WO2024168055A1 - Tnf-alpha binding agents and methods of using the same - Google Patents
Tnf-alpha binding agents and methods of using the same Download PDFInfo
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- WO2024168055A1 WO2024168055A1 PCT/US2024/014831 US2024014831W WO2024168055A1 WO 2024168055 A1 WO2024168055 A1 WO 2024168055A1 US 2024014831 W US2024014831 W US 2024014831W WO 2024168055 A1 WO2024168055 A1 WO 2024168055A1
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K7/00—Peptides having 5 to 20 amino acids in a fully defined sequence; Derivatives thereof
- C07K7/04—Linear peptides containing only normal peptide links
- C07K7/08—Linear peptides containing only normal peptide links having 12 to 20 amino acids
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- 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
- A61K47/54—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 compound
- A61K47/55—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 compound the modifying agent being also a pharmacologically or therapeutically active agent, i.e. the entire conjugate being a codrug, i.e. a dimer, oligomer or polymer of pharmacologically or therapeutically active compounds
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- 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
- A61K47/54—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 compound
- A61K47/554—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 compound the modifying agent being a steroid plant sterol, glycyrrhetic acid, enoxolone or bile acid
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P37/00—Drugs for immunological or allergic disorders
- A61P37/02—Immunomodulators
- A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
-
- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/52—Cytokines; Lymphokines; Interferons
- C07K14/525—Tumour necrosis factor [TNF]
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K38/00—Medicinal preparations containing peptides
Definitions
- the FDA-approved anti-TNF ⁇ therapies include four antibodies, HUMIRA® (adalimumab), REMICADE® (infliximab), CIMZIA® (certolizumab pegol), and SIMPONI ARIA® (golimumab) and one soluble form of TNFR, ENBREL® (etanercept). These drugs are used to treat a wide range of inflammatory conditions, including ulcerative colitis, Crohn’s disease, rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, and psoriasis among others.
- the peptides inhibit TNF ⁇ activity by binding to TNF ⁇ . In some embodiments, the peptides inhibit TNF ⁇ activity by binding to TNF ⁇ and blocking its binding to its receptors, TNFR1 and/or TNFR2.
- the TNFi peptides comprise a core TNF ⁇ binding domain composed of D-amino acids.
- a D-peptide or a salt thereof wherein the peptide comprises a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence, C-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 -X 8 -X 9 -X 10 -X 11 -C (SEQ ID NO:111), wherein each of X 2 through X 11 is a D-amino acid; and X 2 is the D form of any of the canonical L- amino acids other than cysteine; X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) or Leu (L); X 4 is a Polar amino acid comprising Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G
- a D-peptide or a salt thereof wherein the peptide comprises a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence, C*-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 -X 8 -X 9 -X 10 -X 11 -C* (SEQ ID NO:112), wherein each of X 2 through X 11 is a D-amino acid; and X 2 is the D form of any of the canonical L-amino acids other than cysteine; X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) and Leu (L); X 4 is a Polar amino acid comprising Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A),
- a D-peptide or a salt thereof wherein the peptide comprises a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence, C*-X 2 -[W/F/Y]-[Polar]-X 5 -X 6 -F-N-N-[W/Y]-W-C* (SEQ ID NO:113), wherein X 2 is the D form of any of the canonical L-amino acids other than Cys, X 5 is the D form of any of the canonical L-amino acids other than cysteine, X 6 is the D form of any of the canonical L-amino acids other than cysteine, Polar represents a D-amino acid comprising one of R, K, H, E, D, Q, N, T, S, P, A, or G, and the * indicate an optional intramolecular disulfide bond.
- a D-peptide or a salt thereof wherein the peptide comprises a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence, C-X 2 -X 3 -X 4 -X 5 -X 6 -F-F-N-X 10 -X 11 -C (SEQ ID NO:1), wherein each of X 2 through X 6 , X 10 is a D-amino acid or a D- ⁇ -amino acid analog thereof; and a.
- X 2 is the D form of any of Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W), or a D- ⁇ - amino acid analog thereof;
- X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) or Leu (L), or a D- ⁇ -amino acid analog thereof; c.
- X 4 is a Polar amino acid comprising the D form of Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G), or a D- ⁇ -amino acid analog thereof; d.
- X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, Ala, Val or Leu, or a D- ⁇ -amino acid thereof; e.
- X 6 is the D form of Arg (R), His (H), Lys (K), Glu (E), Gln (Q), Val (V), Leu (L), Ser (S), or Ala (A), or a D- ⁇ -amino acid analog thereof;
- X 10 is the D form of Trp (W) or Tyr (Y), or a D- ⁇ -amino acid analog thereof;
- X 11 is the D form of Trp (W), Tyr (Y), Gln (Q) or His (H) or a D- ⁇ -amino acid analog thereof; and h.
- the TNFi peptides comprise a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence: C*-X 2 -X 3 -X 4 - X 5 -X 6 -F-N-N-X 10 -X 11 -C* (SEQ ID NO:2), wherein each of X 1 through X6, X 10 , and X11 is a D-amino acid; and a.
- X 2 is the D form of Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W), or a D- ⁇ -amino acid analog thereof;
- X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) or Leu (L) , or a D- ⁇ -amino acid analog thereof; c.
- X 4 is a Polar amino acid comprising the D forms of Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G), or a D- ⁇ -amino acid analog thereof; d.
- X 5 is the D form of Pro (P), Trp (W), His (H), Gln (Q), Arg (R), Ala (A), Val (V), Leu (L), or Gly (G), or a D- ⁇ -amino acid analog thereof; e.
- X 6 is the D form of Arg (R), His (H), Lys (K), Glu (E), Gln (Q), Val (V), Leu (L), Ser (S), or Ala (A), or a D- ⁇ -amino acid analog thereof;
- X 10 is the D form of Trp (W) or Tyr (Y), or a D- ⁇ -amino acid analog thereof;
- X 11 is the D form of Trp (W), Tyr (Y), Gln (Q) or His (H);
- C denotes the D form of Cysteine; wherein F denotes the D form of phenylalanine; N denotes the D for of asparagine; and the * indicate an optional intramolecular disulfide bond.
- a D-peptide or a salt thereof wherein the core TNF ⁇ binding domain has the following amino acid sequence: C-X 2 -[W/F/Y]-X 4 -X 5 - X 6 -F-N-N-[W/Y]-W-C (SEQ ID NO:3).
- X 2 is the D form Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W);
- X 4 is the D form of Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G);
- X 5 is the D form of Pro (P), Trp (W), His (H), Gln (Q), Arg (R), Ala (A), Val (V), Leu (L), or Gly (G),
- X 6 is the D form of Arg (R), His (H), Lys (K), Glu (E), Gln (Q), Val (V), Leu (L), Ser (S), or Ala (A); and the * indicate an optional intramolecular disulfide bond between the indicated cysteine residues.
- a D-peptide or a salt thereof further comprising an intramolecular disulfide bond between the cysteine residues of the core TNF ⁇ binding domain.
- a D-peptide or a salt thereof having the amino acid sequence set forth in any of SEQ ID Nos:1 to 3, wherein: a. X 2 is the D form of Thr, Val, His, Leu, Gln, Ala, Ile, Met or Trp, or a D- ⁇ - amino acid analog thereof; b. X 2 is the D form of Thr, Val, His, Leu, or Gln, or a D- ⁇ -amino acid analog thereof; c.
- X 2 is the D form of Thr, Val, His or Leu, or a D- ⁇ -amino acid analog thereof; d. X 2 is the D form of Thr, Val or His, or a D- ⁇ -amino acid analog thereof; e. X 2 is the D form of Thr or Val, or a D- ⁇ -amino acid analog thereof; f. X 2 is the D form of Thr, or a D- ⁇ -amino acid analog thereof; or g. X 2 is the D form of Val, or a D- ⁇ -amino acid analog thereof.
- a D-peptide or a salt thereof having the amino acid sequence set forth in any of SEQ ID Nos:1 or 2, wherein: a. X 3 is the D form of Trp, Phe, Tyr, or Ser, or a D- ⁇ -amino acid analog thereof; b. X 3 is the D form of Trp, Phe, or Tyr, or a D- ⁇ -amino acid analog thereof; c. X 3 is the D form of Trp or Phe, or a D- ⁇ -amino acid analog thereof; d. X 3 is the D form of Trp or a D- ⁇ -amino acid analog thereof; or e.
- X 3 is the D form of Phe, or a D- ⁇ -amino acid analog thereof.
- a D-peptide or a salt thereof having the amino acid sequence set forth in any of SEQ ID Nos:1 to 3, wherein: a. X 4 is the D forms of Arg, His, Gln, Asn, Lys, Thr, or Ser, or a D- ⁇ -amino acid analog thereof; b. X 4 is the D form of Arg, His, Gln or Asn, or a D- ⁇ -amino acid analog thereof; c. X 4 is the D form of Arg, His or Gln, or a D- ⁇ -amino acid analog thereof; d.
- X 4 is the D form of Arg, Gln or Asn, or a D- ⁇ -amino acid analog thereof; or e. X 4 is the D form of Gln, or a D- ⁇ -amino acid analog thereof.
- a D-peptide or a salt thereof having the amino acid sequence set forth in any of SEQ ID Nos:1 to 3, wherein: a. X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, Ala, Val or Leu, or a D- ⁇ -amino acid analog thereof; b.
- X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, or Val, or a D- ⁇ -amino acid analog thereof; c. X 5 is the D form of Pro, Trp or His, or a D- ⁇ -amino acid analog thereof; d. X 5 is the D form of Pro or Trp, or a D- ⁇ -amino acid analog thereof; or e. X 5 is the D form of Pro, or a D- ⁇ -amino acid analog thereof. [0018] In some embodiments, provided is a D-peptide or a salt thereof having the amino acid sequence set forth in any of SEQ ID Nos:1 to 3, wherein: a.
- X 6 is the D-form of Arg, His, Lys, Glu, Gln, Val, Leu, Ser or Ala, or a D- ⁇ -amino acid analog thereof; b. X 6 is the D-form of Arg, His, Lys, Glu, Gln, Val or Leu, or a D- ⁇ -amino acid analog thereof; c. X 6 is the D-form of Arg, His, Lys, Glu, or Gln, or a D- ⁇ -amino acid analog thereof; d. X 6 is the D-form of Arg, His, Lys, or Glu, or a D- ⁇ -amino acid analog thereof; e.
- X 6 is the D-form of Arg, His, or Lys, or a D- ⁇ -amino acid analog thereof; f. X 6 is the D-form of Arg, or a D- ⁇ -amino acid analog thereof; g. X 6 is the D-form of Lys, of a D- ⁇ -amino acid analog thereof, or h. X 6 is the D-form of His, or a D- ⁇ -amino acid analog thereof. [0019] In some embodiments, provided is a D-peptide or a salt thereof having the amino acid sequence set forth in any of SEQ ID Nos:1 or 2, wherein: a.
- X 10 is the D form of Trp, or a D- ⁇ -amino acid analog thereof; or b. X 10 is the D form of Tyr, or a D- ⁇ -amino acid analog thereof.
- a D-peptide or a salt thereof having the amino acid sequence set forth in any of SEQ ID Nos:1 to 3, wherein: a. X 11 is the D form of Trp (W), Tyr (Y), or Gln (Q), or a D- ⁇ -amino acid analog thereof; b. X 11 is the D form of Tyr (Y), or c. X 11 is the D form of Trp (W), or a D- ⁇ -amino acid analog thereof.
- a D-peptide or a salt thereof wherein each of X 1 through X 6 , X 10 and X 11 is a D-amino acid. And C is the D-form of cysteine. F is the D-form of phenylalanine, and N is the D-form of asparagine.
- a D-peptide or a salt thereof wherein the core TNF ⁇ binding domain has an amino acid sequence selected from: a. CVWQPKFNNYWC (SEQ ID NO:4); b. CVWQPRFNNYWC (SEQ ID NO:5); c. CTFQPRFNNYWC (SEQ ID NO:6); d.
- CTFQPRFNNWWC (SEQ ID NO:7); e. CSFQPRFNNYWC (SEQ ID NO:8); f. CSFQPRFNNWWC (SEQ ID NO:9); g. CVFQPRFNNYWC (SEQ ID NO:10); h. CVFQPRFNNWWC (SEQ ID NO:11); i. CTFQWRFNNYWC (SEQ ID NO:12); j. CLYQPVFNNWWC (SEQ ID NO:13); k. CVFQAAFNNYWC (SEQ ID NO:14); l. CVFQHHFNNWWC (SEQ ID NO:15); m. CHFNPRFNNWWC (SEQ ID NO:16); n.
- CVWQPHFNNYWC (SEQ ID NO:17); o. CVFQGRFNNWWC (SEQ ID NO:18); p. CVFQHRFNNWWC (SEQ ID NO:19); q. CVFNPRFNNWWC (SEQ ID NO:20); r. CVFKPRFNNWWC (SEQ ID NO:21); s. CAYQRQFNNWWC (SEQ ID NO:22); t. CWFEHRFNNWHC (SEQ ID NO:23); u. CHFQHRFNNWWC (SEQ ID NO:24); v. CHFQPRFNNWWC (SEQ ID NO:25); w. CTYQPRFNNWWC (SEQ ID NO:26); x.
- a D-peptide or a salt thereof wherein the core TNF ⁇ binding domain has comprises an amino acid amino acid sequence set forth in SEQ ID NO:77 to 110.
- a D-peptide or a salt thereof further comprising a tag sequence attached to the N-terminus of the peptide.
- the tag comprises the amino acid sequence D-Asp or D-Asp D-Asp (DD).
- a D-peptide or a salt thereof further comprising a tag sequence attached to the C-terminus of the peptide.
- the tag comprises the amino acid sequence D-GGEEEK (SEQ ID NO:30) or D-GGRRRK (SEQ ID NO:31), wherein each amino acid residue is a D-amino acid.
- the N-terminus of the peptide comprises a cap.
- PEG polyethylene glycol
- a D-peptide or a salt thereof having an amino acid sequence selected from at least one of: a. DDCVWQPKFNNYWC (SEQ ID N:32); b. DGACVWQPKFNNYWC (SEQ ID NO:38); c. DDCVWQPRFNNYWC (SEQ ID NO:39); d. DDCVWQPRFNNYWCGGRRRK (SEQ ID NO:40); e. DCVWQPKFNNYWC (SEQ ID NO:56); f.
- DDDCVWQPRFNNYWC (SEQ ID NO:60); g. DDCTFQPRFNNWWC (SEQ ID NOL61); h. DDCVFQPRFNNYWC (SEQ ID NO:62); i. DDCSFQPRFNNYWC (SEQ ID NO:63); and j. DDCVFQPRFNNWWC (SEQ ID NO:64).
- DGACVWQPKFNNYWC (SEQ ID NO:38); c. DDCVWQPRFNNYWC (SEQ ID NO:39); d. DDCVWQPRFNNYWCGGRRRK (SEQ ID NO:40); e. DCVWQPKFNNYWC (SEQ ID NO:56); f. DDDCVWQPRFNNYWC (SEQ ID NO:60); g. DDCTFQPRFNNWWC (SEQ ID NOL61); h. DDCVFQPRFNNYWC (SEQ ID NO:62); i. DDCSFQPRFNNYWC (SEQ ID NO:63); and j. DDCVFQPRFNNWWC (SEQ ID NO:64).
- a pharmaceutical composition comprising at least one D-peptide described herein or multimer thereof, or pharmaceutically acceptable salt thereof, and at least one pharmaceutically acceptable excipient or carrier.
- a pharmaceutical composition which is formulated for parenteral administration.
- a pharmaceutical composition which is formulated for intravenous, intramuscular, or subcutaneous administration.
- provided is such a pharmaceutical composition, which is formulated for oral administration.
- provided is such a pharmaceutical composition which is formulated for topical administration.
- a lyophilized composition comprising at least one D-peptide or multimer described herein, or a salt or pharmaceutically acceptable salt thereof and a stabilizing agent.
- a lyophilized composition of any of the pharmaceutical compositions described herein and a stabilizing agent is provided.
- a method of treating a TNF ⁇ -mediated disease comprising administering an effective amount of any of the D-peptides described herein, or a salt or pharmaceutically acceptable salt thereof, or any of the multimers described herein, or a salt thereof or any of the pharmaceutical compositions described herein.
- the TNF ⁇ -mediated disease is adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenitis suppurativa, Uveitis (intermediate, posterior, or panuveitis), or non-radiographic axial spondyloarthritis.
- the TNF ⁇ -mediated disease is an inflammatory bowel disease.
- the inflammatory bowel disease is adult Crohn’s Disease, pediatric Crohn’s Disease, or Ulcerative Colitis.
- the administration of any of the D-peptides described herein, or pharmaceutically acceptable salt thereof, or any of the multimers described herein, or pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein is oral.
- the administration of any of the D-peptides described herein, or pharmaceutically acceptable salt thereof, or any of the multimers described herein, or pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein is rectal.
- the administration of any of the D- peptides described herein, or pharmaceutically acceptable salt thereof, or any of the multimers described herein, or pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein is parenteral.
- the TNF ⁇ -mediated disease is an inflammatory skin disease.
- the inflammatory skin disease is selected from Plaque Psoriasis and Cutaneous Lupus.
- the administration of any of the D- peptides described herein, or pharmaceutically acceptable salt thereof, or any of the multimers described herein, or pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein is topical.
- the administration of any of the D-peptides described herein, or pharmaceutically acceptable salt thereof, or any of the multimers described herein, or pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein is parenteral. In some embodiments, the administration of any of the D-peptides described herein, or a pharmaceutically acceptable salt thereof, or any of the multimers described herein, or a pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein, is oral.
- the TNF ⁇ -mediated disease is an inflammatory disease, such as, for example, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, idiopathic arthritis (polyarticular), or non- radiographic axial spondyloarthritis.
- the administration of any of the D-peptides described herein, or pharmaceutically acceptable salt thereof, or any of the multimers described herein, or pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein is parenteral.
- parenteral administration can be intravenous, subcutaneous, and intramuscular.
- a method of inhibiting TNF ⁇ comprising administering any of the D-peptides described herein, or a pharmaceutically acceptable salt thereof, or any of the multimers described herein, or a pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein, to a subject.
- a method of reducing an inflammatory response mediated by TNF ⁇ comprising administering any of the D-peptides described herein, or a pharmaceutically acceptable salt thereof, or any of the multimers described herein, or a pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein, to a subject.
- the administering is by oral administration, by parenteral administration, by topical (dermal), or by rectal administration.
- any of the D-peptides described herein, or a pharmaceutically acceptable salt thereof, or any of the multimers described herein, or a pharmaceutically acceptable salt thereof or any of the pharmaceutical compositions described herein are administered locally to reduce TNF ⁇ activity or inflammation or an inflammatory response.
- the subject has a TNF ⁇ - mediated disease.
- the TNF ⁇ - mediated disease is adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenitis suppurativa, Uveitis (intermediate, posterior, or panuveitis), or non-radiographic axial spondyloarthritis.
- a D-peptide as described herein a multimer of any of the D-peptides described herein, or a salt thereof, for use as a medicament.
- the subject has a TNF ⁇ - mediated disease.
- the TNF ⁇ - mediated disease is adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenitis suppurativa, Uveitis (intermediate, posterior, or panuveitis), or non-radiographic axial spondyloarthritis.
- FIGURE 1 shows a comparison of the TNF ⁇ binding by selected peptides isolated by mirror image phage screening from all libraries.
- FIGURE 2 shows a comparison of the binding of Peptide 18 and two Peptide 18 variants to TNF ⁇ in a solid phase binding assay.
- FIGURE 3 shows that Peptide 18 can block binding of TNF ⁇ to its receptor, TNFR1, in a solid phase binding assay.
- FIGURE 4A shows that Peptide 18 can block cellular activity of TNF ⁇ in an L-929 cell killing assay.
- FIGURE 4B shows that Peptide 18 can block cellular activity of TNF ⁇ in a concentration-dependent manner in the L-929 cell killing assay.
- FIGURE 5 shows the effects of amino acid changes at the N-terminus, C-terminus and an internal position of Peptide 18 on TNF ⁇ binding.
- FIGURE 6 shows the effects of amino acid changes at the N-terminus, C-terminus and an internal position of Peptide 18 using the TNF ⁇ /TNFR blocking assay.
- FIGURE 7 shows the effects of amino acid changes at the N-terminus, C-terminus and internal positions of Peptide 18 using the TNF ⁇ /TNFR blocking assay.
- FIGURE 8 shows the effects of amino acid changes at the N-terminus, C-terminus and internal positions of Peptide 18 using the L-929 cell killing assay.
- FIGURE 9 shows the effects of insertion of an N-terminal PEG4 spacer and insertion or deletion of an amino acid residue on Peptide 18 using the TNF ⁇ binding assay.
- FIGURE 10 shows the effects of insertion of an N-terminal PEG spacer and insertion or deletion of an amino acid residue on Peptide 18 using the L-929 cell killing assay.
- FIGURE 11 compares the activity of Peptide 18 KtoR dimers and trimers using the L-929 cell killing assay.
- FIGURE 12 compares the activity of Peptide 18 mutants and other library hits using the TNF ⁇ binding assay.
- FIGURE 13 compares the activity of Peptide 18 KtoR trimers having different PEG lengths using the L-929 cell killing assay.
- FIGURE 14 compares the activity of Peptide 18 and Peptide 18 mutants using the L-929 cell killing assay.
- FIGURE 15A shows the structures of three multimer scaffolds used to make peptide trimers.
- FIGURE 15B compares the activity of three Peptide 18 KtoR trimers using the L-929 cell killing assay.
- FIGURE 16A shows the structures of six multimer scaffolds used to make peptide trimers.
- FIGURE 16B compares the activity of six Peptide 18 KtoR trimers using the L-929 cell killing assay.
- FIGURE 17 compares the activity of Peptide 18 KtoR trimers having different PEG lengths using the L-929 cell killing assay.
- FIGURE 18 compares the activity of Peptide 18 mutants using the L-929 cell killing assay.
- FIGURE 19 shows the effects of replacement of an N-terminal aspartate residue with succinic acid using the L-929 cell killing assay.
- FIGURE 20 shows the activity of Peptide 18 mutants that contain non-standard amino acids using the L-929 cell killing assay.
- FIGURE 21 shows that fluorescently-labeled Peptide DD-018 binds to native TNF ⁇ .
- FIGURES 22A and B compare the activity of Peptide TF-018-KtoR-WW and oligomers thereof and an anti-TNF ⁇ antibody using the TNF ⁇ /TNFR blocking assay.
- FIGURES 23A and B compare the activity of Peptide TF-018-KtoR-WW and oligomers and an anti-TNF ⁇ antibody using the L-929 cell killing assay.
- FIGURE 24 shows that Peptide TF-18-KtoR-WW C-Trimer can block the activity of membrane-bound TNF ⁇ .
- FIGURE 25 shows the inhibition of IL-8 levels by Peptide TF-18-KtoR- WW C-Trimer following stimulation of blood samples with recombinant human TNF, LPS and anti-CD3 + anti-CD28 antibodies.
- FIGURE 26 shows the results of Peptide TF-18-KtoR-WW C-Trimer administration in a human TNF ⁇ mouse challenge model.
- FIGUREs 27 and 28 show Peptide TF-18-KtoR-WW C-Trimer plasma levels following a single subcutaneous dose in CD1mice.
- FIGURE 29 shows Peptide TF-18-KtoR-WW C-Trimer levels in plasma following administration of 5.0 mg/kg IV or 50 mg/kg SC.
- FIGURE 30 shows Peptide TF-18-KtoR-WW C-Trimer levels in small intestine, liver, plasma, large intestine and kidney following oral administration.
- FIGURE 31 shows inhibition of IL-6 following subcutaneous administration of Peptide TF-18-KtoR-WW C-Trimer to Tg1278 mice.
- FIGURE 32 shows inhibition of mouse KC following subcutaneous administration of Peptide TF-18-KtoR-WW C-Trimer to Tg1278 mice.
- the terms “decrease,” “reduce,” “reduced”, “reduction”, “decrease,” and “inhibit” are all used herein generally to mean a decrease by a statistically significant amount relative to a reference.
- the terms “increased”, “increase” or “enhance” or “activate” are all used herein to generally mean an increase by a statically significant amount relative to a reference.
- the terms “protein” and “polypeptide” are used interchangeably herein to designate a series of amino acid residues each connected to each other by peptide bonds between the alpha-amino and carboxyl groups of adjacent residues.
- protein and polypeptide also refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, and the like) and amino acid analogs, regardless of its size or function.
- modified amino acids e.g., phosphorylated, glycated, glycosylated, and the like
- amino acid analogs regardless of its size or function.
- Protein and polypeptide are often used in reference to relatively large polypeptides, whereas the term “peptide” is often used in reference to small polypeptides, but usage of these terms in the art overlaps.
- protein and polypeptide are used interchangeably herein when referring to an encoded gene product and fragments thereof.
- TNF ⁇ (also referred to as TNFalpha or TNF-alpha or TNF) is a protein that is expressed on a variety of cell types, including monocytes, macrophages, NK cells and regulatory T cells. TNF ⁇ has both a membrane and a soluble form. TNF ⁇ proteins include, but are not limited to, those having the amino acid sequences set forth in accession numbers AQY77150.1, P01375-1, and NP_000585.2; these sequences are incorporated by reference herein.
- D-amino acid and D-amino acid residue”, as used herein, refer to an ⁇ -amino acid residue having the same absolute configuration as D-glyceraldehyde.
- amino acids are named herein using either their 1-letter or 3-letter code according to the recommendations from IUPAC. Unless otherwise indicated by context, an amino acid is of the D-form.
- D-forms of the canonical L-amino acids and “D-forms of any of the canonical L-amino acids” refer to D-forms of alanine, arginine, asparagine, aspartic acid (aspartate), cysteine, glutamine, glutamic acid (glutamate), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine and valine. For convenience, this phrase also refers to glycine, although this amino acid is achiral.
- D-peptide refers to a peptide composed of D- amino acid residues.
- “specifically binds” refers to the ability of a binding agent (e.g., a D-peptide as described herein) to bind to a target with a KD 10 -5 M (10000 nM) or less, e.g., 10 -6 M, 10 -7 M, 10 -8 M, 10 -9 M, 10 -10 M, 10 -11 M, 10 -12 M, or less. Specific binding can be influenced by, for example, the affinity and avidity of the binding agent and the concentration of target polypeptide.
- a person of ordinary skill in the art can determine appropriate conditions under which the binding agent selectively bind to a target using any suitable methods, such as titration of a binding agent in a suitable cell binding assay or in a suitable solid phase binding assay.
- a binding agent specifically bound to a target is not displaced by a non-similar competitor.
- a binding agent is said to specifically bind to its target when it preferentially recognizes its target in a complex mixture of proteins and/or macromolecules.
- the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment.
- pharmaceutically acceptable salt generally means those salts which retain the biological effectiveness and properties of the free bases and which is not biologically or otherwise undesirable formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and organic acids, such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid.
- inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and organic acids, such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, malic acid,
- “Pharmaceutically acceptable salt” includes solvates, particularly hydrates, of such salts. [0096] Other terms are defined herein within the description of the various aspects of the invention. DETAILED DESCRIPTION [0097] The present disclosure is based on the discovery of a highly potent and specific class of D-peptide-based inhibitors of TNF ⁇ (also referred to herein as TNFi peptides).
- the peptides inhibit TNF ⁇ activity by binding to TNF ⁇ .
- the peptides inhibit TNF ⁇ activity by binding to TNF ⁇ and blocking its binding to its receptors, TNFR1 and/or TNFR2.
- the peptides inhibit TNF ⁇ activity by blocking its binding to TNFR1.
- the peptides inhibit TNF ⁇ activity by blocking its binding to TNFR2.
- the TNFi peptides comprise a core TNF ⁇ binding domain composed of D-amino acids.
- the TNFi peptides specifically bind to both soluble and membrane bound TNF ⁇ .
- the TNFi peptides specifically bind to soluble TNF ⁇ .
- the TNFi peptides specifically bind to membrane bound TNF ⁇ .
- the TNFi-peptides are resistant to proteolysis in the environment of the gastrointestinal tract. [0098] Also provided are methods of using the TNFi peptides for the treatment of TNF ⁇ -mediated diseases, including inflammatory and autoimmune diseases and disorders.
- the term “TNF ⁇ -mediated diseases” means diseases or disorders in which TNF ⁇ signaling pathways and/or the cell biological effects of TNF ⁇ are involved in the disease or a symptom thereof.
- the TNFi peptides are administered by parenteral administration, by intravenous administration, by intramuscular administration, by subcutaneous administration, by oral administration, by topical administration or by rectal administration. These and other embodiments are further described herein.
- Peptides [0100] Provided herein are D-peptide-based inhibitors of TNF ⁇ . In some embodiments, the peptides inhibit TNF ⁇ activity by binding to TNF ⁇ .
- the peptides inhibit TNF ⁇ activity by binding to TNF ⁇ and blocking its binding to its receptors, TNFR1 and/or TNFR2.
- the TNFi peptides comprise a core TNF ⁇ binding domain composed of D-amino acids.
- a D-peptide or a salt thereof wherein the peptide comprises a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence, C-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 -X 8 -X 9 -X 10 -X 11 -C (SEQ ID NO:111), wherein each of X 2 through X 11 is a D-amino acid; and X 2 is the D form of any of the canonical L- amino acids other than cysteine; X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) or Leu (L); X 4 is a Polar amino acid comprising Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G
- a D-peptide or a salt thereof wherein the peptide comprises a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence, C*-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 -X 8 -X 9 -X 10 -X 11 -C* (SEQ ID NO:112), wherein each of X 2 through X 11 is a D-amino acid; and X 2 is the D form of any of the canonical L-amino acids other than cysteine; X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) and Leu (L); X 4 is a Polar amino acid comprising Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A),
- a D-peptide or a salt thereof wherein the peptide comprises a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence, C*-X 2 -[W/F/Y]-[Polar]-X 5 -X 6 -F-N-N-[W/Y]-W-C* (SEQ ID NO:113), wherein X 2 is the D form of any of the canonical L-amino acids other than Cys, X 5 is the D form of any of the canonical L-amino acids other than cysteine, X 6 is the D form of any of the canonical L-amino acids other than cysteine, Polar represents a D-amino acid comprising one of R, K, H, E, D, Q, N, T, S, P, A, or G, and the * indicate an optional intramolecular disulfide bond.
- the TNFi peptides comprise a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence: C-X 2 -X 3 -X 4 -X 5 - X 6 -F-N-N-X 10 -X 11 -C (SEQ ID NO:1), wherein each of X 1 through X 6 , X 10 , and X 11 is a D- amino acid; and X 2 is the D form of Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W), or a D- ⁇ -amino acid analog thereof; X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) or Leu (L), or a D- ⁇ -amino acid analog thereof; X 4 is the D form of Arg (R), Lys (K), His (H (H
- the TNFi peptides comprise a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence: C*-X 2 -X 3 -X 4 - X 5 -X 6 -F-N-N-X 10 -X 11 -C* (SEQ ID NO:2), wherein each of X 1 through X 6 , X 10 , and X 11 is a D-amino acid; and X 2 is the D form of Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W), or a D- ⁇ -amino acid analog thereof; X 3 is the D form of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) or Leu (L) , or a D- ⁇ -amino acid analog thereof; X 4 is a Polar amino acid comprising the D forms of
- X 2 is the D-form of Thr, Val, His, Leu, Gln, Ala, Ile, Met or Trp. In some embodiments, X 2 is the D form of Thr, Val, His, Leu, or Gln. In some embodiments, X 2 is the D form of Thr, Val, His or Leu. In some embodiments, X 2 is the D form of Thr, Val or His. In some embodiments, X 2 is the D form of Thr or Val. In some embodiments, X 2 is the D form of Thr. In some embodiments, X 2 is the D form of Val.
- X 3 is the D form of Trp, Phe, Tyr, or Ser. In some embodiments, X 3 is the D form of Trp, Phe, or Tyr. In some embodiments, X 3 is the D form of Trp or Phe. In some embodiments, X 3 is the D form of Trp. In some embodiments, X 3 is the D form of Phe. [0108] In some embodiments of the TNFi peptides set forth in SEQ ID NO:1 or 2, X 4 is the D form of Arg, His, Gln, Lys, Asn, Thr, or Ser.
- X 4 is the D form of Arg, His, Gln, Lys or Asn. In some embodiments, X 4 is the D form of Arg, His or Gln. In some embodiments, X 4 is the D form of Arg, Gln or Asn. In some embodiments, X 4 is the D form of Gln. [0109] In some embodiments of the TNFi peptides set forth in SEQ ID NO:1 or 2, X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, Ala, Val or Leu. In some embodiments, X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, or Val.
- X 5 is the D form of Pro, Trp or His. In some embodiments, X 5 is the D form of Pro or Trp. In some embodiments, X 5 is the D form of Pro. [0110] In some embodiments of the TNFi peptides set forth in SEQ ID NO:1 or 2, X 6 is the D-form of Arg, His, Lys, Glu, Gln, Val, Leu, Ser or Ala. In some embodiments, X 6 is the D-form of Arg, His, Lys, Glu, Gln, Val or Leu. In some embodiments, X 6 is the D-form of Arg, His, Lys, Glu, or Gln.
- X 6 is the D-form of Arg, His, Lys, or Glu. In some embodiments, X 6 is the D-form of Arg, Lys, or His. In some embodiments, X 6 is the D-form of Arg. In some embodiments, X 6 is the D-form of Lys, In some embodiments, X 6 is the D-form of His. [0111] In some embodiments of the TNFi peptides set forth in SEQ ID NO:1 or 2, X 10 is the D form of Trp. In some embodiments, X 10 is the D form of Tyr.
- X 11 is the D form of Trp (W), Tyr (Y), or Gln (Q). In some embodiments, X 11 is the D form of Trp (W).
- the TNFi peptides comprise a core TNF ⁇ binding domain of D-amino acids and having the following amino acid sequence: C*-X 2 -[W/F/Y]- X 4 -X 5 -X 6 -F-N-N-[W/Y]-W-C* (SEQ ID NO:3), wherein X 2 is the D form Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W); X 4 is the D form of Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G); X 5 is the D form of Pro (P), Trp (W), His (H), Gln (Q), Arg (R), Ala (A), Val (V), Le
- X 2 is the D form of Thr, Val, His, Leu, Gln, Ala, Ile, Met or Trp. In some embodiments, X 2 is the D form of Thr, Val, His, Leu, or Gln. In some embodiments, X 2 is the D form of Thr, Val, His or Leu. In some embodiments, X 2 is the D form of Thr, Val or His. In some embodiments, X 2 is the D form of Thr or Val. In some embodiments, X 2 is the D form of Thr. In some embodiments, X 2 is the D form of Val.
- X 4 is selected from the D forms of Arg, His, Lys, Gln, Asn, Thr, or Ser.
- X 4 is the D form of Arg, His, Lys, Gln or Asn.
- X 4 is the D form of Arg, His, Lys or Gln.
- X 4 is the D form of Arg, Gln or Asn.
- X 4 is the D form of Arg, Gln or Lys.
- X 4 is the D form of Gln.
- X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, Ala, Val or Leu. In some embodiments, X 5 is the D form of Pro, Trp, His, Lys, Gln, Gly, Arg, or Val. In some embodiments, X 5 is the D form of Pro, Trp, or His. In some embodiments, X 5 is the D form of Pro or Trp. In some embodiments, X 5 is the D form of Pro.
- X 6 is the D form of Arg, His, Lys, Glu, Gln, Val, Leu, Ser or Ala. In some embodiments, X 6 is the D form of Arg, His, Lys, Glu, Gln, Val or Leu. In some embodiments, X 6 is the D form of Arg, His, Lys, Glu, or Gln. In some embodiments, X 6 is selected from the D form of Arg, His, Lys, or Glu. In some embodiments, X 6 is the D form of Arg or His. In some embodiments, X 6 is the D form of Arg or Lys.
- X 6 is the D form of Arg. In some embodiments, X 6 is the D form of His. In some embodiments, X 6 is the D- form of Lys.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVWQPKFNNYWC (SEQ ID NO:4), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVWQPRFNNYWC (SEQ ID NO:5), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQPRFNNYWC (SEQ ID NO:6), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQPRFNNWWC (SEQ ID NO:7), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CSFQPRFNNYWC (SEQ ID NO:8), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CSFQPRFNNWWC (SEQ ID NO:9), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQPRFNNYWC (SEQ ID NO:10), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQPRFNNWWC (SEQ ID NO:11), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQWRFNNYWC (SEQ ID NO:12), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CLYQPVFNNWWC (SEQ ID NO:13), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQAAFNNYWC (SEQ ID NO:14), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQHHFNNWWC (SEQ ID NO:15), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CHFNPRFNNWWC (SEQ ID NO:16), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVWQPHFNNYWC (SEQ ID NO:17), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQGRFNNWWC (SEQ ID NO:18), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQHRFNNWWC (SEQ ID NO:19), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFNPRFNNWWC (SEQ ID NO:20), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFKPRFNNWWC (SEQ ID NO:21), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CAYQRQFNNWWC (SEQ ID NO:22), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CWFEHRFNNWHC (SEQ ID NO:23), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CHFQHRFNNWWC (SEQ ID NO:24), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CHFQPRFNNWWC (SEQ ID NO:25), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTYQPRFNNWWC (SEQ ID NO:26), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CQFQPRFNNWQC (SEQ ID NO:27), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CHFSQRFNNWWC (SEQ ID NO:28), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CIFQQQFNNYWC (SEQ ID NO:77), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CMHQQRFNNWWC (SEQ ID NO:78), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFRVRFNNYWC (SEQ ID NO:79), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CIFQWRFNNYWC (SEQ ID NO:80), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQWHFNNYWC (SEQ ID NO:81), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQHLFNNWWC (SEQ ID NO:82), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQWLFNNYWC (SEQ ID NO:83), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CAFQWRFNNYWC (SEQ ID NO:84), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFRWRFNNYWC (SEQ ID NO:85), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTSQWRFNNYWC (SEQ ID NO:86), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQLRFNNYWC (SEQ ID NO:87), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQVRFNNYWC (SEQ ID NO:88), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CIWQPKFNNYWC (SEQ ID NO:89), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQRRFNNYWC (SEQ ID NO:90), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTFQWSFNNYWC (SEQ ID NO:91), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQRHFNNWWC (SEQ ID NO:92), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVSTHHFNNWWC (SEQ ID NO:93), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CAFQHHFNNWWC (SEQ ID NO:94), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CAYQRHFNNWWC (SEQ ID NO:95), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CHFNPLFNNWWC (SEQ ID NO:96), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CHFNRRFNNWWC (SEQ ID NO:97), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CHFSQLFNNWWC (SEQ ID NO:98), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CLYQLVFNNWWC (SEQ ID NO:99), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CQFRPRFNNWQC (SEQ ID NO:100), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTLQQQFNNYWC (SEQ ID NO:101), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CTSRWRFNNYWC (SEQ ID NO:102), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQASFNNYWC (SEQ ID NO:103), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFQHSFNNWWC (SEQ ID NO:104), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFRHHFNNWWC (SEQ ID NO:105), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVFTHHFNNWWC (SEQ ID NO:106), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVSQHHFNNWWC (SEQ ID NO:107), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVWQPEFNNYWC (SEQ ID NO:108), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVWQQKFNNYWC (SEQ ID NO:109), optionally comprising an intramolecular disulfide bond.
- the TNFi peptide comprises a core TNF ⁇ binding domain having the following amino acid sequence: CVWRPKFNNYWC (SEQ ID NO:110), optionally comprising an intramolecular disulfide bond.
- a TNFi peptide comprises a core TNF ⁇ binding domain selected from the following amino acid sequences: CVWQPKFNNYWC (SEQ ID NO:4); CVWQPRFNNYWC (SEQ ID NO:5); CTFQPRFNNYWC (SEQ ID NO:6); CTFQPRFNNWWC (SEQ ID NO:7); CSFQPRFNNYWC (SEQ ID NO:8); CSFQPRFNNWWC (SEQ ID NO:9); CVFQPRFNNYWC (SEQ ID NO:10); CVFQPRFNNWWC (SEQ ID NO:11); CTFQWRFNNYWC (SEQ ID NO:12); CHFNPRFNNWWC (SEQ ID NO:16); CVFQGRFNN
- a TNFi peptide comprises a core TNF ⁇ binding domain selected from the amino acid sequences set forth in SEQ ID NO:4-28 and 77-110.
- TNFi Peptides Comprising D-Amino Acid Analogs
- one or more D-amino acids in a TNFi peptide can be replaced with a D- ⁇ -amino acid analog of the D-amino acid(s).
- a D- ⁇ -amino acid analog is a D- ⁇ -amino acid analog that has both an amine functional group, either as NH 2 , NHR, or NR2, and a carboxylic acid functional group.
- a TNFi peptide having a core TNF ⁇ binding domain set forth in any of SEQ ID NOs:1 to 3 and 111 to 113 has at least one D- ⁇ -amino acid analog substitution in the core TNF ⁇ binding domain. In some embodiments, a TNFi peptide having a core TNF ⁇ binding domain set forth in any of SEQ ID NOs:1 to 3 and 111 to 113 has at least two D- ⁇ -amino acid analog substitutions in the core TNF ⁇ binding domain.
- a TNFi peptide having a core TNF ⁇ binding domain set forth in any of SEQ ID NOs:1 to 3 and 111 to 113 has at least three D- ⁇ -amino acid analog substitutions in the core TNF ⁇ binding domain.
- Charged D- ⁇ -amino acid analogs include the D forms of 4-methyl glutamate, mono-4-fluoro glutamate, 4,4-difluoro-glutamate, gamma-hydroxy glutamate, L-threo- ⁇ -hydroxyaspartate, epsilon-N,N,N-trimethyllysine, epsilon-N-acetyllysine, aza- leucine, O-phosphoserine, 3-methylhistidine, 5-hydroxylysine, and methylarginine.
- Polar uncharged D-amino acid analogs include the D forms of L-Glu ⁇ -hydrazide, L-albizziin, L-theanine, ⁇ -hydroxy norvaline, aspartate methyl ester and glutamate methyl ester.
- Aromatic D-amino acid analogs include the D forms of ⁇ -2-thiazolyl- alanine, triazole alanine, 3-fluoro-L-tyrosine, 3-nitro-L-tyrosine, 3-fluoro phenyalanine, 2- thienyl alanine, ⁇ -methyl phenylalanine), ⁇ -thienyl serine, N-acetylserine, N- formylmethionine, p-azido phenylalanine, p-ethynyl phenylalanine, p-nitro-phenylalanine, 7-aza-tryptophan, 5-hydroxy tryptophan, 5-fluoro tryptophan, 5-methoxy tryptophan, 3- (thianapthen-3-yl)-L-alanine, 2-thienyl glycine and L-phenylglycine.
- Non-polar D-amino acid analogs include the D forms of 2-amino hex-5- ynoic acid, norleucine, norvaline, ethionine, ⁇ -azidohomoalanine, trifluoro norleucine, trifluoro norvaline, L-C-propargyl glycine, L-allyl glycine, ⁇ -cyclopropyl alanine, 3- fluoro-valine, methyl ether L-threonine, methyl ether L-allo-threonine, 4-thia-isoleucine, L-cyclohexyl-glycine, 5′,5′,5′-trifluoro leucine, ⁇ -cyclopentyl alanine, thiazolidine-2- carboxylic acid, thiazolidine-4-carboxylic acid, pseutdoproline, 3,4-dehydro proline, and 4-hydroxyproline.
- a TNFi peptide comprises a core TNF ⁇ binding domain having a D- ⁇ -amino acid analog has the following amino acid sequence: XTFQPRFNNWWC (SEQ ID NO:114), optionally comprising an intramolecular disulfide bond, wherein X is Penicillamine (Pen).
- a TNFi peptide comprises a core TNF ⁇ binding domain having a D- ⁇ -amino acid analog has the following amino acid sequence: CTFQPRFNNWWX (SEQ ID NO:115), optionally comprising an intramolecular disulfide bond, wherein X is Penicillamine (Pen).
- a TNFi peptide comprises a core TNF ⁇ binding domain having a D- ⁇ -amino acid analog has the following amino acid sequence: CXFQPRFNNWWC (SEQ ID NO:74), optionally comprising an intramolecular disulfide bond, wherein X is homoleucine (homoLeu).
- a TNFi peptide comprises a core TNF ⁇ binding domain having a D- ⁇ -amino acid analog has the following amino acid sequence: CXFQPRFNNWWC (SEQ ID NO:75), optionally comprising an intramolecular disulfide bond, wherein X is norleucine (norLeu).
- the TNFi peptides are capped at the N-terminus and/or the C-terminus. In some embodiments, a TNFi peptide is capped at the N-terminus. In some embodiments, a TNFi peptide is capped at the N-terminus with, for example, an acetyl group. In some embodiments, a TNFi peptide is capped at the N-terminus with, for example, a protecting group. In some embodiments, a TNFi peptide is capped at the C- terminus.
- a TNFi peptide is capped at the C-terminus with, for example, an amide group. In some embodiments, a TNFi peptide is capped at the C- terminus with, for example, a protecting group. [0191] In some embodiments, a TNFi peptide has a core TNF ⁇ binding domain that is flanked by an additional amino acid residue(s) attached to the N-terminus and/or the C-terminus (a flanking sequence or tag). In some embodiments, a TNFi peptide has a core TNF ⁇ binding domain that is flanked by an additional D-amino acid residue(s) attached to the N-terminus and/or the C-terminus (a flanking sequence or tag).
- a tag can, for example, increase the solubility of a TNFi peptide (e.g., in an aqueous solution).
- the tags can be the same or different.
- a tag is attached to the N-terminus of the core-TNF ⁇ binding domain.
- a tag is attached to the C-terminus of the core TNF ⁇ binding domain.
- a tag is attached to the N-terminus and to the C-terminus of the core TNF ⁇ binding domain. [0192]
- a tag is attached to the N-terminus of the core TNF ⁇ binding domain.
- a tag attached to the N-terminus of the core TNF ⁇ binding domain is 1 to 20 amino acids in length, 1 to 10 amino acids in length, 1 to 6 amino acids in length, or 1 to 3 amino acids in length, 2 to 3 amino acids in length or 1 to 2 amino acids in length or 2 amino acids in length.
- a tag having 1, 2 or 3 D-aspartate residues is attached to the N-terminus of the core-TNF ⁇ peptide binding domain.
- a tag having the amino acid sequence DGA is attached to the N-terminus of the core TNF ⁇ binding domain.
- a tag of 1 or 2 D-aspartate residues is attached to the N-terminus of the core TNF ⁇ binding domain. In some embodiments, a tag of 2 D-aspartate residues is attached to the N-terminus of the core TNF ⁇ binding domain. In some embodiments, a tag of 1 D-aspartate residue is attached to the N-terminus of the core TNF ⁇ binding domain. [0193] In some embodiments, a tag is attached to the C-terminus of the core TNF ⁇ binding domain. In some embodiments, a tag attached to the C-terminus of the core TNF ⁇ binding domain is 1 to 10 amino acids in length, or 1 to 8 amino acids in length, 2 to 8 amino acids in length or 2 to 6 amino acids in length.
- a tag comprises a single glycine attached to the C-terminus of the core TNF ⁇ binding domain. In some embodiments, a tag comprises a pair of glycine residues attached to the C-terminus of the core TNF ⁇ binding domain. In some embodiments, a tag has the D-amino acid sequence GGEEEK (SEQ ID NO:30) and is attached to the C-terminus of the core TNF ⁇ binding domain. In some embodiments, a tag has the D-amino acid sequence GGRRRK (SEQ ID NO:31) and is attached to the C-terminus of the core TNF ⁇ binding domain.
- the TNFi peptides are capped at the N-terminus and/or the C-terminus of a tag. In some embodiments, the TNFi peptides are capped at the N-terminus of a tag. In some embodiments, the TNFi peptides are capped at the N-terminus with, for example, an acetyl group. In some embodiments, the TNFi peptides are capped at the C-terminus of a tag. In some embodiments, the TNFi peptides are capped at the C- terminus with, for example, an amide group.
- a TNFi peptide can comprise additional amino acids in addition to the core TNF ⁇ binding domain and any attached tags. Such additional amino acids can be D-amino acids or L-amino acids.
- a TNFi peptide, including a tag at the N-terminus and/or C-terminus is from 12 to 50 amino acids in length, or 12 to 40 amino acids in length, or 12 to 30 amino acids in length, or 12 to 20 amino acids in length.
- a TNFi peptide, including a tag at the N-terminus and/or C-terminus is from 12 to 50 amino acids in length.
- a TNFi peptide, including a tag at the N-terminus and/or C-terminus is from 12 to 40 amino acids in length. In some embodiments, a TNFi peptide, including a tag at the N-terminus and/or C- terminus, is from 12 to 30 amino acids in length. In some embodiments, a TNFi peptide, including a tag at the N-terminus and/or C-terminus, is from 12 to 20 amino acids in length. [0196] Linkers [0197] In some embodiments, a TNFi peptide includes a Linker attached to its N-terminus and/or its C-terminus. In some embodiments, a Linker comprises L-amino acids.
- a Linker comprises D-amino acids. In some embodiments, a Linker comprises chemical groups other than amino acids. In some embodiments, a Linker comprises chemical groups (other than amino acids) and an amino acid(s). In some embodiments, a Linker comprises both chemical groups (other than amino acids) and an L-amino acid(s). In some embodiments, a Linker comprises chemical groups (other than amino acids) and a D-amino acid(s). [0198] In some embodiments, a Linker comprises a repeating polymer unit. In some embodiments, a polymer unit is attached to the N-terminus of a TNFi peptide.
- a polymer unit is attached to the C-terminus of a TNFi peptide. In some embodiments, a polymer unit is attached to the N-terminus and to the C-terminus of a TNFi peptide. The polymer units attached to the N-terminus and the C-terminus can be the same or different.
- a polymer unit comprises a polyethylene glycol chain (PEG group). In some embodiments, a polymer unit comprises a polysaccharide chain. In some embodiments, a polymer unit comprises an alkyl polyol chain. In some embodiments, a polymer unit comprises an elastin-like polypeptide.
- a polymer unit comprises a poly-sarcosine chain. In some embodiments, a polymer unit comprises an alkyl chain. In some embodiments, a polymer unit comprises a polypeptide chain, such as albumin or other polypeptide.
- a Linker comprises a polymer unit having a polyethylene glycol chain (PEG group). In some embodiments, a Linker comprises a polyethylene glycol chain (PEG group) that is linear or branched. In some embodiments, a PEG group is attached to the N-terminus of the TNFi peptide. In some embodiments, a PEG group is attached to the C-terminus of the TNFi peptide.
- a PEG group is attached to the N-terminus and to the C-terminus of a TNFi peptide. PEG groups attached to the N-terminus and the C-terminus can be the same or different.
- a PEG group has from 1 to 48 (ethylene glycol) subunits and is either linear or branched. In some embodiments, a PEG group has from 1 to 30 subunits and is either linear or branched. In some embodiments, a PEG group has from 1 to 24 subunits and is either linear or branched. In some embodiments, a PEG group has from 1 to 12 subunits.
- a PEG group has from 4 to 30 subunits and is either linear or branched. In some embodiments, a PEG group has from 4 to 24 subunits and is either linear or branched. In some embodiments, a PEG group has from 4 to 12 subunits and is either linear or branched. In some embodiments, a PEG group has from 4 to 10 subunits and is either linear or branched. In some embodiments, a PEG group has 4 subunits and is either linear or branched. In some embodiments, a PEG group has 6 subunits and is either linear or branched. In some embodiments, a PEG group has 8 subunits and is either linear or branched.
- a PEG group has 10 subunits and is either linear or branched. In some embodiments, a PEG group has 12 subunits and is either linear or branched.
- a Linker includes a functional group at an end opposite from its attachment site to a TNFi peptide. A functional group can serve as a cap and/or provide an attachment site for another molecule, such as a multimer scaffold group or an auxiliary molecule.
- the functional group is, for example, an acetate group, a carboxylic acid group, an amine group, an amide group, a carboxamide group, a thiol group, a hydrazide group, an NHS-ester or a o-pentafluorophenyl ester.
- the functional group is an amino acid residue or residues.
- the amino acid residue or residues of the functional group are in the L- configuration.
- the amino acid residues of the functional group are in the D-configuration.
- the functional group is an amino acid residue, such as a lysine residue.
- the functional group is an attachment site for a multimer scaffold.
- the functional group comprises one or more lysine residues, one or more hydrazide groups or one or more thiols or other groups.
- the TNFi peptides can be in the form of a multimer, such as a dimer or a trimer or a higher order multimer.
- the dimer can be comprised of two identical TNFi peptides (i.e., a homodimeric), or can be comprised of two different TNFi peptides (i.e., heterodimeric).
- a multimer can also be a trimer.
- the trimer can be comprised of two identical TNFi peptides and one different TNFi peptide (i.e., heterotrimeric), or three identical TNFi peptides (i.e., homotrimeric), or three different TNFi peptides, each of which is distinct from each other (i.e., heterotrimeric).
- two or more TNFi peptides can be linked via a Linker (e.g., a linker of amino acid residues or other chemical moieties, as described herein or as known to the skilled artisan) to form a multimer, such a dimer, trimer, or higher order multimer.
- the TNFi peptides form a dimer. In some embodiments, the TNFi peptides form a trimer. In some embodiments, the TNFi peptides form a multimer comprising at least four TNFi peptides. In some embodiments, a higher order multimer can include 5, 6, 7, 8, 9, 10, 11, 12, or more TNFi peptides. A multimer can be heteromeric or homomeric. [0207] In some embodiments, TNFi peptides are joined in a dimeric format and form a linear chain.
- the TNFi peptides are linked via the C-terminus of one peptide joined to the N-terminus of a second peptide, optionally comprising a Linker connecting the two TNFi peptides. In some embodiments, the TNFi peptides are linked via the C-terminus of one peptide joined to the C-terminus of the second peptide, optionally comprising a Linker connecting the two TNFi peptides. In some embodiments, the TNFi peptides are linked via the N-terminus of one peptide joined to the N-terminus of the second peptide, optionally comprising a Linker connecting the two TNFi peptides.
- the TNFi peptides may be the same or different.
- TNFi peptides are joined in a trimeric format and form a linear chain.
- the TNFi peptides are linked via the C-terminus of one peptide joined to the N-terminus of the next peptide, the C-terminus of which is connected to the N-terminus of the third peptide, optionally comprising a Linker connecting the pairs of TNFi peptides.
- the TNFi peptides are linked in any suitable orientation of N-termini and C-termini. In any of these embodiments, the TNFi peptides may be the same or different.
- TNFi peptides are joined in a linear multimeric format comprising at least four TNFi peptides and form a linear chain.
- a higher order multimer can include 5, 6, 7, 8, 910, 1112 or more peptides per chain.
- the multimers are linked via the C-terminus of one peptide joined to the N-terminus of the next peptide, optionally comprising a Linker connecting the pairs of TNFi peptides.
- the multimers are linked in any suitable orientation of N-termini and C-termini, optionally comprising a Linker connecting the pairs of TNFi peptides.
- the peptides may be the same or different.
- the TNFi peptides are crosslinked to form a multimer, such as a branched multimer. TNFi peptides are crosslinked via their N- and/or C-termini.
- a crosslinker is a polyethylene glycol (PEG) group derivatized with a reactive group, such as an N-hydroxysuccinimide (NHS)-ester (which reacts with a Lys residue) and/or a maleimide group (which reacts with a thiol group).
- a crosslinker can contain two distinct linkage chemistries (e.g., NHS- ester on one end and maleimide on the other end).
- the peptides may be the same or different.
- TNFi peptides are crosslinked through the use of a multimer scaffold(s).
- a multimer scaffold can include two or more functional groups for attachment of TNFi peptides, each TNFi peptide optionally attached to a multimer scaffold via a Linker.
- each TNFi peptide is attached to a reactive group on a multimer scaffold via a Linker, such as a PEG group.
- each TNFi peptide is attached to a reactive group on a multimer scaffold via a Linker, such as a PEG group.
- a multimer scaffold can be a dimeric scaffold comprising two functional groups, such as NHS ester groups.
- a multimer scaffold may comprise two of the same functional groups, such as NHS ester groups.
- a multimer scaffold may comprise at least two different functional groups, such as an NHS ester group and a maleimide group.
- a multimer scaffold can be a trimeric scaffold comprising three functional groups, such as NHS ester groups or o-pentafluorophenyl ester groups.
- a multimer scaffold may comprise three of the same functional groups, such as NHS ester groups or o-pentafluorophenyl ester groups. In some embodiments, a multimer scaffold may comprise at least two different functional groups, such as NHS ester groups or o-pentafluorophenyl ester groups and maleimide groups. In some embodiments, a multimer scaffold may be a tetrameric scaffold comprising four functional groups, such as three NHS ester groups, or o-pentafluorophenyl ester groups and a fourth orthogonal group.
- a multimer scaffold may comprise different functional groups, for example, NHS ester groups, o-pentafluorophenyl ester groups, maleimide groups and a fourth orthogonal group.
- a functional group can be Fmoc-amine, nitro, amine, or carboxylate.
- an orthogonal group can be a functional group for attachment of an auxiliary molecule.
- an orthogonal group can be, for example, a PEG chain, a cholesterol moiety, a biotin group, a lipid (fatty acid group), a nitro group, or a protected amine.
- a PEG chain of an orthogonal group has from 2 to 48 ethylene glycol repeats, or 2 to 24 ethylene glycol repeats.
- a TNFi peptide is attached to a multimer scaffold via a Linker.
- the Linker comprises a PEG group having functional groups at its termini.
- the PEG group has an NHS ester at two termini.
- the PEG group has an o-pentafluorophenyl ester at two termini.
- the PEG group has an amine group at one terminus and an NHS ester at the other terminus. In some embodiments, the PEG group has an amine group at one terminus and an o-pentafluorophenyl ester at the other terminus. In some embodiments, the PEG group has a carboxyl group at one terminus and an o- pentafluorophenyl ester at the other terminus. In some embodiments, the PEG group has an amine or carboxyl group at one terminus and an NHS ester or o-pentafluorphenyl ester at the other terminus.
- a multimer scaffold is a trifunctional cross-linker, such as tris(succinimidyl) aminotriacetate (TSAT), which contains three N- hydroxysuccinimide (NHS) ester groups.
- TSAT tris(succinimidyl) aminotriacetate
- NHS N- hydroxysuccinimide
- a multimer scaffold is a trifunctional cross-linker, such as Tris-succinimidyl (6-aminocaproyl)aminotriacetate (LC- TSAT).
- a multimer scaffold is a heterotetrameric PEG scaffold, having three functional groups of one type and a further reactive group orthogonal to the other functional groups.
- a multimer scaffold is a heterotetrameric PEG scaffold, having three NHS ester functional groups and a further maleimide reactive group.
- the Linkers connecting the TNFi peptides to the scaffold have different PEG lengths than a PEG group attached to the orthogonal reactive group.
- a multimer scaffold is an Fmoc scaffold (bis(2,5- dioxopyrrolidin-1-yl) 4-((((9H-fluoren-9-yl)methoxy)carbonyl)amino)-4-(3-((2,5-dioxo pyrrolidin-1-yl)oxy)-3-oxopropyl)heptanedioate.
- the multimer scaffold is an Fmoc scaffold having a PEG27 chain (see Figure 15A).
- the multimer scaffold is a cyclohex scaffold (tris(2,5-dioxopyrrolidin-1-yl) cyclohexane-1,3,5-tricarboxylate). In some embodiments, the multimer scaffold is a nitro scaffold (bis(2,5-dioxopyrrolidin-1-yl) 4-(3-((2,5-dioxopyrrolidin-1-yl)oxy)-3- oxopropyl)-4-nitroheptane dioate).
- the multimer scaffold is an Amine scaffold (bis(2,5-dioxopyrrolidin-1-yl) 4-amino-4-(3-((2,5-dioxopyrrolidin-1- yl)oxy)-3-oxopropyl) heptane dioate).
- the multimer scaffold is an Amine-PEG27 scaffold, as shown in Figure 16A.
- the multimer scaffold is a cholesterol scaffold, as shown in Figure 16A.
- a heterotetrameric PEG scaffold is based on a 3- ⁇ 2-Amino-3-(2-carboxyethoxy)-2-[(2- carboxyethoxy)-methyl]propoxy ⁇ propionic acid scaffold.
- the multimer scaffold is based on 4-amino-4-(2-carboxyethyl)heptanedioic acid.
- a TNFi peptide comprises a C-terminal D-lysine residue that is attached to a carboxyl group of 4-amino-4-(2-carboxyethyl)heptanedioic acid.
- the TNFi peptide multimer comprises three TNFi peptides, each TNFi peptide having a C- terminal D-lysine residue that is attached to a carboxyl group of 4-amino-4-(2- carboxyethyl)heptanedioic acid.
- such a TNFi peptide multimer further comprises an auxiliary molecule attached to the free amino group of the carboxyl group of 4-amino-4-(2-carboxyethyl)heptanedioic acid scaffold.
- the auxiliary molecule is a PEG group.
- a PEG group of a Linker attached to a multimer scaffold has from 1 to 48 subunits. In some embodiments, the PEG group of a Linker has from 1 to 30 subunits. In some embodiments, the PEG group of a Linker has from 1 to 24 subunits. In some embodiments, the PEG group of a Linker has from 1 to 12 subunits.
- the PEG group of a Linker has from 4 to 30 subunits. In some embodiments, the PEG group of a Linker has from 4 to 24 subunits. In some embodiments, the PEG group of a Linker has from 4 to 12 subunits. In some embodiments, the PEG group of a Linker has from 4 to 10 subunits. In some embodiments, the PEG group of a Linker has 4 subunits. In some embodiments, the PEG group of a Linker has 6 subunits. In some embodiments, the PEG group of a Linker has 8 subunits. In some embodiments, the PEG group of a Linker has 10 subunits. In some embodiments, the PEG group of a Linker has 12 subunits.
- the PEG group of a Linker as part of the multimer can have the same or different length.
- the PEG group may be composed of a single PEG chain, or a first PEG chain and a second PEG chain linked in series.
- the PEG group may include an internal NHS-ester or other bond, such as is formed by linking multiple PEG groups together.
- a Linker or multimer scaffold can comprise a tris, di-lysine, benzene ring, phosphate, or peptide core as a functional or reactive group.
- a cross-linking group includes a bis(sulfosuccinimidyl)suberate (B3S), a Disuccinimidyl glutarate (DSG) or a bis(sulfosuccinimidyl)suberate (DST) group.
- a crosslinking group comprises a thiol-reactive group, e.g., haloacetyls (e.g., iodoacetate), pyridyl disulfides (e.g., HPDP), and other thiols.
- a TNFi peptide or multimer thereof can be modified or linked to an auxiliary molecule, such as a potency-enhancing molecule, a stabilizing molecule or other molecule that provides an increase in activity, potency, binding, pharmacokinetic, membrane-localizing, or other property(ies).
- an auxiliary molecule such as a potency-enhancing molecule, a stabilizing molecule or other molecule that provides an increase in activity, potency, binding, pharmacokinetic, membrane-localizing, or other property(ies).
- a multimer scaffold can include auxiliary molecule, such as a PEG molecule (e.g., linear or branched), sterol (e.g., cholesterol) or analog thereof (e.g., thiocholesterol), a sugar, a maltose binding protein, a biotin group, a lipid (a fatty acid), serum albumin, ubiquitin, streptavidin, immunoglobulin domains, keyhole limpet hemacyanin, sperm whale myoovalbumin, green fluorescent protein, gold particle, magnetic particle, agarose bead, lactose bead, an alkane chain (e.g., C 8 , C 1 -C 6 , or a C 1- C 8 alkyl chain or the like), or a fatty acid (e.g., C8 fatty acid, C16 fatty acid, C18 fatty acid, palmitate, or the like).
- PEG molecule e.g., linear or branched
- sterol
- auxiliary molecule can be the linking of multiple multimers, such as the linking of multiple trimers (e.g., to increase molecular weight and reduce renal filtration).
- a TNFi peptide or a multimer thereof comprises an auxiliary molecule such as a label or other detectable marker.
- a label or other detectable marker is attached at the N-terminus and/or the C-terminus of the TNFi peptide.
- the TNFi peptide is labeled at the N-terminus.
- the TNFi peptide is labeled at the N-terminus with, for example, a biotin group.
- the TNFi peptide is labeled at the C-terminus. In some embodiments, the TNFi peptide is labeled at the C-terminus with, for example, a biotin group.
- a TNFi peptide multimer comprises a label or other detectable marker. In some embodiments, such a label or other detectable marker is attached at the N-terminus and/or the C-terminus of the TNFi peptide or to an orthogonal arm of a multimer scaffold. In some embodiments, the label or other detectable marker is a biotin group.
- an auxiliary molecule is attached to a TNFi peptide or a multimer thereof via a PEG group.
- Various chemistries that are known in the art may be used to attach an auxiliary molecule to a PEG group.
- the auxiliary molecule may be attached to a PEG group via carbamate, formed via a halide formate molecule reacting with an amine.
- the auxiliary molecule may be attached to a PEG group via an amide bond, formed by condensation between a carboxylic acid molecule and an amine.
- the auxiliary molecule may be attached to a PEG group via an amide bond, formed by an-NHS molecule or any other active ester.
- the auxiliary molecule may be attached to a PEG molecule chain via an amide bond, formed by reaction of a ketone with an amine (isourea).
- the auxiliary molecule may be attached to a PEG chain via a thioether bond, formed by reaction of a thiol with a maleimide ester.
- the auxiliary molecule may be attached to a PEG group via an ether bond, for example via a dehydration reaction with a terminal hydroxyl on an auxiliary molecule and a PEG group.
- the auxiliary molecule may be attached to a PEG group via click chemistry, for example Huisgen 1,3-diploar cycloaddition between an azide and an alkyne.
- a PEG group attached to an auxiliary molecule may be composed of a single PEG chain or a first PEG chain and a second PEG chain linked in series.
- the PEG group auxiliary molecule may include an internal NHS-ester or other bond, such as is formed by linking multiple PEG groups together.
- Multimers of the TNFi peptides can have an increased affinity for a TNF ⁇ molecule, when compared with the affinity of a single TNFi peptide, or control peptide, for the TNF ⁇ molecule.
- multimers of the TNFi peptides can have an increased affinity for trimeric TNF ⁇ , when compared with the affinity of a single TNFi peptide, or control peptide, for trimeric TNF ⁇ .
- the TNFi peptide multimer is a dimer.
- the TNFi peptide multimer is a trimer.
- the single peptide, or control peptide can be identical to one of the components of the multimer, or the single peptide can be a different peptide which is not contained in the multimer.
- a TNFi peptide multimer can exhibit about a 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 20-fold, 25-fold, 30-fold, 40-fold, 50-fold, 100-fold, 200-fold, 300-fold, 400-fold, 500-fold, 1000-fold, 2000- fold, 3000-fold, 4000-fold, 5000-fold, or 10,000-fold increase in affinity for trimeric TNF ⁇ when compared with the affinity of a TNFi peptide alone.
- compositions [0230] The TNFi peptides and multimers thereof can be administered in vivo in a pharmaceutical composition.
- a pharmaceutical composition typically includes a pharmaceutically acceptable excipient, carrier and/or other components.
- pharmaceutically acceptable is meant that the components of the composition are not biologically or otherwise undesirable, i.e., the components may be administered to a subject (e.g., a human) along with TNFi peptide or multimer thereof, without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained.
- a pharmaceutically acceptable excipient is selected to minimize any degradation of the active ingredient (e.g., TNFi peptides or multimers thereof) and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
- Pharmaceutical compositions may be formulated for any suitable form of administration.
- Pharmaceutical compositions may be formulated for oral administration, for parenteral administration (e.g., for intravenous administration, for intramuscular administration, or for subcutaneous administration), for topical administration (e.g., dermal), for rectal administration, and the like.
- the dosage of a pharmaceutical composition required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the disease, its mode of administration and the like.
- Parenteral administration of pharmaceutical composition is generally characterized by injection.
- Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions.
- Parenteral administration may also include use of a slow release or sustained release system (i.e., depot) such that a constant dosage is maintained.
- depot a slow release or sustained release system
- Suitable excipients and carriers and formulations thereof are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A.R. Gennaro, Mack Publishing Company, Easton, PA 1995.
- an appropriate amount of a pharmaceutically acceptable salt is used in a formulation to render the formulation isotonic.
- the pharmaceutically-acceptable carrier include, but are not limited to, saline, Ringer’s solution, and dextrose solution.
- the pH of the solution may be from about 5 to about 8, and alternatively from about 7 to about 7.5.
- Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing TNFi peptides or multimers thereof, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles.
- Carriers for inclusion in a pharmaceutical composition are known to those skilled in the art. These most typically are standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. The compositions can be administered intramuscularly or subcutaneously.
- Pharmaceutical compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents, and the like, in addition to the TNFi peptides or multimers thereof.
- a pharmaceutical composition may also include one or more other active ingredients such as an antimicrobial agent, an anti-inflammatory agent, an anesthetic, and the like.
- Preparations for parenteral administration include sterile aqueous or nonaqueous solutions, suspensions, and emulsions.
- non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate.
- Aqueous carriers include water, alcoholic/aqueous solutions, emulsions, or suspensions including, for example, saline and buffered media.
- Parenteral vehicles include sodium chloride solution, Ringer’s dextrose, dextrose and sodium chloride, lactated Ringer’s, or fixed oils.
- Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer’ s dextrose), and the like. Preservatives and other additives may also be present such as, for example, an antimicrobial, an anti-oxidant, a chelating agent, an inert gas, and the like.
- Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets.
- compositions designed for oral administration can further comprise a gut permeabilizing agent.
- a TNFi peptide or multimers thereof may be administered as a pharmaceutically acceptable acid- or base-addition salt, formed by reaction with an inorganic acid such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and an organic base such as, for example, a mono-,
- a pharmaceutical composition of a TNFi peptide or a multimer thereof is lyophilized.
- Formulations of the TNFi peptide or multimers thereof can be lyophilized for reconstitution or in liquid form.
- the terms “lyophilization,” “lyophilized,” and “freeze-dried” refer to a process by which the material to be dried is first frozen and then the ice or frozen solvent is removed by sublimation in a vacuum environment. An excipient may be included in a pre-lyophilized formulation to enhance stability of the lyophilized product upon storage.
- a “reconstituted” formulation is one that has been prepared by dissolving a lyophilized protein formulation in a diluent such that the protein is dispersed in the reconstituted formulation.
- the reconstituted formulation is suitable for administration, (e.g., parenteral administration), and may optionally be suitable for subcutaneous administration or other route of administration.
- a TNFi peptide and multimers thereof can be used to reduce TNF ⁇ - mediated inflammation in a subject.
- the TNFi peptide or multimer thereof is administered to reduce TNF ⁇ -mediated inflammation in a subject.
- the TNFi peptide or multimer thereof is administered to reduce TNF ⁇ activity in a subject.
- the TNFi peptide or a multimer thereof is administered to reduce an inflammatory response mediated by TNF ⁇ .
- a TNFi peptide or a multimer thereof can be administered by oral administration, by parenteral administration, by intravenous administration, by intramuscular administration, by subcutaneous administration, by topical administration, by rectal administration, or the like.
- the TNFi peptide or a multimer thereof is administered locally, so as to achieve local inhibition of TNF ⁇ activity or TNF ⁇ -mediated inflammation or a TNF ⁇ -mediated inflammatory response.
- a TNFi peptide and multimers thereof can be used to treat subjects having a TNF ⁇ -mediated disease.
- the TNFi peptide or multimers thereof are administered to a subject in need thereof for the treatment of a TNF ⁇ - mediated disease.
- the TNF ⁇ - mediated disease is an inflammatory disease or condition.
- the TNF ⁇ - mediated disease is an autoimmune disorder.
- the TNFi peptide or multimers thereof are administered orally.
- the TNFi peptide or multimers thereof are administered parenterally.
- the TNFi peptide or multimers thereof are administered intravenously.
- the TNFi peptide or multimers thereof are administered intramuscularly.
- the TNFi peptide or multimers thereof are administered subcutaneously. In some embodiments, the TNFi peptides or multimers thereof are administered topically. In some embodiments, the TNFi peptide or multimers thereof are administered by rectal administration.
- the term “subject” refers to a human or an animal. Usually, the animal is a vertebrate such as a primate, rodent, domestic animal, or game animal. Primates include chimpanzees, cynomolgus monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits, and hamsters.
- Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish, and salmon.
- the subject is a mammal, e.g., a primate, e.g., a human.
- the subject is a human, monkey, and dog.
- the subject is human.
- a TNFi peptide or multimers thereof are administered to a subject in need thereof for the treatment of a TNF ⁇ -mediated disease, such as adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenitis suppurativa, Uveitis (intermediate, posterior, or panuveitis), or non- radiographic axial spondyloarthritis.
- a TNF ⁇ -mediated disease such as adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arth
- a TNFi peptide or a multimer thereof is administered to a subject in need thereof having an inflammatory bowel disease, such as adult or pediatric Crohn’s Disease or Ulcerative Colitis. In some embodiments, the TNFi peptide is administered orally to the subject. [0247] In some embodiments, a TNFi peptide or a multimer thereof is administered to a subject in need thereof having an inflammatory bowel disease, such as adult or pediatric Crohn’s Disease or Ulcerative Colitis. In some embodiments, the TNFi peptide is administered rectally (e.g., by enema) to the subject.
- a TNFi peptide or a multimer thereof is administered to a subject in need thereof having an inflammatory skin disease, such as Plaque Psoriasis, Hidradenitis suppurativa, or Cutaneous Lupus.
- the TNFi peptide is administered topically to the subject.
- a TNFi peptide or a multimer thereof is administered to a subject in need thereof having an inflammatory skin disease, such as Plaque Psoriasis, Hidradenitis suppurativa, or Cutaneous Lupus.
- the TNFi peptide or a multimer thereof is administered parenterally (such as subcutaneously, intramuscularly, or intravenously) to the subject. In some embodiments, the TNFi peptide or a multimer thereof is administered subcutaneously to the subject. In some embodiments, the TNFi peptide or a multimer thereof is administered intramuscularly to the subject. In some embodiments, the TNFi peptide or a multimer thereof is administered intravenously to the subject.
- a TNFi peptide or a multimer thereof is administered to a subject in need thereof having an inflammatory disease, such as Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, or Ankylosing Spondylitis.
- the TNFi peptide or a multimer thereof is administered parenterally (such as subcutaneously, intramuscularly, or intravenously) to the subject.
- the TNFi peptide or a multimer thereof is administered subcutaneously to the subject.
- the TNFi peptide or a multimer thereof is administered intramuscularly to the subject.
- the TNFi peptide or a multimer thereof is administered intravenously to the subject.
- Effective dosages and schedules for administering a TNFi peptide or a multimer thereof may be determined empirically, and making such determinations is within the skill in the art.
- the dosage ranges for the administration of the TNFi peptide or multimer and compositions thereof are those large enough to produce the desired effect in which the symptoms/disorder is affected.
- the dosage is typically not so large as to cause serious adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like.
- the dosage will vary with the age, condition, sex, and extent of the disease in the subject, route of administration, or whether other drugs are included in the regimen, and can be determined by one of skill in the art.
- the dosage can be adjusted by the individual physician in the event of any contraindications.
- Dosage can vary, and can be administered in one or more dose administrations daily, for one, or several days.
- a typical daily dosage of the TNFi peptide or multimer thereof used might range from about 1 ⁇ g/kg to up to 100 mg/kg of body weight or more per day, depending on the factors mentioned above.
- a typical daily dosage of the TNFi peptide or multimer thereof used might range from about 0.01 ⁇ g/kg to up to 1 mg/kg of body weight or more per day.
- the TNFi peptide or multimer thereof can be administered several times daily, daily, weekly, monthly, or yearly, depending on the condition of the subject, other modes of therapy, and the like.
- One of skill in the art could readily ascertain an appropriate dosing schedule.
- the TNFi peptide or multimer thereof may be administered prophylactically to a patient or a subject who is at risk for a TNF ⁇ -mediated disease or at risk for recurrence of a TNF ⁇ -mediated disease.
- a TNFi peptide or a multimer thereof can be made using any method known to those of skill in the art for preparation of a D-peptide or a multimer thereof.
- the TNFi peptide can be linked, for example, by disulfide crosslinks.
- the D-peptides disclosed herein have two Cys residues connected by a disulfide bond, which circularizes the peptide and creates a more compact and structured peptide. This disulfide is known to have enhanced TNF ⁇ binding activity.
- Two or more TNFi peptides can also be linked together by protein chemistry techniques.
- a peptide or a polypeptide can be chemically synthesized using currently available laboratory equipment using either FMOC (fluorenylmethyloxycarbonyl) or Boc (tert butyloxycarbonoyl) chemistry (Applied Biosystems, Inc., Foster City, CA).
- FMOC fluorenylmethyloxycarbonyl
- Boc tert butyloxycarbonoyl
- a peptide corresponding to any of the disclosed TNFi peptides for example, can be synthesized by standard chemical reactions.
- a TNFi peptide can be synthesized and not cleaved from its synthesis resin whereas another fragment of a peptide can be synthesized and subsequently cleaved from the resin, thereby exposing a terminal group which is functionally blocked on the other fragment.
- enzymatic ligation of cloned or synthetic peptide segments allow relatively short peptide fragments to be joined to produce larger a peptide (Abrahmsen L., et al., Biochemistry, 30:4151 (1991)).
- native chemical ligation of synthetic peptides can be utilized to synthetically construct larger peptides from shorter peptide fragments. This method consists of a two-step chemical reaction (Dawson et al., Synthesis of Proteins by Native Chemical Ligation. Science, 266:776779 (1994)).
- the first step is the chemoselective reaction of an unprotected synthetic peptide thioester with another unprotected peptide segment containing an amino terminal Cys residue to give a thioester linked intermediate as the initial covalent product. Without a change in the reaction conditions, this intermediate undergoes a spontaneous, rapid intramolecular reaction to form a native peptide bond at the ligation site (Baggiolini M. et al., (1992) FEBS Lett. 307:97-101; Clark-Lewis I. et al., J. Biol. Chem., 269:16075 (1994); Clark-Lewis I. et al., Biochemistry, 30:3128 (1991); Rajarathnam K.
- X 2 is the D form of Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W), or a D- ⁇ - amino acid analog thereof;
- X 3 is selected from the D forms of Trp (W), Phe (F), Tyr (Y), Ser (S), His (H) or Leu (L), or a D- ⁇ -amino acid analog thereof; c.
- X 4 is a Polar amino acid selected from the D form of Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G), or a D- ⁇ -amino acid analog thereof; d.
- X 5 is D form of Pro (P), Trp (W), His (H), Gln (Q), Arg (R), Ala (A), Val (V), Leu (L), or Gly (G), or a D- ⁇ -amino acid analog thereof; e.
- X 6 is the D form of Arg (R), His (H), Lys (K), Glu (E), Gln (Q), Val (V), Leu (L), Ser (S), or Ala (A), or a D- ⁇ -amino acid analog thereof;
- X 10 is the D form of Trp (W) or Tyr (Y), or a D- ⁇ -amino acid analog thereof;
- X 11 is the D form of Trp (W), Tyr (Y), Gln (Q) or His (H), or a D- ⁇ -amino acid analog thereof; and h.
- C denotes the D form of Cysteine, or a D- ⁇ -amino acid analog thereof
- F denotes the D form of phenylalanine, or a D- ⁇ -amino acid analog thereof
- N denotes the D form of asparagine, or a D- ⁇ amino acid analog thereof.
- the D-peptide or a salt thereof of embodiment 1, wherein the core TNF ⁇ binding domain has the following amino acid sequence: C-X 2 -[W/F/Y]-X 4 -X 5 -X 6 - F-N-N-[W/Y]-W-C (SEQ ID NO:3).
- the D-peptide or a salt thereof of any of embodiments 1 to 3 wherein: a. X 2 is the D form of Thr, Val, His, Leu, Gln, Ala, Ile, Met or Trp, or a D- ⁇ -amino acid analog thereof; b. X 2 is the D form of Thr, Val, His, Leu, or Gln, or a D- ⁇ -amino acid analog thereof; c.
- X 2 is selected from the D form of Thr, Val, His and Leu, or a D- ⁇ - amino acid analog thereof; d. X 2 is selected from the D form of Thr, Val and His, or a D- ⁇ -amino acid analog thereof; e. X 2 is selected from the D form of Thr and Val, or a D- ⁇ -amino acid analog thereof; f. X 2 is the D form of Thr, or a D- ⁇ -amino acid analog thereof; or g. X 2 is the D form of Val, or a D- ⁇ -amino acid analog thereof. 5. The D-peptide or a salt thereof of any of embodiments 1 or 3 to 4, wherein: a.
- X 3 is selected from the D forms of Trp, Phe, Tyr, and Ser, or a D- ⁇ - amino acid analog thereof; b. X 3 is selected from the D forms of Trp, Phe, and Tyr, or a D- ⁇ -amino acid analog thereof; c. X 2 is selected from the D forms of Trp and Phe, or a D- ⁇ -amino acid analog thereof; d. X 3 is the D form of Trp or a D- ⁇ -amino acid analog thereof; or e. X 3 is the D form of Phe, or a D- ⁇ -amino acid analog thereof. 6. The D-peptide or a salt thereof of any of embodiments 1 to 5, wherein: a.
- X 4 is the D form of Arg, His, Gln, Asn, Lys, Thr, or Ser, or a D- ⁇ - amino acid analog thereof; b. X 4 is selected from the D forms of Arg, His, Gln and Asn, or a D- ⁇ - amino acid analog thereof; c. X 4 is the D form of Arg, His or Gln, or a D- ⁇ -amino acid analog thereof; d. X 4 is the D form of Arg, Gln or Asn, or a D- ⁇ -amino acid analog thereof; or e. X 4 is the D form of Gln, or a D- ⁇ -amino acid analog thereof. 7.
- X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, Ala, Val or Leu, or a D- ⁇ -amino acid analog thereof; b. X 5 is the D form of Pro, Trp, His, Gln, Gly, Arg, or Val, or a D- ⁇ - amino acid analog thereof; c. X 5 is the D forms of Pro, Trp or His, or a D- ⁇ -amino acid analog thereof; d. X 5 is the D forms of Pro or Trp, or a D- ⁇ -amino acid analog thereof; or e.
- X 5 is the D form of Pro, or a D- ⁇ -amino acid analog thereof.
- X 6 is the D-form of Arg, His, Lys, or Glu, or a D- ⁇ -amino acid analog thereof; e. X 6 is the D-form of Arg or His, or a D- ⁇ -amino acid analog thereof; f. X 6 is the D-form of Arg, or a D- ⁇ -amino acid analog thereof; or g. X 5 is the D-form of His, or a D- ⁇ -amino acid analog thereof.
- X 10 is the D form of Tyr, or a D- ⁇ -amino acid analog thereof.
- the D-peptide or a salt thereof of any of embodiments 1 to 10 wherein each of X 1 through X 6 , X 10 , and X 11 is a D- ⁇ -amino acid. 12.
- CTFQWRFNNYWC (SEQ ID NO:12); j. CLYQPVFNNWWC (SEQ ID NO:13); k. CVFQAAFNNYWC (SEQ ID NO:14); l. CVFQHHFNNWWC (SEQ ID NO:15); m. CHFNPRFNNWWC (SEQ ID NO:16); n. CVWQPHFNNYWC (SEQ ID NO:17); o. CVFQGRFNNWWC (SEQ ID NO:18); p. CVFQHRFNNWWC (SEQ ID NO:19); q. CVFNPRFNNWWC (SEQ ID NO:20); r. CVFKPRFNNWWC (SEQ ID NO:21); s.
- CAYQRQFNNWWC (SEQ ID NO:22); t. CWFEHRFNNWHC (SEQ ID NO:23); u. CHFQHRFNNWWC (SEQ ID NO:24); v. CHFQPRFNNWWC (SEQ ID NO:25); w. CTYQPRFNNWWC (SEQ ID NO:26); x. CQFQPRFNNWQC (SEQ ID NO:27); or y. CHFSQRFNNWWC (SEQ ID NO:28).
- the D-peptide or a salt thereof of any of the preceding embodiments, wherein the core TNF ⁇ binding domain has an amino acid sequence of SEQ ID NO:77 to 110. 14.
- the D-peptide or a salt thereof of any of the preceding embodiments further comprising a tag sequence attached to the N-terminus of the peptide.
- the D-peptide or a salt thereof of embodiment 14 wherein the tag comprises the amino acid sequence D-Asp or D-AspAsp (DD).
- the D-peptide or a salt thereof of any of the preceding embodiments further comprising a tag sequence attached to the C-terminus of the peptide.
- the D-peptide or a salt thereof of embodiment 16 wherein the tag comprises the amino acid sequence D-GGEEEK (SEQ ID NO:30) or D-GGRRRK (SEQ ID NO:31). 18.
- the D-peptide or a salt thereof of any of the preceding embodiments wherein the N-terminus of the peptide comprises a cap. 19. The D-peptide or a salt thereof of embodiment 18, wherein the cap comprises an acetyl group or a protecting group. 20. The D-peptide or a salt thereof of any of the preceding embodiments, wherein the C-terminus of the peptide comprises a cap. 21. The D-peptide or a salt thereof of embodiment 20, wherein the cap comprises an amide group or a protecting group. 22. The D-peptide or a salt thereof of any of the preceding embodiments, further comprising a polyethylene glycol (PEG) group. 23.
- PEG polyethylene glycol
- each PEG group is selected from a PEG group having from 1 to 48 subunits, 1 to 30 subunits, 1 to 24 subunits or 1 to 12 subunits.
- 28. The D-peptide or a salt thereof of embodiment 27, wherein each PEG group is selected from a PEG group having from 6 subunits, 8 subunits, 10 subunits or 12 subunits.
- 29. A multimer of the D-peptide of any of the preceding embodiments, or a salt thereof.
- the D-peptide or a salt thereof of any of embodiments 1 to 28 having an amino acid sequence selected from at least one of the following: a. DDCVWQPKFNNYWC (SEQ ID N:32); b. DGACVWQPKFNNYWC (SEQ ID NO:38); c. DDCVWQPRFNNYWC (SEQ ID NO:39); d. DDCVWQPRFNNYWCGGRRRK (SEQ ID NO:40); e. DCVWQPKFNNYWC (SEQ ID NO:56); f. DDDCVWQPRFNNYWC (SEQ ID NO:60); g. DDCTFQPRFNNWWC (SEQ ID NOL61); h.
- DDCVFQPRFNNYWC (SEQ ID NO:62); i. DDCSFQPRFNNYWC (SEQ ID NO:63); and j. DDCVFQPRFNNWWC (SEQ ID NO:64).
- DCVWQPKFNNYWC (SEQ ID NO:56); f. DDDCVWQPRFNNYWC (SEQ ID NO:60); g. DDCTFQPRFNNWWC (SEQ ID NOL61); h. DDCVFQPRFNNYWC (SEQ ID NO:62); i. DDCSFQPRFNNYWC (SEQ ID NO:63); and j. DDCVFQPRFNNWWC (SEQ ID NO:64).
- a pharmaceutical composition comprising at least one D-peptide or multimer, or a pharmaceutically acceptable salt thereof, as set forth in any of the preceding embodiments, and at least one pharmaceutically acceptable excipient or carrier. 40.
- the pharmaceutical composition of embodiment 39 which is formulated for parenteral administration. 41.
- the pharmaceutical composition of embodiment 40 which is formulated for intravenous, intramuscular, or subcutaneous administration. 42.
- the pharmaceutical composition of embodiment 39 which is formulated for oral administration. 43.
- the pharmaceutical composition of embodiment 39 which is formulated for topical administration. 44.
- the pharmaceutical composition of embodiment 43 which is formulated for topical administration to the skin (dermal) or to the eye.
- the pharmaceutical composition of embodiment 39 which is formulated for rectal administration.
- 46. A lyophilized composition comprising at least one D-peptide or multimer, or a salt or pharmaceutically acceptable salt thereof, of any of embodiments 1 to 38, and a stabilizing agent.
- a method of treating a TNF ⁇ -mediated disease comprising administering an effective amount of the D-peptide of any of embodiments 1 to 28 or 37, the multimer of any of embodiments 29 to 36 and 38 or the pharmaceutical composition of any of embodiments 39 to 45, or a pharmaceutically acceptable salt thereof. 50.
- TNF ⁇ -mediated disease is adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenitis suppurativa, Uveitis (intermediate, posterior, or panuveitis), or non-radiographic axial spondyloarthritis. 51. The method of embodiment 49, wherein the TNF ⁇ -mediated disease is an inflammatory bowel disease. 52.
- the method of embodiment 51 wherein the inflammatory bowel disease is adult Crohn’s Disease, pediatric Crohn’s Disease, or Ulcerative Colitis. 53.
- the method of embodiment 51 or 52, wherein the administration is oral.
- the method of embodiment 51 or 52, wherein the administration is rectal. 55.
- the method of embodiment 51 or 529, wherein the administration is parenteral.
- the method of embodiment 49, wherein the TNF ⁇ -mediated disease is an inflammatory skin disease.
- the method of embodiment 56, wherein the inflammatory skin disease is Plaque Psoriasis, Hidradenitis suppurativa, or Cutaneous Lupus.
- the method of embodiment 56 or 57, wherein the administration is topical. 59.
- a method of reducing TNF ⁇ -mediated inflammation comprising administering a D-peptide or multimer thereof, or a pharmaceutically acceptable salt thereof, of any of embodiments 1 to 38, or a pharmaceutical composition of any of embodiments 39 to 45, to a subject.
- a method of inhibiting TNF ⁇ comprising administering a D-peptide or multimer thereof, or a pharmaceutically acceptable salt thereof, of any of embodiments 1 to 38, or a pharmaceutical composition of any of embodiments 39 to 45, to a subject.
- a method of reducing an inflammatory response mediated by TNF ⁇ comprising administering a D-peptide or multimer thereof, or a pharmaceutically acceptable salt thereof, of any of embodiments 1 to 38, or a pharmaceutical composition of any of embodiments 39 to 45, to a subject.
- the method of any of embodiments 63 to 65, wherein the administering is by oral administration, by parenteral administration, by topical (dermal), or by rectal administration.
- 67. The method of any of embodiments 63 to 65, wherein the D-peptide or the multimer thereof, or a pharmaceutically acceptable salt thereof is administered locally to reduce TNF ⁇ activity or inflammation or an inflammatory response. 68.
- TNF ⁇ - mediated disease is adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenitis suppurativa, Uveitis (intermediate, posterior, or panuveitis), or non-radiographic axial spondyloarthritis. 70.
- TNF ⁇ - mediated disease is adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenitis suppurativa, Uveitis (intermediate, posterior, or panuveitis), or non-radiographic axial spondyloarthritis.
- TNF ⁇ -mediated disease is adult Crohn’s Disease, pediatric Crohn’s Disease, Ulcerative Colitis, Plaque Psoriasis, Cutaneous Lupus, Systemic Lupus Erythematosus, Rheumatoid Arthritis, Psoriatic Arthritis, Ankylosing Spondylitis, Juvenile idiopathic arthritis (polyarticular), Hidradenit
- EXAMPLE 1 Screening of Phage Display Libraries for TNF ⁇ Antagonist Peptides [0265] To identify D-peptides that bind to and inhibit human TNF ⁇ activity, peptide libraries were screened using an enantiomeric screening technique, mirror-image phage display.
- a synthetic, biotinylated D-amino acid form of human TNF ⁇ (i.e., the mirror image of the natural L-amino acid form) was used to identify L-amino acid peptides (L-peptides) that specifically bound to that D-form of TNF ⁇ .
- L-peptides L-amino acid peptides
- the sequences of the L- peptides that bound to the D-amino acid form of human TNF ⁇ were determined by deep sequencing and Sanger sequencing. Based on the sequencing results, D-amino acid peptides of selected L-peptide hits were synthesized and screened for their ability to bind to native human TNF ⁇ (L-amino acid form) and to inhibit its activity.
- the final linear protein target was then refolded by first forming the single intramolecular disulfide and then dialyzing step-by-step from 6 M, 2 M, 0.5 M, to 0 M guanidine hydrochloride buffers.
- the folded, biotinylated L-TNF ⁇ trimer was isolated by SEC (size-exclusion chromatography) to remove any aggregated or misfolded species (i.e., separation of trimer from monomer or higher-order aggregates).
- Synthetic and recombinant L-TNF ⁇ proteins were further characterized by biophysical (LC and ESI-MS), biochemical (multiple assays on binding to TNFR), and activity assays (L-929 cell killing assay) to ensure they were equivalent (data not shown).
- Mirror-image phage display was performed against the folded biotinylated D-TNF ⁇ trimeric protein by screening phage libraries of L-peptides having nine different geometries (one linear and eight disulfide-constrained).
- Twenty-eight (28) that were identified during the selection process were further validated using an assay that quantified binding of different phage clones to the biotinylated D-TNF ⁇ protein.
- 28 phage that were identified during the selection process were further validated using an assay that quantified binding of different phage clones to the biotinylated D-TNF ⁇ protein.
- peptides identified by sequencing include those having the core TNF ⁇ binding domains set forth below in the following Examples as well as in SEQ ID NOs:78 to 111.
- TNF ⁇ -018 emerged as the leading hit based on its binding to recombinant TNF ⁇ (L-form) and its high aqueous solubility.
- Another hit, TNF ⁇ -001 was insoluble in aqueous buffers although it showed strong binding to TNF ⁇ based on phage display.
- Validation of TNF ⁇ -binding by the D-peptide hits was confirmed in three different ELISA formats: “solid-phase” (as described above), “solution-phase” (all components mixed in solution then captured onto Neutravidin surface), and “sequential solid-phase” (mixed biotinylated D-peptide with TNF ⁇ in solution, captured on Neutravidin surface, and then a secondary Ab was added).
- Binding to L-TNF ⁇ by the D- peptide hits was also confirmed using a direct fluorescent readout assay (immobilized recombinant biotinylated TNF ⁇ was treated with fluorescently-labeled D-peptides). These same fluorescent peptides were also used to document TNF ⁇ -binding by co-elution with recombinant TNF ⁇ (L-form) on an analytical size exclusion column (SEC) under native conditions. As described below, select D-peptide point mutants abrogated binding in these assays.
- a thermal shift dye-binding assay (Lavinder et al., 2009, J. Am. Chem. Soc.
- Peptide 18 contained a core TNF ⁇ binding domain, CVWQPKFNNYWC (SEQ ID NO:4), with an N-terminal biotin molecule attached to a D-AspAsp (DD) dipeptide tag attached to the N-terminus of the peptide core TNF ⁇ binding domain; the dipeptide tag increased the solubility of the peptide.
- Peptide 18 also contained a C-terminal amide group.
- Peptide 18-V1 and Peptide 18-V2 contained the same core TNF ⁇ binding domain, were acetylated at their N-termini and contained a C-terminal GGEEEK (SEQ ID NO:30) or GGRRRK (SEQ ID NO:31) peptide, respectively, and a biotin-amide group. These C-terminal sequences were included in Peptide 18-V1 and Peptide 18-V2 to determine whether they increased solubility and/or binding.
- a Peptide 18 mutant was prepared that had similar structure to Peptide 18, except for a W to G substitution at the penultimate C-terminal residue of the core TNF ⁇ binding domain.
- Peptide Biotin DD-18 Biotin-DDCVWQPKFNNYWC-amide (SEQ ID NO:32)
- Peptide 18-V1 Ac-CVWQPKFNNYWCGGEEEK(Biotin)-amide (SEQ ID NO:33)
- Peptide 18-V2 Ac-CVWQPKFNNYWCGGRRRK(Biotin)-amide (SEQ ID NO:34)
- the peptides were immobilized on a neutravidin plate and washed with wash buffer (PBS pH 7.4 containing 0.1% BSA and 0.01% Tween-20).
- His6- TEV-TNF ⁇ was then added followed by washing.
- the TNF ⁇ used in the assay was recombinantly expressed human TNF ⁇ with an N-terminal His6 tag.
- the amount of TNF ⁇ bound to the peptides was then measured using an anti-His6 tag antibody conjugated to Horse Radish Peroxidase (HRP) followed by detection using a QuantaBlu TM fluorogenic peroxidase substrate (Thermo Scientific).
- HRP Horse Radish Peroxidase
- QuantaBlu TM fluorogenic peroxidase substrate Thermo Scientific.
- the Trp (W) to Gly (G) substitution adjacent the C-terminal Cys residue of the core TNF ⁇ binding domain abolished binding of that peptide to TNF ⁇ .
- the BSA control also showed negligible TNF ⁇ binding.
- the number above each bar indicates the fold increase in peptide binding to TNF ⁇ , as compared to the BSA control.
- differences in the amount of peptide binding to TNF ⁇ were dependent, in part, on the relative position and composition of the peptide tags and the location of the biotin molecule.
- EXAMPLE 3 Peptide 18 Blocked Binding of TNF ⁇ to TNFR1
- Peptide Biotin DD-18 Biotin-DDCVWQPKFNNYWC-amide (SEQ ID NO:32) was tested in a binding assay that measures disruption of binding between TNF ⁇ and one of its receptors, TNFR1 (Tumor Necrosis Factor Receptor 1).
- TNFR1 Tumor Necrosis Factor Receptor 1
- a soluble, extracellular domain of TNFR1 with C-terminal biotin tag was immobilized onto neutravidin plates.
- TNF ⁇ with an N-terminal His6 tag (as described in Example 2) was pre-incubated with Peptide 18 at concentrations of 10, 25 and 50 micromolar. Following preincubation, the TNF ⁇ -Peptide 18 mixtures were then added to the immobilized TNFR1. BSA protein was included as a negative control. A llama anti- TNF ⁇ nanobody VHH2 was recombinantly expressed (Beirnaert et al., 2017, Front. Immunol.8:867) was used as a positive control. [0284] Referring to Figure 3, Peptide 18 showed concentration-dependent blocking of TNF ⁇ -TNFR1 binding.
- EXAMPLE 4 Peptide 18 Blocked Cellular Activity of TNF ⁇ by L-929 Cells [0286] The ability of Peptide 18 to block TNF ⁇ -mediated cell killing was demonstrated using an L-929 cell killing assay (Trost and Lemasters, 1994, Anal. Biochem. 220(1):149-153).
- TNF ⁇ in the presence of actinomycin D causes TNF ⁇ -TNFR-mediated cell death in this cell line.
- the sequence of Peptide 18 was: Ac-DDCVWQPKFNNYWC- amide (SEQ ID NO:32; Peptide DD-18).
- TNF ⁇ induced L-929 cell killing (compare first and second columns on left). The addition of Peptide 18 at 50 micromolar blocked TNF ⁇ - induced cell death (compare columns 2 and 3 from left).
- TNF ⁇ induced cell killing was comparable to that shown by soluble TNFR1 (2.5 microgram/mL) while the anti-TNF ⁇ VHH2 nanobody (30 microgram/mL) and anti-TNF ⁇ monoclonal antibody (research grade adalimumab; R&D Systems) exhibited greater inhibition of TNF ⁇ -induced L-929 cell killing.
- concentration of Peptide 18 was also varied in this assay from 50 micromolar to 0.78125 micromolar and cell killing was measured as described above (by absorbance at 450 nm).
- the left bar in each triplet shows the result of Peptide 18 (designated B-D-P 18; Peptide Biotin DD-18; SEQ ID NO:32) alone at the indicated concentration
- the middle bar shows the results of addition of recombinant human TNF ⁇ at a concentration of 0.5 nM with the indicated amount of Peptide 18 (designated B-D-P 18; Peptide Biotin DD-18; SEQ ID NO:32)
- the right bar shows the results of addition of TNF ⁇ at a concentration of 0.1 nM with the indicated amount of Peptide 18.
- the screened peptides were Peptide 18 (Biotin-DDCVWQPKFNNYWC-amide; Peptide Biotin DD-18; SEQ ID NO:32), a Peptide 18 mutant (Biotin-DDCVWQPKFNNYGC-amide; SEQ ID NO: 35; Peptide Biotin DD-18 mutant), and a second mutant, Peptide 18 di-mutant (Biotin-DDCDWQDKFNNYWC-amide; SEQ ID NO:36; Peptide Biotin DD-18 di- mutant).
- the differences between Peptide 18 and Peptide 18 mutant and Peptide 18 di- mutant are underlined in the Peptide 18 mutant and Peptide 18 di-mutant sequences.
- Figure 5 shows the results.
- Example 2 two other variants of Peptide 18 having C-terminal tags (GGEEEK (SEQ ID NO:30) and GGRRRK (SEQ ID NO:31)), Peptide 18-V1 SEQ ID NO:33) and Peptide 18-V2 (SEQ ID NO:34), respectively, were tested and shown to retain TNF ⁇ binding activity.
- Peptide 18-V1 designated Peptide 18-E3 (Ac- CVWQPKFNNYWCGGEEEK(Biotin)-amide; SEQ ID NO: 33)
- Peptide 18-V2 designated Peptide 18-R3 (Ac-CVWQPKFNNYWCGGRRRK(Biotin)-amide); SEQ ID NO:34
- L-929 cell killing assay described in Example 4.
- Peptide 18 and the variants are underlined in the variant sequences.
- an extended peptide based on the sequence of the peptide isolated from the phage library (Example 1), Peptide Biotin DD-18-ex (Biotin-DDCVWQPKFNNYWCGGGSAETVE- amide; SEQ ID NO:37) was tested.
- Peptide 18, having an N-terminal DD dipeptide exhibited greater inhibition of TNF ⁇ -induced cell death than Peptide 18-E3 and Peptide 18-R3.
- Peptide 18-ex exhibited inhibition of TNF ⁇ -induced cell killing that was about the same as or slightly greater than that of Peptide 18.
- EXAMPLE 7 Comparing the Binding of Additional Peptide 18 Sequence Variants in TNF ⁇ Binding Assays [0300] The TNF ⁇ binding assay described above (Example 2) was used to compare the binding of Peptide 18 with additional sequence variants. In addition, another peptide from the same CX 10 C library, Hit 16, was tested. The following peptides were tested, where the sequence differences from Peptide 18 are underlined.
- Peptide 18 Biotin-DD-18 - Biotin-DDCVWQPKFNNYWC-amide (SEQ ID NO:32) Biotin-DGA-18: Biotin-DGACVWQPKFNNYWC-amide (SEQ ID NO:38) Biotin-DD-18-KtoR: Biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Biotin-DD-18-KtoR-R3: Biotin-DDCVWQPRFNNYWCGGRRRK-amide (SEQ ID NO:40) Biotin2-DD-18-KtoR-R3: Biotin-DDCVWQPRFNNYWCGGRRRK(biotin)- amide (SEQ ID NO:40) Biotin-DD-hit16: Biotin-DDCHFNPRFNNWWC-amide (SEQ ID NO:41) [0301] The results of these binding assays are shown in Figure 6.
- DD-18 DDCVWQPKFNNYWC-amide (SEQ ID NO:32) Biotin-DD-18: Biotin-DDCVWQPKFNNYWC-amide (SEQ ID NO:32) Biotin-DD-18-ex: Biotin-DDCVWQPKFNNYWCGGGSAETVE-amide (SEQ ID NO:37) Biotin-DGA-18: Biotin-DGACVWQPKFNNYWC-amide (SEQ ID NO:38) DGA-18: DGACVWQPKFNNYWC-amide (SEQ ID NO:38) DD-18-KtoR: DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Biotin-DD-18-KtoR: Biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Biotin-DD-18-KtoR: Biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Biotin-DD-18-KtoR3: Biotin
- EXAMPLE 9 Comparing Additional Peptide 18 Sequence Variants in L- 929 Cell Killing Assay [0314] The L-929 cell killing assay described above (Example 4) was used to compare the ability of Peptide 18 (designated DD-18; SEQ ID NO:32) and additional sequence variants to block TNF ⁇ -induced cell killing. Biotinylated and non-biotinylated forms of Hit 16 were also included. The peptides tested are shown below. The amino acid sequence differences from Peptide 18 are underlined. Some peptides were not biotinylated in this study.
- DD-18 DDCVWQPKFNNYWC-amide (SEQ ID NO:32) Biotin-DD-18: Biotin-DDCVWQPKFNNYWC-amide (SEQ ID NO:32) Biotin-DD-18-ex: Biotin-DDCVWQPKFNNYWCGGGSAETVE-amide (SEQ ID NO:37) Biotin-DGA-18: Biotin-DGACVWQPKFNNYWC-amide (SEQ ID NO:38) DGA-18: DGACVWQPKFNNYWC-amide (SEQ ID NO:38) DD-18-KtoR: DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Biotin-DD-18-KtoR: Biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Biotin-DD-18-KtoR3: Biotin-DDCVWQPRFNNYWCGGRRRK-amide (SEQ ID NO:40) Biotin2-DD-18-KtoR-R3
- Peptide 18 without a biotin tag (DD-18) blocked cell killing more than Peptide 18 with biotin (Biotin-DD-18) (compare second, third and fourth columns from the left).
- Peptide 18 without biotin (DD-18) blocked more cell killing than Peptide Biotin-DD-18-ex (SEQ ID NO:37) (compare first and fourth columns from the left).
- EXAMPLE 10 Determination of an EC 50 Value for Peptide 18 and Variants [0322] The three most active peptides from the above assays were tested in the L- 929 cell killing assay (described above in Example 4) at peptide concentrations ranging from 50 micromolar to 0.78125 micromolar (in serial two-fold dilutions) and the EC 50 value for each peptide was determined (data not shown).
- EXAMPLE 12 Comparison of Peptide 18 and Variant Binding in the TNF ⁇ Binding Assay [0328] Peptide 18 and the variants described below with altered spacing between the biotin molecule and the AspAsp (DD) N-terminal tag were tested for TNF ⁇ binding using the (TNF ⁇ binding assay described in Example 2. N-terminal spacing variants with PEG4 (4 PEG subunits) were prepared by insertion of a PEG4 at the N-terminus between biotin and the N-terminus of the DD-core TNF ⁇ binding domain of Peptide 18.
- Peptide 18 cyclizes by formation of a disulfide bond between the terminal cysteine residues of the core TNF ⁇ binding domain. To determine whether a single amino acid deletion or insertion between the cysteine residues might alter the activity of the peptide, a valine deletion (Biotin-DD-18-noVal) and an alanine insertion (Biotin-DD-18- plusAla) were prepared.
- Peptide 18 and its variants were tested in the L-929 cell killing assay described in Example 4. Initially, monomeric Peptide 18 having the Lys to Arg substitution in the core TNF ⁇ binding domain (Peptide DD-18KtoR; SEQ ID NO:39) was tested, with and without an N-terminal Lys-PEG12 (12 PEG subunits) or C-terminal peg12-Lys addition.
- the monomeric peptides had the following structures: DD-18KtoR: DDCVWQPRFNNYWC-amide (SEQ ID NO:39) DD-18-KtoR-PEG12-K: Ac-DDCVWQPRFNNYWC-PEG12-K-amide (SEQ ID NO:44) K-PEG12-DD-18-KtoR: Ac-K-PEG12-DDCVWQPRFNNYWC-amide (SEQ ID NO:45) [0334] Referring to Figure 10, addition of a Lys-PEG12 at the N-terminus or PEG12-Lys at the C-terminus did not significantly alter blocking of TNF ⁇ -induced cell killing (compare column 1 and columns 8 and 9).
- Peptide 18 was trimerized by the method in which it was assembled on the solid phase resin to form Peptide DD-18-tricasso.
- Semi-orthogonal protecting groups Dde and Fmoc were used to assemble the trimeric peptide DD-18 trimer (tricasso) directly (see WO2017/040350 for a general description of the tricasso trimerization method).
- Peptide 18 with the Lys to Arg substitution (DD-18- KtoR; SEQ ID NO:39) was trimerized using a naturally forming trimeric IZ coiled-coil sequence (IKKEIEAIKKEQEAIKKKIEAIEKEA (SEQ ID NO:46) and a PEG12 spacer to form Peptide DD-18-KtoR-IZ.
- the IZ forms a non-covalent trimer.
- DD-18-tricasso [DDCVWQPKFNNYWC-PEG12]3-KK-amide
- DD-18-KtoR-IZ DDCVWQPRFNNYWC-PEG12-IKKEIEAIKKEQEAIKKK IEAIEKEA-hydrazide (SEQ ID NO:39 linked through PEG12 to SEQ ID NO:47)
- trimerization of these peptides did not significantly reduce the ability of the peptides to block TNF ⁇ -induced cell death (compare columns 2 and 6 and columns 1 and 7).
- each trimeric Peptides DD-18-tricasso and DD-18-KtoR- IZ in the L-929 cell killing assay were determined by varying the concentrations of peptides from 50 micromolar to 0.78125 micromolar (in serial two-fold dilutions).
- the EC50 value of trimeric Peptide DD-18-KtoR-IZ in PBS and water was determined to be 2.4 micromolar and 2.1 micromolar, respectively.
- the EC50 value of Peptide DD-18-tricasso was determined to be 3.4 micromolar.
- EXAMPLE 14 Preparation and Testing of Covalently-Linked Dimeric and Trimeric Peptides
- Covalently linked dimers and trimers of Peptide DD-18-KtoR were prepared and tested for activity in the L-929 cell killing assay.
- Covalently linked dimers and trimers of DD-18-KtoR were prepared using amine-NHS chemistry.
- the DD-18-KtoR monomers were prepared with terminal amine groups by installing a lysine residue and a PEG group at the N-terminus or C-terminus of the peptide.
- dimers and trimers were prepared by NHS-amine chemistry using linkers with multiple NHS groups. The dimers and trimers were purified using standard HPLC purification methods.
- DD-18-KtoR two different monomers of DD-18-KtoR were prepared: either a N-terminal or C-terminal Lysine was added, separated from the DD-18-KtoR peptide by a PEG12 spacer (SEQ ID NOs: 45 and 46).
- dimers the DD-18-KtoR peptides, with PEG12-Lys, were reacted with an NHS-PEG6-NHS linker.
- trimers the DD-18-KtoR peptides, with PEG12-Lys, were reacted with an Fmoc-amino-tri-NHS linker; in this case, the Fmoc was retained on the amine of the trimeric linker.
- DD-18-KtoR DDCVWQPRFNNYWC-amide SEQ ID NO:39
- DD-18-KtoR-N-dimer (Ac-K-PEG12-DDCVWQPRFNNYWC-amide)2-PEG6
- DD-18-KtoR-C-dimer (Ac-DDCVWQPRFNNYWC-PEG12-K-amide)2-PEG6
- DD-18-KtoR-N-trimer Fmoc-[Ac-K-PEG12-DDCVWQPRFNNYWC-amide]3
- DD-18-KtoR-C-trimer Fmoc-[Ac-DDCVWQPRFNNYWC-PEG12-K-amide]3
- both the covalently linked dimers and trimers of Peptide DD-18-KtoR exhibited significantly more inhibition of TNF ⁇ -mediated cell killing than monomeric P
- Example 15 Determination of EC 50 Values for Dimers and Trimers of Peptide DD-18-KtoR
- concentrations of the following dimers and trimers of Peptide DD-18-KtoR are varied from 10 micromolar to 0.0015 micromolar (in eight two-fold dilutions) in the L-929 cell killing assay.
- DD-18-KtoR-N-dimer (Ac-K-PEG12-DDCVWQPRFNNYWC-amide)2-PEG6 DD-18-KtoR-C-dimer: (Ac-DDCVWQPRFNNYWC-PEG12-K-amide)2-PEG6 DD-18-KtoR-N-trimer: Fmoc-[Ac-K-PEG12-DDCVWQPRFNNYWC-amide]3 DD-18-KtoR-C-trimer: Fmoc-[Ac-DDCVWQPRFNNYWC-PEG12-K-amide]3 [0349]
- the calculated EC50 values were as follows: DD-18-KtoR-N-dimer: 10 nM DD-18-KtoR-C-dimer: 2.6 nM DD-18-KtoR-N-trimer: 2 nM DD-18-KtoR-C-trimer: ⁇ 1.5nM [
- Example 16 Determination of the Species Selectivity of the DD-18-KtoR Trimer
- the C-terminal linked DD-18-KtoR trimer from Example 14 was tested for binding activity against TNF ⁇ proteins from multiple species in the L-929 cell killing assay: Recombinantly expressed soluble TNF ⁇ from human, monkey, dog and rat were tested at concentrations ranging from 10 micromolar to 41 nM (in three-fold dilutions).
- TNF ⁇ from these species can bind to human TNFR, so the L-929 cell killing assay could be used to evaluate the blocking activity of Peptide DD-18-KtoR by the different TNF ⁇ proteins.
- the trimer used was DD-18-KtoR-C-trimer: Fmoc-[Ac- DDCVWQPRFNNYWC-PEG12-K-amide]3. [0353] The C-terminal linked trimer was active against human, monkey, and dog TNF ⁇ in the cell killing assay at all concentrations tested (data not shown). The trimer was not active against rat TNF ⁇ in this assay at any of the concentrations tested (data not shown).
- Example 17 Identification of Residues in Monomeric Peptide DD-18 Involved in Interaction with TNF ⁇ [0355] To identify residues of Peptide DD-18 that are involved in its interaction with TNF ⁇ , additional mutants of Peptide DD-18 (Peptide 18) were prepared. The peptides were tested in the TNF ⁇ binding assay described in Example 2.
- Biotin-DD-018 biotin-DDCVWQPKFNNYWC-amide (SEQ ID NO:32) Biotin-DD-018(K2R): biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Bio-018-WtoG: biotin-DDCVGQPKFNNYWC-amide (SEQ ID NO:47) Bio-018-NtoG: biotin-DDCVWQPKFNGYWC-amide (SEQ ID NO:48) [0356]
- the N-terminal DD tag was changed to DDD in the following peptide: Bio-DDD-018: biotin-DDDCVWQPKFNNYWC-amide (SEQ ID NO:49) [0357] Referring to Figure 12, peptides have substitutions of Trp and Asn to Gly (at positions 3 and 9 of the core TNF ⁇ binding domain, respectively) significantly reduced binding activity
- Peptide Biotin-DD-18K2R (having the Lys to Arg substitution at position 6 of the core TNF ⁇ binding domain; SEQ ID NO:39) exhibited more binding activity than Peptide Bio-DD-18 (SEQ ID NO:32), as shown previously (compare columns 10 and 11).
- Addition of one more D-Asp residue at the N-terminal end of the Peptide Biotin-DD-018 (Peptide Bio-DDD-018; SEQ ID NO:50) reduced its binding activity to some extent (compare columns 3 and 11 from the left).
- other hits from the CX10C peptide libraries were tested in the TNF ⁇ binding assay.
- Bio-DD-Hit19 biotin-DDCQFQPRFNNWQC-amide
- Bio-DD-Hit33 biotin-DDCHFSQRFNNWWC-amide
- Bio-DD-Hit92 biotin-DDCAYQRQFNNWWC-amide
- Bio-DD-Hit193 biotin-DDCWFEHRFNNWHC-amide
- Peptides Bio-DD-Hit19, Bio-DD-Hit92 and Bio-DD-Hit193 exhibited some, but reduced TNF ⁇ binding activity compared to Peptide DD-018, while Peptide Bio-DD-Hit33 exhibited significant binding activity (compare bars 6, 7, and 9 with bar 11 from left).
- Bio-DD-PEG4-018 biotin-DD-PEG4-CVWQPKFNNYWC-amide (SEQ ID NO:55)
- Bio-PEG4-DD-018 biotin-PEG4-DDCVWQPKFNNYWC-amide (SEQ ID NO:54)
- separation of the DD tag from the N-terminus of the core TNF ⁇ peptide binding domain reduced TNF ⁇ binding activity to some extent (compare bars 4, 5 and 11 from the left).
- the EC 50 values were as follows: Bio-DD-018: 16.6 micromolar Bio-DDD-018: 4.1 micromolar Bio-D-018: 38 micromolar Biotin-DD-018(K2R): 2.1 micromolar Biotin-PEG4-DD-018: 15 micromolar Bio-DD-PEG4-018: > 50 micromolar [0366] Referring to these results, compared to Peptide Bio-DD-018 (SEQ ID NO:32), addition of an additional Asp residue in the N-terminal tag (SEQ ID NO:50) results in a more effective (lower) EC50 value while removing an Asp residue (SEQ ID NO:57) results in a less effective (higher) EC50 value.
- Example 19 Thermal Stability of Complexes of TNF ⁇ and Monomeric Peptide Biotin-DD-18 and Selected Variants [0368] The thermal stabilities of complexes of TNF ⁇ and Peptide Biotin-DD-18 and the following mutants were determined using the high-throughput thermal scanning method described by Lavinder et al., J. Am. Chem. Soc.2009, 131(11):3794-3795.
- a fluorescent dye SYPRO TM
- complexes with protein (or protein-peptide) complexes in solution The dye fluoresces after denaturation of the complexes. The results are determined as TNF ⁇ - ⁇ Tm in degrees centigrade.
- Example 20 Thermostability of Monomeric Peptide Biotin-DD-18 and Spacer Changes [0373] The thermostability of the DD spacer changes on Peptide Biotin-DD-18 was determined using the thermostability assay described in Example 19.
- Biotin-PEG4-DD-018 biotin-PEG4-DDCVWQPKFNNYWC-amide (SEQ ID NO:54)
- Bio-DD-PEG4-018 biotin-DD-PEG4-CVWQPKFNNYWC-amide (SEQ ID NO:55)
- the results were as follows: Biotin-PEG4-DD-018: 80.3 (+5.5 over TNF ⁇ alone)
- Example 21 Thermostability of Monomeric Peptides Having Modifications of the N-terminal DD Tag of Peptide DD-18 [0377]
- the thermostability assay described in Example 19 was performed on the following peptides to further assess changes in sequence of the N-terminal DD tag of Peptide Biotin-DD-18.
- Example 22 Thermostability of Peptide Bio-DD-018 and Variants [0381] The thermostability assay described in Example 19 was performed on the following peptides from the library screen described in Example 1 to further assess the effects of changes in the sequence of Peptide Biotin-DD-18 on the binding to TNF ⁇ .
- Example 23 Analysis of the Effects of Changing PEG Spacer Length in Peptide DD-18-KtoR Trimers
- Trimers with different PEG spacers were prepared to determine the effect of PEG spacer length on activity of trimer of Peptide DD-18-KtoR (SEQ ID NO:39) activity in the L-929 cell killing assay.
- the Peptide DD-018-KtoR-C-trimer (PEG12) from Example 14 was used.
- Two different preparations of 018-KtoR-C-trimer (PEG12) were tested in this study. They are designated -1 and -2.
- trimers with PEG spacers of 4 and 8 PEG subunits were prepared.
- the trimeric peptides tested were the following: 018-KtoR-C-trimer (PEG12) – 1: Fmoc-[Ac-DDCVWQPRFNNYWC-PEG12-K- amide] 3 018-KtoR-C-trimer (PEG12) – 2: Fmoc-[Ac-DDCVWQPRFNNYWC-PEG12-K- amide] 3 018-KtoR-C-trimer (PEG4): Fmoc-[Ac-DDCVWQPRFNNYWC-PEG4-K- amide] 3 018-KtoR-C-trimer (PEG8): Fmoc-[Ac-DDCVWQPRFNNYWC-PEG8-K- amide] 3 [0386] Referring to Figure 13, the PEG8 spacer and the PEG12 spacer were about the same in activity while the PEG4 spacer consistently yielded less binding activity (compare bars 2, 3, and 4 with bar 1 within each series).
- Example 24 Activity of Peptide DD-18-Dimers and Trimers in Cell Killing assay Using Mouse TNF [0388]
- the Peptide 018-KtoR-C-trimer and Peptide 018-KtoR-C- dimer were shown to bind to human, monkey, and dog TNF ⁇ , but not rat TNF ⁇ . In this study, the dimers and trimers were tested against mouse TNF ⁇ in the L-929 cell killing assay.
- DD-18-KtoR-N-dimer (Ac-K-PEG12-DDCVWQPRFNNYWC-amide) 2 -PEG6 DD-18-KtoR-C-dimer: (Ac-DDCVWQPRFNNYWC-PEG12-K-amide) 2 -PEG6 DD-18-KtoR-N-trimer: Fmoc-[Ac-K-PEG12-DDCVWQPRFNNYWC-amide] 3 DD-18-KtoR-C-trimer: Fmoc-[Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 [0390] In this study, none of the dimers or trimers showed significant activity in binding to mouse TNF ⁇ (data not shown).
- Example 25 Modification of the Peptide DD-18 Sequence
- Peptide 001 from the CX 10 C library was a strong binder in the phage display screen but was insoluble under the aqueous assay conditions used in these studies. Based on the similarity of Peptide 001 and Peptide 018-KtoR, a modified Peptide 018 was designed.
- Peptide 001 and Peptide 018-KtoR and the modified Peptide 18 are shown below, where differences from Peptide 018-KtoR are underlined: Peptide 001: CTFQWRFNNYWC (SEQ ID NO:12) Peptide 018-KtoR: CVWQPRFNNYWC (SEQ ID NO:5) Modified Peptide 18-KtoR: CTFQPRFNNYWC (SEQ ID NO:6) [0393] Another variant of Peptide DD-018 was also tested; this variant had an N to Q substitution near the C-terminal end of the peptide (at the penultimate C-terminal position of the core TNF ⁇ binding domain) was prepared.
- Bio-DD-018-KtoR Biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) Bio-DD-TF-018-KtoR: Biotin-DDCTFQPRFNNYWC-amide (SEQ ID NO:58) Bio-DD-TF-018-KtoR-W: Biotin-DDCTFQPRFNNWWC-amide (SEQ ID NO:61) Bio-DD-VF-018-KtoR: Biotin-DDCVFQPRFNNYWC-amide (SEQ ID NO:62) Bio-DD-SF-018-KtoR: Biotin-DDCSFQPRFNNYWC-amide (SEQ ID NO:63) [0402] The EC 50 values determined were as follows: Bio-DD-018-KtoR: 2.25 micromolar Bio-DD-TF-018-KtoR: 1.16 micromolar Bio-DD-TF-018-
- Example 28 Activity of Peptide DD-TF-018-KtoR Trimer as compared to anti-TNF ⁇ antibody and VHH2 in The L-929 Cell Killing Assay [0405] The activity of a trimeric form of the DD-TF-018-KtoR (SEQ ID NO:59) that has linked to it a PEG8-K spacer in each arm was compared against the activity of other TNF ⁇ -blocking agents in the L-929 cell killing assay and the EC 50 values were determined. Anti-TNF ⁇ antibody was from R&D Systems (research grade).
- Anti-TNF ⁇ VHH2 nanobody was as described in Beirnaert et al., 2017, Front. Immunol. 8:867.
- the peptide tested was the following: DD-TF-018-KtoR C-trimer (PEG8): Fmoc-[Ac-DDCTFQPRFNNYWC-PEG8-K- amide] 3 [0406]
- the EC 50 values were as follows: DD-TF-018-KtoR C-trimer (PEG8): 1 pM to 1 fM Anti-TNF ⁇ antibody: 90.5 pM Anti-TNF ⁇ VHH2 nanobody: 16.9 pM [0407]
- Peptide DD-TF-018-KtoR trimer was more potent than the anti-TNF ⁇ antibody and anti-TNF ⁇ VHH2.
- Example 29 Analysis of Variations of the Trimeric Scaffold Structure and Spacer Length in the L-929 CELL Killing Assay [0409] To determine whether and/or how different trimeric scaffolds affect the activity of Peptide DD-018-KtoR (SEQ ID NO:32), three different scaffolds were tested. In addition, Peptide DD-TF-018-KtoR (SEQ ID NO:58) was included in one trimer construct.
- the scaffolds tested were an Fmoc-scaffold (Quanta BioDesign), an Fmoc-PEG27 scaffold (Quanta BioDesign) and a cyclohex scaffold (the cyclohex tri-NHS ester was prepared from cyclohexanetricarboxylic acid, also called 1,3,5- cyclohexanetricarboxylic acid, by conversion of tri-carboxylic acid compounds with NHS (N-hydroxysuccinimide) in presence with a carbodiimide (such as DIC or DCC)).
- the Fmoc-scaffold was used previously in Example 14.
- the length of the PEG spacer was changed from PEG8 to PEG6.
- the trimeric peptides were tested in the L-929 cell killing assay using peptide concentrations of 0.2 micromolar to 0.51 pM (in five-fold dilutions).
- the trimeric peptides tested were as follows: 018-KtoR-C-trimer (PEG6)-Fmoc: [Ac-DDCVWQPRFNNYWC-PEG6-K-amide] 3 -Fmoc 018-KtoR-C-trimer (PEG12)-PEG27-Fmoc: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -PEG27-Fmoc 018-KtoR-C-trimer (PEG12)-Fmoc: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -Fmoc DD-TF-018-KtoR-trimer (PEG12)-Fmoc: [Ac-DDCTFQPRFNNYWC
- Example 30 Further Analysis of Variations of the Trimeric Scaffold Structure in the L-929 Cell Killing Assay [0412] To determine whether other trimeric scaffolds increased the activity of Peptide DD-018-KtoR (SEQ ID NO:39) in trimeric form, five different scaffolds were tested in addition to the Fmoc-PEG27 scaffold used in Example 29.
- the scaffolds tested were a Nitro-scaffold (prepared from 4-(2-Carboxyethyl)-4- nitroheptanedioic acid by conversion of tri-carboxylic acid compounds with NHS (N- hydroxysuccinimide) in presence with a carbodiimide (such as DIC or DCC)), an Amine- PEG27-scaffold (Quanta BioDesign), the Fmoc-scaffold (see Example 29), an Amine- scaffold (Quanta BioDesign), a cholesterol-scaffold (Quanta BioDesign) and a Biotin- PEG27-scaffold (Quanta BioDesign).
- Nitro-scaffold prepared from 4-(2-Carboxyethyl)-4- nitroheptanedioic acid by conversion of tri-carboxylic acid compounds with NHS (N- hydroxysuccinimide) in presence with a carbodiimide (such as DIC or DCC)
- the trimeric peptides were tested in the L-929 cell killing assay using peptide concentrations of 0.2 micromolar to 2.6 pM (in five-fold- dilutions).
- the trimeric peptides tested were as follows: 018-KtoR-C-trimer (PEG12)-nitro: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -nitro 018-KtoR-C-trimer (PEG12)-PEG27-amine: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -PEG27-amine 018-KtoR-C-trimer (PEG12)-Fmoc: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -Fmoc 018-KtoR-C-trimer (PEG12)-amine: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -amine 018
- Example 31 Activity of Certain Trimeric Peptides at Lower Concentrations
- Trimers of Peptide DD-018-KtoR (SEQ ID NO:39) or Peptide TF-DD-018- KtoR (SEQ ID NO:59) using the Fmoc-scaffold, amine-scaffold or cyclohex-scaffold from Examples 29 and 30 were tested in L-929 cell killing assay at lower concentrations than in prior examples to determine the EC50 values.
- the trimeric peptide concentrations ranged from 0.32 nM to 0.16 fM (in 5-fold dilutions).
- the trimeric peptides tested were the following: 018-KtoR-C-trimer (PEG12)-Fmoc: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -Fmoc 018-KtoR-C-trimer (PEG12)-amine: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -amine 018-KtoR-C-trimer (PEG12)-cyclohex: [Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 -cyclohex TF-018-KtoR-C-trimer (PEG12)-Fmoc: [Ac-DDCTFQPRFNNYWC-PEG12-K-amide] 3 -Fmoc [0416]
- the EC50 values were as follows: 018-KtoR-C-trimer (PEG12)-Fmoc: 5.1 pM 018-K
- Example 32 Analysis of Further Modifications to Monomeric DD-VF- 018-KtoR-WW Peptide in the L-929 Cell Killing Assay [0419] Based on the above examples, Peptide TF-018-KtoR-WW (DDCTFQPRFNNWWC; SEQ ID NO:61) yielded the best activity in the L-929 cell killing assay.
- Bio-VF-018-KtoR-WW Biotin-DDCVFQPRFNNWWC-amide (SEQ ID NO:64) Bio-DtoE-VF-018-KtoR-WW: Biotin-EDCVFQPRFNNWWC-amide (SEQ ID NO:65) Bio-VF-018-QtoK-KtoR-WW: Biotin-DDCVFKPRFNNWWC-amide (SEQ ID NO:66) VF-018-QtoKbio-KtoR-WW: Ac-DDCVFX 6 PRFNNWWC-amide; wherein X6 is K(bio); SEQ ID NO:67) Bio-018-KtoR: Biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) [0420] Referring to Figure 17, changing the N-terminal Aspartate to Glutamate in the tag did not significantly modify activity of Peptide Bio-VF-018-KtoR-WW (SEQ ID NO:65).
- Example 33 Analysis of Further Modifications to Monomeric DD-VF- 018-KtoR-WW Peptide in the L-929 Cell Killing Assay [0422] To determine whether further modifications to Peptide VF-018-KtoR-WW (SEQ ID NO:65) could improve its activity, additional substitutions were made and tested in the L-929 cell killing assay. The peptides tested were as follows, where differences from Peptide VF-018-KtoR-WW (SEQ ID NO:65) are underlined. Peptide Bio-018-KtoR (SEQ ID NO:39) was also included as a control.
- Bio-VF-018-KtoR-WW Biotin-DDCVFQPRFNNWWC-amide (SEQ ID NO:64) Bio-VF-018-PtoG-KtoR-WW: Biotin-DDCVFQGRFNNWWC-amide (SEQ ID NO:68) Bio-VF-018-PtoH-KtoR-WW: Biotin-DDCVFQHRFNNWWC-amide (SEQ ID NO:69) Bio-VF-018-QtoN-KtoR-WW: Biotin-DDCVFNPRFNNWWC-amide (SEQ ID NO:70) Bio-018-KtoR: Biotin-DDCVWQPRFNNYWC-amide (SEQ ID NO:39) [0423] Referring to Figure 18, Peptides Bio-VF-018-PtoG-KtoR-WW, Bio-018- KtoR-WW and Bio-VF-018-PtoH-KtoR-WW had comparable activity at the highest concentration.
- Example 34 Analysis of Further Modifications to Peptide DD-018-KtoR in Monomeric and Dimeric Forms in the L-929 Cell Killing Assay [0425]
- the DD tag at the N-terminus of the peptides provides a negative charge at neutral pH, which helps improve the solubility of the peptides.
- Two Aspartate (D) residues in the N-terminal tag maintained high solubility and good activity.
- suc (succinate) group was replaced by a mimic suc (succinate) group.
- Succinic acid is a di- carboxylic acid. One acid group is conjugated to the Asp through an amide bond, while the other acid is free to introduce a negatively-charged carboxylate.
- Both monomeric and dimeric forms of Peptide DD-018-KtoR-PEG8-K were tested in the L-929 cell killing assay. The dimeric forms were made using amine-NHS chemistry and an NHS-PEG8- NHS crosslinker (Quanta BioDesign). Peptide Bio-DD-TF-018-KtoR-WW (SEQ ID NO:62) was also included.
- DD-018-KtoR-PEG8-K Ac-DDCVWQPRFNNYWC-PEG4-PEG4-K-amide
- sucD-018-KtoR-PEG8-K suc-DCVWQPRFNNYWC-PEG4-PEG4-K-amide
- DD-018-KtoR-PEG8-K Dimer (Ac-DDCVWQPRFNNYWC-PEG4-PEG4-K-amide) 2 -PEG6 sucD-018-KtoR-PEG8-K Dimer: (suc-DCVWQPRFNNYWC-PEG4-PEG4-K-amide) 2 -PEG6 Bio-DD-TF-018-KtoR-WW: Biotin-DDCTFQPRFNNWWC-amide (SEQ ID NO:61) [0426] Referring to Figure 19, replacement of one Asp residue of the tag with
- Example 35 Analysis of Further Modifications to Peptide TF-018-KtoR- WW in the L-929 Cell Killing Assay
- D- ⁇ -amino acid analogs were site-selectively introduced to determine whether potency of monomeric Peptide TF-018-KtoR-WW (SEQ ID NO:62) was increased in the L-929 cell killing assay.
- the D- ⁇ -amino acid analogs used were penicillamine (Pen), a methyl cysteine analog; Homoleucine (homoLeu), an analog of Leucine (Leu); and Norleucine (norLeu), an analog of Leucine (Leu).
- Bio-DD-TF-018-KtoR-WW Biotin-DDXTFQPRFNNWWC-amide (SEQ ID NO:72), where X in this peptide is D-penicillamine Bio-TF-018-KtoR-WW-Pen: Biotin-DDCTFQPRFNNWWX-amide (SEQ ID NO:73), where X in this peptide is D-penicillamine Bio-homoLeu-F-018-KtoR-WW: Biotin-DDCXFQPRFNNWWC-amide (SEQ ID NO:74), where X in this peptide is D-homoleucine Bio-norLeu-F-018-KtoR-WW: Biotin-DDCXFQPRFNNWWC-amide (SEQ ID NO:75), where X
- Example 36 Thermostability of Complexes of TNF ⁇ with Peptide DD-018- KtoR (SEQ ID NO:39) and Oligomeric Variants [0431]
- the thermostability assay described in Example 19 was performed on the following complexes of TNF ⁇ and peptides to further assess the effects of oligomerization on TNF ⁇ binding stability.
- DD-18-KtoR DD-18-KtoR: DDCVWQPRFNNYWC-amide (SEQ ID NO:39)
- DD-18-KtoR-C-dimer (Ac-DDCVWQPRFNNYWC-PEG12-K-amide) 2 -PEG6
- DD-18-KtoR-C-trimer Fmoc-[Ac-DDCVWQPRFNNYWC-PEG12-K-amide] 3 [0432]
- TNF ⁇ alone was included as a reference.
- DD-018 Fluor-DDCVWQPKFNNYWC-amide (SEQ ID NO:32)
- DD-018-WtoG2 Fluor-DDCVGQPKFNNYGC-amide (SEQ ID NO:76)
- P1 identifies the elution peak corresponding to TNF ⁇ .
- P2 identifies the elution peak for free peptide.
- the top panel shows the elution profile for TNF ⁇ alone.
- the middle panel shows the elution profile for TNF ⁇ plus fluorescently labeled Peptide DD-018. Some peptide co-elutes with TNF ⁇ (P1), indicating that it bound to TNF ⁇ . P2 is the excess peptide.
- the bottom panel shows the elution profile for TNF ⁇ plus fluorescently labeled Peptide DD-018-WtoG2, a non-binding control. Peptide DD-018-WtoG2 does not coelute with TNF ⁇ .
- Example 38 Peptide TF-018-KtoR-WW and Oligomers Thereof Were Tested in the TNF ⁇ /TNFR blocking assay and L-929 Cell Killing Assay.
- TF-018-KtoR-WW Monomer Ac-DDCTFQPRFNNWWC-amide (SEQ ID NO:61)
- TF-18-KtoR-WW C-Dimer (Ac-DDCTFQPRFNNWWC-PEG12-K-amide) 2 - PEG6
- TF-18-KtoR-WW C-Trimer amine-[Ac-DDCTFQPRFNNWWC-PEG8-K- amide] 3
- the activities of the peptide monomers and trimers were compared to an anti-TNF ⁇ antibody (R&D Systems (research grade)).
- Figure 22A shows a comparison of the binding affinities of monomeric, dimeric and trimeric Peptide TF-018-KtoR-WW in the TNF ⁇ /TNFR blocking assay. Multimerization of the peptide improved the IC50.
- Figure 22B shows a comparison of the monomeric trimeric Peptide TF-018-KtoR-WW with an anti-TNF ⁇ antibody (R&D Systems (research grade)). The IC50 of trimeric Peptide TF-018-KtoR-WW was better than that of the anti-TNF ⁇ antibody in the TNF ⁇ /TNFR blocking assay.
- Figure 23A shows a comparison of the activities of monomeric, dimeric, and trimeric Peptide TF-018-KtoR-WW in the L-929 cell killing assay. Multimerization of the peptide improved the EC 50 .
- Figure 23B shows a comparison of the monomeric and trimeric Peptide TF-018-KtoR-WW with an anti-TNF ⁇ antibody (R&D Systems (research grade)). The EC 50 value of trimeric Peptide TF-018-KtoR-WW was better than that of the anti-TNF ⁇ antibody in this assay.
- Example 39 Example 39.
- Peptide TF-018-KtoR- WW Monomer and Trimer The binding affinities of Peptide TF-018-KtoR-WW (SEQ ID NO:62) monomer and trimer were determined by surface plasmon resonance (SPR). Recombinant biotin-TNF ⁇ was immobilized to an SPR chip surface through interaction with neutravidin- modified chips. Then different concentrations of monomer or trimer were introduced across the surface, and relative binding parameters were determined. Peptide TF-018- KtoR-WW monomer had an affinity of ⁇ 50 nM, as determined using concentrations of 1200 nM, 625 nM, and 312.5 nM of monomer.
- Peptide TF-18-KtoR- WW C-trimer Can Block the Activity of Membrane-Bound TNF ⁇
- Peptide TF-18-KtoR-WW C-Trimer was tested for its ability to specifically block the activity of membrane-bound TNF ⁇ using the L-929 cell killing assay.
- TNF ⁇ has a deletion ( ⁇ 1-12 aa) of the substrate cleavage site for TACE (TNF ⁇ converting enzyme).
- TACE TNF ⁇ converting enzyme
- L-929 (TNFR-expressing) cells were overlayed against HEK293T cell lines (expressing either WT or membrane-restricted ( ⁇ 1-12 aa) TNF ⁇ ) in the absence or presence of trimer.
- the TF-18-KtoR-WW C-Trimer could rescue TNF ⁇ - mediated cell killing for both WT and membrane-restricted TNF ⁇ .
- Example 41 Stability of Peptide TF-18-KtoR-WW C-Trimer in Simulated Gastric and Intestinal Fluids
- the stability of Peptide TF-18-KtoR-WW C-Trimer was assessed in simulated gastric and intestinal fluids (SGF and SIF, respectively).
- the TF-18-KtoR-WW C-Trimer has three PEG8 arms and a free amino group.
- Simulated gastric fluid (SGF – RICCA Chemical Company, Product Number 7108) contained 0.2 % (w/v) sodium chloride in 0.7 % (v/v) hydrochloric acid with 3.2 mg of freshly added purified pepsin (derived from porcine stomach mucosa, with an activity of 800 to 2500 units per mg of protein) added per mL of solution.
- the pH of the simulated gastric fluid was 1 to 1.6.
- Simulated intestinal fluid (SIF – RICCA Chemical Company, Product Number 7109) contained 0.68 % (w/v) potassium phosphate, 0.06 % (w/v) sodium hydroxide and 1 % (w/v) pancreatin. The pH of this solution was 6.7 to 6.9.
- Example 42 Whole Blood Cytokine Release Assay.
- Whole blood assays were carried out under sterile conditions in a laminar flow hood. All conditions were tested in triplicate.
- the stimulation of whole blood was done in U bottom 96-well plates as follows.
- Peptide TF-18-KtoR-WW C-Trimer and TNF (10 ng/mL) were preincubated for 30 min at room temperature before being added to diluted blood and further incubated at 37 °C, 5 % CO 2 for 24 hours.
- Peptide TF-18-KtoR-WW C-Trimer was first mixed with diluted blood before the stimulus was added according to the plate layout. The controls were prepared in a similar manner.
- the blood samples were incubated at 37 °C, 5 % CO2 in RPMI containing stabilized L-glutamine. After a 24 hours incubation at 37 °C, 5 % CO 2 , supernatants were harvested and stored at -20 °C. The final reaction volume was 300 ⁇ L per well and the final blood concentration was 50 %. IL-8 released in the culture supernatants was measured using a specific ELISA kit according to the supplier’s instructions (Human IL-8 ELISA kit, R&D Systems, #DY208). [0456] After 24 hours of incubation, no sign of hemolysis was observed in the harvested supernatants. In the absence of stimulation, IL-8 levels were between 450 and 1070 pg/mL on average.
- TNF-induced IL-8 was completely inhibited by Peptide TF-18-KtoR-WW C-Trimer at 100 nM (and 10 nM for donor 2).
- LPS-induced IL-8 was partly inhibited in blood from donors 1 and donor 3 but was not modulated in blood from donor 2.
- Anti-CD3 plus anti-CD28-antibodies induced IL-8 was also fully (donors 1 and 3) or partly (donor 2) inhibited in the presence of Peptide TF-18-KtoR-WW C-Trimer. Referring to Figure 25, the average IL-8 inhibition for the three samples for each condition are shown. [0457] Example 43.
- Peptide TF-18-KtoR-WW C-Trimer Promotes Survival In Vivo in a Human TNF ⁇ Mouse Challenge Model.
- anti-TNF ⁇ monoclonal antibody inhibits both mouse and human TNF-alpha while Peptide TF-18- KtoR-WW C-Trimer inhibits only human TNF-alpha.
- Example 44. Single Dose Subcutaneous Dosing with Peptide TF-18-KtoR- WW C-Trimer mice were dosed with Peptide TF-18-KtoR-WW C-Trimer diluted in PBS and administered as a single subcutaneous dose in 2 male and 2 female CD1mice.
- FIGS. 27 and 28 show the average amount of Peptide TF-18-KtoR-WW C- Trimer in the plasma for each group of four animals, two males and two females. Panels A and B show two different graphical representations of the data.
- Example 45 Peptide TF-18-KtoR-WW C-Trimer Plasma Levels Following Oral Dosing
- Peptide TF-18-KtoR-WW C-Trimer was diluted in PBS to 50 mg/kg and administered to mice, 2 males and 2 females, by a single oral gavage prior to serum collection.
- Peptide TF-18-KtoR-WW C-Trimer was administered intravenously (IV; 5 mg/kg), subcutaneously (SC; 50 mg/kg), and orally (po; 100 mg/kg) to C57Bl/6 mice (3 animals per group).
- the vehicle was 91 % sodium phosphate buffer (20 mM) and 9 % sucrose.
- Peptide TF-18-KtoR-WW C-Trimer concentration (nM) was measured in plasma or kidney (in the case of 50 mg/kg sc dosing) by mass spec.
- Peptide TF-18-KtoR-WW C-Trimer was extracted from serum by precipitating serum components using organic solvent (acetonitrile crash), separated from remaining contaminating proteins by C18 reverse-phase HPLC at 40 °C, and the peptide identified by ESI-MS.
- Peptide TF-18-KtoR-WW C-Trimer levels were quantified by comparing signal in unknown samples to that a standard curve and quality control samples. All samples were spiked with a known amount of a “heavy” internal standard to control for extraction, injection, and ionization variabilities.
- Peptide TF-18-KtoR-WW C-Trimer was detected in the plasma following administration of 5.0 mg/kg IV or 50 mg/kg SC. It was also detected in the kidney following 50 mg/kg SC dosing; ten percent of the initial exposure present in the kidney after 24 hours. The long terminal half-life of Peptide TF- 18-KtoR-WW C-Trimer was 18 hours following intravenous administration.
- Tg1278 mTNF KO/hTNF KI mice are a transgenic strain with a normally regulated and expressed human TNF ⁇ (hTNF ⁇ ) in the absence of murine TNF ⁇ .
- hTNF ⁇ human TNF ⁇
- IL-6 was detected by ELISA.
- Peptide TF-18-KtoR-WW C-Trimer subcutaneous administration of Peptide TF-18-KtoR-WW C-Trimer at 5, 15, and 50 mg/kg per mouse one hour prior to LPS treatment resulted in full inhibition of TNF- mediated IL-6 production at all doses.
- the activity of Peptide TF-18-KtoR-WW C-Trimer was equal to a 10 mg/kg per mouse dose of research grade entanercept (labeled Enbrel in the figure) administered 16 hours prior to LPS treatment.
- Peptide TF-18-KtoR-WW C-Trimer was able to inhibit production of mouse KC (chemokine (C- X-C motif) ligand 1 (CXCL1)), in a similar manner.
- X 2 is the D form of Thr (T), Val (V), His (H), Leu (L), Gln (Q), Ala (A), Ile (I), Met (M), or Trp (W), or a D- ⁇ - amino acid analog thereof
- X 4 is a Polar amino acid selected from the D form of Arg (R), Lys (K), His (H), Glu (E), Asp (D), Gln (Q), Asn (N), Thr (T), Ser (S), Pro (P), Ala (A), or Gly (G), or a D- ⁇ -amino acid analog thereof
- X 5 is D form of Pro (P), Trp (W), His (H), Gln (Q), Arg (R), Ala (A), Val (V), Leu (L), or
- SEQ ID NO: 113 C*-X 2 -[W/F/Y]-[Polar]-X 5 -X 6 -F-N-N-[W/Y]-W-C* (SEQ ID NO:3), wherein X 2 is the D form of any of the canonical L-amino acids other than Cys, X 5 is the D form of any of the canonical L-amino acids other than cysteine, X 6 is the D form of any of the canonical L-amino acids other than cysteine, Polar represents a D-amino acid comprising one of R, K, H, E, D, Q, N, T, S, P, A, or G, and the * indicate an optional intramolecular disulfide bond.
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| KR1020257029726A KR20250163313A (en) | 2023-02-08 | 2024-02-07 | TNF-alpha binders and methods of using the same |
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| WO2007009233A2 (en) * | 2005-07-18 | 2007-01-25 | University Of Manitoba | Peptide-based cytokine vaccines in the treatment of autoimmune and inflammatory diseases |
| US20070172516A1 (en) * | 2002-09-04 | 2007-07-26 | Procom Biotechnologische Produktions Gmbh | Increasing of the resorption of substances via skin and mucous membranes |
| US20180327476A1 (en) * | 2013-03-06 | 2018-11-15 | Protalix Ltd. | Chimeric polypeptides, polynucleotides encoding same, cells expressing same and methods of producing same |
| US20210230237A1 (en) * | 2012-03-26 | 2021-07-29 | Uti Limited Partnership | Methods and compositions for treating inflammation |
| US20210346465A1 (en) * | 2010-03-19 | 2021-11-11 | Immatics Biotechnologies Gmbh | Immunotherapy against several tumors including gastrointestinal and gastric cancer |
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| US20070172516A1 (en) * | 2002-09-04 | 2007-07-26 | Procom Biotechnologische Produktions Gmbh | Increasing of the resorption of substances via skin and mucous membranes |
| WO2007009233A2 (en) * | 2005-07-18 | 2007-01-25 | University Of Manitoba | Peptide-based cytokine vaccines in the treatment of autoimmune and inflammatory diseases |
| US20210346465A1 (en) * | 2010-03-19 | 2021-11-11 | Immatics Biotechnologies Gmbh | Immunotherapy against several tumors including gastrointestinal and gastric cancer |
| US20210230237A1 (en) * | 2012-03-26 | 2021-07-29 | Uti Limited Partnership | Methods and compositions for treating inflammation |
| US20180327476A1 (en) * | 2013-03-06 | 2018-11-15 | Protalix Ltd. | Chimeric polypeptides, polynucleotides encoding same, cells expressing same and methods of producing same |
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