CA2744317A1

CA2744317A1 - Substituted tetracycline compounds

Info

Publication number: CA2744317A1
Application number: CA2744317A
Authority: CA
Inventors: Mark L. Nelson; Kwasi Ohemeng; Victor Amoo; Oak K. Kim; Paul Abato; Haregewein Assefa; Joel Berniac; Beena Bhatia; Todd Bowser; Jackson Chen; Mark Grier; Laura Honeyman; Mohamed Y. Ismail; Rachid Mechiche; Jude Mathews
Original assignee: Paratek Pharmaceuticals Inc
Current assignee: Paratek Pharmaceuticals Inc
Priority date: 2003-07-09
Filing date: 2004-06-25
Publication date: 2005-02-03

Abstract

The present invention pertains, at least in part, to novel substituted tetracycline compounds. These tetracycline compounds can be used to treat numerous tetracycline compound-responsive states, such as bacterial infections and neoplasms, as well as other known applications for tetracycline compounds such as blocking tetracycline efflux and modulation of gene expression.

Description

SUBSTITUTED TETRACYCLINE COMPOUNDS

This application is a divisional application of co-pending Application Serial No. CA 2,531,728, filed June 25, 2004.

Background of the Invention The development of the tetracycline antibiotics was the direct result of a systematic screening of soil specimens collected from many parts of the world for evidence of microorganisms capable of producing bacteriocidal and/or bacteriostatic compositions. The first of these novel compounds was introduced in 1948 under the name chlortetracycline. Two years later, oxytetracycline became available. The elucidation of the chemical structure of these compounds confirmed their similarity and furnished the analytical basis for the production of a third member of this group in 1952, tetracycline. A new family of tetracycline compounds, without the ring-attached methyl group present in earlier tetracyclines, was prepared in 1957 and became publicly available in 1967; and minocycline was in use by 1972.
Recently, research efforts have focused on developing new tetracycline antibiotic compositions effective under varying therapeutic conditions and routes of administration. New tetracycline analogues have also been investigated which may prove to be equal to or more effective than the originally introduced tetracycline compounds. Examples include U.S. Patent Nos. 2,980,584; 2,990,331; 3,062,717;
3,165,531; 3,454,697; 3,557,280; 3,674,859; 3,957,980; 4,018,889; 4,024,272;
and 4,126,680. These patents are representative of the range of pharmaceutically active tetracycline and tetracycline analogue compositions.
Historically, soon after their initial development and introduction, the tetracyclines were found to be highly effective pharmacologically against rickettsiae; a number of gram positive and gram negative bacteria; and the agents responsible for lymphogranuloma venereum, inclusion conjunctivitis, and psittacosis. Hence, tetracyclines became known as "broad spectrum" antibiotics. With the subsequent establishment of their in vitro antimicrobial activity, effectiveness in experimental infections, and pharmacological properties, the tetracyclines as a class rapidly became widely used for therapeutic purposes. However, this widespread use of tetracyclines for both major and minor illnesses and diseases led directly to the emergence of resistance to these antibiotics even among highly susceptible bacterial species both commensal and pathogenic (e.g., pneumococci and Salmonella). The rise of tetracycline-resistant organisms has resulted in a general decline in use of tetracyclines and tetracycline analogue compositions as antibiotics of choice.
Summary of the Invention:
In one embodiment, the invention pertains to a 7,9-substituted tetracycline compound of Formula I:
R7 Rs R4 x ow OR
R0 O R" (j) wherein:
Xis CHC(R13Y'Y), CR6'R6, S, NR6, or 0;
R2, R2', R4', and e' are 'each independently hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is I~R4R4", alkyl, alkenyl, alkynyl, hydroxyl, halogen, or hydrogen;
RZ*, R3, R' , Rn and Rte are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy, R6 and R6' are each independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R' ethyl, perhalogenated alkenyl, substituted pyridinyl, pyrazinyl, furanyl, or pyrazolyl;
R$ is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R9 -CH2NR9R9b;
R9a and R91' are each independently hydrogen, alkyl, alkenyl or linked to form a heterocycle;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl; and Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts thereof.

In another embodiment, the invention pertains to a 9-substituted tetracycline compound of formula II:

x OR?
I NIORr ORja R10 0 OR" 0 0 (II) wherein:
Xis CHC(R13Y'Y), CR6'R6, S, NR6, or 0;
R2, R4', R4", R7' and R7" are each hydrogen, alkyl, alketiyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, 0, R" and RI2 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy, R6 and R6' are independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alk}myl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is NR7'R7", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
s i R is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R9 is -CH2NR fte, or linked with R10 to form a furanyl ring;
R9a is hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic,or heteroaromatic;
e is hydrogen or alkyl;
R$ is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy,, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
RP is hydrogen, hydroxy, alkyl, alkeny1, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.

In another embodiment, the invention pertains to 7-substituted tetracycline compounds of formula III:

Rs X R3 I I NR2Rr _ R9 =
ORS' R10 O R~~ 0 0 lhl Wherein:
X is CHC(Ri3Y'Y), CR6'R6, C=CR6'R6, S, NR6, or 0;
R2, R2', R4', and R4" are each independently hydrogen, alkyl, alkenyl, alkynyl, alkoxy, aikyltbio, alkylsulfonyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, R10, R1' and R12 are each hydrogen or a pro-drug moiety;
RS is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy, R6 and R6' are each independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is substituted or unsubstituted pyrazolyl, furanyl, thiophenyl, or thiazolyl;
R8 is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R4 is hydrogen;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, or an arylalkyl; and Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulnyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts thereof In another embodiment, the invention pertains to 8-substituted tetracycline compound of formula IV:

wherein:
X is CHC(R13Y'Y), CR6'R6, S, NR6, or 0;
R2, e, R4'; R7 and RT' are each hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, R10, R" and Rig are each hydrogen or a pro-drug moiety, R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy, R6 and R6' are independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or-(CH2)as (NR'`)o.iC(w')wR7a;
R8 is an aminomethyl substituted phenyl or substituted pyridinyl;
R9 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or-(CH2)a3NR9C(=Z')ZR9a;
R7a, Rye, e, R7d, R7e, e, R9a, R91', R9c, R9d, R9e, and R81 are each independently absent, hydrogen, acyl, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
W is CRrdRRe, S, 0 or NRh;
W' is 0, W1. or S;
Z is CR9dR9e, S, 0 or NR9b;
Z'is 0,NR9,or S;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.
In one embodiment, a 13-substituted tetracycline compound is of formula V:
Rt3 R7 I R5_ R4 Rs OW

(V) wherein:
R2, R4', R4", R7' and RT' are each hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety, RR is NR4'R4õ, alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen, R2', R3, R10, R" and R'2 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, amyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy, R7 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)0-3 (NR7`)o-iC(=W')WRia;
R8 is substituted phenyl or substituted pyridinyl;
R9 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkenyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)o-3NR9oC(=Z')ZR9a;
R7a, RT', R7c, R7d, R7e, R7 , R9a, R9b, R9o, R9d, R9, and R8 are each independently absent, hydrogen, acyl, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
W is CR7dR7e, S, 0 or NR7 W' is 0,NR7,orS;
R13 is 4-alkyl substituted phenyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.
In another f irther embodiment, the invention pertains, at least in part, to methods for treating subjects for tetracycline responsive states by administering to them an effective amount of a tetracycline compound of the invention, e.g., a compound of formula I, II, III, IV, V, or a tetracycline compound otherwise described herein.
Detailed Description of the Invention:
The present invention pertains, at least in part, to novel substituted tetracycline compounds. These tetracycline compounds can be used to treat numerous tetracycline compound-responsive states, such as bacterial infections and neoplasms, as well as other known applications for minocycline and tetracycline compounds in general, such as blocking tetracycline efflux and modulation of gene expression.
The term "tetracycline compound" includes many compounds with a similar ring structure to tetracycline. Examples of tetracycline compounds include:
chlortetracycline, oxytetracycline, demeclocycline, methacycline, sancycline, chelocardin, rolitetracycline, lymecycline, apicycline; clomocycline, guamecycline, meglucycline, mepylcycline, penimepicycline, pipacycline, etamocycline, penimocycline, etc. Other derivatives and analogues comprising a similar four ring structure are also included (See Rogalski, "Chemical Modifications of Tetracyclines."
Table 1 depicts tetracycline and several known other tetracycline derivatives.

Table 1 H OH H H h 2h i x OH
O O OH O
Oxybelracycline Demecloc line Minocycline co H 'h p nc +h H x M0" 0 ON 0 ethacycline Doxycycliae Chlortetra cline F{,C H N(+Mh N"). H, Pfth ii %-J~

o Sancycline Chelocardm Tetracycline Other tetracycline compounds which maybe modified using the methods of the invention include, but are not limited to, 6-demethyl-6-deoxy-4-dedimethylaminotetracycline; tetracyclino-pyrazole; 7-chloro-4-dedimethylaminotetracycline; 4-hydroxy-4-dedimethylaminotetracycline; 12a-deoxy-4-dedimethylaminotetracycline; 5-hydroxy-6a-deoxy-4-ded methylaminotetracycline;

dedimethylamino-l2a-deoxyanhydrotetracycline; 7-dimethylamino-6-demethyl-6-deoxy-4-dedimethylaminotetracycline; tetracyclinonitrile; 4-oxo-4-dedimethylaminotetracycline 4,6-hemiketal; 4-oxo-11a C1-4-dedimethylaminotetracycline-4,6-hemiketal; 5a,6-anhydro-4-hydrazon-4-dedimethylamino tetracycline; 4-hydroxyimino-4-dedimethylamino tetracyclines;

hydroxyimino-4-dedimethylamino 5a,6-anhydrotetracyclines; 4-amino-4-dedimethylamino-5a, 6 anhydrotetracycline; 4-methylamino-4-dedimethylamino tetracycline; 4-hydrazono-1la-chloro-6-deoxy-6-demethyl-6-methylene-4-dedimethylamino tetracycline; tetracycline quaternary ammonium compounds;
anhydrotetracycline betaines; 4-hydroxy-6-methyl pretetramides; 4-keto tetracyclines; 5-keto tetracyclines; 5a, 1l a dehydro tetracyclines; 11 a CI-6, 12 hemiketal tetracyclines;
11a CI-6-methylene tetracyclines; 6, 13 diol tetracyclines; 6-benzylthiomethylene tetracyclines; 7, 11 a -dichloro-6-fluoro-methyl-6-deoxy tetracyclines; 6-fluoro ((x)-6-denlethyl-6-deoxy tetracyclines; 6-fluoro ((3)-6-demethyl-6-deoxy tetracyclines;6-a acetoxy-6-demethyl tetracyclines; 6-P acetoxy-6-demethyl tetracyclines; 7, 13-epithiotetracyclines; oxytetracyclines; pyrazolotetracyclines; 1la halogens of tetracyclines; 12a formyl and other esters of tetracyclines; 5, 12a esters of tetracyclines;
10, 12a- diesters of tetracyclines; isotetracycline; 12-a-deoxyanhydro tetracyclines; 6-domethyl-12a-deoxy-7-chloroanhydrotetracyclines; B-nortetracyclines; 7-methoxy-demethyl-6-deoxytetracyclines; 6-demethyl-6-deoxy-5aepitetracyclines; 8-hydroxy-6-demethyl-6-deoxy tetracyclines; monardene; chromocycline; 5a methyl-6-demethyl-deoxy tetracyclines; 6-oxa tetracyclines, and 6 thia tetracyclines.

1. 7,9-Substituted Tetracycline Compounds The invention also pertains, at least in part to 7,9-substituted tetracycline compounds.
The term "7,9-substituted tetracycline compounds" includes tetracycline compounds with substitution at the 7 and 9- positions. In one embodiment, the substitution at the 7- and 9- positions enhances the ability of the tetracycline compound to perform its intended function, e.g., treat tetracycline responsive states.
In an embodiment, the 7,9-substituted tetracycline compound is 7,9-substituted tetracycline (e.g., wherein R4 is NR4'R4"; R4' and R4" are methyl, R5 is hydrogen and X is CR6R6', wherein R6 is methyl and R6' is hydroxy); 7,9-substituted doxycycline (e.g., wherein R4 is NR4'R4"; R4' and R4" are methyl, R5 is hydroxyl and X is CR6R6', wherein R6 is methyl and R6' is hydrogen); or 7,9- substituted sancycline (wherein R4 is NR4'R4";
R4' and R4..
are methyl; R5 is hydrogen and X is CR6R6' wherein R6 and R6' are hydrogen atoms. In an embodiment, the substitution at the 7 position of the 7, 9-substituted tetracycline compound is not chlorine or trimethylamino. In one embodiment, R4 is hydrogen.
In one embodiment, the invention pertains to 7,9-substituted tetracycline compounds of Formula I:

R7 RS e s R X ORS

OR~Z
Rio O OR"' O O
wherein:
X is CHC(R13Y'Y), CR6R6, S, NR6, or 0;
e, R , e, and R are each independently hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, hydroxyl, halogen, or hydrogen;
R2', R3, R' , R" and R12 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, amyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy;
R6 and R6' are each independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is ethyl, perhalogenated alkenyl, substituted pyridinyl, pyx"azinyl, furanyl, or pyrazolyly R$ is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R9 is -CH2NR9aR9b; `
R9a and R9b are each independently hydrogen, alkyl, alkenyl or linked to form a heterocycle;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkenyl, alkoxy, alkylthio, alkylsufnyl, alkylsulfonyl, alkylamino, or an arylalkyl; and Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulilnyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts thereof, provided that R7 and R9 are not both unsubstituted phenyl.
In a further embodiment, X is CR6R6'; R2, R2', e, R6', e, Rio, R", and R12 are each hydrogen; R4 is NR4'R4"; R4' and R4" are lower alkyl; and R5 is hydroxy or hydrogen. In another further embodiment, R4' and R4" are each methyl and R5 is hydrogen.

In an embodiment, R7 is ethyl and R9a is alkyl and R9b is alkenyl. In another embodiment, R7 is substituted pyrazinyl Examples of possible substituents include halogens, such as fluorine. In another embodiment, R9a is alkyl and R9b is alkenyl. In another further embodiment, RR' and R9b are linked to form a heterocycle. In a further embodiment, the linked heterocycle is substituted piperidinyl. In a further embodiment, the piperdinyl is substituted with one or more fluorines or halogenated alkyl groups, e.g., at the 2, 3, 4, or 5 position. In another embodiment, the R9 moiety is (4'trifluoromethyl-piperdin-1-yl) methyl, (4', 4'-difluoro-piperdin-l-yl) methyl, or (4'-fluoropiperdin-l-yl) methyl.
In another embodiment, R9a is hydrogen and R9b is alkyl. Other examples of compounds include those wherein R7 is furanyl, and R9a is hydrogen or alkyl and R9b is alkenyl, e.g., 1, 2, 2-trifluoroethenyl.
In another embodiment, R9a is hydrogen or alkyl and R9b is alkenyl. In another embodiment, R7 is pyrazolyl and R9a is hydrogen or alkyl and R9b is alkenyl or alkyl.
In a further embodiment, the invention pertains to tetracycline compounds selected from the group consisting of-cH, H,C .CHa H_ kl 0NH, H Hi-tea H ~H
OOV~ _ a OH, OH O O
OH 0 OtP

F HaC- -CH, H,C.N.CH2 Hac CHa H H -x {~_ _ - OH - ` OH
O' H _ NHs N
ONO o O OH 0HH - O CH3 OH O O
F F H HiH -tea N ..CH, F F H.C'N.CH, D OH H H H H H OH
H OH

F OH O OH O OH O

^ S'~ 4FF
- Hs V HsU H H

F - ' NH, F F H O O
rc lot NCF'H H C~ NH, CF{, Oti i. N=C OH a H N'~+
1_ OH
- OH F _ NHz Ha 2 NH2 I / \ NH, OH O
ON O OH O OFf CH3 Ha-dii CHt H,C.N.CH, a fa F \ H_ H - OH F \ H H tNJ H,C N.CH, F~N / a ( H2 N NH, F`^ OH
OH O OH O OH O OH O N_ NH, OH O

H=N H C pH\N'C~ F F or oH ~
H C C I\ I NHs HC.N.CH, H ~H OH
H H ~ - -H,c off o off o o _ off I M4 HZN I I H2 OH o o& o off o otP o H,C.N_CH, I / H,C-N,OH, H,N I / _ I NH, and pharmaceutically acceptable salts, esters, and prodrugs thereof.
2. 9-Substituted Tetracycline Compounds In another embodiment, the invention pertains to 9-substituted tetracycline compounds.
The term "9-substituted tetracycline compounds" includes tetracycline compounds with substitution at the 9 position. In one embodiment, the substitution at the 9- position enhances the ability of the tetracycline compound to perform its intended function, e.g., treat tetracycline responsive states. In an embodiment, the 9-substituted 10. tetracycline compound is 9-substituted tetracycline (e.g., wherein Ra is NR4'R`r', R4' and Ra,. are methyl, RS is hydrogen and X is CR6R6', wherein R6 is methyl and R6' is hydroxy, and R7 is hydrogen); ; 9-substituted doxycycline i a' R 4 xycycline (e.g., wherein e is NR , R4' and R4' are methyl, R5 is hydroxyl and X is CR6R6', wherein R6 is methyl and R6' is hydrogen, and R7 is hydrogen); 9- substituted minocycline (wherein Ra is NR4'R4", Ra' and e are methyl; RS is hydrogen and X is CR6R6' wherein R6 and R6' are hydrogen atoms, and R7 is dimethylamino); 9-substituted 4-dedimethylamino tetracycline compound, wherein X is CR6R6', R4, R5, R6', R6, and R7 are hydrogen; and 9-substituted sancycline (wherein Ra is NR4'R4õ, Ra' and R4" are methyl; R5 and R7 are hydrogen and X is CR6R6' wherein R6 and e are hydrogen atoms).
In another embodiment, the invention pertains to tetracycline compounds of formula 11-R v I R NR2Rr gage OR10 0 OR" 0 0 wherein:

X is CHC(R13Y'Y), CR6'R6, S, NR6, or 0;
R2, R4', R4", R'' and RT' are each hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
RR is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, R10, Rl l and R12 are each hydrogen or a pro-drug moiety, R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkenyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy;
R6 and R6' are independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is NR7'Rr, alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R$ is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkenyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R9 is -CH2NR9aR9b, or linked with R10 to form a furanyl ring;
R9a is hydrogen, alkyl, alkenyl,. alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic,or heteroaromatic;
R9b is alkoxycarbonyl, arylaminocarbonyl, or aryloxycarbonyl;
R$ is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkenyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
Y' and Y are each independently hydrogen, halogen, hydroxyl, cyan, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.
In a further embodiment, R4 is NR4'R4"; X is CR6R6'; R7 is NR7'Rr, R2, R2', R5, R6, R6" Rs, R9, Rlo, R", and R12 are each hydrogen; and, e, R4", RT, and R7"
are each lower alkyl. In another embodiment, R9a is alkyl, alkenyl, or arylalkyl.
Examples of R9b include alkoxycarbonyl, alkaminocarbonyl, aryloxycarbonyl, and arylaminocarbonyl. In another embodiment,R9a and R9b are linked to form a heterocyle, e.g., a substituted or unsubstituted piperdinyl ring. In a further embodiment, the piperdinyl is substituted with one or more fluorines or halogenated alkyl groups, e.g., at the 2, 3, 4, or 5 position.
In another embodiment, the R9 moiety is (4'trifluoromethyl-piperdin-l-yl) methyl, (4', 4'-difluoro-piperdin-l-yl) methyl, or (4'-fluoropiperdin-l-yl) methyl.
In another embodiment, R4 is NR4'R4", R4' and R4 are methyl, R5 is hydroxyl and X is CR6R6', wherein R6 is methyl and R6' is hydrogen, and R7 is hydrogen In another embodiment, R9a is alkyl, alkenyl, or arylalkyl. In a further embodiment, the piperdinyl is substituted with one or more fluorines or halogenated alkyl groups, e.g., at the 2, 3, 4, or 5 position. In another embodiment, the R9 moiety is (4'trifluoromethyl-piperdin-1-yl) methyl, (4', 4'-difluoro piperdin-l-yl) methyl, or (4'-fluoropiperdin-l-yl) methyl.
In another further embodiment, R9a is substituted alkyl. Examples include alkoxy substituted alkyl (e.g., -(CH2)2-O-CH3), alkenyl substituted alkyl (e.g., -CH2-CH=C(CH3)2, -CH2-C(CH3)=CHCH3, -CH2-CH=CH-phenyl, etc.), heterocyclic substituted alkyl (e.g., -CH2-furanyl, -CH2-CH=CH furanyl, -CH2-pyridinyl, optionally substituted), cyano substituted alkyl (e.g., (CH2)2-CN, etc.), alkynyl substituted alkyl (e.g., -(CH2)2-C sCH, etc.), halogen substituted alkyl (e.g., (CH2)2-CF3, (CH2)3-CF3, -CH2-CF3, -CH2-CH2F, etc.), amido substituted alkyl (e.g., -CH2-C(=O)-N(CH3)2, -C(=O)-NH2, etc.), carbonyl substituted alkyl (e.g., CH2-C(=O)-CH3, -CH2-C(=O)-C(CH3)3, etc.), hydroxy substituted alkyl (e.g., (CH2-CH(OH)-CH3, -CH2-C(OH)(CH3)2, etc.), -CH2-C(=N-O-CH3)-CH3, cycloalkyl (e.g., adamantyl;etc.).
In another embodiment, R9 is substituted or unsubstituted benzyl. Ina further embodiment, R9a is substituted with one or more fluorines (e.g., at the 2, 3, 4, 5, or 6 positions).
In a further embodiment, R9b is hydrogen, substituted or unsubstituted alkyl (e.g., methyl, ethyl, -CH2-CH=CH-furanyl, -CH2-CH=C(CH3)2, -(CH2)3-CF3, -(CH2)2-CH2F, -CH2-CH2F, -(CH2)2-CF3, -CH2-CF3, etc.).
In another further embodiment, R9a and 0 may be linked to form a pyrrolidinyl, .piperazinyl, piperidinyl, pyrazinyl, azapanyl, thiomorpholinyl, morpholinyl, ttrahydroquinolinyl, or a decahydroquinolinyl ring. The ring maybe substituted with one or more fluorines at the 2, 3, 4, or 5 position. The ring may also be substituted with one or more fluorinated alkyl groups (e.g., CH2F, -CHF2, CF3, etc.), cyano groups, hydroxy groups, alkyl groups (e.g., methyl, ethyl, spiro-cyclohexyl, t-butyl, etc.), heterocyclic (e.g., optionally substituted morpholinyl), thiol groups, alkoxy groups, alkyloxycarbonyl groups, carbonyl groups (optionally bonded directly to an atom in the ring), and exocyclic and endocyclic double bonds. In one embodiment, the ring is substituted with a =CF2 group. The ring may also be linked to a -O-(CH2)2-0-group which maybe attached to the pyrollidinyl or piperidinyl ring through one carbons or through two adjacent carbons.
When R9 is linked to R10 to form a furanyl ring, the ring can be further subsituted, e.g., with phenyl or other substituents which allow the compound of the invention to perform its intended function.
In a further embodiment, the tetracycline compound is selected from the group consisting of-H,C.N.CH, H,C.N.CFI, H3C.N.CH3 H,C.N.CH, HC-NCH, H'C.N.CHI
H H ~__ H_ H - H F{

NH, OH O O O ON O OFD O P- ~, cw, OH O O O
H .-CH, H3C.N.CH2 H,C.NCH3 H,C CHr,0.H cHI H,C N.CH, CHN H ON H N ON
GGHa \ OH =
N I / \ NH, N/~N OH O OF1 O' ~C OH O oFP CH. CH, OH 00 H,C-N-CH, H O N-CH, ",%-CH. H,C-N.CH3 H,C.N.CH3 H,C.N.CH, OH
N @ ON ~V-- HON WO&

H,C a Y ~F pig. N I / NHt OIZ OH O O OOH O HaC.tea Hac- N-c-+, -+,c-N- H,O-N- -~c-N-H H - OH F H _H OH H Li = OH

~x N - NH6 F`- NHt k OH 0 WP
H,C. CH, H,H .CH, H,C.N.CH3 H,c.N.CH, H,C..CH, H,C.CH, jJ_ _ ON H H OH H H -NHa OH O HF0^t" ! H~ O C 0 ON O - x H,C, .CH, H,C..CH, H,C.N-CH1 H,C.CH, H3C-N.CH3 H,C.N
Ha .CH, VIC L-t1 U R H, H,C. CH, OH O CH6 _ OH 0 H Oti__,~'.AOb 01 ON O
H,C.N.CH3 H H,C.N-CW, H,C.N.CH, H,C.N.CH, H3C-N.CH3 H3C.N-CH, H
ON
OH
H H - OH 6~1 0 NH, H2c NH, I / \ - I NH2 H,C.NCHI H3C.N-CFI6 FyC.N.crt, H,C.N.cH, H,C=N.CH, H3C.N-CH, H N OH H_ H OH ~x5 NC.ll- ~, OH O F~ 1IOII F O
H O O
N,C.N'Cfii H,GN.CFt, k,c=N-CK H,C'N-CH, v N -K
F H kl 3 ON H N ON H H- ON
OH O H OFf OI F ON O O
, 7 ~0, Plr-H3 CH, H %..CHI HaC HaC-N CH+ HiG CH, FIaC-N-Cf~a H H e N 014 F H H_ -~1 NH, - NFi, I/ a - NH1 at off O O O ON 0 ON O O.
H3C.N.CH3 H,A,N.CHi }~3C WON' H,C.N.CH, H,C.N.CH, 0...
_ - tl H O
9~ U_ U_ F` T N N
CDJ~
N NH, r'Y~ve ON O F ON O'O O ON O
H,O.N-CHa FIaC^N-C~ F H+C, CK, HaC,N-CHa H,CrN-CHa Har^~I-CHa H_ - F \ H_ H OH H H - OH
F

cxix A O ON OH O ON OF O OFf'O O
F
H,C.N.CH3 H,C.N.CH, F F H,C.N-CH3 H3C.N.CH3OH H,C,N.CH3 H1C.N.CH, H e F H H e H H- OH
6NN N ~~ F ON O O
OH O OH O ON O Olp O

H3C.N-CH6 HIC=N-CH3 H,C.N.CH, H,C.N-CH, H,C,N.CH, H,C.N.CH, //--O W=H~ ~~-- H OH /_ b,~ H H OH

OH O O OHOH O Oho 0 OH O OHO O

-- H' HaG -CHa HaC- CH6 HaC- .CHa HaC. -' H,C-H-CHa y ~Jl H H_ OH F NHs NH.
O OH O OH O OH 0' N'C~ FIaC.N.CIia H FIaH =
F N_ - ~~ N
Ql-k ON
C-A OH ' - - I~
F~N I I NHz Fy - NH= FF~I/~NN - N"2 O

FIaC. "~Yl^,j~ HaC. +' bOHF Ha~N-tea Ha.N- 'NHc 0 CH3 ~t~. OH 0 O i H 01 HSC.N.CH8 H6C.N.CH3 Hac.N.CHl H HaCC.N.CHa H HaC.N.CH8 H H = - = ~~~NHCIH
a Ha OH O O 0 OH 0 O F OH 0 0 C
FIaC.N.CH3 HaC N.CH3 H3C.N.CH3 H3C N.CHa NcC I.CF6 H HaH N.CH3 V H OH H ti - OH O OH
Qy 2N H3 Hc 916 OH 0 0 O' " 0 O F OH O O O OH 0 OFP O
F
%c N-CH. H3O-pr l+ HaC.N.CH. %C-N-Cla H3C. CH% Hac cH3 tl H v F H H- F N OH
co _ NHa o c tai. N c I NHZ
OH O OFP O OH O p OH O O O
HaC. CHa HaC .CHa Ha CHa NC CFIa HaC. CHa HaC .CHa U u N N Ham- OH N " OH
w rya O_ NHz Fp NHa Ha _ N
OH O OF 0 F OH 0 OFf 0 CHa OH O
HaC.N-CHa H3C.N.CHa H H3C,N,CH3 H3C.N.CHa H,C.M.cAO
OH H OH F F

NHs H ~~1,=NNz H O OO OH O OfQu0 H F 1` HaC.N.CHa H H3C.N-Chia HaC, CHa HaH
ICON

r r OH OH

N i`,~~^oD
I ' O N w o' NH.
OH O O OH O O L~~.1 O OH O
HaC.N.CH3 HaC.N.CH8 /~ HaC.N.CH3 HVC.N.CH3 ~Ha HaC N_CHa H = OH ) H H_ OH^ k! H
CN - NHZ \{ N p/~fp+c ~~QcH2 O Ot~ 0 H3G N.CH3 H,~. .CHa H,C. CH, H, rCt% c H8C
OH H~ - F Fla - b N OH
-- NH2 - NHa I _ _ Nkia OH O ~i o OH O O O
F HaC.N.CHa HaCN.CH% H3C'WCH3 HaC N.CH3 H ~a H~ry Ca off OH - off F 1 `~1 N ~~ - NHz NHa V " OH O 0 HaC. ,CH3 F1aC. CH3 HaC. CHa N- .CHa Ha CHa H3C. .CH, N H OH N OH SH N' FI Fi N OH
N _ `'NHa I NHzN NHi OH O OFP 0 OH 0 0& O HaC pH 0 OI r 0 HaC.N.CHa ' N.CH' 1 0 N.CHa N.CHa YSH H H pH N H OH = OH Cth NHz C H I - ' NHS HzN~/~ I I NHa ON~ _' Y o CHa OH O OH O O\1~~~
HP ~'r H6C-N.CHa H,C.~.CH, H,C-N.CH3 H3C.N.CH3 H,C-N,CH3 H3C,N.CH, H H- OH OH O H H' OH
F
HHI ~C NH, -ON \ \ ~~NHz OH O OH O OH O O O pH p pF{" b p C
L~ 4 tl\N-C~ F -~ N ~N OH F HaG H QH\N.CHI
OH ON

1 OH O 01? O ON O O
P-O
HIC- - -CNa H,c CH3 H,c CH, F F ",c= H,L-N-F H H OH F N N= off F !1 ~ = ON
N MH, HO I NH, OH O O OH O Of? O OH O Oli O
H3C.N.CH, tw-U-C"3 No, H,C~ -F r Cris N _ F r 4 s -C"3 CH.
OH _I OH
h'Yv_~'=,=1 I p_' I NH, NHI
OHO Otf O ~ O O
H,C-N.CH, H, C- rc%
N N - OHt OH
_ = NH,N NH, H3C \ I \ NH2 OH , O OH O
OH O O
y N. \ CF~ 'N"di H,C.N CH, _ H, - H. H
ON ON _ OH
0H Q ~ ` NH
V=0 H H -~
i^ r r~ - I NHt H,C- O O OH O
1s HyC a 1 `~
F p~~-+[r~' V- OHS
_ OH OH
NH: Ha' 0 0 H,N
N-OI HaC ~-CH, ~W \ -I 0 OH OH NH, and pharmaceutically acceptable salts, est ers, and prodrugs thereof.
3. 7-Substituted Tetracycline Compounds In one embodiment, the invention pertains to novel 7-substituted tetracycline compounds.
The term "7-substituted tetracycline compounds" includes tetracycline compounds with substitution at the 7 position. In one embodiment, the substitution at the 7- position enhances the ability of the tetracycline compound to perform its intended function, e.g., treat tetracycline responsive states. In an embodiment, the 7-substituted tetracycline compound is 7-substituted tetracycline (e.g., wherein R4 is NR4'R4', R4' and e are methyl, R5 is hydrogen and X is CR6R6', wherein R6 is methyl and R6' is hydroxy); 7-substituted doxycycline (e.g., wherein R4 is NR4'R4 , R4' and R4"
are methyl, R5 is hydroxyl and X is CR6R6', wherein R6 is methyl and R6' is hydrogen); 7-substituted tetracycline compound, wherein X is CR6R6', R4, R5, e'. and R6 are hydrogen;
or 7-substituted sancycline (wherein R4 is NR4'R4", R4' and R4"are methyl; R5 is hydrogen and X is CR6R6. wherein R6 and R6' are hydrogen atoms).
The invention pertains, at least in part, to 7-substituted tetracycline compound of Formula III:

x OR3 ORu RIO Rtt 0 wherein:
X is CHC(R13Y'Y), CR6'R6, C=CR6'R6, S, NR6, or 0;
R2, R , R4', and R4" are each independently hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, R' , Ru and R12 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy, R6 and R6' are each independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsuf nyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is substituted or unsubstituted pyrazolyl, furanyl, thiophenyl, or thiazolyl;
R8 is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R9 is hydrogen;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, or an arylalkyl; and Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, suliihydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsufnyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts thereof In a further embodiment, R4 is NR4'R4"; X is CR6R6', R2, R2', R5, R6, R6', Rs, R9, R' , Rtt, and R12 are each hydrogen; and, R4', and R4 are each lower alkyl, e.g., methyl.
In one embodiment, the tetracycline compound is a doxycycline compound and R7 is substituted or unsubstituted aminomethyl (e.g., -CH2NR7aRn').

In one embodiment, R7 is substituted (e.g., N-alkyl substituted) or unsubstituted pyrazolyl. In another embodiment, R7 is diethyl amino. In another, R7 is substituted amino methyl. In a further embodiment, the substituted aminomethyl is substituted with a pentyl group (e.g., -CH2-C(CH3)3), two methyl groups, or fluorinated alkyl (e.g., fluorinated propyl, e.g., -CH2-CH2-CF3).
In another embodiment, R7 is substituted phenyl. In a further embodiment, R7 is phenyl substituted at the 5 position (of the phenyl ring) with an alkyl substituted amino methyl group (e.g., (-CH2- N(CH3)2, -CH2-NH-CH(CH3)2, -CH2-N(CH3)-CH(CH3)2, -CH2-N-piperdinyl), -CH2NH-CH3a -CH2-NH-cyclopropyl, CH2-NH-t butyl, -CH2-N(CH3)-benzyl, -CH2-N(CH3)-CH2-CH=CH2, CHi NH-(CH2)2-CF3i CH2-NH-CH2-C(=O)-NH2, or -CH2 NH-cyclohexyl, ). In a further embodiment, the piperdine may be substituted at its 4 position (e.g., with fluorine, methyl, etc.).
In another embodiment, when R7 is a phenyl substituted at the 5 position with an alkyl substituted amino methyl group, the phenyl may also be substituted with a fluorine (e.g., at the 2, 3, 4, or 6 position) or an alkoxy (e.g., methoxy group) at the 2, 3, 4, or 6 position.
In another embodiment, R7 is phenyl with a 2 -position amino alkyl substituent.
In a further embodiment, the substituent is dialkylanunomethyl (e.g., dimethylaminomethyl, -CH2-N piperazinyl). In a further embodiment, the piperazine is substituted with one or more fluorine or methyl groups. In another further embodiment, the phenyl R7 is further substituted at the 3, 4, 5, or 6 position with a methoxy group. In another embodiment, the phenyl is linked to a methylene dioxy group through its 4 and 5 positions.
In another embodiment, R7 is phenyl with a 4-position amino alkyl (e.g.., aminomethyl) substituent. In a further embodiment, the aminoalkyl substituent is -CH2-NH-CH(CH3)2, -C(CH3)-NH-(CH2)2-CH2F, -CH2-NH-CH2-cyclohexenyl, -CH2-N-piperidinyl, -CHZ N(CH3)-CH2-CH=CH2, or -CH2 NH-(CH2)2-CF3).
In another embodiment, R7 is phenyl substituted with a -C(=N-O-R)-R' group, wherein R and R' are each alkyl. In a further embodiment, the substituent is at the 4-position of the phenyl ring. In another embodiment, R7 is phenyl substituted at the 4-position with an alkoxyalkyl group (-CH2-O-CH3). In another embodiment, R7 is phenyl substituted with an alkylcarbonylamino group.
In another embodiment, R7 is substituted furanyl. In a further embodiment, the furanyl is attached at the 2-position of the furanyl ring. In a further embodiment, the furanyl is substituted with an amino alkyl, e.g., aminomethyl group at its 5-position.
Examples of aminomethyl groups include: -CH2N(CH3)-CH2-C6H5, -CH2 N(CH3)-CH2-CH=CH2, -CH2-N(CH3)-CH(CH3)2, or -CH2-N-piperidinyl. In another embodiment, the furanyl is substituted at the 3-position, e.g., with an aminoalkyl substituent. Examples of such substituents include -CH2-N(CH3)2, -CHZ N piperidinyl In another embodiment, R7 is substituted furanyl attached at its 3-position.
In a further embodiment, the furanyl is substituted with an aminoalkyl substituent.
In another further embodiment, the aminoalkyl substituent is -CH2 N piperazinyl or -CH2-N-(CH3)2-In another embodiment, R7 is substituted or unsubstituted thiophenyl. In a further embodiment R7 is is substituted with an aminoalkyl moiety. In another further embodiment, the aminoalkyl moiety is -CH2 N (CH3)2.
In another further embodiment, R7 is substituted pyridinyl. In a further embodiment, R7 is attached to the phenyl ring at its 3 -position. In another further embodiment, it is substituted with a aminoalkyl moiety at its 5-position.
Examples of aminoalkyl moieties include -CH2-N-(CH3)2, -CH2-N-piperidinyl, -CH2-N(CH3)-CH2 CH=CH2, Or -CH2-N(CH3)-CH(CH3)2.
In another further embodiment, R7 is alkylcarbonylaminoalkyl. In another further embodiment, R7 is -CH2 NH-C(am)-CH3.
In another further embodiment, R7 is amino substituted alkenyl. In another further embodiment, R7 is -CH=CH-CH2 N(CH3)2 or -CH=CH-M2N piperid nyL In another embodiment, R7 is amino substituted alkynyl (e.g., -C M-CH2-N(CH3)-(CH2)2-CF3 or -C r=C-(CH2)rN-piperidinyI.
In another further embodiment, R7 is substituted -CH2-N-piperidinyl. In certain embodiments, the piperidinyl is substituted with one or more fluorines, e.g., at the 4-position of the piperdine ring.
In another embodiment, the R7 substitutuent is alkylaminocarbonyL In a further embodiment, the substituent is -C(0)-NH-(CH2)2-N(CH3)2.
In another further embodiment, the R7 substituent is aminoalkylcarbonyl. In a further embodiment, the substituent is -C(=O)-CH2 N(CH3)2, -C(am)-CH2-NH-(CH2)r OCH3, -C(0)-CH2 N piperidinyl and -C(am)-CH2-N pyrollidinyl.
In another further embodiment, the R7 substituent is N-piperdinyl substituted alkyl. In a further embodiment, the R7 substituent is -(CH2)4 N piperdinyl or -(CH2)2-N-piperdinyl.
In another embodiment, the R7 substituted is -(CH2)2-N(CH3)2 or C(0)-CH3.
In another further embodiment, the R7 substituent is aminoalkyloxycarbonyl.
Examples of aminoalkyloxycarbonyl substituents include C(=O)-O-(CH2)2 N-piperdinyl and -C(0)-O-(CH2)Z N(CH3)2.
In a further embodiment, the compounds of the invention are:

-N HA
H3C.N,CHs Fi C C H,(- CFt~
H OH sH.H,Ctis H,(- H N OH
I I ON

I_ + NHZ Nf~ OH O OH 0 OH 0 0 H+O/~ HZN C Ha \ H'C.N,CH' NN off N O_y CH' y H OH I

OH o O I/ \ - I NHZ H H OH
ON 0 OHO 0 I \p I NHZ
H20.p OH O OH 0 H CH, 9N HsC O H+O-N-CHs IWl CH. I \ H,C.wat rHsNN- H H. I\ H_ H OH
p_ I Nit HH~Ctis FtsC_ CFIs H H N' OH Hs0. ,CH2 H H OH H Li N'oH
OHO O I _ NF6 NH2 yF~ OH O O 0 0110 OH 0 H. NF IWYCH' H2C7.~OH2 I ~ _ TT _ c H H HsC y CHs - - OH \ H HH H H_ OH O O O

O KC,,-CHs Ha Q% U G Hy OFI H PY OH

O
off 0 0 OH O O 0 QHs Hr- CHs H,C-N O Hs0.trca N U- H

0 oFP o t+ U tr:"N H,cH2 ~ ~
p NH=
OH O off O OHO 0 n H
N N6jN%%rCH3 N.C ti~C,N.cH~
yCHs OH
H H \ -- I NHS

M OH O OI f O

N.CH3 ' IMF o HC_ .CH3 N
N
44ou H,C .cH, I H3C,N_CH3 H H H H OH
NH, I/ pp_ I NH, OH 0 0I-r O NH3 OHO ,0 OH O ~OFi O
0 ' \ /l cl, HN" HNJ~ 6av-H,C_ H3C, CH3 H3C_O t%C'N CH3 O H H !~" OH H=
NH=

O
HN CH N,Ct%
OH N
H H
H k3H=N'CH3 / - I NH, OH
OH OH O O NH, I / I NH' OH O OH O

CH3 H3C' NN NH= F
O
N HC,N,CH3 H,C H CH, \ H H = OH \ H_ H
H Nc PYct a / NH3 q- NHz OH off 0 011 o p OH 0 OH 0 OH O 0 O F HUN'CH3 CHI
N,/,, CH2 N H3C,H=cf - OH O NH H3C,N,CFi3 H_ H NH3 _ ~ H H , / H3C,N,CH3 _ ~~I~NH.

' OH 0 OH 0 O p O
Hz OH O 0 P3C=NCH2 F
N H3C,N,CH3 i H, cH, \
H Hz OH H off H3C, CH3 H H_ OH
/ _. NH2 - NH3 NHz OH 0 O OH O O I/ p nOH O OFi 0 H3C,Ni,,,.pCH2 H3C,Ni"-'CH2 N / H C. CH H3C,NCH3 HF.Tc*%
H 3H N' 3 H H= H OH
\ - OH OH NH=
/ \p NH2 NH2 OH 0 IHI OH O OH O OH O OH O

/NCH= n HaGN'~
O C H,C.N-CH, N O O H HsC.N.CHs H O 0 H3 C_ -CH, OH
OH Ft H N H \p NH2 NH= O
\ _ I NH OH O OIi O
OH O O O a OH O O
\ Ni-CH= H,C.N-CH3 ~N'I O I a0N-cHa 0 f%CCN, -CH.
H,O rfq4, H=
OH H OH
OH \
l i I NH2 I \ I NH2 NHi -off O O OH O OH O O
H,C,N.CH3 -CHs H3 CH3 Ntia4 H_ H = CI1, Cli, 4'0~v ~di O NH, H OH
OH O OH" O ~
o OH O O
/C16si,QN.CH, HN N~CHa N~\'CH2 6OMP Fs H H = OH \
NH, \ H H N OH

NH, I \ NH.
OH 0&. O

~o N F F
O H,C.~-CHs HN C`NICH3 H H - OH O ' .N-CH3 H = OH
H H - OH
Nl-~ NH, OH O 0 \ NH, OH O O
OH O O
/~ H3C-N-CH3 H'C.N'CN H3C. -CH, H H OH
N' - NH=
4 \
T OH
H- H H N~OOCNH
off o ori' NH2 OH O Oti O
OH O OHP O
,aia CHs HsC. CHs H,a H, c, -CH. H H - OH
H H OH N tl V off I \
NHS ' H
0 o OH O O

O CH3 H,0. -CHs H,C~
\ H H N OH H,C. cls 0 HsC_ CHs NH, HsC, Ctls H H N OH

NH, OH O OttQ o o OH O 0 O

YN, CH, F G
H HaH' HaC-N^ H,4J, F _ - off H H_ - HH. p OHO OH O NH:
VYC.
H.
GO
Ha H C,_j= OH H. KC-0 ~~~=
{ _- ON
C H
N
O Ha CHs rHWOFHPOP
O O OHO
o HHa O
H.C.N_Ct%

6(H.CINWICH3 HN- CH, H C'O HN
Ha0.N.C %

NH2 oHo o / \Q NH, HaG a HN X) ~' HN Hip- CH4HC ' HaC,WGla H t CH.

H -NHa OH O / _ NHt NH, OHO O o O

N
O H3C.N'CHa N
H OH I / H,C~N.CH, 16-C

H H OH
OH
OH O OH O ~/ gyp. i NHZ OH O OH 0 0 V NHa 40.~
OH and pharmaceutically acceptable esters, prodrugs, and salts thereof.

4. 8-Substituted Tetracycline Compounds The invention also pertains, at least in part to 8-substituted tetracycline compounds.
The term "8-substituted tetracycline compounds" includes tetracycline compounds with substitution at the 8- position. In one embodiment, the substitution at the 8- position enhances the ability of the tetracycline compound to perform its intended function, e.g., treat tetracycline responsive states. In an embodiment, the 8-substituted tetracycline compound is 8-substituted tetracycline (e.g., wherein R4 is NR4'R4"; R4' and R4" are methyl, R5 is hydrogen and X is CR6R6', wherein R6 is methyl and R6' is hydroxy); 8-substituted doxycycline (e.g., wherein R4 is NR4'R4"; R4' and R4"
are methyl, R is hydroxyl and X is CR 6', wherein R6 is methyl and R is hydrogen); or 8-substituted sancycline (wherein R4 is NR4R4'; R4' and e are methyl; R5 is hydrogen and X is CR6R6' wherein R6 and R6' are hydrogen atoms. In an embodiment, the substitution at the 7 position of the 8-substituted tetracycline compound is not chlorine or trimethylamino. In one embodiment, R4 is hydrogen.
In one embodiment, the 8-substituted tetracycline compound is of formula IV:
R1 RS R~
R / X W
\ I \ ( 2RF
R9 =

OR10 O R" O O lj = J
wherein:
X is CHC(R13Y'Y), CR6'R6, S, NR6, or 0;
R2, R4', R4", R7' and R7" are each hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen, R2', R3, Rio, R'1 and Rte are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy;
R6 and R6' are independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)a3 (NRlc)aiC(=W')WR7B;
R$ is substituted phenyl or substituted pyridinyl;
R9 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsuffmyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or-(CH2)a3NR9cC(=Z')ZR9a;

R7a, e, R'0, R7d, R7e, R' , R9a, R9b, R9c, R9d, R9e, and Rsf are each independently absent, hydrogen, acyl, alkyl, alkenyl, alkynyl, alkoxy, alkyltbio, alkylsulfnyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
W is CR7dR7e, S, 0 or NRT;
W' is 0, NR~ or S;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfnyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.
In a further embodiment, the invention pertains to compounds wherein Xis CR6R6'; R2, R2=, R6, R6', R8, R10, R", and R12 are each hydrogen; R4 is NR4'R4"; R4. and R4" are lower alkyl; and R5 is hydroxy or hydrogen-In a further embodiment, R8 is substituted phenyl, e.g., o-substituted phenyl, e.g., aminomethyl substituted phenyl. In a further embodiment, the 8-substituted tetracycline compound is:

OH
F~~N ~ ~ _ I HH=
OH 0 ' and pharmaceutically acceptable salts, esters, and prodrugs thereof..
In another further embodiment, R8 is substituted pyridinyl, e.g., halo-substituted pyridinyl, e.g., 6-fluoro-pyrindin-3-yl. In a further embodiment, R9 is amino.
In yet a further embodiment, the 8-substituted tetracycline compound is:
F N FI,C rCH,, H- OH
FIiN
H o o and pharmaceutically acceptable salts, esters, and prodrugs thereof..

5. 13-Substituted Methacycline Compounds In one embodiment, a 13-substituted tetracycline compound is of formula V:

Rs OW
R9 =
ORIZ
OR10 0 OR" O O (V) wherein:
R2, R4', R4", RT and RT' are each hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety, R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2 , R3, Rio, R" and R12 are each hydrogen or a pro-drug moiety, R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy, R7 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or-(CH2)a3 (NR7c)o-iC(=W7)WR7a;
R8 is substituted phenyl or substituted pyridinyl;
R9 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)o.3NR9cC(=Z')ZR?a;
R7a, R7', R7c, R7d, R'e, R7, R9a, R91i, R9c, R9d, R9e, and R81 are each independently absent, hydrogen, acyl, alkyl, alkenyl, alkynyl,.alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
W is CR7dR7c, S. O or NO;
W' is 0, NR7 or S;
R13 is 4-alkyl substituted phenyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.
In a further embodiment, the invention pertains to compounds wherein R2, R2', R8, R1 , Rl1, and R12 are each hydrogen; R4 is NR4'R4"; R4' and kr are lower alkyl; and R5 is hydroxy or hydrogen.

In a further embodiment, the phenyl R13 group is substituted with an aminomethyl substituent. In another further embodiment, the aminomethyl substituent is dimethylaminomethyl. In another further embodiment, the invention pertains to compounds of the formula:

H3C.N
CHa I,C.N.CH3 H _ OH
(, _ I NHZ

OH O O O
and pharmaceutically acceptable salts, esters, and prodrugs thereof_ In one embodiment, the tetracycline compounds of the invention do not include those described in U.S.S.N. 09/660,598, 09/823,884, 09/852,908, 10/819,343, 10/820,456, 09/894,805, 09/895,796, 09/895,812, 09/895,797, 09/895,857, 10/097,634, 10/759,484, 10/337,914,10/636,437, 10/752,378, or 10/740,961.

6. Methods for Synthesizing Tetracycline Compounds of the Invention The tetracycline compounds of this invention can be synthesized using the methods described in the Schemes and/or by other techniques known to those of ordinary skill in the art.
The substituted tetracycline compounds of the invention can be synthesized using the methods described in the following schemes and by using art recognized techniques. All novel substituted tetracycline compounds described herein are included in the invention as compounds.

x m. + wlj~
Ic u Pt H2 P& III

oM
IF Yc ~H u 9- and 7- substituted tetracyclines can be synthesized by the method shown in Scheme 1. As shown in Scheme 1, 9- and 7-substituted tetracycline compounds can be synthesized by treating a tetracycline compound (e.g., doxycycline, 1A), with sulfuric acid and sodium nitrate. The resulting product is a mixture of the 7 -nitro and 9-nitro isomers (1B and 1C, respectively). The 7-nitro (1B) and 9- nitro (1C) derivatives are treated by hydrogenation using hydrogen gas and a platinum catalyst to yield amines 1D
and 1E. The isomers are separated at this time by conventional methods. To synthesize 7- or 9-substituted alkenyl derivatives, the 7- or 9-amino tetracycline compound (lE and 1F, respectively) is treated with HONO, to yield the diazonium salt (1G and 1H). The salt (1 G and 1H) is treated with an appropriate reactive reagent to yield the desired compound(e.g., in Scheme 1, 7-cyclopent-l-enyl doxycycline (1H) and 9-cyclopent-l-enyl doxycycline (11)).

. "g NM.h Ha XWO, oN O ox O 0 R Ny7R
I'mo' gyp{
Oak m WO
x "Pak wit As shown in Scheme 2, tetracycline compounds of the invention wherein R7 is a carbamate or a urea derivative can be synthesized using the following protocol.
Sancycline (2A) is treated with NaNO2 under acidic conditions forming 7-nitro sancycline (2B) in a mixture of positional isomers. 7-nitrosancycline (2B) is then treated with H2 gas and a platinum catalyst to form the 7-amino sancycline derivative (2C). To form the urea derivative (2E), isocyanate (2D) is reacted with the 7-amino sancycline derivative (2C). To form the carbamate (2G), the appropriate acid chloride ester (2F) is reacted with 2C.

'CH3 FmodiN H

N,42 Fmoc-NCS NHZ
HOH H HO

~b jj2 H i 3E s' 1) -Fmoc R' H
HZ
H
H OH HO

As shown in Scheme 3, tetracycline compounds of the invention, wherein R7 is a heterocyclic (i.e. thiazole) substituted amino group can be synthesized using the above protocol. 7-amino sancycline (3A) is reacted with Fmoc-isotbiocyanate (3B) to produce the protected thiourea (3C). The protected thiourea (3C) is then deprotected yielding the active sancycline thiourea (3D) compound. The sancycline thiourea (3D) is reacted with an a-haloketone (3E) to produce a thiazole substituted 7-amino sancycline (3F).

cH,h h (CH3)2 H NI~H/FfCI OH
HI or H H
x Pd/C
H H O O H H H OH

7- alkenyl tetracycline compounds, such as 7-alkynyl sancycline (4A) and 7-alkenyl sancycline (4B), can be hydrogenated to form 7-alkyl substituted tetracycline compounds (e.g., 7-alkyl sancycline, 4C). Scheme 4 depicts the selective hydrogenation of the 7- position double or triple bond, in saturated methanol and hydrochloric acid solution with a palladium/carbon catalyst under pressure, to yield the product.

ti NMe2 OH
N-iodosuccinimide OH

OH O OHIO O OH O OHIO O

x Pd(OAc}2, Na2COy McOH I
NMe2 = OH
~ OH
B\OH NH2 SC OH O OH O O

In Scheme 5., a general synthetic scheme for synthesizing 7 -position aryl derivatives is shown. A Suzuki coupling of an aryl boronic acid with an iodosancycline compound is shown. An iodo sancycline compound (5B) can be synthesized from sancycline by treating sancycliine (5A) with at least one equivalent N-iodosuccinimide (NIS) under acidic conditions. The reaction is quenched, and the resulting 7-iodo sancycline (5B) can then be purified using standard techniques known in the art. To form the aryl derivative, 7-iodo sancycline (5B) is treated with an aqueous base (e.g., Na2CO3) and an appropriate boronic acid (5C) and under an inert atmosphere.
The reaction is catalyzed with a palladium catalyst (e.g., Pd(OAc)2). The product (5D) can be purified by methods known in the art (such as HPLC). Other 7-aryl, alkenyl, and alkynyl tetracycline compounds can be synthesized using similar protocols.
The 7-substituted tetracycline compounds of the invention can also be synthesized using Stille cross couplings. Stille cross couplings can be performed using an appropriate tin reagent (e.g., R-SnBu3) and a halogenated tetracycline compound, (e.g., 7-iodosancycline). The tin reagent and the iodosancycline compound can be treated with a palladium catalyst (e.g., Pd(PPh3)2C12 or Pd(AsPh3)2C12) and, optionally, with an additional copper salt, e.g., CaL The resulting compound can then be purified using techniques known in the art.

R N(CH )2 TraaslUOU Mctd 7XIPZJNE
2~z H O
( OH Phm b6vLpnd 6C

H H HO TrnzIoiMwi cdolyzt R
6A PbOVMWLtW
(CHA
H

The compounds of the invention can also be synthesized using Heck-type cross coupling reactions. As shown in Scheme 6, Heck type cross-couplings can be performed by suspending a halogenated tetracycline compound (e.g., 7-iodosancycline, 6A) and an appropriate palladium or other transition metal catalyst (e.g., Pd(OAc)2 and Cul) in an appropriate solvent (e.g., degassed acetonitrile). The substrate, a reactive alkene (6B) or alkyne (6D), and triethylamine are then added and the mixture is heated for several hours, before being cooled to room temperature. The resulting 7-substituted alkenyl (6C) or 7-substituted alkynyl (6E) tetracycline compound can then be purified using techniques known in the art.

6UV(CH3)2 CI U(CH3h H MeowIia OH

H OH

To prepare 7-(2'-Chloro-alkenyl)-tetracycline compounds, the appropriate 7-(alkynyl)-sancycline (7A) is dissolved in saturated methanol and hydrochloric acid and stirred. The solvent is then removed to yield the product (7B).

F~, CK~No Cw RI H3C' ,CH3 H carboxylic acid OH
NH: ""6 anhydrous R bH
H B OH HO O
O OH O O

As depicted in Scheme 8, 5-esters of 9- substituted tetracycline compounds can be formed by dissolving the 9- substituted compounds (8A) in strong acid (e.g.
HF, methanesulphonic acid, and trifluoromethanesulfonic acid) and adding the appropriate carboxylic acid to yield the corresponding esters (8B).

As shown in Scheme9 below, 7 and 9 aminomethyl tetracyclines may be synthesized using reagents such as hydroxymethyl-carbamic acid benzyl ester.
H2N i (CH3)2 H
(CH3)2 ~Vd H -H Ip H2 H TFA H li H2 +
~I(CH3)2 OH 24hr.,25C H

H If The term "alkyl" includes saturated aliphatic groups, including straight-chain alkyl groups (e.g., methyl, ethyl, propyl, butyl, pentyl, hexyl, heptyl, octyl, nonyl, decyl, etc.), branched-chain alkyl groups (isopropyl, tert-butyl, isobutyl, etc.), cycloalkyl (alicyclic) groups (cyclopropyl, cyclopentyl, cyclohexyl, cycloheptyl, cyclooctyl), alkyl substituted cycloalkyl groups, and cycloalkyl substituted alkyl groups. The term alkyl further includes alkyl groups, which can frther include oxygen, nitrogen, sulfur or phosphorous atoms replacing one or more carbons of the hydrocarbon backbone.
In certain embodiments, a straight chain or branched chain alkyl has 6 or fewer carbon atoms in its backbone (e.g., Cl-C6 for straight chain, C3-C6 for branched chain), and more preferably 4 or fewer. Likewise, preferred cycloalkyls have from 3-8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure. The terra C1-C6 includes alkyl groups containing 1 to 6 carbon atoms.
Moreover, the term alkyl includes both "unsubstituted alkyls" and "substituted alkyls", the latter of which refers to alkyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone. Such substituents can include, for example, alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, suifamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
Cycloalkyls can be further substituted, e.g., with the substituents described above. An "alkylaryl" or an "arylalkyl" moiety is an alkyl substituted with an aryl (e.g., phenylmethyl (benzyl)).
The term "alkyl" also includes the side chains of natural and unnatural amino acids.
The term "aryl" includes groups, including 5- and 6-membered single-ring aromatic groups that may include from zero to four heteroatoms, for example, benzene, phenyl, pyrrole, furan, thiophene, thiazole, isothiaozole, imidazole, triazole, tetrazole, pyrazole, oxazole, isooxazole, pyridine, pyrazine, pyridazine, and pyrimidine, and the like. Furthermore, the term "aryl" includes multicyclic aryl groups, e.g., tricyclic, bicyclic, e.g., naphthalene, benzoxazole, benzodioxazole, benzothiazole, benzoimidazole, benzothiophene, methylenedioxyphenyl, quinoline, isoquinoline, napthridine, indole, benzofuran, purine, benzofuran, deazapurine, or indolizine. Those aryl groups having heteroatoms in the ring structure may also be referred to as "aryl heterocycles", "heterocycles," "heteroaryls" or "heteroaromatics". The aromatic ring can be substituted at one or more ring positions with such substituents as described above, as for example, halogen, hydroxyl, alkoxy, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, alkylaminoacarbonyl, arylalkyl aminocarbonyl, alkenylaminocarbonyl, alkylcarbonyl, arylcarbonyl, arylalkylcarbonyl, alkenylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylthiocarbonyl, phosphate, phosphonato, phosphinato, cyan, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl; sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety. Aryl groups can also be fused or bridged with alicyclic or heterocyclic rings which are not aromatic so as to form a polycycle (e.g., tetralin).
The term "alkenyl" includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double bond.

For example, the term "alkenyl" includes straight-chain alkenyl groups (e.g., ethylenyl, propenyl, butenyl, pentenyl, hexenyl, heptenyl, octenyl, nonenyl, decenyl, etc.), branched-chain alkenyl groups, cycloalkenyl (alicyclic) groups (cyclopropenyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, cyclooctenyl), alkyl or alkenyl substituted cycloalkenyl groups, and cycloalkyl or cycloalkenyl substituted alkenyl groups. The term alkenyl further includes alkenyl groups which include oxygen, nitrogen, sulfur or phosphorous atoms replacing one or more carbons of the hydrocarbon backbone.
In certain embodiments, a straight chain or branched chain alkenyl group has 6 or fewer carbon atoms in its backbone (e.g., C2-C6 for straight chain, C3-C6 for branched chain).
Likewise, cycloalkenyl groups may have from 3-8 carbon atoms in their ring structure, and more preferably have 5 or 6 carbons in the ring structure. The term C2-C6 includes alkenyl groups containing 2 to 6 carbon atoms.
Moreover, the term alkenyl includes both "unsubstituted alkenyls" and "substituted alkenyls", the latter of which refers to alkenyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone. Such substituents can include, for example, alkyl groups, alkynyl groups, halogens, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulthydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfmyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
The term "alkynyl" includes unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but which contain at least one triple bond.
For example, the term "alkynyl" includes straight-chain alkynyl groups (e.g., ethynyl, propynyl, butynyl, pentynyl, hexynyl, heptynyl, octynyl, nonynyl, decynyl, etc.), branched-chain alkynyl groups, and cycloalkyl or cycloalkenyl substituted alkynyl groups. The term alkynyl further includes alkynyl groups which include oxygen, nitrogen, sulfur or phosphorous atoms replacing one or more carbons of the hydrocarbon backbone. In certain embodiments, a straight chain or branched chain alkynyl group has 6 or fewer carbon atoms in its backbone (e.g., C2-C6 for straight chain, C3-C6 for branched chain). The term C2-C6 includes alkynyl groups containing 2 to 6 carbon atoms.

Moreover, the term alkynyl includes both "unsubstituted alkynyls" and "substituted alkynyls", the latter of which refers to alkynyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone. Such substituents can include, for example, alkyl groups, alkynyl groups, halogens, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyan, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), arylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
Unless the number of carbons is otherwise specified, "lower alkyl" as used herein means an alkyl group, as defined above, but having from one to five carbon atoms in its backbone structure. "Lower alkenyl" and "lower alkynyl" have chain lengths of, for example, 2-5 carbon atoms.
The term "acyl" includes compounds and moieties which contain the acyl radical (CH3CO-) or a carbonyl group. It includes substituted acyl moieties. The term "substituted acyl" includes acyl groups where one or more of the hydrogen atoms are replaced by for example, alkyl groups, alkynyl groups, halogens, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyan, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylaxnino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyan, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.
The term "acylamino" includes moieties wherein an acyl moiety is bonded to an amino group. For example, the tenn includes alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido groups.
The term "aroyl" includes compounds and moieties with an aryl or heteroaromatic moiety bound to a carbonyl group. Examples of aroyl groups include phenylcarboxy, naphthyl carboxy, etc.
The terms "alkoxyalkyl", "alkylaminoalkyl" and "thioalkoxyalkyl" include alkyl groups, as described above, which further include oxygen, nitrogen or sulfur atoms replacing one or more carbons of the hydrocarbon backbone, e.g., oxygen, nitrogen or sulfur atoms.
The term "alkoxy" includes substituted and unsubstituted alkyl, alkenyl, and alkynyl groups covalently linked to an oxygen atom. Examples of alkoxy groups include methoxy, ethoxy, isopropyloxy, propoxy, butoxy, and pentoxy groups.
Examples of substituted alkoxy groups include halogenated alkoxy groups. The alkoxy groups can be substituted with groups such as alkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amino (including alkyl amino, dialkylamino, arylamino, diarylamino, and alkylarylamino), aclamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulthydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moieties. Examples of halogen substituted alkoxy groups include, but are not limited to, fluoromethoxy, difluoromethoxy, trifluoromethoxy, chloromethoxy, dichloromethoxy, trichloromethoxy, etc.
The term "amine" or "amino" includes compounds where a nitrogen atom is covalently bonded to at least one carbon or heteroatom. The term includes "alkyl amino" which comprises groups and compounds wherein the nitrogen is bound to at least one additional alkyl group. The term "dialkyl amino" includes groups wherein the nitrogen atom is bound to at least two additional alkyl groups. The tern "arylamino"
and "diarylamino" include groups wherein the nitrogen is bound to at least one or two aryl groups, respectively. The term "alkylarylan'iino," "alkylaminoaryl" or "arylaminoalkyl" refers to an amino group which is bound to at least one alkyl group and at least one aryl group. The term "alkaminoalkyl" refers to an alkyl, alkenyl, or alkynyl group bound to a nitrogen atom which is also bound to an alkyl group.
The term "amide," "amido" or "aminocarbonyl" includes compounds or moieties which contain a nitrogen atom which is bound to the carbon of a carbonyl or a thiocarbonyl group. The term includes "alkaminocarbonyl" or "alkylaminocarbonyl"
groups which include alkyl, alkenyl, aryl or alkynyl groups bound to an amino group bound to a carbonyl group. It includes arylaminocarbonyl and arylcarbonylamino groups which include aryl or heteroaryl moieties bound to an amino group which is bound to the carbon of a carbonyl or thiocarbonyl group. The terms "alkylaminocarbonyl," "alkenylaminocarbonyl," "alkynylaminocarbonyl,"
"arylaminocarbonyl," "alkylcarbonylamino," "alkenylcarbonylamino,"
"alkynylcarbonylamino," and "arylcarbonylamino" are included in term "amide."

Amides also include urea groups (aminocarbonylamino) and carbamates (oxycarbonylamino).
The term "carbonyl" or "carboxy" includes compounds and moieties which contain a carbon connected with a double bond to an oxygen atom. The carbonyl can be further substituted with any moiety which allows the compounds of the invention to perform its intended function. For example, carbonyl moieties maybe substituted with alkyls, alkenyls, alkynyls, aryls, alkoxy, aminos, etc. Examples of moieties which contain a carbonyl include aldehydes, ketones, carboxylic acids, amides, esters, anhydrides, etc.
The term "thiocarbonyl" or "thiocarboxy" includes compounds and moieties which contain a carbon connected with a double bond to a sulfur atom.
The term "ether" includes compounds or moieties which contain an oxygen bonded to two different carbon atoms or heteroatoms. For example, the term includes "alkoxyalkyl" which refers to an alkyl, alkenyl, or alkynyl group covalently bonded to an oxygen atom which is covalently bonded to another alkyl group.
The term "ester" includes compounds and moieties which contain a carbon or a heteroatom bound to an oxygen atom which is bonded to the carbon of a carbonyl group.
The term "ester" includes alkoxycarboxy groups such as methoxycarbonyl, ethoxycarbonyl, propoxycarbonyl, butoxycarbonyl, pentoxycarbonyl, etc. The alkyl, alkenyl, or alkynyl groups are as defined above.
The term "thioether" includes compounds and moieties which contain a sulfur atom bonded to two different carbon or hetero atoms. Examples of thioethers include, but are not limited to alkthioalkyls, alkthioalkenyls, and alkthioalkynyls.
The term "alkthioalkyls" include compounds with an alkyl, alkenyl, or alkynyl group bonded to a sulfur atom which is bonded to an alkyl group. Similarly, the term "alkthioalkenyls"
and alkthioalkynyls" refer to compounds or moieties wherein an alkyl, alkenyl, or alkynyl group is bonded to a sulfur atom which is covalently bonded to an alkynyl group.
The term "hydroxy" or "hydroxyl" includes groups with an -OH or -0-.
The term "halogen" includes fluorine, bromine, chlorine, iodine, etc. The term "perhalogenated" generally refers to a moiety wherein all hydrogens are replaced by halogen atoms.
The terms "polycyclyl" or "polycyclic radical" refer to two or more cyclic rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls and/or heterocyclyls) in which two or more carbons are common to two adjoining rings, e.g., the rings are "fused rings".
Rings that are joined through non-adjacent atoms are termed "bridged" rings.
Each of the rings of the polycycle can be substituted with such substituents as described above, as for example, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, aryoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl, alkoxycarbonyl, alkylaminoacarbonyl, arylalkylaminocarbonyl, alkenylaminocarbonyl, alkylcarbonyl, arylcarbonyl, arylalkyl carbonyl, alkenylcarbonyl, aminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, cyano, amido, amino (including alkyl amino, dialkylamino, aryyamino, diarylamino, and alkylarylamino), acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino, imino, suithydryl, alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl, alkyl, alkylaryl, or an aromatic or heteroaromatic moiety.
/ The term "heteroatom" includes atoms of any element other than carbon or hydrogen. Preferred heteroatoms are nitrogen, oxygen, sulfur and phosphorus.
The term "prodrug moiety" includes moieties which can be metabolized in vivo to a hydroxyl group and moieties which may advantageously remain esterified in vivo.
Preferably, the prodrugs moieties are metabolized in vivo by esterases or by other mechanisms to hydroxyl groups or other advantageous groups. Examples of prodrugs and their uses are well known in the art (See, e.g., Berge et al. (1977) "Pharmaceutical Salts", J. Pharm. Sci. 66:1-19). The prodrugs can be prepared in situ during the final isolation and purification of the compounds, or by separately reacting the purified compound in its free acid form or hydroxyl with a suitable esterifying agent.
Hydroxyl groups can be converted into esters via treatment with a carboxylic acid.
Examples of prodrug moieties include substituted and unsubstituted, branch or unbranched lower alkyl ester moieties, (e.g., propionoic acid esters), lower alkenyl esters, di-lower alkyl-amino lower-alkyl esters (e.g., dimethylaminoethyl ester), acylamino lower alkyl esters (e.g., acetyloxymethyl ester), acyloxy lower alkyl esters (e.g., pivaloyloxymethyl ester), aryl esters (phenyl ester), aryl-lower alkyl esters (e.g., benzyl ester), substituted (e.g., with methyl, halo, or methoxy substituents) aryl and aryl-lower alkyl esters, amides, lower-alkyl amides, di-lower alkyl amides, and hydroxy amides. Preferred prodrug moieties are propionoic acid esters and acyl esters.
It will be noted that the structure of some of the tetracycline compounds of this invention includes asymmetric carbon atoms. It is to be understood accordingly that the isomers arising from such asymmetry (e.g., all enantiomers and diastereomers) are included within the scope of this invention, unless indicated otherwise. Such isomers can be obtained in substantially pure form by classical separation techniques and by stereochemically controlled synthesis., Furthermore, the structures and other compounds and moieties discussed in this application also include all tautomers thereof.

7. Methods for Treating Tetracycline Responsive States The invention also pertains to methods for treating a tetracycline responsive states in subjects, by administering to a subject an effective amount of a tetracycline compound of the invention (e.g., a compound of Formula I, II, III, IV, V or otherwise described herein), such that the tetracycline responsive state is treated.
The term "treating" includes curing as well as ameliorating at least one symptom of the state, disease or disorder, e.g., the tetracycline compound responsive state.
The language "tetracycline compound responsive state" or "tetracycline responsive state" includes states which can be treated, prevented, or otherwise ameliorated by the administration of a tetracycline compound of the invention, e.g., a 3, 10, and/or 12a substituted tetracycline compound. Tetracycline compound responsive states include bacterial, viral, and fungal infections (including those which are resistant to other tetracycline compounds), cancer (e.g., prostate, breast, colon, lung melanoma and lymph cancers and other disorders characheterized by unwanted cellular proliferation, including, but not limited to, those described in U.S.
6,100,248), arthritis, osteoporosis, diabetes, and other states for which tetracycline compounds have been found to be active (see, for example, U.S. Patent Nos. 5,789,395; 5,834,450;
6,277,061 and 5,532,227).
Compounds of the invention can be used to prevent or control important mammalian and veterinary diseases such as diarrhea, urinary tract infections, infections of skin and skin structure, ear, nose and throat infections, wound infection, mastitis and the like. In addition, methods for treating neoplasms using tetracycline compounds of the invention are also included (van der Bozert et al., Cancer Res., 48:6686-6690 (1988)).
In a further embodiment, the tetracycline responsive state is not a bacterial infection. In another embodiment, the tetracycline compounds of the invention are essentially non-antibacterial. For example, non-antibacterial tetracycline compounds of the invention may have MIC values greater than about 4 pg/ml (as measured by assays known in the art and/or the assay given in Example 2).
Tetracycline compound responsive states also include inflammatory process associated states (IPAS). The term "inflammatory process associated state"
includes states in which inflammation or inflammatory factors (e.g., matrix metalloproteinases (MMPs), nitric oxide (NO), TNF, interleukins, plasma proteins, cellular defense systems, cytoldnes, lipid metabolites, proteases, toxic radicals, adhesion molecules, etc.) are involved or are present in an area in aberrant amounts, e.g., in amounts which may be advantageous to alter, e.g., to benefit the subject. The inflammatory process is the response of living tissue to damage. The cause of inflammation may be due to physical damage, chemical substances, micro-organisms, tissue necrosis, cancer or other agents.

Acute inflammation is short-lasting, lasting only a few days. If it is longer lasting however, then it may be referred to as chronic inflammation.
IPAF's include inflammatory disorders. Inflammatory disorders are generally characterized by heat, redness, swelling, pain and loss of function. Examples of causes of inflammatory disorders include, but are not limited to, microbial infections (e.g., bacterial and fungal infections), physical agents (e.g., burns, radiation, and trauma), chemical agents (e.g., toxins and caustic substances), tissue necrosis and various types of immunologic reactions.
Examples of inflammatory disorders include, but are not limited to, osteoarthritis, rheumatoid arthritis, acute and chronic infections (bacterial and fungal, including diphtheria and pertussis); acute and chronic bronchitis, sinusitis, and upper respiratory infections, including the common cold; acute and chronic gastroenteritis and colitis; acute and chronic cystitis and urethritis; acute and chronic dermatitis; acute and chronic conjunctivitis; acute and chronic serositis (pericarditis, peritonitis, synovitis, pleuritis and tendinitis); uremic pericarditis; acute and chronic cholecystis;
acute and chronic vaginitis; acute and chronic uveitis; drug reactions; insect bites;
burns (thermal, chemical, and electrical); and sunburn.
Tetracycline compound responsive states also include NO associated states. The term "NO associated state" includes states which involve or are associated with nitric oxide (NO) or inducible nitric oxide synthase (iNOS). NO associated state includes states which are characterized by aberrant amounts of NO and/or iNOS.
Preferably, the NO associated state can be treated by administering tetracycline compounds of the invention, e.g., a 3, 10, and/or 12a substituted tetracycline compound. The disorders, diseases and states described in U.S. Patents Nos. 6,231,894; 6,015,804;
5,919,774; and 5,789,395 are also included as NO associated states. -Other examples of NO associated states include, but are not limited to, malaria, senescence, diabetes, vascular stroke, neurodegenerative disorders (Alzheimer's disease & Huntington's disease), cardiac disease (reperfusion-associated injury following infarction), juvenile diabetes, inflammatory disorders, osteoartbritis, rheumatoid arthritis, acute, recurrent and chronic infections (bacterial, viral and fungal); acute and chronic bronchitis, sinusitis, and respiratory infections, including the common cold;
acute and chronic gastroenteritis and colitis; acute and chronic cystitis and urethritis;
acute and chronic dermatitis; acute and chronic conjunctivitis; acute and chronic serositis (pericarditis, peritonitis, synovitis, pleuritis and tendonitis);
uremic pericarditis;
acute and chronic cholecystis; cystic fibrosis, acute and chronic vaginitis;
acute and chronic uveitis; drug reactions; insect bites; burns (thermal, chemical, and electrical);
and sunburn.

The term "inflammatory process associated state" also includes, in one embodiment, matrix metalloproteinase associated states (MMPAS). NIMPAS include states charachterized by abberrant amounts of MMPs or MMP activity. These are also include as tetracycline compound responsive states which may be treated using compounds of the invention, e.g., 3, 10, and/or 12a substituted tetracycline compounds.
Examples of matrix metalloproteinase associated states ("MMPAS's") include, but are not limited to, arteriosclerosis, corneal ulceration, emphysema, osteoarthritis, multiple sclerosis(Liedtke et al., Ann. Neurol. 1998, 44:35-46; Chandler et aL, I
Neuroimmunol.1997, 72:155-71), osteosarcoma, osteomyelitis, bronchiectasis, chronic pulmonary obstructive disease, skin and eye diseases, periodontitis, osteoporosis, rheumatoid arthritis, ulcerative colitis, inflammatory disorders, tumor growth and invasion (Stetler-Stevenson et al., Annu. Rev. Cell Biol. 1993, 9:541-73;
Tryggvason et aL, Biochim. Biophys. Acta 1987, 907:191-217; Li et al., MoL Carcinog. 1998, 22:84-89)),metastasis, acute lung injury, stroke, ischemia, diabetes, aortic or vascular aneurysms, skin tissue wounds, dry eye, bone and cartilage degradation (Greenwald et al., Bone 1998, 22:33-38; Ryan et al., Curr. Op. Rheumatol. 1996, 8;238-247).
Other M WAS include those described in U.S. Pat. Nos. 5,459,135; 5,321,017;
5,308,839;
5,258,371; 4,935,412; 4,704,383, 4,666,897, and RE 34,656..

In another embodiment, the tetracycline compound responsive state is cancer.
Examples of cancers which the tetracycline compounds of the invention may be useful to treat include all solid tumors, i.e., carcinomas e.g., adenocarcinomas, and sarcomas.
Adenocarcinomas are carcinomas derived from glandular tissue or in which the tumor cells form recognizable glandular structures. Sarcomas broadly include tumors whose cells are embedded in a fibrillar or homogeneous substance like embryonic connective tissue. Examples of carcinomas which may be treated using the methods of the invention include, but are not limited to, carcinomas of the prostate, breast, ovary, testis, lung, colon, and breast. The methods of the invention are not limited to the treatment of these tumor types, but extend to any solid tumor derived from any organ system.
Examples of treatable cancers include, but are not limited to, colon cancer, bladder cancer, breast cancer, melanoma, ovarian carcinoma, prostatic carcinoma, lung cancer, and a variety of other cancers as well. The methods of the invention also cause the inhibition of cancer growth in adenocarcinomas, such as, for example, those of the prostate, breast, kidney, ovary, testes, and colon.
In an embodiment, the tetracycline responsive state of the invention is cancer.
The invention pertains to a method for treating a subject suffering or at risk of suffering from cancer, by administering an effective amount of a substituted tetracycline compound, such that inhibition cancer cell growth occurs, i.e., cellular proliferation, invasiveness, metastasis, or tumor incidence is decreased, slowed, or stopped.
The inhibition may result from inhibition of an inflammatory process, down-regulation of an inflammatory process, some other mechanism, or a combination of mechanisms.
Alternatively, the tetracycline compounds maybe useful for preventing cancer recurrence, for example, to treat residual cancer following surgical resection or radiation therapy. The tetracycline compounds useful according to the invention are especially advantageous as they are substantially non-toxic compared to other cancer treatments.
In a further embodiment, the compounds of the invention are administered in combination with standard cancer therapy, such as, but not limited to, chemotherapy.
Examples of tetracycline responsive states also include neurological disorders which include both neuropsychiatric and neurodegenerative disorders, but are not limited to, such as Alzheimer's disease, dementias related to Alzheimer's disease (such as Pick's disease), Parkinson's and other Lewy diffuse body diseases, senile dementia, Huntington's disease, Gilles de la Tourette's syndrome, multiple sclerosis, amylotrophic lateral sclerosis (ALS), progressive supranuclear palsy, epilepsy, and Creutzfeldt-Jakob disease; autonomic function disorders such as hypertension and sleep disorders, and neuropsychiatric disorders, such as depression, schizophrenia, schizoaffective disorder, Korsakoff's psychosis, mania, anxiety disorders, or phobic disorders; learning or memory disorders, e.g., amnesia or age-related memory loss, attention deficit disorder, dysthymic disorder, major depressive disorder, mania, obsessive-compulsive disorder, psychoactive substance use disorders, anxiety, phobias, panic disorder, as well as bipolar affective disorder, e.g., severe bipolar affective (mood) disorder (BP-1), bipolar affective neurological disorders, e.g., migraine and obesity. Further neurological disorders include, for example, those listed in the American Psychiatric Association's Diagnostic and Statistical manual of Mental Disorders (DSM).

Other examples of tetracycline compound responsive states are described in WO
03/005971A2, U.S.S.N. 60/421,248, and U.S.S.N. 60/480,482.

The language "in combination with" another therapeutic agent or treatment includes co-administration of the tetracycline compound, (e.g., inhibitor) and with the other therapeutic agent or treatment, administration of the tetracycline compound first, followed by the other therapeutic agent or treatment and administration of the other therapeutic agent or treatment first, followed by the tetracycline compound.
The other therapeutic agent may be any agent which is known in the art to treat, prevent, or reduce the symptoms of an IPAS. Furthermore, the other therapeutic agent may be any agent of benefit to the patient when administered in combination with the administration of an tetracycline compound. In one embodiment, the cancers treated by methods of the invention include those described in U.S. Patent Nos. 6,100,248; 5,843,925;
5,837,696;
or 5,668,122, In another embodiment, the tetracycline compound responsive state is diabetes, e.g., juvenile diabetes, diabetes mellitus, diabetes type I, or diabetes type H. In a further embodiment, protein glycosylation is not affected by the administration of the tetracycline compounds of the invention. In another embodiment, the tetracycline compound of the invention is administered in combination with standard diabetic therapies, such as, but not limited to insulin therapy. In a further embodiment, the IPAS
includes disorders described in U.S. Patents Nos. 5,929,055; and 5,532,227, In another embodiment, the tetracycline compound responsive state is a bone mass disorder. Bone mass disorders include disorders where a subjects bones are disorders and states where the formation, repair or remodeling of bone is advantageous.
For examples bone mass disorders include osteoporosis (e.g., a decrease in bone strength and density), bone fractures, bone formation associated with surgical procedures (e.g., facial reconstruction), osteogenesis imperfecta (brittle bone disease), hypophosphatasia, Paget's disease, fibrous dysplasia, osteopetrosis, myeloma bone disease, and the depletion of calcium in bone, such as that which is related to primary hyperparathyroidism. Bone mass disorders include all states in which the formation, repair or remodeling of bone is advantageous to the subject as well as all other disorders associated with the bones or skeletal system of a subject which can be treated with the tetracycline compounds of the invention. In a further embodiment, the bone mass disorders include those described in U.S. Patents Nos. 5,459,135; 5,231,017;
5,998,390;
5,770,588; RE 34,656; 5,308,839; 4,925,833; 3,304,227; and 4,666,897.
In another embodiment, the tetracycline compound responsive state is acute lung injury. Acute lung injuries include adult respiratory distress syndrome (ARDS), post-pump syndrome (PPS), and trauma. Trauma includes any injury to living tissue caused by an extrinsic agent or event. Examples of trauma include, but are not limited to, crush injuries, contact with a hard surface, or cutting or other damage to the lungs.
The invention also pertains to a method for treating acute lung injury by administering a substituted tetracycline compound of the invention.
The tetracycline responsive states of the invention also include chronic lung disorders. The invention pertains to methods for treating chronic lung disorders by administering a tetracycline compound, such as those described herein. The method includes administering to a subject an effective amount of a substituted tetracycline compound such that the chronic lung disorder is treated. Examples of chronic lung disorders include, but are not limited, to asthma, cystic fibrosis, and emphesema. In a further embodiment, the tetracycline compounds of the invention used to treat acute and/or chronic lung disorders such as those described in U.S. Patents No.
5,977,091;
-6,043,231; 5,523,297; and 5,773,430!b' In yet another embodiment, the tetracycline compound responsive state is ischemia, stroke, or ischemic stroke. The invention also pertains to a method for treating ischemia, stroke, or ischemic stroke by administering an effective amount of a substituted tetracycline compound of the invention. In a further embodiment, the tetracycline compounds of the invention are used to treat such disorders as described in U.S. Patents No. 6,231,894; 5,773,430; 5,919,775 or 5,789,395.

In another embodiment, the tetracycline compound responsive state is a skin wound. The invention also pertains, at least in part, to a method for improving the healing response of the epithelialized tissue (e.g., skin, mucusae) to acute traumatic injury (e.g., cut, burn, scrape, etc.). The method may include using a tetracycline compound of the invention (which may or may not have antibacterial activity) to improve the capacity of the epithelialized tissue to heal acute wounds. The method may increase the rate of collagen accumulation of the healing tissue. The method may also decrease the proteolytic activity in the epthithelialized tissue by decreasing the collagenolytic and/or gellatinolytic activity of MMPs. In a further embodiment, the tetracycline compound of the invention is administered to the surface of the skin (e.g., topically). In a further embodiment, the tetracycline compound of the invention used to treat a skin wound, and other such disorders as described in, for example, U.S. Patent Nos. 5,827,840; 4,704,383; 4,935,412; 5,258,371; 5,308,83915,459,135;
5,532,227; and 6,015,804a In'yet another embodiment, the tetracycline compound responsive state is an aortic or vascular aneurysm in vascular tissue of a subject (e.g., a subject having or at risk of having an aortic or vascular aneurysm, etc.). The tetracycline compound may by effective to reduce the size of the vascular aneurysm or it may be administered to the subject prior to the onset of the vascular aneurysm such that the aneurysm is prevented.
In one embodiment, the vascular tissue is an artery, e.g., the aorta, e.g., the abdominal aorta. In a further embodiment, the tetracycline compounds of the invention are used to treat disorders described in U.S. Patent Nos. 6,043,225 and 5,834,449.

Bacterial infections maybe caused by a wide variety of gram positive and gram negative bacteria. The compounds of the invention are useful as antibiotics against organisms which are resistant to other tetracycline compounds. The antibiotic activity of the tetracycline compounds of the invention may be determined using the method discussed in Example 2, or by using the in vitro standard broth dilution method described in Waitz, J.A., National Commission for Clinical Laboratory Standards, Document M7 A2, vol. 10, no. 8, pp. 13-20, 2nd edition, Villanova, PA (1990).
The tetracycline compounds may also be used to treat infections traditionally treated with tetracycline compounds such as, for example, rickettsiae; a number of gram-positive and gram-negative bacteria; and the agents responsible for lymphogranuloma venereum, inclusion conjunctivitis, psittacosis. The tetracycline compounds may be used to treat infections of, e.g., K. pneumoniae, Salmonella, E. hirae, A.
baumanii, B.
catarrhalis, H. influenzae, P. aeruginosa, E. faecium, E. coli, S. aureus or E. faecalis. In one embodiment, the tetracycline compound is used to treat a bacterial infection that is resistant to other tetracycline antibiotic compounds. The tetracycline compound of the invention may be administered with a pharmaceutically acceptable carrier.
The language "effective amount" of the compound is that amount necessary or sufficient to treat or prevent a tetracycline compound responsive state. The effective amount can vary depending on such factors as the size and weight of the subject, the type of illness, or the particular tetracycline compound. For example, the choice of the tetracycline compound can affect what constitutes an "effective amount". One of ordinary skill in the art would be able to study the aforementioned factors and make the determination regarding the effective amount of the tetracycline compound without undue experimentation.
The invention also pertains to methods of treatment against microorganism infections and associated diseases. The methods include administration of an effective amount of one or more tetracycline compounds to a subject. The subject can be either a plant or, advantageously, an animal,.e.g., a mammal, e.g., a human.
In the therapeutic methods of the invention, one or more tetracycline compounds of the invention may be administered alone to a subject, or more typically a compound of the invention will be administered as part of a pharmaceutical composition in mixture with conventional excipient, i.e., pharmaceutically acceptable organic or inorganic carrier substances suitable for parenteral, oral or other desired administration and which do not deleteriously react with the active compounds and are not deleterious to the recipient thereof.

8. Pharmaceutical Compositions of the Invention The invention also pertains to pharmaceutical compositions comprising a therapeutically effective amount of a tetracycline compound (e.g., a compound of Formula 1,11,111, IV, V or any other compound described herein) and, optionally, a pharmaceutically acceptable carrier.

=

The language "pharmaceutically acceptable carrier" includes substances capable of being coadministered with the tetracycline compound(s), and which allow both to perform their intended function, e.g., treat or prevent a tetracycline responsive state.
Suitable pharmaceutically acceptable carriers include but are not limited to water, salt solutions, alcohol, vegetable oils, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, perfume oil, fatty acid monoglycerides and diglycerides, petroethral fatty acid esters, hydroxymethyl-cellulose, polyvinylpyrrolidone, etc. The pharmaceutical preparations can be sterilized and if desired mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously react with the active compounds of the invention.
The tetracycline compounds of the invention that are basic in nature are capable of forming a wide variety of salts with various inorganic and organic acids.
The acids that may be used to prepare pharmaceutically acceptable acid addition salts of the tetracycline compounds of the invention that are basic in nature are those that form non-toxic acid addition salts, i.e., salts containing pharmaceutically acceptable anions, such as the hydrochloride, hydrobromide, hydroiodide, nitrate, sulfate, bisulfate, phosphate, acid phosphate, isonicotinate, acetate, lactate, salicylate, citrate, acid citrate, tartrate, pantothenate, bitartrate, ascorbate, succinate, maleate, gentisinate, fumarate, gluconate, glucaronate, saccharate, formate, benzoate, glutamate, methanesulfonate, ethanesulfonate, benzenesulfonate, p-toluenesulfonate and palmoate [i.e., 1,1'-methylene-bis-(2-hydro)y-3 naphthoate)] salts. Although such salts must be pharmaceutically acceptable for administration to a subject, e.g., a mammal, it is often desirable in practice to initially isolate a tetracycline compound of the invention from the reaction mixture as a pharmaceutically unacceptable salt and then simply convert the latter back to the free base compound by treatment with an alkaline reagent and subsequently convert the latter free base to a pharmaceutically acceptable acid addition salt. The acid addition salts of the base compounds of this invention are readily prepared by treating the base compound with a substantially equivalent amount of the chosen mineral or organic acid in an aqueous solvent medium or in a suitable organic solvent, such as methanol or ethanol Upon careful evaporation of the solvent, the desired solid salt is readily obtained. The preparation of other tetracycline compounds of the invention not specifically described in the foregoing experimental section can be accomplished using combinations of the reactions described above that will be apparent to those skilled in the art.
The preparation of other tetracycline compounds of the invention not specifically described in the foregoing experimental section can be accomplished using combinations of the reactions described above that will be apparent to those skilled in the art.
The tetracycline compounds of the invention that are acidic in nature are capable of forming a wide variety of base salts. The chemical bases that maybe used as reagents to prepare pharmaceutically acceptable base salts of those tetracycline compounds of the invention that are acidic in nature are those that form non-toxic base salts with such compounds. Such non-toxic base salts include, but are not limited to those derived from such pharmaceutically acceptable cations such as alkali metal cations (e.g., potassium and sodium) and alkaline earth metal cations (e.g., calcium and magnesium), ammonium or water-soluble amine addition salts such as N-methylglucamine-(meglumine), and the lower alkanolammonium and other base salts of pharmaceutically acceptable organic amines. The pharmaceutically acceptable base addition salts of tetracycline compounds of the invention that are acidic in nature maybe formed with pharmaceutically acceptable cations by conventional methods. Thus, these salts maybe readily prepared by treating the tetracycline compound of the invention with an aqueous solution of the desired pharmaceutically acceptable cation and evaporating the resulting solution to dryness, preferably under reduced pressure. Alternatively, a lower alkyl alcohol solution of the tetracycline compound of the invention may be mixed with an alkoxide of the desired metal and the solution subsequently evaporated to dryness.
The preparation of other tetracycline compounds of the invention not specifically described in the foregoing experimental section can be accomplished using combinations of the reactions described above that will be apparent to those skilled in the art.
The tetracycline compounds of the invention and pharmaceutically acceptable salts thereof can be administered via either the oral, parenteral or topical routes. In general, these compounds are most desirably administered in effective dosages, depending upon the weight and condition of the subject being treated and the particular route of administration chosen. Variations may occur depending upon the species of the subject being treated and its individual response to said medicament, as well as on the type of pharmaceutical formulation chosen and the time period and interval at which such administration is carried out.
The pharmaceutical compositions of the invention may be administered alone or in combination with other known compositions for treating tetracycline responsive states in a subject, e.g., a mammal. Preferred mammals include pets (e.g., cats, dogs, ferrets, etc.), farm animals (cows, sheep, pigs, horses, goats, etc.), lab animals (rats, mice, monkeys, etc.), and primates (chimpanzees, humans, gorillas). The language "in combination with" a known composition is intended to include simultaneous administration of the composition of the invention and the known composition, administration of the composition of the invention first, followed by the known composition and administration of the known composition first, followed by the composition of the invention. Any of the therapeutically composition known in the art for treating tetracycline responsive states can be used in the methods of the invention.
The tetracycline compounds of the invention may be administered alone or in combination with pharmaceutically acceptable carriers or diluents by any of the routes previously mentioned, and the administration may be carried out in single or multiple doses. For example, the novel therapeutic agents of this invention can be administered advantageously in a wide variety of different dosage forms, i.e., they may be combined with various pharmaceutically acceptable inert carriers in the form of tablets, capsules, lozenges, troches, hard candies, powders, sprays (e.g., aerosols, etc.), creams, salves, suppositories, jellies, gels, pastes, lotions, ointments, aqueous suspensions, injectable solutions, elixirs, syrups, and the like. Such carriers include solid diluents or fillers, sterile aqueous media and various non-toxic organic solvents, etc. Moreover, oral pharmaceutical compositions can be suitably sweetened and/or flavored. In general, the therapeutically-effective compounds of this invention are present in such dosage forms at concentration levels ranging from about 5.0% to about 70% by weight.
For oral administration, tablets containing various excipients such as microcrystalline cellulose, sodium citrate, calcium carbonate, dicalcium phosphate and glycine may be employed along with various disintegrants such as starch (and preferably corn, potato or tapioca starch), alginic acid and certain complex silicates, together with granulation binders like polyvinylpyrrolidone, sucrose, gelatin and acacia.
Additionally, lubricating agents such as magnesium stearate, sodium lauryl sulfate and talc are often very useful for tabletting purposes. Solid compositions of a similar type may also be employed as fillers in gelatin capsules; preferred materials in this connection also include lactose or milk sugar as well as high molecular weight polyethylene glycols.
When aqueous suspensions and/or elixirs are desired for oral administration, the active ingredient may be combined with various sweetening or flavoring agents, coloring matter or dyes, and, if so desired, emulsifying and/or suspending agents as well, together with such diluents as water, ethanol, propylene glycol, glycerin and various like combinations thereof. The compositions of the invention may be formulated such that the tetracycline compositions are released over a period of time after administration.
For parenteral administration (including intraperitoneal, subcutaneous, intravenous, intradermal or intramuscular injection), solutions of a therapeutic compound of the present invention in either sesame or peanut oil or in aqueous propylene glycol may be employed. The aqueous solutions should be suitably buffered (preferably pH greater than 8) if necessary and the liquid diluent first rendered isotonic.
These aqueous solutions are suitable for intravenous injection purposes. The oily solutions are suitable for intraarticular, intramuscular and subcutaneous injection purposes. The preparation of all these solutions under sterile conditions is readily accomplished by standard pharmaceutical techniques well known to those skilled in the art. For parenteral application, examples of suitable preparations include solutions, preferably oily or aqueous solutions as well as suspensions, emulsions, or implants, including suppositories. Therapeutic compounds may be formulated in sterile form in multiple or single dose formats such as being dispersed in a fluid carrier such as sterile physiological saline or 5% saline dextrose solutions commonly used with injectables.
Additionally, it is also possible to administer the compounds of the present invention topically when treating inflammatory conditions of the skin.
Examples of methods of topical administration include transdermal, buccal or sublingual application.
For topical applications, therapeutic compounds can be suitably admixed in a pharmacologically inert topical carrier such as a gel, an ointment, a lotion or a cream.
Such topical carriers include water, glycerol, alcohol, propylene glycol, fatty alcohols, triglycerides, fatty acid esters, or mineral oils. Other possible topical carriers are liquid petrolatum, isopropylpalmitate, polyethylene glycol, ethanol 95%, polyoxyethylene monolauriate 5% in water, sodium lauryl sulfate 5% in water, and the like. In addition, materials such as anti-oxidants, humectants, viscosity stabilizers and the like also may be added if desired.
For enteral application, particularly suitable are tablets, dragees or capsules having talc and/or carbohydrate carrier binder or the like, the carrier preferably being lactose and/or corn starch and/or potato starch. A syrup, elixir or the like can be used wherein a sweetened vehicle is employed. Sustained release compositions can be formulated including those wherein the active component is protected with differentially degradable coatings, e.g., by microencapsulation, multiple coatings, etc.
In addition to treatment of human subjects, the therapeutic methods of the invention also will have significant veterinary applications, e.g. for treatment of livestock such as cattle, sheep, goats, cows, swine and the like; poultry such as chickens, ducks, geese, turkeys and the like; horses; and pets such as dogs and cats.
Also, the compounds of the invention may be used to treat non-animal subjects, such as plants.
It will be appreciated that the actual preferred amounts of active compounds used in a given therapy will vary according to the specific compound being utilized, the particular compositions formulated, the mode of application, the particular site of administration, etc. Optimal administration rates for a given protocol of administration can be readily ascertained by those skilled in the art using conventional dosage determination tests conducted with regard to the foregoing guidelines.
In general, compounds of the invention for treatment can be administered to a subject in dosages used in prior tetracycline therapies. See, for example, the Physicians' Desk Reference. For example, a suitable effective dose of one or more compounds of the invention will be in the range of from 0.01 to 100 milligrams per kilogram of body weight of recipient per day, preferably in the range of from 0.1 to 50 milligrams per kilogram body weight of recipient per day, more preferably in the range of 1 to 20 milligrams per kilogram body weight of recipient per day. The desired dose is suitably administered once daily, or several sub-doses, e.g. 2 to 5 sub-doses, are administered at appropriate intervals through the day, or other appropriate schedule.
It will also be understood that normal, conventionally known precautions will be taken regarding the administration of tetracyclines generally to ensure their efficacy under normal use circumstances. Especially when employed for therapeutic treatment of humans and animals in vivo, the pracctitioner should take all sensible precautions to avoid conventionally known contradictions and toxic effects. Thus, the conventionally recognized adverse reactions of gastrointestinal distress and inflammations, the renal toxicity, hypersensitivity reactions, changes in blood, and impairment of absorption through aluminum, calcium, and magnesium ions should be duly considered in the conventional manner.
Furthermore, the invention also pertains to the use of a tetracycline compound of formula I, II, III, N, V, or any other compound described herein, for the preparation of a medicament. The medicament may include a pharmaceutically acceptable carrier and the tetracycline compound is an effective amount, e.g., an effective amount to treat a tetracycline responsive state.

EXEMPLIFICATION OF THE INVENTION

.25 Example 1: Synthesis of Selected Compounds of the Invention F
N
H3C1 .CH3 H H N OH

C~iN I / \ = ( NH2 OH O OH O
The above compound was prepared from 7-iodo-sancycline (15.0g, 22.9mmol) combined with Pd(dppf)2C12 (1.7g, 2.29mmol) and DMF (300mL) in a 1L round bottom 2 neck flask. Na2CO3 (7.2g, 68.2mmol) was dissolved in water (15mL) was added to reaction solution. 2-fluoro-pyridine-5-boronic acid (6.4g, 45.9mmol) was dissolved in DMF (25mL) and also added to reaction solution. Reaction mixture was stirred at 65 C
(oil bath temperature) under an argon atmosphere and reaction was monitored by HPLC
and LCIMS. Reaction shown to be complete within 3hr. Filtered through celite and evaporated solvent in vacuo. Redissolved in MeOH (30mL) and precipitated in MTBE
(3L) to produce a yellow precipitate. Filtered and dried under vacuum overnight to yield 15g of yellow powder. This crude material (9g, 17.8mmol) was dissolved in TFA/Triflic acid (83mIJ7mL) and cooled to 0 C using an ice bath. N-iodo-succinimide (8g, 35.6mmol) was added portionwise to reaction solution over 2hr. Reaction complete after 3hrs - and 20% more NIS added to reaction. Evaporated TFA in vacuo and precipitated remaining acid in MTBE (1.4L) at room temp. Yellow precipitate.
Filtered and dried under vacuum overnight to yield 8.4g of crude product. This crude material (4g, 6.3mmol) was combined with NaOAc (0.52g, 6.3mmol) in an oven-dried 25OmL

neck round bottom flask. Anhydrous DMF (6OmL) was syringed into reaction flask.
Stirred under argon at room temp lhr. Diluted with more anhydrous DMF (120mL) and a CO-filled balloon was placed on top neck of reaction flask. CO was purged through reaction direction from lecture bottle for 15min. Flask then open to CO-filled balloon and allowed to stir at 60 C (oil bath temp) while Pd(PPh3)4 (2.2g, 1.9mmol) was added as a DMF slurry via syringe. Stirred at temperature Ihr. SnBu3H (1.6g, 6.3mmol) was added via syringe pump over 2hr. Reaction monitored by HPLC and LC/MS and shown to be complete upon completion of tin addition. Evaporated solvent in vacuo.
Purified by preparative HPLC in 20% yield in preparation for final synthesis step. This purified material (0.25g, 0.46mmol) was combined with anhydrous DMF (15mL) in an oven-dried 100mL flask. InC13 (0.005g, 0.023mmol), N-methyl-allylamine (0.178, 0.23mmol) were added to reaction and stirred at room temperature under argon lhr.
NaCNBH3 (0.035g, 0.55mmol) was added to reaction solution and was monitored by HPLC
and LC/MS. Reaction 80% complete within 6hrs of reaction time. Evaporated solvent in vacuo. Final product was isolated by preparative HPLC in 10% yield as a yellow solid.
ESI-MS: m/z (M + H) 593.

7-Ethyl-9-(4'. 4' Difluoro-N-Piperidinyl methyl)-Sang cy line CH3 H3C..N.CH3 F H H -F
N NH, OH O OH O
The compound was prepared from 7-ethyl-9-formyl-sancycline (0.23g, 0.49mmol) combined with IUCl3 (0.011g, 0.049mmol), 4,4-difluoropiperidine.HCI
(0.17g, 0.98mmol), Et3N (0.099g, 0.98mmol), and DMF (8mL) in a glass vial.
Stirred under argon at room temperature 30min. NaCNBH3 (0.043g, 0.69mmol) was added to reaction vial and continued to stir at room temperature under argon. Reaction was monitored by LC/MS and HPLC and shown to be complete in 2hrs. Quenched reaction with McOH (15mL) and evaporated solvent in vhcuo. Product was isolated by preparative BPLC in 20% yield as a yellow solid. ESI-MS: m/z (M + H) 576.
7-(Trifluoroalkenyl)-9-(2'- trans-2-methyl-2-butene) aminomethy1 Sanccline F
F F H3C,N.CH3 H H = OH

H3C~,N I _ ' NH2 To a stirred solution of powered Zn (5.00 g, 76.5 mmol) in dry THE (50.0 mL) at 0 C was added iodo-trifluor alkene (2.00 mL, 4.50 g, 21.0 mmol) slowly over a 0.5 h time period. The reaction was stirred for an additional 1.5 h before it was filtered under an inert atmosphere and reduced of all solvent using rotary evaporation (25.0 C, 5.00 mm Hg) to yield the trifluoro-zinc-iodo-aikene reagent (approximately 3 mL).
Dry DMF (10 mL) was added to the above zinc-reagent and this solution was added to a stirred solution of 7-Iodo-9-trans-2-methyl-2 butene sancycline free base (1.00 g, 1.57 mmol) and tetralds(triphenylphosphine)palladium (0.181 g, 0.156 mmol) in dry DMF
(10 mL). The contents were heated to 40 C and allowed to stir for 20 minutes.
The reaction was then filtered and purified using reverse phase HPLC to give 7-trifluoroalkene sancycline product (557 mg, 0.0942 mmol, 60% yield) LCMS m/z =
592.2392 (M + H).

7-(2' P E, zinyl)-9-(3',3',3'-Trifluoro-propylamino)-methyl-Sancycline N iN HC. CH
H 3H N' 3 H OH
F~~1/~2~N NHZ
FF OH O OIPO O
Step 1:
7-Iodo-9-aminomethyl sancycline (569 mg, 1 mmol), indium trichloride (22 mg, 0.1 mmol) and trifluoropropionaldehyde (224 L, 2 mmol) were taken in DMF (25 mL) and stirred at room temperature for 10 minutes. To this solution, sodium triacetoxyborohydride (635 mg, 3 mmol) was added at once and the reaction mixture was stirred at room temperature for another 30 minutes. Progress of the reaction was monitored by HPLC and LC/MS. Reaction was completed in 30 minutes. DMF was then removed and the crude material obtained was then precipitated using diethyl ether/
MeOH (100/10 mL). Filteration of the precipitate gave a yellow powder, which was used for the next step without further purification.

Step 2:
7-Iodo-9- (3,3,3-trifluoro-propylamino)-methyl-sancycline (665 mg, 1 mmol), Pd(PPh3)4 (115mg, 0.1 mmol), Pd(OAc)2 (22 mg, "0.1 mmol), CuI (19 mg, 0.1 mmol) were taken in anhydrous DMF (30 mL) and purged with argon for 5 minutes. To this solution, 2-pyrazine-stannane (738 mg, 2 mmol) was added and the reaction mixture was stirred at room temperature for 2 hours. Reaction was completed by then (monitored by BPLC/LCMS). It was then filtered through celite, washed with 5 mL of methanol.
Solvent was evaporated to dryness. The crude material obtained was purified using preparative HPLC. A yellow solid was obtained after evaporating the fractions, which was converted to its HCl salt using MeOH/HCI solution. LC-MS (M+1 618).
7-Amino-9-Iodo-Doxycycline C. CH3 NH2 CF-h N
OH
+/ _ I NH2 OH 0 tH&O 0 To 500 mg of 9-Iodo-doxycycline in 10 ml of methanesulfonic acid was added 1.1 eq. of sodium nitrate. The reaction mixture was left stirring for several hrs and was monitored by analytical HPLC. The intermediate (9-Iodo-7-nitro-doxycycline) was isolated by diluting he solution with ice-water, adjusting the pH with sodium hydroxide (pH -4) and extracting the product with n-butanol. The solvent was evaporated under reduced pressure and the crude material was subjected to hydrogenation using 10% Pd/C
in methanol. The final product was obtained via preparative HPLC. The LCMS
showed the desired material; MS: 586. The structure was confirmed by NMR

7-(Dimethvlamino)-9-(4'.4'-Difluoropiperdin lll-Doxycycline H3C`N/CH HOH \NCF6 F H OH
F-N I / _ I NH, To a solution of 105 mg (0.16 mmol) of 9-(4-difluoropiperdinyl)-doxycycline dihydrochloride in 10 mL of methanesulfonic acid at room temperature, was added 19.4 mg (0.19 mmol) of potassium nitrate dissolved in 4 mL of methanesulfonic acid.
The reaction was monitored by LCMS. After 30 minutes, the reaction mixture was poured over ice and diluted to 160 mL with ice water. The solution was. loaded onto a 2.5 x 1 cm column of divinylbenzene resin (1000 angstrom, 5-25 pm) equilibrated with water.
The crude reaction mixture was washed with excess water to remove methanesulfonic acid followed an excess of IN ammonium acetate to neutralize the crude mixture. The excess ammonium acetate was removed by a water wash and the crude compound was purified by elution with 40% methanol in water with 0.1 % HCL The purified material was evaporated to dryness to yield 70 mg of 9-(4-difluoropiperdinyl)-7-nitro-doxycycline as the dihydrochloride salt (Yield = 63%). LCMS (MH+) 623. To 70 mg (0.10 mmol) of 9-(4-difluoropiperdinyl)-7 nitro-doxycycline dihydrochloride in 20 mL
of methoxyethanol was added 200 mL of sulfuric acid and 162 mL (2 mmol) of 37%
formaldehyde in water. The reaction mixture was purged with Argon gas and 40 mg of 10% wet Palladium on carbon was added with stirring. The reaction was hydrogenated at room temperature and 760 torr hydrogen gas for 12 hours. The crude reaction was passed through Celite and evaporated to dryness. The crude reaction mixture was purified by preparative HPLC (1 inch x 25 cm, Phenomenex Luna C18, 10 mm, Gradient 5-40% B buffer, A = water + 0.1% TFA, B = acetonitrile + 0.1 % TEA, detection at 280 nm) to yield 20 mg of the product as the dihydrochloride salt (Yield =
30%). LCMS (MH+) 621.
7 Diethvlamino-9-(4'-Fluoro-N-Piperidinyl methyl)-Sancycline LNJ H3C.N.CH3 F H H= OH
N I NHZ
OH O OH O
7 NH2-sancycline (4.0g, 9.32mmol) was combined with 2-methoxyethanol (100mL), H2SO4 (5mL of IN solution) in a 2 -neck 250mL round bottom flask.
Acetaldehyde (5.2mL, 9.32mmol) was added to reaction solution and contents were stirred at room temperature under argon for 20 minutes. Pd/C (1.25g) was added to reaction and contents were evacuated/flushed with argon 3 times. A balloon filled with H2 was placed on top neck of reaction flask and reaction solution was evacuated/flushed with H2 three times. The reaction was stirred overnight under H2 pressure at room temperature. The reaction was monitored by HPLC and LCIMS and shown to be complete by morning. The mixture was filtered through celite and solvent evaporated in vacuo. The residue was redissolved in water (IL) and the pH was adjusted with Et3N to pH 5. The mixture was filtered again through celite and loaded onto a DVB
column.

The compound eluted at 15% CH3CN. Clean fractions were evaporated and dried overnight under vacuum. A yellow/brown solid (7-diethylamino sancycline) was isolated in 40% yield.
7-diethylamino sancycline (1.4g, 2.88mmol)was dissolved in TFA/Triflie acid (22mL/6mL) in a 100mL flask. N-iodosuccinimide (12g, 5.78mmol) was added portionwise to reaction solution every 20 minutes. The reaction monitored by HPLC
and LCMMS and shown to be complete within 3 hours. The reaction solution was diluted with H2O (0.1% TFA) (3OmL) and the solvent was evaporated. The residue was redissolved in H2O (100mL) and loaded onto a 5g DVB cartridge. The crude product eluted at 30-50% CH3CN. A yellow/brown crude product was isolated in 90%
yield.
This crude material, 7-diethylamino-9-iodo-sancycline, (1.8g, 2.95mmol) was dissolved in anhydrous DMF (IOOmL) in a 2 neck IL round bottom flask and placed under argon. NaOAc (0.61g, 7.36mmol) was added to reaction solution and stirred at room temperature 45min. Pd(PPh3)4 (1.028, 8.85mmol) was added to reaction and a CO-filled balloon was placed on top neck of reaction flask. CO was bubbled through reaction solution for 10min. then flask opened to CO balloon. SnBu3H (0.8g, 2.95mmol) was added via syringe pump to reaction solution over 1 hour while heating to 65 C (oil bath temperature). The reaction was monitored by LCMMS and shown to be complete upon addition of tin hydride. H2O (0.1 % TFA, 0.3L) was added to the reaction flask and a precipitate formed. The mixture was filtered through celite and the filtrate was evaporated in vacuo. A brown solid in 90% yield (crude material) was isolated.
7-diethylamino-9-formyl-sancycline (0.25g, 0.49mmol) was dissolved in DMF
(lOmL). InCl3 (0.01g, 0.049mmol), 4-fluoropiperidine.HCl (0.15g, 0.98mmol), and Et3N (0.09g, 0.98mmol) were added to reaction solution. The reaction was stirred at room temperature under argon 45 minutes. NaCNBH3 (0.043g, 0.68mmol) was added to the reaction and it was monitored by HPLC and LCMMS. The reaction was shown to be complete in 3 hours and it was quenched with McOH (3OmL). The final product was isolated by preparative HPLC in 10% yield as a yellow solid. ESI MS: m/z (M +
H) 601.
Synthesis of 7-Aminomethyl Doxycycline HP HaC~NiOHa ON

NH, OH

To 1 gram of 9-tert-butyl-doxycycline, dissolved in 15 ml of methanesulfonic acid, was added an excess of HMBC (Hydroxymethyl-carbamic acid benzyl ester).
The reaction mixture was monitored by analytical HPLC. The LCMS showed MS: 530 corresponding to the desired material, 7-aminomethyl-9-t-butyl doxycycline.
The product was isolated via preparative HPLC and the structure confirmed by NMR.
Removal of the t-butyl in triflic acid afforded the 7-aminomethyl doxycycline in good yield.
Synthesis of 9-(3'.3'.3'-Trifluoro~ropylamino methyl Minocycline H3C..N.CH3 H3C.N.CH3 H H OH
F F ~F N NH2 F OH O OH O
9-formyl-minocycline (0.2g, 0.42mmol) was combined with InC13 (0.01g, 0.005mmol), 3,3,3-trifluoropropylamine.HC1(0.25g, 1.7mmol), Et3N (0.17g, 1.7mmol), and DMF (l OmL) in a glass vial. The reaction was stirred at room temperature under argon for 1 hour. NaCNBH3 (0.032g, 0.50mmol) was added to reaction solution and was monitored by HPLC and LC/MS. The reaction was complete within 1 hour, quenched with MeOH (2OmL) and the solvent evacuated in vacuo. The final product was isolated by preparative HPLC in 25% yield as a yellow solid. ESI-MS: m/z (M + H) 583.

9-(4'-Difluoromethylene-N-pineridinyl methyl Minocycline F H3C,N,CH3 H3C.N,CH3 H H ' F OH
N I / \ _ I NH2 OH O OH

o Anhydrous tetrahydrofuran (THF, 200 mL) was placed in a flame-dried 500 mL
round bottom flask at 0 C in an ice bath. Dibromodifluoromethane (97%, Aldrich, 10.00 mL, 106.19 mniol, 4.3 eq.) was added via syringe. Ten minutes later, Hexamethylphosphorous triamide (HMPT, 97%, Aldrich, 19.50 n2I,104.07 mmol, 4.2 eq.) was added dropwise. The clear solution turned milky white and was stirred for I
hour at 0 C. A solution of tent Butyl 4-oxo-l-piperidinecarboxylate (98%, Aldrich, 5.00 g, 24.59 mmol, 1.0 eq.) in anhydrous THE (50 mL) was then added dropwise via syringe at 0 C and the solution was allowed to warm up slowly to room temperature over 1 hour by removing the ice bath The powdered zinc (99.998%, Aldrich, powdered, -100 mesh, 6.56 g, 98.34 mmol, 4.0 eq.) was then added followed by HMPT (1.15 mL, 6.14 mmol, 25%) and the reaction mixture was refluxed for 3 hours. Water (250 mL) and Diethyl ether (Et20, 250 mL) were added and the mixture was extracted with Et2O
(3 times 100 mL). The combined organic layers were washed with a saturated solution of Copper(fl) sulfate (CuSO4) in Water (150 mL) then with water (150 mL). The organic layer was dried over Magnesium sulfate (MgSO4), filtered, and evaporated under reduced pressure to yield the desired fluorinated piperidine as a yellow oil, which was used without further purification in the next step.
A 100 mL round bottom flask equipped with a magnetic stirring bar was loaded with the BOC-protected piperidine (2.00 g, 8.57 mmol, 1.0 eq.) in a saturated solution in Methanol (50 mL) at room temperature. The mixture was then stirred at 40 C for 30 minutes and the solvent was evaporated under reduced pressure to a minimal volume. The HCl salt was then precipitated from Et2O, filtered, and dried in vacuo to yield the desired fluorinated piperidine (1.10 g, 6.49 mmol, 76%
yield) as a beige solid used without further purification in the next step.
A flame-dried 50 mL round bottom flask equipped with a magnetic stirring bar was loaded with 9-Formyl-minocycline (500 mg, 1.03 mmol,1.0 eq.) in anhydrous Dimethylformamide (DMF, 10.00 mL) at room temperature. Indium chloride (InC13, 99.999%, Aldrich, 59 mg, 0.27 mmol, 26%) was added and the reaction mixture was stirred at 30 C for 10 minutes. The amine (350 mg, 2.06 mmol, 2.0 eq.) was added in anhydrous DMF (2 mL), followed by Triethylamine (NEt3, 99.5%, Alfa-Aesar, 290 L, 2.08 mmol, 2.0 eq.). The mixture was then stirred at 30 C for 1 hour and Sodium triacetoxyborohydride (NaBH(OAc)3, 95%, Aldrich, 220 mg, 1.04 mmol, 1.0 eq.) was added followed by more NEt3 (300 L). After 2 hours, the reaction was done and the solvent evaporated under reduced pressure. The residue was purified by preparative BPLC (Acetonitrile / Water / 0.1% Trifluoroacetic acid gradient) to yield the desired product as a yellow solid. MS m/z 603.

Synthesis of 9-(4'-Fluoro-N-PiperdinyI) methyl Doxycycline ?aH O~H~uia'~a F~ " - OH

H .
OH

The compound was prepared from Doxycycline (2.5g, 5.0mmol) dissolved in MeOH (anhydrous) (25mL) and combined with AgSO4 (3.7g, 1lmmol) and 12 (3.1g, 11mmol) in a 100mL round bottom flask. H2SO4rr, (2 drops) was added to the reaction solution and stirred at room temperature under argon for 1 hour. The reaction solution turned bright yellow after 30 minutes and the reaction was monitored by LC/MS
and shown to be complete in 1 hour. Sodium sulfite (sat) (8mL) was added to the reaction solution and a thick yellow precipitate was formed. The mixture was stirred at room temperature for 20 minutes. The mixture was diluted with CH3CN (75mL), filtered through celite and evaporated solvent in vacuo to yield 1.7g of crude 9-iodo-doxycycline material.

9-iodo-doxycycline (1.3g, 2.4mmol) was dissolved in anhydrous DMF (2OmL) in a 200mL 2 neck round bottom flask and Pd(PPh3)4 (0.82g, 0.71mmol) was added. A
CO-filled balloon was placed on top neck of reaction flask and CO was bubbled directly into reaction from lecture bottole. The flask was then opened to the balloon and SnBu3H
(0.70g, 2.7mmol) was added via syringe pump over 1 hour. The reaction solution was heated to 65 C during the tin addition. The reaction was monitored by LCIMS
and it was shown to be complete once the tin addition was complete. Water (0.1 % TFA) (200mL) was then added to reaction solution and a yellow precipitate formed.
The mixture was then filtered through celite and the filtrate was evaporated in vacuo. A
brown/yellow solid in 50% yield was isolated.
(9-formyl-doxycycline (0.20g, 0.42mmol) combined with InC13 (0.01g, 0.042mmol), 4-fluoropiperidine (0.13g, 0.84mmol), Et3N (0.09g, 0.84mmol), and DMF
(5mL) in a glass vial. The mixture was stirred under argon at room temperature for 30 minutes. NaCNBH3 (0.037g, 0.59mmol) was added to the reaction vial and the reaction continued to be stirred at room temperature under argon. The reaction was monitored by LC/MS and HPLC and shown to be complete after 1 hour. The reaction was quenched with MeOH (15mL) and the solvent was evacuated in vacuo. The product was isolated by preparative HPLC in 10% yield as a yellow solid. ESI-MS: m/z (M + H) 559.

Synthesis of 9-(Benzyl methyl-amino)-Propynyl)-Minocycline H3C.N,CH3 HSC..N..CH3 H H OH

QJH,4~)~;NOH O OH O
7-Iodo-minocycline (1.08 g, 1.86 mmol ), taken in 25 mL of acetonitrile was degassed and purged with nitrogen (three times). To this suspension Pd(OAc)2 (20 mg, .089 mmol), CuI (10 mg, .053 mmol), (o-tolyl)3P (56 mg, .186 mmol) were added and purged with nitrogen for few minutes. Benzyl-methyl-prop-2-ynyl-amine (318 L, mmol) and triethylamine (1 mL) were added to the suspension. It turned into a brown solution after the addition of Et3N. The reaction mixture was then heated to 70 C for 2 hours. The progress of the reaction was monitored by HPLC/LCMS. It was then cooled down to room temperature and was filtered through celite. Evaporation of the solvent gave a brown solid, which was then purified on preparative HPLC to afford the desired compound. LC-MS (M+1615).

Synthesis of 8-(2'-1(2'-Fluoro-eth)lamino)-methyll-phen +y )1-Sancycline H3C. CH3 H H N' OH
F~~N I c _ I NH2 Step 1:
To a stirred solution (cooled at 00 C, ice-bath) of 9-amino-sancycline (7 g, 16.3 mmol) in 200 mL of McOH, 48% HBF4 solution (5.32 mL, 40.75 mmol) was added slowly under an argon atmosphere. After 5 minutes, n-BuNO2 (2.1 MI, 17.93 mnaol ) was added slowly (dropwise). The reaction mixture was then stitrred at 0 C for 3 hours (monitored by HPLC/LC-MS). NaN3 (1.06g, 16.3 mmol) was then added the reaction mixture (all at once). The reaction mixture was stirred at 0 C for another 3 hours (monitored by BPLC/LC-MS). The reaction mixture was then poured slowly into stirring diethyl ether (1L at ice-bath temperature). A yellow precipitate was obtained and it was filtered, washed with ether (20m1 x 3) and dried under vaccum, sealed in a vial and stored at 0 C. Isolated yield 7g.
Step 2:
Hydrobromic acid (30% in acetic acid) (14 mL) was added to a flask and cooled to 0 C. 9-Azido-sancycline (1g, 2.2 mmol) was added to the flask and the reaction was left to stir for one hour. After 1 hour, the reaction was complete. The reaction mixture was precipitated in 300 mL of diethyl ether. After letting the solution settle, the top layer of diethyl ether was decanted and the reaction mixture was dried under vaccum. A
brown-black solid was then dissolved in methanol and precipitated using diethyl ether.
The solid obtained was filtered and dried under vaccum.

Step 3:
To a stirred solution (cooled at 0 C, ice-bath) of 8-bromo-9-amino-sancycline (828 mg, 1.6 mmol) in 200 mL of McOH, 48% HBF4 solution (0.53 mL, 4.0 mmol) was added slowly under an argon atmosphere. After 5 minutes, n BuNO2 (0.2 mL, 1.79 nnnol ) was added slowly (dropwise). The reaction mixture was then stitrred at 0 C for 2 hours and left overnight at room temperature (monitored by HPLC/LC-MS). The solvent was evaporated and the crude material obtained was precipitated using diethyl ether (300 mL). The solid obtained was filtered and dried under vaccum.

Step 4:
8-Bromo-sancycline (492 mg, 1 mmol) and Pd(OAc)2 (22 mg, 0.1 mmol) were taken in methanol (150 mL) and purged with argon while heating the reaction mixture at 65 C (oil bath temperature). After 10 minutes, an aqueous solution of sodium carbonate (315 mg, 3 mmol in 10 mL of water) was added. A yellow precipitate was obtained which was fisher heated for another 10 minutes, before adding a DMF solution of the boronic acid( 300 mg, 2 mmol in 10 mL of DMF). The reaction was then heated at 65 C
for 3 hours. The reaction was monitored by BPLC/LCMS. The mixture was cooled down to room temperature and then filtered through celite. The solvent was then evaporated and the crude materialobtained was precipitated using methanol/diethyl ether (10/200 mL).
The crude material was then filtered and dried under vacuum. The yellow-brown material obtained was used as such without further purification.

Step 5:
To a solution of 8-(2-formyl-phenyl)-sancycline (518 mg, 1 mmol) in 30 mL of DCE under an argon atmosphere, 2-fluoro-ethylamine hydrochloride (198 mg, 2 mmol) and triethylamine (202 L, 2 mmol) were added. The reaction mixture was then stirred at room temperature for 2 hours. The reaction was monitored by using HPLC/LCMS, and was completed in 2 hours. The solvent was then evaporated and the crude material was purified using preparative HPLC to afford the desired compound. LC-MS (M+1 566).

7-Pyrazolyl-S ancycline H
N-N

To a stirred solution of 7-Iodo sancycline (100 mg, 0.153 mmol) in DMF (1 mL) was added pyrozole-4-boronic acid pinacole cyclic ester (77 mg, 0.40 mmol), methanol (1.5 mL), tetrakis(triphenylphosphine)palladium (18 mg, 0.015 mmol) and a solution containing 250 mg CsCO3 in 0.7 mL water. The reaction mixture was then subject to microwave irradiation at a temperature of 100 C for 5 minutes. The reaction was then diluted with 100 mL of water and TFA was used to lower the pH to 2. This solution was then filtered through celite, and loaded onto a plug of divinyl benzene resin (DVB). The plug containing the product was washed with water (200 mL) before the final compound was eluted with MeCN and reduced by rotary evaporation. The crude material was purified by reverse phase HPLC to give the final product (64 mg, 0.12 mmol, 75% yield) LCMS m/z=481.2115 (M+H).

Synthesis of 9-[(2,2,2-Trifluoro-ethyl)-hydrazonomethylj-Minocycline H3C1 N,CH3 H,C,N,CH3 H H OH
F~'H NI _ NHZ
F OH O OH O
To a solution of 9-formyl minocycline (485 mg, 1 mmol) in 30 mL of DMF
under an argon atmosphere, indium trichloride (22 mg, 0.1 mmol) and trifluoroethylhydrazine (228 L, 2 mmol) were added. The reaction mixture was then stirred at room temperature for 30 minutes. The reaction was monitored by using HPLC/LCMS, and was completed in 30 minutes. The solvent was then evaporated and the crude material was purified using preparative HPLC to afford the desired compound.
LC-MS (M+1 582).

Synthesis of 9-(l'-Isopropy1-4'-piperidinyl) amino Sancycline CH3 . H3C.N.CH3 ~N H Fi OH
H 3 C \
N NHZ
OH O OHO O O
To a solution of 9-amino sancycline HCl salt (0.5g, lmmol) in 40 ml of methanol and was added 1-isopropyl-4-piperidone (0.14g, 2 mmol). The solution was stirred for 5 minutes at room temperature. Sodium cyanoborohydride (62.5 mg, 1 mmol) was introduced, followed by the addition of 4 ml of AcOH. The mixture was stirred at room temperature for 1 hour until all starting material disappeared. The suspension was filtered and purified by HPLC to afford the title compound (210mg). LC-MS (M+1 555).
S3mjkesis of 9-(3-t-butyl-N inudazolvl)-methy1)-Minocycline H3C. N CH3 H3C.N CH3 H OH
H3C{N-N NHZ

To a stirred solution of 9-aminomethyl- minocycline (2.50 g, 4.14 mmol) in DMF (25 mL) and MeOH (15 mL) was added 1-bromopinacolone (1.34 mL, 1.01 g, 5.63 mmol) and Cs2CO3 (5.0 mL of a IN aqueous solution, 5.0 mmol). The reaction was heated to 100 C for 15 minutes in a pressure vesicle using microwave irradiation.
The contents were then diluted with water (1.0 L) and Na2CO3 was used to adjust the pH

to 6. This solution was then filtered through celite and loaded onto a plug of divinyl benzene resin. The product was washed with water (500 mL) before it was eluted with MeCN and reduced by rotary evaporation. The crude material was purified by reverse phase HPLC to give the tert-butyl-ketone intermediate (680 mg, 1.90 mmol, 50%
yield).
To a stirred solution of the tert-butyl-ketone intermediate (68 mg, 0.190 mmol) in formamide (1.0 mL) was added triethyl-amine (0.020 mL, 28 mg, 0.27 mmol) to adjust the pH to 8. The reaction was heated to 100 C for 5 minutes in a pressure vesicle using microwave irradiation. The contents were then diluted with water (100 mL) and TFA
was used to adjust the pH to 2. This solution was then filtered through celite, and loaded onto a plug of divinyl benzene resin. The product was washed with water (200 mL) before it was eluted with MeCN and reduced by rotary evaporation. The crude material was purified by reverse phase HPLC to give the final compound (6.0 mg, 10 mol, 4%
yield) LCMS m/z = 594.4863 (M +H).

Synthesis of 9-(2-thiol 5-methyl-N-imidazolyll-methyl Minocycline H3C.N.CH3 HaC,N.CH3 H H OH
~49XNH2 To a stirred solution of 9-am inomethyl-minocycline (2.00 g, 4.12 mmol) in DMF
(12 mL), MeOH (6.0 nL) and acetic acid (3.0 nL) was added KSCN (0.400 g, 4.12 mmol) and Acetol 0.400 mL, 0.370 g, 5.00 mmol). The reaction was heated to 100 C
for 15 minutes in a pressure vesicle using microwave irradiation. The contents were then diluted with water (1.0 L) and Na2CO3 was used to adjust the pH to 6.
This solution was then filtered through celite and loaded onto a plug of divinyl benzene resin.
The product was washed with water (500 mL) before it was eluted with MeCN and reduced by rotary evaporation. The crude material was purified by reverse phase HPLC
to give the final product (620 mg, 1.06 mmol, 26% yield) LCMS m/a = 584.3998 (M +
H).

Synthesis of 7-(2',2'-dimethyl-propyl)amino methyl Sanevcline H3C.N.CH3 OH O OHO O O
1 g of 7-aminomethyl-sancycline, 3 equivalents of trimethylacetaldehyde and one equivalent of indium trichloride were dissolved in 10 ml of DMF. The mixture was stirred at room temperature for 15 minutes. To this mixture was added 3 equivalents of sodium triacetoxyborohydride. The resulting reaction mixture was left stirring for several hours. The reaction was monitored by analytical HPLC. The LCMS showed MS: 514 which corresponds to the desired material. The product was isolated via preparative HPLC and the structure was confirmed by NMR
Synthesis of 9-Benzoimidazoly1l-Minoce H3C.N.CH3 H3C.N.CH3 H H OH
N~ I / _ I NH, NH OH O OH O

To a stirred solution of the trifluoroacetic acid (TFA) salt of 9-formyl minocycline (488 mg, 1.47 mmol) in DMF (3 mL) and MeOH (2 mL) was added 1,2-phenylenediamine (80 mg, 0.74 mmol). The reaction was heated to 50 C and was complete in 5 minutes. The contents were then diluted with water (500 mL) and TFA
was used to adjust the pH to 2. This solution was then filtered through celite, and loaded onto a plug of divinyl benzene resin. The plug containing the product was washed with water (300 mL) before it was eluted with MeCN and reduced by rotary evaporation.
The crude material was purified by reverse phase HPLC to give the Benzoimidazol product (100 mg, 0.175 mmol, 10% yield) LCMS m/z = 574.3637 (M + H).
Example 2: In vitro Minimum Inhibitory Concentration (NIIC) Assay The following assay is used to determine the efficacy of the tetracycline compounds against common bacteria. 2 mg of each compound is dissolved in 100 l of DMSO. The solution is then added to cation-adjusted Mueller Hinton broth (CAMHB), which results in a final compound concentration of 200 g per ml. The tetracycline compound solutions are diluted to 50 pL volumes, with a test compound concentration of .098 g/ml. Optical density (OD) determinations are made from fresh log-phase broth cultures of the test strains. Dilutions are made to achieve a final cell density of 1x106 CFU/ml. At OD=1, cell densities for different genera should be approximately:
E. coli - 1x109 CFU/ml S. aureus 5x10$ CFU/ml Enterococcus sp. 2.5x 109 CFU/ml 50 l of the cell suspensions are added to each well of microtiter plates.
The final cell density should be approximately 5x105 CFU/ml. These plates are incubated at 35 C in an ambient air incubator for approximately 18 hr. The plates are read with a microplate reader and are visually inspected when necessary . The MIC is defined as the lowest concentration of the tetracycline compound that inhibits growth.
EQUIVALENTS
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures described herein. Such equivalents are considered to be within the scope of the present invention and are covered by the following claims.
The appropriate components, processes, and methods of those patents, applications and other documents may be selected for the present invention and embodiments thereof.

Claims

1. A substituted tetracycline compound of Formula I:

wherein:
X is CHC(R13Y'Y), CR6'R6, S, NR6, or O;
R2, R2', R4', and R4" are each independently hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, hydroxyl, halogen, or hydrogen;
R2', R3, R10, R11 and R12 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy;
R6 and R6' are each independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is ethyl, perhalogenated alkenyl, substituted pyridinyl, pyrazinyl, furanyl, or pyrazolyl;
R8 is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R9 -CH2NR9a R9b;
R9a and R9b are each independently hydrogen, alkyl, alkenyl or linked to form a heterocycle;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl; and Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts thereof.

2. The tetracycline compound of claim 1, wherein X is CR6R6'; R2, R2', R6, R6', R8, R10, R11, and R12 are each hydrogen; R4 is NR4'R4"; R4' and R4" are lower alkyl;
and R5 is hydroxy or hydrogen.

3. The tetracycline compound of claim 2, wherein R4' and R4" are each methyl and R5 is hydrogen.

4. The tetracycline compound of any one of claims 1-3, wherein R7 is ethyl and R9a is alkyl and R9b is alkenyl.

5. The tetracycline compound of any one of claims 1-3, wherein R7 is substituted pyrazinyl.

6. The tetracycline compound of claim 5, wherein R7 is substituted with a fluorine.

7. The tetracycline compound of claim 5 or 6, wherein R9a is alkyl and R9b is alkenyl.

8. The tetracycline compound of claim 5 or 6, wherein R9a and R9b are linked to form a heterocycle.

9. The tetracycline compound of claim 5 or 6, wherein R9a is hydrogen and R9b is alkyl.

10. The tetracycline compound of anyone of claims 1-3, wherein R7 is furanyl, and R9a is hydrogen or alkyl and R9b is alkenyl.

11. The tetracycline compound of any one of claims 1-3, wherein R7 is 1, 2, 2-trifluoroethenyl.

12. The tetracyline compound of claim 11, wherein R9a is hydrogen or alkyl and R9b is alkenyl.

13. The tetracycline compound of any one of claims 1-3, wherein R7 is pyrazolyl and R9a is hydrogen or alkyl and R9b is alkenyl or alkyl.

14. A tetracycline compound selected from the group consisting of:
and pharmaceutically acceptable salts, esters, and prodrugs thereof.

15. A tetracycline compound of formula III:

wherein:
X is CHC(R13Y'Y), CR6'R6, C=CR6'R6, S, NR6, or O;
R2, R2', R4', and R4" are each independently hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, R10, R11 and R12 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy;
R6 and R6' are each independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is substituted or unsubstituted pyrazolyl, furanyl, thiophenyl, thiazolyl, aminoalkyl substituted phenyl;
R8 is hydrogen, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R9 is hydrogen;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl; and Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts thereof.

16. The tetracycline compound of claim 15, wherein R4 is NR4'R4"; X is CR6R6', R2, R2', R5, R6, R6', R8, R10, R11, and R12 are each hydrogen; and, R4', and R4 are each methyl.

17. The tetracycline compound of claim 15, wherein R7 is phenyl substituted with -CH2- N(CH3)2, -CH2-NH-CH(CH3)2, -CH2-N(CH3)-CH(CH3)2, -CH2-N-piperdinyl), -CH3, -CH2-NH-cyclopropyl, CH2-NH-t-butyl, -CH2-N(CH3)-benzyl, -CH2-N(CH3)-CH2-CH=CH2, CH2-NH-(CH2)2-CF3, CH2-NH-CH2-C(=O)-NH2, or -CH2-NH-cyclohexyl.

18. The tetracycline compound of claim 17, wherein said phenyl is further substituted with a fluorine, methoxy, or alkyl group.

19. The tetracycline compound of claim 15, wherein R7 is substituted furanyl.

20. The tetracycline compound of claim 19, wherein said furanyl is substituted with an aminoalkyl moiety.

21. The tetracycline compound of claim 15, wherein R7 is substituted or unsustituted thiophenyl.

22. The tetracycline compound of claim 15, wherein R7 is substituted pyridinyl.

23. The tetracycline compound of claim 15, wherein said compound is:

24. A tetracycline compound is of formula IV:

wherein:
X is CHC(R13Y'Y), CR6'R6, S, NR6, or O;
R2, R4', R4", R7' and R7" are each hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, R10, R11 and R12 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy;
R6 and R6' are independently hydrogen, methylene, absent, hydroxyl, halogen, thiol, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
R7 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)0-3 (NR7c)0-1C(=W')WR7a;
R8 is an aminomethyl substituted phenyl or substituted pyridinyl;
R9 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)0-3NR9c C(=Z')ZR9a;

R7a, R7b, R7c, R 7d, R7e, R7f, R9a, R9b, R9c, R9a, R9e, and R9f are each independently absent, hydrogen, acyl, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
Z is CR9d R9e, S, NR9b or O;
Z is O, NR9f, or S;
W is CR7d R7e, S, O or NR7b;
W' is O, NR7f, or S;
R13 is hydrogen, hydroxy, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl;
Y' and Y are each independently hydrogen, halogen, hydroxyl, cyano, sulfhydryl, amino, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, or an arylalkyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.

25. The tetracycline compound of claim 24, wherein X is CR6R6'; R2, R2', R6, R6', R8, R10, R11, and R12 are each hydrogen; R4 is NR4'R4"; R4' and R4" are lower alkyl;
and R5 is hydroxy or hydrogen.

26. The tetracycline compound of claim 25, wherein said substituted tetracycline compound is:

27. A tetracycline compound of the formula V:

wherein:

R2, R4', R4", R" and R7" are each hydrogen, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
R4 is NR4'R4", alkyl, alkenyl, alkynyl, aryl, hydroxyl, halogen, or hydrogen;
R2', R3, R10, R11 and R12 are each hydrogen or a pro-drug moiety;
R5 is hydroxyl, hydrogen, thiol, alkanoyl, aroyl, alkaroyl, aryl, heteroaromatic, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, alkyl carbonyloxy, or aryl carbonyloxy;
R7 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)0-3 (NR7c)0-1C(=W')WR7a;
R8 is substituted phenyl or substituted pyridinyl;
R9 is hydrogen, hydroxyl, halogen, thiol, nitro, alkyl, alkenyl, alkynyl, aryl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, arylalkyl, amino, arylalkenyl, arylalkynyl, acyl, aminoalkyl, heterocyclic, thionitroso, or -(CH2)0-3NR9c C(=Z')ZR9a;
R7a, R7b, R7c, R7d, R7e, R7f, R9a, R9b, R9c, R9d, R9e, and R8f are each independently absent, hydrogen, acyl, alkyl, alkenyl, alkynyl, alkoxy, alkylthio, alkylsulfinyl, alkylsulfonyl, alkylamino, arylalkyl, aryl, heterocyclic, heteroaromatic or a prodrug moiety;
W is CR7d R7e, S, O or NR7b;
W' is O, NR7f, or S;
R13 is 4-alkyl substituted phenyl, and pharmaceutically acceptable salts, esters and prodrugs thereof.

28. The tetracycline compound of claim 27, wherein said tetracycline compound is:

29. A method for treating a tetracycline responsive state in a subject, comprising administering to said subject an effective amount of a tetracycline compound of any one of claims 1, 14, 15, 23, 24, and 27, such that said subject is treated.

30. The method of claim 29, wherein said tetracycline responsive state is a bacterial infection, a viral infection, or a parasitic infection.

31. The method of claim 30, wherein said bacterial infection is associated with E. coli.

32. The method of claim 30, wherein said bacterial infection is associated with S. aureus.

33. The method of claim 30, wherein said bacterial infection is associated with E. faecalis.

34. The method of claim 29, wherein said bacterial infection is resistant to other tetracycline antibiotics.

35. The method of claim 29, wherein said tetracycline associated state is malaria.

36. The method of claim 29, wherein said subject is a human.

37. The method of anyone of claims 29, wherein said tetracycline compound is administered with a pharmaceutically acceptable carrier.

38. A pharmaceutical composition comprising a therapeutically effective amount of a tetracycline compound of any one of claims 1, 14, 15, 23, 24, and 27 and a pharmaceutically acceptable carrier.