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WO2019032961A1 - Trioxacarcin-antibody conjugates and uses thereof - Google Patents

Trioxacarcin-antibody conjugates and uses thereof Download PDF

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Publication number
WO2019032961A1
WO2019032961A1 PCT/US2018/046210 US2018046210W WO2019032961A1 WO 2019032961 A1 WO2019032961 A1 WO 2019032961A1 US 2018046210 W US2018046210 W US 2018046210W WO 2019032961 A1 WO2019032961 A1 WO 2019032961A1
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substituted
unsubstituted
cyclic
acyclic
branched
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PCT/US2018/046210
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French (fr)
Inventor
Andrew G. Myers
Ethan L. MAGNO
Wei Yang
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President And Fellows Of Harvard College
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Publication of WO2019032961A1 publication Critical patent/WO2019032961A1/en

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/335—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin
    • A61K31/35—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin having six-membered rings with one oxygen as the only ring hetero atom
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/68—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an antibody, an immunoglobulin or a fragment thereof, e.g. an Fc-fragment
    • A61K47/6801—Drug-antibody or immunoglobulin conjugates defined by the pharmacologically or therapeutically active agent
    • A61K47/6803—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates
    • A61K47/6807—Drugs conjugated to an antibody or immunoglobulin, e.g. cisplatin-antibody conjugates the drug or compound being a sugar, nucleoside, nucleotide, nucleic acid, e.g. RNA antisense
    • A61K47/6809—Antibiotics, e.g. antitumor antibiotics anthracyclins, adriamycin, doxorubicin or daunomycin
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D493/00—Heterocyclic compounds containing oxygen atoms as the only ring hetero atoms in the condensed system
    • C07D493/22—Heterocyclic compounds containing oxygen atoms as the only ring hetero atoms in the condensed system in which the condensed system contains four or more hetero rings
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/32—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products of oncogenes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/56—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule
    • A61K47/59—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
    • A61K47/60—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes the organic macromolecular compound being a polyoxyalkylene oligomer, polymer or dendrimer, e.g. PEG, PPG, PEO or polyglycerol
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/62—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being a protein, peptide or polyamino acid
    • A61K47/65—Peptidic linkers, binders or spacers, e.g. peptidic enzyme-labile linkers

Definitions

  • ADCs Antibody-drug conjugates
  • a target-specific antibody e.g., a monoclonal antibody, mAb
  • antibody fragment e.g., a single-chain variable fragment (scFv)
  • scFv single-chain variable fragment
  • a payload often a cytotoxic drug
  • a linker connecting the drug to the antibody often a cytotoxic drug
  • the antibody binds to a target cell and the drug exerts its therapeutic effect, for example, by optional cleavage from the ADC and/or by internalization in the cell or proximity to the outside of the cell.
  • Targeted therapies are envisioned to provide many advantages including, but not limited to, decreased side effects and a wider therapeutic window as compared to untargeted therapies.
  • linker used is an important consideration in the design of the ADC.
  • ADCs with cleavable linkers are thought to have a less favorable therapeutic window, and are best designed for targets, such as tumor cell surface antigens that are internalized efficiently.
  • the linker should also be designed in a manner that ensures stability during circulation in blood but allows for the rapid release of the drug, preferably inside the target cell.
  • cleavable acid- and peptidase-labile linkers and non- cleavable linkers such as thioethers. See, e.g., Ducry et al., Bioconjugate Chemistry (2010) 21: 5-13.
  • trioxacarcins are a class of DNA- modifying natural products with antiproliferative effects.
  • the trioxacarcins were first described in 1981 by Tomita and coworkers. See, e.g., Tomita et al., J. Antibiotics,
  • Trioxacarcin A, B, and C were isolated by Tomita and coworkers from the culture broth of Streptomyces bottropensis DO-45 and shown to possess anti-tumor activity in murine models as well as gram-positive antibiotic activity. Subsequent work led to the discovery of other members of this family.
  • Trioxacarcin A is a powerful anticancer agent with subnanmolar IC 70 values against lung (LXFL 529L, H-460), mammary (MCF-7), and CNS (SF-268) cancer cell lines.
  • the trioxacarcins have also been shown to have antimicrobial activity, e.g., anti-bacterial and anti-malarial activity. See, e.g., Maskey et ah, J. Antibiotics (2004) 57:771-779.
  • trioxacarcin A bound to ⁇ - ⁇ of a guanidylate residue in a duplex DNA oligonucleotide substrate has provided compelling evidence for a proposed pathyway of DNA modification that proceeds by duplex intercalation and alkylation. See, e.g., Pfoh et ah, Nucleic Acids Research (2008) 36:3508-3514. All trioxacarcins appear to be derivatives of the aglycone, which is itself a bacterial isolate referred to in the patent literature as DC-45-A 2 .
  • U.S. Patent 4,459,291 issued July 10, 1984, describes the preparation of DC-45-A 2 by fermentation.
  • DC-45-A 2 is the algycone of trioxacarcins A, B, and C and is prepared by the acid hydrolysis of the fermentation products trioxacarcins A and C or the direct isolation from the fermentation broth of Streptomyces bottropensis.
  • the present disclosure provides access to novel trioxacarcin-antibody drug conjugates and trioxacarcin-antibody drug conjugate precursor compounds with
  • trioxacarcins are highly toxic to a variety of cell types. Linking a trioxacarcin to an antibody preserves the trioxacarcin' s potency against a particular cell type while increasing specificity to the target cell, and optionally increasing endocytosis of the trioxacarcin. These effects enable lowering the overall amount of trioxacarcin to be delivered, thereby reducing the associated toxicity.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R D1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is -L-B
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • NR uz C( 0)OR ul ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • R 11 is substituted or unsubstituted alkylene
  • R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • A is a group of the formula
  • Q is -S-, or - -;
  • R wl is independently hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group
  • B is an antibody or an antibody fragment.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R D1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is - ⁇ ⁇
  • NR 1 "C( 0)OR il ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • NR uz C( 0)OR ul ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R B2 is
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • L 1 is of the formula:
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • heteroalk lene ; heterocyclylene; or heteroarylene;
  • R 11 is substituted or unsubstituted alkylene
  • R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring; R is h drogen; substituted or unsubstituted alkyl; substituted or unsubstituted
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • Q is -S-, or -0-
  • R is a leaving group (e.g., halogen, tosylate, or mesylate);
  • R is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group;
  • R wl is independently hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
  • the compound of Formula (I) or Formula (II) is of the formula:
  • the compound of Formula (I) or Formula (II) is of the formula:
  • the compound of Formula (I) or Formula (II) is of the formula:
  • novel trioxacarcin analogs (without linker groups or antibodies conjugated thereto).
  • compositions comprising any of the compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, and optionally a pharmaceutically acceptable carrier.
  • cardiovascular disease e.g., cardiovascular disease
  • proliferative disease e.g., cancer
  • diabetic retinopathy e.g., inflammatory disease
  • autoimmune disease e.g., rhinitis
  • infectious disease e.g., rhinitis
  • kits comprising compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, or pharmaceutical compositions comprising such.
  • the kits further comprise instructions for administration (e.g., human administration).
  • compositions comprising any of the compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, and a pharmaceutically acceptable carrier for use in treating cardiovascular disease, proliferative disease (e.g., cancer), diabetic retinopathy, inflammatory disease, autoimmune disease, or infectious disease, as well as uses of any of the compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, for manufacturing a medicament for use in treating any of the target diseases.
  • Compounds described herein may comprise one or more asymmetric centers, and thus may exist as stereoisomers, e.g., enantiomers and/or diastereomer s.
  • the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer.
  • Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et ah,
  • Compounds may exist as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.
  • alkyl refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms (“Ci_io alkyl”). In some embodiments, an alkyl group has 1 to 9 carbon atoms (“Ci_9 alkyl”). In some embodiments, an alkyl group has 1 to 8 carbon atoms (“Ci_ 8 alkyl”). In some embodiments, an alkyl group has 1 to 7 carbon atoms (“Ci_7 alkyl”). In some embodiments, an alkyl group has 1 to 6 carbon atoms (“Ci_6 alkyl").
  • an alkyl group has 1 to 5 carbon atoms (“Ci_5 alkyl”). In some embodiments, an alkyl group has 1 to 4 carbon atoms ("C ⁇ alkyl”). In some embodiments, an alkyl group has 1 to 3 carbon atoms (“Ci_ 3 alkyl”). In some embodiments, an alkyl group has 1 to 2 carbon atoms (“Ci_ 2 alkyl”). In some embodiments, an alkyl group has 1 carbon atom (“Q alkyl”). In some embodiments, an alkyl group has 2 to 6 carbon atoms (“C 2 -6 alkyl”).
  • Ci_6 alkyl groups include methyl (CO, ethyl (C 2 ), n-propyl (C 3 ), isopropyl (C 3 ), n-butyl (C 4 ), tert-butyl (C 4 ), sec-butyl (C 4 ), iso-butyl (C 4 ), n-pentyl (C5), 3-pentanyl (C5), amyl (C5), neopentyl (C5), 3-methyl-2-butanyl (C5), tertiary amyl (C5), and n-hexyl (C 6 ).
  • Additional examples of alkyl groups include n-heptyl (C 7 ), n-octyl (C 8 ) and the like. Unless otherwise specified, each instance of an alkyl group is
  • the alkyl group is an unsubstituted Ci_io alkyl (e.g., -CH 3 ). In certain embodiments, the alkyl group is a substituted Ci_io alkyl.
  • heteroalkyl refers to an alkyl group as described herein which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain.
  • a heteroalkyl group refers to a saturated group having from 1 to 10 carbon atoms and 1 or more
  • heteroalkyl group is a saturated group having 1 to 9 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi_9 alkyl”).
  • a heteroalkyl group is a saturated group having 1 to 8 carbon atoms and 1 or more heteroatoms within the parent chain (“heteroCi_ 8 alkyl”).
  • a heteroalkyl group is a saturated group having 1 to 7 carbon atoms and 1 or more heteroatoms within the parent chain (“heteroCi_7 alkyl").
  • a heteroalkyl group is a saturated group having 1 to 6 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi_6 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 5 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroCi_5 alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 to 4 carbon atoms and 1 or 2 heteroatoms within the parent chain (“heteroCi ⁇ alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 3 carbon atoms and 1 heteroatom within the parent chain
  • heteroCi_3 alkyl a heteroalkyl group is a saturated group having 1 to 2 carbon atoms and 1 heteroatom within the parent chain (“heteroCi_ 2 alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 1 carbon atom and 1 heteroatom (“heteroCi alkyl”). In some embodiments, a heteroalkyl group is a saturated group having 2 to 6 carbon atoms and 1 or 2 heteroatoms within the parent chain (“heteroC 2 -6 alkyl").
  • each instance of a heteroalkyl group is independently unsubstituted (an "unsubstituted heteroalkyl") or substituted (a "substituted heteroalkyl") with one or more substituents.
  • the heteroalkyl group is an unsubstituted heteroCi_io alkyl.
  • the heteroalkyl group is a substituted heteroCi_io alkyl.
  • alkenyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more double bonds (e.g., 1, 2, 3, or 4 double bonds).
  • an alkenyl group has 2 to 9 carbon atoms ("C 2 -9 alkenyl”).
  • an alkenyl group has 2 to 8 carbon atoms ("C 2 - 8 alkenyl”).
  • an alkenyl group has 2 to 7 carbon atoms (“C 2 -7 alkenyl”).
  • an alkenyl group has 2 to 6 carbon atoms (“C 2 -6 alkenyl”).
  • an alkenyl group has 2 to 5 carbon atoms (“C 2 -5 alkenyl”).
  • an alkenyl group has 2 to 4 carbon atoms ("C 2 ⁇ alkenyl"). In some
  • an alkenyl group has 2 to 3 carbon atoms ("C 2 -3 alkenyl"). In some
  • an alkenyl group has 2 carbon atoms ("C 2 alkenyl").
  • the one or more carbon- carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl).
  • Examples of C 2 ⁇ alkenyl groups include ethenyl (C 2 ), 1-propenyl (C 3 ), 2-propenyl (C 3 ), 1- butenyl (C 4 ), 2-butenyl (C 4 ), butadienyl (C 4 ), and the like.
  • C 2 -6 alkenyl groups include the aforementioned C 2 ⁇ alkenyl groups as well as pentenyl (C 5 ), pentadienyl (C 5 ), hexenyl (C 6 ), and the like. Additional examples of alkenyl include heptenyl (C 7 ), octenyl (C 8 ), octatrienyl (C 8 ), and the like. Unless otherwise specified, each instance of an alkenyl group is independently unsubstituted (an "unsubstituted alkenyl") or substituted (a
  • substituted alkenyl with one or more substituents.
  • the alkenyl group is an unsubstituted C 2 -io alkenyl.
  • the alkenyl group is a substituted C 2 -io alkenyl.
  • heteroalkenyl refers to an alkenyl group as described herein which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain.
  • a heteroalkenyl group refers to a group having from 2 to 10 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (“heteroC 2 -io alkenyl").
  • a heteroalkenyl group has 2 to 9 carbon atoms at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -9 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 8 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -8 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 7 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain (“heteroC 2 -7 alkenyl").
  • a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -6 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 5 carbon atoms, at least one double bond, and 1 or 2
  • heteroalkenyl group has 2 to 4 carbon atoms, at least one double bond, and 1 or 2
  • heteroalkenyl group has 2 to 3 carbon atoms, at least one double bond, and 1 heteroatom within the parent chain ("heteroC 2 -3 alkenyl”). In some embodiments, a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain ("heteroC 2 -6 alkenyl”). Unless otherwise specified, each instance of a heteroalkenyl group is independently unsubstituted (an "unsubstituted heteroalkenyl") or substituted (a "substituted heteroalkenyl") with one or more substituents. In certain embodiments, the heteroalkenyl group is an unsubstituted heteroC 2 -io alkenyl. In certain embodiments, the heteroalkenyl group is a substituted heteroC 2 -io alkenyl.
  • alkynyl refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more triple bonds (e.g., 1, 2, 3, or 4 triple bonds) ("C 2 -io alkynyl"). In some embodiments, an alkynyl group has 2 to 9 carbon atoms ("C 2 -9 alkynyl”). In some embodiments, an alkynyl group has 2 to 8 carbon atoms (“C 2 -8 alkynyl”). In some embodiments, an alkynyl group has 2 to 7 carbon atoms (“C 2 -7 alkynyl").
  • an alkynyl group has 2 to 6 carbon atoms ("C 2 -6 alkynyl”). In some embodiments, an alkynyl group has 2 to 5 carbon atoms ("C 2 -5 alkynyl”). In some embodiments, an alkynyl group has 2 to 4 carbon atoms ("C 2 ⁇ alkynyl”). In some embodiments, an alkynyl group has 2 to 3 carbon atoms ("C 2 -3 alkynyl”). In some embodiments, an alkynyl group has 2 carbon atoms ("C 2 alkynyl”). The one or more carbon- carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl).
  • Examples of C 2 ⁇ alkynyl groups include, without limitation, ethynyl (C 2 ), 1-propynyl (C 3 ), 2-propynyl (C 3 ), 1-butynyl (C 4 ), 2-butynyl (C 4 ), and the like.
  • Examples of C 2 -6 alkenyl groups include the aforementioned C 2 ⁇ alkynyl groups as well as pentynyl (C 5 ), hexynyl (C 6 ), and the like. Additional examples of alkynyl include heptynyl (C 7 ), octynyl (C 8 ), and the like.
  • each instance of an alkynyl group is independently unsubstituted (an "unsubstituted alkynyl") or substituted (a "substituted alkynyl") with one or more substituents.
  • the alkynyl group is an unsubstituted C 2 10 alkynyl.
  • the alkynyl group is a substituted C 2 10 alkynyl.
  • heteroalkynyl refers to an alkynyl group as described herein which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain.
  • a heteroalkynyl group refers to a group having from 2 to 10 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (“heteroC 2 -io alkynyl").
  • a heteroalkynyl group has 2 to 9 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -9 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 8 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -s alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 7 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain (“heteroC 2 -7 alkynyl").
  • a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC 2 -6 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 5 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain ("heteroC 2 -5 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain (“heteroC 2 ⁇ alkynyl").
  • a heteroalkynyl group has 2 to 3 carbon atoms, at least one triple bond, and 1 heteroatom within the parent chain ("heteroC 2 - 3 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain ("heteroC 2 -6 alkynyl"). Unless otherwise specified, each instance of a heteroalkynyl group is independently unsubstituted (an "unsubstituted heteroalkynyl") or substituted (a "substituted heteroalkynyl") with one or more substituents. In certain embodiments, the heteroalkynyl group is an unsubstituted heterod-io alkynyl. In certain embodiments, the heteroalkynyl group is a substituted heterod-io alkynyl.
  • Carbocyclyl or “carbocyclic” refers to a radical of a non- aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms ("C 3 _io
  • carbocyclyl and zero heteroatoms in the non-aromatic ring system.
  • a carbocyclyl group has 3 to 8 ring carbon atoms ("C 3 _ 8 carbocyclyl").
  • a carbocyclyl group has 3 to 7 ring carbon atoms ("C 3 _ 7 carbocyclyl”). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms (“C 3 _6 carbocyclyl”). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms ("Cs-io
  • C 3 _ 6 carbocyclyl groups include, without limitation, cyclopropyl (C 3 ), cyclopropenyl (C 3 ), cyclobutyl (C 4 ), cyclobutenyl (C 4 ), cyclopentyl (C 5 ), cyclopentenyl (C 5 ), cyclohexyl (C 6 ), cyclohexenyl (C 6 ), cyclohexadienyl (C 6 ), and the like.
  • Exemplary C 3 _ 8 carbocyclyl groups include, without limitation, the aforementioned C 3 _ 6 carbocyclyl groups as well as cycloheptyl (C 7 ), cycloheptenyl (C 7 ), cycloheptadienyl (C 7 ), cycloheptatrienyl (C 7 ), cyclooctyl (C 8 ), cyclooctenyl (C 8 ), bicyclo[2.2.1]heptanyl (C 7 ), bicyclo[2.2.2]octanyl (C 8 ), and the like.
  • Exemplary C 3 _io carbocyclyl groups include, without limitation, the
  • C 3 _ 8 carbocyclyl groups as well as cyclononyl (C9), cyclononenyl (C9), cyclodecyl (C 10 ), cyclodecenyl (C 10 ), octahydro-lH-indenyl (C9), decahydronaphthalenyl (Cio), spiro[4.5]decanyl (C 10 ), and the like.
  • the carbocyclyl group is either monocyclic (“monocyclic carbocyclyl”) or polycyclic (e.g., containing a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic carbocyclyl”) or tricyclic system (“tricyclic carbocyclyl”)) and can be saturated or can contain one or more carbon-carbon double or triple bonds.
  • Carbocyclyl also includes ring systems wherein the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system.
  • each instance of a carbocyclyl group is independently unsubstituted (an "unsubstituted carbocyclyl") or substituted (a "substituted carbocyclyl”) with one or more substituents.
  • the carbocyclyl group is an unsubstituted C 3 _io carbocyclyl.
  • the carbocyclyl group is a substituted C 3 _io carbocyclyl.
  • “carbocyclyl” is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms ("C 3 _io cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms ("C 3 _ 8 cycloalkyl”). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms ("C 3 _6 cycloalkyl”). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms ("Cs_6 cycloalkyl").
  • a cycloalkyl group has 5 to 10 ring carbon atoms ("Cs_io cycloalkyl").
  • Cs_ 6 cycloalkyl groups include cyclopentyl (C 5 ) and cyclohexyl (C5).
  • C 3 _6 cycloalkyl groups include the aforementioned Cs_6 cycloalkyl groups as well as cyclopropyl (C 3 ) and cyclobutyl (C 4 ).
  • Examples of C 3 _ 8 cycloalkyl groups include the aforementioned C 3 _ 6 cycloalkyl groups as well as cycloheptyl (C 7 ) and cyclooctyl (C 8 ).
  • each instance of a cycloalkyl group is independently unsubstituted (an
  • the cycloalkyl group is an unsubstituted C 3 _io
  • the cycloalkyl group is a substituted C 3 _io cycloalkyl.
  • heterocyclyl or “heterocyclic” refers to a radical of a 3- to 14- membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("3-14 membered heterocyclyl").
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • a heterocyclyl group can either be monocyclic (“monocyclic heterocyclyl”) or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system (“bicyclic heterocyclyl”) or tricyclic system (“tricyclic heterocyclyl”)), and can be saturated or can contain one or more carbon- carbon double or triple bonds.
  • Heterocyclyl polycyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heterocyclyl also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system.
  • each instance of heterocyclyl is independently unsubstituted (an "unsubstituted heterocyclyl") or substituted (a "substituted heterocyclyl") with one or more substituents.
  • the heterocyclyl group is an unsubstituted 3-14 membered heterocyclyl. In certain embodiments, the heterocyclyl group is a substituted 3-14 membered heterocyclyl.
  • a heterocyclyl group is a 5-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heterocyclyl").
  • a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is
  • a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is
  • the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • Exemplary 3-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azirdinyl, oxiranyl, thiorenyl.
  • Exemplary 4-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl.
  • Exemplary 5-membered heterocyclyl groups containing 1 heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl,
  • Exemplary 5- membered heterocyclyl groups containing 2 heteroatoms include, without limitation, dioxolanyl, oxathiolanyl and dithiolanyl.
  • Exemplary 5-membered heterocyclyl groups containing 3 heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl.
  • Exemplary 6-membered heterocyclyl groups containing 1 heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl.
  • Exemplary 6-membered heterocyclyl groups containing 2 heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, dioxanyl.
  • heterocyclyl groups containing 3 heteroatoms include, without limitation, triazinyl.
  • Exemplary 7-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl.
  • Exemplary 8-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl.
  • Exemplary bicyclic heterocyclyl groups include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, tetrahydrobenzothienyl, tetrahydrobenzofuranyl, tetrahydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyl,
  • decahydronaphthyridinyl decahydro-l,8-naphthyridinyl, octahydropyrrolo[3,2-b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyl, lH-benzo[e] [l,4]diazepinyl, l,4,5,7-tetrahydropyrano[3,4-b]pyrrolyl, 5,6-dihydro-4H-furo[3,2-b]pyrrolyl, 6,7-dihydro- 5H-furo[3,2-b]pyranyl, 5,7-dihydro-4H-thieno[2,3-c]pyranyl, 2,3-dihydro-lH- pyrrolo[2,3-b]pyridinyl, 2,3-dihydrofuro[2,3-b]pyridinyl, 4,5,6,7-
  • aryl refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 ⁇ electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system ("C 6 -i 4 aryl”).
  • an aryl group has 6 ring carbon atoms ("C 6 aryi”; e.g., phenyl).
  • an aryl group has 10 ring carbon atoms ("Cio aryi”; e.g., naphthyl such as 1-naphthyl and 2-naphthyl).
  • an aryl group has 14 ring carbon atoms ("C 14 aryl”; e.g., anthracyl).
  • Aryl also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system.
  • each instance of an aryl group is independently unsubstituted (an "unsubstituted aryl") or substituted (a "substituted aryl") with one or more substituents.
  • the aryl group is an unsubstituted C 6 - 14 aryl.
  • the aryl group is a substituted C 6 -i 4 aryl.
  • alkyl is a subset of “alkyl” and refers to an alkyl group, as described herein, substituted by an aryl group, as described herein, wherein the point of attachment is on the alkyl moiety.
  • heteroaryl refers to a radical of a 5-14 membered monocyclic or polycyclic (e.g., bicyclic, tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 ⁇ electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur ("5-14 membered heteroaryl").
  • the point of attachment can be a carbon or nitrogen atom, as valency permits.
  • Heteroaryl polycyclic ring systems can include one or more heteroatoms in one or both rings.
  • Heteroaryl includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system.
  • Heteroaryl also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused polycyclic (aryl/heteroaryl) ring system.
  • Polycyclic heteroaryl groups wherein one ring does not contain a heteroatom e.g., indolyl, quinolinyl, carbazolyl, and the like
  • the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indolyl).
  • a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heteroaryl").
  • a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heteroaryl").
  • a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heteroaryl").
  • the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur.
  • the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.
  • each instance of a heteroaryl group is independently unsubstituted (an "unsubstituted heteroaryl") or substituted (a "substituted heteroaryl") with one or more substituents.
  • the heteroaryl group is an unsubstituted 5-14 membered heteroaryl.
  • the heteroaryl group is a substituted 5-14 membered heteroaryl.
  • Exemplary 5-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl.
  • Exemplary 5-membered heteroaryl groups containing 2 heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl.
  • Exemplary 5-membered heteroaryl groups containing 3 heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl.
  • 5- membered heteroaryl groups containing 4 heteroatoms include, without limitation, tetrazolyl.
  • Exemplary 6-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyridinyl.
  • Exemplary 6-membered heteroaryl groups containing 2 heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl.
  • 6- membered heteroaryl groups containing 3 or 4 heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively.
  • Exemplary 7-membered heteroaryl groups containing 1 heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl.
  • Exemplary 5,6- bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl,
  • Exemplary 6,6-bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl.
  • Exemplary tricyclic heteroaryl groups include, without limitation, phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl, phenothiazinyl, phenoxazinyl and phenazinyl.
  • Heteroaralkyl is a subset of “alkyl” and refers to an alkyl group, as described herein, substituted by a heteroaryl group, as described herein, wherein the point of attachment is on the alkyl moiety.
  • partially unsaturated refers to a ring moiety that includes at least one double or triple bond.
  • the term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl moieties) as herein defined.
  • saturated refers to a ring moiety that does not contain a double or triple bond, i.e. , the ring contains all single bonds.
  • alkylene is the divalent moiety of alkyl
  • alkenylene is the divalent moiety of alkenyl
  • alkynylene is the divalent moiety of alkynyl
  • heteroalkylene is the divalent moiety of heteroalkyl
  • heteroalkenylene is the divalent moiety of heteroalkenyl
  • heteroalkynylene is the divalent moiety of heteroalkynyl
  • carbocyclylene is the divalent moiety of carbocyclyl
  • heterocyclylene is the divalent moiety of heterocyclyl
  • arylene is the divalent moiety of aryl
  • heteroarylene is the divalent moiety of heteroaryl.
  • alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as described herein, are, in certain embodiments, optionally substituted.
  • Optionally substituted refers to a group which may be substituted or unsubstituted (e.g., "substituted” or "unsubstituted” alkyl, "substituted” or “unsubstituted” alkenyl, "substituted” or “unsubstituted” alkynyl,
  • substituted means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction.
  • a "substituted” group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position.
  • substituted is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound.
  • the present invention contemplates any and all such combinations in order to arrive at a stable compound.
  • heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
  • R aa is, independently, selected from Ci_io alkyl, Ci_io perhaloalkyl, C 2 _io alkenyl, C 2 _io alkynyl, heteroCi_io alkyl, heteroC 2 _io alkenyl, heteroC 2 _ioalkynyl, C 3 _io carbocyclyl, 3-14 membered heterocyclyl, C 6 -i 4 aryl, and 5-14 membered heteroaryl, or two R aa groups are joined to form a 3-14 membered heterocyclyl,
  • each instance of R bb is, independently, selected from hydrogen, -OH, -OR aa , -
  • each instance of R cc is, independently, selected from hydrogen, Ci_io alkyl, Ci_io perhaloalkyl, C 2 _io alkenyl, C 2 _io alkynyl, heteroCi-ioalkyl, heteroC 2 _ioalkenyl, heteroC 2 _ l oalkynyl, C 3 _io carbocyclyl, 3-14 membered heterocyclyl, C 6 -i 4 aryl, and 5-14 membered heteroaryl, or two R cc groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R dd groups; each instance of R is, independently, selected from
  • each instance of R ee is, independently, selected from Ci_ 6 alkyl, Ci_ 6 perhaloalkyl, C 2 6 alkenyl, C 2 _ 6 alkynyl, heteroCi_6alkyl, heteroC 2 _6alkenyl, heteroC 2 _6alkynyl, C 3 _io
  • each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups;
  • each instance of R is, independently, selected from hydrogen, Ci_ 6 alkyl, Ci_ 6 perhaloalkyl, C 2 _ 6 alkenyl, C 2 _ 6 alkynyl, heteroCi_ 6 alkyl, heteroC 2 _ 6 alkenyl, heteroC 2 _ 6 alkynyl, C 3 _io carbocyclyl, 3-10 membered heterocyclyl, C 6 -io aryl and 5-10 membered heteroaryl, or two R ff groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 R gg groups; and
  • halo refers to fluorine (fluoro, -F), chlorine (chloro, -CI), bromine (bromo, -Br), or iodine (iodo, -I).
  • R xl is hydrogen; halogen; substituted or unsubstituted hydroxyl; substituted or unsubstituted thiol; substituted or unsubstituted amino; substituted or unsubstituted acyl, cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched alkyl; cyclic or acyclic, substituted or unsubstituted, branched or unbranched alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted aryl,
  • heteroaryloxy aliphaticthioxy, heteroaliphaticthioxy, alkylthioxy, heteroalkylthioxy, arylthioxy, heteroarylthioxy, mono- or di- aliphaticamino, mono- or di- heteroaliphaticamino, mono- or di- alkylamino, mono- or di- heteroalkylamino, mono- or di-arylamino, or mono- or di-heteroarylamino; or two R groups taken together form a 5- to 6-membered heterocyclic ring.
  • acyl groups include aldehydes (-CHO), carboxylic acids (-C0 2 H), ketones, acyl halides, esters, amides, imines, carbonates, carbamates, and ureas.
  • Acyl substituents include, but are not limited to, any of the substituents described herein, that result in the formation of a stable moiety (e.g., aliphatic, alkyl, alkenyl, alkynyl, heteroaliphatic, heterocyclic, aryl, heteroaryl, acyl, oxo, imino, thiooxo, cyano, isocyano, amino, azido, nitro, hydroxyl, thiol, halo, aliphaticamino, heteroaliphaticamino, alkylamino, heteroalkylamino, arylamino, heteroarylamino, alkylaryl, arylalkyl, aliphaticoxy, heteroaliphaticoxy, alky
  • a "counterion” or “anionic counterion” is a negatively charged group associated with a positively charged group in order to maintain electronic neutrality.
  • An anionic counterion may be monovalent (i.e., including one formal negative charge).
  • An anionic counterion may also be multivalent (i.e., including more than one formal negative charge), such as divalent or trivalent.
  • Exemplary counterions include halide ions (e.g., F , Cl ⁇ , Br , ⁇ ), N0 3 , C10 4 , OH , H 2 P0 4 , HC0 ⁇ HS0 4 , sulfonate ions (e.g., methansulfonate,
  • exemplary counterions which may be multivalent include C0 3 , HP0 4 ,
  • carboxylate anions e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the like
  • carboxylate anions e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the like
  • carboranes e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the
  • leaving group is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile. See, for example, Smith, March Advanced Organic Chemistry 6th ed. (501-502).
  • suitable leaving groups include, but are not limited to, halogen (such as F, CI, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy,
  • alkyl-carbonyloxy e.g., acetoxy
  • arylcarbonyloxy aryloxy
  • methoxy N,0-dimethylhydroxylamino, pixyl
  • haloformates e.g., acetoxy
  • the leaving group is a brosylate, such as /?-bromobenzenesulfonyloxy.
  • the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy.
  • the leaving group may also be a phosphineoxide (e.g. , formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate.
  • phosphineoxide e.g. , formed during a Mitsunobu reaction
  • an internal leaving group such as an epoxide or cyclic sulfate.
  • Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties.
  • hydroxyl refers to the group -OH.
  • thiol refers to the group -SH.
  • amino refers to the group -NH 2 .
  • substituted amino by extension, refers to a monosubstituted amino, a disubstituted amino, or a trisubstituted amino, as described herein. In certain embodiments, the "substituted amino” is a monosubstituted amino or a disubstituted amino group.
  • trisubstituted amino refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with three groups, and includes groups selected from -N(R bb ) 3 and -N(R bb ) 3 + X ⁇ , wherein R bb and X are as described herein.
  • a "counterion” is a negatively charged group associated with a positively charged quarternary amine in order to maintain electronic neutrality.
  • exemplary counterions include halide ions (e.g., F , CI , Br , ⁇ ), N0 3 , C10 4 , OH , H 2 P0 4 , HS0 4 , sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-l-sulfonic acid-5-sulfonate, ethan-1 -sulfonic acid-2-sulfonate, and the like), and carboxylate ions (e.g., acetate, ethanoate, propanoate, benzoate,
  • Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms.
  • the substituent present on the nitrogen atom is an nitrogen protecting group (also referred to herein as an "amino protecting group").
  • Nitrogen protecting groups such as carbamate groups include, but are not limited to, methyl carbamate, ethyl carbamate, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethyl carbamate, 2,7-di-i-butyl-[9-( 10, 10-dioxo-lO, 10, 10, 10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1- (l-adamantyl)-l-methylethyl
  • Nitrogen protecting groups such as sulfonamide groups include, but are not limited to, /?-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4- methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6- dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5, 6-tetramethyl-4- methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6- trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7, 8-pentamethylchroman-6-sulfonamide (Pmc), methanes
  • Ts /?-toluenesulfonamide
  • Mtr
  • nitrogen protecting groups include, but are not limited to, phenothiazinyl- (10)-acyl derivative, N'-p-toluenesulfonylaminoacyl derivative, N'-phenylaminothioacyl derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine derivative, 4,5-diphenyl- 3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-l,l,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted l,3-dimethyl-l,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl- l,3,5-triazacyclohexan-2-one, 1-
  • benzenesulfenamide o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide,
  • triphenylmethylsulfenamide triphenylmethylsulfenamide
  • 3-nitropyridinesulfenamide Npys
  • a nitrogen protecting group is benzyl (Bn), tert-butyloxycarbonyl (BOC), carbobenzyloxy (Cbz), 9-flurenylmethyloxycarbonyl (Fmoc), trifluoroacetyl,
  • triphenylmethyl triphenylmethyl, acetyl (Ac), benzoyl (Bz), p-methoxybenzyl (PMB), 3,4-dimethoxybenzyl (DMPM), p-methoxyphenyl (PMP), 2,2,2-trichloroethyloxycarbonyl (Troc), triphenylmethyl (Tr), tosyl (Ts), brosyl (Bs), nosyl (Ns), mesyl (Ms), triflyl (Tf), or dansyl (Ds).
  • the substituent present on an oxygen atom is an oxygen protecting group (also referred to herein as an "hydroxyl protecting group").
  • Oxygen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3 edition, John Wiley & Sons, 1999, incorporated herein by reference.
  • oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), i-butylthiomethyl,
  • DPMS diphenylmethylsilyl
  • TMPS i-butylmethoxyphenylsilyl
  • benzoylformate acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, /?-chlorophenoxyacetate, 3- phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p- phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9- fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(
  • an oxygen protecting group is silyl.
  • an oxygen protecting group is t-butyldiphenylsilyl (TBDPS), t- butyldimethylsilyl (TBDMS), triisoproylsilyl (TIPS), triphenylsilyl (TPS), triethylsilyl (TES), trimethylsilyl (TMS), triisopropylsiloxymethyl (TOM), acetyl (Ac), benzoyl (Bz), allyl carbonate, 2,2,2-trichloroethyl carbonate (Troc), 2-trimethylsilylethyl carbonate,
  • methoxymethyl (MOM), 1-ethoxyethyl (EE), 2-methyoxy-2-propyl (MOP), 2,2,2- trichloroethoxyethyl, 2-methoxyethoxymethyl (MEM), 2-trimethylsilylethoxymethyl (SEM), methylthiomethyl (MTM), tetrahydropyranyl (THP), tetrahydrofuranyl (THF), p- methoxyphenyl (PMP), triphenylmethyl (Tr), methoxytrityl (MMT), dimethoxytrityl (DMT), allyl, p-methoxybenzyl (PMB), t-butyl, benzyl (Bn), allyl, or pivaloyl (Piv).
  • the substituent present on a sulfur atom is a sulfur protecting group (also referred to as a "thiol protecting group").
  • a sulfur protecting group is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl.
  • salts and “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio.
  • Pharmaceutically acceptable salts are well known in the art. For example, Berge et ah, describes pharmaceutically acceptable salts in detail in . Pharmaceutical Sciences (1977) 66: 1-19.
  • Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases.
  • Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid
  • organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange.
  • salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate,
  • glycerophosphate gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy- ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like.
  • Pharmaceutically acceptable salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N + (Ci ⁇ alkyl) 4 salts.
  • Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like.
  • Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.
  • a "peptidyl group” refers to a divalent amino acid moiety.
  • a “polypeptidyl” group refers to a divalent moiety comprising three or more consecutively linked amino acid residues (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 19, 20, or more linked amino acid residues).
  • Peptidyl, dipeptidyl, and polypeptidyl moieties may contain only natural amino acids, although non-natural amino acids (i.e., compounds that do not occur in nature but that can be incorporated into a polypeptide chain) and/or amino acid analogs as are known in the art may alternatively be employed.
  • one or more of the amino acids in a peptidyl, dipeptidyl, or polypeptidyl moiety may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation,
  • cysteine (-CH 2 SH) side chain may be modified to a formyl (-CHO) side chain.
  • Exemplary amino acids contemplated useful in providing the peptidyl, dipeptidyl, and polypeptidyl moieties of interest include, without limitation, natural alpha-amino acids such as D- and L-isomers of the 20 common naturally occurring alpha-amino acids found in peptides (e.g., A, R, N, C, D, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V), natural beta-amino acids (e.g., beta-alanine), and unnnatural amino acids.
  • natural alpha-amino acids such as D- and L-isomers of the 20 common naturally occurring alpha-amino acids found in peptides (e.g., A, R, N, C, D, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V)
  • natural beta-amino acids e.g., beta-alanine
  • amino acids contemplated useful in providing the peptidyl, dipeptidyl, and polypeptidyl moieties of interest include without limitation, ornithine, citrulline (Cit), -methyl- Alanine (Aib), 4-hydroxyproline, desmosine, gamma-aminobutyric acid, beta-cyanoalanine, norvaline, 4-(E)-butenyl-4(R)-methyl-N-methyl-L-threonine, N-methyl-L-leucine, 1- amino-cyclopropanecarboxylic acid, l-amino-2-phenyl-cyclopropanecarboxylic acid, 1- amino-cyclobutanecarboxylic acid, 4-amino-cyclopentenecarboxylic acid, 3-amino- cyclohexanecarboxy
  • a "subject" to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g, infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult)) and/or other non-human animals, for example mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as rodents (e.g., mice, rats), guinea pigs, cattle, pigs, horses, sheep, goats, cats, and/or dogs.
  • the non-human animal may be male or female and at any stage of development.
  • a non-human animal may be a transgenic animal.
  • the terms “treat,” “treating” and “treatment” contemplate an action that occurs while a subject is suffering from the specified disease, disorder, or condition, which reduces the severity of the disease, disorder, or condition, or retards or slows the progression of the disease, disorder, or condition
  • therapeutic treatment or “therapeutically treating”
  • therapeutically treating an action that occurs before a subject begins to suffer from the specified disease, disorder, or condition, and which inhibits or reduces the severity of the disease, disorder, or condition.
  • the "effective amount" of a compound refers to an amount sufficient to elicit the desired biological response.
  • the effective amount of a compound of the invention may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the disease being treated, the mode of administration, and the age, health, and condition of the subject.
  • the effective amount of a compound with anti-proliferative activity is the amount that results in a sufficient concentration to inhibit the proliferation of cells.
  • An effective amount encompasses therapeutic and prophylactic treatment.
  • a "therapeutically effective amount" of a compound is an amount sufficient to provide a therapeutic benefit in the treatment of a disease, disorder, or condition, or to delay or minimize one or more symptoms associated with the disease, disorder, or condition.
  • a therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the disease, disorder, or condition.
  • the term "therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the disease, disorder, or condition, or enhances the therapeutic efficacy of another therapeutic agent.
  • a prophylactic ally effective amount of a compound is an amount sufficient to prevent a disease, disorder, or condition, or one or more symptoms associated with the disease, disorder, or condition, or prevent its recurrence.
  • a prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the disease, disorder, or condition.
  • the term “prophylactically effective amount” can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.
  • At least one instance refers to 1, 2, 3, 4, or more instances, but also encompasses a range, e.g., for example, from 1 to 4, from 1 to 3, from 1 to 2, from 2 to 4, from 2 to 3, or from 3 to 4 instances, inclusive.
  • Figure 1 is a graph showing the stability of exemplary trioxacarcin-linker species R02-B5, R02-B4, R02-B8, R02-A3, and R02-A8 at 37 °C in pH 5.0 buffer.
  • Figure 2 is a graph showing the stability of exemplary trioxacarcin-linker species R02-B5, R02-B4, R02-B8, R02-A3, and R02-A8 under physiological conditions at 37 °C in pH 7.4 buffer.
  • Figure 3 is a graph showing the stability of exemplary free drug trioxacarcin species R02-B1, R02-A9, R02-B7, R02-A1, and R02-A7 under physiological conditions at 37 °C in pH 7.4 buffer.
  • Figure 4 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-A3 upon exposure to Cathepsin B (ti /2 of R02-A3: 0.45 hours).
  • Figure 5 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-A8 upon exposure to Cathepsin B (ti /2 of R02-A8: 0.21 hours).
  • Figure 6 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-B4 upon exposure to Cathepsin B (ti /2 of R02-B4: 0.44 hours).
  • Figure 7 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-B5 upon exposure to Cathepsin B (ti /2 of R02-B5: 0.25 hours).
  • Trioxacarcins are highly toxic to a variety of cell types. Linking a trioxacarcin to an antibody preserves the trioxacarcin' s potency against the cell type while increasing specificity to the target cell, and optionally increasing endocytosis of the trioxacarcin. These effects enable lowering the overall amount of trioxacarcin to be delivered, thereby reducing the associated toxicity. By taking advantage of established synthetic methods, complex and therapeutically relevant trioxacarcins are accessible. In turn, conjugating these trioxacarcins to antibodies through linking groups provide trioxacarcin-antibody drug conjugates.
  • trioxacarcin-antibody drug conjugates e.g., compounds of Formula (I)
  • trioxacarcin-antibody drug conjugate precursors comprising a trioxacarcin and a linking group
  • novel trioxacarcin analogs e.g., free drug species.
  • the compounds may be provided for use in any composition, kit, or method described herein as a pharmaceutically acceptable salt.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two R A2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is -L-B;
  • NR 1 "C( 0)OR il ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • NR uz C( 0)OR ul ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • heteroalk lene ; heterocyclylene; or heteroarylene;
  • R 11 is substituted or unsubstituted alkylene
  • R 21 is independently substituted or unsubstituted alkyl; substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
  • N R 1 carbocyclyl; or V ⁇ ⁇ N(R W112 ;
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • A is a group of the formula
  • Q is - -, or -0-
  • R wl is independently hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group
  • B is an antibody or an antibody fragment.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two R A2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R D1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is -L-B;
  • NR 1 "C( 0)OR il ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • NR uz C( 0)OR ul ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • A is a grou of the formula
  • Q is -S-, or -0-
  • R wl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group
  • B is an antibody or an antibody fragment.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R D1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is -L-B;
  • NR 1 "C( 0)OR il ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • NR uz C( 0)OR ul ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; R is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • A is a grou of the formula
  • Q is -S-, or -0-
  • R wl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and B is an antibody or an antibody fragment.
  • the compound of Formula (I) is of Formula (I-a):
  • the compound of Formula (I) is of Formula (I-b):
  • the com ound of Formula (I) is of Formula (I-c):
  • the compound of Formula (I) is of Formula (I-d):
  • the antibody or antibody fragment B is a large molecule with many sites of attachment, and thus may have many instances of a compound of Formula (I) attached thereto.
  • the antibody or antibody fragment comprises 1 to 200 independent instances of a compound of Formula (I) attached thereto, inclusive, e.g. , 1 to 150, 1 to 100, 1 to 75, 1 to 50, 1 to 25, 1 to 15, 1 to 10, inclusive, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 independent instances.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • F2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is - ⁇ ⁇
  • NR 1 "C( 0)OR il ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R G2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • L 1 is of the formula:
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • R 11 is substituted or unsubstituted alkylene
  • R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
  • R 22 is h drogen; substituted or unsubstituted alkyl; substituted or unsubstituted
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • R is halogen, tosylate, mesylate, or triflate
  • R X2 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
  • R wl is independently hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R D1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • F2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is - ⁇ ⁇
  • NR 1 "C( 0)OR il ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R G2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R B2 is
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted
  • R is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • R is halogen, tosylate, mesylate, or triflate
  • R is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group;
  • R wl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R D1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • F2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R 7 is - ⁇ ⁇
  • NR 1 "C( 0)OR il ; or -C(R ⁇ ) 3 ; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
  • dialkylamino or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R G2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R G2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
  • R B2 is
  • cyclic or acyclic independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 1 and R 10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 1 0 U and R 3 J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 1 and R 4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 4 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • R 6 and R 9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety
  • L 1 is of the formula: j— R 20 -X-CH 2 -Ar-NH-Z m -Y m -E-C(O)-R 40 — j .
  • R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • R is halogen, tosylate, mesylate, or triflate
  • R X2 is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
  • R wl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
  • the compound of Formula (II) is of Formula (Il-a):
  • the compound of Formula (II) is of Formula (Il-b):
  • the com ound of Formula (II) is of Formula (II-c):
  • the compound of Formula (II) is of Formula (Il-d):
  • Compounds of Formula (I) are prepared by coupling a compound of Formula (II) with an antibody or antibody fragment.
  • an antibody may couple with 1 to 200 compounds of Formula (II) and form corresponding compounds of Formula (I).
  • R 1 is hydrogen; and R 2 is hydrogen. 1 2
  • R is halogen (e.g., -F, -CI, Br, or -I); and R is hydrogen.
  • R 1 is substituted or unsubstituted alkyl, e.g. , substituted or unsubstituted Ci 6 alkyl, substituted or unsubstituted Ci_ 2 alkyl, substituted or unsubstituted C 2 - 3 alkyl, substituted or unsubstituted C 3 ⁇ alkyl, substituted or unsubstituted C ⁇ salkyl, or
  • R Ci_ 6 alkyl groups include, but are not limited to, substituted or unsubstituted methyl (Ci), ethyl (C 2 ), n-propyl (C 3 ), isopropyl (C 3 ), n-butyl (C 4 ), tert-butyl (C 4 ), sec-butyl (C 4 ), iso-butyl (C 4 ), n-pentyl (C 5 ), 3-pentanyl (C 5 ), amyl (C 5 ), neopentyl (C 5 ), 3-methyl-2-butanyl (C 5 ), tertiary amyl (C 5 ), n-hexyl (C 6 ).
  • R 1 is substituted or unsubstituted alkenyl, e.g. , substituted or unsubstituted C 2 - 6 alkenyl, substituted or unsubstituted C 2 - 3 alkenyl, substituted or unsubstituted C 3 ⁇ alkenyl, substituted or unsubstituted C 4 _salkenyl, or substituted or unsubstituted C5_ 6 alkenyl, and R is hydrogen.
  • R 1 is substituted or unsubstituted alkynyl, e.g. , substituted or unsubstituted C 2 - 6 alkynyl, substituted or unsubstituted C 2 - 3 alkynyl, substituted or unsubstituted C 3 ⁇ alkynyl, substituted or unsubstituted C 4 _salkynyl, or substituted or unsubstituted C5_ 6 alkynyl, and R is hydrogen.
  • R 1 is substituted or unsubstituted carbocyclyl, e.g. , substituted or unsubstituted C 3 _ 6 carbocyclyl, substituted or unsubstituted C 3 ⁇ carbocyclyl, substituted or unsubstituted C 4 _ 5 carbocyclyl, or substituted or unsubstituted Cs_ 6 carbocyclyl, and R is hydrogen.
  • R 1 is substituted or unsubstituted heterocyclyl, e.g. , substituted or unsubstituted 3-6 membered heterocyclyl, substituted or unsubstituted 3-4 membered heterocyclyl, substituted or unsubstituted 4-5 membered heterocyclyl, or substituted or unsubstituted 5-6 membered heterocyclyl, and R is hydrogen.
  • R 1 is substituted or unsubstituted aryl, e.g., substituted or unsubstituted phenyl, and R is hydrogen.
  • R 1 is substituted or unsubstituted heteroaryl, e.g., substituted or unsubstituted 5-6 membered heteroaryl, and R is hydrogen.
  • R A1 or R A2 represent a group of Formula (i):
  • M 1 is -0-, -NR A8 -, or -CHR A - wherein R A8 is hydrogen; substituted or
  • R is independently hydrogen; substituted or unsubstituted alkyl; acyl; or an oxygen protecting group.
  • R A1 or R A2 is hydrogen.
  • R ⁇ is hydrogen.
  • R ⁇ is substituted or unsubstituted alkyl, e.g., methyl.
  • R ⁇ is -OR A9 , e.g., -OH or -O-alkyl.
  • R A4 is hydrogen.
  • R A4 is substituted or unsubstituted alkyl, e.g., methyl.
  • R A4 is -OR A9 , e.g., -OH or -O-alkyl.
  • R ⁇ is hydrogen.
  • R ⁇ is substituted or unsubstituted alkyl, e.g., methyl.
  • R ⁇ is -OR A9 , e.g., -OH or -O-alkyl.
  • R A6 is hydrogen.
  • R A6 is substituted or unsubstituted alkyl, e.g., methyl.
  • R A6 is -OR A9 , e.g., -OH or -O-alkyl.
  • R A7 is hydrogen.
  • R A7 is substituted or unsubstituted alkyl, e.g., methyl.
  • R A7 is -OR A9 , e.g., -OH or -O-alkyl.
  • M 1 is -0-, -NR A8 -, or -CHR A8 - wherein R A8 is hydrogen; substituted or unsubstituted alkyl; a nitrogen protecting group if attached to nitrogen; or -OR A9 ; wherein R A9 is independently hydrogen; substituted or unsubstituted alkyl; acyl; or an oxygen protecting group.
  • R A3 is a non-hydrogen equatorial group.
  • R C 1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • R C2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
  • heteroaliphatic acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring.
  • R 3 is hydrogen or -OR CI , wherein R CI is hydrogen; an oxygen protecting group; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl;
  • R is hydrogen.
  • R 3 is -OR cl , e.g., -OH or -OCH 3 .
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino;
  • R 4 is hydrogen or -OR D1 , wherein R D1 is hydrogen; an oxygen protecting group; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl;
  • R 4 is hydrogen. In certain embodiments, R 4 is -OR D1 , e.g., -OH or -OCH 3 .
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted
  • R is hydrogen or -OR , wherein R is hydrogen; an oxygen protecting group; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl;
  • R 5 is hydrogen. In certain embodiments, R 5 is -OR E1 , e.g. , -OH or -OCH 3 .
  • R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
  • R 6 is hydrogen; halogen; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or
  • R 6 is hydrogen
  • R 6 is halogen; e.g., -F, -CI, Br, or -I.
  • R 6 is substituted or unsubstituted alkyl, e.g. , substituted or unsubstituted Q 6 alkyl, substituted or unsubstituted Q 2 alkyl, substituted or unsubstituted
  • R 6 Ci_ 6 alkyl groups include, but are not limited to, substituted or unsubstituted methyl (CO, ethyl (C 2 ), n-propyl (C 3 ), isopropyl (C 3 ), n-butyl (C 4 ), tert-butyl (C 4 ), sec-butyl (C 4 ), iso-butyl (C 4 ), n-pentyl (C 5 ), 3-pentanyl (C 5 ), amyl (C 5 ), neopentyl (C 5 ), 3-methyl-2-butanyl (C 5 ), tertiary amyl (C 5 ), n-hexyl (C 6 ).
  • R 6 is substituted or unsubstituted alkenyl, e.g. , substituted or unsubstituted C 2 _ 6 alkenyl, substituted or unsubstituted C 2 _ 3 alkenyl, substituted or unsubstituted C 3 ⁇ alkenyl, substituted or unsubstituted C 4 _salkenyl, or substituted or unsubstituted Cs ⁇ alkenyl.
  • R 6 is substituted or unsubstituted alkynyl, e.g. , substituted or unsubstituted C 2 _ 6 alkynyl, substituted or unsubstituted C 2 _ 3 alkynyl, substituted or unsubstituted C 3 ⁇ alkynyl, substituted or unsubstituted C 4 _salkynyl, or substituted or unsubstituted Cs ⁇ alkynyl.
  • R 6 is substituted or unsubstituted carbocyclyl, e.g. , substituted or unsubstituted C 3 _ 6 carbocyclyl, substituted or unsubstituted C 3 ⁇ carbocyclyl, substituted or unsubstituted C 4 _ 5 carbocyclyl, or substituted or unsubstituted Cs_ 6 carbocyclyl.
  • R 6 is substituted or unsubstituted cyclopropyl.
  • R 6 is substituted or unsubstituted heterocyclyl, e.g. , substituted or unsubstituted 3-6 membered heterocyclyl, substituted or unsubstituted 3-4 membered heterocyclyl, substituted or unsubstituted 4-5 membered heterocyclyl, or substituted or unsubstituted 5-6 membered heterocyclyl.
  • R 6 is substituted or unsubstituted aryl, e.g., substituted or unsubstituted phenyl.
  • R 6 is substituted or unsubstituted heteroaryl, e.g., substituted or unsubstituted5-6 membered heteroaryl.
  • each occurrence of R is independently hydrogen; an oxygen protecting group if attached to oxygen; a sulfur protecting group if attached to sulfur; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or acyl; and each occurrence of R F2 is independently hydrogen; a nitrogen protecting group if attached to nitrogen; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted
  • R Fl or R F2 is hydrogen
  • R 3 is hydrogen or -OH
  • R 4 is -OCH 3
  • R 5 is -OH
  • R 3 is hydrogen or -OH
  • R 4 is -OCH 3
  • R 5 is -OH
  • R 6 substituted or unsubstituted alkyl or -OR Fl .
  • R is -L-B; wherein L is a group of the formula:
  • R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted
  • R 11 is substituted or unsubstituted alkylene
  • R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
  • Ar is substituted or unsubstituted arylene; each occurrence of Z is independently an amino acid;
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • A is a group of the formula
  • Q is -S-, or -0-
  • R wl is independently hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group
  • B is an antibody or an antibody fragment.
  • R is -L-B; wherein L is a group of the formula:
  • R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • X is ⁇ / or O ;
  • R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • Q is -S- or -0-
  • R wl is hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group
  • B is an antibody or an antibody fragment.
  • R is -L-B; wherein L is a group of the formula
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalk lene;
  • R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
  • Ar is substituted or unsubstituted arylene
  • each occurrence of Z is independently an amino acid
  • each occurrence of Y is independently an amino acid
  • E is a bond or an amino acid
  • n is independently 1, 2, or 3;
  • R 40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • A is a group of the formula:
  • Q is -S-, or -0-
  • R wl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group
  • B is an antibody or an antibody fragment.
  • R is -L-B; wherein L is a group of the formula:
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
  • R 11 is substituted or unsubstituted alkylene
  • R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
  • R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
  • B is an antibody or an antibody fragment.
  • R is -L-B; wherein L is a group of the formula:
  • R 20 is substituted or unsubstituted alkylene
  • R 11 is substituted or unsubstituted alkylene
  • R 22 is hydrogen; or substituted or unsubstituted alkyl
  • B is an antibody or an antibody fragment.
  • R 20 is substituted or unsubstituted alkylene. In certain embodiments, R 20 is unsubstituted alkylene. In certain embodiments, R 20 is unsubstituted Ci_ 6 alkylene. In certain embodiments, R 20 is unsubstituted C 1-5 alkylene. In certain embodiments,
  • R 20 is unsubstituted C 1-4 alkylene. In certain embodiments, R 20 is unsubstituted C 2 _ 6 alkylene.
  • R 20 is unsubstituted C 20
  • R is unsubstituted C 2 _ 4 alkylene.
  • R 20 is unsubstituted C 2 _ 3 alkylene.
  • R 20 is unsubstituted ethylene.
  • R 20 is unsubstituted propylene.
  • R 20 is unsubstituted butylene.
  • R 20 is unsubstituted pentylene.
  • R 20 is unsubstituted hexylene.
  • X is ; and R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are oined
  • X is and R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted
  • X is independently substituted or
  • X is and R is independently
  • X is ; and R is independently R 21 R 2
  • X is ⁇ ® f ; and R 21 is independently
  • R 21 R 2 unsubstituted C 1-3 alkyl.
  • X is ⁇ ® f ; and R 21 is independently
  • Ci_ 2 alkyl unsubstituted Ci_ 2 alkyl.
  • X ; and two R 21 groups are joined to form an optionally substituted heterocyclyl ring.
  • X is ; and two R 21 groups are optionally joined to form an optionally substituted 5-6
  • R 2 R 21 membered heterocyclyl ring.
  • X is V ⁇ ® ' ; and two R 21 groups are joined to form an optionally substituted 6 membered heterocyclyl ring.
  • X is V * ® ' ; and two R 21 groups are joined to form an unsubstituted 6
  • R 21 membered heterocyclyl ring.
  • X is v ⁇ ® N y ' ; and two R 21 groups are joined to form an optionally substituted pyrrolidine, piperidine, piperazine, thiomorpholine
  • X is v ⁇ ® N y ' ; and two R 21 groups are
  • R 2 R 21 joined to form an optionally substituted morpholine.
  • X is Y ⁇ ft ⁇ y ' and two R 21 groups are joined to form an unsubstituted morpholine.
  • X is ; and R 22 is hydrogen; substituted or
  • X is y O y ; and R 22 is hydrogen; substituted or unsubstituted
  • R is hydrogen; or substituted or unsubstituted alkyl.
  • X is R 22
  • R 22 is hydrogen; or substituted or unsubstituted Ci_6 alkyl.
  • X is O ; and R 22 is hydrogen; or substituted or unsubstituted Ci_ 2
  • X is v A Y
  • alkyl O°y alkyl O°y ; and R 22 is hydrogen; or substituted or
  • R 22 unsubstituted Q_ 2 alkyl.
  • X is y O ; and R 22 is hydrogen; or
  • R 22 substituted Ci_ 2 alkyl.
  • X is vV O v ; and R 22 is hydrogen; or
  • R 22 unsubstituted Q_ 2 alkyl.
  • X is y O ; and R 22 is hydrogen.
  • R 22 certain embodiments, X is y O ; and R 22 is substituted or unsubstituted Q_ 2 alkyl.
  • X is y O ; and R 22 is substituted Ci_ 2 alkyl (e.g., haloalkyl).
  • X is O ; and R 22 is unsubstituted Ci_ 2 alkyl.
  • X is yl (e.g., C3 cycloalkyl).
  • X is ; and R is .
  • X is .
  • X is heterocyclylene or heteroarylene. In certain embodiments, X is heterocyclylene. In certain embodiments, X is a 6-membered
  • X is a piperazinylene. In certain embodiments, X is heteroarylene. In certain embodiments, X is a 5-membered heteroarylene. In certain embodiments, X is an imidazolylene.
  • Ar is substituted or unsubstituted arylene. In certain embodiments, Ar is substituted or unsubstituted phenylene. In certain embodiments, Ar is unsubstituted phenylene.
  • each occurrence of Z is independently an amino acid.
  • Z is independently a naturally occurring amino acid.
  • Z is independently lysine, arginine, histidine, ornithine, or citrulline.
  • Z is lysine or citrulline.
  • Z is citrulline.
  • each occurrence of Y is independently an amino acid. In certain embodiments, Y is independently a naturally occurring amino acid. In certain embodiments, Y is alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan. In certain embodiments, Y is valine or phenylalanine. In certain embodiments, Y is valine.
  • each occurrence of m is 1, 2, or 3. In certain embodiments, each occurrence of m is 1 or 2. In certain embodiments, each occurrence of m is 1.
  • -Z m -Y m - is -citrulline- valine-.
  • E is a bond or an amino acid. In certain embodiments, E is a bond or a naturally occurring amino acid. In certain embodiments, E is a bond or a substituted naturally occurring amino acid. In certain embodiments, E is a bond. In certain embodiments, E is a naturally occurring amino acid. In certain embodiments, E is a substituted naturally occurring amino acid. In certain embodiments, E is a substituted lysine. [00162] In certain embodiments, E is of the formula:
  • R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl.
  • E is of the formula:
  • n 2-30.
  • E is of the formula:
  • R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene.
  • R 40 is substituted or unsubstituted Ci_6 alkylene; or substituted or unsubstituted Ci_ 4 o heteroalkylene.
  • R 40 is substituted or unsubstituted alkylene.
  • R 40 is substituted or unsubstituted C 1-6 alkylene.
  • R 40 is substituted C 1-6 alkylene.
  • R 40 is unsubstituted C 1-6 alkylene.
  • R 40 is substituted or unsubstituted heteroalkylene.
  • R 40 is substituted or unsubstituted Ci_ 4 o heteroalkylene. In certain embodiments, R 40 is substituted Ci_ 4 o heteroalkylene. In certain embodiments, R 40 is unsubstituted C 1-4 o heteroalkylene. In certain embodiments, R 40 is , Ci_6 unsubstituted alkylene, or ; wherein p is
  • R 40 is . In certain embodiments, R 40 is Ci_ 6 unsubstituted alkylene. In certain embodiments, R is P ; wherein p is 1-8. In certain R 40 is P ; wherein p is 2-8. In certain embodiments, R 40 is ; wherein p is 2, 4, or 8. In certain embodiments, R 40 is 2 . In certain embodiments, R 40 is 4 . In certain embodiments, R 40 is
  • A is a group of the formula:
  • Q is -S-, or -0-; and R wl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
  • A is a group of the formula:
  • A is a group of the formula:
  • L is a group of Formula (L-1):
  • R is substituted or unsubstituted C 1-6 alkylene
  • R 22 is hydrogen, or substituted or unsubstituted Ci_ 6 alkyl
  • R 40 is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene
  • R 50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine
  • R 60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
  • L is a group of Formula (L-2):
  • R 20 is substituted or unsubstituted Ci_ 6 alkylene
  • R 22 is hydrogen, or substituted or unsubstituted Ci_ 6 alkyl
  • R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene
  • R 50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine
  • R 60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
  • L is a group of Formula (L-3):
  • R 20 is substituted or unsubstituted Ci_ 6 alkylene
  • R 22 is hydrogen, or substituted or unsubstituted Ci_ 6 alkyl
  • R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene.
  • L is a group of Formula (L-4):
  • R is substituted or unsubstituted C 1-6 alkylene; and R 22 is hydrogen or substituted or unsubstituted Ci_ 6 alkyl.
  • R is unsubstituted C 2 -5 alkylene; and R is hydrogen or methyl.
  • L is a group of Formula (L-5):
  • R 20 is substituted or unsubstituted C 1-6 alkylene;
  • R 22 is hydrogen, or substituted or unsubstituted Ci_ 6 alkyl; and
  • p is 1- 10.
  • R ⁇ is unsubstituted C 2 -5 alkylene; R is hydrogen or methyl; and p is 2-8.
  • L is a group of Formula (L-6):
  • R u is substituted or unsubstituted Ci- alkylene; and R 22 is hydrogen or substituted or unsubstituted Ci_ 6 alkyl.
  • R 20 is unsubstituted C 2 -5 alkylene; and R 22 is hydrogen or methyl.
  • L is a group of Formula (L-7):
  • R u is substituted or unsubstituted Ci_ 6 alkylene; and R 22 is hydrogen or substituted or unsubstituted C 1-6 alkyl.
  • R 20 is unsubstituted C 2 -5 alkylene; and R 22 is hydrogen or methyl.
  • L is a group of Formula (L-8):
  • R is substituted or unsubstituted C 1-6 alkylene;
  • R 22 is hydrogen or substituted or unsubstituted C 1-6 alkyl;
  • R 40 is substituted or
  • R 20 is unsubstituted C 2 -5 alkylene; R 22 is hydrogen or methyl; R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted C 1-4 o heteroalkylene; and R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl.
  • R 20 is unsubstituted C 2 -5 alkylene; R 22 is hydrogen or methyl; R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted C 1-4 o heteroalkylene; and R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl.
  • R 20 is unsubstituted C 2 -5 alkylene
  • R 22 is hydrogen or methyl; R 40 is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted C 1-4 o heteroalkylene; and R 70 is unsubstituted C 1-4 o heteroalkylene.
  • R 20 is unsubstituted C 2 22
  • R is hydrogen or methyl; R is substituted or unsub alkylene, or substituted or unsubstituted Ci_ 4 o heteroalkylene; and R is ; wherein p is 1-30.
  • R is unsubstituted C 2 -5 alkylene;
  • R is hydrogen or methyl;
  • R is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted Ci_ 4 o heteroalkylene;
  • L is a group of Formula (L-9):
  • n 2-30.
  • R 20 is substituted or unsubstituted Ci_ 6 alkylene; R 22 is hydrogen or substituted or unsubstituted 40
  • R is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene; and n is 1-9.
  • R 20 is unsubstituted 22
  • R 20 is hydrogen or methyl;
  • R 40 is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted Ci_ heteroalkylene; and
  • n is 1-9.
  • R 20 is hydrogen or methyl;
  • R 20 is unsubstituted 22
  • R is hydrogen or methyl
  • R 40 is unsubstituted Ci_ 4 o heteroalkylene
  • n is 1-9.
  • L is a group of Formula (L-10):
  • R is substituted or unsubstituted C 1-6 alkylene;
  • R 21 is independently substituted or unsubstituted Ci_ 6 alkyl;
  • R 40 is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene;
  • R 50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
  • R 60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
  • L is a group of Formula (L-11):
  • R is substituted or unsubstituted Ci_ 6 alkylene
  • R 21 is independently substituted or unsubstituted C 1-6 alkyl
  • R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene
  • R 50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline
  • R 60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
  • L is a group of Formula (L-12):
  • R 20 is substituted or unsubstituted C 1-6 alkylene;
  • R 21 is independently substituted or unsubstituted Ci_ 6 alkyl; and
  • R 40 is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene.
  • L is a group of Formula (L-13):
  • R 20 is substituted or unsubstituted Ci_ 6 alkylene; and R 21 is independently substituted or unsubstituted C 1-6 alkyl.
  • R 20 is unsubstituted C 2 -5 alkylene; and R 21 is methyl.
  • L is a group of Formula (L-14):
  • R is substituted or unsubstituted Ci_ 6 alkylene; R 21 is independently substituted or unsubstituted Ci_ 6 alkyl; and p is 1-10.
  • R 20 is unsubstituted C 2 _5 alkylene; R 21 is methyl; and p is 2-
  • L is a group of Formula (L-15):
  • R is substituted or unsubstituted Ci_ 6 alkylene; and R 21 is independently substituted or unsubstituted Ci_ 6 alkyl.
  • R 20 is unsubstituted C 2 _5 alkylene; and R 21 is methyl.
  • L is a group of Formula (L-16):
  • R is substituted or unsubstituted Ci_ 6 alkylene; and R 21 is independently substituted or unsubstituted Ci_ 6 alkyl.
  • R is unsubstituted C 2 _5 alkylene; and R 1 is methyl.
  • L is a group of Formula (L-17):
  • R is substituted or unsubstituted Ci_ 6 alkylene; R 21 is independently substituted or unsubstituted Ci_ 6 alkyl; R 40 is substituted or
  • R 20 is unsubstituted C 2 -5 alkylene; R 21 is methyl; R 40 is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted Ci_ 4 o heteroalkylene; and R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl.
  • R 20 is unsubstituted C 2 -5 alkylene; R 21 is methyl; R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted C 1-4 o
  • R 20 is unsubstituted C 2 -5 alkylene; R 21 is methyl; R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted C 1-4 o heteroalkylene; and R 70 is unsubstituted alkylene.
  • R 20 is unsubstituted C 2 -5 alkylene; R 21 is methyl; R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted C 1-4 o heteroalkylene; and R 70 is unsubstituted alkylene.
  • R 20 is unsubstituted C 2 -5 alkylene; R 21 is methyl; R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted C 1-4 o heteroalkylene; and R 70 is unsubstituted alkylene.
  • R 21 is methyl
  • R 40 is substituted d Ci_ 6 alkylene
  • Ci_ 4 o heteroalkylene or substituted or unsubstituted Ci_ 4 o heteroalkylene; and R is P ; wherein p is
  • R is unsubstituted C 2 -5 alkylene; R is bstituted or unsubstituted Ci_ 4 o
  • L is a group of Formula (L-18):
  • n 2-30.
  • R is substituted or unsubstituted Ci_ 6 alkylene
  • R 21 is independently substituted or unsubstituted Ci_ 6 alkyl
  • R 40 is substituted or unsubstituted Ci_ 6 alkylene, or substituted or unsubstituted Ci ⁇ o heteroalkylene
  • n is 1-9.
  • R 20 is unsubstituted ;
  • C 2 -5 alkylene is independently unsubstituted C 1-6 alkyl; R 40 is substituted or unsubstituted C 1-6 alkylene, or substituted or unsubstituted Ci_ 4 o heteroalkylene; and n is 1-9.
  • R 20 is unsubstituted C 2 -5 alkylene; R 21 is methyl; R 40 is substituted or unsubstituted C 1-6 alkylene; and n is 1-9.
  • R 20 is unsubstituted C 2 -5 alkylene; R 21 is methyl; R 40 is unsubstituted C 1-4 o heteroalkylene; and n is 1-9.
  • R 7 is -L 1 -T; wherein is a group of the formula:
  • R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;

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Abstract

Provided herein are trioxacarcin-antibody drug conjugates of Formula (I): and pharmaceutically acceptable salts thereof, wherein R7 is -L-B, wherein L is a linking group, and B is an antibody or antibody fragment. Also provided are methods of preparing the antibody-drug conjugates, pharmaceutically acceptable compositions thereof, and methods of their use and treatment. Further provided are precursors to the trioxacarcin- antibody drug conjugates (e.g., compounds of Formula (II), novel trioxacarcins without an antibody conjugated thereto), pharmaceutical compositions thereof, and methods of their use and treatment.

Description

TRIOXACARCIN-ANTIBODY CONJUGATES AND USES THEREOF
Related Applications
[0001] This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional
Applications, U.S.S.N. 62/544,614, filed August 11, 2017, and U.S.S.N. 62/578,997, filed October 30, 2017. The entire content of each is incorporated herein by reference.
Background of the Invention
[0002] Antibody-drug conjugates (ADCs) are a targeted therapy consisting of three components: a target-specific antibody (e.g., a monoclonal antibody, mAb) or antibody fragment (e.g., a single-chain variable fragment (scFv)); a payload, often a cytotoxic drug; and a linker connecting the drug to the antibody. Upon administration, the antibody binds to a target cell and the drug exerts its therapeutic effect, for example, by optional cleavage from the ADC and/or by internalization in the cell or proximity to the outside of the cell. See, e.g., Ducry et al., Bioconjugate Chemistry (2010) 21: 5-13; Kovtun et al., Cancer Research (2006) 66: 3214-21; and Kovtun et al, Cancer Letters (2007) 255 (2): 232-40. Targeted therapies are envisioned to provide many advantages including, but not limited to, decreased side effects and a wider therapeutic window as compared to untargeted therapies.
[0003] The type of linker used is an important consideration in the design of the ADC. For example, ADCs with cleavable linkers are thought to have a less favorable therapeutic window, and are best designed for targets, such as tumor cell surface antigens that are internalized efficiently. The linker should also be designed in a manner that ensures stability during circulation in blood but allows for the rapid release of the drug, preferably inside the target cell. Several types of enzymatically degradable and non-degradable linkers for ADCs have also been explored, such as cleavable acid- and peptidase-labile linkers and non- cleavable linkers such as thioethers. See, e.g., Ducry et al., Bioconjugate Chemistry (2010) 21: 5-13.
[0004] Natural products that bind and often covalently modify duplex DNA figure prominently in chemotherapy for human cancers. The trioxacarcins are a class of DNA- modifying natural products with antiproliferative effects. The trioxacarcins were first described in 1981 by Tomita and coworkers. See, e.g., Tomita et al., J. Antibiotics,
34(12): 1520-1524, 1981; Tamaoki et al, J. Antibiotics 34(12): 1525-1530, 1981; Fujimoto et al., J. Antibiotics 36(9): 1216— 1221, 1983. Trioxacarcin A, B, and C were isolated by Tomita and coworkers from the culture broth of Streptomyces bottropensis DO-45 and shown to possess anti-tumor activity in murine models as well as gram-positive antibiotic activity. Subsequent work led to the discovery of other members of this family. Trioxacarcin A is a powerful anticancer agent with subnanmolar IC70 values against lung (LXFL 529L, H-460), mammary (MCF-7), and CNS (SF-268) cancer cell lines. The trioxacarcins have also been shown to have antimicrobial activity, e.g., anti-bacterial and anti-malarial activity. See, e.g., Maskey et ah, J. Antibiotics (2004) 57:771-779. An X-ray crystal structure of trioxacarcin A bound to Ν-Ί of a guanidylate residue in a duplex DNA oligonucleotide substrate has provided compelling evidence for a proposed pathyway of DNA modification that proceeds by duplex intercalation and alkylation. See, e.g., Pfoh et ah, Nucleic Acids Research (2008) 36:3508-3514. All trioxacarcins appear to be derivatives of the aglycone, which is itself a bacterial isolate referred to in the patent literature as DC-45-A2. U.S. Patent 4,459,291, issued July 10, 1984, describes the preparation of DC-45-A2 by fermentation. DC-45-A2 is the algycone of trioxacarcins A, B, and C and is prepared by the acid hydrolysis of the fermentation products trioxacarcins A and C or the direct isolation from the fermentation broth of Streptomyces bottropensis.
[0005] Prior to this work, the inventors developed a fully synthetic method to access known trioxacarcins and novel trioxacarcin analogs. See, e.g., PCT Application Publication No. WO 2011/119549 and PCT Application Publication No. WO 2014/082065, both of which are incorporated herein by reference. A wide variety of fully synthetic natural and nonnatural trioxacarcin compounds have been prepared by a process that is amenable to scaling.
Summary of the Invention
[0006] The present disclosure provides access to novel trioxacarcin-antibody drug conjugates and trioxacarcin-antibody drug conjugate precursor compounds with
advantageous properties (e.g., stability, release kinetics). The trioxacarcins are highly toxic to a variety of cell types. Linking a trioxacarcin to an antibody preserves the trioxacarcin' s potency against a particular cell type while increasing specificity to the target cell, and optionally increasing endocytosis of the trioxacarcin. These effects enable lowering the overall amount of trioxacarcin to be delivered, thereby reducing the associated toxicity. [0007] In one aspect, provided is a com ound of Formula (I):
Figure imgf000005_0001
(I)
or a pharmaceutically acceptable salt thereof;
wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CO^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -NCR^k; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two R^ groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000006_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000007_0001
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -L-B;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NRI2C(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
Figure imgf000007_0002
wherein each occurrence of R II is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R 12 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB 1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB 1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl;
B2
or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40-A— I Qr j— R20~X-R1 1— S— j.
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
R22
R2 R21
X S \ J / ; O ; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carbocyclyl; or
Figure imgf000009_0001
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
A is a group of the formula
Figure imgf000010_0001
Q is -S-, or - -;
Rwl is independently hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
[0008] In another aspect, provided is a compound of Formula (II):
Figure imgf000010_0002
or a pharmaceutically acceptable salt thereof;
wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CO^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two R^ groups are optionally joined to form a heterocyclyl or heteroaryl ring; R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring; R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000012_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000012_0002
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -ΐ Τ;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR ; -C(=0)Ri ; -C02Ru; -CN; -SCN; -SRn; -SOR11; -S02Ru; -N02; -N3; -N(R^)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB 1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R B2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L1 is of the formula:
Figure imgf000014_0001
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000014_0002
; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring; R is h drogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carbocyclyl; or
Figure imgf000015_0001
;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000015_0002
Figure imgf000015_0003
Q is -S-, or -0-;
R is a leaving group (e.g., halogen, tosylate, or mesylate);
X2
R is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is independently hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
[0009] In certain embodiments, the compound of Formula (I) or Formula (II) is of the formula:
Figure imgf000015_0004
or a pharmaceutically acceptable salt thereof. [0010] In certain embodiments, the compound of Formula (I) or Formula (II) is of the formula:
Figure imgf000016_0001
or a pharmaceutically acceptable salt thereof.
[0011] In certain embodiments, the compound of Formula (I) or Formula (II) is of the formula:
Figure imgf000016_0002
or a pharmaceutically acceptable salt thereof.
[0012] In another aspect, provided are novel trioxacarcin analogs (without linker groups or antibodies conjugated thereto).
[0013] In another aspect, provided are pharmaceutical compositions comprising any of the compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, and optionally a pharmaceutically acceptable carrier.
[0014] In another aspect, provided are methods of treating cardiovascular disease, proliferative disease (e.g., cancer), diabetic retinopathy, inflammatory disease, autoimmune disease, or infectious disease in a subject in need thereof, the method comprising
administering to the subject an effective amount of any of the compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, or a pharmaceutical composition comprising such to the subject.
[0015] In another aspect, provided are kits comprising compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, or pharmaceutical compositions comprising such. In certain embodiments, the kits further comprise instructions for administration (e.g., human administration).
[0016] Also within the scope of the present disclosure are pharmaceutical compositions comprising any of the compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, and a pharmaceutically acceptable carrier for use in treating cardiovascular disease, proliferative disease (e.g., cancer), diabetic retinopathy, inflammatory disease, autoimmune disease, or infectious disease, as well as uses of any of the compounds of Formula (I), Formula (II), or novel trioxacarcin analogs as described herein, or pharmaceutically acceptable salts thereof, for manufacturing a medicament for use in treating any of the target diseases.
[0017] Also provided are methods of preparing compounds of Formula (I), Formula (II), and the novel trioxacarcin analogs as described herein.
[0018] The details of one or more embodiments of the invention are set forth in the accompanying Figures and the Detailed Description below. Other features, objects, and advantages of the invention will be apparent from the Examples and the Claims.
Definitions
Chemical definitions
[0019] Definitions of specific functional groups and chemical terms are described in more detail below. The chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75th Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito, 1999; Smith and March March 's Advanced Organic Chemistry, 5th Edition, John Wiley & Sons, Inc., New York, 2001; Larock, Comprehensive Organic Transformations, VCH Publishers, Inc., New York, 1989; and Carruthers, Some Modern Methods of Organic Synthesis, 3 Edition, Cambridge University Press, Cambridge, 1987.
[0020] Compounds described herein may comprise one or more asymmetric centers, and thus may exist as stereoisomers, e.g., enantiomers and/or diastereomer s. For example, the compounds described herein can be in the form of an individual enantiomer, diastereomer or geometric isomer, or can be in the form of a mixture of stereoisomers, including racemic mixtures and mixtures enriched in one or more stereoisomer. Isomers can be isolated from mixtures by methods known to those skilled in the art, including chiral high pressure liquid chromatography (HPLC) and the formation and crystallization of chiral salts; or preferred isomers can be prepared by asymmetric syntheses. See, for example, Jacques et ah,
Enantiomers, Racemates and Resolutions (Wiley Interscience, New York, 1981); Wilen et al., Tetrahedron 33:2725 (1977); Eliel, E.L. Stereochemistry of Carbon Compounds
(McGraw-Hill, NY, 1962); and Wilen, S.H. Tables of Resolving Agents and Optical Resolutions p. 268 (E.L. Eliel, Ed., Univ. of Notre Dame Press, Notre Dame, IN 1972).
Compounds may exist as individual isomers substantially free of other isomers, and alternatively, as mixtures of various isomers.
[0021] When a range of values is listed, it is intended to encompass each value and subrange within the range. For example "Ci_6 alkyl" is intended to encompass, Q, C2, C3, C4,
C5, C6, Ci_6, Ci_5, Ci^, Ci_3, Q_2, C2-6, C2-5, C2- , C2-3, C3_6, C3_5, C3^, C4_6, C4_5, and Cs_6 alkyl.
[0022] As used herein, "alkyl" refers to a radical of a straight-chain or branched saturated hydrocarbon group having from 1 to 10 carbon atoms ("Ci_io alkyl"). In some embodiments, an alkyl group has 1 to 9 carbon atoms ("Ci_9 alkyl"). In some embodiments, an alkyl group has 1 to 8 carbon atoms ("Ci_8 alkyl"). In some embodiments, an alkyl group has 1 to 7 carbon atoms ("Ci_7 alkyl"). In some embodiments, an alkyl group has 1 to 6 carbon atoms ("Ci_6 alkyl"). In some embodiments, an alkyl group has 1 to 5 carbon atoms ("Ci_5 alkyl"). In some embodiments, an alkyl group has 1 to 4 carbon atoms ("C^ alkyl"). In some embodiments, an alkyl group has 1 to 3 carbon atoms ("Ci_3 alkyl"). In some embodiments, an alkyl group has 1 to 2 carbon atoms ("Ci_2 alkyl"). In some embodiments, an alkyl group has 1 carbon atom ("Q alkyl"). In some embodiments, an alkyl group has 2 to 6 carbon atoms ("C2-6 alkyl"). Examples of Ci_6 alkyl groups include methyl (CO, ethyl (C2), n-propyl (C3), isopropyl (C3), n-butyl (C4), tert-butyl (C4), sec-butyl (C4), iso-butyl (C4), n-pentyl (C5), 3-pentanyl (C5), amyl (C5), neopentyl (C5), 3-methyl-2-butanyl (C5), tertiary amyl (C5), and n-hexyl (C6). Additional examples of alkyl groups include n-heptyl (C7), n-octyl (C8) and the like. Unless otherwise specified, each instance of an alkyl group is
independently unsubstituted (an "unsubstituted alkyl") or substituted (a "substituted alkyl") with one or more substituents. In certain embodiments, the alkyl group is an unsubstituted Ci_io alkyl (e.g., -CH3). In certain embodiments, the alkyl group is a substituted Ci_io alkyl.
[0023] As used herein, "heteroalkyl" refers to an alkyl group as described herein which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkyl group refers to a saturated group having from 1 to 10 carbon atoms and 1 or more
heteroatoms within the parent chain ("heteroCi_io alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 9 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi_9 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 8 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi_8 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 7 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi_7 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 6 carbon atoms and 1 or more heteroatoms within the parent chain ("heteroCi_6 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 5 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroCi_5 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 4 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroCi^ alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 3 carbon atoms and 1 heteroatom within the parent chain
("heteroCi_3 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 to 2 carbon atoms and 1 heteroatom within the parent chain ("heteroCi_2 alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 1 carbon atom and 1 heteroatom ("heteroCi alkyl"). In some embodiments, a heteroalkyl group is a saturated group having 2 to 6 carbon atoms and 1 or 2 heteroatoms within the parent chain ("heteroC2-6 alkyl"). Unless otherwise specified, each instance of a heteroalkyl group is independently unsubstituted (an "unsubstituted heteroalkyl") or substituted (a "substituted heteroalkyl") with one or more substituents. In certain embodiments, the heteroalkyl group is an unsubstituted heteroCi_io alkyl. In certain embodiments, the heteroalkyl group is a substituted heteroCi_io alkyl.
[0024] As used herein, "alkenyl" refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more double bonds (e.g., 1, 2, 3, or 4 double bonds). In some embodiments, an alkenyl group has 2 to 9 carbon atoms ("C2-9 alkenyl"). In some embodiments, an alkenyl group has 2 to 8 carbon atoms ("C2-8 alkenyl"). In some embodiments, an alkenyl group has 2 to 7 carbon atoms ("C2-7 alkenyl"). In some embodiments, an alkenyl group has 2 to 6 carbon atoms ("C2-6 alkenyl"). In some embodiments, an alkenyl group has 2 to 5 carbon atoms ("C2-5 alkenyl"). In some
embodiments, an alkenyl group has 2 to 4 carbon atoms ("C2^ alkenyl"). In some
embodiments, an alkenyl group has 2 to 3 carbon atoms ("C2-3 alkenyl"). In some
embodiments, an alkenyl group has 2 carbon atoms ("C2 alkenyl"). The one or more carbon- carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1-butenyl). Examples of C2^ alkenyl groups include ethenyl (C2), 1-propenyl (C3), 2-propenyl (C3), 1- butenyl (C4), 2-butenyl (C4), butadienyl (C4), and the like. Examples of C2-6 alkenyl groups include the aforementioned C2^ alkenyl groups as well as pentenyl (C5), pentadienyl (C5), hexenyl (C6), and the like. Additional examples of alkenyl include heptenyl (C7), octenyl (C8), octatrienyl (C8), and the like. Unless otherwise specified, each instance of an alkenyl group is independently unsubstituted (an "unsubstituted alkenyl") or substituted (a
"substituted alkenyl") with one or more substituents. In certain embodiments, the alkenyl group is an unsubstituted C2-io alkenyl. In certain embodiments, the alkenyl group is a substituted C2-io alkenyl.
[0025] As used herein, "heteroalkenyl" refers to an alkenyl group as described herein which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkenyl group refers to a group having from 2 to 10 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-io alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 9 carbon atoms at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-9 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 8 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-8 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 7 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-7 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and 1 or more heteroatoms within the parent chain ("heteroC2-6 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 5 carbon atoms, at least one double bond, and 1 or 2
heteroatoms within the parent chain ("heteroC2-5 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 4 carbon atoms, at least one double bond, and 1 or 2
heteroatoms within the parent chain ("heteroC2^ alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 3 carbon atoms, at least one double bond, and 1 heteroatom within the parent chain ("heteroC2-3 alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 6 carbon atoms, at least one double bond, and 1 or 2 heteroatoms within the parent chain ("heteroC2-6 alkenyl"). Unless otherwise specified, each instance of a heteroalkenyl group is independently unsubstituted (an "unsubstituted heteroalkenyl") or substituted (a "substituted heteroalkenyl") with one or more substituents. In certain embodiments, the heteroalkenyl group is an unsubstituted heteroC2-io alkenyl. In certain embodiments, the heteroalkenyl group is a substituted heteroC2-io alkenyl.
[0026] As used herein, "alkynyl" refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 10 carbon atoms and one or more triple bonds (e.g., 1, 2, 3, or 4 triple bonds) ("C2-io alkynyl"). In some embodiments, an alkynyl group has 2 to 9 carbon atoms ("C2-9 alkynyl"). In some embodiments, an alkynyl group has 2 to 8 carbon atoms ("C2-8 alkynyl"). In some embodiments, an alkynyl group has 2 to 7 carbon atoms ("C2-7 alkynyl"). In some embodiments, an alkynyl group has 2 to 6 carbon atoms ("C2-6 alkynyl"). In some embodiments, an alkynyl group has 2 to 5 carbon atoms ("C2-5 alkynyl"). In some embodiments, an alkynyl group has 2 to 4 carbon atoms ("C2^ alkynyl"). In some embodiments, an alkynyl group has 2 to 3 carbon atoms ("C2-3 alkynyl"). In some embodiments, an alkynyl group has 2 carbon atoms ("C2 alkynyl"). The one or more carbon- carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl). Examples of C2^ alkynyl groups include, without limitation, ethynyl (C2), 1-propynyl (C3), 2-propynyl (C3), 1-butynyl (C4), 2-butynyl (C4), and the like. Examples of C2-6 alkenyl groups include the aforementioned C2^ alkynyl groups as well as pentynyl (C5), hexynyl (C6), and the like. Additional examples of alkynyl include heptynyl (C7), octynyl (C8), and the like. Unless otherwise specified, each instance of an alkynyl group is independently unsubstituted (an "unsubstituted alkynyl") or substituted (a "substituted alkynyl") with one or more substituents. In certain embodiments, the alkynyl group is an unsubstituted C2 10 alkynyl. In certain embodiments, the alkynyl group is a substituted C2 10 alkynyl.
[0027] As used herein, "heteroalkynyl" refers to an alkynyl group as described herein which further includes at least one heteroatom (e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen, or sulfur within (i.e., inserted between adjacent carbon atoms of) and/or placed at one or more terminal position(s) of the parent chain. In certain embodiments, a heteroalkynyl group refers to a group having from 2 to 10 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-io alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 9 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-9 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 8 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-s alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 7 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-7 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or more heteroatoms within the parent chain ("heteroC2-6 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 5 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain ("heteroC2-5 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 4 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain ("heteroC2^ alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 3 carbon atoms, at least one triple bond, and 1 heteroatom within the parent chain ("heteroC2-3 alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 6 carbon atoms, at least one triple bond, and 1 or 2 heteroatoms within the parent chain ("heteroC2-6 alkynyl"). Unless otherwise specified, each instance of a heteroalkynyl group is independently unsubstituted (an "unsubstituted heteroalkynyl") or substituted (a "substituted heteroalkynyl") with one or more substituents. In certain embodiments, the heteroalkynyl group is an unsubstituted heterod-io alkynyl. In certain embodiments, the heteroalkynyl group is a substituted heterod-io alkynyl.
[0028] As used herein, "carbocyclyl" or "carbocyclic" refers to a radical of a non- aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms ("C3_io
carbocyclyl") and zero heteroatoms in the non-aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms ("C3_8 carbocyclyl"). In some
embodiments, a carbocyclyl group has 3 to 7 ring carbon atoms ("C3_7 carbocyclyl"). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms ("C3_6 carbocyclyl"). In some embodiments, a carbocyclyl group has 5 to 10 ring carbon atoms ("Cs-io
carbocyclyl"). Exemplary C3_6 carbocyclyl groups include, without limitation, cyclopropyl (C3), cyclopropenyl (C3), cyclobutyl (C4), cyclobutenyl (C4), cyclopentyl (C5), cyclopentenyl (C5), cyclohexyl (C6), cyclohexenyl (C6), cyclohexadienyl (C6), and the like. Exemplary C3_8 carbocyclyl groups include, without limitation, the aforementioned C3_6 carbocyclyl groups as well as cycloheptyl (C7), cycloheptenyl (C7), cycloheptadienyl (C7), cycloheptatrienyl (C7), cyclooctyl (C8), cyclooctenyl (C8), bicyclo[2.2.1]heptanyl (C7), bicyclo[2.2.2]octanyl (C8), and the like. Exemplary C3_io carbocyclyl groups include, without limitation, the
aforementioned C3_8 carbocyclyl groups as well as cyclononyl (C9), cyclononenyl (C9), cyclodecyl (C10), cyclodecenyl (C10), octahydro-lH-indenyl (C9), decahydronaphthalenyl (Cio), spiro[4.5]decanyl (C10), and the like. As the foregoing examples illustrate, in certain embodiments, the carbocyclyl group is either monocyclic ("monocyclic carbocyclyl") or polycyclic (e.g., containing a fused, bridged or spiro ring system such as a bicyclic system ("bicyclic carbocyclyl") or tricyclic system ("tricyclic carbocyclyl")) and can be saturated or can contain one or more carbon-carbon double or triple bonds. "Carbocyclyl" also includes ring systems wherein the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. Unless otherwise specified, each instance of a carbocyclyl group is independently unsubstituted (an "unsubstituted carbocyclyl") or substituted (a "substituted carbocyclyl") with one or more substituents. In certain embodiments, the carbocyclyl group is an unsubstituted C3_io carbocyclyl. In certain embodiments, the carbocyclyl group is a substituted C3_io carbocyclyl.
[0029] In some embodiments, "carbocyclyl" is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms ("C3_io cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms ("C3_8 cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms ("C3_6 cycloalkyl"). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms ("Cs_6 cycloalkyl"). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms ("Cs_io cycloalkyl"). Examples of Cs_6 cycloalkyl groups include cyclopentyl (C5) and cyclohexyl (C5). Examples of C3_6 cycloalkyl groups include the aforementioned Cs_6 cycloalkyl groups as well as cyclopropyl (C3) and cyclobutyl (C4). Examples of C3_8 cycloalkyl groups include the aforementioned C3_6 cycloalkyl groups as well as cycloheptyl (C7) and cyclooctyl (C8). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an
"unsubstituted cycloalkyl") or substituted (a "substituted cycloalkyl") with one or more substituents. In certain embodiments, the cycloalkyl group is an unsubstituted C3_io
cycloalkyl. In certain embodiments, the cycloalkyl group is a substituted C3_io cycloalkyl.
[0030] As used herein, "heterocyclyl" or "heterocyclic" refers to a radical of a 3- to 14- membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("3-14 membered heterocyclyl"). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic ("monocyclic heterocyclyl") or polycyclic (e.g., a fused, bridged or spiro ring system such as a bicyclic system ("bicyclic heterocyclyl") or tricyclic system ("tricyclic heterocyclyl")), and can be saturated or can contain one or more carbon- carbon double or triple bonds. Heterocyclyl polycyclic ring systems can include one or more heteroatoms in one or both rings. "Heterocyclyl" also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. Unless otherwise specified, each instance of heterocyclyl is independently unsubstituted (an "unsubstituted heterocyclyl") or substituted (a "substituted heterocyclyl") with one or more substituents. In certain embodiments, the heterocyclyl group is an unsubstituted 3-14 membered heterocyclyl. In certain embodiments, the heterocyclyl group is a substituted 3-14 membered heterocyclyl.
[0031] In some embodiments, a heterocyclyl group is a 5-10 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heterocyclyl"). In some embodiments, a heterocyclyl group is a 5-8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is
independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heterocyclyl"). In some embodiments, a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is
independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heterocyclyl"). In some embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur.
[0032] Exemplary 3-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azirdinyl, oxiranyl, thiorenyl. Exemplary 4-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary 5-membered heterocyclyl groups containing 1 heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl, tetrahydrothiophenyl,
dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl and pyrrolyl-2,5-dione. Exemplary 5- membered heterocyclyl groups containing 2 heteroatoms include, without limitation, dioxolanyl, oxathiolanyl and dithiolanyl. Exemplary 5-membered heterocyclyl groups containing 3 heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6-membered heterocyclyl groups containing 1 heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary 6-membered heterocyclyl groups containing 2 heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, dioxanyl. Exemplary 6-membered
heterocyclyl groups containing 3 heteroatoms include, without limitation, triazinyl.
Exemplary 7-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered heterocyclyl groups containing 1 heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl.
Exemplary bicyclic heterocyclyl groups include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl, tetrahydrobenzothienyl, tetrahydrobenzofuranyl, tetrahydroindolyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyl,
decahydronaphthyridinyl, decahydro-l,8-naphthyridinyl, octahydropyrrolo[3,2-b]pyrrole, indolinyl, phthalimidyl, naphthalimidyl, chromanyl, chromenyl, lH-benzo[e] [l,4]diazepinyl, l,4,5,7-tetrahydropyrano[3,4-b]pyrrolyl, 5,6-dihydro-4H-furo[3,2-b]pyrrolyl, 6,7-dihydro- 5H-furo[3,2-b]pyranyl, 5,7-dihydro-4H-thieno[2,3-c]pyranyl, 2,3-dihydro-lH- pyrrolo[2,3-b]pyridinyl, 2,3-dihydrofuro[2,3-b]pyridinyl, 4,5,6,7-tetrahydro-lH-pyrrolo- [2,3-b]pyridinyl, 4,5,6,7-tetrahydrofuro[3,2-c]pyridinyl, 4,5,6,7-tetrahydrothieno[3,2- b]pyridinyl, l,2,3,4-tetrahydro-l,6-naphthyridinyl, and the like.
[0033] As used herein, "aryl" refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 π electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system ("C6-i4 aryl"). In some embodiments, an aryl group has 6 ring carbon atoms ("C6 aryi"; e.g., phenyl). In some embodiments, an aryl group has 10 ring carbon atoms ("Cio aryi"; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In some embodiments, an aryl group has 14 ring carbon atoms ("C14 aryl"; e.g., anthracyl). "Aryl" also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each instance of an aryl group is independently unsubstituted (an "unsubstituted aryl") or substituted (a "substituted aryl") with one or more substituents. In certain embodiments, the aryl group is an unsubstituted C6- 14 aryl. In certain embodiments, the aryl group is a substituted C6-i4 aryl.
[0034] "Aralkyl" is a subset of "alkyl" and refers to an alkyl group, as described herein, substituted by an aryl group, as described herein, wherein the point of attachment is on the alkyl moiety.
[0035] As used herein, "heteroaryl" refers to a radical of a 5-14 membered monocyclic or polycyclic (e.g., bicyclic, tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 π electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur ("5-14 membered heteroaryl"). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl polycyclic ring systems can include one or more heteroatoms in one or both rings. "Heteroaryl" includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. "Heteroaryl" also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused polycyclic (aryl/heteroaryl) ring system. Polycyclic heteroaryl groups wherein one ring does not contain a heteroatom (e.g., indolyl, quinolinyl, carbazolyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom (e.g., 2-indolyl) or the ring that does not contain a heteroatom (e.g., 5-indolyl).
[0036] In some embodiments, a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heteroaryl"). In some embodiments, a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heteroaryl"). In some embodiments, a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heteroaryl"). In some embodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unless otherwise specified, each instance of a heteroaryl group is independently unsubstituted (an "unsubstituted heteroaryl") or substituted (a "substituted heteroaryl") with one or more substituents. In certain embodiments, the heteroaryl group is an unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is a substituted 5-14 membered heteroaryl.
[0037] Exemplary 5-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl. Exemplary 5-membered heteroaryl groups containing 2 heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroaryl groups containing 3 heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary
5- membered heteroaryl groups containing 4 heteroatoms include, without limitation, tetrazolyl. Exemplary 6-membered heteroaryl groups containing 1 heteroatom include, without limitation, pyridinyl. Exemplary 6-membered heteroaryl groups containing 2 heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary
6- membered heteroaryl groups containing 3 or 4 heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively. Exemplary 7-membered heteroaryl groups containing 1 heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl. Exemplary 5,6- bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl,
benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplary 6,6-bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplary tricyclic heteroaryl groups include, without limitation, phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl, phenothiazinyl, phenoxazinyl and phenazinyl.
[0038] "Heteroaralkyl" is a subset of "alkyl" and refers to an alkyl group, as described herein, substituted by a heteroaryl group, as described herein, wherein the point of attachment is on the alkyl moiety.
[0039] As used herein, the term "partially unsaturated" refers to a ring moiety that includes at least one double or triple bond. The term "partially unsaturated" is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aromatic groups (e.g., aryl or heteroaryl moieties) as herein defined.
[0040] As used herein, the term "saturated" refers to a ring moiety that does not contain a double or triple bond, i.e. , the ring contains all single bonds.
[0041] Affixing the suffix "-ene" to a group indicates the group is a divalent moiety, e.g. , alkylene is the divalent moiety of alkyl, alkenylene is the divalent moiety of alkenyl, alkynylene is the divalent moiety of alkynyl, heteroalkylene is the divalent moiety of heteroalkyl, heteroalkenylene is the divalent moiety of heteroalkenyl, heteroalkynylene is the divalent moiety of heteroalkynyl, carbocyclylene is the divalent moiety of carbocyclyl, heterocyclylene is the divalent moiety of heterocyclyl, arylene is the divalent moiety of aryl, and heteroarylene is the divalent moiety of heteroaryl. [0042] As understood from the above, alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl groups, as described herein, are, in certain embodiments, optionally substituted. Optionally substituted refers to a group which may be substituted or unsubstituted (e.g., "substituted" or "unsubstituted" alkyl, "substituted" or "unsubstituted" alkenyl, "substituted" or "unsubstituted" alkynyl,
"substituted" or "unsubstituted" heteroalkyl, "substituted" or "unsubstituted" heteroalkenyl, "substituted" or "unsubstituted" heteroalkynyl, "substituted" or "unsubstituted" carbocyclyl, "substituted" or "unsubstituted" heterocyclyl, "substituted" or "unsubstituted" aryl or "substituted" or "unsubstituted" heteroaryl group). In general, the term "substituted", whether preceded by the term "optionally" or not, means that at least one hydrogen present on a group (e.g., a carbon or nitrogen atom) is replaced with a permissible substituent, e.g., a substituent which upon substitution results in a stable compound, e.g., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, or other reaction. Unless otherwise indicated, a "substituted" group has a substituent at one or more substitutable positions of the group, and when more than one position in any given structure is substituted, the substituent is either the same or different at each position. The term "substituted" is contemplated to include substitution with all permissible substituents of organic compounds, any of the substituents described herein that results in the formation of a stable compound. The present invention contemplates any and all such combinations in order to arrive at a stable compound. For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents and/or any suitable substituent as described herein which satisfy the valencies of the heteroatoms and results in the formation of a stable moiety.
[0043] Exemplary carbon atom substituents include, but are not limited to, halogen, -CN, -N02, -N3, -S02H, -S03H, -OH, -ORaa, -ON(Rbb)2, -N(Rbb)2, -N(Rbb)3 +X , -N(ORcc)Rbb, -SH, -SRaa, -SSRCC, -C(=0)Raa, -C02H, -CHO, -C(ORcc)3, -C02Raa, -OC(=0)Raa, - OC02Raa, -C(=0)N(Rbb)2, -OC(=0)N(Rbb)2, -NRbbC(=0)Raa, -NRbbC02Raa, - NRbbC(=0)N(Rbb)2, -C(=NRbb)Raa, -C(=NRbb)ORaa, -OC(=NRbb)Raa, -OC(=NRbb)ORaa, - C(=NRbb)N(Rbb)2, -OC(=NRbb)N(Rbb)2, -NRbbC(=NRbb)N(Rbb)2, -C(=0)NRbbS02Raa, - NRbbS02Raa, -S02N(Rbb)2, -S02Raa, -S02ORaa, -OS02Raa, -S(=0)Raa, -OS(=0)Raa, - Si(Raa)3, -OSi(Raa)3 -C(=S)N(Rbb)2, -C(=0)SRaa, -C(=S)SRaa, -SC(=S)SRaa, -SC(=0)SRaa, -OC(=0)SRaa, -SC(=0)ORaa, -SC(=0)Raa, -P(=0)(Raa)2, -P(=0)(ORcc)2, -OP(=0)(Raa)2, -OP(=0)(ORcc)2, -P(=0)(N(Rbb)2)2, -OP(=0)(N(Rbb)2)2, -NRbbP(=0)(Raa)2,
-NRbbP(=0)(ORcc)2, -NRbbP(=0)(N(Rbb)2)2, -P(RCC)2, -P(ORcc)2, -P(RCC)3 +X", -P(ORcc)3 +X~, -P(RCC)4, -P(ORcc)4, -OP(Rcc)2, -OP(Rcc)3 +X", -OP(ORcc)2, -OP(ORcc)3 +X", -OP(Rcc)4, -OP(ORcc)4, -B(Raa)2, -B(ORcc)2, -BRaa(ORcc), Ci_i0 alkyl, Ci_i0 perhaloalkyl, C2_io alkenyl, C2_io alkynyl, heteroCi_io alkyl, heteroC2_io alkenyl, heteroC2_ioalkynyl, C3_io carbocyclyl, C3_i4 carbocyclyl, 3-14 membered heterocyclyl, C6-i4 aryl, and 5-14 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; wherein X~ is a counterion;
or two geminal hydrogens on a carbon atom are replaced with the group =0, =S, =NN(Rbb)2, =NNRbbC(=0)Raa, =NNRbbC(=0)ORaa, =NNRbbS(=0)2Raa, =NRbb, or =NORcc; each instance of Raa is, independently, selected from Ci_io alkyl, Ci_io perhaloalkyl, C2_io alkenyl, C2_io alkynyl, heteroCi_io alkyl, heteroC2_io alkenyl, heteroC2_ioalkynyl, C3_io carbocyclyl, 3-14 membered heterocyclyl, C6-i4 aryl, and 5-14 membered heteroaryl, or two Raa groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups;
each instance of Rbb is, independently, selected from hydrogen, -OH, -ORaa, -
N(RCC)2, -CN, -C(=0)Raa, -C(=0)N(Rcc)2, -C02Raa, -S02Raa, -C(=NRcc)ORaa, -
C(=NRCC)N(RCC)2, -S02N(Rcc)2, -S02Rcc, -S02ORcc, -SORaa, -C(=S)N(RCC)2, -C(=0)SRcc, -
C(=S)SRCC, -P(=0)(Raa)2, -P(=0)(ORcc)2, -P(=0)(N(Rcc)2)2, Cno alkyl, Ci_io perhaloalkyl,
C2_io alkenyl, C2_io alkynyl, heteroCi_ioalkyl, heteroC2_ioalkenyl, heteroC2_ioalkynyl, C3_io carbocyclyl, 3-14 membered heterocyclyl, C6-i4 aryl, and 5-14 membered heteroaryl, or two Rbb groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; wherein X~ is a counterion;
each instance of Rcc is, independently, selected from hydrogen, Ci_io alkyl, Ci_io perhaloalkyl, C2_io alkenyl, C2_io alkynyl, heteroCi-ioalkyl, heteroC2_ioalkenyl, heteroC2_ loalkynyl, C3_io carbocyclyl, 3-14 membered heterocyclyl, C6-i4 aryl, and 5-14 membered heteroaryl, or two Rcc groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups; each instance of R is, independently, selected from halogen, -CN, -N02, -N3, - S02H, -S03H, -OH, -ORee, -ON(Rff)2, -N(Rff)2, -N(Rff)3 +X , -N(ORee)Rff, -SH, -SRee, - SSRee, -C(=0)Ree, -C02H, -C02Ree, -OC(=0)Ree, -OC02Ree, -C(=0)N(Rff)2, - OC(=0)N(Rff)2, -NRffC(=0)Ree, -NRffC02Ree, -NRffC(=0)N(Rff)2, -C(=NRff)ORee, - OC(=NRff)Ree, -OC(=NRff)ORee, -C(=NRff)N(Rff)2, -OC(=NRff)N(Rff)2, - NRffC(=NRff)N(Rff)2,-NRffS02Ree, -S02N(Rff)2, -S02Ree, -S02ORee, -OS02Ree, -S(=0)Ree, -Si(Ree)3, -OSi(Ree)3, -C(=S)N(Rff)2, -C(=0)SRee, -C(=S)SRee, -SC(=S)SRee, -P(=0)2Ree, - P(=0)(Ree)2, -OP(=0)(Ree)2, -OP(=0)(ORee)2, Ci_6 alkyl, Ci_6 perhaloalkyl, C2_6 alkenyl, C2 6 alkynyl, heteroCi_6alkyl, heteroC2_6 alkenyl, heteroC2_6alkynyl, C3_io carbocyclyl, 3-10 membered heterocyclyl, Ce-io aryl, 5-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups, or two geminal Rdd substituents can be joined to form =0 or =S; wherein X~ is a counterion;
each instance of Ree is, independently, selected from Ci_6 alkyl, Ci_6 perhaloalkyl, C2 6 alkenyl, C2_6 alkynyl, heteroCi_6alkyl, heteroC2_6alkenyl, heteroC2_6alkynyl, C3_io
carbocyclyl, C6-io aryl, 3-10 membered heterocyclyl, and 3-10 membered heteroaryl, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups;
ff
each instance of R is, independently, selected from hydrogen, Ci_6 alkyl, Ci_6 perhaloalkyl, C2_6 alkenyl, C2_6 alkynyl, heteroCi_6alkyl, heteroC2_6alkenyl, heteroC2_ 6alkynyl, C3_io carbocyclyl, 3-10 membered heterocyclyl, C6-io aryl and 5-10 membered heteroaryl, or two R ff groups are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rgg groups; and
each instance of Rgg is, independently, halogen, -CN, -N02, -N3, -S02H, -S03H, - OH, -OCi-6 alkyl, -ON(Ci_6 alkyl)2, -N(Ci_6 alkyl)2, -N(Ci_6 alkyl)3 +X- -NH(Ci_6 alkyl)2 +X~ -NH2(Ci_6 alkyl) +X~ -NH3 +X", -N(OCi_6 alkyl)(Ci_6 alkyl), -N(OH)(Ci_6 alkyl), -NH(OH), -SH, -SCi_6 alkyl, -SS(Ci^, alkyl), -C(=0)(Ci_6 alkyl), -C02H, -C02(Ci_6 alkyl), -OC(=0)(Ci_6 alkyl), -OC02(Ci_6 alkyl), -C(=0)NH2, -C(=0)N(Ci_6 alkyl)2, - OC(=0)NH(Ci_6 alkyl), -NHC(=0)( Ci_6 alkyl), -N(Ci_6 alkyl)C(=0)( Ci_6 alkyl), - NHC02(Ci_6 alkyl), -NHC(=0)N(Ci_6 alkyl)2, -NHC(=0)NH(Ci_6 alkyl), -NHC(=0)NH2, -C(=NH)0(Ci^, alkyl),-OC(=NH)(Ci^, alkyl), -OC(=NH)OCi^, alkyl, -C(=NH)N(Ci_6 alkyl)2, -C(=NH)NH(Ci_6 alkyl), -C(=NH)NH2, -OC(=NH)N(Ci_6 alkyl)2,
-OC(=NH)NH(Ci_6 alkyl), -OC(=NH)NH2, -NHC(=NH)N(Ci_6 alkyl)2, -NHC(=NH)NH2, - NHS02(Ci_6 alkyl), -S02N(Ci_6 alkyl)2, -S02NH(Ci 6 alkyl), -S02NH2, -S02(Ci_6 alkyl), -S020(Ci_6 alkyl), -OS02(Ci_6 alkyl), -SO(Ci_6 alkyl), -Si(Ci_6 alkyl)3, -OSi(Ci_6 alkyl)3 - C(=S)N(Ci_6 alkyl)2, C(=S)NH(d_6 alkyl), C(=S)NH2, -C(=0)S(C^ alkyl), -C(=S)SC^ alkyl, -SC(=S)Sd_6 alkyl, -P(=0)(Od_6 alkyl)2, -P(=0)(d 6 alkyl)2, -OP(=0)(d 6 alkyl)2, -0P(=0)(0Ci_6 alkyl)2, Ci_6 alkyl, Ci_6 perhaloalkyl, C2_6 alkenyl, C2_6 alkynyl, heteroCi- 6alkyl, heteroC2_6 alkenyl, heteroC2_6alkynyl, C3_io carbocyclyl, C6-io aryl, 3-10 membered heterocyclyl, 5-10 membered heteroaryl; or two geminal Rgg substituents can be joined to form =0 or =S; wherein X is a counterion.
[0044] As used herein, the term "halo" or "halogen" refers to fluorine (fluoro, -F), chlorine (chloro, -CI), bromine (bromo, -Br), or iodine (iodo, -I).
[0045] The term "acyl" refers to a group having the general formula -C(=0)R ,
-C(=0)ORxl, -C(=0)-0-C(=0)Rxl, -C(=0)SRxl, -C(=0)N(Rxl)2, -C(=S)RX1,
Figure imgf000031_0001
-C(=NRX1)SRX1, and -C(=NRX1)N(RX1)2, wherein Rxl is hydrogen; halogen; substituted or unsubstituted hydroxyl; substituted or unsubstituted thiol; substituted or unsubstituted amino; substituted or unsubstituted acyl, cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched alkyl; cyclic or acyclic, substituted or unsubstituted, branched or unbranched alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, aliphaticoxy, heteroaliphaticoxy, alkyloxy, heteroalkyloxy, aryloxy,
heteroaryloxy, aliphaticthioxy, heteroaliphaticthioxy, alkylthioxy, heteroalkylthioxy, arylthioxy, heteroarylthioxy, mono- or di- aliphaticamino, mono- or di- heteroaliphaticamino, mono- or di- alkylamino, mono- or di- heteroalkylamino, mono- or di-arylamino, or mono- or di-heteroarylamino; or two R groups taken together form a 5- to 6-membered heterocyclic ring. Exemplary acyl groups include aldehydes (-CHO), carboxylic acids (-C02H), ketones, acyl halides, esters, amides, imines, carbonates, carbamates, and ureas. Acyl substituents include, but are not limited to, any of the substituents described herein, that result in the formation of a stable moiety (e.g., aliphatic, alkyl, alkenyl, alkynyl, heteroaliphatic, heterocyclic, aryl, heteroaryl, acyl, oxo, imino, thiooxo, cyano, isocyano, amino, azido, nitro, hydroxyl, thiol, halo, aliphaticamino, heteroaliphaticamino, alkylamino, heteroalkylamino, arylamino, heteroarylamino, alkylaryl, arylalkyl, aliphaticoxy, heteroaliphaticoxy, alkyloxy, heteroalkyloxy, aryloxy, heteroaryloxy, aliphaticthioxy, heteroaliphaticthioxy, alkylthioxy, heteroalkylthioxy, arylthioxy, heteroarylthioxy, acyloxy, and the like, each of which may or may not be further substituted).
[0046] A "counterion" or "anionic counterion" is a negatively charged group associated with a positively charged group in order to maintain electronic neutrality. An anionic counterion may be monovalent (i.e., including one formal negative charge). An anionic counterion may also be multivalent (i.e., including more than one formal negative charge), such as divalent or trivalent. Exemplary counterions include halide ions (e.g., F , Cl~, Br , Γ), N03 , C104 , OH , H2P04 , HC0 ~ HS04 , sulfonate ions (e.g., methansulfonate,
trifluoromethanesulfonate, /?-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene- 1 -sulfonic acid-5-sulfonate, ethan-1 -sulfonic acid- 2-sulfonate, and the like), carboxylate ions (e.g. , acetate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, gluconate, and the like), BF4 ~, PF4 , PF6 , AsF6 ~, SbF6 , B[3,5- (CF3)2C6H3]4r, B(C6F5)4 ", BPh4 , Al(OC(CF3)3)4 ~, and carborane anions (e.g. , CBuHi2 or
— 2— 2—
(HCBnMe5Br6) ). Exemplary counterions which may be multivalent include C03 , HP04 ,
3— 2— 2— 2—
P04 B407 , S04 , S203 , carboxylate anions (e.g., tartrate, citrate, fumarate, maleate, malate, malonate, gluconate, succinate, glutarate, adipate, pimelate, suberate, azelate, sebacate, salicylate, phthalates, aspartate, glutamate, and the like), and carboranes.
[0047] The term "leaving group" is given its ordinary meaning in the art of synthetic organic chemistry and refers to an atom or a group capable of being displaced by a nucleophile. See, for example, Smith, March Advanced Organic Chemistry 6th ed. (501-502). Examples of suitable leaving groups include, but are not limited to, halogen (such as F, CI, Br, or I (iodine)), alkoxycarbonyloxy, aryloxycarbonyloxy, alkanesulfonyloxy,
arenesulfonyloxy, alkyl-carbonyloxy (e.g., acetoxy), arylcarbonyloxy, aryloxy, methoxy, N,0-dimethylhydroxylamino, pixyl, and haloformates. In some cases, the leaving group is a sulfonic acid ester, such as toluenesulfonate (tosylate, -OTs), methanesulfonate (mesylate, - OMs), /?-bromobenzenesulfonyloxy (brosylate, -OBs), -OS(=0)2(CF2)3CF3 (nonaflate, -ONf), or trifluoromethanesulfonate (triflate, -OTf). In some cases, the leaving group is a brosylate, such as /?-bromobenzenesulfonyloxy. In some cases, the leaving group is a nosylate, such as 2-nitrobenzenesulfonyloxy.The leaving group may also be a phosphineoxide (e.g. , formed during a Mitsunobu reaction) or an internal leaving group such as an epoxide or cyclic sulfate. Other non-limiting examples of leaving groups are water, ammonia, alcohols, ether moieties, thioether moieties, zinc halides, magnesium moieties, diazonium salts, and copper moieties. Further exemplary leaving groups include, but are not limited to, halo (e.g., chloro, bromo, iodo) and activated substituted hydroxyl groups (e.g., -OC(=0)SRaa, -OC(=0)Raa, - OCChR^, -OC(=0)N(Rbb)2, -OC(=NRbb)Raa, -OC(=NRbb)ORaa, -OC(=NRbb)N(Rbb)2, - OS(=0)Raa, -OSO^, -OP(Rcc)2, -OP(Rcc)3, -OP(=0)2Raa, -OP(=0)(Raa)2, - OP(=0)(ORcc)2, -OP(=0)2N(Rbb)2, and -OP(=0)(NRbb)2, wherein Raa, Rbb, and Rcc are as defined herein).
[0048] As used herein, the term "hydroxyl" or "hydroxy" refers to the group -OH. The term "substituted hydroxyl" or "substituted hydroxyl," by extension, refers to a hydroxyl group wherein the oxygen atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from -ORaa, -ON(Rbb)2, - OC(=0)SRaa, -OC(=0)Raa, -OC02Raa, -OC(=0)N(Rbb)2, -OC(=NRbb)Raa, - OC(=NRbb)ORaa, -OC(=NRbb)N(Rbb)2, -OS(=0)Raa, -OS02Raa, -OSi(Raa)3, -OP(Rcc)2, -OP(Rcc)3 +X", -OP(ORcc)2, -OP(ORcc)3 +X~, -OP(=0)(Raa)2, -OP(=0)(ORcc)2, and
-OP(=0)(N(Rbb)2)2, wherein X", Raa, Rbb, and Rcc are as described herein.
[0049] As used herein, the term "thiol" or "thio" refers to the group -SH. The term "substituted thiol" or "substituted thio," by extension, refers to a thiol group wherein the sulfur atom directly attached to the parent molecule is substituted with a group other than hydrogen, and includes groups selected from -SRaa, -S=SRCC, -SC(=S)SRaa, -SC(=0)SRaa, - SC(=0)ORaa, and -SC(=0)Raa, wherein Raa and Rcc are as described herein.
[0050] As used herein, the term, "amino" refers to the group -NH2. The term "substituted amino," by extension, refers to a monosubstituted amino, a disubstituted amino, or a trisubstituted amino, as described herein. In certain embodiments, the "substituted amino" is a monosubstituted amino or a disubstituted amino group.
[0051] As used herein, the term "monosubstituted amino" refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with one hydrogen and one group other than hydrogen, and includes groups selected from -NH(Rbb), - NHC(=0)Raa, -NHC02Raa, -NHC(=0)N(Rbb)2, -NHC(=NRbb)N(Rbb)2, -NHS02Raa, - NHP(=0)(ORcc)2, and -NHP(=0)(N(Rbb)2)2, wherein Raa, Rbb and Rcc are as described herein, and wherein Rbb of the group -NH(Rbb) is not hydrogen.
[0052] As used herein, the term "disubstituted amino" refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with two groups other than hydrogen, and includes groups selected from -N(Rbb)2, -NRbbC(=0)Raa, - NRbbC02Raa, -NRbbC(=0)N(Rbb)2, -NRbbC(=NRbb)N(Rbb)2, -NRbbS02Raa, - NRbbP(=0)(ORcc)2, and -NRbbP(=0)(N(Rbb)2)2, wherein Raa, Rbb, and Rcc are as described herein, with the proviso that the nitrogen atom directly attached to the parent molecule is not substituted with hydrogen.
[0053] As used herein, the term "trisubstituted amino" refers to an amino group wherein the nitrogen atom directly attached to the parent molecule is substituted with three groups, and includes groups selected from -N(Rbb)3 and -N(Rbb)3 +X~, wherein Rbb and X are as described herein.
[0054] As used herein, the term "oxo" refers to the group =0, and the term "thiooxo" refers to the group =S.
[0055] As used herein, a "counterion" is a negatively charged group associated with a positively charged quarternary amine in order to maintain electronic neutrality. Exemplary counterions include halide ions (e.g., F , CI , Br , Γ), N03 , C104 , OH , H2P04 , HS04 , sulfonate ions (e.g., methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate, benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate, naphthalene-l-sulfonic acid-5-sulfonate, ethan-1 -sulfonic acid-2-sulfonate, and the like), and carboxylate ions (e.g., acetate, ethanoate, propanoate, benzoate, glycerate, lactate, tartrate, glycolate, and the like).
[0056] Nitrogen atoms can be substituted or unsubstituted as valency permits, and include primary, secondary, tertiary, and quarternary nitrogen atoms. Exemplary nitrogen atom substitutents include, but are not limited to, hydrogen, -OH, -ORaa, -N(RCC)2, -CN, - C(=0)Raa, -C(=0)N(Rcc)2, -C02Raa, -S02Raa, -C(=NRbb)Raa, -C(=NRcc)ORaa, - C(=NRCC)N(RCC)2, -S02N(Rcc)2, -S02Rcc, -S02ORcc, -SORaa, -C(=S)N(RCC)2, -C(=0)SRcc, - C(=S)SRCC, -P(=0)(ORcc)2, -P(=0)(Raa)2, -P(=0)(N(Rcc)2)2, d_10 alkyl, Cwo perhaloalkyl, C2_io alkenyl, C2_io alkynyl, heteroCi-ioalkyl, heteroC2_ioalkenyl, heteroC2_ioalkynyl, C3_io carbocyclyl, 3-14 membered heterocyclyl, C6-i4 aryl, and 5-14 membered heteroaryl, or two Rcc groups attached to an N atom are joined to form a 3-14 membered heterocyclyl or 5-14 membered heteroaryl ring, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, and wherein Raa, Rbb, Rcc and Rdd are as defined above.
[0057] In certain embodiments, the substituent present on the nitrogen atom is an nitrogen protecting group (also referred to herein as an "amino protecting group"). Nitrogen protecting groups include, but are not limited to, -OH, -ORaa, -N(RCC)2, -C(=0)Raa, - C(=0)N(Rcc)2, -CO^, -S02Raa, -C(=NRcc)Raa, -C(=NRcc)ORaa, -C(=NRCC)N(RCC)2, - S02N(Rcc)2, -S02Rcc, -S02ORcc, -SORaa, -C(=S)N(RCC)2, -C(=0)SRcc, -C(=S)SRCC, Ci_i0 alkyl (e.g., aralkyl, heteroaralkyl), C2_io alkenyl, C2_io alkynyl, heteroCi_ioalkyl, heteroC2_ loalkenyl, heteroC2-ioalkynyl, C3_io carbocyclyl, 3-14 membered heterocyclyl, C6-i4 aryl, and 5-14 membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl, heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5 Rdd groups, and wherein Raa, Rbb, Rcc and Rdd are as described herein. Nitrogen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3 edition, John Wiley & Sons, 1999, incorporated herein by reference.
[0058] For example, nitrogen protecting groups such as amide groups (e.g., -C(=0)Raa) include, but are not limited to, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3- pyridylcarboxamide, N-benzoylphenylalanyl derivative, benzamide, /?-phenylbenzamide, o- nitrophenylacetamide, o-nitrophenoxyacetamide, acetoacetamide, (Ν'- dithiobenzyloxyacylamino)acetamide, 3-(p-hydroxyphenyl)propanamide, 3-(o- nitrophenyl)propanamide, 2-methyl-2-(o-nitrophenoxy)propanamide, 2-methyl-2-(o- phenylazophenoxy)propanamide, 4-chlorobutanamide, 3-methyl-3-nitrobutanamide, o- nitrocinnamide, N-acetylmethionine derivative, o-nitrobenzamide and o- (benzoyloxymethyl)benzamide.
[0059] Nitrogen protecting groups such as carbamate groups (e.g., -C(=0)ORaa) include, but are not limited to, methyl carbamate, ethyl carbamate, 9-fluorenylmethyl carbamate (Fmoc), 9-(2-sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethyl carbamate, 2,7-di-i-butyl-[9-( 10, 10-dioxo-lO, 10, 10, 10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1- (l-adamantyl)-l-methylethyl carbamate (Adpoc), l,l-dimethyl-2-haloethyl carbamate, l,l-dimethyl-2,2-dibromoethyl carbamate (DB-i-BOC), l,l-dimethyl-2,2,2-trichloroethyl carbamate (TCBOC), l-methyl-l-(4-biphenylyl)ethyl carbamate (Bpoc), 1— (3,5— di— f— butylphenyl)-l-methylethyl carbamate (i-Bumeoc), 2-(2'- and 4'-pyridyl)ethyl carbamate (Pyoc), 2-(N,N-dicyclohexylcarboxamido)ethyl carbamate, i-butyl carbamate (BOC), 1- adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1- isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl carbamate, N-hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), /?-methoxybenzyl carbamate (Moz), /?-nitrobenzyl carbamate, p- bromobenzyl carbamate, /?-chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4- methylsulfinylbenzyl carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2-(p- toluenesulfonyl)ethyl carbamate, [2-(l,3-dithianyl)]methyl carbamate (Dmoc), 4- methylthiophenyl carbamate (Mtpc), 2,4-dimethylthiophenyl carbamate (Bmpc), 2- phosphonioethyl carbamate (Peoc), 2-triphenylphosphonioisopropyl carbamate (Ppoc), 1, 1- dimethyl-2-cyanoethyl carbamate, m-chloro-p-acyloxybenzyl carbamate, p- (dihydroxyboryl)benzyl carbamate, 5-benzisoxazolylmethyl carbamate, 2-(trifluoromethyl)- 6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate, phenyl(o- nitrophenyl)methyl carbamate, i-amyl carbamate, S-benzyl thiocarbamate, /?-cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate,
cyclopropylmethyl carbamate, /?-decyloxybenzyl carbamate, 2,2-dimethoxyacylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzyl carbamate, l,l-dimethyl-3-(N,N- dimethylcarboxamido)propyl carbamate, 1, 1-dimethyipropynyl carbamate, di(2- pyridyl)methyl carbamate, 2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p-(p '-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate, 1-methylcyclohexyl carbamate, 1-methyl-l- cyclopropylmethyl carbamate, l-methyl-l-(3,5-dimethoxyphenyl)ethyl carbamate, 1- methyl-l-( ?-phenylazophenyl)ethyl carbamate, 1 -methyl- 1-phenylethyl carbamate, 1- methyl-l-(4-pyridyl)ethyl carbamate, phenyl carbamate, /?-(phenylazo)benzyl carbamate, 2,4,6-tri-i-butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, and 2,4,6- trimethylbenzyl carbamate.
[0060] Nitrogen protecting groups such as sulfonamide groups (e.g., -S(=0)2Raa) include, but are not limited to, /?-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6,-trimethyl-4- methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6- dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5, 6-tetramethyl-4- methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6- trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7, 8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide (Ms), β- trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4-(4' ,8'- dimethoxynaphthylmethyl)benzenesulfonamide (DNMB S ), benzylsulfonamide,
trifluoromethylsulfonamide, and phenacylsulfonamide.
[0061] Other nitrogen protecting groups include, but are not limited to, phenothiazinyl- (10)-acyl derivative, N'-p-toluenesulfonylaminoacyl derivative, N'-phenylaminothioacyl derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine derivative, 4,5-diphenyl- 3-oxazolin-2-one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5-dimethylpyrrole, N-l,l,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5-substituted l,3-dimethyl-l,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl- l,3,5-triazacyclohexan-2-one, 1-substituted 3,5-dinitro-4-pyridone, N-methylamine, N- allylamine, N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine, N- (l-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammonium salts, N- benzylamine, N-di(4-methoxyphenyl)methylamine, N-5-dibenzosuberylamine, N- triphenylmethylamine (Tr), N-[(4-methoxyphenyl)diphenylmethyl] amine (MMTr), N-9- phenylfluorenylamine (PhF), N-2,7-dichloro-9-fluorenylmethyleneamine, N- ferrocenylmethylamino (Fcm), N-2-picolylamino N'-oxide, N-1,1- dimethylthiomethyleneamine, N-benzylideneamine, N-p-methoxybenzylideneamine, N- diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine, N-(N',N'- dimethylaminomethylene)amine, N,N '-isopropylidenediamine, N-p-nitrobenzylideneamine, N-salicylideneamine, N-5-chlorosalicylideneamine, N-(5-chloro-2- hydroxyphenyl)phenylmethyleneamine, N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo- l-cyclohexenyl)amine, N-borane derivative, N-diphenylborinic acid derivative, N- [phenyl(pentaacylchromium- or tungsten)acyl] amine, N-copper chelate, N-zinc chelate, N- nitroamine, N-nitrosoamine, amine N-oxide, diphenylphosphinamide (Dpp),
dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl
phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate,
benzenesulfenamide, o-nitrobenzenesulfenamide (Nps), 2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4-methoxybenzenesulfenamide,
triphenylmethylsulfenamide, and 3-nitropyridinesulfenamide (Npys). In certain
embodiments, a nitrogen protecting group is benzyl (Bn), tert-butyloxycarbonyl (BOC), carbobenzyloxy (Cbz), 9-flurenylmethyloxycarbonyl (Fmoc), trifluoroacetyl,
triphenylmethyl, acetyl (Ac), benzoyl (Bz), p-methoxybenzyl (PMB), 3,4-dimethoxybenzyl (DMPM), p-methoxyphenyl (PMP), 2,2,2-trichloroethyloxycarbonyl (Troc), triphenylmethyl (Tr), tosyl (Ts), brosyl (Bs), nosyl (Ns), mesyl (Ms), triflyl (Tf), or dansyl (Ds).
[0062] In certain embodiments, the substituent present on an oxygen atom is an oxygen protecting group (also referred to herein as an "hydroxyl protecting group"). Oxygen protecting groups include, but are not limited to, -Raa, -N(Rbb)2, -C(=0)SRaa, -C(=0)Raa, - C02Raa, -C(=0)N(Rbb)2, -C(=NRbb)Raa, -C(=NRbb)ORaa, -C(=NRbb)N(Rbb)2, -S(=0)Raa, - S02Raa, -Si(Raa)3, -P(RCC)2, -P(RCC)3 +X", -P(ORcc)2, -P(ORcc)3 +X", -P(=0)(Raa)2,
-P(=0)(ORcc)2, and -P(=0)(N(Rbb) 2)2, wherein X", Raa, Rbb, and Rcc are as described herein. Oxygen protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3 edition, John Wiley & Sons, 1999, incorporated herein by reference.
[0063] Exemplary oxygen protecting groups include, but are not limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM), i-butylthiomethyl,
(phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), /?- methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), i-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2- methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2-chloroethoxy)methyl, 2- (trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3- bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4- methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl, 4- methoxytetrahydrothiopyranyl S ,S-dioxide, l-[(2-chloro-4-methyl)phenyl]-4- methoxypiperidin-4-yl (CTMP), l,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl, 1-ethoxyethyl, l-(2-chloroethoxy)ethyl, 1-methyl-l-methoxyethyl, 1-methyl-l-benzyloxyethyl, 1- methyl-l-benzyloxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2- (phenylselenyl)ethyl, i-butyl, allyl, /?-chlorophenyl, /?-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), /?-methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, /?-nitrobenzyl, p- halobenzyl, 2,6-dichlorobenzyl, /?-cyanobenzyl, /?-phenylbenzyl, 2-picolyl, 4-picolyl, 3- methyl-2-picolyl N-oxido, diphenylmethyl, p,p '-dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl, a-naphthyldiphenylmethyl, /?-methoxyphenyldiphenylmethyl, di(p- methoxyphenyl)phenylmethyl, tri( ?-methoxyphenyl)methyl, 4-(4'- bromophenacyloxyphenyl)diphenylmethyl, 4,4',4"-tris(4,5- dichlorophthalimidophenyl)methyl, 4,4',4"-tris(levulinoyloxyphenyl)methyl, 4,4',4"- tris(benzoyloxyphenyl)methyl, 3-(imidazol-l-yl)bis(4',4"-dimethoxyphenyl)methyl, 1,1- bis(4-methoxyphenyl)-l'-pyrenylmethyl, 9-anthryl, 9-(9-phenyl)xanthenyl, 9-(9-phenyl- 10-oxo)anthryl, l,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, i-butyldimethylsilyl (TBDMS), t- butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p-xylylsilyl, triphenylsilyl,
diphenylmethylsilyl (DPMS), i-butylmethoxyphenylsilyl (TBMPS), formate,
benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, /?-chlorophenoxyacetate, 3- phenylpropionate, 4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, p- phenylbenzoate, 2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9- fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec), 2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkyl /?-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl /?-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl o-nitrobenzyl carbonate, alkyl /?-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate, 4-ethoxy-l- napththyl carbonate, methyl dithiocarbonate, 2-iodobenzoate, 4-azidobutyrate, 4-nitro-4- methylpentanoate, o-(dibromomethyl)benzoate, 2-formylbenzenesulfonate, 2- (methylthiomethoxy)ethyl, 4-(methylthiomethoxy)butyrate, 2-
(methylthiomethoxymethyl)benzoate, 2,6-dichloro-4-methylphenoxyacetate, 2,6-dichloro- 4-( 1 , 1 ,3 ,3-tetramethylbutyl)phenoxyacetate, 2,4-bis( 1 , l-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate, o- (methoxyacyl)benzoate, a-naphthoate, nitrate, alkyl Ν,Ν,Ν',Ν'- tetramethylphosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts). In certain embodiments, an oxygen protecting group is silyl. In certain embodiments, an oxygen protecting group is t-butyldiphenylsilyl (TBDPS), t- butyldimethylsilyl (TBDMS), triisoproylsilyl (TIPS), triphenylsilyl (TPS), triethylsilyl (TES), trimethylsilyl (TMS), triisopropylsiloxymethyl (TOM), acetyl (Ac), benzoyl (Bz), allyl carbonate, 2,2,2-trichloroethyl carbonate (Troc), 2-trimethylsilylethyl carbonate,
methoxymethyl (MOM), 1-ethoxyethyl (EE), 2-methyoxy-2-propyl (MOP), 2,2,2- trichloroethoxyethyl, 2-methoxyethoxymethyl (MEM), 2-trimethylsilylethoxymethyl (SEM), methylthiomethyl (MTM), tetrahydropyranyl (THP), tetrahydrofuranyl (THF), p- methoxyphenyl (PMP), triphenylmethyl (Tr), methoxytrityl (MMT), dimethoxytrityl (DMT), allyl, p-methoxybenzyl (PMB), t-butyl, benzyl (Bn), allyl, or pivaloyl (Piv).
[0064] In certain embodiments, the substituent present on a sulfur atom is a sulfur protecting group (also referred to as a "thiol protecting group"). Sulfur protecting groups include, but are not limited to, -Raa, -N(Rbb)2, -C(=0)SRaa, -C(=0)Raa, -C02Raa, - C(=0)N(Rbb)2, -C(=NRbb)Raa, -C(=NRbb)ORaa, -C(=NRbb)N(Rbb)2, -S(=0)Raa, -S02Raa, - Si(Raa)3, -P(Rcc)2, -P(RCC)3 +X", -P(ORcc)2, -P(ORcc)3 +X", -P(=0)(Raa)2, -P(=0)(ORcc)2, and -P(=0)(N(Rbb) 2)2, wherein X", Raa, Rbb, and Rcc are as described herein. Sulfur protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3rd edition, John Wiley & Sons, 1999, incorporated herein by reference. In certain embodiments, a sulfur protecting group is acetamidomethyl, t-Bu, 3-nitro-2-pyridine sulfenyl, 2-pyridine-sulfenyl, or triphenylmethyl.
[0065] These and other exemplary substituents are described in more detail in the Detailed Description, Examples, and Claims. The invention is not intended to be limited in any manner by the above exemplary listing of substituents.
Other definitions
[0066] The term "salt" and "pharmaceutically acceptable salt" refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, Berge et ah, describes pharmaceutically acceptable salts in detail in . Pharmaceutical Sciences (1977) 66: 1-19. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate,
glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy- ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Pharmaceutically acceptable salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N+(Ci^alkyl)4 salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, lower alkyl sulfonate, and aryl sulfonate.
[0067] As used herein, a "peptidyl group" refers to a divalent amino acid moiety. A "dipeptidyl" group refers to a divalent moiety comprising two amino acid residues linked together by peptide bonds, i.e., -C(=0)-N- (amide) bonds. A "polypeptidyl" group refers to a divalent moiety comprising three or more consecutively linked amino acid residues (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 19, 20, or more linked amino acid residues). Peptidyl, dipeptidyl, and polypeptidyl moieties may contain only natural amino acids, although non-natural amino acids (i.e., compounds that do not occur in nature but that can be incorporated into a polypeptide chain) and/or amino acid analogs as are known in the art may alternatively be employed. Furthermore, one or more of the amino acids in a peptidyl, dipeptidyl, or polypeptidyl moiety may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation,
functionalization, or other modification. For example, a cysteine (-CH2SH) side chain may be modified to a formyl (-CHO) side chain.
[0068] Exemplary amino acids contemplated useful in providing the peptidyl, dipeptidyl, and polypeptidyl moieties of interest include, without limitation, natural alpha-amino acids such as D- and L-isomers of the 20 common naturally occurring alpha-amino acids found in peptides (e.g., A, R, N, C, D, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V), natural beta-amino acids (e.g., beta-alanine), and unnnatural amino acids. There are many known unnatural amino acids any of which may be included in the peptides of the present invention. See for example, S. Hunt, The Non-Protein Amino Acids: In Chemistry and Biochemistry of the Amino Acids, edited by G. C. Barrett, Chapman and Hall, 1985. Additional examples of amino acids contemplated useful in providing the peptidyl, dipeptidyl, and polypeptidyl moieties of interest include without limitation, ornithine, citrulline (Cit), -methyl- Alanine (Aib), 4-hydroxyproline, desmosine, gamma-aminobutyric acid, beta-cyanoalanine, norvaline, 4-(E)-butenyl-4(R)-methyl-N-methyl-L-threonine, N-methyl-L-leucine, 1- amino-cyclopropanecarboxylic acid, l-amino-2-phenyl-cyclopropanecarboxylic acid, 1- amino-cyclobutanecarboxylic acid, 4-amino-cyclopentenecarboxylic acid, 3-amino- cyclohexanecarboxylic acid, 4-piperidylacetic acid, 4-amino-l-methylpyrrole-2-carboxylic acid, 2,4-diaminobutyric acid, 2,3-diaminopropionic acid, 2,4-diaminobutyric acid, 2- aminoheptanedioic acid, 4-(aminomethyl)benzoic acid, 4-aminobenzoic acid, ortho-, meta- and /?ara-substituted phenylalanines (e.g., substituted with -C(=0)C6H5; -CF3; -CN; -halo; -N02; CH3), disubstituted phenylalanines, substituted tyrosines (e.g., further substituted with -C(=0)C6H5; -CF3; -CN; -halo; -N02; CH3), and statine.
[0069] A "subject" to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g, infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult)) and/or other non-human animals, for example mammals (e.g., primates (e.g., cynomolgus monkeys, rhesus monkeys); commercially relevant mammals such as rodents (e.g., mice, rats), guinea pigs, cattle, pigs, horses, sheep, goats, cats, and/or dogs. The non-human animal may be male or female and at any stage of development. A non-human animal may be a transgenic animal.
[0070] "Disease," "disorder," and "condition" are used interchangeably herein.
[0071] As used herein, and unless otherwise specified, the terms "treat," "treating" and "treatment" contemplate an action that occurs while a subject is suffering from the specified disease, disorder, or condition, which reduces the severity of the disease, disorder, or condition, or retards or slows the progression of the disease, disorder, or condition
("therapeutic treatment" or "therapeutically treating"), and also contemplates an action that occurs before a subject begins to suffer from the specified disease, disorder, or condition, and which inhibits or reduces the severity of the disease, disorder, or condition ("prophylactic treatment" or "prophylactically treating").
[0072] In general, the "effective amount" of a compound refers to an amount sufficient to elicit the desired biological response. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound of the invention may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the disease being treated, the mode of administration, and the age, health, and condition of the subject. For example, the effective amount of a compound with anti-proliferative activity is the amount that results in a sufficient concentration to inhibit the proliferation of cells. An effective amount encompasses therapeutic and prophylactic treatment.
[0073] As used herein, and unless otherwise specified, a "therapeutically effective amount" of a compound is an amount sufficient to provide a therapeutic benefit in the treatment of a disease, disorder, or condition, or to delay or minimize one or more symptoms associated with the disease, disorder, or condition. A therapeutically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other therapies, which provides a therapeutic benefit in the treatment of the disease, disorder, or condition. The term "therapeutically effective amount" can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the disease, disorder, or condition, or enhances the therapeutic efficacy of another therapeutic agent.
[0074] As used herein, and unless otherwise specified, a "prophylactic ally effective amount" of a compound is an amount sufficient to prevent a disease, disorder, or condition, or one or more symptoms associated with the disease, disorder, or condition, or prevent its recurrence. A prophylactically effective amount of a compound means an amount of a therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the disease, disorder, or condition. The term "prophylactically effective amount" can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.
[0075] As used herein, use of the phrase "at least one instance" refers to 1, 2, 3, 4, or more instances, but also encompasses a range, e.g., for example, from 1 to 4, from 1 to 3, from 1 to 2, from 2 to 4, from 2 to 3, or from 3 to 4 instances, inclusive.
Brief Description of the Drawings
[0076] Figure 1 is a graph showing the stability of exemplary trioxacarcin-linker species R02-B5, R02-B4, R02-B8, R02-A3, and R02-A8 at 37 °C in pH 5.0 buffer.
[0077] Figure 2 is a graph showing the stability of exemplary trioxacarcin-linker species R02-B5, R02-B4, R02-B8, R02-A3, and R02-A8 under physiological conditions at 37 °C in pH 7.4 buffer.
[0078] Figure 3 is a graph showing the stability of exemplary free drug trioxacarcin species R02-B1, R02-A9, R02-B7, R02-A1, and R02-A7 under physiological conditions at 37 °C in pH 7.4 buffer.
[0079] Figure 4 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-A3 upon exposure to Cathepsin B (ti/2 of R02-A3: 0.45 hours).
[0080] Figure 5 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-A8 upon exposure to Cathepsin B (ti/2 of R02-A8: 0.21 hours).
[0081] Figure 6 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-B4 upon exposure to Cathepsin B (ti/2 of R02-B4: 0.44 hours).
[0082] Figure 7 is a graph showing the release kinetics of exemplary trioxacarcin-linker species R02-B5 upon exposure to Cathepsin B (ti/2 of R02-B5: 0.25 hours). Detailed Description of Certain Embodiments of the Invention
[0083] Trioxacarcins are highly toxic to a variety of cell types. Linking a trioxacarcin to an antibody preserves the trioxacarcin' s potency against the cell type while increasing specificity to the target cell, and optionally increasing endocytosis of the trioxacarcin. These effects enable lowering the overall amount of trioxacarcin to be delivered, thereby reducing the associated toxicity. By taking advantage of established synthetic methods, complex and therapeutically relevant trioxacarcins are accessible. In turn, conjugating these trioxacarcins to antibodies through linking groups provide trioxacarcin-antibody drug conjugates.
[0084] Accordingly, provided herein are novel trioxacarcin-antibody drug conjugates (e.g., compounds of Formula (I)). Also provided are trioxacarcin-antibody drug conjugate precursors comprising a trioxacarcin and a linking group (e.g., compounds of Formula (II)), and novel trioxacarcin analogs (e.g., free drug species). The compounds may be provided for use in any composition, kit, or method described herein as a pharmaceutically acceptable salt.
[0085] Provided is a compound of Formula I):
Figure imgf000044_0001
(I)
or a pharmaceutically acceptable form thereof;
wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -COiR^; -CN; -SCN; -SRA1 ; -SORA1 ; -S02RA; -N02; -N3; =0; =N(RA2); =S; -NCR^k; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1 ; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1 ; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2; -OC(=0)N(RD2)2; - NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000046_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000046_0002
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -L-B; R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
|-R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40— j Qr
Figure imgf000048_0001
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000048_0002
; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene; R 21 is independently substituted or unsubstituted alkyl; substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
N R 1 carbocyclyl; or V \ ^N(RW112 ;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
A is a group of the formula
Figure imgf000049_0001
Q is - -, or -0-;
Rwl is independently hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
[0086] In certain embodiments of the compound of Formula (I),
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CO^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -NCR^k; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000051_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000051_0002
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring; R7 is -L-B;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring; R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
j— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O) -R40-A— j .
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000053_0001
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
A is a grou of the formula
Figure imgf000054_0001
Q is -S-, or -0-;
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
[0087] In certain embodiments of the compound of Formula (I),
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -COiR^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of RA2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000056_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000056_0002
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -L-B; R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
j— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40-A— | .
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000058_0001
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; R is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
A is a grou of the formula
Figure imgf000059_0001
Q is -S-, or -0-;
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and B is an antibody or an antibody fragment.
[0088] In certain embodiments the compound of Formula (I) is of Formula (I-a):
Figure imgf000059_0002
or a pharmaceutically acceptable salt thereof.
[0089] In certain embodiments the compound of Formula (I) is of Formula (I-b):
Figure imgf000059_0003
or a pharmaceutically acceptable salt thereof. [0090] In certain embodiments, the com ound of Formula (I) is of Formula (I-c):
Figure imgf000060_0001
or a pharmaceutically acceptable salt thereof.
[0091] In certain embodiments, the compound of Formula (I) is of Formula (I-d):
Figure imgf000060_0002
or a pharmaceutically acceptable salt thereof.
[0092] The antibody or antibody fragment B is a large molecule with many sites of attachment, and thus may have many instances of a compound of Formula (I) attached thereto. In certain embodiments, the antibody or antibody fragment comprises 1 to 200 independent instances of a compound of Formula (I) attached thereto, inclusive, e.g. , 1 to 150, 1 to 100, 1 to 75, 1 to 50, 1 to 25, 1 to 15, 1 to 10, inclusive, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 independent instances.
[0093] Also provided are precursor compounds to Formula (I), referred to herein as compounds of Formula (II):
Figure imgf000060_0003
or pharmaceutically acceptable salts thereof;
wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -COiR^; -CN; -SCN; -SRA1 ; -SORA1 ; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NR^C^O)^2; -ΝΚ^(=0)Ν(ΚΑ2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of RA2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2; -OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000062_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; - 2
Figure imgf000062_0002
-C(R Fr")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
F2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
F2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -ΐ Τ;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R G2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L1 is of the formula: |-R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40— I Qr |-R i:20 _ X-R 1 1
R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
X S
Figure imgf000065_0001
; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is h drogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carbocyclyl; or
Figure imgf000065_0002
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000065_0003
Figure imgf000065_0004
R is halogen, tosylate, mesylate, or triflate;
R X2 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is independently hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group.
[0094] In certain embodiments of the compound of Formula (II), R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -COiR^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of RA2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - 0RC1; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000067_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NR^C(=0)R^; -NR^C(=0)N(R^)2; -OC(=0)ORJ 1; -OC(=0)R^; -OC(=0)N(R^)2; -
F2 Fl F2 Fl
NRr"C(=0)ORri; or -C(Rr")3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
F2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
F2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -ΐ Τ;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; - NR C(=0)OR ; or -C(R )3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R G2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R G2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R B2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40— | .
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
Figure imgf000070_0001
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted
21
carbocyclyl; or two R groups are joined to form an optionally substituted heterocyclyl ring;
22
R is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
Figure imgf000070_0002
R is halogen, tosylate, mesylate, or triflate;
X2
R is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
[0095] In certain embodiments of the compound of Formula (II),
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CC^R^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of RA2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - 0RC1; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000072_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; - F2
Figure imgf000072_0002
-C(Rr")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
F2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
F2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -ΐ Τ;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1 ; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R G2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R G2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R B2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L1 is of the formula: j— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40— j .
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000075_0001
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000075_0002
R is halogen, tosylate, mesylate, or triflate;
R X2 is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
[0096] In certain embodiments the compound of Formula (II) is of Formula (Il-a):
Figure imgf000075_0003
or a pharmaceutically acceptable salt thereof.
[0097] In certain embodiments, the compound of Formula (II) is of Formula (Il-b):
Figure imgf000076_0001
or a pharmaceutically acceptable salt thereof.
[0098] In certain embodiments, the com ound of Formula (II) is of Formula (II-c):
Figure imgf000076_0002
or a pharmaceutically acceptable salt thereof.
[0099] In certain embodiments the compound of Formula (II) is of Formula (Il-d):
Figure imgf000076_0003
or a pharmaceutically acceptable salt thereof.
[00100] Compounds of Formula (I) are prepared by coupling a compound of Formula (II) with an antibody or antibody fragment. In certain embodiments, an antibody may couple with 1 to 200 compounds of Formula (II) and form corresponding compounds of Formula (I).
1 2
Groups R and R
[00101] As generally defined above, R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -ORA1; -C(=0)RA2; -CC^R^; -CN; -SCN; -SRA1; - SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; - NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; -OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -
C(R A2 )3; and R 2 is hydrogen; or R 1 and R2 are joined to form =0.
[00102] In certain embodiments, R 1 is hydrogen; and R 2 is hydrogen. 1 2
[00103] In certain embodiments, R is halogen (e.g., -F, -CI, Br, or -I); and R is hydrogen.
[00104] In certain embodiments, R1 is substituted or unsubstituted alkyl, e.g. , substituted or unsubstituted Ci 6alkyl, substituted or unsubstituted Ci_2alkyl, substituted or unsubstituted C2-3alkyl, substituted or unsubstituted C3^alkyl, substituted or unsubstituted C^salkyl, or
2 1
substituted or unsubstituted Cs^alkyl, and R is hydrogen. Exemplary R Ci_6 alkyl groups include, but are not limited to, substituted or unsubstituted methyl (Ci), ethyl (C2), n-propyl (C3), isopropyl (C3), n-butyl (C4), tert-butyl (C4), sec-butyl (C4), iso-butyl (C4), n-pentyl (C5), 3-pentanyl (C5), amyl (C5), neopentyl (C5), 3-methyl-2-butanyl (C5), tertiary amyl (C5), n-hexyl (C6).
[00105] In certain embodiments, R1 is substituted or unsubstituted alkenyl, e.g. , substituted or unsubstituted C2-6alkenyl, substituted or unsubstituted C2-3alkenyl, substituted or unsubstituted C3^alkenyl, substituted or unsubstituted C4_salkenyl, or substituted or unsubstituted C5_6alkenyl, and R is hydrogen.
[00106] In certain embodiments, R1 is substituted or unsubstituted alkynyl, e.g. , substituted or unsubstituted C2-6alkynyl, substituted or unsubstituted C2-3alkynyl, substituted or unsubstituted C3^alkynyl, substituted or unsubstituted C4_salkynyl, or substituted or unsubstituted C5_6alkynyl, and R is hydrogen.
[00107] In certain embodiments, R1 is substituted or unsubstituted carbocyclyl, e.g. , substituted or unsubstituted C3_6carbocyclyl, substituted or unsubstituted C3^carbocyclyl, substituted or unsubstituted C4_5 carbocyclyl, or substituted or unsubstituted Cs_6 carbocyclyl, and R is hydrogen.
[00108] In certain embodiments, R1 is substituted or unsubstituted heterocyclyl, e.g. , substituted or unsubstituted 3-6 membered heterocyclyl, substituted or unsubstituted 3-4 membered heterocyclyl, substituted or unsubstituted 4-5 membered heterocyclyl, or substituted or unsubstituted 5-6 membered heterocyclyl, and R is hydrogen.
[00109] In certain embodiments, R1 is substituted or unsubstituted aryl, e.g., substituted or unsubstituted phenyl, and R is hydrogen.
[00110] In certain embodiments, R1 is substituted or unsubstituted heteroaryl, e.g., substituted or unsubstituted 5-6 membered heteroaryl, and R is hydrogen.
[00111] In certain embodiments, R1 is -ORA1, and R2 is hydrogen. In certain embodiments, R1 is -C(=0)RA2 and R2 is hydrogen. In certain embodiments, R1 is -C02RA2 and R2 is
1 2 1 hydrogen. In certain embodiments, R is -CN and R is hydrogen. In certain embodiments, R is -SCN and R2 is hydrogen. In certain embodiments, R1 is -SRA1 and R2 is hydrogen. In certain embodiments, R1 is -SORA1 and R2 is hydrogen. In certain embodiments, R1 is - S02R A2 and R 2 is hydrogen. In certain embodiments, R 1 is -N02 and R2 is hydrogen. In certain embodiments, R1 is -N3 and R2 is hydrogen. In certain embodiments, R1 is -N(RA2)2 and R2 is hydrogen. In certain embodiments, R1 is -NRA2C(=0)RA2 and R2 is hydrogen. In certain embodiments, R1 is -NRA2C(=0)N(RA2)2 and R2 is hydrogen. In certain embodiments, R1 is -OC(=0)ORA1 and R2 is hydrogen. In certain embodiments, R1 is -OC(=0)RA2 and R2 is hydrogen. In certain embodiments, R1 is -OC(=0)N(RA2)2 and R2 is hydrogen. In certain embodiments, R1 is -NRA2C(=0)ORA1 and R2 is hydrogen. In certain embodiments, R1 is - C(RA2)3 and R2 is hydrogen.
[00112] In certain embodiments, R 1 and R 2 are joined to form =0.
[00113] As generally defined above, each occurrence of RA1 is independently hydrogen; an oxygen protecting group if attached to oxygen; a sulfur protecting group if attached to sulfur; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; each occurrence of RA2 is independently hydrogen; a nitrogen protecting group if attached to nitrogen; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or
unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; hydroxyl; substituted hydroxyl; thiol; substituted thiol; amino; or substituted amino; or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring.
[00114] In certain embodiments, RA1 or RA2 represent a group of Formula (i):
Figure imgf000078_0001
each occurrence of R^, RA4, R^, RA6, and RA7 is independently hydrogen, substituted or unsubstituted alkyl; -ORA9; -OC(=0)RA9; -N(RA9)2; or -NHC(=0)RA9; wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; an oxygen protecting group when attached to an oxygen atom; or a nitrogen protecting group when attached to a nitrogen atom; or two RA9 groups are joined to form a substituted or
unsubstituted heterocyclic or substituted or unsubstituted heteroaryl ring; and
M1 is -0-, -NRA8-, or -CHRA - wherein RA8 is hydrogen; substituted or
unsubstituted alkyl; a nitrogen protecting group if attached to nitrogen; or -ORA9; wherein R is independently hydrogen; substituted or unsubstituted alkyl; acyl; or an oxygen protecting group.
[00115] In certain embodiments, RA1 or RA2 is hydrogen.
[00116] In certain embodiments, R^ is hydrogen, substituted or unsubstituted alkyl; - ORA9; -OC(=0)RA9; or -NHC(=0)RA9; wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; or an oxygen protecting group. In certain embodiments, R^ is hydrogen. In certain embodiments, R^ is substituted or unsubstituted alkyl, e.g., methyl. In certain embodiments, R^ is -ORA9, e.g., -OH or -O-alkyl.
[00117] In certain embodiments, RA4 is hydrogen, substituted or unsubstituted alkyl; - ORA9; -OC(=0)RA9; or -NHC(=0)RA9; wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; or an oxygen protecting group. In certain embodiments, RA4 is hydrogen. In certain embodiments, RA4 is substituted or unsubstituted alkyl, e.g., methyl. In certain embodiments, RA4 is -ORA9, e.g., -OH or -O-alkyl.
[00118] In certain embodiments, R^ is hydrogen, substituted or unsubstituted alkyl; - ORA9; -OC(=0)RA9; or -NHC(=0)RA9; wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; or an oxygen protecting group. In certain embodiments, R^ is hydrogen. In certain embodiments, R^ is substituted or unsubstituted alkyl, e.g., methyl. In certain embodiments, R^ is -ORA9, e.g., -OH or -O-alkyl.
[00119] In certain embodiments, RA6 is hydrogen, substituted or unsubstituted alkyl; - ORA9; -OC(=0)RA9; or -NHC(=0)RA9; wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; or an oxygen protecting group. In certain embodiments, RA6 is hydrogen. In certain embodiments, RA6 is substituted or unsubstituted alkyl, e.g., methyl. In certain embodiments, RA6 is -ORA9, e.g., -OH or -O-alkyl.
[00120] In certain embodiments, RA7 is hydrogen, substituted or unsubstituted alkyl; - ORA9; -OC(=0)RA9; or -NHC(=0)RA9; wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; or an oxygen protecting group. In certain embodiments, RA7 is hydrogen. In certain embodiments, RA7 is substituted or unsubstituted alkyl, e.g., methyl. In certain embodiments, RA7 is -ORA9, e.g., -OH or -O-alkyl.
[00121] In certain embodiments, M1 is -0-, -NRA8-, or -CHRA8- wherein RA8 is hydrogen; substituted or unsubstituted alkyl; a nitrogen protecting group if attached to nitrogen; or -ORA9; wherein RA9 is independently hydrogen; substituted or unsubstituted alkyl; acyl; or an oxygen protecting group.
[00122] In certain embodiments, M1 is -0-. In certain embodiments, M1 is -NRA8-, e.g., - NH-. In certain embodiments, M1 is -CHRA8-, e.g., -CH2-. [00123] In certain embodiments, R is hydrogen; R is hydrogen or -OR ; R is methyl, -NHC(=0)RA9; RA6 is hydrogen, -ORA9, -OC(=0)RA9, or -NHC(=0)RA9; RA7 is methyl; and M1 is -0-.
[00124] In certain embodiments, R^ is hydrogen; RA4 is hydrogen or -ORA9; R^ is methyl, -NHC(=0)RA9; RA6 is hydrogen, -ORA9, -OC(=0)RA9, or -NHC(=0)RA9; and RA7 is methyl. In certain embodiments, RA3 is a non-hydrogen equatorial group.
Groups R3, R4, R5, and R6
[00125] As generally defined above, R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; - SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; - NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; -OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -
C(R C2 )3; wherein each occurrence of R C 1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring.
[00126] In certain embodiments, R 3 is hydrogen or -OR CI , wherein R CI is hydrogen; an oxygen protecting group; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl;
substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or acyl. In certain embodiments, R is hydrogen. In certain embodiments, R3 is -ORcl, e.g., -OH or -OCH3.
[00127] As generally defined above, R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; - SORD1; -S02RD2; -N02; -N3; -N(RD2)2; -NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; - OC(=0)ORD1; -OC(=0)RD2; -OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of
D2
R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino;
D2
or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring.
[00128] In certain embodiments, R4 is hydrogen or -ORD1, wherein RD1 is hydrogen; an oxygen protecting group; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl;
substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or acyl. In certain embodiments, R4 is hydrogen. In certain embodiments, R4 is -ORD1, e.g., -OH or -OCH3.
[00129] As generally defined above, R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; - SORE1; -S02RE2; -N02; -N3; -N(RE2)2; -NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -NRE2C(=0)ORE1; or -C(RE2)3; wherein each occurrence of
El
R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted
E2 aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring. 5 El El
[00130] In certain embodiments, R is hydrogen or -OR , wherein R is hydrogen; an oxygen protecting group; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl;
substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or acyl. In certain embodiments, R5 is hydrogen. In certain embodiments, R5 is -ORE1, e.g. , -OH or -OCH3.
[00131] As generally defined above, R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; - SORF1; -S02RF2; -N02; -N3; -N(RF2)2; -NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -NRF2C(=0)ORF1; or -C(RF2)3; wherein each occurrence of
Fl
R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring.
[00132] In certain embodiments, R6 is hydrogen; halogen; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or
F 1 F2 F 1 unsubstituted aryl; substituted or unsubstituted heteroaryl; -OR ; -C(=0)R ; -C02R ; - CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; -NRF2C(=0)RF2; - NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -NRF2C(=0)ORF1; or - C(RF2)3.
[00133] In certain embodiments, R6 is hydrogen.
[00134] In certain embodiments, R6 is halogen; e.g., -F, -CI, Br, or -I.
[00135] In certain embodiments, R6 is substituted or unsubstituted alkyl, e.g. , substituted or unsubstituted Q 6alkyl, substituted or unsubstituted Q 2alkyl, substituted or unsubstituted
C2_3alkyl, substituted or unsubstituted C3^alkyl, substituted or unsubstituted C^alkyl, or substituted or unsubstituted Cs^alkyl. Exemplary R6 Ci_6 alkyl groups include, but are not limited to, substituted or unsubstituted methyl (CO, ethyl (C2), n-propyl (C3), isopropyl (C3), n-butyl (C4), tert-butyl (C4), sec-butyl (C4), iso-butyl (C4), n-pentyl (C5), 3-pentanyl (C5), amyl (C5), neopentyl (C5), 3-methyl-2-butanyl (C5), tertiary amyl (C5), n-hexyl (C6).
[00136] In certain embodiments, R6 is substituted or unsubstituted alkenyl, e.g. , substituted or unsubstituted C2_6alkenyl, substituted or unsubstituted C2_3alkenyl, substituted or unsubstituted C3^alkenyl, substituted or unsubstituted C4_salkenyl, or substituted or unsubstituted Cs^alkenyl.
[00137] In certain embodiments, R6 is substituted or unsubstituted alkynyl, e.g. , substituted or unsubstituted C2_6alkynyl, substituted or unsubstituted C2_3alkynyl, substituted or unsubstituted C3^alkynyl, substituted or unsubstituted C4_salkynyl, or substituted or unsubstituted Cs^alkynyl.
[00138] In certain embodiments, R6 is substituted or unsubstituted carbocyclyl, e.g. , substituted or unsubstituted C3_6carbocyclyl, substituted or unsubstituted C3^carbocyclyl, substituted or unsubstituted C4_5 carbocyclyl, or substituted or unsubstituted Cs_6 carbocyclyl. In certain embodments, R6 is substituted or unsubstituted cyclopropyl.
[00139] In certain embodiments, R6 is substituted or unsubstituted heterocyclyl, e.g. , substituted or unsubstituted 3-6 membered heterocyclyl, substituted or unsubstituted 3-4 membered heterocyclyl, substituted or unsubstituted 4-5 membered heterocyclyl, or substituted or unsubstituted 5-6 membered heterocyclyl.
[00140] In certain embodiments, R6 is substituted or unsubstituted aryl, e.g., substituted or unsubstituted phenyl.
[00141] In certain embodiments, R6 is substituted or unsubstituted heteroaryl, e.g., substituted or unsubstituted5-6 membered heteroaryl.
6 Fl 6 F2
[00142] In certain embodiments, R is -OR . In certain embodiments, R is -C(=0)R . In certain embodiments, R6 is -C02RF1. In certain embodiments, R6 is -CN. In certain embodiments, R6 is -SCN. In certain embodiments, R6 is -SRF1. In certain embodiments, R6
Fl 6 F2 6
is -SOR . In certain embodiments, R is -S02R . In certain embodiments, R is -N02. In certain embodiments, R6 is -N3. In certain embodiments, R6 is -N(RF2)2. In certain embodiments, R6 is -NRF2C(=0)RF2. In certain embodiments, R6 is -NRF2C(=0)N(RF2)2. In
6 Fl 6 F2 certain embodiments, R is -OC(=0)OR . In certain embodiments, R is -OC(=0)R . In certain embodiments, R6 is -OC(=0)N(RF2)2. In certain embodiments, R6 is - NRF2C(=0)ORF1. In certain embodiments, R6 is -C(RF2)3. [00143] In certain embodiments, each occurrence of R is independently hydrogen; an oxygen protecting group if attached to oxygen; a sulfur protecting group if attached to sulfur; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or acyl; and each occurrence of R F2 is independently hydrogen; a nitrogen protecting group if attached to nitrogen; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; hydroxyl; substituted hydroxyl; thiol; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring.
[00144] In certain embodiments, R Fl or R F2 is hydrogen.
[00145] In certain embodiments, R3 is hydrogen or -OH, R4 is -OCH3, and R5 is -OH.
[00146] In certain embodiments, R3 is hydrogen or -OH, R4 is -OCH3, R5 is -OH, and R6 substituted or unsubstituted alkyl or -OR Fl .
Group R - compounds of Formula (I)
[00147] As generally defined above for compounds of Formula (I), R is -L-B; wherein L is a group of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40-A— j Qr |— R20-X-R1 1— S— | . wherein:
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
R22
p21 p21 I
X S \ tt> / . o ; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carbocyclyl; or
Figure imgf000084_0001
2 ;
Ar is substituted or unsubstituted arylene; each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
A is a group of the formula
Figure imgf000085_0001
Q is -S-, or -0-;
Rwl is independently hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
[00148] In certain embodiments of the compound of Formula (I), R is -L-B; wherein L is a group of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O) -R40-A— | . wherein:
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
R22
p21 p21 I
X is © / or O ;
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
Figure imgf000086_0001
Q is -S- or -0-;
Rwl is hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
[00149] In certain embodiments of the compound of Formula (I), R is -L-B; wherein L is a group of the formula
Figure imgf000086_0002
wherein:
R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalk lene;
Figure imgf000086_0003
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene; A is a group of the formula:
Figure imgf000087_0001
Q is -S-, or -0-;
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
[00150] In certain embodiments of the compound of Formula (I), R is -L-B; wherein L is a group of the formula:
h R20-X-R1 1— S— | . wherein:
R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
X iiss
Figure imgf000087_0002
· ; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carbocyclyl; or
Figure imgf000087_0003
; and
B is an antibody or an antibody fragment.
[00151] In certain embodiments of the compound of Formula (I), R is -L-B; wherein L is a group of the formula:
|-R20-X-R1 1— S— | . wherein:
R 20 is substituted or unsubstituted alkylene;
Figure imgf000088_0001
R11 is substituted or unsubstituted alkylene;
R 22 is hydrogen; or substituted or unsubstituted alkyl; and
B is an antibody or an antibody fragment.
[00152] In certain embodiments, R 20 is substituted or unsubstituted alkylene. In certain embodiments, R 20 is unsubstituted alkylene. In certain embodiments, R 20 is unsubstituted Ci_6 alkylene. In certain embodiments, R 20 is unsubstituted C1-5 alkylene. In certain embodiments,
R 20 is unsubstituted C1-4 alkylene. In certain embodiments, R 20 is unsubstituted C2_6 alkylene.
In certain embodiments, R 20 is unsubstituted C 20
2_5 alkylene. In certain embodiments, R is unsubstituted C2_4 alkylene. In certain embodiments, R 20 is unsubstituted C2_3 alkylene. In certain embodiments, R 20 is unsubstituted ethylene. In certain embodiments, R 20 is unsubstituted propylene. In certain embodiments, R 20 is unsubstituted butylene. In certain embodiments, R 20 is unsubstituted pentylene. In certain embodiments, R 20 is unsubstituted hexylene.
[00153] In certain embodiments, X is
Figure imgf000088_0002
; and R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are oined
to form an optionally substituted heterocyclyl ring. In certain embodiments, X is
Figure imgf000088_0003
and R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted
carbocyclyl. In certain embodiments, X is is independently substituted or
unsubstituted alkyl. In certain embodiment ; and R is independently
unsubstituted alkyl. In certain embodiment
Figure imgf000088_0004
s, X is and R is independently
unsubstituted C1-6 alkyl. In certain embodiments, X is
Figure imgf000088_0005
; and R is independently R21 R2
\ /
unsubstituted C1-4 alkyl. In certain embodiments, X is \ ® f ; and R21 is independently
R21 R2 unsubstituted C1-3 alkyl. In certain embodiments, X is \ ® f ; and R21 is independently
unsubstituted Ci_2 alkyl. In certain embodiments, X
Figure imgf000089_0001
; and two R 21 groups are joined to form an optionally substituted heterocyclyl ring. In certain embodiments, X is
Figure imgf000089_0002
; and two R 21 groups are optionally joined to form an optionally substituted 5-6
R2 R21 membered heterocyclyl ring. In certain embodiments, X is V■ ® ' ; and two R21 groups are joined to form an optionally substituted 6 membered heterocyclyl ring. In certain
R21 F
\ /
embodiments, X is V * ® ' ; and two R21 groups are joined to form an unsubstituted 6
R21 R21 membered heterocyclyl ring. In certain embodiments, X is v \ ®Ny ' ; and two R21 groups are joined to form an optionally substituted pyrrolidine, piperidine, piperazine, thiomorpholine
R2 R21
1,1-dioxide, or morpholine. In certain embodiments, X is v \ ®Ny ' ; and two R21 groups are
R2 R21 joined to form an optionally substituted morpholine. In certain embodiments, X is Y \ ft ^y ' and two R 21 groups are joined to form an unsubstituted morpholine.
[00154] In certain embodiments, X is
Figure imgf000089_0003
; and R 22 is hydrogen; substituted or
unsubstituted carbocyclyl; substituted or unsubstituted alkyl; or
Figure imgf000089_0004
. In certain I
Y
embodiments, X is y O y ; and R22 is hydrogen; substituted or unsubstituted
Figure imgf000090_0001
22
and R is hydrogen; or substituted or unsubstituted alkyl. In certain embodiments, X is R22
vV O°y ; and R22 is hydrogen; or substituted or unsubstituted Ci_6 alkyl. In certain
R22 embodiments, X is O ; and R22 is hydrogen; or substituted or unsubstituted Ci_2
R22 . In certain embodiments, X is vAY
alkyl O°y ; and R22 is hydrogen; or substituted or
R22 unsubstituted Q_2 alkyl. In certain embodiments, X is y O ; and R22 is hydrogen; or
R22 substituted Ci_2 alkyl. In certain embodiments, X is vV O v ; and R 22 is hydrogen; or
R22 unsubstituted Q_2 alkyl. In certain embodiments, X is y O ; and R22 is hydrogen. In
R22 certain embodiments, X is y O ; and R22 is substituted or unsubstituted Q_2 alkyl. In
R22 certain embodiments, X is y O ; and R 22 is substituted Ci_2 alkyl (e.g., haloalkyl). In
R22 certain embodiments, X is O ; and R22 is unsubstituted Ci_2 alkyl. In certain embodiments, X is yl (e.g., C3 cycloalkyl).
In certain embodim
Figure imgf000091_0001
ents, X is ; and R is . In certain
embodiments, X is
Figure imgf000091_0002
.
[00155] In certain embodiments, X is heterocyclylene or heteroarylene. In certain embodiments, X is heterocyclylene. In certain embodiments, X is a 6-membered
heterocyclylene. In certain embodiments, X is a piperazinylene. In certain embodiments, X is heteroarylene. In certain embodiments, X is a 5-membered heteroarylene. In certain embodiments, X is an imidazolylene.
[00156] In certain embodiments, Ar is substituted or unsubstituted arylene. In certain embodiments, Ar is substituted or unsubstituted phenylene. In certain embodiments, Ar is unsubstituted phenylene.
[00157] In certain embodiments, each occurrence of Z is independently an amino acid. In certain embodiments, Z is independently a naturally occurring amino acid. In certain embodiments, Z is independently lysine, arginine, histidine, ornithine, or citrulline. In certain embodiments, Z is lysine or citrulline. In certain embodiments, Z is citrulline.
[00158] In certain embodiments, each occurrence of Y is independently an amino acid. In certain embodiments, Y is independently a naturally occurring amino acid. In certain embodiments, Y is alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan. In certain embodiments, Y is valine or phenylalanine. In certain embodiments, Y is valine.
[00159] In certain embodiments, each occurrence of m is 1, 2, or 3. In certain embodiments, each occurrence of m is 1 or 2. In certain embodiments, each occurrence of m is 1.
[00160] In certain embodiments, -Zm-Ym- is -citrulline- valine-.
[00161] In certain embodiments, E is a bond or an amino acid. In certain embodiments, E is a bond or a naturally occurring amino acid. In certain embodiments, E is a bond or a substituted naturally occurring amino acid. In certain embodiments, E is a bond. In certain embodiments, E is a naturally occurring amino acid. In certain embodiments, E is a substituted naturally occurring amino acid. In certain embodiments, E is a substituted lysine. [00162] In certain embodiments, E is of the formula:
Figure imgf000092_0001
wherein R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl.
[00163] In certain embodiments, E is of the formula:
Figure imgf000092_0002
wherein n is 2-30.
[00164] In certain embodiments, E is of the formula:
Figure imgf000092_0003
[00165] In certain embodiments, R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene. In certain embodiments, R40 is substituted or unsubstituted Ci_6 alkylene; or substituted or unsubstituted Ci_4o heteroalkylene. In certain embodiments, R40 is substituted or unsubstituted alkylene. In certain embodiments, R40 is substituted or unsubstituted C1-6 alkylene. In certain embodiments, R40 is substituted C1-6 alkylene. In certain embodiments, R40 is unsubstituted C1-6 alkylene. In certain embodiments, R40 is substituted or unsubstituted heteroalkylene. In certain embodiments, R40 is substituted or unsubstituted Ci_4o heteroalkylene. In certain embodiments, R40 is substituted Ci_4o heteroalkylene. In certain embodiments, R40 is unsubstituted C1-4o heteroalkylene. In certain embodiments, R40 is
Figure imgf000093_0001
, Ci_6 unsubstituted alkylene, or ; wherein p is
1-8. In certain embodiments . In
certain embodiments, R40 is
Figure imgf000093_0002
. In certain embodiments, R40 is Ci_6 unsubstituted alkylene. In certain embodiments, R is P ; wherein p is 1-8. In certain R40 is P ; wherein p is 2-8. In certain embodiments, R40 is
Figure imgf000093_0003
; wherein p is 2, 4, or 8. In certain embodiments, R40 is 2 . In certain embodiments, R40 is 4 . In certain embodiments, R40 is
Figure imgf000093_0004
[00166] In certain embodiments, A is a group of the formula:
Figure imgf000093_0005
Q is -S-, or -0-; and Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
[00167] In certain embodiments, A is a group of the formula:
Figure imgf000093_0006
[00168] In certain embodiments, A is a group of the formula:
Figure imgf000093_0007
[00169] In certain embodiments, L is a group of Formula (L-1):
Figure imgf000094_0001
[00170] In certain embodiments of Formula (L-l), R is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00171] In certain embodiments, L is a group of Formula (L-2):
Figure imgf000094_0002
[00172] In certain embodiments of Formula (L-2), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00173] In certain embodiments L is a group of Formula (L-3):
Figure imgf000094_0003
[00174] In certain embodiments of Formula (L-3), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; and R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene.
[00175] In certain embodiments, L is a group of Formula (L-4):
Figure imgf000095_0001
[00176] In certain embodiments of Formula (L-4), R is substituted or unsubstituted C1-6 alkylene; and R22 is hydrogen or substituted or unsubstituted Ci_6 alkyl. In certain
20 22
embodiments, of Formula (L-4), R is unsubstituted C2-5 alkylene; and R is hydrogen or methyl.
[00177] In certain embodiments L is a group of Formula (L-5):
Figure imgf000095_0002
[00178] In certain embodiments of Formula (L-5), R20 is substituted or unsubstituted C1-6 alkylene; R22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; and p is 1- 10. In certain
T) 22
embodiments, of Formula (L-5), R~ is unsubstituted C2-5 alkylene; R is hydrogen or methyl; and p is 2-8.
[00179] In c rtain embodiments, L is a group of Formula (L-6):
Figure imgf000095_0003
[00180] In certain embodiments of Formula (L-6), R u is substituted or unsubstituted Ci- alkylene; and R22 is hydrogen or substituted or unsubstituted Ci_6 alkyl. In certain embodiments, of Formula (L-6), R20 is unsubstituted C2-5 alkylene; and R22 is hydrogen or methyl. [00181] In certain embodiments L is a group of Formula (L-7):
Figure imgf000096_0001
[00182] In certain embodiments of Formula (L-7), R u is substituted or unsubstituted Ci_6 alkylene; and R 22 is hydrogen or substituted or unsubstituted C1-6 alkyl. In certain
embodiments, of Formula (L-7), R 20 is unsubstituted C2-5 alkylene; and R 22 is hydrogen or methyl.
[00183] In certain embodiments L is a group of Formula (L-8):
Figure imgf000096_0002
[00184] In certain embodiments of Formula (L-8), R is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen or substituted or unsubstituted C1-6 alkyl; R 40 is substituted or
70 unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of Formula (L-8), R 20 is unsubstituted C2-5 alkylene; R 22 is hydrogen or methyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; and R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of Formula (L-8), R 20 is unsubstituted C2-5 alkylene; R 22 is hydrogen or methyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or
70
unsubstituted C1-4o heteroalkylene; and R is substituted or unsubstituted C1-4o
heteroalkylene. In certain embodiments of Formula (L-8), R 20 is unsubstituted C2-5 alkylene;
R 22 is hydrogen or methyl; R 40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; and R 70 is unsubstituted C1-4o heteroalkylene. In certain embodiments of Formula (L-8), R 20 is unsubstituted C2 22
-5 alkylene; R is hydrogen or methyl; R is substituted or unsub alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; and R is
Figure imgf000097_0001
; wherein p is 1-30. In certain embodiments of
Formula (L-8), R is unsubstituted C2-5 alkylene; R is hydrogen or methyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
Figure imgf000097_0002
[00185] In certain embodiments, L is a group of Formula (L-9):
Figure imgf000097_0003
wherein n is 2-30.
[00186] In certain embodiments of Formula (L-9), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen or substituted or unsubstituted 40
C1-6 alkyl; R is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and n is 1-9.
In certain embodiments of Formula (L-9), R 20 is unsubstituted 22
C2-5 alkylene; R is hydrogen or methyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_ heteroalkylene; and n is 1-9. In certain embodiments of Formula (L-9), R 20
40 is unsubstituted
22 is hydrogen or methyl; R 40
C2-5 alkylene; R is substituted or unsubstituted C1-6 alkylene; and n is 1-9. In certain embodiments of Formula (L-9), R 20 is unsubstituted 22
C2-5 alkylene; R is hydrogen or methyl; R40 is unsubstituted Ci_4o heteroalkylene; and n is 1-9.
[00187] In certain embodiments L is a group of Formula (L-10):
Figure imgf000097_0004
[00188] In certain embodiments of Formula (L-10), R is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan. [00189] In certain embodiments L is a group of Formula (L-11):
Figure imgf000098_0001
[00190] In certain embodiments of Formula (L-11), R is substituted or unsubstituted Ci_6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00191] In certain embodiments, L is a group of Formula (L-12):
Figure imgf000098_0002
[00192] In certain embodiments of Formula (L-12), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene.
[00193] In certain embodiments, L is a group of Formula (L-13):
Figure imgf000098_0003
(L-13).
[00194] In certain embodiments of Formula (L-13), R 20 is substituted or unsubstituted Ci_6 alkylene; and R 21 is independently substituted or unsubstituted C1-6 alkyl. In certain embodiments of Formula (L-13), R 20 is unsubstituted C2-5 alkylene; and R 21 is methyl. [00195] In certain embodiments, L is a group of Formula (L-14):
Figure imgf000099_0001
(L.14)
20
[00196] In certain embodiments of Formula (L-14), R is substituted or unsubstituted Ci_6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; and p is 1-10. In certain embodiments of Formula (L-14), R20 is unsubstituted C2_5 alkylene; R21 is methyl; and p is 2-
[00197] In certain embodiments, L is a group of Formula (L-15):
Figure imgf000099_0002
20
[00198] In certain embodiments of Formula (L-15), R is substituted or unsubstituted Ci_6 alkylene; and R21 is independently substituted or unsubstituted Ci_6 alkyl. In certain embodiments of Formula (L-15), R20 is unsubstituted C2_5 alkylene; and R21 is methyl.
[00199] In certain embodiments, L is a group of Formula (L-16):
Figure imgf000099_0003
20
[00200] In certain embodiments of Formula (L-16), R is substituted or unsubstituted Ci_6 alkylene; and R21 is independently substituted or unsubstituted Ci_6 alkyl. In certain
21
embodiments of Formula (L-16), R is unsubstituted C2_5 alkylene; and R 1 is methyl. [00201] In certain embodiments L is a group of Formula (L-17):
Figure imgf000100_0001
[00202] In certain embodiments of formula (L-17), R is substituted or unsubstituted Ci_6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; R40 is substituted or
70 unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of formula (L-17), R20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; and R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of formula (L-17), R20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o
heteroalkylene; and R 70 is substituted or unsubstituted Ci_4o heteroalkylene. In certain embodiments of formula (L-17), R20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; and R 70 is unsubstituted alkylene. In certain embodiments of formula (L-17), R 20
C1-4o hetero
is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted d Ci_6 alkylene,
Figure imgf000100_0002
or substituted or unsubstituted Ci_4o heteroalkylene; and R is P ; wherein p is
1-30. In certain embodiments of formula (L-17), R is unsubstituted C2-5 alkylene; R is bstituted or unsubstituted Ci_4o
Figure imgf000100_0003
[00203] In certain embodiments, L is a group of Formula (L-18):
Figure imgf000101_0001
wherein n is 2-30.
[00204] In certain embodiments of Formula (L-18), R is substituted or unsubstituted Ci_6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and n is 1-9.
In certain embodiments of Formula (L-18), R 20 is unsubstituted ; R 21
C2-5 alkylene is independently unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; and n is 1-9. In certain embodiments of Formula (L-18), R20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted or unsubstituted C1-6 alkylene; and n is 1-9. In certain embodiments of Formula (L-18), R 20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is unsubstituted C1-4o heteroalkylene; and n is 1-9.
Group R - compounds of Formula (II)
[00205] As generally defined above for compounds of Formula (II), R 7 is -L 1 -T; wherein is a group of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40— I Qr J— R20-X~R1 1— S— j . wherein:
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
X 1iSs
Figure imgf000101_0002
■ ; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted carbocyclyl; or
Figure imgf000102_0001
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000102_0002
R is halogen, tosylate, mesylate, or triflate;
R X2 is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
[00206] Rwl is independently hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group. In certain embodiments of Formula (II), R 7 is -L 1 -T; wherein L 1 is a group of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40— | . wherein:
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
R22
R2 R21
s V N 0
X iiss \ ©<±> oorr O ·
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000103_0001
R is halogen, tosylate, mesylate, or triflate;
R X2 is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
[00207] In certain embodiments of Formula (II), R 7 is -L 1 -T; wherein L 1 is a group of the formula:
j— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40— j . wherein:
R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalk lene;
Figure imgf000103_0002
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid; E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000104_0001
R is halogen, tosylate, mesylate, or triflate;
R X2 is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
[00208] In certain embodiments of the compound of Formula (II), R 7 is -L 1 -T; wherein L 1 is a group of the formula:
|-R20-X-R1 1— S— j . wherein:
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
X is
Figure imgf000104_0002
heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring; and
R is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carboc clyl or
Figure imgf000104_0003
Figure imgf000104_0004
[00209] In certain embodiments of the compound of Formula (II), R 7 is -L 1 -T; wherein L 1 is a group of the formula:
|-R20-X-R1 1— S— | . wherein:
R 20 is substituted or unsubstituted alkylene;
Figure imgf000105_0001
R11 is substituted or unsubstituted alkylene;
R 22 is hydro en; or substituted or unsubstituted alkyl; and
Figure imgf000105_0002
[00210] In certain embodiments, R 20 is substituted or unsubstituted alkylene. In certain embodiments, R 20 is unsubstituted alkylene. In certain embodiments, R 20 is unsubstituted C1-6 alkylene. In certain embodiments, R 20 is unsubstituted C1-5 alkylene. In certain embodiments,
R 20 is unsubstituted C1-4 alkylene. In certain embodiments, R 20 is unsubstituted C2-6 alkylene.
In certain embodiments, R 20 is unsubstituted C rtain embodiments, R 20
2_5 alkylene. In ce is unsubstituted C2_4 alkylene. In certain embodiments, R 20 is unsubstituted C2_3 alkylene. In certain embodiments, R 20 is unsubstituted ethylene. In certain embodiments, R 20 is unsubstituted propylene. In certain embodiments, R 20 is unsubstituted butylene. In certain embodiments, R 20 is unsubstituted pentylene. In certain embodiments, R 20 is unsubstituted hexylene.
[00211] In certain embodiments, X
Figure imgf000105_0003
; and R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R group joined
to form an optionally substituted heterocyclyl ring. In certain embodiments, X is
Figure imgf000105_0004
and R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted
R2 R21 carbocyclyl. In certain embodiments, X is * u ' ; and R 21 is independently substituted or unsubstituted alkyl. In certain embodiments, X is
Figure imgf000106_0001
and R 21 i ·s independently
unsubstituted alkyl. In certain embodiments, X is ^ ' ; and R is independently
unsubstituted Ci_6 alkyl. In certain embodiments, X ; and R 21 is independently
unsubstituted Ci_4 alkyl. In certain embodiments, X ; and R 21 is independently
1 unsubstituted C1-3 alkyl. In certain embodiments, X ; and R 21 is independently
1 unsubstituted Ci_2 alkyl. In certain embodiments, X
Figure imgf000106_0002
; and two R 1 groups are joined to form an optionally substituted heterocyclyl ring. In certain embodiments, X is
Figure imgf000106_0003
; and two R , 21 groups are optionally joined to form an optionally substituted 5-6
R2 R 21
\ /
- N .
membered heterocyclyl ring. In certain embodiments, X is V■ ® y ' ; and two R21 groups are joined to form an optionally substituted 6 membered heterocyclyl ring. In certain
embodiments, X is
Figure imgf000106_0004
R21 F
\ /
N ,
m d heterocyclyl ring. In certain embodiments, X is V .
embere V ; and two R21 groups are joined to form an optionally substituted pyrrolidine, piperidine, piperazine, thiomorpholine
R2 R21
1,1-dioxide, or morpholine. In certain embodiments, X is ; and two R 21 groups are
R21 R2'
\ /
N . joined to form an optionally substituted morpholine. In certain embodiments, X is V \ n ^V ' ; and two R 21 groups are joined to form an unsubstituted morpholine. I
[00212] In certain embodiments, X is YV OV ; and R 22 is hydrogen; substituted or
N RW1 unsubstituted carbocyclyl; substituted or unsubstituted alkyl; or * 12 . In certain
R22 embodiments, X is vv Ov ; and R22 is hydrogen; substituted or unsubstituted
R22 carbocyclyl, or substituted or unsubstituted alkyl. In certain embodiments, X is vv Ov
; and R 22 is hydrogen; or substituted or unsubstituted alkyl. In certain embodiments, X is R22
vv Ov ; and R22 is hydrogen; or substituted or unsubstituted Ci_6 alkyl. In certain
R22 embodiments, X is vv Ov ; and R22 is hydrogen; or substituted or unsubstituted Q_2
R22 alkyl. In certain embodiments, X is O ; and R is hydrogen; or substituted or
R22 unsubstituted Q_2 alkyl. In certain embodiments, X is YV OV ; and R22 is hydrogen; or
R22 substituted Ci_2 alkyl. In certain embodiments, X is O ; and R 22 is hydrogen; or
R22 unsubstituted Ci_2 alkyl. In certain embodiments, X is VV OV ; and R 22 is hydrogen. In
R22 certain embodiments, X is YV OV ; and R22 is substituted or unsubstituted Ci_2 alkyl. In I
VNY
certain embodiments, X is O ; and R is substituted Ci_2 alkyl (e.g., haloalkyl). In
certain embodiments, X is
Figure imgf000108_0001
; and R is unsubstituted Ci 2 alkyl. In certain
. In certain embodiments, X is
Figure imgf000108_0002
[00213] In certain embodiments, X is heterocyclylene or heteroarylene. In certain embodiments, X is heterocyclylene. In certain embodiments, X is a 6-membered
heterocyclylene. In certain embodiments, X is a piperazinylene. In certain embodiments, X is heteroarylene. In certain embodiments, X is a 5-membered heteroarylene. In certain embodiments, X is an imidazolylene.
[00214] In certain embodiments, Ar is substituted or unsubstituted arylene. In certain embodiments, Ar is substituted or unsubstituted phenylene. In certain embodiments, Ar is unsubstituted phenylene.
[00215] In certain embodiments, each occurrence of Z is independently an amino acid. In certain embodiments, Z is independently a naturally occurring amino acid. In certain embodiments, Z is independently lysine, arginine, histidine, ornithine, or citrulline. In certain embodiments, Z is lysine or citrulline. In certain embodiments, Z is citrulline.
[00216] In certain embodiments, each occurrence of Y is independently an amino acid. In certain embodiments, Y is independently a naturally occurring amino acid. In certain embodiments, Y is alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan. In certain embodiments, Y is valine or phenylalanine. In certain embodiments, Y is valine.
[00217] In certain embodiments, each occurrence of m is 1, 2, or 3. In certain embodiments, each occurrence of m is 1 or 2. In certain embodiments, each occurrence of m is 1.
[00218] In certain embodiments, -Zm-Ym- is -citrulline- valine-.
[00219] In certain embodiments, E is a bond or an amino acid. In certain embodiments, E is a bond or a naturally occurring amino acid. In certain embodiments, E is a bond or a substituted naturally occurring amino acid. In certain embodiments, E is a bond. In certain embodiments, E is a naturally occurring amino acid. In certain embodiments, E is a substituted naturally occurring amino acid. In certain embodiments, E is a substituted lysine.
[00220] In certain embodiments, E is of the formula:
Figure imgf000109_0001
wherein R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl.
[00221] In certain embodiments, E is of the formula:
Figure imgf000109_0002
wherein n is 2-30.
[00222] In certain embodiments, E is of the formula:
Figure imgf000109_0003
[00223] In certain embodiments, R is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene. In certain embodiments, R40 is substituted or unsubstituted Ci-6 alkylene; or substituted or unsubstituted Ci_4o heteroalkylene. In certain embodiments, R40 is substituted or unsubstituted alkylene. In certain embodiments, R40 is substituted or unsubstituted Ci_6 alkylene. In certain embodiments, R40 is substituted Ci_6 alkylene. In certain embodiments, R40 is unsubstituted Ci_6 alkylene. In certain embodiments, R40 is substituted or unsubstituted heteroalkylene. In certain embodiments, R40 is substituted or unsubstituted Ci_4o heteroalkylene. In certain embodiments, R40 is substituted Ci_4o heteroalkylene. In certain embodiments, R is unsubstituted Ci_4o heteroalkylene. In certain
embodiments, R40 is
Figure imgf000110_0001
, Ci_6 unsubstituted alkylene, or ; wherein p is
1-8. In certain embodiments R is
Figure imgf000110_0002
. In
certain embodiments, R40 is . diments, R40 is C1-6 unsubstituted ; wherein p is 1-8. In certain herein p is 2-8. In certain embo ; wherein p is certain embodiments, R40 is
Figure imgf000110_0003
certain embodiments, R40 is . In certain embodiments, R40 is
[00224] In certain embodiments, T is a group of the formula:
Figure imgf000110_0004
Q is -S-, or -0-; and Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group.
[00225] In certain embodiments, T is a group of the formula:
Figure imgf000110_0005
R is halogen; and
R X2 is substituted or unsubstituted heterocyclyl.
[00226] In certain embodiments, T is a group of the formula:
Figure imgf000111_0001
[00227] In certain embodiments, T is a roup of the formula:
Figure imgf000111_0002
[00228] In certain embodiments, -Ll-T is a group of Formula (ΐ -1):
Figure imgf000111_0003
1 20
[00229] In certain embodiments of Formula (L -1), R is substituted or unsubstituted Ci_6
22 40
alkylene; R is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00230] In certain embodiments, -Ll-T is a group of Formula (L1-2):
Figure imgf000111_0004
1 20
[00231] In certain embodiments of Formula (L -2), R is substituted or unsubstituted Ci_6
22 40
alkylene; R is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00232] In certain embodiments, -Ll-T is a group of Formula (L1-3):
Figure imgf000112_0001
[00233] In certain embodiments of Formula (L1-3), R20 is substituted or unsubstituted C1-6
22 40
alkylene; R is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Q-40 heteroalkylene.
[00234] In certain embodiments, -ΐ τ is a group of Formula (L1-4):
Figure imgf000112_0002
[00235] In certain embodiments of Formula (L1-4), R20 is substituted or unsubstituted C1-6 alkylene; and R22 is hydrogen or substituted or unsubstituted C1-6 alkyl. In certain
1 22
embodiments of Formula (L -4), R~ is unsubstituted C2-5 alkylene; and R is hydrogen or methyl.
[00236] In certain embodiments, -L!-T is a group of Formula (L1-5):
Figure imgf000112_0003
[00237] In certain embodiments of Formula (L1-5), R20 is substituted or unsubstituted C1-6 alkylene; R22 is hydrogen, or substituted or unsubstituted Ci-6 alkyl; and p is 1-10. In certain
20 22
embodiments of Formula (L-5), R is unsubstituted C2-5 alkylene; R is hydrogen or methyl; and p is 2-8.
[00238] In certain embodiments, -ΐ τ is a group of Formula (L1-6):
Figure imgf000113_0001
[00239] In certain embodiments of Formula (L 1 -6), 20
R is substituted or unsubstituted Ci_6 alkylene; and 22
R is hydrogen or substituted or unsubstituted Ci_6 alkyl. In certain embodiments of Formula (L 1 -6), 20 22
R is unsubstituted C2-5 alkylene; and R is hydrogen or methyl.
[00240] In certain embodiments, -Ll-T is a group of Formula (ΐ -7):
Figure imgf000113_0002
[00241] In certain embodiments of Formula (L 1 -7), 20
R is substituted or unsubstituted Ci_6 alkylene; and 22
R is hydrogen or substituted or unsubstituted Ci_6 alkyl. In certain embodiments of Formula (L 1 -7), 20 22
R is unsubstituted C2-5 alkylene; and R is hydrogen or methyl.
[00242] In certain embodiments, -Ll-T is a group of Formula (L1-8):
Figure imgf000113_0003
[00243] In certain embodiments of Formula (L 1 -8), 20
R is substituted or unsubstituted Ci_6 alkylene; 22 is hydrogen or substituted or unsubstituted 40
R C1-6 alkyl; R is substituted or unsubstituted uted 70
C1-6 alkylene, or substituted or unsubstit Ci^o heteroalkylene; and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of Formula (L 1 -8), R 20 is unsubstituted 22
C2-5 alkylene; R is hydrogen or methyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; and R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of Formula (L 1 -8), R 20 is unsubstituted 1
C2-5 alkylene; R ' is hydrogen or methyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted nd R 70
Ci_4o heteroalkylene; a is substituted or unsubstituted Ci_4o heteroalkylene. In certain embodiments of Formula (L 1 -8), R 20 is unsubstituted C2-5 alkylene;
R 22 is hydrogen or methyl; R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted teroalkylene; and R 70
Ci_4o he is unsubstituted Ci_4o heteroalkylene. In certain embodiments of Formula (L 1 -8), R 20 is unsubstituted 22
C2-5 alkylene; R is hydrogen or methyl; R40 is substituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; and R is
Figure imgf000114_0001
wherein p is 1-30. In certain embodiments of
Formula (L 1 -8), R 20 is unsubstituted 22 methyl; R 40
-5 alkylene; R is hydrogen or is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene;
Figure imgf000114_0002
[00244 In certain embodiments, -Ll-T is a group of Formula (L1-9):
Figure imgf000114_0003
wherein n is 2-30.
[00245] In certain embodiments of Formula (L 1 -9), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen or substituted or unsubstituted 40
Ci_6 alkyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and n is 1-9.
In certain embodiments of Formula (L 1 -9), R 20 is unsubstituted 22
C2-5 alkylene; R is hydrogen or methyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci_ 0 heteroalkylene; and n is 1-9. In certain embodiments of Formula (L 1 -9), R 20
4 is
unsubstituted 22 s hydrogen or methyl; R 40
C2-5 alkylene; R i is substituted or unsubstituted Ci_6 alkylene; and n is 1-9. In certain embodiments of Formula (L 1 -9), R 20 is unsubstituted C2-5 alkylene; R 22 is hydrogen or methyl; R 40 is unsubstituted Ci_4o heteroalkylene; and n is 1-9.
[00246] In certain embodiments -Ll-T is a group of Formula (L1-10):
Figure imgf000115_0001
[00247] In certain embodiments of Formula (L 1 -10), R 20 is substituted or unsubstituted Ci_6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00248] In certain embodiments -Ll-T is a group of Formula (L1-!!):
Figure imgf000115_0002
[00249] In certain embodiments of Formula (L 1 -11), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00250] In certain embodiments -Ll-T is a group of Formula (L1-12):
Figure imgf000115_0003
(ΙΛ12).
[00251] In certain embodiments of Formula (L 1 -12), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene.
[00252] In certain embodiments, -Ll-T is a group of Formula (L1-13):
Figure imgf000116_0001
1 20
[00253] In certain embodiments of Formula (L -13), R is substituted or unsubstituted C1-6 alkylene; and R21 is independently substituted or unsubstituted Ci_6 alkyl. In certain embodiments of Formula (L1-13), R20 is unsubstituted C2-5 alkylene; and R21 is methyl.
[00254] In c
Figure imgf000116_0002
[00255] In certain embodiments of Formula (ΐ ΐ4), R20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted Ci-6 alkyl; and p is 1-10. In certain embodiments of Formula (L1-14), R20 is unsubstituted C2-5 alkylene; R21 is methyl; and p is 2-8.
[00256] In certain embodiments, -ΐ τ is a group of Formula (L1-15):
Figure imgf000116_0003
(Li.15).
1 20
[00257] In certain embodiments of Formula (L -15), R is substituted or unsubstituted C1-6 alkylene; and R21 is independently substituted or unsubstituted C1-6 alkyl. In certain embodiments of Formula (L1-15), R20 is unsubstituted C2-5 alkylene; and R21 is methyl.
[00258] In certain embodiments, -ΐ τ is a group of Formula (L1-16):
Figure imgf000117_0001
1 20
[00259] In certain embodiments of Formula (L -16), R is substituted or unsubstituted Ci_6
21
alkylene; and R is independently substituted or unsubstituted Ci_6 alkyl. In certain
1 20 21
embodiments of Formula (L -16), R is unsubstituted C2-5 alkylene; and R is methyl.
[00260] In certain embodiments -Ll-T is a group of the formula (Ll-17)
Figure imgf000117_0002
1 20
[00261] In certain embodiments of Formula (L -17), R is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or
70 unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of Formula (L1-17), R20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene;
70
and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In
1 20 21
certain embodiments of Formula (L -17), R is unsubstituted C2-5 alkylene; R is methyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o
70
heteroalkylene; and R is substituted or unsubstituted C1-4o heteroalkylene. In certain embodiments of Formula (L1-17), R20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
70 20 and R is unsubstituted Ci_4o heteroalkylene. In certain embodiments of Formula (L-17), R is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted d C1-6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; and R7 is
Figure imgf000117_0003
; wherein p is
1 20 21
1-30. In certain embodiments of Formula (L -17), R is unsubstituted C2-5 alkylene; R is methyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; and R70 is 11 ' P' ; wherein p is 7-24.
[00262 In certain embodiments, -Ll-T is a group of Formula (L1-18):
Figure imgf000118_0001
wherein n is 2-30.
[00263] In certain embodiments of Formula (L 1 -18), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and n is 1-9.
In certain embodiments of Formula (L 1 -18), R 20 is unsubstituted 21
C2-5 alkylene; R is independently unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; and n is 1-9. In certain embodiments of Formula (L1-18), R20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is substituted or unsubstituted C1-6 alkylene; and n is 1-9. In certain embodiments of Formula (L 1 -18), R 20 is unsubstituted C2-5 alkylene; R21 is methyl; R40 is unsubstituted C1-4o heteroalkylene; and n is 1-9.
Group R8
[00264] As generally defined above, R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -OR11; -C(=0)RE; -C02RU; -CN; -SCN; -SR11; - SOR11; -SO2R12; -NO2; -N3; -N(RE)2; -NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORu; - OC(=0)RE; -OC(=0)N(RE)2; -NREC(=0)ORu; or -C(RE)3; wherein each occurrence of Ru is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R 12 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy;
heteroaryloxy); substituted thiol (e.g., alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino, dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring.
[00265] In certain embodiments, R is hydrogen; halogen; substituted or unsubstituted alkyl; substituted or unsubstituted alkenyl; substituted or unsubstituted alkynyl; substituted or unsubstituted carbocyclyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -OR11; -C(=0)RE; -CO2R11; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; -NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -NREC(=0)ORn; -CH2(ORn), -CH(ORn)2, -CH2OC(=0)R12, or -C(RE)3.
[00266] In certain embodiments, R is hydrogen.
[00267] In certain embodiments, R is halogen, e.g., -F, -CI, -Br, or -I.
[00268] In certain embodiments, R is substituted or unsubstituted alkyl, e.g. , substituted or unsubstituted Q _6alkyl, substituted or unsubstituted Q _2alkyl, substituted or unsubstituted C2-3alkyl, substituted or unsubstituted C3^alkyl, substituted or unsubstituted C^salkyl, or substituted or unsubstituted C5_6alkyl.
[00269] In certain embodiments, R is substituted or unsubstituted alkenyl, e.g. , substituted or unsubstituted C2-6alkenyl, substituted or unsubstituted C2-3alkenyl, substituted or unsubstituted C3^alkenyl, substituted or unsubstituted C4_salkenyl, or substituted or unsubstituted Cs^alkenyl.
[00270] In certain embodiments, R is substituted or unsubstituted alkynyl, e.g. , substituted or unsubstituted C2-6 alkynyl, substituted or unsubstituted C2-3alkynyl, substituted or unsubstituted C3^ alkynyl, substituted or unsubstituted C4_5 alkynyl, or substituted or unsubstituted Cs_6 alkynyl.
[00271] In certain embodiments, R is substituted or unsubstituted carbocyclyl, e.g. , substituted or unsubstituted C3_6 carbocyclyl, substituted or unsubstituted C3^ carbocyclyl, substituted or unsubstituted C4_5 carbocyclyl, or substituted or unsubstituted Cs_6 carbocyclyl.
[00272] In certain embodiments, R is substituted or unsubstituted heterocyclyl, e.g. , substituted or unsubstituted 3-6 membered heterocyclyl, substituted or unsubstituted 3-4 membered heterocyclyl, or substituted or unsubstituted 4-5 membered heterocyclyl. [00273] In certain embodiments, R is substituted or unsubstituted aryl, e.g., substituted or unsubstituted phenyl.
[00274] In certain embodiments, R is substituted or unsubstituted heteroaryl, e.g., substituted or unsubstituted 5-6 membered heteroaryl.
8 II 8 12
[00275] In certain embodiments, R is -OR . In certain embodiments, R is -C(=0)R . In
8 II 8
certain embodiments, R is -C02R . In certain embodiments, R is -CN. In certain
8 8 II 8 embodiments, R is -SCN. In certain embodiments, R is -SR . In certain embodiments, R
II 8 12 8
is -SOR . In certain embodiments, R is -S02R . In certain embodiments, R is -N02. In
8 8 12 certain embodiments, R is -N3. In certain embodiments, R is -N(R )2. In certain embodiments, R8 is -NREC(=0)RE. In certain embodiments, R8 is -NREC(=0)N(RI2)2. In
8 II 8 12 certain embodiments, R is -OC(=0)OR . In certain embodiments, R is -OC(=0)R . In
8 12 8
certain embodiments, R is -OC(=0)N(R )2. In certain embodiments, R is - NREC(=0)ORn. In certain embodiments, R8 is -CH2(ORn). In certain embodiments, R8 is -
II 8 12 8
CH(OR )2. In certain embodiments, R is -CH2OC(=0)R . In certain embodiments, R is - C(RE)3.
[00276] In certain embodiments, at least one instance of R11 is independently hydrogen.
[00277] In certain embodiments, at least one instance of R11 is an oxygen protecting group if attached to oxygen or a sulfur protecting group if attached to sulfur.
[00278] In certain embodiments, at least one instance of R11 is substituted or unsubstituted alkyl, e.g., substituted or unsubstituted Ci_6alkyl, substituted or unsubstituted Ci_2alkyl, substituted or unsubstituted C2 3alkyl, substituted or unsubstituted C3^alkyl, substituted or unsubstituted C4_salkyl, or substituted or unsubstituted Cs_6alkyl.
[00279] In certain embodiments, at least one instance of R11 is substituted or unsubstituted alkenyl, e.g. , substituted or unsubstituted C2-6alkenyl, substituted or unsubstituted C2 3alkenyl, substituted or unsubstituted C3^alkenyl, substituted or unsubstituted C4_salkenyl, or substituted or unsubstituted Cs^alkenyl.
[00280] In certain embodiments, at least one instance of R11 is substituted or unsubstituted alkynyl, e.g., substituted or unsubstituted C2-6alkynyl, substituted or unsubstituted C2 3alkynyl, substituted or unsubstituted C3^alkynyl, substituted or unsubstituted C4_salkynyl, or substituted or unsubstituted Cs^alkynyl.
[00281] In certain embodiments, at least one instance of R11 is substituted or unsubstituted carbocyclyl, e.g. , substituted or unsubstituted C3_6carbocyclyl, substituted or unsubstituted C3^carbocyclyl, substituted or unsubstituted C4_5 carbocyclyl, or substituted or unsubstituted C5_6 carbocyclyl. [00282] In certain embodiments, at least one instance of R is substituted or unsubstituted heterocyclyl, e.g. , substituted or unsubstituted 3-6 membered heterocyclyl, substituted or unsubstituted 3-4 membered heterocyclyl, substituted or unsubstituted 4-5 membered heterocyclyl, or substituted or unsubstituted 5-6 membered heterocyclyl.
[00283] In certain embodiments, at least one instance of R11 is substituted or unsubstituted aryl, e.g., substituted or unsubstituted phenyl.
[00284] In certain embodiments, at least one instance of R11 is substituted or unsubstituted heteroaryl, e.g., substituted or unsubstituted 5-6 membered heteroaryl.
[00285] In certain embodiments, at least one instance of R11 is acyl.
12
[00286] In certain embodiments, at least one instance of R is independently hydrogen.
12
[00287] In certain embodiments, at least one instance of R is a nitrogen protecting group if attached to nitrogen.
12
[00288] In certain embodiments, at least one instance of R is substituted or unsubstituted alkyl, e.g., substituted or unsubstituted Ci_6alkyl, substituted or unsubstituted Ci_2alkyl, substituted or unsubstituted C2_3alkyl, substituted or unsubstituted C3^alkyl, substituted or unsubstituted C4_salkyl, or substituted or unsubstituted Cs^alkyl.
12
[00289] In certain embodiments, at least one instance of R is substituted or unsubstituted alkenyl, e.g. , substituted or unsubstituted C2_6alkenyl, substituted or unsubstituted C2
3alkenyl, substituted or unsubstituted C3^alkenyl, substituted or unsubstituted C4_salkenyl, or substituted or unsubstituted Cs^alkenyl.
12
[00290] In certain embodiments, at least one instance of R is substituted or unsubstituted alkynyl, e.g., substituted or unsubstituted C2_6alkynyl, substituted or unsubstituted C2
3alkynyl, substituted or unsubstituted C3^alkynyl, substituted or unsubstituted C4_salkynyl, or substituted or unsubstituted Cs^alkynyl.
12
[00291] In certain embodiments, at least one instance of R is substituted or unsubstituted carbocyclyl, e.g. , substituted or unsubstituted C3_6carbocyclyl, substituted or unsubstituted C3^carbocyclyl, substituted or unsubstituted C4_5 carbocyclyl, or substituted or unsubstituted C5_6 carbocyclyl.
12
[00292] In certain embodiments, at least one instance of R is substituted or unsubstituted heterocyclyl, e.g. , substituted or unsubstituted 3-6 membered heterocyclyl, substituted or unsubstituted 3-4 membered heterocyclyl, substituted or unsubstituted 4-5 membered heterocyclyl, or substituted or unsubstituted 5-6 membered heterocyclyl.
12
[00293] In certain embodiments, at least one instance of R is substituted or unsubstituted aryl, e.g. , substituted or unsubstituted phenyl. [00294] In certain embodiments, at least one instance of R is substituted or unsubstituted heteroaryl, e.g., substituted or unsubstituted 5-6 membered heteroaryl.
[00295] In certain embodiments, at least one instance of R 12 is acyl.
[00296] In certain embodiments, at least one instance of R 12 is hydroxyl; substituted hydroxyl; thiol; substituted thiol; amino; or substituted amino.
[00297] In certain embodiments, two R 12 groups are optionally joined to form a heterocyclyl or heteroaryl ring.
Group R9
As generally defined herein, R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; - SORG1; -S02RG2; -N02; -N3; -N(RG)2; -NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; - OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -NRG2C(=0)ORG1; or -C(RG2)3; wherein each occurrence of R Gl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of
R G2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R G2 groups are optionally joined to form a heterocyclyl or heteroaryl ring; or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00298] In certain embodiments, R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety. In certain embodiments, R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00299] In certain embodiments, R9 is hydrogen. Group R
[00300] As generally defined herein, R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; -ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; - SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; - NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; -OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -
C(R )3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R B2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring; or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R 10 and R 3 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00301] In certain embodiments, R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety. In certain embodiments, R 10 and R 3 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00302] In certain embodiments, R10 is hydrogen.
Additional embodiments of Formula (I)
[00303] Various combinations of the above embodiments are further contemplated herein. One of skill in the art would appreciate that the various embodiments described herein may be combined in various ways and are contemplated by the inventors.
[00304] In certain embodiments of the compound of Formula (I), R 1 and R 2 are each hydrogen or together form =0; and R10 and R3 are hydrogen; or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00305] In certain embodiments of the compound of Formula (I), R1 is -ORA1; wherein RA1 is hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and R10 and R3 are hydrogen; or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00306] In certain embodiments of the compound of Formula (I), R1 is hydrogen or -ORA1; R2 is hydrogen; or R1 and R2 are joined to form =0; RA1 is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; or RA1 is a group of Formula (i):
Figure imgf000124_0001
wherein each occurrence of R^, RA^, R^, RA6, and RA7 is independently hydrogen, substituted or unsubstituted alkyl; -ORA9; -OC(=0)RA9; -N(RA9)2; or -NHC(=0)RA9;
wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; an oxygen protecting group when attached to an oxygen atom; or a nitrogen protecting group when attached to a nitrogen atom; or two RA9 groups are joined to form a substituted or unsubstituted heterocyclic or substituted or unsubstituted heteroaryl ring; and M1 is -0-;
R 3 is hydrogen or -OR CI , wherein R CI is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; R4 is hydrogen or -ORD1, wherein RD1 is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; R 5 is hydrogen or -OR El , wherein R El is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; R6 is substituted or unsubstituted alkyl; R8 is -CH(ORu)2; and each occurrence of Ru is substituted or unsubstituted alkyl.
[00307] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-e):
Figure imgf000125_0001
or a pharmaceutically acceptable salt thereof.
[00308] In certain embodiments of the compound of Formula (I-e), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00309] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-f):
Figure imgf000125_0002
or a pharmaceutically acceptable salt thereof.
[00310] In certain embodiments of the compound of Formula (I-f), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00311] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-g):
Figure imgf000126_0001
or a pharmaceutically acceptable salt thereof.
20
[00312] In certain embodiments of the compound of Formula (I-g), R is substituted or
22 40 unsubstituted Ci_6 alkylene; R is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00313] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-h):
Figure imgf000126_0002
or a pharmaceutically acceptable salt thereof.
20
[00314] In certain embodiments of the compound of Formula (I-h), R is substituted or
22
unsubstituted C1-6 alkylene; R is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00315] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-i):
Figure imgf000127_0001
or a pharmaceutically acceptable salt thereof.
[00316] In certain embodiments of the compound of Formula (I-i), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00317] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-j):
Figure imgf000127_0002
or a pharmaceutically acceptable salt thereof.
[00318] In certain embodiments of the compound of Formula (I-j), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00319] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-k):
Figure imgf000128_0001
or a pharmaceutically acceptable salt thereof.
[00320] In certain embodiments of the compound of Formula (I-k), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00321] In certain embodiments, the compound of Formula (I) is a compound of Formula (1-1):
Figure imgf000128_0002
or a pharmaceutically acceptable salt thereof.
[00322] In certain embodiments of the compound of Formula (1-1), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00323] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-m):
Figure imgf000129_0001
or a pharmaceutically acceptable salt thereof.
20
[00324] In certain embodiments of the compound of Formula (I-m), R is substituted or
22 40 unsubstituted Ci_6 alkylene; R is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
70
and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In
20
certain embodiments of the compound of Formula (I-m), R is substituted or unsubstituted
22 40
Ci_6 alkylene; R is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R is substituted or
70 unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and R is unsubstituted heteroalkyl.
[00325] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-n):
Figure imgf000129_0002
or a pharmaceutically acceptable salt thereof.
20
[00326] In certain embodiments of the compound of Formula (I-n), R is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00327] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-o):
Figure imgf000130_0001
or a pharmaceutically acceptable salt thereof.
[00328] In certain embodiments of the compound of Formula (I-o), R 20 is substituted or unsubstituted Ci_6 alkylene; R 21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
[00329] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-P):
Figure imgf000130_0002
or a pharmaceutically acceptable salt thereof.
[00330] In certain embodiments of the compound of Formula (I-p), R is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citruUine; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan. In certain embodiments, the compound of Formula (I) is a compound of Formula
Figure imgf000131_0001
or a pharmaceutically acceptable salt thereof.
[00332] In certain embodiments of the compound of Formula (I-q), R 20 is substituted or unsubstituted C1-6 alkylene; R 21 is independently substituted or unsubstituted C1-6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
[00333] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-r):
Figure imgf000131_0002
or a pharmaceutically acceptable salt thereof.
[00334] In certain embodiments of the compound of Formula (I-r), R is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00335] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-s):
Figure imgf000132_0001
or a pharmaceutically acceptable salt thereof.
[00336] In certain embodiments of the compound of Formula (I-s), R 20 is substituted or unsubstituted Ci_6 alkylene; R 21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00337] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-t):
Figure imgf000132_0002
or a pharmaceutically acceptable salt thereof.
[00338] In certain embodiments of the compound of Formula (I-t), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00339] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-u):
Figure imgf000133_0001
or a pharmaceutically acceptable salt thereof.
[00340] In certain embodiments of the compound of Formula (I-u), R 20 is substituted or unsubstituted Ci_6 alkylene; R 21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
[00341] In certain embodiments, the compound of Formula (I) is a compound of Formula (I-v):
Figure imgf000133_0002
or a pharmaceutically acceptable salt thereof.
[00342] In certain embodiments of the compound of Formula (I-v), R 20 is substituted or unsubstituted Ci_6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; and R 70 is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of the compound of Formula (I-v), R 20 is substituted or unsubstituted
Ci kylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40
_6 al is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and R is unsubstituted heteroalkyl.
[00343] In certain embodiments, the compound of Formula (I) is
Figure imgf000134_0001
Figure imgf000135_0001
ı33
Figure imgf000136_0001

Figure imgf000137_0001

Figure imgf000138_0001

Figure imgf000139_0001
or a pharmaceutically acceptable salt thereof, wherein B is an antibody or an antibody fragment.
[00344] In certain embodiments the compound of Formula (I) is
Figure imgf000139_0002
or a pharmaceutically acceptable salt thereof, wherein B is an antibody or an antibody fragment.
[00345] In certain embodiments the compound of Formula (I) is not
Figure imgf000139_0003
Figure imgf000140_0001

Figure imgf000141_0001
Additional embodiments of Formula (II)
[00346] Various combinations of the above embodiments are further contemplated herein. One of skill in the art would appreciate that the various embodiments described herein may be combined in various ways and are contemplated by the inventors.
[00347] In certain embodiments of the compound of Formula (II), R 1 and R 2 are each hydrogen or together form =0; and R10 and R3 are hydrogen; or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00348] In certain embodiments of the compound of Formula (II), R1 is -ORA1; wherein RA1 is hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and R10 and R3 are hydrogen; or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety; or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
[00349] In certain embodiments of the compound of Formula (II), R1 is hydrogen or - ORA1; R2 is hydrogen; or R1 and R2 are joined to form =0; RA1 is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; or RA1 is a group of Formula (i):
wherein each occurrence
Figure imgf000142_0001
is independently hyd:
substituted or unsubstituted alkyl;— OR ; -OC(=0)RAy; -N(R )2; or -NHC(=0)RAy;
wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; an oxygen protecting group when attached to an oxygen atom; or a nitrogen protecting group when attached to a nitrogen atom; or two RA9 groups are joined to form a substituted or unsubstituted heterocyclic or substituted or unsubstituted heteroaryl ring; and M1 is -0-;
R 3 is hydrogen or -OR CI , wherein R CI is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; R4 is hydrogen or -ORD1, wherein RD1 is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; R 5 is hydrogen or -OR El , wherein R El is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; R6 is substituted or unsubstituted alkyl; R8 is -CH(ORu)2; and each occurrence of Ru is substituted or unsubstituted alkyl.
[00350] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-e):
Figure imgf000142_0002
or a pharmaceutically acceptable salt thereof.
[00351] In certain embodiments of the compound of Formula (Il-e), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00352] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-f):
Figure imgf000143_0001
or a pharmaceutically acceptable salt thereof.
[00353] In certain embodiments of the compound of Formula (II-f), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00354] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-g):
Figure imgf000143_0002
or a pharmaceutically acceptable salt thereof. [00355] In certain embodiments of the compound of Formula (Il-g), R is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00356] In certain embodiments, the compound of Formula (II) is a compound of Formula (Il-h):
Figure imgf000144_0001
or a pharmaceutically acceptable salt thereof.
[00357] In certain embodiments of the compound of Formula (Il-h), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
[00358] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-i):
Figure imgf000144_0002
or a pharmaceutically acceptable salt thereof.
[00359] In certain embodiments of the compound of Formula (II-i), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00360] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-j):
Figure imgf000145_0001
or a pharmaceutically acceptable salt thereof.
[00361] In certain embodiments of the compound of Formula (II-j), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00362] In certain embodiments, the compound of Formula (II) is a compound of Formula (Il-k):
Figure imgf000145_0002
or a pharmaceutically acceptable salt thereof.
[00363] In certain embodiments of the compound of Formula (Il-k), R 20 is substituted or unsubstituted Ci_6 alkylene; R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00364] In certain embodiments, the compound of Formula (II) is a compound of Formula (Π-1):
Figure imgf000146_0001
or a pharmaceutically acceptable salt thereof.
[00365] In certain embodiments of the compound of Formula (II-l), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00366] In certain embodiments, the compound of Formula (II) is a compound of Formula (Il-m :
Figure imgf000146_0002
or a pharmaceutically acceptable salt thereof.
[00367] In certain embodiments of the compound of Formula (Il-m), R 20 is substituted or unsubstituted C1-6 alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; R 40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In certain embodiments of the compound of Formula (I-m), R 20 is substituted or unsubstituted
Ci alkylene; R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; R 40
-6 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and R 70 is unsubstituted heteroalkyl.
[00368] In certain embodiments, the compound of Formula (II) is a compound of Formula (Il-n):
Figure imgf000147_0001
or a pharmaceutically acceptable salt thereof.
[00369] In certain embodiments of the compound of Formula (Il-n), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00370] In certain embodiments, the compound of Formula (II) is a compound of Formula (Π-ο):
Figure imgf000147_0002
or a pharmaceutically acceptable salt thereof. [00371] In certain embodiments of the compound of Formula (II-o), R is substituted or unsubstituted Ci_6 alkylene; R 21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
[00372] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-p):
Figure imgf000148_0001
or a pharmaceutically acceptable salt thereof.
[00373] In certain embodiments of the compound of Formula (II-p), R 20 is substituted or unsubstituted Ci_6 alkylene; R21 is independently substituted or unsubstituted Ci_6 alkyl; R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00374] In certain embodiments, the compound of Formula (II) is a compound of Formula (Il-q):
Figure imgf000148_0002
or a pharmaceutically acceptable salt thereof.
[00375] In certain embodiments of the compound of Formula (Il-q), R 20 is substituted or unsubstituted C1-6 alkylene; R 21 is independently substituted or unsubstituted C1-6 alkyl; and R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
[00376] In certain embodiments, the compound of Formula (II) is a compound of Formula (Il-r):
Figure imgf000149_0001
or a pharmaceutically acceptable salt thereof.
[00377] In certain embodiments of the compound of Formula (Il-r), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00378] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-s):
Figure imgf000149_0002
or a pharmaceutically acceptable salt thereof.
[00379] In certain embodiments of the compound of Formula (II-s), R 20 is substituted or unsubstituted Ci_6 alkylene; R 21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene. In certain embodiments, the compound of Formula (II) is a compound of Formula
Figure imgf000150_0001
or a pharmaceutically acceptable salt thereof.
[00381] In certain embodiments of the compound of Formula (Il-t), R 20 is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene; R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
[00382] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-u):
Figure imgf000150_0002
or a pharmaceutically acceptable salt thereof.
[00383] In certain embodiments of the compound of Formula (II-u), R 20 is substituted or unsubstituted Ci_6 alkylene; R 21 is independently substituted or unsubstituted Ci_6 alkyl; and R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene. [00384] In certain embodiments, the compound of Formula (II) is a compound of Formula (II-v):
Figure imgf000151_0001
or a pharmaceutically acceptable salt thereof.
20
[00385] In certain embodiments of the compound of Formula (II-v), R is substituted or unsubstituted C1-6 alkylene; R21 is independently substituted or unsubstituted C1-6 alkyl; R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
70
and R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl. In
20
certain embodiments of the compound of Formula (II-v), R is substituted or unsubstituted
22 40
Ci-6 alkylene; R is hydrogen, or substituted or unsubstituted C1-6 alkyl; R is substituted or
70 unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci^o heteroalkylene; and R is unsubstituted heteroalkyl.
[00386] In certain embodiments the compound of Formula (II) is
Figure imgf000151_0002
Figure imgf000152_0001
150
Figure imgf000153_0001
151
Figure imgf000154_0001
ı52
Figure imgf000155_0001
ı53
Figure imgf000156_0001
ı54
Figure imgf000157_0001
or a pharmaceutically acceptable salt thereof.
[00387] In certain embodiments, the compound of Formula (II) is
Figure imgf000157_0002
or a pharmaceutically acceptable salt thereof.
[00388] In certain embodiments, the compound of Formula (II) is not
Figure imgf000157_0003
Figure imgf000158_0001

Figure imgf000159_0001
Group B
[00389] As generally defined herein, B is an antibody or antibody fragment. It is generally understood that the antibody or antibody fragment B is a large molecule with many possible sites of attachment of the trioxacarcin-linker moiety, i.e., a [trioxacarcin-L-] moiety. In certain embodiments, the antibody or antibody fragment comprises 1 to 200 independent instances of a trioxacarcin-linker moiety attached thereto, inclusive, e.g., 1 to 150, 1 to 100, 1 to 75, 1 to 50, 1 to 25, 1 to 15, 1 to 10, inclusive, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 independent instances.
[00390] An antibody, as described herein, refers to a full-length (i.e., naturally occurring or formed by normal immunoglobulin gene fragment recombinatorial processes)
immunoglobulin molecule (e.g., an IgG antibody) or an immunologically active (i.e., specifically binding) portion of an immunoglobulin molecule, like an antibody fragment. An antibody is a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds. Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region. The heavy chain constant region is comprised of three subdomains, CHI, CH2 and CH3- Each light chain is comprised of a light chain variable region (abbreviated herein as VL) and a light chain constant region. The light chain constant region is comprised of one subdomain, CL- The VH and VL regions can be further subdivided into regions of hypervariability, termed
complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (Clq) of the classical complement system.
[00391] As used herein, the term "monoclonal antibody" may refer to an antibody obtained from a single clonal population of immunoglobulins that bind to the same epitope of an antigen. Monoclonal antibodies have the same Ig gene rearrangement and thus demonstrate identical binding specificity. Methods for preparing monoclonal antibodies, as described herein, are known in the art. Monoclonal antibodies can be prepared by a variety of methods. For example, monoclonal antibodies may be made by a hybridoma method (see, e.g., Kohler et ah, Nature, 1975, 256: 495), or may be made by recombinant DNA methods (see, e.g., U.S. Patent No. 4,816,567). The monoclonal antibodies may also be isolated from phage antibody libraries. (See e.g., Clarkson et ah, Nature, 1991, 352: 624-628 and Marks et al, J. Mol. Biol, 1991, 222: 581-597).
[00392] Human monoclonal antibodies may be made by any of the methods known in the art, including those disclosed in U.S. Patent No. 5567610, U.S. Patent No. 5565354, U.S. Patent No. 5571893, Kozber, J. Immunol., 1984, 133: 3001, Brodeur, et ah, Monoclonal Antibody Production Techniques and Applications, p. 51-63 (Marcel Dekker, Inc., new York, 1987), and Boerner et ah, J. Immunol., 1991, 147: 86-95. Human antibodies may be obtained by recovering antibody-producing lymphocytes from the blood or other tissues of humans producing antibody to an antigen of interest {e.g., CD20 or EGFR). These lymphocytes can be treated to produce cells that grow independently in the laboratory under appropriate culture conditions. The cell cultures can be screened for production of antibodies to the antigen of interest and then cloned. Clonal cultures can be used to produce human monoclonal antibodies to CD20 and/or EGFR, or the genetic elements encoding the variable portions of the heavy and light chain of the antibodies can be cloned and inserted into nucleic acid vectors for production of antibodies of different types. In addition to the conventional methods for preparing human monoclonal antibodies, such antibodies may also be prepared by immunizing transgenic animals that are capable of producing human antibodies {e.g., Jakobovits et al, PNAS USA, 1993, 90: 2551, Jakobovits et al, Nature, 1993, 362: 255-258, Bruggermann et ah, Year in Immunol., 1993, 7:33 and U.S. Patent No. 5569825).
[00393] As used herein, "humanized monoclonal antibody" may refer to monoclonal antibodies having at least human constant regions and an antigen-binding region, such as one, two, or three CDRs, from a non-human species. Humanized antibodies specifically recognize antigens of interest, but will not evoke an immune response in humans against the antibody itself. As an example, murine CDRs may be grafted into the framework region of a human antibody to prepare the humanized antibody {e.g., Riechmann et ah, Nature, 1988, 332, 323, and Neuberger et ah, Nature, 1985, 314, 268). Alternatively, humanized monoclonal antibodies may be constructed by replacing the non-CDR regions of non-human antibodies with similar regions of human antibodies while retaining the epitopic specificity of the original antibodies. For example, non-human CDRs and optionally some of the framework regions may be covalently joined to human FR and/or Fc/pFc' regions to produce functional antibodies.
[00394] As used herein, the term "chimeric antibody" may refer to a monoclonal antibody comprising a variable region from one source {e.g., species) and at least a portion of a constant region derived from a different source. In some embodiments, chimeric antibodies are prepared by recombinant DNA techniques. In some embodiments, the chimeric antibodies comprise a murine variable region and a human constant region. Such chimeric antibodies may, in some embodiments, be the product of expressed immunoglobulin genes comprising DNA segments encoding murine immunoglobulin variable regions and DNA segments encoding human immunoglobulin constant regions. Methods for producing chimeric antibodies involve conventional recombinant DNA and gene transfection techniques (see, e.g., Morrison et ah, Proc. Natl. Acad. Sci. USA, 1984, 81: 6851-6855; U.S. Patent No. 5,202,238; and U.S. Patent No. 5,204,244).
[00395] An antibody fragment is a portion of an antibody such as F(ab').sub.2, F(ab).sub.2, Fab', Fab, Fv, scFv (single chain Fv) and the like. Such fragments may be prepared by standard methods. See, e.g., Coligan et al. Current Protocols in Immunology, John Wiley & Sons, 1991-1997. Regardless of structure, an antibody fragment binds with the same antigen that is recognized by the intact antibody. An antibody fragment may comprise one or more proteolytic fragments (i.e., fragments produced by cleavage with papain), e.g., a Fab fragment, each containing a light chain domain and a heavy chain domain (designated herein as a "Fab heavy chain domain"), and/or Fc fragment containing two Fc domains. Each light chain domain contains a VL and a CL subdomain, each Fab heavy chain domain contains a VH and a CHI subdomain, and each Fc domain contains a CH2 and CH3 subdomain.
[00396] In certain embodiments, antigen-binding antibody fragments is only a small portion of an antibody molecule, the paratope, is involved in the binding of the antibody to its epitope (see, in general, Clark, W.R. (1986) The Experimental Foundations of Modern Immunology Wiley & Sons, Inc., New York; Roitt, I. (1991) Essential Immunology, 7th Ed., Blackwell Scientific Publications, Oxford). The pFc' and Fc regions of the antibody, for example, are effectors of the complement cascade but are not involved in antigen binding. An antibody from which the pFc' region has been enzymatically cleaved, or which has been produced without the pFc' region, designated an F(ab')2 fragment, retains both of the antigen binding sites of an intact antibody. An isolated F(ab')2 fragment is referred to as a bivalent monoclonal fragment because of its two antigen binding sites. Similarly, an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region, designated an Fab fragment, retains one of the antigen binding sites of an intact antibody molecule. Further, Fab fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain denoted Fd (heavy chain variable region, referred to herein as Fab heavy chain domain). The Fd fragments are the major determinant of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity) and Fd fragments retain epitope-binding ability in isolation.
[00397] The terms Fab, Fc, pFc', F(ab')2 and Fv are employed with either standard immunological meanings (Klein, Immunology (John Wiley, New York, NY, 1982); Clark, W.R. (1986) The Experimental Foundations of Modern Immunology (Wiley & Sons, Inc., New York); Roitt, I. (1991) Essential Immunology, 7th Ed., (Blackwell Scientific Publications, Oxford)). Well-known functionally active antibody fragments include but are not limited to F(ab')2, Fab, Fv and Fd fragments of antibodies. These fragments, which lack the Fc fragment of intact antibody, clear more rapidly from the circulation, and may have less non-specific tissue binding than an intact antibody (Wahl et ah, J. Nucl. Med. 24:316-325 (1983)). For example, single-chain antibodies may be constructed in accordance with the methods described in U.S. Patent No. 4,946,778. Such single-chain antibodies include the variable regions of the light and heavy chains joined by a flexible linker moiety. Methods for obtaining a single domain antibody ("Fd") which comprises an isolated variable heavy chain single domain, also have been reported {see, e.g., Ward et ah, Nature, 1989, 341:644-646, disclosing a method of screening to identify an antibody heavy chain variable region (VR single domain antibody) with sufficient affinity for its target epitope to bind thereto in isolated form). Methods for making recombinant Fv fragments based on known antibody heavy chain and light chain variable region sequences are known in the art and have been described, (see, e.g., Moore et ah, U.S. Patent No. 4,462,334). Other references describing the use and generation of antibody fragments include, e.g., Fab fragments (Tijssen, Practice and Theory of Enzyme Immunoassays (Elsevieer, Amsterdam, 1985)), Fv fragments
(Hochman et ah, Biochemistry, 1973, 12: 1130; Sharon et ah, Biochemistry, 1976, 15: 1591; Ehrilch et ah, U.S. Patent No. 4,355,023) and portions of antibody molecules (Audilore- Hargreaves, U.S. Patent No. 4,470,925). Thus, antibody fragments may be constructed from intact antibodies without destroying the specificity of the antibodies for the CD20 or EGFR epitope.
[00398] In certain embodiments, the antibody fragment is a camelid antibody; e.g., a functional antibody devoid of light chains of which the single N-terminal domain is fully capable of antigen binding; i.e., a single-domain antibody fragment.
[00399] Exemplary antibodies and their cell markers (targets) contemplated for use include, but are not limited to, antibodies listed in Table A, and antibody fragments thereof.
Figure imgf000163_0001
Figure imgf000164_0001
pritumumab vimentin
Figure imgf000165_0001
[00400] Additional antibodies include, but are not limited to, pembrolizumab, nivolumab, pidilizumab, tremelimumab, durvalumab, atezolizumab, avelumab, PF-06801591, utomilumab, PDR001, PBF-509, MGB453, LAG525, AMP-224, INCSHR1210,
INCAGN1876, INCAGN1949, samalizumab, PF-05082566, urelumab, lirilumab, lulizumab, BMS-936559, BMS-936561, BMS-986004, BMS-986012, BMS-986016, BMS-986178, IMP321, IPH2101, IPH2201, varilumab, ulocuplumab, monalizumab, MEDI0562,
MEDI0680, MEDI1873, MEDI6383, MEDI6469, MEDI9447, AMG228, AMG820, CC- 90002, CDX- 1127, CGEN15001T, CGEN15022, CGEN15029, CGEN15049, CGEN15027, CGEN15052, CGEN15092, CX-072, CX-2009, CP-870893, Chi Lob 7/4, RG6058, RG7686, RG7876, RG7888, TRX518, MK-4166, MGA271, IMC-CS4, emactuzumab, obinutuzumab, cabiralizumab, margetuximab, enoblituzumab, mogamulizumab, carlumab, fresolimumab, FAZ053, TSR022, MBG453, REGN2810, REGN3767, MOXR0916, PF-04518600,
RO7009789, BMS986156, GWN323, JTX-2011, NKTR-214, GSK3174998, DS-8273a, NIS793, or BGB-A317
[00401] In certain embodiments, the antibody is trastuzumab (HERCEPTIN) or an antibody fragment thereof. Methods of Preparation
[00402] As is generally understood from the above disclosure, the compound of Formula (II), comprising a group T, is coupled to an antibody to form an antibody-drug conjugate of Formula (I). See, e.g., Scheme 1. In certain embodiments, the coupling takes place between a nucleophilic sidechain of an amino acid residue (e.g., cysteine, lysine, serine) of the antibody and an electrophilic T group. Exemplary coupling reactions include, but are not limited to, formation of esters, thioesters, amides (e.g., such as peptide coupling) from activated acids or acyl halides; nucleophilic displacement reactions (e.g., such as nucleophilic displacement of a halide); and Michael additions (e.g., maleimide addition).
Scheme 1.
B
(trioxacarcin)— L1— T ► (trioxacarcin)— L— B
[00403] In certain embodiments, the method of preparing a compound of Formula (I)
comprises coupling an antibody with a compound of Formula (II), wherein T is
Figure imgf000166_0001
X2
Q is -S-, or -0-; and R is hydrogen, substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl (e.g., succinimide); substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group, to provide a corresponding compound of Formula (I). See, for example, Scheme 2.
Scheme 2. Preparation of compounds of Formula (I) via amide, thioester, and ester formation
Figure imgf000166_0002
(trioxacarcin)— L— B
[00404] In certain embodiments, the method of preparing a compound of Formula (I)
comprises coupling an antibody with a compound of Formula (II), wherein T is
Figure imgf000166_0003
; Q is -S-, or -0-; and R is a leaving group (e.g., halogen, tosylate, mesylate, or triflate), to provide a compound of Formula (I). See, for example, Scheme 3. Scheme 3. Nucleophilic displacement of a halide or other leaving group
Figure imgf000167_0001
(trioxacarcin)— L— B
[00405] In certain embodiments, the method of preparing a compound of Formula (I) comprises coupling an antibody with a compound of Formula (II), wherein T is -N=C=S {i.e., isothiocyanate) to provide a compound of Formula (I). See, for example, Scheme 4.
Scheme 4. Nucleophilic addition to isothiocyanate
B
(trioxacarcin)— L1— N=C=S (trioxacarcin)— L— B
[00406] In certain embodiments, the method of preparing a compound of Formula (I) comprises coupling an antibody with a compound of Formula (II), wherein T is a maleimide group to provide a compound of Formula (I). See, for example, Scheme 5.
Scheme 5. Maleimide addition
B
(trioxacarcin)-L1-T ioxacarcin)-L-B
Figure imgf000167_0002
[00407] In certain embodiments, the method of preparing a compound of Formula (I) comprises coupling an antibody with a compound of Formula (II), wherein T is 4- nitrobenzenethiol (e.g., wherein the sulfur is attached to a sulfur atom of L1) to provide a compound of Formula (I). See, for example, Scheme 6. Scheme 6. Nucleophilic displacement of a thiol
(trioxacarcin)— L— B
Figure imgf000168_0001
Pharmaceutical Compositions
[00408] The present disclosure provides pharmaceutical compositions comprising an active ingredient and, optionally, a pharmaceutically acceptable carrier. In certain embodiments, the active ingredient is present in an effective amount, e.g., a therapeutically effective amount or a prophylactically effective amount.
[00409] An "active ingredient," as used herein, refers to trioxacarcin-antibody conjugates of Formula (I), precursor compounds of Formula (II), or novel trioxacarcin compounds without an antibody conjugated thereto, and pharmaceutically acceptable salts thereof.
[00410] A pharmaceutical composition of the present disclosure can be administered via one or more routes of administration using one or more of a variety of methods known in the art. As will be appreciated by the skilled artisan, the route and/or mode of administration will vary depending upon the desired results. Preferred routes of administration include intravenous, intramuscular, intradermal, intraperitoneal, subcutaneous, spinal or other parenteral routes of administration, for example by epidermal administration (e.g., by injection or infusion). The phrase "parenteral administration" as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal,
intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal,
subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal, epidural and intrasternal injection and infusion.
[00411] Alternatively, the pharmaceutical composition can be administered via a non- parenteral route, such as a topical, epidermal or mucosal route of administration, for example, intranasally, orally, vaginally, rectally, sublingually or topically.
[00412] Depending on the route of administration, the pharmaceutical composition or active ingredient may be coated in a material to protect the compound from the action of acids and other natural conditions that may inactivate the compound. [00413] Pharmaceutically acceptable excipients include any and all solvents, diluents or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. General considerations in the formulation and/or manufacture of pharmaceutical compositions agents can be found, for example, in
Remington 's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980), and Remington: The Science and Practice of Pharmacy, 21st Edition (Lippincott Williams & Wilkins, 2005).
[00414] Pharmaceutical compositions described herein can be prepared by any method known in the art of pharmacology. In general, such preparatory methods include the steps of bringing the active ingredient into association with the excipient and/or one or more other accessory ingredients, and then, if necessary and/or desirable, shaping and/or packaging the product into a desired single- or multi-dose unit.
[00415] Pharmaceutical compositions can be prepared, packaged, and/or sold in bulk, as a single unit dose, and/or as a plurality of single unit doses. As used herein, a "unit dose" is discrete amount of the pharmaceutical composition comprising a predetermined amount of the active ingredient. The amount of the active ingredient is generally equal to the dosage of the active ingredient which would be administered to a subject and/or a convenient fraction of such a dosage such as, for example, one-half or one-third of such a dosage.
[00416] Relative amounts of the active ingredient, the pharmaceutically acceptable carrier, and/or any additional ingredients in a pharmaceutical composition of the invention will vary, depending upon the identity, size, and/or condition of the subject treated and further depending upon the route by which the composition is to be administered. By way of example, the composition may comprise between 0.1% and 100% (w/w) active ingredient.
[00417] Pharmaceutically acceptable excipients used in the manufacture of provided pharmaceutical compositions include inert diluents, dispersing and/or granulating agents, surface active agents and/or emulsifiers, disintegrating agents, binding agents, preservatives, buffering agents, lubricating agents, and/or oils. Excipients such as cocoa butter and suppository waxes, coloring agents, coating agents, sweetening, flavoring, and perfuming agents may also be present in the composition.
[00418] Exemplary diluents include calcium carbonate, sodium carbonate, calcium phosphate, dicalcium phosphate, calcium sulfate, calcium hydrogen phosphate, sodium phosphate lactose, sucrose, cellulose, microcrystalline cellulose, kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch, cornstarch, powdered sugar, etc., and combinations thereof.
[00419] Exemplary granulating and/or dispersing agents include potato starch, corn starch, tapioca starch, sodium starch glycolate, clays, alginic acid, guar gum, citrus pulp, agar, bentonite, cellulose and wood products, natural sponge, cation-exchange resins, calcium carbonate, silicates, sodium carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone), sodium carboxymethyl starch (sodium starch glycolate), carboxymethyl cellulose, cross- linked sodium carboxymethyl cellulose (croscarmellose), methylcellulose, pregelatinized starch (starch 1500), microcrystalline starch, water insoluble starch, calcium carboxymethyl cellulose, magnesium aluminum silicate (Veegum), sodium lauryl sulfate, quaternary ammonium compounds, etc., and combinations thereof.
[00420] Exemplary surface active agents and/or emulsifiers include natural emulsifiers {e.g. acacia, agar, alginic acid, sodium alginate, tragacanth, chondrux, cholesterol, xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol, wax, and lecithin), colloidal clays {e.g.
bentonite [aluminum silicate] and Veegum [magnesium aluminum silicate]), long chain amino acid derivatives, high molecular weight alcohols {e.g. stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin monostearate, ethylene glycol distearate, glyceryl monostearate, and propylene glycol monostearate, polyvinyl alcohol), carbomers {e.g. carboxy polymethylene, polyacrylic acid, acrylic acid polymer, and carboxyvinyl polymer), carrageenan, cellulosic derivatives {e.g. carboxymethylcellulose sodium, powdered cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose, hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty acid esters {e.g. polyoxyethylene sorbitan monolaurate [Tween 20],
polyoxyethylene sorbitan [Tween 60], polyoxyethylene sorbitan monooleate [Tween 80], sorbitan monopalmitate [Span 40], sorbitan monostearate [Span 60], sorbitan tristearate [Span 65], glyceryl monooleate, sorbitan monooleate [Span 80]), polyoxyethylene esters {e.g.
polyoxyethylene monostearate [Myrj 45], polyoxyethylene hydrogenated castor oil, polyethoxylated castor oil, polyoxymethylene stearate, and Solutol), sucrose fatty acid esters, polyethylene glycol fatty acid esters {e.g. Cremophor), polyoxyethylene ethers, {e.g.
polyoxyethylene lauryl ether [Brij 30]), poly(vinyl-pyrrolidone), diethylene glycol monolaurate, triethanolamine oleate, sodium oleate, potassium oleate, ethyl oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic F 68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride, benzalkonium chloride, docusate sodium, etc. and/or combinations thereof. [00421] Exemplary binding agents include starch (e.g. cornstarch and starch paste), gelatin, sugars (e.g. sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol, mannitol, etc.), natural and synthetic gums (e.g. acacia, sodium alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage of isapol husks, carboxymethylcellulose, methylcellulose,
ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose, hydroxypropyl
methylcellulose, microcrystalline cellulose, cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum silicate (Veegum), and larch arabogalactan), alginates, polyethylene oxide, polyethylene glycol, inorganic calcium salts, silicic acid, polymethacrylates, waxes, water, alcohol, etc., and/or combinations thereof.
[00422] Exemplary preservatives include antioxidants, chelating agents, antimicrobial preservatives, antifungal preservatives, alcohol preservatives, acidic preservatives, and other preservatives.
[00423] Exemplary antioxidants include alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated hydroxyanisole, butylated hydroxytoluene, monothioglycerol, potassium
metabisulfite, propionic acid, propyl gallate, sodium ascorbate, sodium bisulfite, sodium metabisulfite, and sodium sulfite.
[00424] Exemplary chelating agents include ethylenediaminetetraacetic acid (EDTA) and salts and hydrates thereof (e.g., sodium edetate, disodium edetate, trisodium edetate, calcium disodium edetate, dipotassium edetate, and the like), citric acid and salts and hydrates thereof (e.g., citric acid monohydrate), fumaric acid and salts and hydrates thereof, malic acid and salts and hydrates thereof, phosphoric acid and salts and hydrates thereof, and tartaric acid and salts and hydrates thereof. Exemplary antimicrobial preservatives include benzalkonium chloride, benzethonium chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium chloride, chlorhexidine, chlorobutanol, chlorocresol, chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine, imidurea, phenol, phenoxyethanol, phenylethyl alcohol, phenylmercuric nitrate, propylene glycol, and thimerosal.
[00425] Exemplary antifungal preservatives include butyl paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate, sodium benzoate, sodium propionate, and sorbic acid.
[00426] Exemplary alcohol preservatives include ethanol, polyethylene glycol, phenol, phenolic compounds, bisphenol, chlorobutanol, hydroxybenzoate, and phenylethyl alcohol.
[00427] Exemplary acidic preservatives include vitamin A, vitamin C, vitamin E, beta- carotene, citric acid, acetic acid, dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid. [00428] Other preservatives include tocopherol, tocopherol acetate, deteroxime mesylate, cetrimide, butylated hydroxyanisol (BHA), butylated hydroxytoluened (BHT),
ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium sulfite, potassium metabisulfite, Glydant Plus, Phenonip, methylparaben, Germall 115, Germaben II, Neolone, Kathon, and Euxyl. In certain embodiments, the preservative is an anti-oxidant. In other embodiments, the preservative is a chelating agent.
[00429] Exemplary buffering agents include citrate buffer solutions, acetate buffer solutions, phosphate buffer solutions, ammonium chloride, calcium carbonate, calcium chloride, calcium citrate, calcium glubionate, calcium gluceptate, calcium gluconate, D- gluconic acid, calcium glycerophosphate, calcium lactate, propanoic acid, calcium levulinate, pentanoic acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium phosphate, calcium hydroxide phosphate, potassium acetate, potassium chloride, potassium gluconate, potassium mixtures, dibasic potassium phosphate, monobasic potassium phosphate, potassium phosphate mixtures, sodium acetate, sodium bicarbonate, sodium chloride, sodium citrate, sodium lactate, dibasic sodium phosphate, monobasic sodium phosphate, sodium phosphate mixtures, tromethamine, magnesium hydroxide, aluminum hydroxide, alginic acid, pyrogen-free water, isotonic saline, Ringer's solution, ethyl alcohol, etc., and combinations thereof.
[00430] Exemplary lubricating agents include magnesium stearate, calcium stearate, stearic acid, silica, talc, malt, glyceryl behanate, hydrogenated vegetable oils, polyethylene glycol, sodium benzoate, sodium acetate, sodium chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate, etc. , and combinations thereof.
[00431] Exemplary natural oils include almond, apricot kernel, avocado, babassu, bergamot, black current seed, borage, cade, camomile, canola, caraway, carnauba, castor, cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol, gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba, kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut, mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange, orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed, pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood, sasquana, savoury, sea buckthorn, sesame, shea butter, silicone, soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut, and wheat germ oils.
Exemplary synthetic oils include, but are not limited to, butyl stearate, caprylic triglyceride, capric triglyceride, cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone oil, and combinations thereof.
[00432] Liquid dosage forms for oral and parenteral administration include
pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredients, the liquid dosage forms may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (e.g., cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the conjugates of the invention are mixed with solubilizing agents such as Cremophor, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and combinations thereof.
[00433] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions can be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation can be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer' s solution, U.S. P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.
[00434] The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
[00435] In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This can be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.
[00436] Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing the conjugates of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
[00437] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may comprise buffering agents.
[00438] Solid compositions of a similar type can be employed as fillers in soft and hard- filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. Solid compositions of a similar type can be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.
[00439] The active ingredient can be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active ingredient can be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may comprise, as is normal practice, additional substances other than inert diluents, e.g. , tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may comprise buffering agents. They may optionally comprise opacifying agents and can be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner.
Examples of embedding compositions which can be used include polymeric substances and waxes.
[00440] The active ingredient can be prepared with carriers that will protect the active ingredient against rapid release, such as a controlled release formulation, including implants, transdermal patches, and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are patented or generally known to those skilled in the art. See, e.g., Sustained and Controlled Release Drug Delivery Systems, J. R. Robinson, ed., Marcel Dekker, Inc., New York, 1978.
[00441] Pharmaceutical compositions can be administered with medical devices known in the art. For example, in a preferred embodiment, a pharmaceutical composition of this disclosure can be administered with a needleless hypodermic injection device, such as the devices disclosed in U.S. Pat. Nos. 5,399,163; 5,383,851 ; 5,312,335; 5,064,413; 4,941,880; 4,790,824; or 4,596,556. Examples of well-known implants and modules useful in the present disclosure include: U.S. Pat. No. 4,487,603, which discloses an implantable micro-infusion pump for dispensing medication at a controlled rate; U.S. Pat. No. 4,486,194, which discloses a therapeutic device for administering medicants through the skin; U.S. Pat. No. 4,447,233, which discloses a medication infusion pump for delivering medication at a precise infusion rate; U.S. Pat. No. 4,447,224, which discloses a variable flow implantable infusion apparatus for continuous drug delivery; U.S. Pat. No. 4,439,196, which discloses an osmotic drug delivery system having multi-chamber compartments; and U.S. Pat. No. 4,475, 196, which discloses an osmotic drug delivery system. These patents are incorporated herein by reference. Many other such implants, delivery systems, and modules are known to those skilled in the art. [00442] Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation. General considerations in the formulation and/or manufacture of pharmaceutical compositions can be found, for example, in Remington: The Science and Practice of Pharmacy 21st ed., Lippincott Williams & Wilkins, 2005.
[00443] The exact amount of the active ingredient required to achieve an effective amount will vary from subject to subject, depending, for example, on species, age, and general condition of a subject, severity of the side effects or disorder, identity of the particular compound(s), mode of administration, and the like. The desired dosage can be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage can be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations).
[00444] In certain embodiments, an effective amount of an active ingredient for administration one or more times a day to a 70 kg adult human may comprise about 0.0001 mg to about 3000 mg, about 0.0001 mg to about 2000 mg, about 0.0001 mg to about 1000 mg, about 0.001 mg to about 1000 mg, about 0.01 mg to about 1000 mg, about 0.1 mg to about 1000 mg, about 1 mg to about 1000 mg, about 1 mg to about 100 mg, about 10 mg to about 1000 mg, or about 100 mg to about 1000 mg, of the active ingredient per unit dosage form.
[00445] In certain embodiments, the active ingredient may be administered orally or parenterally at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, and from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.
[00446] It will be appreciated that dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.
[00447] It will be also appreciated that the active ingredient or composition, as described herein, can be administered in combination with one or more additional therapeutically active agents. The active ingredient or compositions can be administered in combination with additional therapeutically active agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body. It will also be appreciated that the therapy employed may achieve a desired effect for the same disorder (for example, a compound can be administered in combination with an anti-cancer agent, etc.), and/or it may achieve different effects (e.g. , control of adverse side- effects, e.g. , emesis controlled by an anti-emetic).
[00448] The active ingredient or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In will further be appreciated that the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions. The particular combination to employ in a regimen will take into account compatibility of the active ingredient with the additional therapeutically active agent and/or the desired therapeutic effect to be achieved. In general, it is expected that additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.
[00449] Exemplary additional therapeutically active agents include, but are not limited to, cancer therapies, antibiotics, anti-viral agents, anesthetics, anti-coagulants, inhibitors of an enzyme, steroidal agents, steroidal or non-steroidal anti-inflammatory agents, antihistamine, immunosuppressant agents, anti-neoplastic agents, antigens, vaccines, antibodies, decongestant, sedatives, opioids, pain-relieving agents, analgesics, anti-pyretics, hormones, prostaglandins, progestational agents, anti-glaucoma agents, ophthalmic agents, anticholinergics, anti-depressants, anti-psychotics, hypnotics, tranquilizers, anti- convulsants/anti-epileptics (e.g., Neurontin, Lyrica, valproates (e.g., Depacon), and other neurostabilizing agents), muscle relaxants, anti-spasmodics, muscle contractants, channel blockers, miotic agents, anti-secretory agents, anti-thrombotic agents, anticoagulants, anticholinergics, β-adrenergic blocking agents, diuretics, cardiovascular active agents, vasoactive agents, vasodilating agents, anti-hypertensive agents, angiogenic agents, modulators of cell- extracellular matrix interactions (e.g., cell growth inhibitors and anti-adhesion molecules), or inhibitors/intercalators of DNA, RNA, protein-protein interactions, protein-receptor interactions, etc. Therapeutically active agents include small organic molecules such as drug compounds (e.g., compounds approved by the Food and Drugs Administration as provided in the Code of Federal Regulations (CFR)), peptides, proteins, carbohydrates, monosaccharides, oligosaccharides, polysaccharides, nucleoproteins, mucoproteins, lipoproteins, synthetic polypeptides or proteins, small molecules linked to proteins, glycoproteins, steroids, nucleic acids, DNAs, RNAs, nucleotides, nucleosides, oligonucleotides, antisense oligonucleotides, lipids, hormones, vitamins and cells.
[00450] In certain embodiments, the additional therapeutic agent is a cancer therapy.
Cancer therapies include, but are not limited to, surgery and surgical treatments, radiation therapy, and administration of additional therapeutic cancer agents (e.g., biotherapeutic and chemotherapeutic cancer agents).
[00451] Exemplary biotherapeutic cancer agents include, but are not limited to, interferons, cytokines (e.g., tumor necrosis factor, interferon a, interferon γ), vaccines, hematopoietic growth factors, monoclonal serotherapy, immunostimulants and/or immunodulatory agents (e.g., IL-1, 2, 4, 6, or 12), immune cell growth factors (e.g., GM-CSF) and antibodies (e.g. HERCEPTIN (trastuzumab), T-DM1, AVASTIN (bevacizumab), ERBITUX (cetuximab), VECTIBIX (panitumumab), RITUXAN (rituximab), BEXXAR (tositumomab)).
[00452] Exemplary chemotherapeutic cancer agents include, but are not limited to, anti- estrogens (e.g. tamoxifen, raloxifene, and megestrol), LHRH agonists (e.g. goscrclin and leuprolide), anti-androgens (e.g. flutamide and bicalutamide), photodynamic therapies (e.g. vertoporfin (BPD-MA), phthalocyanine, photosensitizer Pc4, and demethoxy-hypocrellin A (2BA-2-DMHA)), nitrogen mustards (e.g. cyclophosphamide, ifosfamide, trofosfamide, chlorambucil, estramustine, and melphalan), nitrosoureas (e.g. carmustine (BCNU) and lomustine (CCNU)), alkylsulphonates (e.g. busulfan and treosulfan), triazenes (e.g.
dacarbazine, temozolomide), platinum containing compounds (e.g. cisplatin, carboplatin, oxaliplatin), vinca alkaloids (e.g. vincristine, vinblastine, vindesine, and vinorelbine), taxoids (e.g. paclitaxel or a paclitaxel equivalent such as nanoparticle albumin-bound paclitaxel (Abraxane), docosahexaenoic acid bound-paclitaxel (DHA-paclitaxel, Taxoprexin), polyglutamate bound-paclitaxel (PG-paclitaxel, paclitaxel poliglumex, CT-2103,
XYOTAX), the tumor-activated prodrug (TAP) ANG1005 (Angiopep-2 bound to three molecules of paclitaxel), paclitaxel-EC-1 (paclitaxel bound to the erbB2-recognizing peptide EC-1), and glucose-conjugated paclitaxel, e.g., 2 -paclitaxel methyl 2-glucopyranosyl succinate; docetaxel, taxol), epipodophyllins (e.g. etoposide, etoposide phosphate, teniposide, topotecan, 9-aminocamptothecin, camptoirinotecan, irinotecan, crisnatol, mytomycin C), anti-metabolites, DHFR inhibitors (e.g. methotrexate, dichloromethotrexate, trimetrexate, edatrexate), IMP dehydrogenase inhibitors (e.g. mycophenolic acid, tiazofurin, ribavirin, and EICAR), ribonuclotide reductase inhibitors (e.g. hydroxyurea and deferoxamine), uracil analogs (e.g. 5-fluorouracil (5-FU), floxuridine, doxifluridine, ratitrexed, tegafur-uracil, capecitabine), cytosine analogs (e.g. cytarabine (ara C), cytosine arabinoside, and
fludarabine), purine analogs (e.g. mercaptopurine and Thioguanine), Vitamin D3 analogs (e.g. EB 1089, CB 1093, and KH 1060), isoprenylation inhibitors (e.g. lovastatin), dopaminergic neurotoxins (e.g., l-methyl-4-phenylpyridinium ion), cell cycle inhibitors (e.g. staurosporine), actinomycin (e.g., actinomycin D, dactinomycin), bleomycin (e.g.
bleomycin A2, bleomycin B2, peplomycin), anthracycline (e.g. daunorubicin, doxorubicin, pegylated liposomal doxorubicin, idarubicin, epirubicin, pirarubicin, zorubicin,
mitoxantrone), MDR inhibitors (e.g. verapamil), Ca2+ ATPase inhibitors (e.g. thapsigargin), imatinib, thalidomide, lenalidomide, tyrosine kinase inhibitors (e.g., axitinib (AG013736), bosutinib (SKI-606), cediranib (RECENTIN™, AZD2171), dasatinib (SPRYCEL®, BMS- 354825), erlotinib (TARCEVA®), gefitinib (IRESSA®), imatinib (Gleevec®, CGP57148B, STI-571), lapatinib (TYKERB®, TYVERB®), lestaurtinib (CEP-701), neratinib (HKI-272), nilotinib (TASIGNA®), semaxanib (semaxinib, SU5416), sunitinib (SUTENT®, SU11248), toceranib (PALLADIA®), vandetanib (ZACTIMA®, ZD6474), vatalanib (PTK787,
PTK/ZK), trastuzumab (HERCEPTIN®), bevacizumab (AVASTIN®), rituximab
(RITUXAN®), cetuximab (ERBITUX®), panitumumab (VECTIBIX®), ranibizumab (Lucentis®), nilotinib (TASIGNA®), sorafenib (NEXAVAR®), everolimus (AFINITOR®), alemtuzumab (CAMPATH®), gemtuzumab ozogamicin (MYLOTARG®), temsirolimus (TORISEL®), ENMD-2076, PCI-32765, AC220, dovitinib lactate (TKI258, CHIR-258), BIBW 2992 (TOVOK™), SGX523, PF-04217903, PF-02341066, PF-299804, BMS- 777607, ABT-869, MP470, BIBF 1120 ( VARGATEF® ) , AP24534, JNJ-26483327,
MGCD265, DCC-2036, BMS-690154, CEP-11981, tivozanib (AV-951), OSI-930, MM- 121, XL-184, XL-647, and/or XL228), proteasome inhibitors (e.g., bortezomib
(VELCADE)), mTOR inhibitors (e.g., rapamycin, temsirolimus (CCI-779), everolimus (RAD-001), ridaforolimus, AP23573 (Ariad), AZD8055 (AstraZeneca), BEZ235 (Novartis), BGT226 (Norvartis), XL765 (Sanofi Aventis), PF-4691502 (Pfizer), GDC0980 (Genetech), SF1126 (Semafoe) and OSI-027 (OSI)), oblimersen, gemcitabine, carminomycin, leucovorin, pemetrexed, cyclophosphamide, dacarbazine, procarbizine, prednisolone, dexamethasone, campathecin, plicamycin, asparaginase, aminopterin, methopterin, porfiromycin, melphalan, leurosidine, leurosine, chlorambucil, trabectedin, procarbazine, discodermolide,
carminomycin, aminopterin, and hexamethyl melamine.
[00453] In certain embodiments, the additional pharmaceutical agent is an immunotherapy. In certain embodiments, the immunotherapy is useful in the treatment of a cancer. Exemplary immunotherapies include, but are not limited to, T-cell therapies, interferons, cytokines (e.g., tumor necrosis factor, interferon a, interferon γ), vaccines, hematopoietic growth factors, monoclonal serotherapy, immuno stimulants and/or immunodulatory agents (e.g., IL- 1, 2, 4, 6, or 12), immune cell growth factors (e.g., GM-CSF) and antibodies. In certain
embodiments, the immunotherapy is a T-cell therapy. In certain embodiments, the T-cell therapy is chimeric antigen receptor T cells (CAR-T). In certain embodiments, the
immunotherapy is an antibody. In certain embodiments, the antibody is an anti-PD- 1 antibody, an anti-PD-Ll antibody, an anti-CTLA-4 antibody, an anti-TIM3 antibody, an anti- OX40 antibody, an anti-GITR antibody, an anti-LAG-3 antibody, an anti-CD 137 antibody, an anti-CD27 antibody, an anti-CD28 antibody, an anti-CD28H antibody, an anti-CD30 antibody, an anti-CD39 antibody, an anti-CD40 antibody, an anti-CD47 antibody, an anti- CD48 antibody, an anti-CD70 antibody, an anti-CD73 antibody, an anti-CD96 antibody, an anti-CD 160 antibody, an anti-CD200 antibody, an anti-CD244 antibody, an anti-ICOS antibody, an anti-TNFRSF25 antibody, an anti-TMIGD2 antibody, an anti-DNAMl antibody, an anti-BTLA antibody, an anti-LIGHT antibody, an anti-TIGIT antibody, an anti- VISTA antibody, an anti-HVEM antibody, an anti-Siglec antibody, an anti-GALl antibody, an anti- GAL3 antibody, an anti-GAL9 antibody, an anti-BTNL2 (butrophylins) antibody, an anti-B7- H3 antibody, an anti-B7-H4 antibody, an anti-B7-H5 antibody, an anti-B7-H6 antibody, an anti-KIR antibody, an anti-LIR antibody, an anti-ILT antibody, an anti-MICA antibody, an anti-MICB antibody, an anti-NKG2D antibody, an anti-NKG2A antibody, an anti-TGFp antibody, an anti-TGFpR antibody, an anti-CXCR4 antibody, an anti-CXCL12 antibody, an anti-CCL2 antibody, an anti-IL- 10 antibody, an anti-IL- 13 antibody, an anti-IL-23 antibody, an anti-phosphatidylserine antibody, an anti-neuropilin antibody, an anti-GalCer antibody, an anti-HER2 antibody, an anti-VEGFA antibody, an anti-VEGFR antibody, an anti-EGFR antibody, or an anti-Tie2 antibody. In certain embodiments, the antibody is pembrolizumab, nivolumab, pidilizumab, ipilimumab, tremelimumab, durvalumab, atezolizumab, avelumab, PF-06801591, utomilumab, PDR001, PBF-509, MGB453, LAG525, AMP-224,
INCSHR1210, INCAGN1876, INCAGN1949, samalizumab, PF-05082566, urelumab, lirilumab, lulizumab, BMS-936559, BMS-936561, BMS-986004, BMS-986012, BMS- 986016, BMS-986178, IMP321, IPH2101, IPH2201, varilumab, ulocuplumab, monalizumab, MEDI0562, MEDI0680, MEDI1873, MEDI6383, MEDI6469, MEDI9447, AMG228, AMG820, CC-90002, CDX- 1127, CGEN15001T, CGEN15022, CGEN15029, CGEN15049, CGEN15027, CGEN15052, CGEN15092, CX-072, CX-2009, CP-870893, lucatumumab, dacetuzumab, Chi Lob 7/4, RG6058, RG7686, RG7876, RG7888, TRX518, MK-4166, MGA271, IMC-CS4, emactuzumab, trastuzumab, pertuzumab, obinutuzumab, cabiralizumab, margetuximab, enoblituzumab, mogamulizumab, panitumumab, carlumab, bevacizumab, rituximab, or cetuximab.
[00454] In certain embodiments, the compounds or pharmaceutical compositions described herein can be administered in combination with an anti-cancer therapy including, but not limited to, surgery, radiation therapy, and transplantation (e.g., stem cell transplantation, bone marrow transplantation).
[00455] In other embodiments, the additional therapeutically active agent is an antiinflammatory agent. Exemplary anti-inflammatory agents include, but are not limited to, aspirin; ibuprofen; ketoprofen; naproxen; etodolac (LODINE®); COX-2 inhibitors such as celecoxib (CELEBREX®), rofecoxib (VIOXX®), valdecoxib (BEXTRA®}, parecoxib, etoricoxib (MK663), deracoxib, 2-(4-ethoxy-phenyl)-3-(4-methanesulfonyl-phenyl)- pyrazolo[ 1 ,5-b] pyridazine, 4-(2-oxo-3-phenyl-2,3-dihydrooxazol-4- yl)benzenesulfonamide, darbufelone, flosulide, 4-(4-cyclohexyl-2-methyl-5-oxazolyl)-2- fluorobenzenesulfonamide), meloxicam, nimesulide, l-Methylsulfonyl-4-(l,l-dimethyl-4- (4-fluorophenyl)cyclopenta-2,4-dien-3-yl)benzene, 4-( 1 ,5-Dihydro-6-fluoro-7-methoxy- 3-(trifluoromethyl)-(2)-benzothiopyrano(4,3-c)pyrazol-l-yl)benzenesulfonamide, 4,4- dimethyl-2-phenyl-3-(4-methylsulfonyl)phenyl)cyclo- butenone, 4-Amino-N-(4-(2- fluoro-5-trifluoromethyl)-thiazol-2-yl)-benzene sulfonamide, l-(7-tert-butyl-2,3- dihydro-3,3-dimethyl-5-benzo-furanyl)-4-cyclopropyl butan-l-one, or their
physiologically acceptable salts, esters or solvates; sulindac (CLINORIL®); diclofenac (VOLTAREN®); piroxicam (FELDENE®); diflunisal (DOLOBID®), nabumetone
(RELAFEN®), oxaprozin (DAYPRO®), indomethacin (INDOCIN®); or steroids such as PEDIAPED® prednisolone sodium phosphate oral solution, SOLU-MEDROL®
methylprednisolone sodium succinate for injection, PRELONE brand prednisolone syrup.
[00456] Further examples of anti-inflammatory agents include naproxen, which is commercially available in the form of EC-NAPROSYN delayed release tablets, NAPROSYN®, ANAPROX® and ANAPROX® DS tablets and NAPROSYN® suspension from Roche Labs, CELEBREX® brand of celecoxib tablets, VIOXX® brand of rofecoxib, CELESTONE® brand of betamethasone, CUPRAMINE® brand penicillamine capsules, DEPEN® brand titratable penicillamine tablets, DEPO-MEDROL brand of
methylprednisolone acetate injectable suspension, ARAVA™ leflunomide tablets,
AZULFIDIINE EN-tabs® brand of sulfasalazine delayed release tablets, FELDENE® brand piroxicam capsules, CATAFLAM® diclofenac potassium tablets, VOLTAREN® diclofenac sodium delayed release tablets, VOLTAREN -XR diclofenac sodium extended release tablets, or ENBREL etanerecept products.
[00457] In certain embodiments, the additional therapeutically active agent is a pain- relieving agent. Exemplary pain relieving agents include, but are not limited to, analgesics such as non-narcotic analgesics [e.g., salicylates such as aspirin, ibuprofen (MOTRIN®, ADVIL®), ketoprofen (ORUDIS®), naproxen (NAPROSYN®), acetaminophen,
indomethacin] or narcotic analgesics [e.g., opioid analgesics such as tramadol, fentenyl, sufentanil, morphine, hydromorphone, codeine, oxycodone, and buprenorphine] ; nonsteroidal anti-inflammatory agents (NSAIDs) [e.g., aspirin, acetaminophen, COX-2 inhibitors]; steroids or anti-rheumatic agents; migraine preparations such as beta adrenergic blocking agents, ergot derivatives; tricyclic antidepressants (e.g., amitryptyline, desipramine, imipramine); anti-epileptics (e.g. , clonaxepam, valproic acid, phenobarbital, phenytoin, tiagaine, gabapentin, carbamazepine, topiramate, sodium valproate); 2 agonists; selective serotonin reuptake inhibitors (SSRIs), selective norepinepherine uptake inhibitors;
benzodiazepines; mexiletine (MEXITIL); flecainide (TAMBOCOR); NMD A receptor antagonists (e.g., ketamine, detromethorphan, methadone); and topical agents (e.g., capsaicin (Zostrix), EMLA cream, lidocaine, prilocaine).
Kits
[00458] Still further contemplated herein are pharmaceutical packs and/or kits.
Pharmaceutical packs and/or kits provided may comprise a provided composition and a container (e.g., a vial, ampoule, bottle, syringe, and/or dispenser package, or other suitable container). In some embodiments, provided kits may optionally further include a second container comprising a suitable aqueous carrier for dilution or suspension of the provided composition for preparation of administration to a subject. In some embodiments, contents of provided formulation container and solvent container combine to form at least one unit dosage form.
[00459] Optionally, a single container may comprise one or more compartments for containing a provided composition, and/or appropriate aqueous carrier for suspension or dilution. In some embodiments, a single container can be appropriate for modification such that the container may receive a physical modification so as to allow combination of compartments and/or components of individual compartments. For example, a foil or plastic bag may comprise two or more compartments separated by a perforated seal which can be broken so as to allow combination of contents of two individual compartments once the signal to break the seal is generated. A pharmaceutical pack or kit may thus comprise such multi-compartment containers including a provided composition and appropriate solvent and/or appropriate aqueous carrier for suspension.
[00460] Optionally, instructions for use are additionally provided in such kits of the invention. Such instructions may provide, generally, for example, instructions for dosage and administration. In other embodiments, instructions may further provide additional detail relating to specialized instructions for particular containers and/or systems for administration. Still further, instructions may provide specialized instructions for use in conjunction and/or in combination with additional therapy.
Methods of Use and Treatment
[00461] Further provided are methods of using compounds as described herein {e.g., trioxacarcin-antibody conjugates of Formula (I) and precursor compounds of Formula (II), or novel trioxacarcin compounds which do not comprise an antibody conjugated thereto, and pharmaceutically acceptable salts thereof).
[00462] For example, in one aspect, provided is a method of treating a disease, disorder, or condition selected from the group consisting of cardiovascular disease, proliferative disease {e.g., cancer, benign tumors), diabetic retinopathy, inflammatory disease, autoimmune disease, and infectious disease {e.g., bacterial infections, fungal infections, parasitic infections) comprising administering an effective amount of a compound of the present disclosure to a subject in need thereof.
[00463] In certain embodiments, the compound of the present disclosure is useful in the treatment of cardiovascular disease. Exemplary cardiovascular diseases include, but are not limited to, coronary heart disease, cardiomyopathy, hypertensive heart disease, heart failure, inflammatory heart disease, valvular heart disease, stroke, cerebrovascular disease, and peripheral arterial disease.
[00464] In certain embodiments, the compound of the present disclosure is useful in the treatment of a proliferative disease. Exemplary proliferative diseases include, but are not limited to, cancers and benign neoplasms. In certain embodiments, the proliferative disease is cancer. Exemplary cancers include, but are not limited to, acoustic neuroma,
adenocarcinoma, adrenal gland cancer, anal cancer, angiosarcoma (e.g., lymphangio sarcoma, lymphangio-endotheliosarcoma, hemangio sarcoma), appendix cancer, benign monoclonal gammopathy, biliary cancer (e.g., cholangiocarcinoma), bladder cancer, breast cancer (e.g., adenocarcinoma of the breast, papillary carcinoma of the breast, mammary cancer, medullary carcinoma of the breast), brain cancer (e.g., meningioma; glioma, e.g., astrocytoma, oligodendroglioma; medulloblastoma), bronchus cancer, carcinoid tumor, cervical cancer (e.g., cervical adenocarcinoma), choriocarcinoma, chordoma, craniopharyngioma, colorectal cancer (e.g., colon cancer, rectal cancer, colorectal adenocarcinoma), epithelial carcinoma, ependymoma, endothelio sarcoma (e.g., Kaposi's sarcoma, multiple idiopathic hemorrhagic sarcoma), endometrial cancer (e.g. , uterine cancer, uterine sarcoma), esophageal cancer (e.g., adenocarcinoma of the esophagus, Barrett' s adenocarinoma), Ewing sarcoma, eye cancer (e.g., intraocular melanoma, retinoblastoma), familiar hypereosinophilia, gall bladder cancer, gastric cancer (e.g., stomach adenocarcinoma), gastrointestinal stromal tumor (GIST), head and neck cancer (e.g., head and neck squamous cell carcinoma, oral cancer (e.g., oral squamous cell carcinoma (OSCC), throat cancer (e.g., laryngeal cancer, pharyngeal cancer, nasopharyngeal cancer, oropharyngeal cancer)), hematopoietic cancers (e.g., leukemia such as acute lymphocytic leukemia (ALL) (e.g., B-cell ALL, T-cell ALL), acute myelocytic leukemia (AML) (e.g., B-cell AML, T-cell AML), chronic myelocytic leukemia (CML) (e.g., B-cell CML, T-cell CML), and chronic lymphocytic leukemia (CLL) (e.g., B-cell CLL, T-cell CLL); lymphoma such as Hodgkin lymphoma (HL) (e.g., B-cell HL, T-cell HL) and non-Hodgkin lymphoma (NHL) (e.g., B-cell NHL such as diffuse large cell lymphoma (DLCL) (e.g., diffuse large B-cell lymphoma (DLBCL)), follicular lymphoma, chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), mantle cell lymphoma (MCL), marginal zone B-cell lymphomas (e.g., mucosa-associated lymphoid tissue (MALT) lymphomas, nodal marginal zone B-cell lymphoma, splenic marginal zone B-cell lymphoma), primary mediastinal B-cell lymphoma, Burkitt lymphoma, lymphoplasmacytic lymphoma (i.e., "Waldenstrom's macroglobulinemia"), hairy cell leukemia (HCL), immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma and primary central nervous system (CNS) lymphoma; and T-cell NHL such as precursor T- lymphoblastic lymphoma/leukemia, peripheral T-cell lymphoma (PTCL) (e.g., cutaneous T- cell lymphoma (CTCL) (e.g., mycosis fungiodes, Sezary syndrome), angioimmunoblastic T- cell lymphoma, extranodal natural killer T-cell lymphoma, enteropathy type T-cell lymphoma, subcutaneous panniculitis-like T-cell lymphoma, anaplastic large cell lymphoma); a mixture of one or more leukemia/lymphoma as described above, e.g. , mixed leukemia lymphoma (MLL); and multiple myeloma (MM)), heavy chain disease (e.g., alpha chain disease, gamma chain disease, mu chain disease), hemangioblastoma, inflammatory myofibroblastic tumors, immunocytic amyloidosis, kidney cancer (e.g., nephroblastoma a.k.a. Wilms' tumor, renal cell carcinoma), liver cancer (e.g., hepatocellular cancer (HCC), malignant hepatoma), lung cancer (e.g., bronchogenic carcinoma, small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC), adenocarcinoma of the lung),
leiomyosarcoma (LMS), mastocytosis (e.g., systemic mastocytosis), myelodysplastic syndrome (MDS), mesothelioma, myeloproliferative disorder (MPD) (e.g., polycythemia Vera (PV), essential thrombocytosis (ET), agnogenic myeloid metaplasia (AMM) a.k.a. myelofibrosis (MF), chronic idiopathic myelofibrosis, chronic myelocytic leukemia (CML), chronic neutrophilic leukemia (CNL), hypereosinophilic syndrome (HES)), neuroblastoma, neurofibroma (e.g., neurofibromatosis (NF) type 1 or type 2, schwannomatosis),
neuroendocrine cancer (e.g., gastroenteropancreatic neuroendoctrine tumor (GEP-NET), carcinoid tumor), osteosarcoma, ovarian cancer (e.g., cystadenocarcinoma, ovarian embryonal carcinoma, ovarian adenocarcinoma), papillary adenocarcinoma, pancreatic cancer (e.g., pancreatic andenocarcinoma, intraductal papillary mucinous neoplasm (IPMN), Islet cell tumors), penile cancer (e.g., Paget' s disease of the penis and scrotum), pinealoma, primitive neuroectodermal tumor (PNT), prostate cancer (e.g., prostate adenocarcinoma), rectal cancer, rhabdomyosarcoma, salivary gland cancer, skin cancer (e.g., squamous cell carcinoma (SCC), keratoacanthoma (KA), melanoma, basal cell carcinoma (BCC)), small bowel cancer (e.g., appendix cancer), soft tissue sarcoma (e.g., malignant fibrous histiocytoma (MFH), liposarcoma, malignant peripheral nerve sheath tumor (MPNST), chondrosarcoma, fibrosarcoma, myxosarcoma), sebaceous gland carcinoma, sweat gland carcinoma, synovioma, testicular cancer (e.g., seminoma, testicular embryonal carcinoma), thyroid cancer (e.g., papillary carcinoma of the thyroid, papillary thyroid carcinoma (PTC), medullary thyroid cancer), urethral cancer, vaginal cancer and vulvar cancer (e.g., Paget' s disease of the vulva). [00465] Trioxacarcins are known to be useful in the treatment of various cancers, such as ovarian, colorectal, hepatocellular, pancreatic cancer, and andenocarcinomas. See, e.g., Cassidy et al., Cancer Chemother. Pharmacol. (1993) 3i:395-400; Tomita et al., J. Antibiot. (1981) 34: 1519-1524. It is contemplated that various compounds of Formula (I), and (II) conjugated to an antibody, will have even higher efficacy against these and other cancers as described herein.
[00466] In certain embodiments, the compound of the present disclosure is useful in the treatment of diabetic retinopathy.
[00467] In certain embodiments, the compound of the present invention is useful in the treatment of an inflammatory disease. Exemplary inflammatory diseases include, but are not limited to, inflammation associated with acne, anemia {e.g., aplastic anemia, haemolytic autoimmune anaemia), asthma, arteritis {e.g., polyarteritis, temporal arteritis, periarteritis nodosa, Takayasu's arteritis), arthritis {e.g., crystalline arthritis, osteoarthritis, psoriatic arthritis, gouty arthritis, reactive arthritis, rheumatoid arthritis and Reiter's arthritis), ankylosing spondylitis, amylosis, amyotrophic lateral sclerosis, autoimmune diseases, allergies or allergic reactions, atherosclerosis, bronchitis, bursitis, chronic prostatitis, conjunctivitis, Chagas disease, chronic obstructive pulmonary disease, cermatomyositis, diverticulitis, diabetes {e.g., type I diabetes mellitus, type 2 diabetes mellitus), a skin condition {e.g., psoriasis, eczema, burns, dermatitis, pruritus (itch)), endometriosis, Guillain- Barre syndrome, infection, ischaemic heart disease, Kawasaki disease, glomerulonephritis, gingivitis, hypersensitivity, headaches {e.g., migraine headaches, tension headaches), ileus {e.g., postoperative ileus and ileus during sepsis), idiopathic thrombocytopenic purpura, interstitial cystitis (painful bladder syndrome), gastrointestinal disorder {e.g., selected from peptic ulcers, regional enteritis, diverticulitis, gastrointestinal bleeding, eosinophilic gastrointestinal disorders {e.g., eosinophilic esophagitis, eosinophilic gastritis, eosinophilic gastroenteritis, eosinophilic colitis), gastritis, diarrhea, gastroesophageal reflux disease (GORD, or its synonym GERD), inflammatory bowel disease (IBD) {e.g., Crohn's disease, ulcerative colitis, collagenous colitis, lymphocytic colitis, ischaemic colitis, diversion colitis, Behcet's syndrome, indeterminate colitis) and inflammatory bowel syndrome (IBS)), lupus, multiple sclerosis, morphea, myeasthenia gravis, myocardial ischemia, nephrotic syndrome, pemphigus vulgaris, pernicious aneaemia, peptic ulcers, polymyositis, primary biliary cirrhosis, neuroinflammation associated with brain disorders {e.g., Parkinson's disease, Huntington's disease, and Alzheimer's disease), prostatitis, chronic inflammation associated with cranial radiation injury, pelvic inflammatory disease, reperfusion injury, regional enteritis, rheumatic fever, systemic lupus erythematosus, schleroderma, scierodoma, sarcoidosis, spondyloarthopathies, Sjogren's syndrome, thyroiditis, transplantation rejection, tendonitis, trauma or injury (e.g. , frostbite, chemical irritants, toxins, scarring, burns, physical injury), vasculitis, vitiligo and Wegener's granulomatosis. In certain embodiments, the inflammatory disorder is selected from arthritis (e.g. , rheumatoid arthritis), inflammatory bowel disease, inflammatory bowel syndrome, asthma, psoriasis, endometriosis, interstitial cystitis and prostatistis.
[00468] In certain embodiments, the inflammatory condition is an acute inflammatory condition (e.g. , for example, inflammation resulting from infection). In certain embodiments, the inflammatory condition is a chronic inflammatory condition (e.g. , conditions resulting from asthma, arthritis and inflammatory bowel disease). The compounds may also be useful in treating inflammation associated with trauma and non-inflammatory myalgia. The compounds may also be useful in treating inflammation associated with cancer.
[00469] In certain embodiments, the compound of the present disclosure is useful in the treatment of an autoimmune disease. Exemplary autoimmune diseases include, but are not limited to, arthritis (e.g. , including rheumatoid arthritis, spondyloarthopathies, gouty arthritis, degenerative joint diseases such as osteoarthritis, systemic lupus erythematosus, Sjogren's syndrome, ankylosing spondylitis, undifferentiated spondylitis, Behcet's disease, haemolytic autoimmune anaemias, multiple sclerosis, amyotrophic lateral sclerosis, amylosis, acute painful shoulder, psoriatic, and juvenile arthritis), asthma, atherosclerosis, osteoporosis, bronchitis, tendonitis, bursitis, skin condition (e.g., psoriasis, eczema, burns, dermatitis, pruritus (itch)), enuresis, eosinophilic disease, gastrointestinal disorder (e.g. , selected from peptic ulcers, regional enteritis, diverticulitis, gastrointestinal bleeding, eosinophilic gastrointestinal disorders (e.g., eosinophilic esophagitis, eosinophilic gastritis, eosinophilic gastroenteritis, eosinophilic colitis), gastritis, diarrhea, gastroesophageal reflux disease (GORD, or its synonym GERD), inflammatory bowel disease (IBD) (e.g., Crohn's disease, ulcerative colitis, collagenous colitis, lymphocytic colitis, ischaemic colitis, diversion colitis, Behcet's syndrome, indeterminate colitis) and inflammatory bowel syndrome (IBS)), and disorders ameliorated by a gastroprokinetic agent (e.g., ileus, postoperative ileus and ileus during sepsis; gastroesophageal reflux disease (GORD, or its synonym GERD); eosinophilic esophagitis, gastroparesis such as diabetic gastroparesis; food intolerances and food allergies and other functional bowel disorders, such as non-ulcerative dyspepsia (NUD) and non- cardiac chest pain (NCCP, including costo-chondritis)). [00470] In certain embodiments, the inflammatory disorder and/or the immune disorder is a gastrointestinal disorder. In some embodiments, the gastrointestinal disorder is selected from peptic ulcers, regional enteritis, diverticulitis, gastrointestinal bleeding, eosinophilic gastrointestinal disorders (e.g., eosinophilic esophagitis, eosinophilic gastritis, eosinophilic gastroenteritis, eosinophilic colitis), gastritis, diarrhea, gastroesophageal reflux disease (GORD, or its synonym GERD), inflammatory bowel disease(IBD) (e.g., Crohn's disease, ulcerative colitis, collagenous colitis, lymphocytic colitis, ischaemic colitis, diversion colitis, Behcet's syndrome, indeterminate colitis) and inflammatory bowel syndrome (IBS).
[00471] In certain embodiments, the compound of the present disclosure is useful in the treatment of an infectious disease (e.g., bacterial infection, fungal infection, and/or parasitic infection). In certain embodiments, the compound is useful in treating a parasitic infection (e.g., malaria). In certain embodiments, the compound is useful in treating a bacterial infection. In certain embodiments, the compound is useful in treating a fungal infection.
[00472] Trioxacarcins are known to have antibiotic and antiparasitic (e.g., anti-malarial) activity. See, e.g., U.S. Patent 4,459,291; U.S. Patent 4,511,560; Fujimoto et al, J. Antibiot. (1983) 36: 1216-1221; Maiese et al. J. Antibiot. (1990) 43:253-258; Tomita et al, J. Antibiot. (1981) 34: 1519-1524; and Maskey et al. J. Antibiot. (2004) 57:771-779 (antibacterial and antimalarial activity). It is contemplated that various compounds of Formula (I), and (II) conjugated to an antibody, will have even higher efficacy against an infectious disease, such as a bacterial infection, and other infectious diseases as described herein.
Examples
[00473] In order that the invention described herein may be more fully understood, the following examples are set forth. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting this invention in any manner.
[00474] General Experimental Procedures: All reactions were performed in flame-dried glassware fitted with rubber septa under a positive pressure of argon, unless otherwise noted. Air- and moisture-sensitive liquids were transferred via syringe or stainless steel cannula. Solutions were concentrated by rotary evaporation at or below 40 °C. Analytical thin-layer chromatography (TLC) was performed using glass plates pre-coated with silica gel (0.25- mm, 60-A pore size, 230-400 mesh, Merck KGA) impregnated with a fluorescent indicator (254 nm). TLC plates were visualized by exposure to ultraviolet light (UV), then were stained by submersion in either an aqueous sulfuric acid solution of eerie ammonium molybdate (CAM), an acidic solution of p-anisaldehyde in ethanol (Anis), or an aqueous sodium hydroxide-potassium carbonate solution of potassium permanganate (KMn04), followed by brief heating with a flameless heat gun. Flash column chromatography was performed as described by Still et al., employing silica gel (60 A, standard grade) purchased from Dynamic Adsorbents.
[00475] Materials: Commercial solvents and reagents were used as received with the following exceptions: Dichloromethane, benzene, ether, dioxane, and tetrahydrofuran were purified by passage through Α1203 under argon. Dideoxy-DC-45-A2 (1) can be prepared by procedures in PCT Application Publication No. WO 2011/119549, the entire contents of which are incorporated herein by reference.
[00476] Instrumentation: Proton nuclear magnetic resonance (1H NMR) spectra and carbon nuclear magnetic resonance ( 13 C NMR) spectra were recorded on Varian INOVA 500 (500 MHz/125 MHz) or Varian INOVA 600 (600 MHz/150 MHz) NMR spectrometers at 23 °C. Proton chemical shifts are expressed in parts per million (ppm, δ scale) and are referenced to residual protium in the NMR solvent (CHC13: δ 7.26). Carbon chemical shifts are expressed in parts per million (ppm, δ scale) and are referenced to the carbon resonance of the NMR solvent (CHC13: δ 77.0, CH3OD: δ 49.0). Data are represented as follows: chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, dd = doublet of doublets, dt = doublet of triplets, m = multiplet and/or multiple resonances, br = broad, app = apparent), integration, and coupling constant (J) in Hertz (Hz). Infrared (IR) spectra were obtained using a Shimadzu 8400S FT-IR spectrophotometer. Data are reported as follows: frequencies of absorption (cm 1), intensity of absorption (s = strong, m = medium, w = weak, br = broad). High-resolution mass spectra were obtained at the Harvard University Mass Spectrometry Facility using a Bruker micrOTOF-QII or an Agilent 6220 LC-TOF mass spectrometer. Unless otherwise specified, diastereomeric ratios of products are reported as (major diastereomer) : (sum of minor diastereomers). High performance liquid chromatography purifications were performed using an Agilent Technologies 1200 Series preparative HPLC system. LC-MS analysis was performed on an Agilent 6120 Single Quadrupole LC-MS interfaced to an Agilent 1260 Infinity HPLC instrument equipped with an Agilent Eclipse Plus C18, 1.8 μιη, 2.1 x 50 mm reverse phase column, UV detection at 399 nm, 280 nm, 254 nm, 210 nm. The acidic eluent consisted of a linear gradient of acetonitrile from 10% to 90% in 0.1% aqueous formic acid over 8 min, followed by isocratic 90% acetonitrile for 2 min (flow rate = 0.5 mL/min). Synthesis of Trioxacarcin-Antibody Conjugate Precursors
Figure imgf000190_0001
[00477] A flame-dried 25 mL flask was charged with pyridine (0.350 mL, 4.32 mmol, 1.08 equiv) and dichloromethane (4 mL). The solution was cooled to -20 °C in a dry ice-acetone bath. Trifluoromethanesulfonic anhydride (0.703 mL, 4.16 mmol, 1.04 equiv) was added dropwise. Substantial white precipitate forms, preventing stirring. After 10 min, 2- bromoethan-l-ol (0.282 mL, 4.00 mmol, 1 equiv) was added dropwise. The mixture partially clarifies and stirs more freely. The cooling bath was removed and the mixture allowed to warm slowly to 23 °C. After 10 min, the mixture was diluted with 1: 1 dichloromethane- hexanes (20 mL) and filtered through a pad of silica (1 cm in a 30-mL sintered glass funnel), eluting with 1: 1 dichloromethane-hexanes (80 mL). The filtrate was concentrated, providing 2-bromoethyl trifluoromethanesulfonate as a colorless oil, which was used without further purification.
[00478] An oven-dried 5-mL flask was charged with dideoxy-DC-45-A2 (1) (25 mg, 0.051 mmol, 1 equiv) and dichloromethane (1.03 mL). 4A molecular sieves and proton-sponge (220 mg, 1.028 mmol, 20 equiv) were added and the mixture was stirred at 23 °C for 30 min to dry. 2-bromoethyl trifluoromethanesulfonate (69.5 μί, 0.514 mmol, 10 equiv) was added dropwise and the mixture was stirred at 23 °C under argon for 24 h. The reaction mixture was diluted with dichloromethane (10 mL) and methanol (0.5 mL), stirring for 20 min to quench any unreacted alkyl triflate. The mixture was partitioned between dichloromethane (20 mL) and saturated sodium bicarbonate solution (10 mL). The mixture was shaken vigorously and the layers were separated. The organic layer was dried over sodium sulfate. The dried solution was filtered, and the filtrate was concentrated. The residue was purified by flash column chromatography on silica gel deactivated with triethylamine (25%→35% ethyl acetate-hexanes) to provide alkyl bromide 2 as a yellow oil (22.6 mg, 74%). TLC (50% ethyl acetate-hexanes): Rf = 0.39 (UV); 1H NMR (600 MHz, CDC13) δ 14.83 (s, 1H), 7.44 (s, 1H), 5.20 (d, = 4.1 Hz, 1H), 4.77 (d, = 4.1 Hz, 1H), 4.73 (s, 1H), 4.26 - 4.23 (m, 2H), 3.78 (s, 3H), 3.67 - 3.63 (m, 2H), 3.62 (s, 3H), 3.44 (s, 3H), 3.06 - 3.02 (m, 2H), 2.89 (d, = 5.5 Hz, 1H), 2.83 (d, = 5.6 Hz, 1H), 2.75 - 2.72 (m, 2H), 2.58 (s, 3H), 2.11 - 2.07 (m, 2H); 13C NMR (125 MHz, CDC13) δ 204.67, 162.85, 150.93, 142.62, 141.91, 135.34, 130.47, 116.01, 113.71, 113.29, 111.25, 110.12, 104.51, 102.25, 100.02, 73.03, 69.33, 68.97, 65.78, 61.05, 57.21, 56.82, 48.55, 38.95, 30.61, 23.71, 22.23, 20.50; FTIR (neat), cm"1: 2949 (br w), 1620 (s), 1386 (s), 1119 (m), 1074 (s), 984 (s), 792 (s); HRMS (ESI): Calc'd for (C27H29BrOio + H)+: 593.1017, found: 593.1005.
Figure imgf000191_0001
[00479] A 10-mL round-bottom flask was charged with alkyl bromide 2 (22.6 mg, 0.038 mmol, 1 equiv) and sodium azide (24.76 mg, 0.381 mmol, 10 equiv). Anhydrous
dimethylformamide (0.76 mL) was added, and the reaction flask was wrapped in foil. The suspension was stirred at 23 °C under argon for 22 h. The reaction mixture was partitioned between ethyl acetate (30 mL) and saturated sodium bicarbonate solution (10 mL). The layers were separated, and the organic layer was washed with saturated sodium bicarbonate solution (10 mL), water (2 x 10 mL), and saturated sodium chloride solution (2 x 10 mL). The washed solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash column chromatography (20%→35% ethyl acetate-hexanes) to provide alkyl azide 3 as a yellow foam (19.6 mg, 93%). TLC (50% ethyl acetate-hexanes): Rf = 0.35 (UV); 1H NMR (600 MHz, CDC13) δ 14.84 (s, 1H), 7.45 (s, 1H), 5.20 (d, = 4.2 Hz, 1H), 4.77 (d, = 4.1 Hz, 1H), 4.74 (s, 1H), 4.29 - 4.25 (m, 1H), 4.22 - 4.17 (m, 1H), 3.78 (s, 3H), 3.63 (s, 3H), 3.60 - 3.55 (m, 1H), 3.53 - 3.46 (m, 1H), 3.44 (s, 3H), 3.06 - 3.02 (m, 2H), 2.89 (d, = 5.6 Hz, 1H), 2.83 (d, = 5.7 Hz, 1H), 2.75 - 2.71 (m, 2H), 2.59 (s, 3H), 2.12 - 2.06 (m, 2H); 13C NMR (125 MHz, CDC13) δ 204.70, 162.93, 150.96, 142.64, 141.98, 135.36, 130.43, 116.00, 113.77, 113.31, 111.25, 104.53, 102.10, 100.07, 73.17, 69.49, 68.95, 64.73, 61.05, 57.25, 56.83, 51.17, 48.45, 38.96, 23.71, 22.23, 20.52; FTIR (neat), cm"1: 2949 (br w), 2106 (m), 1622 (s), 1389 (s), 1324 (w), 1094 (s), 1076 (s), 985 (m); HRMS (ESI): Calc'd for (C27H29N3Oio + H)+: 556.1926, found: 556.1917.
Figure imgf000192_0001
(R02-A9)
[00480] To a solution of alkyl azide 3 (22.2 mg, 0.040 mmol, 1 equiv) in THF (1.8 mL) and water (0.18 mL) was added triphenyl phosphine (41.9 mg, 0.160 mmol, 4 equiv). The reaction mixture was stirred at 23 °C under argon for 24 h. The reaction mixture was diluted with ethyl acetate (30 mL) and the mixture was filtered through a plug of cotton and sodium sulfate, rinsing with ethyl acetate (20 mL). Formic acid (100 uL) was added to the solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→50% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide alkyl amine formate 4 (R02-A9) as a yellow oil (11.6 mg, 55%). TLC (10% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): Rf = 0.21 (UV); 1H NMR (600 MHz, CDC13) δ 15.18 (br s, 1H), 8.26 (s, 1H), 8.00 (br s, 3H), 7.45 (s, 1H), 5.21 (d, = 4.0 Hz, 1H), 5.00 (d, = 4.0 Hz, 1H), 4.68 (s, 1H), 4.27 - 4.16 (br m, 2H), 3.76 (s, 3H), 3.58 (s, 3H), 3.41 (s, 3H), 3.26 - 3.21 (br m, 2H), 3.04 - 2.98 (br m, 2H), 2.87 (d, = 5.5 Hz, 1H), 2.77 (d, = 5.5 Hz, 1H), 2.71 - 2.68 (br m, 2H), 2.56 (s, 3H), 2.08 - 2.01 (br m, 2H); 13C NMR (125 MHz, CDC13) δ 205.09, 167.75, 161.85, 150.38, 143.02, 142.04, 135.26, 130.52, 116.41, 114.21, 113.07, 111.47, 104.42, 102.47, 99.98, 72.37, 69.10 (2C), 63.04, 61.05, 56.95, 56.80, 48.56, 39.95, 38.77, 23.61, 22.09, 20.50; FTIR (neat), cm"1: 3216 (br w), 2952 (br w), 1620 (s), 1571 (s), 1388 (s), 1347 (m), 1113 (s), 1094 (s), 984 (m); HRMS (ESI): Calc'd for (C27H3iNOio + H)+: 530.2021, found: 530.2020.
Figure imgf000192_0002
[00481] A flame-dried 25 mL flask was charged with 2,6-lutidine (0.453 mL, 3.89 mmol, 1.08 equiv) and dichloromethane (4 mL). The solution was cooled to -20 °C in a dry ice- acetone bath. Trifluoromethanesulfonic anhydride (0.632 mL, 3.74 mmol, 1.04 equiv) was added dropwise, generating a bright red mixture. After 10 min, 3-bromopropan-l-ol (0.325 mL, 3.60 mmol, 1 equiv) was added dropwise. The mixture partially clarifies and stirs more freely. The cooling bath was removed and the mixture allowed to warm slowly to 23 °C. After 10 min, the mixture was diluted with 1: 1 dichloromethane-hexanes (20 mL) and filtered through a pad of silica (1 cm in a 30-mL sintered glass funnel), eluting with 1: 1 dichloromethane-hexanes (80 mL). The filtrate was concentrated, providing 3-bromopropyl trifluoromethanesulfonate as a colorless oil, which was used without further purification.
[00482] An oven-dried 5-mL flask was charged with dideoxy-DC-45-A2 (1) (25 mg, 0.051 mmol, 1 equiv) and dichloromethane (1.03 mL). 4A molecular sieves and proton-sponge (220 mg, 1.028 mmol, 20 equiv) were added and the mixture was stirred at 23 °C for 30 min to dry. 3-bromopropyl trifluoromethanesulfonate (139 mg, 0.514 mmol, 10 equiv) was added dropwise and the mixture was stirred at 23 °C under argon for 24 h. The reaction mixture was diluted with dichloromethane (10 mL) and methanol (0.5 mL), stirring for 20 min to quench any unreacted alkyl triflate. The mixture was partitioned between dichloromethane (20 mL) and saturated sodium bicarbonate solution (10 mL). The mixture was shaken vigorously and the layers were separated. The organic layer was dried over sodium sulfate. The dried solution was filtered, and the filtrate was concentrated. The residue was purified by flash column chromatography on silica gel deactivated with triethylamine (25%→35% ethyl acetate-hexanes) to provide 5 as a yellow oil (31.2 mg, 100%). TLC (50% ethyl acetate- hexanes): Rf = 0.34 (UV); 1H NMR (600 MHz, CDC13) δ 14.79 (s, 1H), 7.43 (s, 1H), 5.21 (d, = 4.1 Hz, 1H), 4.81 (d, = 4.1 Hz, 1H), 4.13 - 4.06 (m, 2H), 3.77 (s, 3H), 3.65 - 3.56 (m, 2H), 3.62 (s, 3H), 3.44 (s, 3H), 3.05 - 3.01 (m, 2H), 2.87 (d, = 5.8 Hz, 1H), 2.83 (d, = 5.7, 1H), 2.74 - 2.71 (m, 2H), 2.58 (s, 3H), 2.36 - 2.29 (m, 1H), 2.26 - 2.19 (m, 1H), 2.11 - 2.06 (m, 2H); 13C NMR (125 MHz, CDCI3) δ 204.61, 163.06, 151.43, 142.56, 141.95, 135.37, 130.39, 115.81, 113.57, 113.36, 111.18, 104.53, 102.23, 99.88, 72.34, 69.29, 69.08, 63.56, 61.03, 57.01, 56.83, 48.29, 38.96, 33.50, 30.83, 23.72, 22.24, 20.52; FTIR (neat), cm"1: 3295 (br w), 2951 (br w), 1620 (s), 1389 (s), 1113 (s), 1092 (s), 733 (m), 702 (m); HRMS (ESI): Calc'd for (CisHsiBrOio + H)+: 607.1173, found: 607.1148.
Figure imgf000193_0001
[00483] A 10-mL round-bottom flask was charged with alkyl bromide 5 (24.8 mg, 0.041 mmol, 1 equiv) and sodium azide (26.5 mg, 0.408 mmol, 10 equiv). Anhydrous
dimethylformamide (0.82 mL) was added, and the reaction flask was wrapped in foil. The suspension was stirred at 23 °C under argon for 40 h. The reaction mixture was partitioned between ethyl acetate (30 mL) and saturated sodium bicarbonate solution (10 mL). The layers were separated, and the organic layer was washed with saturated sodium bicarbonate solution (10 mL), water (2 x 10 mL), and saturated sodium chloride solution (2 x 10 mL). The washed solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash column chromatography on silica gel deactivated with triethylamine (20%→35% ethyl acetate-hexanes) to provide 6 as a yellow foam (17.6 mg, 76%). TLC (50% ethyl acetate-hexanes): Rf = 0.40 (UV); 1H NMR (600 MHz, CDC13) δ 14.82 (s, 1H), 7.43 (s, 1H), 5.21 (d, J = 4.1 Hz, 1H), 4.78 (d, J = 4.1 Hz, 1H), 4.74 (s, 1H), 4.08 (t, J = 5.9 Hz, 2H), 3.78 (s, 3H), 3.63 (s, 3H), 3.52 (t, J = 6.8 Hz, 2H), 3.44 (s, 3H), 3.07 - 3.00 (m, 2H), 2.88 (d, J = 5.7 Hz, 1H), 2.84 (d, J = 5.7 Hz, 1H), 2.75 - 2.71 (m, 2H), 2.58 (s, 3H), 2.12 - 2.06 (m, 2H), 2.03 - 1.96 (m, 2H); 13C NMR (125 MHz, CDCI3) 5 204.63, 163.04, 151.37, 142.58, 141.95, 135.37, 130.39, 115.83, 113.61, 113.36, 111.19, 104.54, 102.14, 99.93, 72.52, 69.37, 69.07, 62.53, 61.03, 57.07, 56.83, 48.62, 48.32, 38.96, 29.63, 23.71, 22.24, 20.52; FTIR (neat), cm"1: 2951 (br w), 2099 (m), 1622 (s), 1389 (s), 1094 (s), 1074 (s), 984 (m); HRMS (ESI): Calc'd for (C28H31N3O10 + Na)+: 592.1907, found:
592.1822.
Figure imgf000194_0001
(R02-A2)
[00484] To a solution of alkyl azide 6 (5.0 mg, 8.78 μηοΐ, 1 equiv) in THF (400 L) and water (40 μί) was added triphenyl phosphine (9.2 mg, 0.035 mmol, 4 equiv). The reaction mixture was stirred at 23 °C under argon for 24 h. The reaction mixture was diluted with ethyl acetate (20 mL) and washed with saturated aqueous sodium chloride (2 x 5 mL). The washed organic solution was dried over sodium sulfate and filtered. Several drops of formic acid were added to the filtrate and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide 7 (R02-A2) as a yellow oil (3.6 mg, 75%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): Rf = 0.29
(UV); 1H NMR (500 MHz, CDC13) δ 14.98 (br s, 1H), 8.33 (s, 1H), 7.71 (br s, 3H), 7.46 (s, 1H), 5.22 (d, 7 = 4.1 Hz, 1H), 4.86 (d, 7 = 4.1 Hz, 1H), 4.72 (s, 1H), 4.22 - 4.16 (br m, 2H), 3.78 (s, 3H), 3.60 (s, 3H), 3.45 (s, 3H), 3.33 - 3.28 (br m, 2H), 3.06 - 3.01 (br m, 2H), 2.92 (d, 7 = 5.4 Hz, 1H), 2.85 (d, 7 = 5.5 Hz, 1H), 2.74 - 2.69 (br m, 2H), 2.58 (s, 3H), 2.13 - 2.04 (br m, 4H); 13C NMR (125 MHz, CDCI3) δ 204.91, 167.19, 162.39, 150.80, 142.83, 141.90, 135.35, 130.64, 116.35, 113.84, 113.20, 111.45, 104.47, 101.96, 100.22, 77.42, 77.36, 77.16, 76.91, 72.06, 69.33, 69.15, 63.70, 61.09, 57.23, 57.01, 48.81, 38.88, 38.55, 26.88, 23.69, 22.17, 20.51; FTIR (neat), cm"1: 2945 (br w), 1620 (s), 1572 (m), 1389 (s), 1151 (s), 1094 (s), 1076 (s), 984 (w); HRMS (ESI): Calc'd for (C28H33NO10 + H)+: 544.2177, found: 544.2170.
Figure imgf000195_0001
[00485] A flame-dried 25 mL flask was charged with pyridine (0.285 mL, 3.53 mmol, 1.08 equiv) and dichloromethane (4 mL). The solution was cooled to -20 °C in a dry ice-acetone bath. Trifluoromethanesulfonic anhydride (0.574 mL, 3.40 mmol, 1.04 equiv) was added dropwise. Substantial white precipitate forms, preventing stirring. After 10 min, 4- bromobutan-l-ol (500 mg, 3.27 mmol, 1 equiv) was added dropwise. The mixture partially clarifies and stirs more freely. The cooling bath was removed and the mixture allowed to warm slowly to 23 °C. After 10 min, the mixture was diluted with 1: 1 dichloromethane- hexanes (20 mL) and filtered through a pad of silica (1 cm in a 30-mL sintered glass funnel), eluting with 1: 1 dichloromethane-hexanes (80 mL). The filtrate was concentrated, providing 4-bromobutyl trifluoromethanesulfonate as a colorless oil, which was used without further purification.
[00486] An oven-dried 5-mL flask was charged with dideoxy-DC-45-A2 (1) (50 mg, 0.103 mmol, 1 equiv) and dichloromethane (2.06 mL). 4A molecular sieves and proton-sponge (441 mg, 2.056 mmol, 20 equiv) were added and the mixture was stirred at 23 °C for 30 min to dry. 4-bromobutyl trifluoromethanesulfonate (293 mg, 1.028 mmol, 10 equiv) was added dropwise and the mixture was stirred at 23 °C under argon for 24 h. The reaction mixture was diluted with dichloromethane (10 mL) and methanol (0.5 mL), stirring for 20 min to quench any unreacted alkyl triflate. The mixture was partitioned between dichloromethane (20 mL) and saturated sodium bicarbonate solution (10 mL). The mixture was shaken vigorously and the layers were separated. The organic layer was dried over sodium sulfate. The dried solution was filtered, and the filtrate was concentrated. The residue was purified by flash column chromatography on silica gel deactivated with triethylamine (25%→35% ethyl acetate-hexanes) to provide 8 as a yellow oil (42 mg, 66%).. TLC (50% ethyl acetate- hexanes): Rf = 0.38 (UV); 1H NMR (600 MHz, CDC13) δ 14.81 (s, 1H), 7.43 (s, 1H), 5.20 (d, 7 = 4.1 Hz, 1H), 4.76 (d, J = 4.1 Hz, 1H), 4.74 (s, 1H), 4.05 - 4.01 (m, 2H), 3.77 (s, 3H), 3.62 (s, 3H), 3.52 (t, J = 6.8 Hz, 2H), 3.44 (s, 3H), 3.06 - 3.01 (m, 2H), 2.86 (d, J = 5.8 Hz, 1H), 2.82 (d, J = 5.1 Hz, 1H), 2.75 - 2.70 (m, 2H), 2.58 (s, 3H), 2.12 - 2.02 (m, 5H), 1.90 - 1.84 (m, 2H); 13C NMR (125 MHz, CDC13) δ 204.61, 163.07, 151.49, 142.56, 141.97, 135.37, 130.36, 115.76, 113.61, 113.36, 111.16, 104.54, 102.09, 99.94, 72.45, 69.37, 69.07, 64.33, 61.03, 57.06, 56.83, 48.25, 38.96, 34.10, 29.58, 28.60, 23.71, 22.24, 20.52; FTIR (neat), cm"1: 2949 (br w), 1618 (s), 1387 (s), 1234 (w), 1092 (s), 1072 (s), 982 (s), 910 (m), 731 (s);
HRMS (ESI): Calc'd for (C29H33BrOi0 + H)+: 621.1330, found: 621.1337.
Figure imgf000196_0001
[00487] A 10-mL round-bottom flask was charged with alkyl bromide 8 (40.0 mg, 0.064 mmol, 1 equiv) and sodium azide (41.8 mg, 0.644 mmol, 10 equiv). Anhydrous
dimethylformamide (1.3 mL) was added, and the reaction flask was wrapped in foil. The suspension was stirred at 23 °C under argon for 14 h. The reaction mixture was partitioned between ethyl acetate (30 mL) and saturated sodium bicarbonate solution (10 mL). The layers were separated, and the organic layer was washed with saturated sodium bicarbonate solution (10 mL), water (2 x 10 mL), and saturated sodium chloride solution (2 x 10 mL). The washed solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash column chromatography (20%→35% ethyl acetate-hexanes) to provide 9 as a yellow foam (27.1 mg, 72%). TLC (50% ethyl acetate- hexanes): Rf = 0.38 (UV); 1H NMR (600 MHz, CDC13) δ 14.82 (s, 1H), 7.43 (s, 1H), 5.20 (d, J = 4.2 Hz, 1H), 4.76 (d, J = 4.1 Hz, 1H), 4.74 (s, 1H), 4.05 - 4.00 (m, 2H), 3.77 (s, 3H), 3.63 (s, 3H), 3.44 (s, 3H), 3.39 - 3.35 (m, 2H), 3.06 - 3.01 (m, 2H), 2.87 (d, J = 5.7 Hz, 1H), 2.83 (d, = 5.8 Hz, 1H), 2.75 - 2.70 (m, 2H), 2.58 (s, 3H), 2.12 - 2.05 (m, 2H), 1.83 - 1.77 (m, 4H); 13C NMR (125 MHz, CDC13) δ 204.62, 163.07, 151.47, 142.57, 141.97, 135.37, 130.35, 115.75, 113.61, 113.36, 111.16, 104.54, 102.08, 99.95, 72.52, 69.39, 69.06, 64.72, 61.02, 57.07, 56.82, 51.42, 48.27, 38.95, 27.20, 25.75, 23.70, 22.24, 20.52; FTIR (neat), cm"1: 2951 (br w), 2097 (m), 1620 (s), 1389 (s), 1234 (w), 1092 (s), 1074 (m), 910 (s), 731 (s); HRMS (ESI): Calc'd for (C29H33N3O10 + Na)+: 606.2058, found: 606.2031.
Figure imgf000197_0001
[00488] To a solution of alkyl azide 9 (5.0 mg, 8.57 μηοΐ, 1 equiv) in THF (390 iL) and water (39 μί) was added triphenyl phosphine (9.0 mg, 0.034 mmol, 4 equiv). The reaction mixture was stirred at 23 °C under argon for 24 h. The reaction mixture was diluted with ethyl acetate (20 mL) and washed with saturated aqueous sodium chloride (2 x 5 mL). The washed organic solution was dried over sodium sulfate and filtered. Several drops of formic acid were added to the filtrate and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1 % formic acid, flow rate: 15 mL/min) to provide 10 (R02-A1) as a yellow oil (4.2 mg, 88%).
[00489] . TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): Rf = 0.27 (UV); 1H NMR (600 MHz, CDCI3) δ 8.42 (br s, 1H), 7.45 (s, 1H), 5.23 (d, J = 4.1 Hz, 1H), 4.89 (d, J = 4.1 Hz, 1H), 4.74 (s, 1H), 4.10 - 3.98 (br m, 2H), 3.78 (s, 3H), 3.61 (s, 3H), 3.46 (s, 3H), 3.22 - 3.09 (br m, 2H), 3.06 - 3.01 (m, 2H), 2.93 (d, J = 5.5 Hz, 1H), 2.86 (d, = 5.4 Hz, 1H), 2.76 - 2.70 (m, 2H), 2.58 (s, 3H), 2.12 - 2.05 (br m, 2H), 1.98 - 1.86 (br m, 4H); FTIR (neat), cm"1 : 2967 (br w), 1736 (m), 1692 (m), 1620 (s), 1391 (s), 1252 (m), 1175 (m), 1115 (s); HRMS (ESI): Calc'd for (C29H35NO10 + H)+: 558.2334, found: 558.2319.
Figure imgf000198_0001
[00490] A flame-dried 25 mL flask was charged with 2,6-lutidine (0.377 mL, 3.23 mmol, 1.08 equiv) and dichloromethane (4 mL). The solution was cooled to -20 °C in a dry ice- acetone bath. Trifluoromethanesulfonic anhydride (0.526 mL, 3.11 mmol, 1.04 equiv) was added dropwise, generating a bright red mixture. After 10 min, 5-bromopentan-l-ol (0.361 mL, 2.99 mmol, 1 equiv) was added dropwise. The mixture partially clarifies and stirs more freely. The cooling bath was removed and the mixture allowed to warm slowly to 23 °C. After 10 min, the mixture was diluted with 1: 1 dichloromethane-hexanes (20 mL) and filtered through a pad of silica (1 cm in a 30-mL sintered glass funnel), eluting with 1: 1 dichloromethane-hexanes (80 mL). The filtrate was concentrated, providing 5-bromopentyl trifluoromethanesulfonate as a colorless oil, which was used without further purification.
[00491] An oven-dried 10-mL flask was charged with dideoxy-DC-45-A2 (1) (25 mg, 0.051 mmol, 1 equiv) and dichloromethane (1.03 mL). 4A molecular sieves and proton- sponge (220 mg, 1.028 mmol, 20 equiv) were added and the mixture was stirred at 23 °C for 30 min to dry. 5-bromopentyl trifluoromethanesulfonate (154 mg, 0.514 mmol, 10 equiv) was added dropwise and the mixture was stirred at 23 °C under argon for 18 h. The reaction mixture was diluted with dichloromethane (10 mL) and methanol (0.5 mL), stirring for 20 min to quench any unreacted alkyl triflate. The mixture was partitioned between
dichloromethane (20 mL) and saturated sodium bicarbonate solution (10 mL). The mixture was shaken vigorously and the layers were separated. The organic layer was dried over sodium sulfate. The dried solution was filtered, and the filtrate was concentrated. The residue was purified by flash column chromatography on silica gel deactivated with triethylamine (25%→35% ethyl acetate-hexanes) followed by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide 11 as a yellow oil (9.4 mg, 29%). TLC (50% ethyl acetate-hexanes): Rf = 0.34 (UV); 1H NMR (600 MHz, CDC13) δ 14.80 (s, 1H), 7.43 (s, 1H), 5.20 (d, = 4.2 Hz, 1H), 4.77 (d, = 4.1 Hz, 1H), 4.75 (s, 1H), 4.03 - 3.96 (m, 2H), 3.78 (s, 3H), 3.63 (s, 3H), 3.46 - 3.43 (m, 2H), 3.45 (s, 3H), 3.08 - 2.99 (m, 2H), 2.87 (d, = 5.7 Hz, 1H), 2.84 (d, = 5.7 Hz, 1H), 2.75 - 2.71 (m, 2H), 2.58 (s, 3H), 2.12 - 2.06 (m, 2H), 1.98 - 1.91 (m, 2H), 1.79 - 1.73 (m, 2H), 1.64 - 1.58 (m, 2H); 13C NMR (125 MHz, CDC13) δ 204.60, 163.15, 151.59, 142.56, 142.00, 135.39, 130.34, 115.72, 113.59, 113.39, 111.15, 104.56, 102.14, 99.95, 72.40, 69.38, 69.10, 65.24, 61.04, 57.09, 56.84, 48.27, 38.98, 34.04, 32.74, 29.22, 24.89, 23.73, 22.26, 20.54; FTIR (neat), cm"1: 2947 (br w), 1701 (w), 1620 (s), 1389 (s), 1092 (s), 1074 (s), 984 (m); HRMS (ESI): Calc'd for (C30H35BrOio + H)+: 635.1486, found: 635.1480.
Figure imgf000199_0001
[00492] A 10-mL round-bottom flask was charged with alkyl bromide 11 (9.4 mg, 0.015 mmol, 1 equiv) and sodium azide (9.6 mg, 0.148 mmol, 10 equiv). Anhydrous
dimethylformamide (296 μί) was added, and the reaction flask was wrapped in foil. The suspension was stirred at 23 °C under argon for 14 h. The reaction mixture was partitioned between ethyl acetate (30 mL) and saturated sodium bicarbonate solution (10 mL). The layers were separated, and the organic layer was washed with saturated sodium bicarbonate solution (10 mL), water (2 x 10 mL), and saturated sodium chloride solution (2 x 10 mL). The washed solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The residue was purified by flash column chromatography (20%→35% ethyl acetate-hexanes) to provide 12 as a yellow oil (8.84 mg, 100%). TLC (50% ethyl acetate- hexanes): Rf = 0.38 (UV); 1H NMR (600 MHz, CDC13) δ 14.80 (s, 1H), 7.43 (s, 1H), 5.20 (d, = 4.1 Hz, 1H), 4.77 (d, = 4.2 Hz, 1H), 4.75 (s, 1H), 4.02 - 3.95 (m, 2H), 3.78 (s, 3H), 3.63 (s, 3H), 3.44 (s, 3H), 3.30 (t, = 7.0 Hz, 2H), 3.06 - 3.01 (m, 2H), 2.87 (d, = 5.8 Hz, 1H), 2.84 (d, = 5.7 Hz, 1H), 2.75 - 2.71 (m, 2H), 2.58 (s, 3H), 2.12 - 2.06 (m, 2H), 1.79 - 1.73 (m, 2H), 1.71 - 1.65 (m, 2H), 1.57 - 1.50 (m, 2H); 13C NMR (125 MHz, CDC13) δ 204.63, 163.15, 151.60, 142.57, 142.00, 135.39, 130.34, 115.72, 113.59, 113.39, 111.15, 104.56, 102.14, 99.95, 72.41, 69.39, 69.10, 65.24, 61.04, 57.08, 56.84, 51.58, 48.27, 38.98, 29.61, 28.79, 23.73, 23.39, 22.26, 20.54; FTIR (neat), cm"1: 2943 (br w), 2097 (m), 1620 (s), 1389 (s), 1234 (w), 1092 (s), 1072 (s), 984 (m); HRMS (ESI): Calc'd for (C30H35N3Oio + H)+: 598.2395, found: 598.2380.
Figure imgf000200_0001
(R02-A10)
[00493] To a solution of alkyl azide 12 (12.7 mg, 0.021 mmol, 1 equiv) in THF (970 μΐ.) and water (97 μ¾ was added triphenyl phosphine (22.3 mg, 0.085 mmol, 4 equiv). The reaction mixture was stirred at 23 °C under argon for 14 h. The reaction mixture was diluted with ethyl acetate (20 mL) and washed with saturated aqueous sodium chloride (2 x 5 mL). The washed organic solution was dried over sodium sulfate and filtered. Several drops of formic acid were added to the filtrate and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→60% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide 13 (R02-A10) as a yellow oil (4.6 mg, 38%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): Rf = 0.34 (UV); 1H NMR (600 MHz, CDC13) δ 14.77 (br s, 1H), 8.32 - 8.26 (br m, 3H), 7.42 (s, 1H), 5.19 (d, 7 = 3.6 Hz, 1H), 4.84 (d, 7 = 3.8 Hz, 1H), 4.71 (s, 1H), 4.04 - 3.93 (m, 2H), 3.77 (s, 3H), 3.59 (s, 3H), 3.45 (s, 3H), 3.08 - 2.98 (br m, 4H), 2.87 (d, 7 = 5.7 Hz, 1H), 2.82 (d, 7 = 5.7 Hz, 1H), 2.75 - 2.68 (m, 2H), 2.56 (s, 3H), 2.12 - 2.04 (m, 2H), 1.84 - 1.73 (br m, 4H), 1.65 - 1.56 (br m, 2H); 13C NMR (125 MHz, CDC13) δ 204.58, 169.17, 163.10, 151.53, 142.54, 141.99, 135.34, 130.32, 115.69, 113.61, 113.36, 111.13, 104.50, 102.13, 100.06, 77.41, 77.36, 77.16, 76.91, 72.26, 69.35, 69.14, 65.23, 61.02, 57.08, 56.90, 48.28, 39.73, 38.94, 29.36, 28.18, 23.70, 23.28, 22.24, 20.52; FTIR (neat), cm"1: 2947 (br w), 1620 (s), 1572 (m), 1389 (s), 1115 (m), 1094 (s), 984 (m); HRMS (ESI): Calc'd for (C30H37NOio + H)+: 572.2490, found: 572.2491.
Figure imgf000200_0002
[00494] To a solution of dideoxy-DC-45-A2 (1) (48 mg, 0.099 mmol, 1.0 equiv) in allyl bromide (4.5 ml, 51.4 mmol) was added calcium sulfate (53.7 mg, 0.395 mmol, 4.0 equiv) at 23 °C, followed by the addition of Ag20 (45.7 mg, 0.197 mmol, 2.0 equiv). The reaction mixture was stirred at 23 °C for 72 hours. The reaction reaction mixture was diluted with ethyl acetate (10 mL) and filtered through celite. The celite was washed with ethyl acetate (10 mL). The organic solutions were combined and concentrated. The residue was purified by flash column chromatography on silica gel deactivated with triethylamine (40% ethyl acetate-hexanes) to provide 14 as a yellow oil (33 mg, 64%). 1H NMR (500 MHz, CDC13) δ: 7.45 (s, 1H), 6.16 - 6.08 (m, 1H), 5.41 (dd, 1Η, = 17.3, 1.7 Hz); 5.24 - 5.21 (m, 2H), 4.82 (d, 1H, = 3.8 Hz), 4.77 (s, 1H), 4.57 (m, 2H), 3.80 (s, 3H), 3.65 (s, 3H), 3.46 (s, 3H), 3.08 - 3.04 (m, 2H), 2.91 - 2.87 (m, 2H), 2.76 - 2.73 (m, 2H), 2.60 (s, 3H), 2.12 - 2.10 (m, 2H).
Figure imgf000201_0001
[00495] Alkene 14 (97 mg, 0.184 mmol, 1.0 equiv) was dissolved in THF (4.0 mL) and water (2.0 mL) in a 25 mL flask and cooled to 0° C. 2,6-lutidine (42.9 μί, 0.368 mmol, 2.0 equiv), sodium periodate (315 mg, 1.474 mmol, 8.0 equiv) and potassium osmate dihydrate (3.39 mg, 9.21 μιηοΐ, 0.05 equiv) were added to the reaction in sequence. The flask was flushed with argon and sealed with parafilm. The ice bath was removed after 10 min and the reaction was stirred at 23 °C for 4 hours. The reaction was diluted with ethyl acetate (80 mL), washed with brine (30 mL), aqueous copper(II) sulfate solution (1M, 30 mL), water (30 mL), and brine (30 mL) in sequence. The aqueous solution was extracted with ethyl acetate. The organic layers were combined, dried over sodium sulfate and concentrated. The residue was purified by column chromatography (35% ethyl acetate-hexanes) to provide 15 as a yellow oil (84 mg, 86%). 1H NMR (500 MHz, CDCI3) δ: 9.87 (s, 1H), 7.48 (s, 1H), 5.26 (d, 1H, = 4.4 Hz); 4.85 (d, 1H, = 4.4 Hz), 4.76 (s, 1H), 4.62 - 4.52 (m, 2H), 3.80 (s, 3H), 3.66 (s, 3H), 3.47 (s, 3H), 3.07 - 3.04 (m, 2H), 2.95 - 2.85 (m, 2H), 2.75 (t, 2H, = 5.7 Hz), 2.61 (s, 3H), 2.13 - 2.08 (m, 2H).
Figure imgf000202_0001
[00496] Sodium cyanoborohydride (20.0 mg, 0.318 mmol, 4.0 equiv) was added in one portion to a solution of methylamine hydrochloride (107 mg, 1.589 mmol, 20 equiv) in 9: 1 methanol: acetic acid (1 mL) at 0 °C. A solution of aldehyde 15 (42 mg, 0.079 mmol, 1.0 equiv) in 9: 1 methanol: acetic acid (3 mL) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction temperature was increased to 23 °C. After 45 min, the solution was diluted with ethyl acetate (20 mL) and washed with brine (20 mL). The aqueous solution was extracted wtih ethyl acetate (6 x 20 mL). The organic solution was combined and dried over sodium sulfate. Three drops of formic acid were added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μη, 19 x 250 mm, UV detection at 399 nm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 16 (R02-B1) as a yellow oil (25 mg, 58%). 1H NMR (500 MHz, CDC13) δ: 7.51 (s, 1H), 5.28 (d, 1H, J = 3.4 Hz); 5.05 (d, 1H, J = 3.4 Hz), 4.73 (s, 1H), 4.52 - 4.28 (m, 2H), 3.80 (s, 3H), 3.63 (s, 3H), 3.46 (s, 3H), 3.39 - 3.20 (m, 2H), 3.07 (t, 2H, J = 5.9 Hz), 2.93 - 2.83 (m, 2H), 2.78 - 2.75 (m, 5H), 2.61 (s, 3H), 2.16 - 2.09 (m, 2H); HRMS (ESI): Calc'd for (C3oH37NOio+H)+ 544.2177, found 544.2184.
Figure imgf000202_0002
[00497] Proton-sponge (88 mg, 0.411 mmol, 20 equiv) and 4A molecule sieves (10 mg) were added to a solution of dideoxy-DC-45-A2 (1) (10 mg, 0.021 mmol, 1.0 equiv) in dry dichloromethane (307 μί) at 23 °C. The reaction was stirred for 20 min. But-3-en-l-yl trifluoromethanesulfonate (42.0 mg, 0.206 mmol, 10 equiv) was then added dropwise to the reaction. The reaction was flushed with argon and stirred at 23 °C for 4 hours. Three drops of methanol were added to the reaction and stirred for 20 min to consume the remaining triflate. Then the reaction was diluted with ethyl acetate (15 mL) and washed with saturated aqueous sodium bicarbonate solution (5 mL). The organic phase was further washed with 0.1 M HC1 (2 x 5 ml), water (5 ml), and brine (5 ml). The organic solution was dried over sodium sulfate and concentrated. The residue was purified immediately by flash column chromatography on silica gel deactivated with triethylamine (hexanes initially, to 50% ethyl acetate-hexanes) to provide 17 as a yellow oil (8 mg, 72%). 1H NMR (400 MHz, CDC13) δ: 7.41 (s, 1H), 5.82 - 5.93 (m, 1H), 5.20 (d, 1H, J = 3.8 Hz); 5.19 - 5.03 (m, 2H), 4.76 - 4.73 (m, 2H), 4.07 - 4.01 (m, 2H), 3.79 (s, 3H), 3.62 (s, 3H), 3.42 (s, 3H), 3.05 - 3.02 (m, 2H), 2.88 - 2.83 (m, 2H), 2.74 - 2.70 (m, 2H), 2.59 (s, 3H), 2.48 - 2.52 (m, 2H), 2.04 - 2.09 (m, 2H).
Figure imgf000203_0001
[00498] Alkene 17 (40 mg, 0.074 mmol, 1.0 equiv) was dissolved in THF (1.6 mL) and water (0.8 mL) in a 10 mL flask and cooled to 0° C. 2,6-lutidine (17.2 μί, 0.148 mmol, 2.0 equiv), sodium periodate (127 mg, 0.592 mmol, 8.0 equiv) and potassium osmate dihydrate (1.363 mg, 3.70 μιηοΐ, 0.05 equiv) were added to the reaction in sequence. The flask was flushed with argon and sealed with parafilm. The ice bath was removed after 10 min and stirred at 23 °C for 4 hours. The reaction was diluted with ethyl acetate (40 mL), washed with brine (15 mL), aqueous copper(II) sulfate solution (1M, 15 mL), water (15 mL), and brine (15 mL) in sequence. The aqueous solution was extracted with ethyl acetate. The organic layers were combined, dried over sodium sulfate and concentrated. The residue was purified by column chromatography (35% ethyl acetate-hexanes) to provide 18 as a yellow oil (35 mg, 86%). 1H NMR (500 MHz, CDC13) δ: 9.90 (s, 1H), 7.47 (s, 1H), 5.21 (d, 1H, = 3.8 Hz); 4.81 (d, 1H, = 3.8 Hz), 4.74 (s, 1H), 4.48 - 4.36 (m, 2H), 3.80 (s, 3H), 3.64 (s, 3H), 3.46 (s, 3H), 3.08 - 3.04 (m, 2H), 2.92 - 2.83 (m, 4H), 2.75 (t, 2H, = 6.8 Hz), 2.60 (s, 3H), 2.13 - 2.10 (m, 2H).
Figure imgf000204_0001
[00499] Sodium cyanoborohydride (2.3 mg, 0.037 mmol, 4.0 equiv) was added in one portion to a solution of methylamine hydrochloride (12.44 mg, 0.184 mmol, 20 equiv) in 9: 1 methanol: acetic acid (0.1 mL) at 0 °C. A solution of aldehyde 18 (5 mg, 0.009 mmol, 1.0 equiv) in 9: 1 methanol: acetic acid (0.3 mL) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction temperature was increased to 23 °C. After 45 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (5 mL). The aqueous solution was extracted with ethyl acetate (6 x 5 mL). The organic layers were combined and dried over sodium sulfate. Three drops of formic acid were added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide 19 (R02-A5) as a yellow oil (2.7 mg, 53 %). 1H NMR (500 MHz, CDC13) δ: 7.50 (s, 1H), 5.24 (d, 1H, = 3.4 Hz); 4.87 (d, 1H, = 3.4 Hz), 4.71 (s, 1H), 4.24 - 4.13 (m, 2H), 3.81 (s, 3H), 3.63 (s, 3H), 3.48 (s, 3H), 3.39 - 3.20 (m, 2H), 3.08 - 3.05 (m, 2H), 2.98 - 2.85 (m, 2H), 2.78 - 2.72 (m, 5H), 2.61 (s, 3H), 2.16 - 2.09 (m, 4H); HRMS (ESI): Calc'd for (C29H36NOio+H)+ 558.2334, found 558.2342.
Figure imgf000204_0002
[00500] Proton-sponge (352 mg, 1.644 mmol, 20 equiv) and 4A molecule sieves (40 mg) were added to a solution of dideoxy-DC-45-A2 (1) (40 mg, 0.082 mmol, 1.0 equiv) in dry dichloromethane (1.6 mL) at 23 °C. The reaction was stirred for 20 mins. Pent-4-en-l-yl trifluoromethanesulfonate (179 mg, 0.822 mmol, 10 equiv) was then added dropwise to the reaction. The reaction was flushed with argon and stirred at 23 °C for 4 hours. Three drops of methanol were added to the reaction and stirred for 20 mins to consume the remaining triflate. Then the reaction was diluted with ethyl acetate (60 mL) and washed with saturated aqueous sodium bicarbonate solution (20 mL). The organic phase was further washed with 0.1 M HCl (2 x 20 ml), water (20 ml), and brine (20 ml). The organic solution was dried over sodium sulfate and concentrated. The residue was purified immediately by flash column chromatography on silica gel deactivated with triethylamine (hexanes initially, to 50% ethyl acetate-hexanes) to provide 20 as a yellow oil (45 mg, 99%). 1H NMR (500 MHz, CDC13) δ: 7.43 (s, 1H), 5.93 - 5.86 (m, 1H), 5.22 (d, 1H, J = 4.3 Hz); 5.05 - 4.99 (m, 2H), 4.80 (d, 1H, J = 4.3 Hz), 4.77 (s, 1H), 4.05 - 3.96 (m, 2H), 3.79 (s, 3H), 3.65 (s, 3H), 3.46 (s, 3H), 3.08 - 3.04 (m, 2H), 2.89 - 2.86 (m, 2H), 2.76 - 2.73 (m, 2H), 2.60 (s, 3H), 2.26 - 2.21 (m, 2H), 2.13 - 2.09 (m, 2H), 1.89 - 1.83 (m, 2H).
Figure imgf000205_0001
[00501] Alkene 20 (43 mg, 0.078 mmol, 1.0 equiv) was dissolved in THF (1.8 mL) and water (0.9 mL) in a 10 mL flask and cooled to 0° C. 2,6-lutidine (18.0 μΐ, 0.155 mmol, 2.0 equiv), sodium periodate (133 mg, 0.620 mmol, 8.0 equiv) and potassium osmate dihydrate (1.4 mg, 3.88 μιηοΐ, 0.05 equiv) were added to the reaction in sequence. The flask was flushed with argon and sealed with parafilm. The ice bath was removed after 10 mins and stirred at 23 °C for 4 hours. The reaction was diluted with ethyl acetate (40 mL), washed with brine (15 mL), aqueous copper(II) sulfate solution (1M, 15 mL), water (15 mL), and brine (15 mL) in sequence. The aqueous solution was extracted with ethyl acetate. The organic layers waere combined, dried over sodium sulfate and concentrated. The residue was purified by column chromatography (35% ethyl acetate-hexanes) to provide 21 as a yellow oil (30 mg, 70%). 1H NMR (500 MHz, CDC13) δ: 9.85 (s, 1H), 7.43 (s, 1H), 5.21 (d, 1H, = 4.6 Hz); 4.76-4.75 (m, 2H), 4.09 - 4.03 (m, 2H), 3.79 (s, 3H), 3.64 (s, 3H), 3.46 (s, 3H), 3.07 - 3.03 (m, 2H), 2.89 - 2.83 (m, 2H), 2.74 - 2.73 (m, 2H), 2.60 (s, 3H), 2.13 - 2.07 (m, 4H), 1.29 - 1.25 (m, 2H).
Figure imgf000206_0001
23
(R02-B9)
[00502] To a solution of aldehyde 21 (7 mg, 0.013 mmol, 1.0 equiv) in dry 1,2- dichloroethane (0.4 mL) was added methylamine hydrochloride (17 mg, 0.252 mmol, 20 equiv) and triethylamine (35.1 μί, 0.252 mmol, 20 equiv). After stirring for 60 min, sodium triacetoxyborohydride (10.7 mg, 0.05 mmol, 4.0 equiv) was added in one portion. The vial was flushed with argon and sealed. After being stirred at 23 °C for 45 min, the reaction was partitioned between saturated aqueous sodium bicarbonate solution (5 mL) and ethyl acetate (20 mL). The organic phase was dried over sodium sulfate. Three drops of formic acid were added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 22 (R02-A7) as a yellow oil (5 mg, 70%) and 23 (R02-B9) as a yellow oil (2 mg, 14%).
[00503] 22 (R02-A7): 1H NMR (500 MHz, CDC13) δ: 7.48 (s, 1H), 5.25 (d, 1H, = 4.2 Hz); 4.92 (d, 1H, = 4.2 Hz), 4.72 (s, 1H), 4.12 - 4.01 (m, 2H), 3.80 (s, 3H), 3.64 (s, 3H), 3.48 (s, 3H), 3.20 - 3.13 (m, 2H), 3.07 - 3.04 (m, 2H), 2.97 - 2.84 (m, 2H), 2.77 - 2.75 (m, 5H), 2.60 (s, 3H), 2.13-2.07 (m, 4H), 1.98 - 1.93 (m, 2H); HRMS (ESI): Calc'd for
(C3oH37NOio+H)+ 572.2490, found 572.2473.
[00504] 23 (R02-B9): 1H NMR (500 MHz, CDC13) δ: 7.41 (s, 2H), 6.95 (s, 2H), 5.19 (d, 2H, = 4.1 Hz); 4.80 (d, 2H, = 4.1 Hz), 4.75 (s, 2H), 3.99 (t, 4H, = 11.8 Hz), 3.78 (s, 6H), 3.60 (s, 6H), 3.42 (s, 6H), 3.15 - 3.03 (m, 4H), 2.88 - 2.78 (m, 4H), 2.74 - 2.71 (m, 4H), 2.73 (s, 3H), 2.72 - 2.68 (s, 4H), 2.55 (s, 6H), 2.08 - 2.04 (m, 8H), 1.96 - 1.92 (m, 4H); HRMS (ESI): Calc'd for (C59H69N02o+H)+ 1112.4486, found 1112.4486.
Figure imgf000207_0001
[00505] Proton-sponge (352 mg, 1.644 mmol, 20 equiv) and 4A molecule sieves (40 mg) were added to a solution of dideoxy-DC-45-A2 (1) (40 mg, 0.082 mmol, 1.0 equiv) in dry dichloromethane (1.6 mL) at 23 °C. The reaction was stirred for 20 min. Hex-5-en-l-yl trifluoromethanesulfonate (191 mg, 0.822 mmol, 10 equiv) was then added dropwise to the reaction. The reaction was flushed with argon and stirred at 23 °C for 4 hours. Three drops of methanol were added to the reaction and stirred for 20 min to consume the remaining triflate. Then the reaction was diluted with ethyl acetate (60 mL) and washed with saturated aqueous sodium bicarbonate solution (20 mL). The organic phase was further washed with 0.1 M HCl (2 x 20 ml), water (20 ml), and brine (20 ml). The organic solution was dried over sodium sulfate and concentrated. The residue was purified immediately by flash column
chromatography on silica gel deactivated with triethylamine (hexanes initially, to 50% ethyl acetate-hexanes) to provide 24 as a yellow oil (36 mg, 77%). 1H NMR (500 MHz, CDC13) δ: 7.44 (s, 1H), 5.90 - 5.81 (m, 1H), 5.22 (d, 1Η, = 4.0 Hz); 5.06 - 4.96 (m, 2H), 4.80 (d, 1H, = 4.0 Hz), 4.77 (s, 1H), 4.05 - 3.96 (m, 2H), 3.79 (s, 3H), 3.65 (s, 3H), 3.46 (s, 3H), 3.08 - 3.03 (m, 2H), 2.89 - 2.85 (m, 2H), 2.75 - 2.73 (m, 2H), 2.60 (s, 3H), 2.15 - 2.09 (m, 4H), 1.79 - 1.73 (m, 2H), 1.59 - 1.53 (m, 2H).
Figure imgf000207_0002
[00506] Alkene 24 (10 mg, 0.018 mmol, 1.0 equiv) was dissolved in THF (0.4 mL) and water (0.2 mL) in a 5 mL flask and cooled to 0° C. 2,6-lutidine (4.10 μί, 0.035 mmol, 2.0 equiv), sodium periodate (30.1 mg, 0.141 mmol, 8.0 equiv) and potassium osmate dihydrate (0.324 mg, 0.879 μιηοΐ, 0.05 equiv) were added to the reaction in sequence. The flask was flushed with argon and sealed with parafilm. The ice bath was removed after 10 min and stirred at 23 °C for 4 hours. The reaction was diluted with ethyl acetate (10 mL), washed with brine (4 mL), aqueous copper(II) sulfate solution (1M, 4 mL), water (4 mL), and brine (4 mL) in sequence. The aqueous solution was extracted with ethyl acetate. The organic solution was combined, dried over sodium sulfate and concentrated. The residue was purified by column chromatography (35% ethyl acetate-hexanes) to provide 25 as a yellow oil (7 mg, 70%). 1H NMR (500 MHz, CDC13) δ: 9.81 (s, 1H), 7.45 (s, 1H), 5.21 (d, 1H, = 4.6 Hz); 4.78 (d, 1H, = 4.6 Hz), 4.76 (s, 1H), 4.04 (t, 2H, J = 6.0 Hz), 3.80 (s, 3H), 3.65 (s, 3H), 3.46 (s, 3H), 3.08 - 3.04 (m, 2H), 2.89 - 2.84 (m, 2H), 2.76 - 2.73 (m, 2H), 2.60 (s, 3H), 2.56 - 2.54 (m, 2H), 2.12 - 2.09 (m, 2H), 1.87 - 1.78 (m, 4H).
Figure imgf000208_0001
27
(R02-B6)
[00507] To a solution of aldehyde 25 (6 mg, 10.52 μιηοΐ, 1.0 equiv) in dry 1,2- dichloroethane (0.35 mL) was added methylamine hydrochloride (14.20 mg, 0.210 mmol, 20 equiv) and triethylamine (29.3 μί, 0.210 mmol, 20 equiv). After stirring for 60 min, sodium triacetoxyborohydride (8.91 mg, 0.042 mmol, 4.0 equiv) was added in one portion. The vial was flushed with argon and sealed. After being stirred at 23 °C for 45 min, the reaction was partitioned between saturated aqueous sodium bicarbonate solution (5 mL) and ethyl acetate (20 mL). The organic phase was dried over sodium sulfate. Three drops of formic acid were added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 26 (R02-B2) as a yellow oil (3.7 mg, 60%) and 27 (R02-B6) as a yellow oil (2 mg, 16%).
[00508] 26 (R02-B2): 1H NMR (500 MHz, CDC13) δ: 7.44 (s, 1H), 5.21 (d, 1H, = 3.8 Hz); 4.82 (d, 1H, = 3.8 Hz), 4.74 (s, 1H), 4.02 - 3.97 (m, 2H), 3.80 (s, 3H), 3.64 (s, 3H), 3.46 (s, 3H), 3.08 - 3.03 (m, 2H), 2.96 - 2.92 (m, 2H), 2.87 - 2.84 (m, 2H), 2.75 - 2.72 (m, 2H), 2.63 (s, 3H), 2.59 (s, 3H), 2.13 - 2.07 (m, 2H), 1.86 - 1.75 (m, 4H), 1.61 - 1.56 (m, 2H); HRMS (ESI): Calc'd for (C3iH39NOio+H)+ 586.2647, found 586.2468.
[00509] 27 (R02-B6): 1H NMR (500 MHz, CDC13) δ: 7.42 (s, 2H), 6.95 (s, 2H), 5.20 (d, 2H, = 4.3 Hz); 4.78 (d, 2H, = 4.3 Hz), 4.74 (s, 2H), 3.97 (t, 4H, = 6.4 Hz), 3.77 (s, 6H), 3.62 (s, 6H), 3.44 (s, 6H), 3.05 - 3.03 (m, 4H), 2.94 - 2.92 (m, 4H), 2.86 - 2.81 (m, 4H), 2.72 (t, 4H, = 6.8 Hz), 2.66 (s, 3H), 2.57 (s, 6H), 2.11 - 2.07 (m, 4H), 1.86 - 1.72 (m, 8H), 1.53 - 1.48 (m, 4H); HRMS (ESI): Calc'd for (C6iH73N02o+H)+ 1140.4799, found 1140.4849.
Figure imgf000209_0001
(R02-C5)
[00510] Sodium cyanoborohydride (1.9 mg, 0.030 mmol, 4.0 equiv) was added in one portion to a solution of bicyclo[l. l.l]pentan-l-amine hydrochloride (18.1 mg, 0.151 mmol, 20 equiv) in 9: 1 methanol: acetic acid (0.1 mL) at 0 °C. A solution of aldehyde 15 (4 mg, 7.57 μιηοΐ, 1.0 equiv) in 9: 1 methanol: acetic acid (0.3 mL) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction temperature was increased to 23 °C. After 50 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The organic solution was combined and dried over sodium sulfate. Three drops of formic acid were added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 28 (R02-C5) as a yellow oil (2.1 mg, 47%). 1H NMR (600 MHz, CD3OD) δ: 7.54 (s, 1H), 5.26 (d, 1H, = 4.2 Hz); 5.05 (d, 1H, = 4.2 Hz), 4.63 (s, 1H), 4.18 - 4.15 (m, 2H), 3.80 (s, 3H), 3.58 (s, 3H), 3.42 (s, 3H), 3.10 - 3.06 (m, 4H), 2.86 - 2.75 (m, 4H), 2.60 (s, 3H), 2.12 - 2.08 (m, 2H), 2.02 - 1.99 (m, 4H), 0.89 (d, 3H, = 6.8 Hz); HRMS (ESI): Calc'd for (C32H37NOi0+H)+ 596.2490, found 596.2478.
Figure imgf000210_0001
(R02-C6)
[00511] Sodium cyanoborohydride (1.902 mg, 0.030 mmol, 4.0 equiv) was added in one portion to a solution of cyclopropylamine (10.7 μί, 0.151 mmol, 20 equiv) in 9: 1
methanol: acetic acid (0.1 mL) at 0 °C. A solution of aldehyde 15 (4 mg, 7.57 μιηοΐ, 1.0 equiv) in 9: 1 methanol: acetic acid (0.3 mL) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction temperature was increased to 23 °C. After 50 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The organic layers were combined and dried over sodium sulfate. Three drops of formic acid were added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide 29 (R02-C6) as a yellow oil (2.3 mg, 53%). 1H NMR (600 MHz, CD3OD) δ: 7.57 (s, 1H), 5.28 (d, 1H, J = 4.4 Hz); 5.07 (d, 1H, J = 4.4 Hz), 4.63 (s, 1H), 4.28 - 4.32 (m, 2H), 3.80 (s, 3H), 3.56 (s, 3H), 3.50 - 3.42 (m, 5H), 3.08 (t, 2H, J - 5.7 Hz), 2.90 - 2.78 (m, 3H), 2.77 - 2.75 (m, 2H), 2.60 (s, 3H), 2.12 - 2.08 (m, 2H), 0.94 - 0.89 (m, 4H); HRMS (ESI): Calc'd for (C3oH35NOio+H)+ 570.2334, found 570.2339.
Figure imgf000210_0002
(R02-C7)
[00512] Sodium cyanoborohydride (1.902 mg, 0.030 mmol, 4.0 equiv) was added in one portion to a solution of 2,2,2-trifluoroethylamine (12.0 μί, 0.151 mmol, 20 equiv) in 9: 1 methanol: acetic acid (0.1 mL) at 0 °C. A solution of aldehyde 15 (4 mg, 7.57 μιηοΐ, 1.0 equiv) in 9: 1 methanol: acetic acid (0.3 mL) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction temperature was increased to 23 °C. After 50 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The organic layers were combined and dried over sodium sulfate. Three drops of formic acid was added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 30 (R02-C7) as a yellow oil (1.9 mg, 41%). 1H NMR (600 MHz, CD3OD) δ: 7.50 (s, 1H), 5.24 (d, 1H, J = 4.1 Hz); 5.05 (d, 1H, = 4.1 Hz), 4.65 (s, 1H), 4.10 - 4.06 (m, 2H), 3.80 (s, 3H), 3.56 (s, 3H), 3.40 (s, 3H), 3.37 - 3.33 (m, 2H), 3.07 - 3.05 (m, 2H), 3.01 - 2.97 (m, 2H), 2.83 - 2.75 (m, 4H), 2.57 (s, 3H), 2.10 - 2.05 (m, 2H); HRMS (ESI): Calc'd for (C29H32F3NOio+H)+ 612.2051, found 612.2067.
Figure imgf000211_0001
[00513] Sodium cyanoborohydride (4.7 mg, 0.076 mmol, 4.0 equiv) was added in one portion to a solution of dimethylamine hydrochloride (30.9 mg, 0.378 mmol, 20 equiv) in in 9: 1 methanol: acetic acid (0.2 mL) at 0 °C. A solution of aldehyde 15 (10 mg, 0.019 mmol, 1.0 equiv) in in 9: 1 methanol: acetic acid (0.4 mL) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction temperature was increased to 23 °C. After 45 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The organic layers were combined and dried over sodium sulfate. Three drops of formic acid were added to the organic solution and the solution was concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 31 (R02-B7) as a yellow oil (7.3 mg, 69%). 1H NMR (600 MHz, CD3OD) δ: 7.54 (s, 1H), 5.26 (d, 1H, = 4.3 Hz); 5.04 (d, 1H, = 4.3 Hz), 4.65 (s, 1H), 4.44 - 4.36 (m, 2H), 3.80 (s, 3H), 3.56 (s, 3H), 3.52 - 3.49 (m, 2H), 3.41 (s, 3H), 3.08 - 3.05 (m, 2H), 3.01 (s, 6H), 2.88 - 2.78 (m, 2H), 2.76 - 2.73 (m, 2H), 2.58 (s, 3H), 2.09 - 2.06 (m, 2H); HRMS (ESI): Calc'd for (C29H35NOio+H)+ 558.2334, found 558.2339.
Figure imgf000212_0001
(R02-D6)
[00514] To a solution of amine 4 (R02-A9) (4.0 mg, 7.55 μιηοΐ, 1.0 equiv) and ammonium acetate (1.8 mg, 0.023 mmol, 3.0 equiv) in methanol (151 μί) was added aqueous
formaldehyde (37 wt. % in H20, 1.7 μί, 0.023 mmol, 3.0 equiv) and aqueous glyoxal (40 wt. % in H20, 3.3 μί, 0.023 mmol, 3.0 equiv). The reaction was stirred at 23 °C for 18 h. The mixture was diluted with methanol to a total volume of 800 μΐ^ and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 10→70% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide 32 (R02-D6) as a yellow oil (2.1 mg, 48%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.58 (UV); 1H NMR (500 MHz, CDC13) δ 14.89 (s, 1H), 7.74 (s, 1H), 7.45 (d, = 1.0 Hz, 1H), 7.09 - 7.06 (m, 2H), 5.19 (d, = 4.2 Hz, 1H), 4.70 (s, 1H), 4.66 (d, = 4.1 Hz, 1H), 4.40 - 4.25 (m, 4H), 3.78 (s, 3H), 3.63 (s, 3H), 3.45 (s, 3H), 3.08 - 3.02 (m, 2H), 2.89 (d, = 5.5 Hz, 1H), 2.81 (d, = 5.5 Hz, 1H), 2.76 - 2.72 (m, 2H), 2.58 (d, = 0.9 Hz, 3H), 2.10 (p, = 6.4 Hz, 2H); FTIR (neat), cm"1: 2924 (m), 2850 (w), 1621 (s), 1387 (s), 1233 (w), 1093 (s), 1077 (s), 910 (m), 728 (s); HRMS (ESI): Calc'd for (C3oH32N2Oio + H)+: 581.2130, found: 581.2159.
Figure imgf000212_0002
4 (R02-D7)
[00515] To a solution of amine 4 (R02-A9) (3.0 mg, 5.67 μιηοΐ, 1.0 equiv) in anhydrous dimethylformamide (57 μί) was added IH-pyrazole-l-carboxamidine hydrochloride (1.7 mg, 0.011 mmol, 2.0 equiv), followed by triethylamine (4.0 uL, 0.028 mmol, 5.0 equiv). The reaction was stirred at 23 °C for 24 h. The mixture was diluted with dimethylformamide (100 μί) and methanol to a total volume of -900 μΐ^ and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 5→60% acetonitrile in water containing 0.1% trifluoroacetic acid, flow rate: 15 mL/min) to provide 33 (R02-D7) as a yellow oil (2.2 mg, 68%). TLC (15% methanol- dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.28 (UV); 1H NMR (500 MHz, CDC13) δ 14.95 (s, 1H), 7.92 (t, 7 = 6.5 Hz, 1H), 7.48 (s, 1H), 6.85 (br s, 1H), 5.24 (d, 7 = 4.1 Hz, 1H), 4.86 (d, 7 = 4.2 Hz, 1H), 4.67 (s, 1H), 4.21 - 4.15 (m, 1H), 4.07 - 4.01 (m, 1H), 3.78 (s, 3H), 3.59 (s, 3H), 3.56 - 3.49 (m, 2H), 3.47 (s, 3H), 3.33 (br s, 4H), 3.07 - 3.01 (m, 2H), 2.95 (d, 7 = 5.5 Hz, 1H), 2.82 (d, 7 = 5.4 Hz, 1H), 2.75 - 2.70 (m, 2H), 2.58 (s, 3H), 2.08 (p, 7 = 6.6 Hz, 2H); FTIR (neat), cm"1: 3370 (br w), 3189 (br w), 2960 (w), 2922 (s), 2851 (w), 1673 (s), 1622 (s), 1446 (m), 1202 (m), 1094 (s), 1017 (s), 800 (s); HRMS (ESI): Calc'd for (C28H33N3Oio + H)+: 572.2239, found: 572.2260.
Figure imgf000213_0001
(R02-D9)
[00516] Sodium cyanoborohydride (1.43 mg, 0.023 mmol, 4.0 equiv) was added in one portion to a solution of piperidine (9.67 mg, 0.114 mmol, 20 equiv) in 0.1 mL methanol- acetic acid (methanol: acetic acid = 9: 1) at 0 °C. A solution of aldehyde 15 (3 mg, 5.68 μιηοΐ, 1.0 equiv) in 0.3 mL methanol- acetic acid (methanol: acetic acid = 9: 1) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction was warmed to 23 °C. After 45 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The combined organic solutions were dried over sodium sulfate. Drops of formic acid were added to the organic solution before concentration under reduced pressure. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 34 (R02-D9) as a yellow oil (2.5 mg, 74%). 1H NMR (600 MHz, CD3OD) δ 7.55 (s, 1H), 5.29 (d, 1H, 7 = 4.0 Hz), 5.10 (d, 1H, 7 = 4.0 Hz), 4.64 (s, 1H), 4.38 - 4.36 (m, 2H), 3.80 (s, 3H), 3.55 (s, 3H), 3.50 - 3.47 (m, 2H), 3.43 (s, 3H), 3.31 - 3.29 (m, 4H), 3.07 (t, 2H, 7 = 6.2 Hz), 2.91 (d, 1H, 7 = 5.5 Hz), 2.79 - 2.74 (m, 3H), 2.59 (s, 3H), 2.09 - 2.07 (m, 2H), 1.96 - 1.85 (m, 6H); HRMS(ESI): Calc'd for (C32H39F3NOio+H)+ 598.2647, found 598.2661.
Figure imgf000214_0001
(R02-D8)
[00517] Sodium cyanoborohydride (1.43 mg, 0.023 mmol, 4.0 equiv) was added in one portion to a solution of pyrrolidine (8.07 mg, 0.114 mmol, 20 equiv) in 0.1 mL methanol- acetic acid (methanol: acetic acid = 9: 1) at 0 °C. A solution of aldehyde 15 (3 mg, 5.68 μιηοΐ, 1.0 equiv) in 0.3 mL methanol- acetic acid (methanol: acetic acid = 9: 1) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction was warmed to 23 °C. After 45 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The combined organic solutions were dried over sodium sulfate. Drops of formic acid were added to the organic solution before concentration under reduced pressure. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 35 (R02-D8) as a yellow oil (2.5 mg, 75%). 1H NMR (500 MHz, CD3OD) δ 7.55 (s, 1H), 5.28 (d, 1H, J = 4.2 Hz), 5.06 (d, 1H, J = 4.2 Hz), 4.65 (s, 1H), 4.41 - 4.31 (m, 2H), 3.80 (s, 3H), 3.59 - 3.57 (m, 2H), 3.55 (s, 3H), 3.43 (s, 3H), 3.30 - 3.29 (m, 4H), 3.07 (t, 2H, J = 6.2 Hz), 2.89 (d, 1H, J = 5.6 Hz), 2.79 - 2.74 (m, 3H), 2.59 (s, 3H), 2.16 - 2.12 (m, 4H), 2.09 - 2.07 (m, 2H); HRMS(ESI): Calc'd for (C3iH37NOio+H)+ 584.2490, found 584.2471.
Figure imgf000214_0002
(R02-D10) [00518] Sodium cyanoborohydride (1.43 mg, 0.023 mmol, 4.0 equiv) was added in one portion to a solution of tert-butyl piperazine-l-carboxylate (21.14 mg, 0.114 mmol, 20 equiv) in 0.1 mL methanol- acetic acid (methanol: acetic acid = 9: 1) at 0 °C. A solution of aldehyde 15 (3 mg, 5.68 μιηοΐ, 1.0 equiv) in 0.3 mL methanol-acetic acid (methanol: acetic acid = 9: 1) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction was warmed to 23 °C. After 45 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The combined organic solutions were dried over sodium sulfate. Drops of formic acid were added to the organic solution before concentration under reduced pressure. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide the Boc-protected piperazine product as a yellow oil (2.0 mg, 50%).
[00519] The product was charged to a flask, followed by the addition of a solution of trifluoroacetic acid in dichloromethane (100 μί, 10% v/v) at 0 °C. When the reaction was complete, 1.5 mL of dimethylformamide was added to the solution and then concentrated to 0.5 mL. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide 36 (R02- D10) as a yellow oil (1.7 mg, 99%). 1H NMR (500 MHz, CD3OD) δ 7.55 (s, 1H), 5.28 (d, 1H, J = 4.2 Hz), 5.06 (d, 1H, J = 4.2 Hz), 4.66 (s, 1H), 4.35 - 4.27 (m, 2H), 3.81 (s, 3H), 3.56 (s, 3H), 3.46 - 3.43 (m, 7H), 3.31 - 3.24 (m, 4H), 3.09 (t, 2H, J = 6.2 Hz), 2.89 - 2.75 (m, 4H), 2.60 (s, 3H), 2.11 - 2.08 (m, 2H); HRMS(ESI): Calc'd for (C3iH38N2Oio+H)+ 599.2599, found 599.2567.
Figure imgf000215_0001
[00520] Sodium cyanoborohydride (1.43 mg, 0.023 mmol, 4.0 equiv) was added in one portion to a solution of 2,2,2-trifluoro-N-methylethan- 1 -amine (12.84 mg, 0.114 mmol, 20 equiv) in 0.1 mL methanol-acetic acid (methanol: acetic acid = 9: 1) at 0 °C. A solution of aldehyde 15 (3 mg, 5.68 μιηοΐ, 1.0 equiv) in 0.3 mL methanol- acetic acid (methanol: acetic acid = 9: 1) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction was warmed to 23 °C. After 40 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The combined organic solutions were dried over sodium sulfate. Drops of formic acid were added to the organic solution before concentration under reduced pressure. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 37 (R02-E1) as a yellow oil (2.5 mg, 70%). 1H NMR (500 MHz, CD3OD) δ 7.48 (s, 1H), 5.22 - 5.21 (m, 1H), 5.00 - 4.98 (m, 1H), 4.65 (s, 1H), 4.14 - 4.12 (m, 2H), 3.78 (s, 3H), 3.56 (s, 3H), 3.40 (s, 3H), 3.34 - 3.31 (m, 2H), 3.07 - 3.05 (m, 2H), 3.01 - 2.94 (m, 2H), 2.82 - 2.71 (m, 4H), 2.57 - 2.55 (m, 6H), 2.09 - 2.05 (m, 2H); HRMS(ESI): Calc'd for (C30H34F3NOi0+H)+ 626.2208, found 626.2215.
Figure imgf000216_0001
(R02-E2)
[00521] Sodium cyanoborohydride (1.43 mg, 0.023 mmol, 4.0 equiv) was added in one portion to a solution of 2-(2-aminoethoxy)ethan-l-ol (11.94 mg, 0.114 mmol, 20 equiv) in 0.1 mL methanol- acetic acid (methanol: acetic acid = 9: 1) at 0 °C. A solution of aldhyede 15 (3 mg, 5.68 μιηοΐ, 1.0 equiv) in 0.3 mL methanol-acetic acid (methanol: acetic acid = 9: 1) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction was warmed to 23 °C. After 45 min, the solution was diluted with ethyl acetate (20 mL) and washed with brine (20 mL). The aqueous solution was extracted with ethyl acetate (6 x 20 mL). The organic solution was combined and dried over sodium sulfate. Drops of formic acid were added to the organic solution before concentration under reduced pressure. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 38 (R02-E2) as a yellow oil (2.2 mg, 62%). 1H NMR (500 MHz, CD3OD) δ 7.55 (s, 1H), 5.28 (d, 1H, J = 4.1 Hz), 5.05 (d, 1H, J = 4.1 Hz), 4.65 (s, 1H), 4.35 - 4.28 (m, 2H), 3.81 - 3.76 (m, 5H), 3.69 - 3.66 (m, 2H), 3.57 - 3.61 (m, 2H), 3.55 (s, 3H), 3.45 - 3.41 (m, 5H), 3.39 - 3.36 (m, 2H), 3.09 - 3.07 (m, 2H), 2.90 (d, 1H, = 5.4 Hz), 2.80 (d, 1H, = 5.4 Hz), 2.75 (t, 2H, = 6.4 Hz), 2.59 (s, 3H), 2.11 - 2.06 (m, 2H); HRMS(ESI): Calc'd for (C3iH39NOi2+H)+ 618.2545, found 618.2574.
Figure imgf000217_0001
39
(R02-E3)
[00522] Sodium cyanoborohydride (1.43 mg, 0.023 mmol, 4.0 equiv) was added in one portion to a solution of 1-methylpiperazine (11.37 mg, 0.114 mmol, 20 equiv) in 0.1 mL methanol-acetic acid (methanol: acetic acid = 9: 1) at 0 °C. A solution of aldehyde 15 (3 mg, 5.68 μιηοΐ, 1.0 equiv) in 0.3 mL methanol-acetic acid (methanohacetic acid = 9: 1) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction was warmed to 23 °C. After 45 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (5 mL). The aqueous solution was extracted with ethyl acetate (6 x 5 mL). The combined organic solutions were dried over sodium sulfate. Drops of formic acid were added to the organic solution before concentration under reduced pressure. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide 39 (R02-E3) as a yellow oil (2.2 mg, 64%). 1H NMR (600 MHz, CD3OD) δ 7.52 (s, 1H), 5.25 (d, 1H, = 4.2 Hz), 5.03 (d, 1H, = 4.2 Hz), 4.64 (s, 1H), 4.25 - 4.20 (m, 2H), 3.79 (s, 3H), 3.55 (s, 3H), 3.41 (s, 3H), 3.16 - 3.00 (m, 12H), 2.85 (d, 1H, = 5.6 Hz), 2.75 - 2.73 (m, 6H), 2.58 (s, 3H), 2.10 - 2.06 (m, 2H); HRMS(ESI): Calc'd for (C32H4oN2Oio+H)+ 613.2756, found 613.2738.
Figure imgf000218_0001
40
(R02-E4)
[00523] Sodium cyanoborohydride (1.43 mg, 0.023 mmol, 4.0 equiv) was added in one portion to a solution of thiomorpholine 1, 1-dioxide (15.35 mg, 0.114 mmol, 20 equiv) in 0.1 mL methanol- acetic acid (methanol: acetic acid = 9: 1) at 0 °C. A solution of aldehyde 15 (3 mg, 5.68 μιηοΐ, 1.0 equiv) in 0.3 mL methanol-acetic acid (methanol: acetic acid = 9: 1) was added slowly via syringe to the reaction. After being stirred for 10 min, the reaction was warmed to 23 °C. After 40 min, the solution was diluted with ethyl acetate (10 mL) and washed with brine (10 mL). The aqueous solution was extracted with ethyl acetate (6 x 10 mL). The combined organic solutions were dried over sodium sulfate. Drops of formic acid were added to the organic solution before concentration under reduced pressure. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide 40 (R02-E4) as a yellow oil (1.9 mg, 51%). 1H NMR (600 MHz, CD3OD) δ 7.50 (s, 1H), 5.23 (d, 1H, J = 4.1 Hz), 5.00 (d, 1H, J = 4.1 Hz), 4.65 (s, 1H), 4.16 - 4.14 (m, 2H), 3.79 (s, 3H), 3.56 (s, 3H), 3.41 (s, 3H), 3.21 - 3.20 (m, 4H), 3.13 - 3.11 (m, 4H), 3.07 - 3.04 (m, 2H), 2.98 - 2.91 (m, 2 H), 2.81 (d, 1Η, = 5.8 Hz), 2.75 - 2.71 (m, 3H), 2.57 (s, 3H), 2.09 - 2.05 (m, 2H); HRMS(ESI): Calc'd for (C3iH37NOi2S+H)+ 648.2109, found 648.2134.
Figure imgf000218_0002
R01 -D1
[00524] A flame-dried 25-mL flask was charged with 2-morpholinoethan- l-ol (0.312 mL, 2.056 mmol, 1 equiv) and anhydrous dichloromethane (4.1 mL). 2,6-ditert-butyl-4- methylpyridine (0.422 g, 2.056 mmol, 1 equiv) was added and the clear, brown solution was cooled to 0 °C in an ice-water bath. Trifluoromethanesulfonic anhydride (0.347 niL, 2.056 mmol, 1 equiv) was added dropwise. After 10 min, the cooling bath was removed and the mixture was allowed to warm slowly to 23 °C. After 30 min, the mixture was filtered through a cotton plug in a pipette. The filtrate was used directly in the next reaction.
[00525] An oven-dried 20-mL vial was charged with dideoxy-DC-45-A2 (1) (100 mg, 0.206 mmol, 1 equiv) and the residue was dried by sublimation of benzene under high vacuum. 4 A molecular sieves and proton-sponge (485 mg, 2.261 mmol, 11 equiv) were added to the vial. 2-morpholinoethyl trifluoromethanesulfonate (2.056 mmol, 10 equiv) was added as a solution in anhydrous dichloromethane (4.1 mL) and the mixture was stirred at 23 °C under argon for 24 h. The reaction mixture was diluted with dichloromethane (25 mL) and methanol (0.5 mL), stirring for 20 min to quench any unreacted alkyl triflate. The mixture was washed saturated sodium bicarbonate solution (40 mL), and the aqueous layer was extracted with dichloromethane (3 x 25 mL). The combined organic layers were dried over sodium sulfate. The dried solution was filtered, and the filtrate was concentrated. The residue was purified first by flash column chromatography on silica gel deactivated with
triethylamine (25%→80% ethyl acetate-hexanes to recover starting material, then 0%→15% methanol-dichloromethane). The material was further purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→40% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide R01-D1 as a yellow powder after lyophilization (43.5 mg, 35%). TLC (5% methanol-dichloromethane): Rf = 0.38 (UV); 1H NMR (600 MHz, CDC13) δ 14.89 (s, 1H), 8.34 (s, 1H), 7.44 (s, 1H), 5.20 (d, 7 = 4.2 Hz, 1H), 4.84 (d, 7 = 4.1 Hz, 1H), 4.71 (s, 1H), 4.30 (h, 7 = 6.5 Hz, 2H), 3.86 (t, 7 = 4.7 Hz, 4H), 3.77 (s, 3H), 3.61 (s, 3H), 3.44 (s, 3H), 3.18 - 3.06 (m, 2H), 3.07 - 2.96 (m, 6H), 2.88 (d, 7 = 5.7 Hz, 1H), 2.81 (d, 7 = 5.7 Hz, 1H), 2.73 (t, 7 = 6.4 Hz, 2H), 2.58 (s, 3H), 2.09 (p, 7 = 6.4 Hz, 2H); 13C NMR (125 MHz, CDC13) δ 204.76, 162.77, 151.05, 142.67, 141.93, 135.36, 130.49, 116.06, 113.63, 113.26, 111.27, 104.53, 102.12, 100.00, 72.19, 69.28, 69.04, 65.48, 61.17, 61.05, 57.16, 56.99, 56.85, 52.72, 48.31, 38.92, 23.70, 22.21, 20.50; FTIR (neat), cm"1: 3372 (br w), 2951 (m), 2850 (w), 1620 (s), 1388 (s), 1116 (s), 1093 (s), 982 (m), 764 (m); HRMS (ESI): Calc'd for (C3iH37NOi0 + H)+ 600.2439, found 600.2432. Synthesis of Linking Groups and Trioxacarcin-linker species
Figure imgf000220_0001
Val-Cit-PABOH MDpr(Boc)-Val-Cit-PABOH
[00526] A flame-dried 10-mL flask was charged with Val-Cit-PABOH (49.8 mg, 0.131 mmol, 1 equiv) and MDpr(Boc)-OSu (50 mg, 0.393 mmol, 1 equiv). Dimethylformamide (0.66 mL) and N,N-diisopropylethylamine (68.5
Figure imgf000220_0002
0.939 mmol, 3 equiv) were then added. The reaction mixture was stirred at 23 °C under argon for 22 h. The reaction was diluted with DMSO (0.5 mL), filtered through a 0.2 μιη syringe filter, and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 254 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide MDpr(Boc)-Val-Cit-PABOH as a white solid (32.3 mg, 38%). TLC (15% methanol-dichloromethane): Rf = 0.31 (UV, KMn04); 1H NMR (500 MHz, CD3OD) δ 8.09 (d, = 7.5 Hz, 1H), 7.58 (d, = 8.5 Hz, 2H), 7.54 (d, = 8.5 Hz, 1H), 7.30 (d, = 8.7 Hz, 2H), 6.87 (s, 2H), 6.70 (br t, = 6.7 Hz, 1H), 4.84 - 4.78 (m, 1H), 4.55 (s, 2H), 4.49 - 4.43 (m, 1H), 4.18 (d, = 7.3 Hz, 1H), 3.72 - 3.63 (m, 2H), 3.17 (ddt, = 35.8, 13.4, 6.8 Hz, 2H), 2.10 (dq, = 13.5, 6.7 Hz, 1H), 1.99 - 1.89 (m, 1H), 1.85 - 1.76 (m, 1H), 1.65 - 1.54 (m, 2H), 1.38 (s, 9H), 0.98 - 0.94 (m, 6H); HRMS (ESI): Calc'd for (C3oH43N709 + Na)+: 668.3014, found: 668.3033.
Figure imgf000220_0003
MDpr(Boc)-Val-Cit-PABOH MDpr(Boc)-Val-Cit-PABO(CO)pNP
[00527] To a solution of MDpr(Boc)-Val-Cit-PABOH (13.2 mg, 0.02 mmol, 1 equiv) in anhydrous dimethylformamide (0.17 mL) was added bis(4-nitrophenyl) carbonate (12.44 mg, 0.041 mmol, 2 equiv), and N,N-diisopropylethylamine (8.9
Figure imgf000220_0004
0.951 mmol, 2.5 equiv). The reaction mixture was stirred at 23 °C under argon for 15 h, at which time additional bis(4- nitrophenyl) carbonate (6.22 mg, 0.021 mmol, 1 equiv) was added. After further stirring for 4 h, the reaction mixture was diluted with dimethylformamide (800 μί) and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 254 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide MDpr(Boc)-Val-Cit-PABO-pNP as a white solid (13.2 mg, 80%). TLC (15% methanol-dichloromethane): Rf = 0.45 (UV, KMn04); HRMS (ESI):
Calc'd for (C37H46N8Oi3 + H)+: 811.3257, found: 811.3246.
Figure imgf000221_0001
Mal-PEG2-Val-Cit-PABOH 41
[00528] Mal-PEG2-Val-Cit-PABOH (0.217 g, 0.367 mmol, 1.0 equiv) was dissolved in dimethylformamide (1.8 mL) in a dry vial and cooled to 0 °C. Thionyl dichloride (0.029 mL, 0.404 mmol, 1.1 equiv) was added to the reaction dropwise via syringe. The reaction was held at 0 °C for 30 min and then treated slowly with water (4.5 mL). The reaction mixture was extracted with ethyl acetate (20 mL). The organic solution was dried over sodium sulfate and concentrated. The residue was purified by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 41 as a yellow solid (0.1 g, 45%). 1H NMR (600 MHz, ((CD3)2SO) δ: 10.05 (s, 1H), 8.06 (d, 1H, = 7.4 Hz), 7.58 (d, 2H, = 7.7 Hz), 7.34 (d, 2H, = 7.7 Hz), 7.15 (d, 1H, = 7.4 Hz), 7.00 (s, 2H), 5.96 (br, 1H), 5.79 (br, 2H), 4.70 (s, 2H), 4.44 - 4.36 (m, 1H), 4.01 - 3.96 (m, 2H), 3.88 - 3.86 (m, 1H), 3.56 - 3.50 (m, 6H), 3.02 - 2.90 (m, 2H), 1.97 - 1.93 (m, 1H), 1.68 - 1.57 (m, 2H), 1.48 - 1.38 (m, 2H), 0.86 - 0.81 (m, 6H); HRMS (ESI): Calc'd for (C27H37C1N608+Na)+ 631.2254, found 631.2257.
Figure imgf000221_0002
Mal-PEG4-Val-Cit-PABOH [00529] Mal-PEG4-Val-Cit-PABOH (0.21 g, 0.309 mmol, 1.0 equiv) was dissolved in dimethylformamide (1.5 mL) in a dry vial and cooled to 0 °C. Thionyl dichloride (0.025 mL, 0.340 mmol, 1.1 equiv) was added to the reaction dropwise via syringe. The reaction was held at 0 °C for 60 min and then concentrated directly. The residue was purified by flash column chromatography (0%→25% methanol-dichloromethane) to provide 42 as a yellow oil (0.17 g, 79%). 1H NMR (500 MHz, ((CD3)2SO) δ: 10.10 (s, 1H), 8.08 (d, 1H, J = 7.3 Hz), 7.60 (d, 2H, = 8.0 Hz), 7.34 (d, 2H, = 7.9 Hz), 7.25 (d, 1H, = 8.6 Hz), 7.02 (s, 2H), 4.71 (s, 2H), 4.43 - 4.40 (m, 1H), 4.07 - 3.87 (m, 4H), 3.59 - 3.41 (m, 16H), 3.08 - 2.96 (m, 2H), 1.97 - 1.93 (m, 1H), 1.68 - 1.58 (m, 2H), 1.48 - 1.36 (m, 2H), 0.85 - 0.81 (m, 6H); HRMS (ESI): Calc'd for (C3iH45ClN6Oi0+Na)+ 719.2778, found 719.2777.
Figure imgf000222_0001
Mal-Cap-Val-Cit-PABO-pNP
[00530] To a solution of Mal-Cap-Val-Cit-PABO-pNP (9.61 mg, 0.013 mmol, 3 equiv) in anhydrous dimethylformamide (72 μί) was added N,N-diisopropylethylamine (7.6 μί, 0.043 mmol, 10 equiv). Alkyl amine 4 (2.3 mg, 4.3 μιηοΐ, 1 equiv) was then added dropwise as a solution in anhydrous dimethylformamide (72 μΐ^). The reaction mixture was stirred at 23 °C under argon for 30 min. The reaction mixture was diluted with dimethylformamide (800 uL) and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide 43 (R02-B5) as a pale yellow solid (3.4 mg, 67%). 1H NMR (600 MHz, CD3OD) δ 7.51 (s, 1H), 7.47 (d, = 8.2 Hz, 2H), 7.19 (d, = 8.1 Hz, 2H), 6.77 (s, 2H), 5.22 (d, = 4.1 Hz, 1H), 5.04 - 5.00 (m, 2H), 4.94 (d, = 4.1 Hz, 1H), 4.65 (s, 1H), 4.49 (dd, = 9.1, 5.1 Hz, 1H), 4.09 - 4.04 (m, 2H), 3.79 (s, 3H), 3.56 (s, 3H), 3.45 (t, = 7.1 Hz, 2H), 3.43 - 3.41 (m, 2H), 3.40 (s, 3H), 3.24 - 3.17 (m, 1H), 3.14 - 3.07 (m, 1H), 3.06 - 3.02 (m, 2H), 2.82 (d, = 5.8 Hz, 1H), 2.74 (d, = 5.8 Hz, 1H), 2.71 - 2.64 (m, 2H), 2.58 (s, 3H), 2.27 (t, = 7.4 Hz, 2H), 2.11 - 2.06 (m, 1H), 2.06 - 2.00 (m, 2H), 1.93 - 1.85 (m, 1H), 1.79 - 1.71 (m, 1H), 1.63 (p, J = 7.5 Hz, 2H), 1.59 - 1.52 (m, 4H), 1.34 - 1.26 (m, 2H), 0.97 (app t, / = 6.4 Hz, 6H); HRMS (ESI): Calc'd for
(C56H69N7O18 + H)+: 1128.4777, found: 1128.4668.
Figure imgf000223_0001
Mal-Cap-Val-Cit-PABO-pNP
[00531] To a solution of Mal-Cap-Val-Cit-PABO-pNP (12.22 mg, 0.017 mmol, 3.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (9.64 μί, 0.055 mmol, 10 equiv) at 23 °C. Amine 16 (3 mg, 5.52 μιηοΐ, 1.0 equiv) in dry dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 44 (R02-B4) as yellow solid (4 mg, 64%). 1H NMR (600 MHz, CD3OD) δ: 7.52-7.24 (m, 8H), 6.78 (s, 2H), 5.20 - 4.78 (m, 7H), 4.63 (s, 1H), 4.48 - 4.46 (m, 1H), 4.19 - 4.17 (m, 1H), 4.10 - 4.08 (m, 2H), 3.80 (s, 3H), 3.58 (s, 3H), 3.45 - 3.44 (m, 2H), 3.40 (s, 3H), 3.23 - 3.18 (m, 2H), 3.10 - 3.04 (m, 6H), 2.81 - 2.62 (m, 5H), 2.58 (s, 3H), 2.26 - 2.24 (m, 2H), 2.09 - 2.05 (m, 2H), 1.90 - 1.53 (m, 11H), 0.95 - 0.93 (m, 6H); HRMS (ESI): Calc'd for (C57H7iN70i8+Na)+ 1164.4748, found 1164.4851.
Figure imgf000224_0001
Mal-Cap-Val-Cit-PABO-pNP '
[00532] To a solution of Mal-Cap-Val-Cit-PABO-pNP (42.3 mg, 0.057 mmol, 3 equiv) in anhydrous dimethylformamide (319 μί) was added N,N-diisopropylethylamine (33.4 μί, 0.191 mmol, 10 equiv). Alkyl amine 7 (R02-A2) (10.4 mg, 0.019 mmol, 1 equiv) was then added dropwise as a solution in anhydrous dimethylformamide (319 μί). The reaction mixture was stirred at 23 °C under argon for 45 min. The reaction mixture was diluted with dimethylformamide to a total of 900 uL and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1 % formic acid, flow rate: 15 mL/min) to provide 45 (R02-A4) as a yellow solid (8.1 mg, 37%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): Rf = 0.57 (UV); 1H NMR (600 MHz, CD3OD) δ 8.22 (d, J = 7.6 Hz, 1H), 7.96 (d, J = 7.8 Hz, 1H), 7.50 - 7.47 (m, 3H), 7.19 (d, / =
8.2 Hz, 2H), 6.77 (s, 2H), 5.21 (d, = 4.1 Hz, 1H), 5.00 (d, = 4.0 Hz, 1H), 4.99 - 4.92 (m, 2H), 4.64 (s, 1H), 4.49 (dd, J = 9.1, 5.1 Hz, 1H), 4.17 - 4.15 (m, 1H), 4.06 - 4.01 (m, 2H), 3.78 (s, 3H), 3.55 (s, 3H), 3.45 (t, J = 7.1 Hz, 2H), 3.39 (s, 3H), 3.38 - 3.32 (m, 2H), 3.23 - 3.17 (m, 1H), 3.13 - 3.07 (m, 1H), 3.05 - 2.99 (m, 2H), 2.78 (d, 7 = 5.8 Hz, 1H), 2.71 (d, = 5.8 Hz, 1H), 2.69 - 2.63 (m, 2H), 2.56 (s, 3H), 2.26 (t, = 7.4 Hz, 2H), 2.10 - 2.05 (m, 1H),
2.03 - 1.99 (m, 2H), 1.90 - 1.85 (m, 3H), 1.78 - 1.70 (m, 1H), 1.62 (p, 7 = 7.5 Hz, 2H), 1.59 - 1.52 (m, 4H), 1.32 - 1.25 (m, 2H), 0.96 (app t, J = 6.3 Hz, 6H); HRMS (ESI): Calc'd for (C57H71N7O18 + Na)+: 1164.4748, found: 1164.4704.
Figure imgf000225_0001
Mal-Cap-Val-Cit-PABO-pNP
[00533] To a solution of Mal-Cap-Val-Cit-PABO-pNP (39.7 mg, 0.054 mmol, 3.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (31.3 μί, 0.179 mmol, 10 equiv) at 23 °C. Amine 19 (10 mg, 0.018 mmol, 1.0 equiv) in dry
dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 46 (R02-A6) as a yellow solid (7.2 mg, 35%). 1H NMR (600 MHz, CD3OD) δ: 7.59- 7.21 (m, 8H), 6.78 (s, 2H), 5.20 - 4.63 (m, 8H), 4.50 - 4.48 (m, 1H), 4.20 - 4.18 (m, 1H), 4.05 - 3.94 (m, 2H), 3.78 (s, 3H), 3.58 (s, 3H), 3.43 - 3.42 (m, 2H), 3.39 (s, 3H), 3.23 - 3.05 (m, 2H), 3.06 - 2.94 (m, 6H), 2.78 - 2.64 (m, 5H), 2.56 (s, 3H), 2.26 - 2.24 (m, 2H), 2.07 - 2.05 (m, 2H), 1.95 - 1.51 (m, 13H), 0.96 - 0.94 (m, 6H); HRMS ESI): Calc'd for
(C58H73N7Oi8+Na)+ 1178.4904, found 1178.4992.
Figure imgf000225_0002
[00534] To a solution of Mal-Cap-Val-Cit-PABO-pNP (50.8 mg, 0.069 mmol, 3 equiv) in anhydrous dimethylformamide (383 μί) was added N,N-diisopropylethylamine (40.1 μί, 0.230 mmol, 10 equiv). Alkyl amine 10 (R02-A1) (12.8 mg, 0.023 mmol, 1 equiv) was then added dropwise as a solution in anhydrous dimethylformamide (383 μί). The reaction mixture was stirred at 23 °C under argon for 45 min. The reaction mixture was diluted with dimethylformamide to a total of 900 uL and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid, flow rate: 15 mL/min) to provide 47 (R02-A3) as a yellow solid (12.4 mg, 47%). TLC (15% methanol- dichloromethane + 2% 30% aqueous ammonium hydroxide solution): Rf = 0.59 (UV); 1H NMR (600 MHz, CD3OD) δ 8.23 (d, = 7.6 Hz, 1H), 7.96 (d, = 7.9 Hz, 1H), 7.54 (d, = 8.3 Hz, 2H), 7.46 (d, = 1.1 Hz, 1H), 7.26 (d, = 8.5 Hz, 2H), 6.77 (s, 2H), 5.20 (d, = 4.1 Hz, 1H), 5.00 - 4.97 (m, 3H), 4.65 (s, 1H), 4.52 - 4.47 (m, 1H), 4.19 - 4.14 (m, 1H), 4.02 - 3.93 (m, 2H), 3.78 (s, 3H), 3.56 (s, 3H), 3.45 (t, = 7.1 Hz, 2H), 3.39 (s, 3H), 3.25 - 3.18 (m, 3H), 3.10 (dt, = 13.4, 6.6 Hz, 1H), 3.06 - 3.01 (m, 2H), 2.78 (d, = 5.8 Hz, 1H), 2.73 - 2.68 (m, 3H), 2.56 (s, 3H), 2.26 (t, = 7.4 Hz, 2H), 2.10 - 2.04 (m, 3H), 1.93 - 1.86 (m, 1H), 1.77 - 1.71 (m, 3H), 1.70 - 1.65 (m, 2H), 1.65 - 1.59 (m, 2H), 1.60 - 1.50 (m, 2H), 1.39 - 1.35 (m, 2H), 1.33 - 1.25 (m, 2H), 0.96 (app t, = 6.5 Hz, 6H); HRMS (ESI): Calc'd for (C58H73N7Oi8 + Na)+: 1178.4904, found: 1178.4875.
Figure imgf000226_0001
[00535] To a solution of Mal-Cap-Val-Cit-PABO-pNP (11.6 mg, 0.016 mmol, 3.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (9.17 μί, 0.052 mmol, 10 equiv) at 23 °C. Amine 22 (3 mg, 5.25 μιηοΐ, 1.0 equiv) in dry dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 48 (R02-A8) as a yellow solid (3.5 mg, 57%). 1H NMR (600 MHz, CD3OD) δ: 7.95 (br, 1H), 7.59 - 7.18 (m, 7H), 6.78 (s, 2H), 5.20 - 4.93 (m, 7H), 4.64 (s, 1H), 4.48 - 4.46 (m, 1H), 4.19 - 4.16 (m, 1H), 4.00-3.94 (m, 2H), 3.78 (s, 3H), 3.56 (s, 3H), 3.45 - 3.44 (m, 2H), 3.38 (s, 3H), 3.23 - 3.08 (m, 2H), 3.06 - 3.04 (m, 2H), 2.92 - 2.90 (m, 4H), 2.77 - 2.71 (m, 5H), 2.56 (s, 3H), 2.26 - 2.24 (m, 2H), 2.07 - 2.05 (m, 2H), 1.90 - 1.89 (m, 1H), 1.74 - 1.29 (m, 14H), 0.95 - 0.92 (m, 6H); HRMS (ESI): Calc'd for (C59H75N7Oi8+Na)+ 1192.5061, found 1192.5151.
Figure imgf000227_0001
Mal-Cap-Val-Cit-PABO-pNP 49
[00536] To a solution of Mal-Cap-Val-Cit-PABO-pNP (14.0 mg, 0.019 mmol, 3 equiv) in anhydrous dimethylformamide (105 μί) was added N,N-diisopropylethylamine (11.0 μί, 0.063 mmol, 10 equiv). Alkyl amine 13 (R02-A10) (3.6 mg, 6.30 μιηοΐ, 1 equiv) was then added dropwise as a solution in anhydrous dimethylformamide (105 μί). The reaction mixture was stirred at 23 °C under argon for 20 min. The reaction mixture was diluted with dimethylformamide to a total of 900 uL and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1 % formic acid, flow rate: 15 mL/min) to provide 49 as a yellow solid (3.4 mg, 46%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): Rf = 0.60 (UV); 1H NMR (600 MHz, CD3OD) δ 8.52 (s, 1H), 7.55 (d, = 8.3 Hz, 2H), 7.48 (s, 1H), 7.28 (d, = 8.2 Hz, 2H), 6.78 (s, 2H), 5.21 (d, = 4.2 Hz, 1H), 4.99 (s, 2H), 4.98 (d, = 4.1 Hz, 1H), 4.81 (d, = 5.6 Hz, 2H), 4.66 (s, 1H), 4.49 (dd, = 9.0, 5.1 Hz, 1H), 4.15 (d, = 7.4 Hz, 1H), 4.00 - 3.94 (m, 2H), 3.78 (s, 3H), 3.56 (s, 3H), 3.46 (t, = 7.1 Hz, 2H), 3.40 (s, 3H), 3.22 - 3.17 (m, 1H), 3.15 (t, = 6.7 Hz, 2H), 3.13 - 3.07 (m, 1H), 3.07 - 3.03 (m, 2H), 2.80 (d, = 5.8 Hz, 1H), 2.74 - 2.70 (m, 3H), 2.57 (s, 3H), 2.26 (t, = 7.4 Hz, 2H), 2.10 - 2.03 (m, 3H), 1.93 - 1.86 (m, 1H), 1.76 - 1.70 (m, 2H), 1.66 - 1.53 (m, 10H), 1.53 - 1.46 (m, 2H), 1.32 - 1.26 (m, 2H), 0.96 (app t, / = 6.5 Hz, 6H); HRMS (ESI): Calc'd for (C59H75N7O18 + Na)+: 1192.5061, found: 1192.5012.
Figure imgf000228_0001
Mal-Cap-Val-Cit-PABO-pNP 50
[00537] To a solution of Mal-Cap-Val-Cit-PABO-pNP (6.30 mg, 8.54 μηιοΐ, 5.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (2.98 μί, 0.017 mmol, 10 equiv) at 23 °C. Amine 26 (1 mg, 1.708 μιηοΐ, 1.0 equiv) in dry
dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 50 as a yellow solid (1.5 mg, 74%). 1H NMR (600 MHz, CD3OD) δ: 8.53 (s, 1H), 7.56 - 7.18 (m, 7H), 6.77 (s, 2H), 5.22 - 4.85 (m, 7H), 4.65 (s, 1H), 4.48 - 4.47 (m, 1H), 4.15 (d, 1H, 7.5 Hz), 4.02 - 3.94 (m, 2H), 3.78 (s, 3H), 3.56 (s, 3H), 3.45 (t, 2H, = 7.1 Hz), 3.40 (s, 3H), 3.20 - 3.08 (m, 2H), 3.06 - 3.04 (m, 2H), 2.92 - 2.89 (m, 4H), 2.80 - 2.71 (m, 5H), 2.59 (s, 3H), 2.26 - 2.24 (m, 2H), 2.12 - 2.07 (m, 2H), 1.90 - 1.89 (m, 1H), 1.74 - 1.43 (m, 16H), 0.95 - 0.91 (m, 6H); HRMS (ESI): Calc'd for (C6oH77N7Oi8+Na)+ 1206.5217, found 1206.5284.
Figure imgf000229_0001
Mal-PEG2-Val-Cit-PABO-pNP
[00538] To a solution of Mal-PEG2-Val-Cit-PABO-pNP (8.6 mg, 0.011 mmol, 3.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (6.60 μΐ, 0.038 mmol, 10 equiv) at 23 °C. Amine 4 (R02-A9) (2 mg, 3.78 μιηοΐ, 1.0 equiv) in dry
dimethylformamide (200 μί) was added dropwise to the solution and stirred for 1 h. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 51 (R02-C8) as yellow film (2.3 mg, 53%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.52 (UV); 1H NMR (600 MHz, CD3OD) δ 8.53 (s, 1H), 7.72 (dt, = 6.6, 3.3 Hz, 1H), 7.65 - 7.58 (m, 1H), 7.50 (s, 1H), 7.48 (d, = 8.3 Hz, 2H), 7.19 (d, = 8.1 Hz, 2H), 6.93 - 6.88 (m, 1H), 6.78 (s, 2H), 5.21 (d, = 4.1 Hz, 1H), 5.02 (s, 2H), 4.93 (d, = 4.1 Hz, 1H), 4.64 (s, 1H), 4.51 (dd, = 9.2, 5.0 Hz, 1H), 4.18 - 4.03 (m, 4H), 3.95 (d, = 6.5 Hz, 1H), 3.79 (s, 3H), 3.67 - 3.57 (m, 6H), 3.56 (s, 3H), 3.45 - 3.41 (m, 2H), 3.40 (s, 3H), 3.24 - 3.16 (m, 1H), 3.11 (dt, / = 13.5, 6.7 Hz, 1H), 3.06 - 3.00 (m, 2H), 2.81 (d, = 5.8 Hz, 1H), 2.73 (d, = 5.7 Hz, 1H), 2.71 - 2.66 (m, 2H), 2.57 (s, 3H), 2.10 (dq, = 13.5, 6.8 Hz, 1H), 2.06 - 2.01 (m, 2H), 1.97 - 1.89 (m, 1H), 1.79 - 1.70 (m, 1H), 1.65 - 1.52 (m, 2H), 0.99 (d, = 6.8 Hz, 3H), 0.96 (d, = 6.8 Hz, 3H); HRMS (ESI): Calc'd for (CSSHCTNTC^O + H)+ 1146.4514, found 1146.4525.
Figure imgf000230_0001
Mal-PEG2-Val-Cit-PABO-pNP
[00539] To a solution of Mal-PEG2-Val-Cit-PABO-pNP (8.3 mg, 0.011 mmol, 3.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (6.43 μί, 0.037 mmol, 10 equiv) at 23 °C. Amine 16 (2 mg, 3.68 μιηοΐ, 1.0 equiv) in dry dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 52 (R02-B10) as a yellow solid (2.7 mg, 63%). 1H NMR (600 MHz, CD3OD) δ: 7.52 - 7.28 (m, 8H), 6.76 (s, 2H), 5.23 - 4.57 (m, 8H), 4.52 - 4.48 (m, 1H), 4.16 - 4.07 (m, 2H), 3.94 (d, 1H, = 6.3 Hz), 3.80 (s, 3H), 3.62 - 2.58 (m, 8H), 3.56 (s, 3H), 3.40 (s, 3H), 3.20 - 3.18 (m, 2H), 3.10 - 3.03 (m, 6H), 2.80 - 2.62 (m, 5H), 2.57 (s, 3H), 2.10 - 2.04 (m, 2H), 1.95 - 1.53 (m, 5H), 0.95 - 0.90 (m, 6H); HRMS (ESI): Calc'd for (C56H69N702o+Na)+ 1182.4490, found 1182.4817.
Figure imgf000230_0002
Mal-PEG4-Val-Cit-PABO-pNP
[00540] To a solution of Mal-PEG4-Val-Cit-PABO-pNP (14.3 mg, 0.017 mmol, 3.0 equiv) in dry dimethylformamide (300 μί) was added N,N-diisopropylethylamine (9.90 μΐ, 0.057 mmol, 10 equiv) at 23 °C. Amine 4 (R02-A9) (3 mg, 5.67 μιηοΐ, 1.0 equiv) in dry dimethylformamide (300 μί) was added dropwise to the solution and stirred for 45 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 53 (R02-C9) as yellow film (5.1 mg, 73%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.47 (UV); 1H NMR (600 MHz, CD3OD) δ 8.46 (s, 2H), 7.50 (s, 1H), 7.48 (d, 7 = 8.3 Hz, 2H), 7.19 (d, 7 = 8.1 Hz, 2H), 6.90 (t, 7 = 5.3 Hz, 1H), 6.79 (s, 2H), 5.21 (d, 7 = 4.2 Hz, 1H), 5.02 (s, 2H), 4.94 (d, 7 = 4.3 Hz, 1H), 4.64 (s, 1H), 4.51 (dd, 7 = 9.1, 5.1 Hz, 1H), 4.23 - 4.14 (m, 2H), 4.07 - 4.04 (m, 2H), 3.96 (d, 7 = 6.6 Hz, 1H), 3.79 (s, 3H), 3.68 - 3.57 (m, 9H), 3.56 (s, 3H), 3.57 - 3.53 (m, 5H), 3.43 - 3.40 (m, 2H), 3.40 (s, 3H), 3.23 - 3.17 (m, 1H), 3.11 (dt, 7 = 13.4, 6.6 Hz, 1H), 3.05 - 3.01 (m, 2H), 2.81 (d, 7 = 5.7 Hz, 1H), 2.73 (d, 7 = 5.7 Hz, 1H), 2.71 - 2.65 (m, 2H), 2.57 (s, 3H), 2.10 (dq, 7 = 15.6, 8.4, 7.6 Hz, 1H), 2.06 - 2.00 (m, 2H), 1.94 - 1.88 (m, 1H), 1.75 (dtd, 7 = 14.0, 9.4, 4.9 Hz, 1H), 1.64 - 1.52 (m, 2H), 0.99 (d, 7 = 6.8 Hz, 3H), 0.95 (d, 7 = 6.8 Hz, 3H); HRMS (ESI): Calc'd for (C59H75N7O22 + Na)+ 1234.5038, found 1234.5005.
Figure imgf000231_0001
Mal-PEG4-Val-Cit-PABO-pNP
[00541] To a solution of Mal-PEG4-Val-Cit-PABO-pNP (9.31 mg, 0.011 mmol, 3.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (6.43 μί, 0.037 mmol, 10 equiv) at 23 °C. Amine 16 (2 mg, 3.68 μιηοΐ, 1.0 equiv) in dry dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 54 (R02-C1) as yellow solid (2.9 mg, 63%). 1H NMR (600 MHz, CD3OD) δ: 7.52 - 7.27 (m, 8H), 6.78 (s, 2H), 5.23 - 4.64 (m, 7H), 4.52 - 4.48 (m, 1H), 4.18 - 4.14 (m, 2H), 4.08 (s, 1H), 3.96 (d, 1H, 7 = 6.6 Hz), 3.80 (s, 3H), 3.67 - 2.56 (m, 19H), 3.38 (s, 3H), 3.20 - 3.18 (m, 2H), 3.08 - 2.96 (m, 6H), 2.80 - 2.62 (m, 5H), 2.57 (s, 3H), 2.08 - 2.04 (m, 2H), 1.95 - 1.53 (m, 5H), 0.95 - 0.92 (m, 6H); HRMS (ESI): Calc'd for (C6oH77N7022+Na)+ 1270.5014, found 1270.4878.
Figure imgf000232_0001
[00542] To a solution of Mal-PEG8-Val-Cit-PABO-pNP (10.8 mg, 9.63 μιηοΐ, 1.7 equiv) in dry dimethylformamide (300 μί) was added N,N-diisopropylethylamine (9.90 μΐ, 0.057 mmol, 10 equiv) at 23 °C. Amine 4 (R02-A9) (3 mg, 5.67 μιηοΐ, 1.0 equiv) in dry
dimethylformamide (300 μί) was added dropwise to the solution and stirred for 45 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 55 (R02-C10) as yellow film (6.0 mg, 70%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.32 (UV); 1H NMR (600 MHz, CD3OD) δ 8.36 (s, 1H), 8.07 (br s, 1H), 8.01 (d, 7 = 7.7 Hz, 1H), 7.50 (d, 7 = 8.5 Hz, 2H), 7.49 (s, 1H), 7.21 (d, 7 = 8.7 Hz, 2H), 6.90 (t, 7 = 5.4 Hz, 1H), 6.80 (s, 2H), 5.21 (d, 7 = 4.1 Hz, 1H), 5.02 (s, 2H), 4.95 (d, 7 = 4.1 Hz, 1H), 4.64 (s, 1H), 4.50 (dd, 7 = 9.2, 5.0 Hz, 1H), 4.21 (d, 7 = 6.9 Hz, 1H), 4.08 - 4.02 (m, 2H), 3.79 (s, 3H), 3.77 - 3.71 (m, 4H), 3.64 - 3.57 (m, 28H), 3.55 (s, 3H), 3.48 (t, 7 = 5.4 Hz, 2H), 3.44 - 3.40 (m, 2H), 3.39 (s, 3H), 3.29 (t, 7 = 5.4 Hz, 2H), 3.20 (dt, 7 = 13.7, 6.9 Hz, 1H), 3.11 (dt, 7 = 13.4, 6.7 Hz, 1H), 3.05 - 3.01 (m, 2H), 2.81 (d, 7 = 5.7 Hz, 1H), 2.72 (d, 7 = 5.7 Hz, 1H), 2.71 - 2.65 (m, 2H), 2.57 (s, 3H), 2.55 (t, 7 = 6.0 Hz, 2H), 2.45 (t, 7 = 6.9 Hz, 2H), 2.12 (h, 7 = 6.6 Hz, 1H), 2.07 - 2.00 (m, 2H), 1.91 (dq, 7 = 14.0, 6.2 Hz, 1H), 1.74 (dtd, 7 = 14.0, 9.3, 4.9 Hz, 1H), 1.64 - 1.51 (m, 2H), 0.99 (d, 7 = 6.8 Hz, 3H), 0.97 (d, 7 = 6.7 Hz, 3H); HRMS (ESI): Calc'd for
(C72H10oN8027 + Na)+ 1531.6590, found 1531.6557.
Figure imgf000233_0001
[00543] To a solution of Mal-PEG8-Val-Cit-PABO-pNP (7 mg, 6.25 μηιοΐ, 1.7 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (6.43 μί, 0.037 mmol, 10 equiv) at 23 °C. Amine 16 (2 mg, 3.68 μιηοΐ, 1.0 equiv) in dry dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 56 (R02-C3) as yellow solid (3.3 mg, 59%). 1H NMR (600 MHz, CD3OD) δ: 7.54 - 7.27 (m, 8H), 6.79 (s, 2H), 5.23 - 4.57 (m, 8H), 4.48 - 4.44 (m, 1H), 4.22 - 4.18 (m, 1H), 4.08 - 4.06 (m, 2H), 3.96 (d, 1H, J = 6.6 Hz), 3.79 (s, 3H), 3.75 (t, 2 H, J = 7.3 Hz), 3.75 - 3.65 (m, 35H), 3.48 (t, 2H, 7 = 5.4 Hz), 3.39 (s, 3H), 3.22 - 3.18 (m, 2H), 3.14 - 3.06 (m, 6H), 2.80 - 2.62 (m, 5H), 2.57 (s, 3H), 2.56 - 2.53 (m, 2H), 2.45 (t, 2H, J = 4.1 Hz), 2.15 - 2.07 (m, 2H), 1.95 - 1.53 (m, 5H), 0.98 - 0.94 (m, 6H); HRMS (ESI): Calc'd for (C73Hio2N8027+Na)+ 1545.6747, found 1545.6858.
Figure imgf000234_0001
MDpr(Boc)-Val-Cit-PABO-pNP
[00544] To a solution of MDpr(Boc)-Val-Cit-PABO-pNP (9.95 mg, 0.012 mmol, 1.3 equiv) in dry dimethylformamide (300 μί) was added N,N-diisopropylethylamine (8.3 μί, 0.047 mmol, 5.0 equiv) at 23 °C. Amine 4 (R02-A9) (5 mg, 9.44 μιηοΐ, 1.0 equiv) in dry dimethylformamide (300 μί) was added dropwise to the solution and stirred for 1 h. The reaction solution was diluted with methanol to 900 μΐ^ and was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1 % formic acid over 30 min, flow rate: 15 mL/min) to provide 57 as yellow solid (1.7 mg, 76%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.35 (UV); HRMS (ESI): Calc'd for (CSSHTINSOIO + H)+ 1201.4936, found 1201.4892.
Figure imgf000234_0002
[00545] 57 (4.9 mg, 1.646 μιηοΐ) was dissolved in acetonitrile (0.5 mL), transferred to a dry vial and concentrated. To the vial, a solution of trifluoroacetic acid (10% in dichloromethane, 300 μί) was added at -20 °C. The reaction mixture was allowed to warm to 0 °C over 2 h. After stirring for an additional 90 min at 0 °C, 0.5 mL of dimethylformamide was added to the vial and concentrated to remove dichloromethane. The residue was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1 % formic acid over 30 min, flow rate: 15 mL/min) to provide 58 (R02-D1) as yellow solid (2.7 mg, 60%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution):
Figure imgf000235_0001
+ H)+ 1101.4411, found 1101.4387.
Figure imgf000235_0002
MDpr(Boc)-Val-Cit-PABO-PNP
[00546] To a solution of MDpr(Boc)-Val-Cit-PABO-pNP (2.98 mg, 3.68 μιηοΐ, 2.0 equiv) in dry dimethylformamide (200 μί) was added N,N-diisopropylethylamine (1.607 μί, 9.20 μιηοΐ, 5.0 equiv) at 23 °C. Amine 16 (1 mg, 1.840 μιηοΐ, 1.0 equiv) in dry
dimethylformamide (200 μί) was added dropwise to the solution and stirred for 40 min. The reaction solution was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 59 as a yellow solid (1.7 mg, 76 %).
Figure imgf000235_0003
[00547] 59 (2 mg, 1.646 μιηοΐ) was dissolved in dichloromethane (0.5 mL), transferred to a dry vial and concentrated. To the vial, a solution of trifluoroacetic acid (10% in
dichloromethane, 150 μί) was added at 0 °C. After stirring for 70 min at 0 °C, 0.5 mL dimethylformamide was added to the vial and concentrated to remove dichloromethane. The residue was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 30→90% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 60 as a yellow solid (0.7 mg, 38%). HRMS (ESI): Calc'd for (C54H66N8Oi8+H)+ 1115.4568, found 1115.4469.
Figure imgf000236_0001
Mal-Cap-Val-Cit-PABCI
[00548] To a solution of tertiary amine 31 (2 mg, 3.59 μιηοΐ, 1.0 equiv) in
dimethylformamide (100 μΐ) was added Mal-Cap-Val-Cit-PABCI (2.3 mg, 3.95 μιηοΐ, 1.1 equiv) at 23 °C. Tetrabutylammonium iodide (0.397 mg, 1.076 μιηοΐ, 0.3 equiv) and N,N- diisopropylethylamine (1.6 μΐ, 8.97 μιηοΐ, 2.5 equiv) were added in that order. The mixture was stirred until all starting material amine had been consumed (7 h). The mixture was diluted with dimethylformamide (0.5 mL) and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→70% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 61 (R02-B8) as a yellow solid (1.7 mg, 43%). 1H NMR (600 MHz, CD3OD) δ: 7.80 - 7.58 (m, 8H), 6.78 (s, 2H), 5.28 (d, 1H, = 4.3 Hz), 5.09 (d, 1H, = 4.3 Hz), 4.70 - 4.63 (m, 3H), 4.59 - 4.49 (m, 3H), 4.13 (d, 1H, = 7.4 Hz), 3.80 (s, 3H), 7.76 - 3.71 (m, 2H), 3.54 (s, 3H), 3.45 (t, 2H, = 7.2 Hz), 3.41 (s, 3H), 3.22 (s, 3H), 3.18 (s, 3H), 3.13 - 3.08 (m, 4H), 2.90 - 2.80 (m, 2H), 2.75 (t, 2H, = 6.1 Hz), 2.59 (s, 3H), 2.26 - 2.24 (m, 2H), 2.12 - 2.08 (m, 2H), 1.94 - 1.57 (m, 11H), 0.95 - 0.93 (m, 6H); HRMS (ESI):
Calc'd for (C57H74N7Oi6)+ 1112.5187, found 1112.5160.
Figure imgf000237_0001
Mal-PEG2-Val-Cit-PABCI
[00549] To a solution of tertiary amine 31 (2 mg, 3.59 μιηοΐ, 1.0 equiv) in
dimethylformamide (100 μΐ) was added Mal-PEG2-Val-Cit-PABC1 (2.403 mg, 3.95 μιηοΐ, 1.1 equiv) at 23 °C. Tetrabutylammonium iodide (0.397 mg, 1.076 μιηοΐ, 0.3 equiv) and N,N- diisopropylethylamine (1.6 μί, 8.97 μmol, 2.5 equiv) were added in that order. The mixture was stirred until all starting material amine had been consumed (24 h). The mixture was diluted with dimethylformamide (0.5 mL) and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→70% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide 62 as a yellow solid (2.1 mg, 52%). 1H NMR (600 MHz, CD3OD) δ: 7.99
- 7.58 (m, 8H), 6.80 (s, 2H), 5.28 (d, 1H, = 4.2 Hz), 5.09 (d, 1H, = 4.2 Hz), 4.90 - 4.61 (m, 6H), 4.58 - 4.51 (m, 1H), 4.15 - 4.09 (m, 2H), 3.95 (d, 1H, = 6.6 Hz), 3.80 (s, 3H), 3.76
- 3.71 (m, 2H), 3.70 - 3.61 (m, 8H), 3.57 (s, 3H), 3.43 (s, 3H), 3.22 (s, 3H), 3.18 (s, 3H), 3.13 - 3.08 (m, 4H), 2.90 - 2.80 (m, 2H), 2.77 (t, 2H, = 6.1 Hz), 2.60 (s, 3H), 2.16 - 2.08 (m, 2H), 1.98 - 1.57 (m, 5H), 0.95 - 0.93 (m, 6H); HRMS (ESI): Calc'd for (C56H72N7Oi8)+ 1130.4928, found 1130.4955.
Figure imgf000238_0001
Mal-PEG4-Val-Cit-PABCI
[00550] To a solution of tertiary amine 31 (2 mg, 3.59 μιηοΐ, 1.0 equiv) in
dimethylformamide (100 μί) was added Mal-PEG4-Val-Cit-PABC1 (2.75 mg, 3.95 μιηοΐ, 1.1 equiv) at 23 °C. Tetrabutylammonium iodide (0.4 mg, 1.076 μιηοΐ, 0.3 equiv) and N,N- diisopropylethylamine (1.6 μί, 8.97 μmol, 2.5 equiv) were added in that order. The mixture was stirred until all starting material amine was consumed (24 h). The mixture was diluted with dimethylformamide (0.5 mL) and purified directly by preparatory HPLC (Waters Prep- CIS SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→70% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 63 (R02-C2) as a yellow solid (2.5 mg, 57%). 1H NMR (500 MHz, CD3OD) δ: 7.99 - 7.58 (m, 8H), 6.80 (s, 2H), 5.28 (d, 1H, = 4.3 Hz), 5.09 (d, 1H, = 4.3 Hz), 4.90 - 4.61 (m, 6H), 4.58 - 4.53 (m, 1H), 4.22 - 4.19 (m, 2H), 3.98 (d, 1H, = 6.4 Hz), 3.80 (s, 3H), 3.76 - 3.51 (m, 21H), 3.41 (s, 3H), 3.22 (s, 3H), 3.18 (s, 3H), 3.15 - 3.08 (m, 4H), 2.90 - 2.80 (m, 2H), 2.78 - 2.76 (m, 2H), 2.60 (s, 3H), 2.12 - 2.08 (m, 2H), 1.98 - 1.58 (m, 5H), 0.95 - 0.93 (m, 6H); HRMS (ESI): Calc'd for (C6oH8oN702o)+ 1218.5453, found
1218.5426.
Figure imgf000238_0002
64
[00551] To a flame-dried 25 mL flask was added Fmoc-L-lysine (235 mg, 0.638 mmol, 1 equiv) under argon atmosphere. mPEG6-NHS ester (297 mg, 0.638 mmol, 1 equiv) was then added as a solution in anhydrous dichloromethane (12.8 mL), followed by the addition of N,N-diisopropylethylamine (556 μΐ, 3.19 mmol, 5.0 equiv) at 23 °C. After 20 h, the reaction mixture was partitioned between dichloromethane (30 mL) and water (10 mL). The aqueous layer was extracted with dichloromethane (3 x 30 mL). The organic layers were combined and the combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated providing 64 as a clear, colorless oil (425 mg, 93%). The product was taken forward without further purification. TLC (15% methanol- dichloromethane): R = 0.40 (UV, KMn04); 1H NMR (600 MHz, CDC13) δ 7.76 (d, 7 = 7.5 Hz, 2H), 7.63 - 7.59 (m, 2H), 7.40 (t, 7 = 7.3 Hz, 2H), 7.34 - 7.28 (m, 2H), 6.79 (t, 7 = 5.9 Hz, 1H), 5.71 (d, 7 = 7.7 Hz, 1H), 4.40 (d, 7 = 7.1 Hz, 2H), 4.39 - 4.34 (m, 1H), 4.21 (t, 7 = 7.1 Hz, 1H), 3.69 (t, 7 = 5.5 Hz, 2H), 3.66 - 3.58 (m, 22H), 3.56 - 3.52 (m, 2H), 3.37 (s, 3H), 3.29 - 3.23 (m, 2H), 2.46 (t, 7 = 5.5 Hz, 2H), 1.92 - 1.78 (m, 2H), 1.60 - 1.41 (m, 4H);
HRMS (ESI): Calc'd for (C37H54N2Oi2 + H)+ 719.3750, found 719.3757.
Figure imgf000239_0001
[00552] A vial containing Fmoc-(PEG7)-L-Lys 64 (75 mg, 0.104 mmol, 1.0 equiv) was charged with N-hydroxysuccinimide (14.4 mg, 0.125 mmol, 1.2 equiv) and l-ethyl-3-(3- dimethylaminopropyl)carbodiimide (30 mg, 0.157 mmol, 1.5 equiv) under argon atmosphere. The solids were dissolved in anhydrous dichloromethane (1.04 mL) and stirred at 23 °C. After 18 h, the reaction was quenched with water (3 mL). The layers were separated and the aqueous layer was extracted with dichloromethane (3 x 10 mL). The organic layers were combined and the combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated to provide 65 as a clear, colorless oil (70 mg, 83%). 1H NMR (600 MHz, CDC13D δ 7.75 (d, 7 = 7.6 Hz, 2H), 7.61 (t, 7 = 6.7 Hz, 2H), 7.39 (t, 7 = 7.4 Hz, 2H), 7.34 - 7.27 (m, 2H), 6.68 (s, 1H), 6.17 (t, 7 = 6.1 Hz, 1H), 5.90 (d, 7 = 7.8 Hz, 1H), 4.69 - 4.64 (m, 1H), 4.52 - 4.42 (m, 2H), 4.22 (t, 7 = 6.8 Hz, 1H), 3.68 (td, 7 = 6.1, 1.8 Hz, 2H), 3.65 - 3.51 (m, 22H), 3.36 (s, 3H), 3.33 - 3.20 (m, 2H), 2.87 - 2.83 (m, 6H), 2.47 - 2.42 (m, 2H), 2.03 - 1.85 (m, 2H), 1.61 - 1.45 (m, 4H).
Figure imgf000240_0001
Val-Cit-PABOH
[00553] A flame-dried vial was charged with NHS ester 65 (30 mg, 0.037 mmol, 1 equiv) and the oil was dried by azeotropic evaporation with toluene under reduced pressure, followed by drying on high vacuum for 30 min. Val-Cit-PABOH (14 mg, 0.037 mmol, 1 equiv) and powdered 4A molecular sieves were added to the vial. The reactants were dissolved in anhydrous dimethylformamide (735 μί) and N,N-diisopropylethylamine (32.0 μί, 0.184 mmol, 5 equiv) was added. The mixture was stirred at 23 °C under argon atmosphere, monitoring by LC-MS. After complete consumption of the NHS ester, piperidine (72.7 μί, 0.735 mmol, 20 equiv) was added and the reaction was stirred at 23 °C for 30 min. The mixture was filtered through a 0.2-μιη syringe filter and purified by preparatory HPLC (Waters Prep-C 18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 5→50% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide the formate salt as a clear, colorless oil. The product was dissolved in methanol (100 μί) and treated with 500 mg of freshly washed (methanol) Amberlyst A26 hydroxide form beads at 0 °C. The suspension was stirred at 0 °C for 1 h, then the beads were filtered and the filtrate concentrated to provide the free -base 66 as a clear, colorless oil (10.4 mg, 33%). 1H NMR (500 MHz, CD3OD) δ 7.56 (d, / = 8.6 Hz, 2H), 7.30 (d, J = 8.1 Hz, 2H), 4.56 (s, 2H), 4.51 (dd, J = 9.1, 5.1 Hz, 1H), 4.22 (d, J = 7.3 Hz, 1H), 3.80 (dd, J = 7.1, 5.1 Hz, 1H), 3.74 - 3.69 (m, 3H), 3.66 - 3.58 (m, 20H), 3.55 - 3.52 (m, 2H),
3.40 - 3.36 (m, 2H), 3.35 (s, 3H), 3.21 - 3.15 (m, 4H), 3.10 (dt, J = 13.5, 6.7 Hz, 1H), 2.46 -
2.41 (m, 3H), 2.10 (h, 7 = 6.8 Hz, 1H), 1.89 (ddt, J = 14.3, 10.0, 6.0 Hz, 1H), 1.80 - 1.66 (m, 4H), 1.66 - 1.47 (m, 10H), 1.43 - 1.34 (m, 2H), 0.99 (app t, J = 6.5 Hz, 6H); 13C NMR (125 MHz, CD3OD) δ 177.84, 174.99, 173.76, 173.68, 172.16, 162.24, 138.69, 128.58, 121.13, 72.92, 71.48, 71.40, 71.28, 68.31, 64.80, 60.09, 59.09, 55.88, 54.95, 51.16, 49.47, 49.30, 49.15, 47.59, 44.39, 40.21, 40.07, 37.67, 36.15, 36.01, 31.94, 30.50, 30.28, 30.18, 27.88, 27.67, 26.81, 25.50, 24.01, 23.69, 19.83, 18.86; HRMS (ESI): Calc'd for (Q0H71N7O13 + H)+ 858.5183, found 858.5210.
Figure imgf000241_0001
[00554] A 10-mL flask was charged with (PEG7)Lys-Val-Cit-PABOH 66 (15 mg, 0.017 mmol, 1 equiv) and the material was dried by sublimation with benzene (freezing at -78 °C then warming to 23 °C under high vacuum) resulting in a white powder. 2-(2-(2,5-dioxo-2,5- dihydro-lH-pyrrol-l-yl)ethoxy)ethyl (4-nitrophenyl) carbonate (6.43 mg, 0.018 mmol, 1.05 equiv) was added as a solution in anhydrous dimethylformamide (350 μί), followed by addition of N,N-diisopropylethylamine (9.2 μί, 0.052 mmol, 3 equiv). The solution was stirred under argon atmosphere at 23 °C for 36 h. The reaction mixture was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 10→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) providing 67 as a white film (15 mg, 80%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.26 (UV); 1H NMR (600 MHz, CD3OD) δ 8.42 (s, 1H), 7.93 (s, 1H), 7.56 (d, J = 8.2 Hz, 2H), 7.33 - 7.28 (m, 2H), 6.83 (s, 2H), 4.62 (s, 1H), 4.56 (s, 2H), 4.49 (dd, J = 9.2, 5.0 Hz, 1H), 4.19 (d, J = 7.3 Hz, 1H), 4.15 - 4.08 (m, 3H), 3.72 (t, J = 6.1 Hz, 2H), 3.68 (t, J = 5.3 Hz, 2H), 3.65 - 3.59 (m, 24H), 3.55 - 3.53 (m, 2H), 3.36 (s, 3H), 3.22 - 3.16 (m, 3H), 3.11 (dt, J = 13.5, 6.7 Hz, 1H), 2.44 (t, 7 = 6.0 Hz, 2H), 2.10 (h, J = 6.8 Hz, 1H), 1.93 - 1.86 (m, 1H), 1.81 - 1.73 (m, 2H), 1.72 - 1.49 (m, 7H), 1.47 - 1.35 (m, 3H), 0.98 (dd, J = 6.8, 3.9 Hz, 6H); HRMS (ESI): Calc'd for (C49H8oN8Oi8 + Na)+ 1091.5483, found 1091.5458.
Figure imgf000241_0002
[00555] A vial was charged with Mal-2PEG-(PEG7)Lys-Val-Cit-PABOH 67 (27.5 mg, 0.026 mmol, 1 equiv) and the material was dried by sublimation with benzene (freezing at - 78 °C then warming to 23 °C under high vacuum) resulting in a white powder. Bis(4- nitrophenyl) carbonate (15.7 mg, 0.051 mmol, 2.0 equiv) was added and the solids were dissolved in anhydrous dimethylformamide (214 μΐ^). N,N-diisopropylethylamine (11.2 μί, 0.064 mmol, 2.5 equiv) was added, the vial was flushed with argon and sealed, and the mixture was stirred at 23 °C for 17 h. The reaction mixture was diluted with methanol to a total of 900 μL· and was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) providing 68 as a yellow solid (18 mg, 57%). TLC (15% methanol-dichloromethane): R = 0.62 (UV); 1H NMR (500 MHz, CD3OD) δ 8.37 - 8.31 (m, 2H), 7.70 (d, = 8.3 Hz, 2H), 7.52 - 7.44 (m, 4H), 7.39 (d, = 0.7 Hz, 1H), 6.83 (s, 2H), 5.28 (s, 2H), 4.48 (dd, = 9.3, 4.7 Hz, 1H), 4.34 (dd, = 8.2, 4.3 Hz, 1H), 4.18 (d, = 6.8 Hz, 1H), 4.15 - 4.07 (m, 2H), 3.71 (t, = 6.2 Hz, 2H), 3.69 - 3.63 (m, 6H), 3.62 - 3.58 (m, 26H), 3.56 - 3.51 (m, 3H), 3.35 (s, 3H), 3.24 - 3.16 (m, 3H), 3.11 (dt, = 13.4, 6.5 Hz, 1H), 2.43 (t, = 6.1 Hz, 2H), 2.13 (q, = 6.8 Hz, 1H), 1.97 - 1.87 (m, 1H), 1.83 - 1.36 (m, 9H), 1.01 - 0.96 (m, 6H); HRMS (ESI): Calc'd for (C56H83N9022 + Na)+ 1256.5545, found 1256.5507.
Figure imgf000242_0001
[00556] A vial was charged (PEG7)Lys-Val-Cit-PABOH 66 (20 mg, 0.023 mmol, 1 equiv) followed by a solution of MDpr(Boc)-OSu (10.7 mg, 0.028 mmol, 1.2 equiv) in anhydrous dimethylformamide (117 μί). N,N-diisopropylethylamine (20.3 μί, 0.117 mmol, 5.0 equiv) was added, the vial was flushed with argon and sealed, and the mixture was stirred at 23 °C for 1 h. The reaction was quenched with the addition of glacial acetic acid (20 μί), diluted with dimethylformamide to a total of 900 μί, and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 10→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) providing 69 as a white solid (18 mg, 69%). TLC (15% methanol- dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.40 (UV); 1H NMR (600 MHz, D20) δ 7.43 - 7.38 (m, 2H), 7.38 - 7.34 (m, 2H), 6.92 (s, 2H), 4.86 - 4.82 (m, 1H), 4.58 (s, 2H), 4.39 (dd, J = 8.7, 5.6 Hz, 1H), 4.33 (t, = 7.4 Hz, 1H), 4.09 (dd, / = 15.1, 8.1 Hz, 1H), 3.74 - 3.70 (m, 2H), 3.67 - 3.59 (m, 25H), 3.59 - 3.56 (m, 3H), 3.34 (s, 3H), 3.14 - 3.07 (m, 4H), 2.49 - 2.44 (m, 2H), 2.07 (dq, = 16.2, 8.6, 7.7 Hz, 1H), 1.92 - 1.84 (m, 1H), 1.83 - 1.49 (m, 6H), 1.43 (dt, = 17.0, 8.5 Hz, 2H), 1.32 (s, 9H), 0.95 - 0.89 (m, 6H); HRMS (ESI): Calc'd for (C52H85N9Oi8 + Na)+ 1146.5905, found 1146.5870.
Figure imgf000243_0001
[00557] A vial was charged with MDpr(Boc)-(PEG7)Lys-Val-Cit-PABOH 69 (19.7 mg, 0.018 mmol, 1 equiv) and the material was dried by sublimation with benzene (freezing at - 78 °C then warming to 23 °C under high vacuum) resulting in a white powder. Bis(4- nitrophenyl) carbonate (10.7 mg, 0.035 mmol, 2.0 equiv) was added and the solids were dissolved in anhydrous dimethylformamide (146 μί). N,N-diisopropylethylamine (7.7 μί, 0.044 mmol, 2.5 equiv) was added, the vial was flushed with argon and sealed, and the mixture was stirred at 23 °C for 5 h. The reaction was quenched with the addition of glacial acetic acid (7 μΐ^), diluted with dimethylformamide to a total of 900 μί, and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) providing 70 as a yellow solid (13.5 mg, 60%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.24 (UV); 1H NMR (600 MHz, D20) δ 8.73 - 8.68 (m, 2H), 8.06 - 7.98 (m, 2H), 7.86 - 7.81 (m, 4H), 7.30 (s, 2H), 5.66 (s, 2H), 5.20 - 5.15 (m, 1H), 4.67 (dt, = 9.4, 4.6 Hz, 1H), 4.53 - 4.46 (m, 1H), 4.11 - 4.07 (m, 2H), 4.03 - 3.97 (m, 24H), 3.95 - 3.92 (m, 2H), 3.72 (s, 2H), 3.49 (dt, = 20.2, 7.4 Hz, 4H), 2.83 (q, = 6.7 Hz, 2H), 2.55 - 2.43 (m, 1H), 2.43 - 2.40 (m, 1H), 2.31 - 2.21 (m, 1H), 2.20 - 2.09 (m, 2H), 2.09 - 1.79 (m, 5H), 1.73 (s, 9H), 1.31 (dd, = 10.7, 6.8 Hz, 6H); HRMS (ESI): Calc'd for (C59H88Ni0O22 + H)+ 1289.6147, found 1289.6093.
Figure imgf000244_0001
[00558] To a solution of Mal-PEG2-(PEG7)Lys-Val-Cit-PABO-pNP 70 (8.2 mg, 6.61 μιηοΐ, 1.0 equiv) in anhydrous dimethylformamide (220 μί) was added N,N- diisopropylethylamine (5.8 μί, 0.033 mmol, 5.0 equiv) at 23 °C. Amine 4 (R02-A9) (3.5 mg, 6.61 μmol, 1.0 equiv) in anhydrous dimethylformamide (220 μί) was added dropwise to the solution and the reaction mixture was stirred for 40 min. The reaction solution was diluted with methanol to a total volume of 900 μΐ^ and purified directly by preparatory HPLC
(Waters Prep-C 18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 niL/min) to provide 71 (R02-D2) as a yellow film (2.3 mg, 21%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.38 (UV); 1H NMR (600 MHz, CD3OD) δ 8.54 (s, 1H), 7.51 (s, 1H), 7.48 (d, 7 = 8.4 Hz, 2H), 7.20 (d, 7 = 8.2 Hz, 2H), 6.81 (s, 2H), 5.22 (d, 7 = 4.1 Hz, 1H), 5.03 (s, 2H), 4.95 (d, 7 = 4.1 Hz, 1H), 4.87 - 4.83 (m, 2H), 4.65 (s, 1H), 4.47 (dd, 7 = 9.2, 5.0 Hz, 1H), 4.19 (d, 7 = 7.2 Hz, 1H), 4.14 - 4.03 (m, 6H), 3.79 (s, 3H), 3.70 (t, 7 = 6.1 Hz, 2H), 3.68 - 3.65 (m, 2H), 3.65 - 3.57 (m, 29H), 3.56 (s, 3H), 3.54 - 3.51 (m, 2H), 3.44 - 3.40 (m, 2H), 3.40 (s, 3H), 3.35 (s, 3H), 3.20 - 3.15 (m, 3H), 3.10 (dt, 7 = 13.5, 6.7 Hz, 1H), 3.06 - 3.02 (m, 2H), 2.82 (d, 7 = 5.8 Hz, 1H), 2.73 (d, 7 = 5.7 Hz, 1H), 2.71 - 2.65 (m, 2H), 2.58 (s, 3H), 2.43 (t, 7 = 6.1 Hz, 2H), 2.15 - 2.05 (m, 1H), 2.06 - 2.00 (m, 2H), 1.93 - 1.85 (m, 2H), 1.80 - 1.72 (m, 3H), 1.69 - 1.34 (m, 7H), 0.98 (dd, 7 = 6.7, 4.4 Hz, 6H); HRMS (ESI): Calc'd for (C77H109N9O29 + H)+ 1624.7404, found 1624.7367.
Figure imgf000245_0001
[00559] To a solution of MDpr(Boc)-(PEG7)Lys-Val-Cit-PABO-pNP 70 (13.9 mg, 10.76 μηιοΐ, 1.5 equiv) in anhydrous dimethylformamide (360 μί) was added N,N- diisopropylethylamine (12.5 μΐ,, 0.072 mmol, 10.0 equiv) at 23 °C. Amine 4 (R02-A9) (3.8 mg, 7.18 μιηοΐ, 1.0 equiv) in anhydrous dimethylformamide (360 μί) was added dropwise to the solution and the mixture was stirred at 23 °C for 1.5 h. The reaction solution was diluted with dimethylformamide to a total volume of 900 μΐ^ and purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 72 as yellow solid (3.5 mg, 29%). HRMS (ESI):
Calc'd for (C8oHii4Nio029 + H)+ 1679.7826, found 1679.7771.
Figure imgf000245_0002
[00560] 72 (3.5 mg, 2.084 μιηοΐ) was dissolved in acetonitrile (0.5 mL), transferred to a dry vial and concentrated. The residue was suspended in anhydrous dichloromethane (270 μί) under an argon atmosphere. The mixture was cooled to 0 °C and trifluoroacetic acid (30 μί) was added dropwise. The reaction mixture was stirred at 0 °C for 45 min, after which an additional 30 μΐ^ of trifluoroacetic acid was added. After stirring for 15 min, HRMS indicated complete consumption of starting material. 0.5 mL of dimethylformamide was added to the vial and concentrated to remove dichloromethane. The residue was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 15→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 73 (R02-D3) as yellow solid (2.7 mg, 60%). TLC (15% methanol-dichloromethane + 2% 30% aqueous ammonium hydroxide solution): R = 0.29 (UV); HRMS (ESI): Calc'd for (C75H106N10O27 + H)+ 1579.7302, found 1579.7276.
Figure imgf000246_0001
74
( 02-E7)
[00561] To a solution of 4-nitrophenyl (2-((5-nitropyridin-2-yl)disulfanyl)propyl) carbonate (1.514 mg, 3.68 μιηοΐ, 2.0 equiv) in 0.2 mL dimethylformamide was added N,N- diisopropylethylamine (3.21 μί, 0.018 mmol, 10 equiv) at 23 °C, followed by the addition of amine 16 (R02-B1) (1 mg, 1.840 μιηοΐ, 1 equiv) in 0.2 mL dimethylformamide. The reaction mixture was stirred at 23 °C for 30 min or until the reaction was complete. The reaction mixture was purified directly by preparatory HPLC (Waters Prep-C18 SunFire® column, 5 μιη, 19 x 250 mm, UV detection at 399 nm, gradient elution with 20→80% acetonitrile in water containing 0.1% formic acid over 30 min, flow rate: 15 mL/min) to provide 74 (R02- E7) as a yellow oil (0.7 mg, 48%, mixture of diastereomers). 1H NMR (500 MHz, CDCI3) δ: 9.25 - 9.16 (m, 1H), 8.37 - 8.33 (m, 1H), 7.94 - 7.88 (m, 1H), 7.46 - 7.42 (m, 1H), 5.24 - 5.19 (m, 1H), 4.85 - 4.76 (m, 1H), 4.71 (s, 1H), 4.24 - 4.14 (m, 4H), 3.78 (s, 3H), 3.65 - 3.62 (m, 2H), 3.60 (s, 3H), 3.48 - 3.46 (m, 3H), 3.36 - 3.31 (m, 1H), 3.11 - 3.03 (m, 5H), 2.92 - 2.81 (m, 2H), 2.74 - 2.71 (m, 2H), 2.58 (s, 3H), 2.12 - 2.07 (m, 2H), 1.39-1.35 (m, 3H); HRMS(ESI): Calc'd for (C37H4iN3Oi4S2+H)+ 816.2103, found 816.2040.
Preparation of Trioxacarcin-Antibody Conjugates
[00562] Exemplary trioxacarcin-antibody conjugates were prepared from the anti-HER2 monoclonal antibody trastuzumab and each of the trioxacarcin-linker species R02-A3, R02- B4, R02-B5, R02-B10, R02-C1, R02-C2, R02-C3, R02-C4, R02-C9, R02-C10, and R02-
D2. The methods used for preparing and characterizing the antibody-drug conjugates are described below. [00563] Partial reduction of interchain disulfides: To a solution of trastuzumab (500 μg, 25 μΐ^ of 20 mg/niL in PBS) was added a solution of tris(2-carboxyethyl)phosphine hydrochloride (1.7 μί, 5 mM in water, 2.5 equiv) and diluted to 15 mg/niL final antibody concentration using DPBS pH 7.4 containing ethylenediaminetetraacetic acid (5 mM, 8.3 μί). The reaction was incubated at 37 °C for 2 h and then cooled to 23 °C.
[00564] Conjugation of maleimide containing trioxacarcin-linker: To a solution of partially reduced trastuzumab was added the trioxacarcin-linker species (6.9 μί, 5 mM in DMSO, 10 equiv). DPBS pH 7.4 containing ethylenediaminetetraacetic acid (5 mM, 8.3 μί) was added to achieve 10 mg/mL final antibody concentration. DMSO (1 μί) was added to achieve 15% (v/v) total organic solvent component in the final reaction mixture. The reaction was incubated for 2h at 23 °C with agitation at 500 rpm. After conjugation, the antibody solution was desalted into DPBS by three rounds of dilution and centrifugation at 4,000 x g through a 10 kDa MWCO filter. The resulting antibody-drug conjugate was analyzed by LC- MS, and stored at -80 °C.
[00565] LC-MS analysis: Trioxacarcin-antibody conjugates (50 μg, 20 μΐ^ solution in DPBS) were optionally deglycosylated before analysis by addition of PNGase F (0.5 μί, New England Biolabs) and PNGase F lOx buffer (2 μί, New England Biolabs). The solution was incubated at 27 °C for 16 h. Antibody was fully reduced by addition of tris(2- carboxyethyl)phosphine hydrochloride solution (20 μΐ^ of 20 mM in water) immediately before analysis. LC-MS analysis was performed at the Harvard University Mass
Spectrometry Facility using a Bruker Impact II q-TOF mass spectrometer.
[00566] Between 0 and 1 conjugations were observed per light chain, and between 0 and 3 conjugations were observed per heavy chain.
Antiproliferative Assays
[00567] Cell Culture: Cell lines NCI-H460, HT-29, and NCI-N87 were purchased from American Type Culture Collection (ATCC). H460 and N87 cells were maintained in RPMI- 1640 medium and HT-29 cells were maintained in McCoy's 5 A medium, all supplemented with 10% fetal bovine serum (Life Technologies, UK).
[00568] Cell Proliferation Assay: Cells were plated in black-walled 96-well plates (3000- 4000 cells per well for H460, 4000-5000 cells per well for HT-29, and 5000-6000 cells per well for N87). Stock solutions of each compound were diluted serially and the resulting solutions were administrated to cells to achieve final concentrations of 1.1 nM to 2.5 μΜ in 100 μΐ, total volume. After incubating at 37 °C (5% C02) for 2 days (H460 and N87) or 3 days (HT-29), 20 μL· of resazurin solution (Promega CellTiter-Blue® Cell Viability Assay) was added to each well. After incubating at 37 °C for 4.0 h, the fluorescence (560 nm excitation/590 nm emission) was recorded using a microplate reader (SpectraMax i3) as a measure of viable cells. IC50 values, determined in triplicate, were calculated using a four- parameter logistic equation.
[00569] Table 1 reports the IC50 values of exemplary trioxacarcin ADC precursors with and without linking groups evaluated in H460, HT-29, and N87 cell lines. Notably, several free drugs containing amine groups exhibited low nanomolar IC50 values across all evaluated cell lines. Corresponding trioxacarcin-linker species incorporating these trioxacarcin analogs did not exhibit toxicity even at concentrations 100-fold higher than free drug, indicating no free drug was released under cell culture conditions.
Table 1.
Figure imgf000248_0001
Stability of the Trioxacarcin-linker Species
[00570] To determine the stability of several representative exemplary free drug (R02-B1, R02-A9, R02-B7, R02-A1, and R02-A7) and trioxacarcin-linker species (R02-B5, R02-B4, R02-B8, R02-A3, and R02-A8) under physiological pH and temperature, trioxacarcin analogs and corresponding trioxacarcin-linkers were incubated at 37 °C in pH 7.4 or pH 5.0 buffer. The trioxacarcin-linker species were stable and all but one had half-lives of 50 hours or greater, even in acidic media. No free drug release was seen at any time point, and the primary mode of degradation of drug-linkers was hydrolysis of the maleimide, thus demonstrating that the exemplary trioxacarcin-linkers comprising amine-functionalized trioxacarcins exhibit favorable stability.
[00571] Compound Stability Assay: In a 1.5 mL screw-top conical plastic vial, the desired compound as a solution in DMSO (5 mM, 6 μί, 30 nmol) was mixed with a solution of N- acetylcysteine in DMSO (10 mM, 6
Figure imgf000249_0001
30 nmol, 2 equiv) to quench the maleimide. The mixture was diluted with either pH 5.0 sodium acetate or pH 7.4 phosphate buffer containing 8 mM N-acetylcysteine (282 μί). 1-naphthalene acetic acid in DMSO (5 mM, 6 μί, 30 nmol) was added as an internal standard. In the case of testing free drug stability, no N- acetylcysteine solution was added and instead the amount of buffer added was increased an equivalent amount to compensate (288
Figure imgf000249_0002
total buffer). The vial was placed in a heating block at 37 °C and protected from direct light. 25
Figure imgf000249_0003
aliquots of the reaction mixture were removed at various time points and analyzed by LC-MS. LC-MS peaks were integrated within the Agilent LC-MS software and the areas of each peak were normalized to 1- napthalene acetic acid at 280 nm. Percent compound remaining is defined as the normalized peak area at a given time point divided by the normalized peak area at 0 hours x 100%. The results are shown in Figures 1-3.
Release Kinetics of the Trioxacarcin-linker Species
[00572] To determine whether free drug would be effectively released upon exposure to Cathepsin B, the enzyme most responsible for intracellular cleavage of the linker, exemplary trioxacarcin-linker species (R02-A3, R02-A8, R02-B4, and R02-B5) were incubated with Cathepsin B at pH 5.0 at 37 °C. These conditions simulate the environment of the lysosome. All linkers evaluated exhibited excellent release kinetics, with half-lives on the order of 15-30 minutes. Half-lives for the evaluated compounds were as follows: R02-A3: 0.45 hours; R02- A8: 0.21 hours; R02-B4: 0.44 hours; R02-B5: 0.25 hours. The results are shown in Figures 4-7. [00573] Release Kinetics Assay: In a 1.5 niL screw-top conical plastic vial, the desired compound as a solution in DMSO (5 mM, 6 μί, 30 nmol) was mixed with a solution of N- acetylcysteine in DMSO (10 mM, 6 μί, 30 nmol, 2 equiv) to quench the maleimide. The mixture was diluted with pH 5.0 sodium acetate buffer containing 8 mM N-acetylcysteine (255 μί). 1-napthalene acetic acid in DMSO (5 mM, 6 μί, 30 nmol) was added as an internal standard. A 9.2 U/mL solution of Cathepsin B in pH 5.0 buffer was added. The vial was placed in a heating block at 37 °C and protected from direct light. 25 μΐ^ aliquots of the reaction mixture were removed at various time points and analyzed by LC-MS. LC-MS peaks were integrated within the Agilent LC-MS software and the areas of each peak were normalized to 1-napthalene acetic acid at 280 nm. Percent drug-linker remaining is defined as the normalized peak area at a given time point divided by the normalized peak area at 0 hours x 100%.
Other Embodiments
[00574] In the claims articles such as "a," "an," and "the" may mean one or more than one unless indicated to the contrary or otherwise evident from the context. Claims or descriptions that include "or" between one or more members of a group are considered satisfied if one, more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process unless indicated to the contrary or otherwise evident from the context. The invention includes embodiments in which exactly one member of the group is present in, employed in, or otherwise relevant to a given product or process. The invention includes embodiments in which more than one, or all of the group members are present in, employed in, or otherwise relevant to a given product or process.
[00575] Furthermore, the invention encompasses all variations, combinations, and permutations in which one or more limitations, elements, clauses, and descriptive terms from one or more of the listed claims is introduced into another claim. For example, any claim that is dependent on another claim can be modified to include one or more limitations found in any other claim that is dependent on the same base claim. Where elements are presented as lists, e.g., in Markush group format, each subgroup of the elements is also disclosed, and any element(s) can be removed from the group. It should it be understood that, in general, where the invention, or aspects of the invention, is/are referred to as comprising particular elements and/or features, certain embodiments of the invention or aspects of the invention consist, or consist essentially of, such elements and/or features. For purposes of simplicity, those embodiments have not been specifically set forth in haec verba herein. It is also noted that the terms "comprising" and "containing" are intended to be open and permits the inclusion of additional elements or steps. Where ranges are given, endpoints are included. Furthermore, unless otherwise indicated or otherwise evident from the context and understanding of one of ordinary skill in the art, values that are expressed as ranges can assume any specific value or sub-range within the stated ranges in different embodiments of the invention, to the tenth of the unit of the lower limit of the range, unless the context clearly dictates otherwise.
[00576] This application refers to various issued patents, published patent applications, journal articles, and other publications, all of which are incorporated herein by reference. If there is a conflict between any of the incorporated references and the instant specification, the specification shall control. In addition, any particular embodiment of the present invention that falls within the prior art may be explicitly excluded from any one or more of the claims. Because such embodiments are deemed to be known to one of ordinary skill in the art, they may be excluded even if the exclusion is not set forth explicitly herein. Any particular embodiment of the invention can be excluded from any claim, for any reason, whether or not related to the existence of prior art.
[00577] Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments described herein. The scope of the present embodiments described herein is not intended to be limited to the above Description, but rather is as set forth in the appended claims. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims.

Claims

Claims
What is claimed is:
1. A compound of Formula I) :
Figure imgf000252_0001
(I)
or a pharmaceutically acceptable salt thereof;
wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CO^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -NCR^k; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two R^ groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -0C(=0)0RC1; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)0RC1; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; - E2 El E2 El
NR^C(=0)ORE1; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000254_0001
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -L-B;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NRI2C(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
Figure imgf000254_0002
wherein each occurrence of R II is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB 1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB 1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl;
B2
or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40-A— I Qr j— R20~X-R1 1— S— j.
R 20 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
R22
p21 p21 I
X is \ ' o ; heterocyclylene; or heteroarylene;
R11 is substituted or unsubstituted alkylene;
R 21 is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is h drogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carbocyclyl; or
Figure imgf000256_0001
;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid; m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
A is a group of the formula
Figure imgf000257_0001
Q is -S- or -0-;
Rwl is independently hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
2. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -COiR^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two R^ groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -0C(=0)0RC1; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)0RC1; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; - E2 El E2 El
NR^C(=0)ORE1; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000259_0001
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -L-B;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NRI2C(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
Figure imgf000259_0002
wherein each occurrence of R II is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB 1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB 1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl;
B2
or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
|— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O) -R40-A— | .
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000261_0001
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
A is a group of the formula
Figure imgf000262_0001
Q is -S-, or -0-;
R is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
3. The compound of claim 1 or 2, or a pharmaceutically acceptable salt thereof, wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CC^R^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of RA2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - 0RC1; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000263_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000264_0001
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -L-B;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NRI2C(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
Figure imgf000264_0002
wherein each occurrence of R II is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R 12 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB 1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB 1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl;
B2
or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L is of the formula:
j— R20-X-CH2-Ar-NH-Zm-Ym-E-C(O)-R40-A— J .
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000266_0001
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
A is a group of the formula:
Figure imgf000267_0001
Q is -S-, or -0-;
Rwl is hydrogen, substituted or unsubstituted alkyl; or a nitrogen protecting group; and
B is an antibody or an antibody fragment.
4. A compound of Formula (II):
Figure imgf000267_0002
(II)
or a pharmaceutically acceptable salt thereof;
wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CO^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two R^ groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring; R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000269_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000269_0002
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -ΐ Τ;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR ; -C(=0)Ri ; -C02Ru; -CN; -SCN; -SRn; -SOR11; -S02Ru; -N02; -N3; -N(R^)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB 1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R B2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L1 is of the formula:
Figure imgf000271_0001
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000271_0002
; heterocyclylene; or heteroarylene;
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R 21 groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is h drogen; substituted or unsubstituted alkyl; substituted or unsubstituted
carbocyclyl; or
Figure imgf000271_0003
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
Figure imgf000272_0001
Q is -S-, or -0-;
R is a leaving group;
R X2 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is independently hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group.
5. The compound of claim 4, or a pharmaceutically acceptable salt thereof, wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -CO^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R^ is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000274_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000274_0002
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring; R7 is -ΐ Τ;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L1 is of the formula:
j— R20-X-CH2-Ar-NH-Zm-Yn -C(0)-R40— | .
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
Figure imgf000276_0001
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; or two R groups are joined to form an optionally substituted heterocyclyl ring;
R 22 is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalkylene;
Figure imgf000277_0001
Q is -S- or -0-;
R is a leaving group;
R X2 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is hydrogen: substituted or unsubstituted alkyl; or a nitrogen protecting group.
6. The compound of claim 4 or 5, or a pharmaceutically acceptable salt thereof, wherein:
R1 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORA1; -C(=0)RA2; -COiR^; -CN; -SCN; -SRA1; -SORA1; -S02RA; -N02; -N3; =0; =N(RA2); =S; -N(RA2)2; -NRA2C(=0)RA2; -NRA2C(=0)N(RA2)2; -OC(=0)ORA1; -OC(=0)RA2; - OC(=0)N(RA2)2; -NRAC(=0)ORA1; or -C(RA2)3; wherein each occurrence of RA1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of RA2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino, or two RA2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R 2 is hydrogen; or R 1 and R2 are joined to form =0;
R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORcl; -C(=0)RC2; -C02RC1; -CN; -SCN; -SRC1; -SORcl; -S02RC2; -N02; -N3; =0; =N(RC2); =S; -N(RC2)2; -NHC(=0)RC2; -NRC2C(=0)N(RC2)2; -OC(=0)ORcl; -OC(=0)RC2; - OC(=0)N(RC2)2; -NRC2C(=0)ORcl; or -C(RC2)3; wherein each occurrence of RC1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R C2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R C2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R4 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORD1; -C(=0)RD2; -C02RD2; -CN; -SCN; -SRD1; -SORD1; -S02RD2; -N02; -N3; -N(RD2)2; - NRD2C(=0)RD2; -NRD2C(=0)N(RD2)2; -OC(=0)ORD1; -OC(=0)RD2;
-OC(=0)N(RD2)2; -NRD2C(=0)ORD1; or -C(RD2)3; wherein each occurrence of RD1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R D2 is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R D2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R5 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORE1; -C(=0)RE2; -C02RE1; -CN; -SCN; -SRE1; -SORE1; -S02RE2; -N02; -N3; -N(RE2)2; - NRE2C(=0)RE2; -NRE2C(=0)N(RE2)2; -OC(=0)ORE1; -OC(=0)RE2; -OC(=0)N(RE2)2; -
Figure imgf000279_0001
or -C(R E"2)3; wherein each occurrence of R El is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R E2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R E2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R6 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORF1; -C(=0)RF2; -C02RF1; -CN; -SCN; -SRF1; -SORF1; -S02RF2; -N02; -N3; -N(RF2)2; - NRF2C(=0)RF2; -NRF2C(=0)N(RF2)2; -OC(=0)ORF1; -OC(=0)RF2; -OC(=0)N(RF2)2; -
Figure imgf000279_0002
-C(R Fr2")3; wherein each occurrence of R Fl is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R F2 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R F2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R7 is -ΐ Τ; R is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - OR11; -C(=0)R12; -C02Rn; -CN; -SCN; -SR11; -SOR11; -S02RE; -N02; -N3; -N(RE)2; - NREC(=0)R12; -NREC(=0)N(RI2)2; -OC(=0)ORn; -OC(=0)RE; -OC(=0)N(RE)2; -
12 II 12 II
NR1"C(=0)ORil; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
12
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl (e.g. , alkoxy; aryloxy; heteroaryloxy); substituted thiol (e.g. , alkylthio; arylthio; heteroarylthio); amino; or substituted amino (e.g., alkylamino,
12
dialkylamino); or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R9 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORG1; -C(=0)RG2; -C02RG1; -CN; -SCN; -SRG1; -SORG1; -S02RG2; -N02; -N3; -N(RG)2; - NRG2C(=0)RG2; -NRG2C(=0)N(RG2)2; -OC(=0)ORG1; -OC(=0)RG2; -OC(=0)N(RG2)2; -
G2 Gl G2 Gl
NRuzC(=0)ORul; or -C(R^)3; wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2
heteroaryl; and wherein each occurrence of R is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched
heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted
G2 heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R groups are optionally joined to form a heterocyclyl or heteroaryl ring;
R10 is hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; - ORB1; -C(=0)RB2; -C02RB2; -CN; -SCN; -SRB1; -SORB1; -S02RB2; -N02; -N3; =0; =N(RB2); =S; -N(RB2)2; -NRB2C(=0)RB2; -NRB2C(=0)N(RB2)2; -OC(=0)ORB1; -OC(=0)RB2; - OC(=0)N(RB2)2; -NRB2C(=0)ORB1; or -C(RB2)3; wherein each occurrence of RB1 is independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and wherein each occurrence of R is
independently hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or
unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; substituted hydroxyl; substituted thiol; amino; or substituted amino; or two R B2 groups are optionally joined to form a heterocyclyl or heteroaryl ring;
or R1 and R10 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R 110U and R 3J are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
L1 is of the formula:
Figure imgf000281_0001
R is substituted or unsubstituted alkylene; or substituted or unsubstituted
heteroalk lene;
Figure imgf000281_0002
R is independently substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl; R is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstituted carbocyclyl;
Ar is substituted or unsubstituted arylene;
each occurrence of Z is independently an amino acid;
each occurrence of Y is independently an amino acid;
E is a bond or an amino acid;
m is independently 1, 2, or 3;
R40 is substituted or unsubstituted alkylene; or substituted or unsubstituted heteroalkylene;
Figure imgf000282_0001
Q is -S-, or -0-;
R is a leaving group;
R X2 is hydrogen; substituted or unsubstituted alkyl; substituted or unsubstituted heterocyclyl; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; or an oxygen protecting group; and
Rwl is hydrogen; substituted or unsubstituted alkyl; or a nitrogen protecting group.
7. The compound of any of claims 1-6, wherein the compound is of the formula:
Figure imgf000282_0002
or a pharmaceutically acceptable salt thereof.
8. The compound of an of claims 1-6, wherein the compound is of the formula:
Figure imgf000282_0003
or a pharmaceutically acceptable salt thereof.
9. The compound of an of claims 1-6, wherein the compound is of the formula:
Figure imgf000283_0001
or a pharmaceutically acceptable salt thereof.
10. The compound of any of claims 1-6, or a pharmaceutically acceptable salt thereof, wherein:
R 1 and R 2 are each hydrogen or together form =0; and
R 10 and R 3 are hydrogen;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
11. The compound of any of claims 1-6, or a pharmaceutically acceptable salt thereof, wherein:
R1 is -ORA1; wherein RA1 is hydrogen; carbohydrate; a protecting group; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; acyl; substituted or unsubstituted aryl; or substituted or unsubstituted heteroaryl; and
R 10 and R 3 are hydrogen;
or R1 and R4 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R4 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety;
or R6 and R9 are optionally taken together with the intervening carbon atoms to form an optionally substituted cyclic moiety.
12. The compound of any of claims 1-6, or a pharmaceutically acceptable salt thereof, wherein: R1 is hydrogen or -ORA1;
2 1 2
R is hydrogen; or R and R are joined to form =0;
RA1 is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl; or RA1 is a group of Formula (i):
Figure imgf000284_0001
wherein each occurrence of R^, RA^, R^, RA6, and RA7 is independently hydrogen, substituted or unsubstituted alkyl; -ORA9; -OC(=0)RA9; -N(RA9)2; or -NHC(=0)RA9;
wherein each occurrence of RA9 is independently hydrogen; substituted or unsubstituted alkyl; an oxygen protecting group when attached to an oxygen atom; or a nitrogen protecting group when attached to a nitrogen atom; or two RA9 groups are joined to form a substituted or unsubstituted heterocyclic or substituted or unsubstituted heteroaryl ring; and M1 is -0-;
3 CI CI
R is hydrogen or -OR , wherein R is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl;
R4 is hydrogen or -ORD1, wherein RD1 is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl;
5 El El
R is hydrogen or -OR , wherein R is hydrogen; an oxygen protecting group; or substituted or unsubstituted alkyl;
R6 is substituted or unsubstituted alkyl;
R8 is -CH(ORu)2; and
each occurrence of Ru is substituted or unsubstituted alkyl.
13. The compound of any of claims 1-6 or 10-12, or a pharmaceutically acceptable salt
1 2
thereof, wherein R and R are hydrogen.
14. The compound of any of claims 1-6 or 10-13, or a pharmaceutically acceptable salt thereof, wherein R is hydrogen.
15. The compound of any of claims 1-6 or 10-14, or a pharmaceutically acceptable salt
1 2 3
thereof, wherein R , R , and R are each hydrogen.
16. The compound of any of claims The compound of any of claims 1-6 or 10-15, or a pharmaceutically acceptable salt thereof, wherein R4 is -ORD1.
17. The compound of any of claims The compound of any of claims 1-6 or 10-16, or a pharmaceutically acceptable salt thereof, wherein R 5 is -OR El .
18. The compound of any of claims 1-8, or 10-17, or a pharmaceutically acceptable salt thereof, wherein R 6 is substituted or unsubstituted alkyl or -OR Fl .
19. The compound of any of claims 1-8, or 10-18, or a pharmaceutically acceptable salt thereof, wherein R8 is hydrogen, -CH2(ORn), -CH(ORn)2, or -CH2OC(=0)RE
20. The compound of any of claims 1-19, or a pharmaceutically acceptable salt thereof, wherein R 20 is substituted or unsubstituted alkylene.
21. The compound of any of claims 1-19, or a pharmaceutically acceptable salt thereof, wherein R 20 is unsubstituted alkylene.
22. The compound of any of claims 1-21, or a pharmaceutically acceptable salt thereof, wherein:
Figure imgf000285_0001
R is independently substituted or unsubstituted alkyl.
23. The compound of any of claims 1-21, or a pharmaceutically acceptable salt thereof, wherein:
Figure imgf000285_0002
two R groups are joined to form an optionally substituted heterocyclyl ring.
24. The compound of any of claims 1-21, or a pharmaceutically acceptable salt thereof, wherein:
Figure imgf000286_0001
R is hydrogen; substituted or unsubstituted alkyl; or substituted or unsubstitued carbocyclyl.
25. The compound of any of claims 1-24, or a pharmaceutically acceptable salt thereof, wherein Ar is substituted or unsubstituted phenylene.
26. The compound of any of claims 1-25, or a pharmaceutically acceptable salt thereof, wherein Z is lysine, arginine, histidine, ornithine, or citrulline.
27. The compound of any of claims 1-25, or a pharmaceutically acceptable salt thereof, wherein Z is lysine or citrulline.
28. The compound of any of claims 1-25, or a pharmaceutically acceptable salt thereof, wherein Z is citrulline.
29. The compound of any of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein Y is alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
30. The compound of any of claims 1-28, or a pharmaceutically acceptable salt thereof, wherein Y is valine.
31. The compound of any of claims 1-30, or a pharmaceutically acceptable salt thereof, wherein each occurrence of m is 1.
32. The compound of any of claims 1-31, or a pharmaceutically acceptable salt thereof, wherein -Zm-Ym- is -citrulline- valine-.
33. The compound of any of claims 1-32, or a pharmaceutically acceptable salt thereof, wherein E is a bond.
34. The compound of any of claims 1-32, or a pharmaceutically acceptable salt thereof, wherein E is lysine or a substituted lysine.
35. The compound of any of claims 1-32, or a pharmaceutically acceptable salt thereof, wherein E is of the formula:
Figure imgf000287_0001
wherein R is substituted or unsubstituted alkyl, or substituted or unsubstituted heteroalkyl.
36. The compound of any of claims 1-35, or a pharmaceutically acceptable salt thereof, wherein R40 is substituted or unsubstituted alkylene.
37. The compound of any of claims 1-35, or a pharmaceutically acceptable salt thereof, wherein R40 is substituted or unsubstituted heteroalkylene.
38. The compound of any of claims 1-3 or 7-37, or a pharmaceutically acceptable salt thereof, wherein A is a group of the formula:
Figure imgf000287_0002
39. The compound of any of claims 1-3 or 7-38, or a pharmaceutically acceptable salt thereof, wherein -L- is a roup of the formula:
Figure imgf000287_0003
wherein:
R 20 is substituted or unsubstituted Ci_6 alkylene;
R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
40. The compound of any of claims 1-3 or 8-38, or a pharmaceutically acceptable salt thereof, wherein -L- is a group of the formula:
Figure imgf000288_0001
wherein:
R 20 is substituted or unsubstituted Ci_6 alkylene;
R 22 is hydrogen; or substituted or unsubstituted Ci_6 alkyl;
R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
41. The compound of any of claims 1-3 or 7-38, or a pharmaceutically acceptable salt thereof, wherein -L- is a group of the formula:
Figure imgf000288_0002
wherein:
R is substituted or unsubstituted Ci_6 alkylene;
R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
42. The compound of any of claims 1-3 or 7-38, or a pharmaceutically acceptable salt thereof, wherein -L- is a roup of the formula:
Figure imgf000289_0001
wherein:
R 20 is substituted or unsubstituted C1-6 alkylene;
R 21 is independently substituted or unsubstituted Ci_6 alkyl;
R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
43. The compound of any of claims 1-3 or 7-38, or a pharmaceutically acceptable salt thereof, wherein -L- is a roup of the formula:
Figure imgf000289_0002
wherein:
R 20 is substituted or unsubstituted C1-6 alkylene;
R 21 is independently substituted or unsubstituted C1-6 alkyl;
R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
44. The compound of any of claims 1-3 or 7-38, or a pharmaceutically acceptable salt thereof, wherein -L- is a group of the formula:
Figure imgf000290_0001
wherein:
R 20 is substituted or unsubstituted Ci_6 alkylene;
R 21 is independently substituted or unsubstituted C1-6 alkyl; and
R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
45. The compound of any of claims 1-3 or 7-38, wherein the compound is of Formula (I- e):
Figure imgf000290_0002
(I-e)
or a pharmaceutically acceptable salt thereof,
wherein:
R 20 is substituted or unsubstituted Ci_6 alkylene;
R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl;
R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
46. The compound of any of claims 1-3 or 7-38, wherein the compound is of Formula (I-
Figure imgf000291_0001
(i-f)
or a pharmaceutically acceptable salt thereof,
wherein:
R20 is substituted or unsubstituted Ci_6 alkylene;
R22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl; and
R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
47. The compound of any of claims 4-37, or a pharmaceutically acceptable salt thereof, wherein T is a group of formula:
Figure imgf000291_0002
48. The compound of any of claims 4-37, or a pharmaceutically acceptable salt thereof, wherein -Lx-T is a group of the formula:
Figure imgf000291_0003
wherein:
R is substituted or unsubstituted Ci_6 alkylene;
R22 is hydrogen, or substituted or unsubstituted C\ R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
49. The compound of any of claims 4-37, or a pharmaceutically acceptable salt thereof, wherein -Ll-T is a group of the formula:
Figure imgf000292_0001
wherein:
R 20 is substituted or unsubstituted Ci_6 alkylene;
R 22 is hydrogen, or substituted or unsubstituted Ci_6 alkyl;
R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
50. The compound of any of claims 4-37, or a pharmaceutically acceptable salt thereof, wherein -Ll-T is a group of the formula:
Figure imgf000292_0002
wherein:
R is substituted or unsubstituted Ci_6 alkylene;
R 22 is hydrogen, or substituted or unsubstituted C1-6 alkyl; and R is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
51. The compound of any of claims 4-37, or a pharmaceutically acceptable salt thereof, wherein -Ll-T is a grou of the formula:
Figure imgf000293_0001
wherein:
R 20 is substituted or unsubstituted C1-6 alkylene;
R 21 is independently substituted or unsubstituted Ci_6 alkyl;
R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
52. The compound of any of claims 4-37, or a pharmaceutically acceptable salt thereof, wherein -Ll-T is a grou of the formula:
Figure imgf000293_0002
wherein:
R 20 is substituted or unsubstituted C1-6 alkylene;
R 21 is independently substituted or unsubstituted C1-6 alkyl;
R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
53. The compound of any of claims 4-37, or a pharmaceutically acceptable salt thereof, wherein -Ll-T is a group of the formula:
Figure imgf000294_0001
wherein:
R 20 is substituted or unsubstituted Ci_6 alkylene;
R 21 is independently independently substituted or unsubstituted C1-6 alkyl; and R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene.
The compound of an of claims 4-37, wherein the compound is of Formula (Il-e):
Figure imgf000294_0002
(H e)
or a pharmaceutically acceptable salt thereof,
wherein:
R 20 is substituted or unsubstituted Ci_6 alkylene;
22
R is hydrogen or Ci_6 alkyl;
R40 is substituted or unsubstituted C1-6 alkylene, or substituted or unsubstituted C1-4o heteroalkylene;
R50 is the sidechain of lysine, arginine, histidine, ornithine, or citrulline; and
R60 is the sidechain of alanine, valine, leucine, isoleucine, methionine, phenylalanine, or tryptophan.
55. The compound of any of claims 4-37, wherein the compound is of Formula (Il-f):
Figure imgf000295_0001
(II-f)
or a pharmaceutically acceptable salt thereof,
wherein:
R 20 is substituted or unsubstituted C1-6 alkylene;
R 22 is hydrogen or Ci_6 alkyl; and
R40 is substituted or unsubstituted Ci_6 alkylene, or substituted or unsubstituted Ci_4o heteroalkylene.
56. The compound of any of claims 1-3 or 7-46, wherein B is an antibody selected from the group consisting of Adecatumumab, Afutuzumab, Alemtuzumab (CAMPATH), Bavituximab, Belimumab, Bevacizumab (AVASTIN), Brentuximab, Cantuzumab, Cetuximab (ERBITUX), Citatuzumab, Cixutumumab, Conatumumab, Dacetuzumab, Elotuzumab, Etaracizumab, Farletuzumab, Figitumumab, Gemtuzumab, Ibritumomab, Inotuzumab, Ipilimumab (YERVOY), Iratumumab, Labetuzumab, Lexatumumab,
Lintuzumab, Lucatumumab, Mapatumumab, Matuzumab, Milatuzumab, Necitumumab, Nimotuzumab, Ofatumumab (ARZERRA), Olaratumab, Oportuzumab, Panitumumab (VECTIBIX), Pertuzumab (PERJETA), Pritumumab, Rituximab (RITUXAN),
Robatumumab, Sibrotuzumab, Siltuximab, Tacatuzumab, Tigatuzumab, Tositumomab (BEXXAR), Trastuzumab (HERCEPTIN), Tucotuzumab, Veltuzumab, Votumumab, and Zalutumumab, or an antibody fragment thereof.
57. The compound of any of claims 1-3, wherein the compound is
Figure imgf000296_0001
294
Figure imgf000297_0001
295
Figure imgf000298_0001
296
Figure imgf000299_0001
297
Figure imgf000300_0001
298
Figure imgf000301_0001
or a pharmaceutically acceptable salt thereof, wherein B is an antibody or antibody fragment.
58. The compound of any of claims 1-3, wherein the compound is
Figure imgf000301_0002
or a pharmaceutically acceptable salt thereof, wherein B is an antibody or antibody fragment.
59. The compound of any of claims 4-6, wherein the compound is
Figure imgf000302_0001
Figure imgf000303_0001
301
Figure imgf000304_0001
302
Figure imgf000305_0001
303
Figure imgf000306_0001
304
Figure imgf000307_0001
or a pharmaceutically acceptable salt thereof.
60. The com ound of any of claims 4-6, wherein the compound is
Figure imgf000307_0002
or a pharmaceutically acceptable salt thereof. A compound of the formula:
Figure imgf000308_0001
R02-A7 R02-C7 R02-A10
Figure imgf000308_0002
R02-D7 R02-D9 R02-D8
Figure imgf000309_0001
or a pharmaceutically acceptable salt thereof.
62. A pharmaceutical composition comprising a compound of any of claims 1-61, or pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
63. A method of treating a cardiovascular disease, a proliferative disease, diabetic retinopathy, an inflammatory disease, an autoimmune disease, or an infectious disease in a subject in need thereof, the method comprising administering to the subject an effective amount of the compound of any of claims 1-61, or a pharmaceutically acceptable salt thereof, or the pharmaceutical composition of claim 62.
64. The method of claim 63, wherein the proliferative disease is a cancer.
65. The method of claim 63, wherein the infectious disease is a bacterial, fungal, or parasitic infection.
66. The method of claim 63, wherein the parasitic infection is malaria.
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WO2023096904A2 (en) 2021-11-24 2023-06-01 President And Fellows Of Harvard College C-16 modified trioxacarcins, antibody drug conjugates, and uses thereof

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US20150297747A1 (en) * 2012-11-26 2015-10-22 President And Fellows Of Harvard College Trioxacarcins, trioxacarcin-antibody conjugates, and uses thereof
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WO2021252708A1 (en) 2020-06-11 2021-12-16 President And Fellows Of Harvard College Stabilized trioxacarcin antibody drug conjugates and uses thereof
WO2023096904A2 (en) 2021-11-24 2023-06-01 President And Fellows Of Harvard College C-16 modified trioxacarcins, antibody drug conjugates, and uses thereof

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