WO2012047907A1

WO2012047907A1 - Synthesis of c5-substituted tetracyclines, uses thereof, and intermediates thereto

Info

Publication number: WO2012047907A1
Application number: PCT/US2011/054791
Authority: WO
Inventors: Andrew G. Myers; Peter M. Wright; Evan Hecker
Original assignee: President And Fellows Of Harvard College
Priority date: 2010-10-04
Filing date: 2011-10-04
Publication date: 2012-04-12
Also published as: WO2012047907A9

Abstract

The tetracycline class of antibiotics has played a major role in the treatment of infectious diseases for the past 50 years. However, the increased use of the tetracyclines in human and veterinary medicine has led to resistance among many organisms previously susceptible to tetracycline antibiotics. The recent development of a modular synthesis of tetracycline analogs through a chiral enone intermediate has allowed for the efficient synthesis of novel tetracycline analogs never prepared before. The present invention provides more efficient routes for preparing the enone intermediate and allows for a wide variety of substituents at position 5 of the tetracycline ring system.

Description

SYNTHESIS OF C5-SUBSTITUTED TETRACYCLINES,

USES THEREOF, AND INTERMEDIATES THERETO

Government Support

[0001] This invention was made with Government support under grant AI048825 awarded by the National Institutes of Health. The Government has certain rights in the invention.

Background of the Invention

[0002] The tetracyclines are broad spectrum antimicrobial agents that are widely used in human and veterinary medicine (Schappinger et al., "Tetracyclines: Antibiotic Action, Uptake, and Resistance Mechanisms" Arch. Microbiol. 165:359-69, 1996; Mitscher, Medicinal Research Series, Vol. 9, The Chemistry of the Tetracycline Antibiotics, Marcel Dekker Inc. New York, 1978). The tetracyclines are broad spectrum antimicrobial agents that are widely used in human and veterinary medicine. The primary tetracyclines of clinical importance today include tetracycline (Boothe et ah, J. Am. Chem. Soc. 75:4621, 1953), oxytetracycline (Terramycin™) (Finlay et ah, Science 111:85, 1950), (-)-doxycycline (Stephens et ah, J. Am. Chem. Soc. 85:2643, 1963), (-) -minocycline (Martell et ah, J. Med. Chem. 10:44, 1967; Martell et al, J. Med. Chem. 10:359, 1967), and tigecycline. The tetracyclines exert their antimicrobial activity by inhibition of bacterial protein synthesis (Bentley and O'Hanlon, Eds., Anti-Infectives: Recent Advances in Chemistry and Structure- Activity Relationships The Royal Society of Chemistry: Cambridge, UK, 1997). Most tetracyclines are bacteriostatic rather than bactericidal (Rasmussen et al., Antimicrob. Agents Chemother. 35:2306-11, 1991; Primrose and Wardlaw, Ed. "The Bacteriostatic and

Bacteriocidal Action of Antibiotics" Sourcebook of Experiments for the Teaching of

Microbiology Society for General Microbiology, Academic Press Ltd., London, 1982). It has been proposed that after tetracycline passes through the cytoplasmic membrane of a bacterium it chelates Mg⁺², and this tetracycline-Mg⁺² complex binds the 30S subunit of the bacterial ribosome (Goldman et al., Biochemistry 22:359-368, 1983). Binding of the complex to the ribosome inhibits the binding of aminoacyl-tRNAs, resulting in inhibition of protein synthesis (Wissmann et al., Forum Mikrobiol. 292-99, 1998; Epe et al., EMBO J. 3: 121-26, 1984).

Tetracycline

[0003] Structure-activity relationships for the tetracycline antibiotics have been determined empirically from 50 years of semi-synthetic modification of the parent structure (Sum et al. , Curr. Pharm. Design 4: 119-32, 1998). Permutations of the upper left-hand portion of the natural product, also known as the hydrophobic domain, have provided new therapeutically active agents, while modifications of the polar hydrophobic domain result in a loss of activity. However, semi- synthesis by its very nature has limited the number of tetracycline analogs that can be prepared and studied.

Tetracycline

[0004] Recently, a novel convergent synthetic route to tetracyclines and various analogs, including pentacycline and heterocycle-containing tetracyclines, has been developed by Myers and co-workers. See PCT Application WO 2005/112945, published December 1, 2005; incorporated herein by reference; and Charest et al., Science, 308:395-398, 15 April 2005; Charest et al., J. Am. Chem. Soc. 127:8292-93, 2005. This route proceeds through the highly functionalized chiral enone intermediate (A) which is prepared starting from benzoic acid in ten steps (11 % yield, >95 ee). See Charest et al, Science 308:395-398, April 15, 2005; Charest et al, J. Am. Chem. Soc. 127:8292-8293, 2005; Myers et al, Org. Lett.

3(18):2923-26, 2001. A second generation route to the enone intermediate was later developed starting from an isoxazole aldehyde. The second generation route yields the highly functionalized chiral enone in eight steps in an improved yield. See PCT Application WO2008/127361, published October 23, 2008, incorporated herein by reference.

A

[0005] Several approaches were developed to form the tetracycline core ring system from enone. For example, one approach involves the reaction of an enone with an anion formed by the deprotonation of a toluate or metallation of a benzylic halide. Other approaches involve reacting the enone in a Diels- Alder type reaction with a diene or benzocyclobutenol. In each of these approaches, the chiral enone provides the functionalized A and B rings of the tetracycline core, and the D-ring is derived from a toluate, benzylic halide, diene or benzocyclobutenol. In bringing the two portions of the tetracycline core together the C-ring is formed, preferably in a stereoselective manner. These new synthetic approaches to tetracycline analogs not only allow for the stereoselective and efficient synthesis of a wide variety of tetracycline analogs never before prepared, but they also allow for preparation of tetracycline analogs in which the D-ring is replaced with a heterocycle, 5- membered ring, or other ring systems. The new methodologies also allow for the prepartion of various pentacyclines or higher cyclines containing aromatic and non-aromatic carbocycles and heterocycles. See PCT Application WO 2005/112985, published December 1, 2005; PCT Application WO 2007/117639, published October 18, 2007; and PCT Application WO 2008/127361, published October 23, 2008; each of which is incorporated herein by reference.

[0006] Although the above approaches to tetracycline analogs are much more efficient than earlier approaches and allow for synthetic variability, there remains a need for improving the efficiency and versatility of these routes to new tetracycline analogs.

Summary of the Invention

[0007] The present invention provides C5-tetracycline analogs of the formula (I):

(I)

or pharmaceutically acceptable salts thereof, wherein R₃ is hydrogen and R₄ is a group other than hydrogen to provide beta C5-analogs, or R₄ is hydrogen and R₃ is a group other than hydrogen to provide alpha C5-analogs, and wherein n, R_P1, R_P2, Rp₃, Rp₄, Ri, R₂, R5, R₆, R7, R8, R9, Rio, and Rn, are as described herein.

[0008] For example, in one aspect, provided are alpha C5-tetracycline analogs of the formula (I-b23):

(I-b23)

or pharmaceutically acceptable salts thereof, wherein n, Rpi, Rp₂, Rp₃, RD, R₃, and R₇, are as described herein.

[0009] In another aspect, provided are beta C5-tetracycline analogs of the formula (I- a23):

(I-a23)

or pharmaceutically acceptable salts thereof, wherein n, Rpi, Rp₂, Rp₃, RD, R₄ and R₇, are as described herein. [0010] In yet another aspect, provided are C5-tetracycline analogs of the formula (I- t):

(I-t)

or pharmaceutically acceptable salts thereof, wherein R₃, R4 and R₇, are as described herein.

[0011] Also provided are C5-substituted intermediates useful in the synthesis of compounds of formula (I), e.g., compounds of formulae (II) and (IV):

(II) (IV)

or pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, Rp₄, Ri, R₂, R₃, R₄, R5, R₆, R₇, R8, R9, Rio, and R_{11 ;} are as described herein.

[0012] In certain embodiments, provided is an alpha C5- substituted enone of the formula (II-x-i):

(II-x-i)

or pharmaceutically acceptable salts thereof, wherein Rp₄, R₃ and RD are as described herein.

[0013] In certain embodiments, provided is a beta C5- substituted enone of the formula (II-y-i):

(II-y-i)

or pharmaceutically acceptable salts thereof, wherein R_P4, R₄ and R_D are as described herein.

[0014] In certain embodiments, provided is an alpha C5-pentacycline isoxazole of the formula (IV-b23):

(IV-b23)

or pharmaceutically acceptable salts thereof, wherein n, Rp_1; Rp₄, R₃, R₇, and R_D, are as described herein.

[0015] In certain embodiments, provided is a beta C5-pentacycline isoxazole of the formula (IV-a23):

(IV-a23)

or pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P4, R₄, R₇, and R_D, are as described herein.

[0016] Also provided are methods of preparing compounds of formula (II). For example, in one aspect, provided is a method of preparing a compound of formula (II-x):

(II-x)

or a salt thereof, from a compound of formula (III):

(III)

or a salt thereof, the method comprising reacting an electrophile with a compound of formula (III) to provide a compound of formula (II-x); wherein R_P4, R_P5, R₃, R4, R5, R₉, R₁₀, and R_{11 ;} are as described herein.

[0017] In one embodiment, provided is a method of preparing a compound of the formula (II-c):

(II-c)

or a salt thereof, from a compound of formula (III):

(III)

or a salt thereof, the method comprising:

(i) reacting the compound of formula (III) with an electrophilic halogenating reagent to provide a compound of formula (Il-a):

(Il-a)

or a salt thereof;

(ii) reacting a compound of formula (Il-a) with a hydroxide reagent to provide a compound of formula (Il-b):

(Il-b)

or a salt thereof, wherein R_B is hydrogen; and

(iii) reacting a compound of formula (Il-b) with a nucleophilic fluorinating reagent to provide a compound of formula (II-c); wherein R_P4, R_P5, Hal, R_B, R5, R9, Rio, and Rn, are as described herein.

[0018] Other embodiments of C5-tetracycline analogs of formula (I), and

intermediates thereto (e.g., compounds of formula (II) and (IV)), pharmaceutical compositions thereof, and methods of their preparation and use are described in more detail herein.

Definitions

[0019] Definitions of specific functional groups and chemical terms are described in more detail below. For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75^th Ed., inside cover, and specific functional groups are generally defined as described therein. Additionally, general principles of organic chemistry, as well as specific functional moieties and reactivity, are described in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito: 1999; Strategic Applications of Named Reactions in Organic Synthesis, Laszlo Kurti and Barbara Czako, Academic Press, 1^st edition: March 18, 2005; Comprehensive Organic Transformations: A Guide to Functional Group Preparations, Richard C. Larock, Wiley- VCH, 2^nd edition: November 3, 1999; Name Reactions of

Functional Group Transformations, Comprehensive Name Reactions, Jie Jack Li and E.J. Corey, Wiley: July 16, 2007; Greene 's Protective Groups in Organic Synthesis, Peter G.M. Wuts and Theodora W. Greene, Wiley-Interscience, 4^th edition: October 30, 2006; and March' s Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, Michael B. Smith and Jerry March, Wiley-Interscience, 6^th edition: January 16, 2007, the entire contents of which are incorporated herein by reference.

[0020] It should be understood that any atom described herein includes all isotope forms of that atom. For example, -H may be - 1 H, -2 H (-D), - 3 H, etc. Accordingly, the structures described herein include all isotopologues thereof.

[0021] Certain compounds of the present invention may exist in particular geometric or stereoisomeric forms. The present invention contemplates all such compounds, including cis- and inms-isomers, R- and S-enantiomers, diastereomers, (D)-isomers, (L)-isomers, the racemic mixtures thereof, and other mixtures thereof, as falling within the scope of the invention. Additional asymmetric carbon atoms may be present in a substituent such as an alkyl group. All such isomers, as well as mixtures thereof, are intended to be included in this invention.

[0022] Isomeric mixtures containing any of a variety of isomer ratios may be utilized in accordance with the present invention. For example, where only two isomers are combined, mixtures containing 50:50, 60:40, 70:30, 80:20, 90: 10, 95:5, 96:4, 97:3, 98:2, 99: 1, or 100:0 isomer ratios are all contemplated by the present invention. Those of ordinary skill in the art will readily appreciate that analogous ratios are contemplated for more complex isomer mixtures.

[0023] If, for instance, a particular enantiomer of a compound of the present invention is desired, it may be prepared by asymmetric synthesis, or by derivation with a chiral auxiliary, where the resulting diastereomeric mixture is separated and the auxiliary group cleaved to provide the pure desired enantiomers. Alternatively, where the molecule contains a basic functional group, such as amino, or an acidic functional group, such as carboxyl, diastereomeric salts are formed with an appropriate optically- active acid or base, followed by resolution of the diastereomers thus formed by fractional crystallization or chromatographic means well known in the art, and subsequent recovery of the pure enantiomers. [0024] The term "diastereomerically enriched" as used herein refers to a particular synthetic mixture wherein one of at least two diastereomers is generated in preference to the other, i.e., wherein the percent by weight of one diastereomer is greater than the percent by weight of the other diastereomer. For example, a diastereomerically enriched preparation of a particular diastereomer means a preparation of the compound having greater than 50% by weight of one diastereomer relative to another diastereomer, more preferably at least 75% by weight, and even more preferably at least 80% by weight. In some embodiments, the enrichment can be much greater than 80% by weight, providing a "substantially diastereomerically enriched" preparation, which refers to preparations of compositions which have at least 85% by weight of one diastereomer relative to other diastereomer, more preferably at least 90% by weight, and even more preferably at least 95% by weight. In certain embodiments, the enrichment is greater than 99% by weight, providing a "diastereomerically pure" preparation.

[0025] One of ordinary skill in the art will appreciate that the synthetic methods, as described herein, utilize a variety of protecting groups. By the term "protecting group", as used herein, it is meant that a particular functional moiety, e.g., O, S, or N, is temporarily blocked so that a reaction can be carried out selectively at another reactive site in a multifunctional compound. In preferred embodiments, a protecting group reacts selectively in good yield to give a protected substrate that is stable to the projected reactions; the protecting group should be selectively removable in good yield by readily available, preferably non-toxic reagents that do not attack the other functional groups; the protecting group forms an easily separable derivative (more preferably without the generation of new stereogenic centers); and the protecting group has a minimum of additional functionality to avoid further sites of reaction. As used herein, "protecting groups" refers to oxygen, sulfur, nitrogen, and carbon protecting groups.

[0026] "Hydroxyl protecting groups", "hydroxy protecting groups" and "oxygen protecting groups" as used herein refer to methyl, methoxylmethyl (MOM),

methylthiomethyl (MTM), t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM), benzyloxymethyl (BOM), /?-methoxybenzyloxymethyl (PMBM), (4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM), i-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl, 2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl, bis(2- chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR), tetrahydropyranyl (THP), 3- bromotetrahydropyranyl, tetrahydrothiopyranyl, 1-methoxycyclohexyl, 4- methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl, 4- methoxytetrahydrothiopyranyl S,S-dioxide, 1 - [(2-chloro-4-methyl)phenyl] -4- methoxypiperidin-4-yl (CTMP), l,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl, 2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl, 1-ethoxyethyl, 1- (2-chloroethoxy)ethyl, 1 -methyl- 1-methoxyethyl, 1 -methyl- 1-benzyloxyethyl, 1 -methyl- 1- benzyloxy-2-fluoroethyl, 2,2,2-trichloroethyl, 2-trimethylsilylethyl, 2-(phenylselenyl)ethyl, t- butyl, allyl, /7-chlorophenyl, /7-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), /?- methoxybenzyl, 3,4-dimethoxybenzyl, o-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6- dichlorobenzyl, p-cyanobenzyl, p-phenylbenzyl, 2-picolyl, 4-picolyl, 3-methyl-2-picolyl N- oxido, diphenylmethyl, p,p '-dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl, a- naphthyldiphenylmethyl, p-methoxyphenyldiphenylmethyl, di(p- methoxyphenyl)phenylmethyl, tri(p-methoxyphenyl)methyl, 4-(4'- bromophenacyloxyphenyl)diphenylmethyl, 4,4',4"-tris(4,5- dichlorophthalimidophenyl)methyl, 4,4',4"-tris(levulinoyloxyphenyl)methyl, 4,4',4"- tris(benzoyloxyphenyl)methyl, 3-(imidazol-l-yl)bis(4',4"-dimethoxyphenyl)methyl, 1, 1- bis(4-methoxyphenyl)- -pyrenylmethyl, 9-anthryl, 9-(9-phenyl)xanthenyl, 9-(9-phenyl-10- oxo)anthryl, l,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido, trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl (TIPS), dimethylisopropylsilyl (IPDMS),

diethylisopropylsilyl (DEIPS), dimethylthexylsilyl, i-butyldimethylsilyl (TBDMS), t- butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-/?-xylylsilyl, triphenylsilyl,

diphenylmethylsilyl (DPMS), i-butylmethoxyphenylsilyl (TBMPS), formate, benzoylformate, acetate, chloroacetate, dichloroacetate, trichloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, phenoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate, 4- oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate (levulinoyldithioacetal), pivaloate, adamantoate, crotonate, 4-methoxycrotonate, benzoate, /?-phenylbenzoate, 2,4,6- trimethylbenzoate (mesitoate), alkyl methyl carbonate, 9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl 2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl carbonate (TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec), 2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl carbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkyl p-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate, alkyl onitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkyl S-benzyl thiocarbonate, 4-ethoxy- l-napththyl carbonate, methyl

dithiocarbonate, 2-iodobenzoate, 4-azidobutyrate, 4-nitro-4-methylpentanoate, o- (dibromomethyl)benzoate, 2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl, 4- (methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate, 2,6-dichloro-4- methylphenoxyacetate, 2,6-dichloro-4-(l,l,3,3-tetramethylbutyl)phenoxyacetate, 2,4-bis(l,l- dimethylpropyl)phenoxyacetate, chlorodiphenylacetate, isobutyrate, monosuccinoate, (E)-2- methyl-2-butenoate, o(methoxycarbonyl)benzoate, a-naphthoate, nitrate, alkyl Ν,Ν,Ν',Ν'- tetramethylphosphorodiamidate, alkyl N-phenylcarbamate, borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate, sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate (Ts).

[0027] Other "oxygen protecting groups", i.e., for protecting 1,2- or 1,3-diols, include methylene acetal, ethylidene acetal, 1-i-butylethylidene ketal, 1-phenylethylidene ketal, (4- methoxyphenyl)ethylidene acetal, 2,2,2-trichloroethylidene acetal, acetonide,

cyclopentylidene ketal, cyclohexylidene ketal, cycloheptylidene ketal, benzylidene acetal, p- methoxybenzylidene acetal, 2,4-dimethoxybenzylidene ketal, 3,4-dimethoxybenzylidene acetal, 2-nitrobenzylidene acetal, methoxymethylene acetal, ethoxymethylene acetal, dimethoxymethylene ortho ester, 1-methoxyethylidene ortho ester, 1-ethoxyethylidine ortho ester, 1,2-dimethoxyethylidene ortho ester, a-methoxybenzylidene ortho ester, l-(N,N- dimethylamino)ethylidene derivative, a-(N,N'-dimethylamino)benzylidene derivative, 2- oxacyclopentylidene ortho ester, di-i-butylsilylene group (DTBS), 1,3-(1, 1,3,3- tetraisopropyldisiloxanylidene) derivative (TIPDS), tetra-i-butoxydisiloxane-l,3-diylidene derivative (TBDS), cyclic carbonates, cyclic boronates, ethyl boronate, and phenyl boronate.

[0028] "Amino-protecting groups" or "nitrogen protecting groups" include methyl carbamate, ethyl carbamante, 9-fluorenylmethyl carbamate (Fmoc), 9-(2- sulfo)fluorenylmethyl carbamate, 9-(2,7-dibromo)fluoroenylmethyl carbamate, 2,7-di-i-butyl- [9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl carbamate (DBD-Tmoc), 4- methoxyphenacyl carbamate (Phenoc), 2,2,2-trichloroethyl carbamate (Troc), 2- trimethylsilylethyl carbamate (Teoc), 2-phenylethyl carbamate (hZ), 1 -(1-adamantyl)- 1- methylethyl carbamate (Adpoc), l,l-dimethyl-2-haloethyl carbamate, l,l-dimethyl-2,2- dibromoethyl carbamate (DB-i-BOC), l,l-dimethyl-2,2,2-trichloroethyl carbamate

(TCBOC), 1 -methyl- l-(4-biphenylyl)ethyl carbamate (Bpoc), l-(3,5-di-i-butylphenyl)-l- methylethyl carbamate (i-Bumeoc), 2-(2'- and 4'-pyridyl)ethyl carbamate (Pyoc), 2-(N,N- dicyclohexylcarboxamido)ethyl carbamate, i-butyl carbamate (BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl carbamate (Alloc), 1-isopropylallyl carbamate (Ipaoc), cinnamyl carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl carbamate, N- hydroxypiperidinyl carbamate, alkyldithio carbamate, benzyl carbamate (Cbz), p- methoxybenzyl carbamate (Moz), p-nitobenzyl carbamate, p-bromobenzyl carbamate, p- chlorobenzyl carbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzyl carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl carbamate, 2-(p-toluenesulfonyl)ethyl carbamate, [2-(l,3- dithianyl)] methyl carbamate (Dmoc), 4-methylthiophenyl carbamate (Mtpc), 2,4- dimethylthiophenyl carbamate (Bmpc), 2-phosphonioethyl carbamate (Peoc), 2- triphenylphosphonioisopropyl carbamate (Ppoc), l,l-dimethyl-2-cyanoethyl carbamate, m- chloro-/?-acyloxybenzyl carbamate, /?-(dihydroxyboryl)benzyl carbamate, 5- benzisoxazolylmethyl carbamate, 2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc), m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate, onitrobenzyl carbamate, 3,4- dimethoxy-6-nitrobenzyl carbamate, phenyl(onitrophenyl)methyl carbamate, phenothiazinyl- (lO)-carbonyl derivative, N'-/?-toluenesulfonylaminocarbonyl derivative, N'- phenylaminothiocarbonyl derivative, i-amyl carbamate, S-benzyl thiocarbamate, p- cyanobenzyl carbamate, cyclobutyl carbamate, cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl carbamate, p-decyloxybenzyl carbamate, 2,2-dimethoxycarbonylvinyl carbamate, o-(N,N-dimethylcarboxamido)benzyl carbamate, l, l-dimethyl-3-(N,N- dimethylcarboxamido)propyl carbamate, 1, 1-dimethylpropynyl carbamate, di(2- pyridyl)methyl carbamate, 2-furanylmethyl carbamate, 2-iodoethyl carbamate, isoborynl carbamate, isobutyl carbamate, isonicotinyl carbamate, p-(p '-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl carbamate, 1-methylcyclohexyl carbamate, 1 -methyl- 1- cyclopropylmethyl carbamate, l-methyl-l-(3,5-dimethoxyphenyl)ethyl carbamate, 1-methyl- l-(p-phenylazophenyl)ethyl carbamate, 1 -methyl- 1-phenylethyl carbamate, 1 -methyl- 1- (4- pyridyl)ethyl carbamate, phenyl carbamate, /?-(phenylazo)benzyl carbamate, 2,4,6-tri-i- butylphenyl carbamate, 4-(trimethylammonium)benzyl carbamate, 2,4,6-trimethylbenzyl carbamate, formamide, acetamide, chloroacetamide, trichloroacetamide, trifluoroacetamide, phenylacetamide, 3-phenylpropanamide, picolinamide, 3-pyridylcarboxamide, N- benzoylphenylalanyl derivative, benzamide, p-phenylbenzamide, o-nitophenylacetamide, o- nitrophenoxyacetamide, acetoacetamide, (N'-dithiobenzyloxycarbonylamino)acetamide, 3-(p- hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide, 2-methyl-2-(o- nitrophenoxy)propanamide, 2-methyl-2-(o-phenylazophenoxy)propanamide, 4- chlorobutanamide, 3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethionine derivative, onitrobenzamide, o-(benzoyloxymethyl)benzamide, 4,5-diphenyl-3-oxazolin-2- one, N-phthalimide, N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide, N-2,5- dimethylpyrrole, N-l,l,4,4-tetramethyldisilylazacyclopentane adduct (STABASE), 5- substituted l,3-dimethyl-l,3,5-triazacyclohexan-2-one, 5-substituted 1,3-dibenzyl- 1,3,5- triazacyclohexan-2-one, 1-substituted 3,5-dinitro-4-pyridone, N-methylamine, N-allylamine, N-[2-(trimethylsilyl)ethoxy]methylamine (SEM), N-3-acetoxypropylamine, N-(l-isopropyl-4- nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary ammonium salts, N-benzylamine, N-di(4- methoxyphenyl)methylamine, N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr), N- [(4-methoxyphenyl)diphenylmethyl]amine (MMTr), N-9-phenylfluorenylamine (PhF), N-2,7- dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino (Fcm), N-2-picolylamino N'- oxide, N-l,l-dimethylthiomethyleneamine, N-benzylideneamine, N-p- methoxybenzylideneamine, N-diphenylmethyleneamine, N-[(2- pyridyl)mesityl] methyleneamine, N- (Ν',Ν' -dimethylaminomethylene)amine , Ν,Ν'- isopropylidenediamine, N-/?-nitrobenzylideneamine, N-salicylideneamine, N-5- chlorosalicylideneamine, N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamine, N- cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-l-cyclohexenyl)amine, N-borane derivative, N-diphenylborinic acid derivative, N- [phenyl (pentacarbonylchromium- or

tungsten)carbonyl] amine, N-copper chelate, N-zinc chelate, N-nitroamine, N-nitrosoamine, amine N-oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide (Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates, dibenzyl phosphoramidate, diphenyl phosphoramidate, benzenesulfenamide, onitrobenzenesulfenamide (Nps), 2,4- dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide, 2-nitro-4- methoxybenzenesulfenamide, triphenylmethylsulfenamide, 3-nitropyridinesulfenamide (Npys), /7-toluenesulfonamide (Ts), benzenesulfonamide, 2,3,6, -trimethyl-4- methoxybenzenesulfonamide (Mtr), 2,4,6-trimethoxybenzenesulfonamide (Mtb), 2,6- dimethyl-4-methoxybenzenesulfonamide (Pme), 2,3,5,6-tetramethyl-4- methoxybenzenesulfonamide (Mte), 4-methoxybenzenesulfonamide (Mbs), 2,4,6- trimethylbenzenesulfonamide (Mts), 2,6-dimethoxy-4-methylbenzenesulfonamide (iMds), 2,2,5,7, 8-pentamethylchroman-6-sulfonamide (Pmc), methanesulfonamide (Ms), β- trimethylsilylethanesulfonamide (SES), 9-anthracenesulfonamide, 4-(4',8'- dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS), benzylsulfonamide,

trifluoromethylsulfonamide, and phenacylsulfonamide..

[0029] Other exemplary protecting groups are detailed herein, however, it will be appreciated that the present invention is not intended to be limited to these protecting groups; rather, a variety of additional equivalent protecting groups can be readily identified using the above criteria and utilized in the method of the present invention. Additionally, a variety of protecting groups are described in Protective Groups in Organic Synthesis, Fourth Ed. Greene, T.W. and Wuts, P.G., Eds., John Wiley & Sons, New York: 2007, the entire contents of which are hereby incorporated by reference.

[0030] It will be appreciated that the compounds, as described herein, may be substituted with any number of substituents or functional moieties. In general, the term "substituted" whether preceded by the term "optionally" or not, and substituents contained in formulas of this invention, refer to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. When more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. As used herein, the term "substituted" is contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic substituents of organic compounds. For purposes of this invention, heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valencies of the heteroatoms. Furthermore, this invention is not intended to be limited in any manner by the permissible substituents of organic compounds. Combinations of substituents and variables envisioned by this invention are preferably those that result in the formation of stable compounds useful in the treatment, for example, of infectious diseases or proliferative disorders.

[0031] The term "stable", as used herein, preferably refers to compounds which possess stability sufficient to allow manufacture and which maintain the integrity of the compound for a sufficient period of time to be detected and preferably for a sufficient period of time to be useful for the purposes detailed herein.

[0032] When a range of values is listed, it is intended to encompass each value and sub-range within the range. For example "C^ alkyl" is intended to encompass, Q, C₂, C₃,

C₄, C₅, C₆, Ci_6, Ci_5, Ci^, Ci_₃, Ci-2, C₂-6, C₂_5, C-2-A, C₂_3, C₃_₆, C₃_₅, C₃^, C4-6, C₄_₅, and C5-6 alkyl.

[0033] The term "aliphatic", as used herein, includes both saturated and unsaturated, straight chain {i.e., unbranched), branched, acyclic, cyclic, or polycyclic aliphatic hydrocarbons, which are optionally substituted with one or more functional groups. As will be appreciated by one of ordinary skill in the art, "aliphatic" is intended herein to include, but is not limited to, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, and cycloalkynyl moieties. Thus, as used herein, the term "alkyl" includes straight, branched and cyclic alkyl groups. An analogous convention applies to other generic terms such as "alkenyl", "alkynyl", and the like. Furthermore, as used herein, the terms "alkyl", "alkenyl", "alkynyl", and the like encompass both substituted and unsubstituted groups. In certain embodiments, as used herein, "lower alkyl" is used to indicate those alkyl groups (cyclic, acyclic, substituted, unsubstituted, branched or unbranched) having 1-6 carbon atoms.

[0034] In certain embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-20 aliphatic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-4 carbon atoms. Illustrative aliphatic groups thus include, but are not limited to, for example, methyl, ethyl, n-propyl, isopropyl, cyclopropyl, -CH₂-cyclopropyl, vinyl, allyl, n-butyl, sec- butyl, isobutyl, tert-butyl, cyclobutyl, -CH₂-cyclobutyl, n-pentyl, sec-pentyl, isopentyl, tert- pentyl, cyclopentyl, -CH₂-cyclopentyl, n-hexyl, sec-hexyl, cyclohexyl, -CH₂-cyclohexyl moieties and the like, which again, may bear one or more substituents. Alkenyl groups include, but are not limited to, for example, ethenyl, propenyl, butenyl, l-methyl-2-buten-l- yl, and the like. Representative alkynyl groups include, but are not limited to, ethynyl, 2- propynyl (propargyl), 1-propynyl, and the like.

[0035] "Alkyl" refers to a radical of a straight-chain or branched saturated

hydrocarbon group having from 1 to 20 carbon atoms ("C^o alkyl"). In some embodiments, an alkyl group has 1 to 10 carbon atoms ("Q-io alkyl"). In some embodiments, an alkyl group has 1 to 9 carbon atoms ("Q-g alkyl"). In some embodiments, an alkyl group has 1 to 8 carbon atoms ("Ci-g alkyl"). In some embodiments, an alkyl group has 1 to 7 carbon atoms ("Ci-7 alkyl"). In some embodiments, an alkyl group has 1 to 6 carbon atoms ("Ci-6 alkyl"). In some embodiments, an alkyl group has 1 to 5 carbon atoms ("Q-s alkyl"). In some embodiments, an alkyl group has 1 to 4 carbon atoms ("C^ alkyl"). In some embodiments, an alkyl group has 1 to 3 carbon atoms ("C^ alkyl"). In some embodiments, an alkyl group has 1 to 2 carbon atoms ("Ci-₂ alkyl"). In some embodiments, an alkyl group has 1 carbon atom ("Ci alkyl"). In some embodiments, an alkyl group has 2 to 6 carbon atoms ("C₂-6 alkyl"). Examples of Q_6 alkyl groups include methyl (CO, ethyl (C₂), n-propyl (C₃), isopropyl (C₃), n-butyl (C₄), tert-butyl (C₄), sec-butyl (C₄), iso-butyl (C₄), n-pentyl (C₅), 3- pentanyl (C₅), amyl (C₅), neopentyl (C₅), 3-methyl-2-butanyl (C₅), tertiary amyl (C₅), and n- hexyl (C₆). Additional examples of alkyl groups include n-heptyl (C₇), n-octyl (C₈) and the like. Unless otherwise specified, each instance of an alkyl group is independently optionally substituted, i.e. , unsubstituted (an "unsubstituted alkyl") or substituted (a "substituted alkyl") with one or more substituents. In certain embodiments, the alkyl group is unsubstituted Ci-w alkyl (e.g., -CH₃). In certain embodiments, the alkyl group is substituted Ci-w alkyl.

[0036] "Perhaloalkyl" or "haloaliphatic" refers to a substituted alkyl group as defined herein wherein all of the hydrogen atoms are independently replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. In some embodiments, the alkyl moiety has 1 to 8 carbon atoms ("Ci-₈ perhaloalkyl"). In some embodiments, the alkyl moiety has 1 to 6 carbon atoms ("Ci_6 perhaloalkyl"). In some embodiments, the alkyl moiety has 1 to 4 carbon atoms ("C^ perhaloalkyl"). In some embodiments, the alkyl moiety has 1 to 3 carbon atoms ("Ci_₃ perhaloalkyl"). In some embodiments, the alkyl moiety has 1 to 2 carbon atoms ("C^ perhaloalkyl"). In some embodiments, all of the hydrogen atoms are replaced with fluoro. In some embodiments, all of the hydrogen atoms are replaced with chloro. Examples of perhaloalkyl groups include -CF₃, -CF₂CF₃, -CF₂CF₂CF₃, -CC1₃, -CFC1₂, -CF₂C1, and the like.

[0037] "Alkenyl" refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon double bonds, and no triple bonds ("C₂_₂o alkenyl"). In some embodiments, an alkenyl group has 2 to 10 carbon atoms ("C₂_io alkenyl"). In some embodiments, an alkenyl group has 2 to 9 carbon atoms ("C₂_9 alkenyl"). In some embodiments, an alkenyl group has 2 to 8 carbon atoms ("C₂_₈ alkenyl"). In some embodiments, an alkenyl group has 2 to 7 carbon atoms ("C₂_7 alkenyl"). In some embodiments, an alkenyl group has 2 to 6 carbon atoms ("C₂_₆ alkenyl"). In some embodiments, an alkenyl group has 2 to 5 carbon atoms ("C₂_₅ alkenyl"). In some embodiments, an alkenyl group has 2 to 4 carbon atoms ("C₂^ alkenyl"). In some embodiments, an alkenyl group has 2 to 3 carbon atoms ("C₂_₃ alkenyl"). In some embodiments, an alkenyl group has 2 carbon atoms ("C₂ alkenyl"). The one or more carbon-carbon double bonds can be internal (such as in 2-butenyl) or terminal (such as in 1- butenyl). Examples of C₂^ alkenyl groups include ethenyl (C₂), 1-propenyl (C₃), 2-propenyl (C₃), 1-butenyl (C₄), 2-butenyl (C₄), butadienyl (C₄), and the like. Examples of C2-6 alkenyl groups include the aforementioned C₂- alkenyl groups as well as pentenyl (C₅), pentadienyl (C₅), hexenyl (C₆), and the like. Additional examples of alkenyl include heptenyl (C₇), octenyl (C₈), octatrienyl (C₈), and the like. Unless otherwise specified, each instance of an alkenyl group is independently optionally substituted, i.e., unsubstituted (an "unsubstituted alkenyl") or substituted (a "substituted alkenyl") with one or more substituents. In certain embodiments, the alkenyl group is unsubstituted C₂_₁₀ alkenyl. In certain embodiments, the alkenyl group is substituted C2-10 alkenyl.

[0038] "Alkynyl" refers to a radical of a straight-chain or branched hydrocarbon group having from 2 to 20 carbon atoms, one or more carbon-carbon triple bonds, and optionally one or more double bonds ("C2-20 alkynyl"). In some embodiments, an alkynyl group has 2 to 10 carbon atoms ("C2-10 alkynyl"). In some embodiments, an alkynyl group has 2 to 9 carbon atoms ("C2-9 alkynyl"). In some embodiments, an alkynyl group has 2 to 8 carbon atoms ("C₂_₈ alkynyl"). In some embodiments, an alkynyl group has 2 to 7 carbon atoms ("C2-7 alkynyl"). In some embodiments, an alkynyl group has 2 to 6 carbon atoms ("C2-6 alkynyl"). In some embodiments, an alkynyl group has 2 to 5 carbon atoms ("C2-5 alkynyl"). In some embodiments, an alkynyl group has 2 to 4 carbon atoms ("C₂^ alkynyl"). In some embodiments, an alkynyl group has 2 to 3 carbon atoms ("C₂_₃ alkynyl"). In some embodiments, an alkynyl group has 2 carbon atoms ("C₂ alkynyl"). The one or more carbon- carbon triple bonds can be internal (such as in 2-butynyl) or terminal (such as in 1-butynyl). Examples of alkynyl groups include, without limitation, ethynyl (C₂), 1-propynyl (C₃), 2-propynyl (C₃), 1-butynyl (C₄), 2-butynyl (C₄), and the like. Examples of C2-6 alkenyl groups include the aforementioned

alkynyl groups as well as pentynyl (C₅), hexynyl (C₆), and the like. Additional examples of alkynyl include heptynyl (C₇), octynyl (C₈), and the like. Unless otherwise specified, each instance of an alkynyl group is independently optionally substituted, i.e., unsubstituted (an "unsubstituted alkynyl") or substituted (a "substituted alkynyl") with one or more substituents. In certain embodiments, the alkynyl group is unsubstituted C₂_₁₀ alkynyl. In certain embodiments, the alkynyl group is substituted C2-10 alkynyl.

[0039] The term "alkoxy" as used herein refers to an alkyl group, as previously defined, attached to the parent molecule through an oxygen atom. In certain embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-20 alipahtic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-4 aliphatic carbon atoms. Examples of alkoxy, include but are not limited to, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, tert-butoxy, neopentoxy, and n-hexoxy.

[0040] The term "thioalkyl" or "alkylthio" as used herein refers to an alkyl group, as previously defined, attached to the parent molecule through a sulfur atom. In certain embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-20 alipahtic carbon atoms. In certain other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-10 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-6 aliphatic carbon atoms. In yet other embodiments, the alkyl, alkenyl, and alkynyl groups contain 1-4 aliphatic carbon atoms. Examples of thioalkyl include, but are not limited to, methylthio, ethylthio, propylthio, isopropylthio, n- butylthio, and the like.

[0041] The term "alkylamino" refers to a group having the structure -NHR', wherein

R' is aliphatic, as defined herein. In certain embodiments, the aliphatic group contains 1-20 aliphatic carbon atoms. In certain other embodiments, the aliphatic group contains 1-10 aliphatic carbon atoms. In yet other embodiments, the aliphatic group employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the aliphatic group contains 1-6 aliphatic carbon atoms. In yet other embodiments, the aliphatic group contains 1-4 aliphatic carbon atoms. Examples of alkylamino groups include, but are not limited to, methylamino, ethylamino, n-propylamino, iso-propylamino, cyclopropylamino, n- butylamino, tert-butylamino, neopentylamino, n-pentylamino, hexylamino, cyclohexylamino, and the like.

[0042] The term "dialkylamino" refers to a group having the structure -NRR', wherein R and R' are each an aliphatic group, as defined herein. R and R' may be the same or different in an dialkyamino moiety. In certain embodiments, the aliphatic groups contains 1- 20 aliphatic carbon atoms. In certain other embodiments, the aliphatic groups contains 1-10 aliphatic carbon atoms. In yet other embodiments, the aliphatic groups employed in the invention contain 1-8 aliphatic carbon atoms. In still other embodiments, the aliphatic groups contains 1-6 aliphatic carbon atoms. In yet other embodiments, the aliphatic groups contains 1-4 aliphatic carbon atoms. Examples of dialkylamino groups include, but are not limited to, dimethylamino, methyl ethylamino, diethylamino, methylpropylamino, di(n-propyl)amino, di(iso-propyl)amino, di(cyclopropyl)amino, di(n-butyl)amino, di(tert-butyl)amino, di(neopentyl)amino, di(n-pentyl)amino, di(hexyl)amino, di(cyclohexyl)amino, and the like. In certain embodiments, R and R' are linked to form a cyclic structure (e.g. , to form a heterocycle group). The resulting cyclic structure may be aromatic or non-aromatic.

Examples of cyclic diaminoalkyl groups include, but are not limted to, aziridinyl, pyrrolidinyl, piperidinyl, morpholinyl, pyrrolyl, imidazolyl, 1,3,4-trianolyl, and tetrazolyl.

[0043] Some examples of substituents of the above-described aliphatic (and other) moieties of compounds of the invention include, but are not limited to aliphatic;

heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; -F; -CI; -Br; -I; -OH; -N₃; - N0₂; -CN; -CF₃; -CH₂CF₃; -CHC1₂; -CH₂OH; -CH₂OR_x; -CH₂R_X; -CH₂CH₂OH; -CH₂NH₂; - CH₂N(R_X)₂; =C(R_X)₂; -CH₂S0₂CH₃; -C(0)R_x; -C0₂(R_x); -OC(0)R_x; -OC0₂R_x; -OC(R_x)₃; - OCON(R_x)₂; -CON(R_x)₂; -NR_x(CO)R_x, -N(R_X)₂; -S(0)₂R_x; and -S(0)R_x; wherein each occurrence of R_x independently includes, but is not limited to, hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substituents are illustrated by the specific embodiments shown in the Examples that are described herein.

[0044] "Aryl" refers to a radical of a monocyclic or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring system (e.g., having 6, 10, or 14 π electrons shared in a cyclic array) having 6-14 ring carbon atoms and zero heteroatoms provided in the aromatic ring system ("C6-i₄ aryl"). In some embodiments, an aryl group has six ring carbon atoms ("C₆ aryl"; e.g., phenyl). In some embodiments, an aryl group has ten ring carbon atoms ("Cio aryl"; e.g., naphthyl such as 1-naphthyl and 2-naphthyl). In some embodiments, an aryl group has fourteen ring carbon atoms ("C₁₄ aryl"; e.g., anthracyl). "Aryl" also includes ring systems wherein the aryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the radical or point of attachment is on the aryl ring, and in such instances, the number of carbon atoms continue to designate the number of carbon atoms in the aryl ring system. Unless otherwise specified, each instance of an aryl group is independently optionally substituted, i.e., unsubstituted (an "unsubstituted aryl") or substituted (a "substituted aryl") with one or more substituents. In certain embodiments, the aryl group is unsubstituted Ce_₁₄ aryl. In certain embodiments, the aryl group is substituted C₆-i4 aryl.

[0045] As used herein, the term "aralkyl" or "arylalkyl" refers to an aryl group, as defined herein, attached to the parent molecule through an alphatic group as defined herein. Likewise, "aryloxy" refers to an aryl group, as defined herein, attached to an alkoxy group, wherein the oxygen atom of the alkoxy group is point of attachment to the parent molecule. "Arylthio" refers to an aryl group, as defined herein, attached to an alkylthio group, wherein the sulfur atom of the alkylthio group is point of attachment to the parent molecule.

[0046] "Heteroaryl" refers to a radical of a 5-10 membered monocyclic or bicyclic

4n+2 aromatic ring system {e.g., having 6 or 10 π electrons shared in a cyclic array) having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen and sulfur ("5-10 membered heteroaryl"). In heteroaryl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. Heteroaryl bicyclic ring systems can include one or more heteroatoms in one or both rings. "Heteroaryl" includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more carbocyclyl or heterocyclyl groups wherein the point of attachment is on the heteroaryl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heteroaryl ring system. "Heteroaryl" also includes ring systems wherein the heteroaryl ring, as defined above, is fused with one or more aryl groups wherein the point of attachment is either on the aryl or heteroaryl ring, and in such instances, the number of ring members designates the number of ring members in the fused (aryl/heteroaryl) ring system. Bicyclic heteroaryl groups wherein one ring does not contain a heteroatom {e.g., indolyl, quinolinyl, carbazolyl, and the like) the point of attachment can be on either ring, i.e., either the ring bearing a heteroatom {e.g., 2-indolyl) or the ring that does not contain a heteroatom {e.g., 5-indolyl).

[0047] In some embodiments, a heteroaryl group is a 5-10 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-10 membered heteroaryl"). In some embodiments, a heteroaryl group is a 5-8 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heteroaryl"). In some embodiments, a heteroaryl group is a 5-6 membered aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring system, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heteroaryl"). In some embodiments, the 5-6 membered heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heteroaryl has 1 ring heteroatom selected from nitrogen, oxygen, and sulfur. Unless otherwise specified, each instance of a heteroaryl group is independently optionally substituted, i.e., unsubstituted (an "unsubstituted heteroaryl") or substituted (a "substituted heteroaryl") with one or more substituents. In certain embodiments, the heteroaryl group is unsubstituted 5-14 membered heteroaryl. In certain embodiments, the heteroaryl group is substituted 5-14 membered heteroaryl.

[0048] Exemplary 5-membered heteroaryl groups containing one heteroatom include, without limitation, pyrrolyl, furanyl and thiophenyl. Exemplary 5-membered heteroaryl groups containing two heteroatoms include, without limitation, imidazolyl, pyrazolyl, oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary 5-membered heteroaryl groups containing three heteroatoms include, without limitation, triazolyl, oxadiazolyl, and thiadiazolyl. Exemplary 5-membered heteroaryl groups containing four heteroatoms include, without limitation, tetrazolyl. Exemplary 6-membered heteroaryl groups containing one heteroatom include, without limitation, pyridinyl. Exemplary 6-membered heteroaryl groups containing two heteroatoms include, without limitation, pyridazinyl, pyrimidinyl, and pyrazinyl. Exemplary 6-membered heteroaryl groups containing three or four heteroatoms include, without limitation, triazinyl and tetrazinyl, respectively. Exemplary 7-membered heteroaryl groups containing one heteroatom include, without limitation, azepinyl, oxepinyl, and thiepinyl. Exemplary 5,6-bicyclic heteroaryl groups include, without limitation, indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl, isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl, benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl, benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl. Exemplary 6,6- bicyclic heteroaryl groups include, without limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl, cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. [0049] As used herein, the term "heteroaralkyl" or "heteroarylalkyl" refers to a heteroaryl group, as defined herein, attached to the parent molecule through an alphatic group as defined herein. Likewise, "heteroaryloxy" refers to a heteroaryl group, as defined herein, attached to an alkoxy group, wherein the oxygen atom of the alkoxy group is point of attachment to the parent molecule. "Heteroarylthio" refers to a heteroaryl group, as defined herein, attached to an alkylthio group, wherein the sulfur atom of the alkylthio group is point of attachment to the parent molecule.

[0050] It will be appreciated that aryl and heteroaryl groups can be unsubstituted or substituted, wherein substitution includes replacement of one, two, three, or more of the hydrogen atoms thereon independently with any one or more of the following moieties including, but not limited to: aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl;

heteroarylalkyl; alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio;

heteroalkylthio; heteroarylthio; -F; -CI; -Br; -I; -OH; -N₃; -N0₂; -CN; -CF₃; -CH₂CF₃; - CHC1₂; -CH₂OH; -CH₂OR_x; -CH₂R_X; -CH₂CH₂OH; -CH₂NH₂; -CH₂N(R_X)₂; =C(R_X)₂; - CH₂S0₂CH₃; -C(0)R_x; -C0₂(R_x); -OC(0)R_x; -OC0₂R_x; -OC(R_x)₃; -OCON(R_x)₂; -CON(R_x)₂; -NR_x(CO)R_x, -N(R_X)₂; -S(0)₂R_x; and -S(0)R_x; wherein each occurrence of R_x independently includes, but is not limited to, hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples that are described herein.

[0051] "Carbocyclyl" or "carbocyclic" refers to a radical of a non-aromatic cyclic hydrocarbon group having from 3 to 10 ring carbon atoms (" -io carbocyclyl") and zero heteroatoms in the non-aromatic ring system. In some embodiments, a carbocyclyl group has 3 to 8 ring carbon atoms ("C₃_g carbocyclyl"). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms ("C₃_₆ carbocyclyl"). In some embodiments, a carbocyclyl group has 3 to 6 ring carbon atoms ("C₃_6 carbocyclyl"). In some embodiments, a

carbocyclyl group has 5 to 10 ring carbon atoms ("Cs-io carbocyclyl"). Exemplary C₃_6 carbocyclyl groups include, without limitation, cyclopropyl (C₃), cyclopropenyl (C₃), cyclobutyl (C₄), cyclobutenyl (C₄), cyclopentyl (C₅), cyclopentenyl (C₅), cyclohexyl (C₆), cyclohexenyl (C₆), cyclohexadienyl (C₆), and the like. Exemplary C₃_8 carbocyclyl groups include, without limitation, the aforementioned C₃_₆ carbocyclyl groups as well as cycloheptyl (C₇), cycloheptenyl (C₇), cycloheptadienyl (C₇), cycloheptatrienyl (C₇), cyclooctyl (Cg), cyclooctenyl (Cg), bicyclo[2.2.1]heptanyl (C₇), bicyclo[2.2.2]octanyl (Cg), and the like. Exemplary C₃_₁₀ carbocyclyl groups include, without limitation, the

aforementioned C₃_g carbocyclyl groups as well as cyclononyl (C₉), cyclononenyl (C₉), cyclodecyl (C₁₀), cyclodecenyl (C₁₀), octahydro-lH-indenyl (C₉), decahydronaphthalenyl (Cio), spiro[4.5]decanyl (C₁₀), and the like. As the foregoing examples illustrate, in certain embodiments, the carbocyclyl group is either monocyclic ("monocyclic carbocyclyl") or contain a fused, bridged or spiro ring system such as a bicyclic system ("bicyclic

carbocyclyl") and can be saturated or can be partially unsaturated. "Carbocyclyl" also includes ring systems wherein the carbocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups wherein the point of attachment is on the carbocyclyl ring, and in such instances, the number of carbons continue to designate the number of carbons in the carbocyclic ring system. Unless otherwise specified, each instance of a carbocyclyl group is independently optionally substituted, i.e., unsubstituted (an "unsubstituted carbocyclyl") or substituted (a "substituted carbocyclyl") with one or more substituents. In certain

embodiments, the carbocyclyl group is unsubstituted C₃_io carbocyclyl. In certain

embodiments, the carbocyclyl group is a substituted C₃_io carbocyclyl.

[0052] In some embodiments, "carbocyclyl" is a monocyclic, saturated carbocyclyl group having from 3 to 10 ring carbon atoms ('¾_₁₀ cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 8 ring carbon atoms ("C₃_g cycloalkyl"). In some embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms ("C₃_6 cycloalkyl"). In some embodiments, a cycloalkyl group has 5 to 6 ring carbon atoms ("C₅_6 cycloalkyl"). In some embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms ('¾__½ cycloalkyl"). Examples of C₅_6 cycloalkyl groups include cyclopentyl (C₅) and cyclohexyl (C₅). Examples of C₃_6 cycloalkyl groups include the aforementioned C₅_6 cycloalkyl groups as well as cyclopropyl (C₃) and cyclobutyl (C₄). Examples of C₃_g cycloalkyl groups include the aforementioned C₃_₆ cycloalkyl groups as well as cycloheptyl (C₇) and cyclooctyl (Cg). Unless otherwise specified, each instance of a cycloalkyl group is independently unsubstituted (an

"unsubstituted cycloalkyl") or substituted (a "substituted cycloalkyl") with one or more substituents. In certain embodiments, the cycloalkyl group is unsubstituted C₃_io cycloalkyl. In certain embodiments, the cycloalkyl group is substituted C₃_io cycloalkyl.

[0053] Carbocyclyl groups may optionally be substituted with substituents including, but not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl;

alkoxy; aryloxy; heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio;

heteroarylthio; -F; -CI; -Br; -I; -OH; -N₃; -N0₂; -CN; -CF₃; -CH₂CF₃; -CHC1₂; -CH₂OH; - CH₂OR_x; -CH₂R_X; -CH₂CH₂OH; -CH₂NH₂; -CH₂N(R_X)₂; =C(R_X)₂; -CH₂S0₂CH₃; -C(0)R_x; - C0₂(R_x); -OC(0)R_x; -OC0₂R_x; -OC(R_x)₃; -OCON(R_x)₂; -CON(R_x)₂; -NR_x(CO)R_x, -N(R_X)₂; - S(0)₂R_x; and -S(0)R_x; wherein each occurrence of R_x independently includes, but is not limited to, hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples that are described herein.

[0054] The term "heteroaliphatic," as used herein, refers to aliphatic moieties that contain one or more oxygen, sulfur, nitrogen, phosphorus, or silicon atoms, e.g., in place of carbon atoms. Heteroaliphatic moieties may be branched, unbranched, cyclic or acyclic and include saturated and unsaturated heterocycles such as morpholino, pyrrolidinyl, etc. A cyclic heteroaliphatic is referred to herein as "heterocycloalkyl" or "heterocycle". In certain embodiments, heteroaliphatic moieties are substituted by independent replacement of one or more of the hydrogen atoms thereon with one or more moieties including, but not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl; heteroarylalkyl; alkoxy; aryloxy;

heteroalkoxy; heteroaryloxy; alkylthio; arylthio; heteroalkylthio; heteroarylthio; -F; -CI; -Br; -I; -OH; -N₃; -N0₂; -CN; -CF₃; -CH₂CF₃; -CHC1₂; -CH₂OH; -CH₂OR_x; -CH₂R_X; - CH₂CH₂OH; -CH₂NH₂; -CH₂N(R_X)₂; =C(R_X)₂; -CH₂S0₂CH₃; -C(0)R_x; -C0₂(R_x); -OC(0)R_x; -OC0₂R_x; -OC(R_x)₃; -OCON(R_x)₂; -CON(R_x)₂; -NR_x(CO)R_x, -N(R_X)₂; -S(0)₂R_x; and - S(0)R_x; wherein each occurrence of R_x independently includes, but is not limited to, hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or

heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples that are described herein. [0055] The terms "halo" and "halogen" as used herein refer to an atom selected from fluorine (fluoro, -F), chlorine (chloro, -CI), bromine (bromo, -Br), and iodine (iodo, -I).

[0056] The term "perfluoroalkyl" denotes an aliphatic group, as defined above, having one, two, or three halogen atoms (i.e., chloro, bromo, fluoro, iodo) attached thereto. The term "haloalkyl" is a sub-set of "perfluoroalkyl" and denotes an alkyl group, as defined above, having one, two, or three halogen atoms attached thereto and is exemplified by such groups as chloromethyl, bromoethyl, trifluoromethyl, and the like.

[0057] "Heterocyclyl" or "heterocyclic" refers to a radical of a 3- to 10-membered non-aromatic ring system having ring carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon ("3-10 membered heterocyclyl"). In heterocyclyl groups that contain one or more nitrogen atoms, the point of attachment can be a carbon or nitrogen atom, as valency permits. A heterocyclyl group can either be monocyclic ("monocyclic heterocyclyl") or a fused, bridged or spiro ring system such as a bicyclic system ("bicyclic heterocyclyl"), and can be saturated or can be partially unsaturated. Heterocyclyl bicyclic ring systems can include one or more heteroatoms in one or both rings. "Heterocyclyl" also includes ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more carbocyclyl groups wherein the point of attachment is either on the carbocyclyl or heterocyclyl ring, or ring systems wherein the heterocyclyl ring, as defined above, is fused with one or more aryl or heteroaryl groups, wherein the point of attachment is on the heterocyclyl ring, and in such instances, the number of ring members continue to designate the number of ring members in the heterocyclyl ring system. Unless otherwise specified, each instance of heterocyclyl is independently optionally substituted, i.e., unsubstituted (an "unsubstituted heterocyclyl") or substituted (a "substituted heterocyclyl") with one or more substituents. In certain embodiments, the heterocyclyl group is unsubstituted 3-10 membered heterocyclyl. In certain embodiments, the heterocyclyl group is substituted 3-10 membered heterocyclyl.

[0058] In some embodiments, a heterocyclyl group is a 5-10 membered non- aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, sulfur, boron, phosphorus, and silicon ("5-10 membered heterocyclyl"). In some embodiments, a heterocyclyl group is a 5- 8 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-8 membered heterocyclyl"). In some embodiments, a heterocyclyl group is a 5-6 membered non-aromatic ring system having ring carbon atoms and 1-4 ring heteroatoms, wherein each heteroatom is independently selected from nitrogen, oxygen, and sulfur ("5-6 membered heterocyclyl"). In some embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6 membered heterocyclyl has one ring heteroatom selected from nitrogen, oxygen, and sulfur.

[0059] Exemplary 3-membered heterocyclyl groups containing one heteroatom include, without limitation, azirdinyl, oxiranyl, thiorenyl. Exemplary 4-membered heterocyclyl groups containing one heteroatom include, without limitation, azetidinyl, oxetanyl and thietanyl. Exemplary 5-membered heterocyclyl groups containing one heteroatom include, without limitation, tetrahydrofuranyl, dihydrofuranyl,

tetrahydrothiophenyl, dihydrothiophenyl, pyrrolidinyl, dihydropyrrolyl and pyrrolyl-2,5- dione. Exemplary 5-membered heterocyclyl groups containing two heteroatoms include, without limitation, dioxolanyl, oxasulfuranyl, disulfuranyl, and oxazolidin-2-one. Exemplary 5-membered heterocyclyl groups containing three heteroatoms include, without limitation, triazolinyl, oxadiazolinyl, and thiadiazolinyl. Exemplary 6-membered heterocyclyl groups containing one heteroatom include, without limitation, piperidinyl, tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, piperazinyl, morpholinyl, dithianyl, dioxanyl.

Exemplary 6-membered heterocyclyl groups containing two heteroatoms include, without limitation, triazinanyl. Exemplary 7-membered heterocyclyl groups containing one heteroatom include, without limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8- membered heterocyclyl groups containing one heteroatom include, without limitation, azocanyl, oxecanyl and thiocanyl. Exemplary 5-membered heterocyclyl groups fused to a C₆ aryl ring (also referred to herein as a 5,6-bicyclic heterocyclic ring) include, without limitation, indolinyl, isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl,

benzoxazolinonyl, and the like. Exemplary 6-membered heterocyclyl groups fused to an aryl ring (also referred to herein as a 6,6-bicyclic heterocyclic ring) include, without limitation, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and the like.

[0060] In certain embodiments, a "substituted heterocycloalkyl or heterocycle" group is utilized and as used herein, refers to a heterocycloalkyl or heterocycle group, as defined above, substituted by the independent replacement of one, two or three of the hydrogen atoms thereon with but are not limited to aliphatic; heteroaliphatic; aryl; heteroaryl; arylalkyl;

heteroalkylthio; heteroarylthio; -F; -CI; -Br; -I; -OH; -N₃; -N0₂; -CN; -CF₃; -CH₂CF₃; - CHC1₂; -CH₂OH; -CH₂OR_x; -CH₂R_X; -CH₂CH₂OH; -CH₂NH₂; -CH₂N(R_X)₂; =C(R_X)₂; - CH₂S0₂CH₃; -C(0)R_x; -C0₂(R_x); -OC(0)R_x; -OC0₂R_x; -OC(R_x)₃; -OCON(R_x)₂; -CON(R_x)₂; -NR_x(CO)R_x, -N(R_X)₂; -S(0)₂R_x; and -S(0)R_x; wherein each occurrence of R_x independently includes, but is not limited to, hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted. Additional examples of generally applicable substitutents are illustrated by the specific embodiments shown in the Examples which are described herein.

[0061] The term "carbocyclic" or "carbocycle," as used herein, refers to an aromatic or non-aromatic ring in which each atom of the ring is a carbon atom.

[0062] The term "sulfonyl" refers to a group having the structure -S(0)₂R_x, and the term sulfinyl refers to a group having the structure -S(0)R_x, wherein each R_x is independently aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted.

[0063] The term "acyl" refers to a group -C(0)R_x or -C0₂(R_x), wherein each R_x is independently hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted.

[0064] The term "acyloxy" refers to a group -OC(0)R_x or -OC0₂R_x, wherein each R_x is independently aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted.

[0065] The term "amide" refers to a group -(CO)N(R_x)₂ or -NR_x(CO)R_x wherein each R_x is independently hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted.

[0066] The term "carbamate" refers to a group -0(CO)N(R_x)₂ or -NR_x(CO)OR_x wherein each R_x is independently hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted.

[0067] The term "silyl" as used herein refers to an oxygen or nitrogen protecting group of the formula -Si(R_x)3, wherein each R_x is independently aliphatic, heteroaliphatic, perfluoroalkyl, aryl, heteroaryl, arylalkyl, or heteroarylalkyl, wherein any of the aliphatic, heteroaliphatic, perfluoroalkyl, arylalkyl, or heteroarylalkyl substituents described above and herein may be substituted or unsubstituted, branched or unbranched, cyclic or acyclic, and wherein any of the aryl or heteroaryl substituents described above and herein may be substituted or unsubstituted.

[0068] The term "independently selected" is used herein to indicate that the R groups can be identical or different.

[0069] As used herein, the term "labeled" is intended to mean that a compound has at least one element, isotope, or chemical compound attached to enable the detection of the compound. In general, labels typically fall into three classes: a) isotopic labels, which may be radioactive or heavy isotopes, including, but not limited to, ²H, ³H, ³²P, ³⁵S, ⁶⁷Ga, ^99mTc (Tc-99m), ^mIn, ¹²³I, ¹²⁵1, ¹⁶⁹Yb and ¹⁸⁶Re; b) immune labels, which may be antibodies or antigens,which may be bound to enzymes (such as horseradish peroxidase) that produce detectable agents; and c) colored, luminescent, phosphorescent, or fluorescent dyes. It will be appreciated that the labels may be incorporated into the compound at any position that does not interfere with the biological activity or characteristic of the compound that is being detected. In certain embodiments, hydrogen atoms in the compound are replaced with deuterium atoms ( H) to slow the degradation of compound in vivo. Due to isotope effects, enzymatic degradation of the deuterated tetracyclines may be slowed thereby increasing the half-life of the compound in vivo. The term "isotopologue" refers to a species that has the same chemical structure and formula as a specific compound of this invention, with the exception of the isotopic composition at one or more positions, e.g., H vs. D. Thus, an isotopologue differs from a specific compound of this invention in the isotopic composition thereof. In certain embodiments of the invention, photoaffinity labeling is utilized for the direct elucidation of intermolecular interactions in biological systems. A variety of known photophores can be employed, most relying on photoconversion of diazo compounds, azides, or diazirines to nitrenes or carbenes (See, Bayley, H., Photogenerated Reagents in

Biochemistry and Molecular Biology (1983), Elsevier, Amsterdam.), the entire contents of which are hereby incorporated by reference. In certain embodiments of the invention, the photoaffinity labels employed are o-, m- and p-azidobenzoyls, substituted with one or more halogen moieties, including, but not limited to 4-azido-2,3,5,6-tetrafluorobenzoic acid.

[0070] As used herein, the term "tautomers" are particular isomers of a compound in which a hydrogen and double bond have changed position with respect to the other atoms of the molecule. For a pair of tautomers to exist there must be a mechanism for interconversion. Examples of tautomers include keto-enol forms, imine-enamine forms, amide-imino alcohol forms, amidine-aminidine forms, nitroso-oxime forms, thio ketone-enethiol forms, N-nitroso- hydroxyazo forms, nitro-ad-nitro forms, and pyridione-hydroxypyridine forms.

[0071] It will be appreciated that certain compounds of the present invention can exist in free form, or where appropriate, as a pharmaceutically acceptable derivative thereof.

According to the present invention, a pharmaceutically acceptable derivative includes, but is not limited to, pharmaceutically acceptable salts, esters, salts of such esters, or any other adduct or derivative which upon administration to a subject in need is capable of providing, directly or indirectly, a compound as otherwise described herein, or a metabolite or residue thereof, e.g., a prodrug.

[0072] As used herein, the term "pharmaceutically acceptable salt" refers to those salts which are, within the scope of sound medical judgement, suitable for use in contact with the tissues of a subject without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 66: 1-19, 1977; incorporated herein by reference. The salts can be prepared in situ during the final isolation and purification of the compounds of the invention, or separately by reacting the free base functionality with a suitable organic or inorganic acid. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate,

benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hernisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further

pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate, and aryl sulfonate.

[0073] Additionally, as used herein, the term "pharmaceutically acceptable ester" refers to esters which hydrolyze in vivo and include those that break down readily in the human body to leave the parent compound or a salt thereof. Suitable ester groups include, for example, those derived from pharmaceutically acceptable aliphatic carboxylic acids, particularly alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenyl moiety advantageously has not more than 6 carbon atoms. Examples of particular esters include formates, acetates, propionates, butyrates, acrylates and ethylsuccinates. In certain embodiments, the esters are cleaved by enzymes such as esterases.

[0074] Furthermore, the term "pharmaceutically acceptable prodrugs" as used herein refers to those prodrugs of the compounds of the present invention which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of a subject with undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit/risk ratio, and effective for their intended use, as well as the zwitterionic forms, where possible, of the compounds of the invention. The term "prodrug" refers to compounds that are rapidly transformed in vivo to yield the parent compound of the above formula, for example by hydrolysis in blood. A thorough discussion is provided in T. Higuchi and V. Stella, Prodrugs as Novel Delivery Systems, Vol. 14 of the A.C.S. Symposium Series, and in Edward B. Roche, ed., Bioreversible Carriers in Drug Design, American Pharmaceutical Association and Pergamon Press, 1987, both of which are incorporated herein by reference.

[0075] Definitions of non-chemical terms used throughout the specification include:

[0076] A "subject" or "animal" to which administration is contemplated includes, but is not limited to, humans (i.e., a male or female of any age group, e.g., a pediatric subject (e.g, infant, child, adolescent) or adult subject (e.g., young adult, middle-aged adult or senior adult)); and other non-human animals, such as mammals (e.g., other primates (e.g., cynomolgus monkeys, rhesus monkeys) and commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs); birds (e.g., commercially relevant birds such as chickens, ducks, geese, and/or turkeys); reptiles; amphibians; and fish. Preferably, the non- human animal is a mammal (e.g., a rodent, a mouse, a rat, a rabbit, a monkey, a dog, a cat, a primate, or a pig). A non-human animal may be a transgenic animal.

[0077] When two entities are "associated with" one another as described herein, they are linked by a direct or indirect covalent or non-covalent interaction. Preferably, the association is covalent. Desirable non-covalent interactions include hydrogen bonding, van der Waals interactions, hydrophobic interactions, magnetic interactions, electrostatic interactions, etc.

[0078] As used herein, "effective amount" or "therapeutically effective amount" refers to the amount of an active agent refers to an amount sufficient to elicit the desired biological response; i.e., an amount sufficient to provide a therapeutic benefit in the treatment or management of a disease, disorder or condition, or to delay or minimize one or more symptoms associated with the disease, disorder or condition. As will be appreciated by those of ordinary skill in this art, the effective amount of a compound of the invention may vary depending on such factors as the desired biological endpoint, the pharmacokinetics of the compound, the disease being treated, the mode of administration, and the subject. For example, the effective amount of a tetracycline analog antibiotic is the amount that results in a sufficient concentration at the site of the infection to kill the microorganism causing the infection (bacteriocidal) or to inhibit the reproduction of such microorganisms (bacteriostatic). In another example, the effective amount of tetracycline analog antibiotic is the amount sufficient to reverse clinicals signs and symptoms of the infection, including fever, redness, warmth, pain, chills, cultures, and pus production. The term "therapeutically effective amount" or "effective amount" can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of disease or condition, or enhances the therapeutic efficacy of another therapeutic agent.

[0079] As used herein, and unless otherwise specified, the terms "treat," "treating" and "treatment" contemplate an action that occurs while a subject is suffering from the specified disease, disorder or condition, which reduces the severity of the disease, disorder or condition, or retards or slows the progression of the disease, disorder or condition.

[0080] As used herein, and unless otherwise specified, the terms "manage," "managing" and "management" encompass preventing the recurrence of the specified disease, disorder or condition in a subject who has already suffered from the disease, disorder or condition, and/or lengthening the time that a subject who has suffered from the disease, disorder or condition remains in remission. The terms encompass modulating the threshold, development and/or duration of the disease, disorder or condition, or changing the way that a subject responds to the disease, disorder or condition.

[0081] As used herein, unless otherwise specified, the terms "prevent," "preventing" and "prevention" contemplate an action that occurs before a subject begins to suffer from the specified disease, disorder or condition, which inhibits or reduces the severity of the disease, disorder or condition.

[0082] As used herein, and unless otherwise specified, a "prophylactically effective amount" of a compound is an amount sufficient to prevent a disease, disorder or condition, or one or more symptoms associated with the disease, disorder or condition, or prevent its recurrence. A prophylactically effective amount of a compound means an amount of therapeutic agent, alone or in combination with other agents, which provides a prophylactic benefit in the prevention of the disease, disorder or condition. The term "prophylactically effective amount" can encompass an amount that improves overall prophylaxis or enhances the prophylactic efficacy of another prophylactic agent.

[0083] As used herein "inhibition," "inhibiting," "inhibit" and "inhibitor," and the like, refer to the ability of a compound to reduce, slow, halt or prevent activity of a particular biological process in a cell relative to a control. Brief Description of the Drawing

[0084] Figure 1 depicts an ORTEP plot of alpha C5-substituted enone 4.

[0085] Figures 2A-2I are tables showing IC₅₀ values for C5-alpha and C5-beta substituted tetracyclines tested with various Gram-positive and Gram-negative bacterial strains.

Detailed Description of Certain Embodiments of the Invention

[0086] The present invention is directed, in part, to new methods of making tetracycline analogs substituted at the C5 position (i.e., wherein R₃ or R₄ are a group other than hydrogen).

[0087] As used herein, a "C5-tetracycline analog" refers to a compound of formula

(I), or subgenera thereof, wherein one of R₃ and R₄ is hydrogen, and the other of R₃ and R₄ is a group other than hydrogen. In certain embodiments, wherein R₃ is hydrogen, and R₄ is a group other than hydrogen, the C5-tetracycline analog is referred to as a "beta C5- tetracycline analog." Alternatively, in certain embodiments, wherein R₄ is hydrogen, and R is a group other than hydrogen, the C5-tetracycline analog is referred to as an "alpha C5- tetracycline analog".

[0088] Thus, in one aspect, the present invention provides C5-tetracycline analogs of the formula (I):

(I)

or pharmaceutically acceptable salts thereof, wherein one of R and R₄ is hydrogen and the other of R and R₄ is a group other than hydrogen, and n, R_P1, R_P2, Rp₃, Rp₄, R_{1 ;} R₂, R5, R₆, R₇, R8, R9, Rio, and Rn are as described herein.

[0089] Also provided are C5-substituted intermediates useful in the synthesis of a compound of formula (I) (e.g., compounds of formulae (II) and (IV)).

[0090] For example, in one aspect, the present invention provides compounds of formula (II) (a "C5-substituted enone"):

and pharmaceutically acceptable salts thereof, wherein one of R₃ and R₄ is hydrogen and the other of R₃ and R₄ is a group other than hydrogen, and R_P4, R_P5, R5, R₉, R₁₀, and Rn are as described herein.

[0091] As used herein, a "C5-substituted enone" refers to a compound of formula

(II), or subgenera thereof, generated from a compound of formula (III), or subgenera thereof, wherein one of R and R₄ is hydrogen and the other of R and R₄ is a group other than hydrogen. In certain embodiments, wherein R₃ is hydrogen, and R₄ is a group other than hydrogen, the C5- substituted enone is referred to as a "beta C5-substituted enone".

Alternatively, in certain embodiments, wherein R₄ is hydrogen, and R₃ is a group other than hydrogen, the C5- substituted enone is referred to as an "alpha C5-substituted enone".

[0092] The present invention further describes the synthesis of compounds of formula

(II) from a compound of formula (III), wherein the substituent at the C5 position of (II) is installed by treatment of (III) with an electrophile. Further sythetic modification of (II) allows access to a wide variety of C5- substituted enones.

[0093] In yet another aspect, the present invention provides compounds of formula

(IV (a "C5-pentacycline isoxazole"):

(II) (IV) and pharmaceutically acceptable salts thereof, wherein one of R and R₄ is hydrogen and the other of R and R₄ is a group other than hydrogen, and n, R_P1, R_P2, R_P3, R_P4, R_1; R₂, R5, R₆, R₇, R8, R9, Rio, and R_{11 ;} are as described herein. [0094] As used herein, a "C5-pentacycline isoxazole" refers to a compound of formula (IV), or subgenera thereof, wherein one of R₃ and R4 is hydrogen and the other of R₃ and R₄ is a group other than hydrogen. In certain embodiments, wherein R is hydrogen, and R^ is a group other than hydrogen, the C5-pentacycline isoxazole is referred to as a "beta C5- pentacycline isoxazole". Alternatively, in certain embodiments, wherein R₄ is hydrogen, and R₃ is a group other than hydrogen, the C5-tetracycline analog is referred to as an "alpha C5- pentacycline isoxazole".

[0095] In certain embodiments, a compound of formula (II) is treated with a compound of formulae (V), (VI), (VII) or (VIII) to provide compounds of formula (IV-c):

and pharmaceutically acceptable salts thereof, wherein one of R and R₄ is hydrogen and the other of R₃ and R₄ is a group other than hydrogen, and Hal, R₁₂, n, Rp_1; Rp₂, Rp₃, Rp₄, R_1; R₂, R5, R₆, R7, R8, R9, Rio, and Rn are as described herein.

[0096] Further optional sythetic modification followed by ring opening of the isoxazole ring of (IV) provides C5-tetracycline analogs of the present invention.

[0097] Preferred embodiments of C5-tetracycline analogs of formula (I), and intermediates thereto (e.g., compounds of formula (II) and (IV)), pharmaceutical

compositions thereof and methods of their preparation and use are described in more detail herein. Compounds of Formula (I)

[0098] As described generally above, C5-tetracycline analogs of the present invention are represented by the formula (I):

(I)

and pharmaceutically acceptable salts thereof;

wherein:

represents a single or double bond;

Ri and R₂ are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or

unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -ORA; -CH₂ORA; -CH₂N(RA)₂; =C(RA)₂;

-CH₂R_A; -C(=0)R_A; -C0₂R_A; -CN; -SCN; -SR_A; -SOR_A; -S0₂R_A; -N₃; -N0₂;

-N(R_A)₂; -NHC(0)R_A; -NHS0₂R_A; or -C(R_A)₃; wherein each occurrence of R_A is

independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or _\ and R₂ are taken together to form =0;

one of R and R₄ is hydrogen, and the other is selected from halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -ORB; -CH₂ORB; -CH₂R_B; - CH₂N(R_B)₂; -C(0)R_B; -C0₂R_B; -C(0)N(R_B)₂; -CN; -SCN; -SR_B; -SOR_B; -S0₂R_B; -N0₂; -N₃; -N(R_B)₂; or -C(R_B)₃; wherein each occurrence of R_B is independently hydrogen, halogen, azido, a protecting group, sulfonyl, sulfinyl, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; or two R_B groups, when attached to a nitrogen atom, are joined to form a heterocyclic ring;

R₅, R9, R₁₀, and Rn are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_D; -CH₂OR_D; -CH₂R_D; -CH₂N(R_D)₂; -C(=0) R_D; -C0₂ R_D; -CN; -SCN; -S R_D; -SO R_D; -S0₂R_D; -N0₂; -N₃; -N(R_D)₂; -NHC(0)R_D; or - C(R_D)₃; wherein each occurrence of R_D is independently hydrogen, halogen, azido, a protecting group, silyl, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate,aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

each R₇ is indepedently hydrogen, halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or

unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_c; -CH₂OR_c; -CH₂R_C; -CH₂N(R_C)₂; - C(=0)R_c; -C0₂R_c; -CN; -SCN; -SR_C; -SOR_c; -S0₂R_c; -N₃; -N0₂; -N(R_C)₂; -NR_C C(0)R_c; - NR_cS0₂R_c; -NR_cC(0)CH₂R_c; or -C(R_C)₃; or two R⁷ groups are taken together to form =0 or =C(Rc)₂; wherein each occurrence of R_c is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

R₆ and R₈ are absent if the dashed line between the carbon atoms to which R₆ and R₈ are attached represents a bond, or are each independently selected from hydrogen, halogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, substituted or unsubstituted alkoxy, -OH, -CN, -SCN, -SH, alkylthio, -N0₂, amino, alkylamino, or dialkylamino;

each R_P1, R_P2, R_P4 and R_P5 is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

each R_P is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, a nitrogen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and

n is an integer in the range of 0 to 8, inclusive.

[0099] In certain embodiments, R_P1 is hydrogen. [00100] In certain embodiments, Rp₂ is hydrogen.

[00101] In certain embodiments, each R_P3 is hydrogen.

[00102] In certain embodiments, Ri is hydrogen. In other embodiments, Ri is lower alkyl, alkenyl, or alkynyl. In some embodiments, Ri is C_1-6 alkyl. In yet other embodiments, Ri is methyl, ethyl, n-propyl, cyclopropyl, or isopropyl. In still other embodiments Ri is methyl.

[00103] In certain embodiments, R₂ is hydrogen. In other embodiments, R₂ is -OR_A-

In certain embodiments, R₂ is -OH. In certain embodiments, R₂ is alkoxy. In yet other embodiments, R₂ is a lower alkyl, alkenyl, or alkynyl group. In some embodiments, R₂ is Ci_ ₆ alkyl.

[00104] In certain embodiments, Ri is methyl, and R₂ is hydroxyl. In other

embodiments, Ri is methyl, and R₂ is hydrogen. In certain embodiments, Ri and R₂ are both hydrogen. In certain other embodiments, Ri and R₂ are taken together to form a carbocyclic or heterocyclic ring system spiro-linked to the C ring of the tetracycline analog.

[00105] In certain embodiments, R₃ is hydrogen, and R₄ is selected from halogen, -

OR_B; -CH₂OR_B; -CH₂R_B; -CH₂N(R_B)₂; -C(0)R_B; -C0₂R_B; -C(0)N(R_B)₂; -SR_B; -SOR_B; - S0₂R_B; -N₃; -N(R_B)₂; or -C(R_B)₃; wherein each occurrence of R_B is independently hydrogen, halogen, azido, a protecting group, sulfonyl, sulfinyl, aliphatic, heteroaliphatic,

perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio. Compounds having this stereochemistry at the C5 position are referred to herein as "beta C5 isomers".

[00106] In certain embodiments, R₃ is selected from halogen, -OR_B; -CH₂OR_B; -

CH₂R_B; -CH₂N(R_B)₂; -C(0)R_B; -C0₂R_B; -C(0)N(R_B)₂; -SR_B; -SOR_B; -S0₂R_B; -N₃; -N(R_B)₂; or -C(R_B)₃; wherein each occurrence of R_B is independently hydrogen, halogen, azido, a protecting group, sulfonyl, sulfinyl, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio, and Rj is hydrogen. Compounds having this stereochemistry at the C5 position are referred to herein as "alpha-C5 isomers".

[00107] In certain embodiments, the C5 position is substituted with a halogen. For example, in certain embodiments, R₃ is halogen and R₄ is hydrogen. In certain embodiments, R is fluoro and Rj is hydrogen. In certain embodiments, R is bromo and R₄ is hydrogen. In certain embodiments, R is chloro and Rj is hydrogen. In certain embodiments, R is iodo and Ri is hydrogen. In certain embodiments, R₄ is halogen and R₃ is hydrogen. In certain embodiments, R₄ is fluoro and R₃ is hydrogen. In certain embodiments, R₄ is bromo and R₃ is hydrogen. In certain embodiments, R^ is chloro and R is hydrogen. In certain

embodiments, R₄ is iodo and R is hydrogen.

[00108] In certain embodiments, the C5 position is substituted with an -ORB group.

For example, in certain embodiments, R₃ is -ORB and R^ is hydrogen. In certain

embodiments, R₄ is -ORB and R is hydrogen. In certain embodiments, R_B is hydrogen. In certain embodiments, R_B is an oxygen protecting group. In certain embodiments, R_B is sulfonyl. In certain embodiments, RB is aliphatic (e.g., optionally substituted C_1-6 alkyl, C₂_ ealk l, C_3-6 alkyl, C_4-6 alkyl, C₅_₆ alkyl, Cialk l, C₂alkyl, C₃alkyl, C₄alkyl, C₅alkyl, C₆alkyl). In certain embodiments, R_B is heteroaliphatic. In certain embodiments, R_B is perfluoroalkyl (e.g., -CF ). In certain embodiments, R_B is acyl (e.g., -C(0)CH ). In certain embodiments, RB is amide. In certain embodiments, RB is aryl (e.g., optionally substituted phenyl). In certain embodiments, RB is heteroaryl. However, in certain embodiments, compounds wherein R is -OH or wherein R^ is -OH is specifically excluded.

[00109] In certain embodiments, the C5 position is substituted with an -N(RB)₂ group.

For example, in certain embodiments, R₃ is -N(RB)₂ and R^ is hydrogen. In certain embodiments, R₄ is -N(RB)₂ and R₃ is hydrogen. In certain embodiments, at least one RB is hydrogen. In certain embodiments, at least one R_B is a amino protecting group. In certain embodiments, at least one R_B is sulfonyl. In certain embodiments, at least one R_B is aliphatic (e.g., optionally substituted C_1-6 alkyl, Cialkyl, C₃_₆ alkyl, C₄_₆ alkyl, C5-6 alkyl, Qalkyl, C₂alkyl, C₃alkyl, C₄alkyl, C₅alkyl, C₆alkyl). In certain embodiments, at least one RB is heteroaliphatic. In certain embodiments, RB is at least one perfluoroalkyl (e.g., -CF₃). In certain embodiments, R_B is at least one acyl (e.g., -C(=0)CH ) group. In certain

embodiments, R_B is at least one amino acid group, e.g., -C(=0)C(RAA)NHR_BB or

-C(=0)(C(RAA))₂NHR_bb, or derivative thereof, e.g., -C(=0)C(R_AA)OR_BB or

-C(=0)(C(RAA))₂ORBB, wherein RAA is optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted aryl, optionally substituted heteroaryl, and R_BB is hydrogen or an amino protecting group when attached to a nitrogen atom, or hydrogen or an oxygen protecting group when attached to an oxygen atom. In certain embodiments, RAA is an amino acid side chain group selected from hydrogen, optionally substituted alkyl (e.g., -CH₂OH, -CH(OH)CH₃, -CH₂C(=0)NH₂,

-CH₂CH₂C(=0)NH₂, -CH₂SH, -CH₂NH₂, -CH₃, -CH(CH₃)₂, -CH(CH₃)CH₂CH₃,

-CH₂CH(CH₃)₂, -CH₂CH₂SCH₃, -CH₂Ph, -CH₂Ph(4-OH), -CH₂-indolyl, -CH₂CH₂CH₂NHC(=NH)NH₂, -CH₂CH₂CH₂CH₂NH₂, -CH₂C0₂H, -CH₂CH₂C0₂H), or optionally substituted heterocyclyl (e.g., -pyrrolidinyl). In certain embodiments, at least one R_B is aryl (e.g., optionally substituted phenyl). In certain embodiments, at least one R_B is heteroaryl. In certain embodiments, two R_B groups are joined to form a heterocyclic ring.

[00110] In certain embodiments, the C5 position is substituted with an -N₃ group. For example, in certain embodiments, R₃ is -N₃ and R4 is hydrogen. In certain embodiments, R₄ is -N₃ and R₃ is hydrogen.

[00111] In certain embodiments, the C5 position is substituted with a -CH₂N(R_B)₂ group. For example, in certain embodiments, R₃ is -CH₂N(R_B)₂ and R^ is hydrogen. In certain embodiments, R₄ is -CH₂N(R_B)₂ and R₃ is hydrogen. In certain embodiments, at least one R_B is hydrogen. In certain embodiments, at least one R_B is a amino protecting group. In certain embodiments, at least one R_B is sulfonyl. In certain embodiments, at least one R_B is aliphatic (e.g., optionally substituted C_1-6 alkyl, Csalkyl, C₃_₆ alkyl, C₄_₆ alkyl, C5-₆ alkyl, Cialkyl, C₂alkyl, C₃alkyl, C₄alkyl, C₅alkyl, C₆alkyl). In certain embodiments, at least one R_B is heteroaliphatic. In certain embodiments, R_B is at least one perfluoroalkyl (e.g., - CF₃). In certain embodiments, R_B is at least one acyl (e.g., -C(0)CH₃). In certain

embodiments, at least one R_B is aryl (e.g., optionally substituted phenyl). In certain embodiments, at least one R_B is heteroaryl. In certain embodiments, two R_B groups are joined to form a heterocyclic ring.

[00112] In certain embodiments, the C5 position is substituted with a -CH₂OR_B group.

For example, in certain embodiments, R₃ is -CH₂OR_B and R^ is hydrogen. In certain embodiments, R₄ is -CH₂OR_B and R₃ is hydrogen. In certain embodiments, R_B is hydrogen. In certain embodiments, R_B is an oxygen protecting group. In certain embodiments, R_B is sulfonyl. In certain embodiments, R_B is aliphatic (e.g., optionally substituted C_1-6 alkyl, C₂_ ealk l, C_3-6 alkyl, C_4-6 alkyl, C₅_₆ alkyl, Cialk l, C₂alkyl, C₃alkyl, C₄alkyl, C₅alkyl, C₆alkyl). In certain embodiments, R_B is heteroaliphatic. In certain embodiments, R_B is perfluoroalkyl (e.g., -CF₃). In certain embodiments, R_B is acyl (e.g., -C(0)CH₃). In certain embodiments, R_B is amide. In certain embodiments, R_B is aryl (e.g., optionally substituted phenyl). In certain embodiments, R_B is heteroaryl.

[00113] In certain embodiments, the C5 position is substituted with a -CH₂F group.

For example, in certain embodiments, R₃ is -CH₂F and R₄ is hydrogen. In certain

embodiments, R₄ is -CH₂F and R₃ is hydrogen. [00114] In certain embodiments, the C5 position is substituted with a -CH₂N₃ group.

For example, in certain embodiments, R₃ is -CH₂N₃ and R4 is hydrogen. In certain embodiments, R₄ is -CH₂N₃ and R is hydrogen.

[00115] In certain embodiments, the C5 position is substituted with a -C(0)RB; -

C0₂RB; or -C(0)N(RB)₂ group (i. e. , -C0₂H, -CHO, and the like). For example, in certain embodiments, R is -C(0)RB; -C0₂RB; or -C(0)N(RB)₂ and R^ is hydrogen. In certain embodiments, R₄ is -C(0)RB; -C0₂RB; or -C(0)N(RB)₂ and R is hydrogen. In certain embodiments, RB is hydrogen. In certain embodiments, RB is an oxygen protecting group. In certain embodiments, RB is sulfonyl. In certain embodiments, RB is aliphatic (e.g., optionally substituted C_1-6 alkyl, C₂_₆alkyl, C₃_₆ alkyl, C₄_₆ alkyl, C₅_₆ alkyl, Qalkyl, C₂alkyl, C₃alkyl, C₄alkyl, C₅alkyl, C₆alkyl). In certain embodiments, R_B is heteroaliphatic. In certain embodiments, RB is perfluoroalkyl (e.g., -CF₃). In certain embodiments, RB is acyl (e.g., - C(0)CH₃). In certain embodiments, RB is amide. In certain embodiments, RB is aryl (e.g., optionally substituted phenyl). In certain embodiments, R_B is heteroaryl. In certain embodiments, two R_B groups, when attached to a nitrogen atom, are joined to form a heterocyclic ring.

[00116] In certain embodiments, the C5 position is substituted with a -C(RB)₃ group

(e.g. , -CH₂F, -CHF₂, -CF ). For example, in certain embodiments, R is -C(RB)₃ and R^ is hydrogen. In certain embodiments, R^ is -C(RB)₃ and R is hydrogen.

[00117] In some embodiments, R₅ is -N(RD)₂- In certain embodiments, R₅ is -N(RD)₂, wherein RD is hydrogen or Ci_₆ alkyl. In certain other embodiments, R₅ is -N(RD)₂, wherein RD is methyl. In some embodiments, R₅ is amino, alkylamino, or dialkylamino. In certain embodiments, R5 is dimethylamino, diethylamino, methyl(ethyl)amino, dipropylamino, methyl(propyl)amino, or ethyl (prop yl)amino. In other embodiments, R5 is (tert- butyldiphenylsilyl)amino. In some embodiments, R₅ is -ORD or -SRD- In some

embodiments, R₅ is -C(RD)₃, wherein RD is as defined and described herein. In other embodiments, R5 is substituted or unsubstituted aliphatic. In certain embodiments, R5 is C . alkyl. In yet other embodiments, R5 is substituted or unsubstituted heteroaliphatic. In certain other embodiments, R₅ is hydrogen. In some embodiments, R₅ is -CH₂N(RD)₂, wherein RD is as defined and described herein. In some embodiments, R₅ is -CH₂N(CH₃)₂.

[00118] In some embodiments, R₉ is -ORD- In certain embodiments, R₉ is hydroxyl.

In certain other embodiments, R₉ is methoxy. In some embodiments, R₉ is alkoxy. In certain embodiments, R₉ is -ORD wherein RD is silyl. In some embodiments, R₉ is -OC(RD)₃, wherein at least one RD is a halogen. In certain embodiments, R9 is -OCF₃, -OCHF2, or - OCH₂F. In certain embodiments, R₉ is ethoxy. In certain embodiments, R₉ is propoxy. In certain embodiments, R₉ is butoxy. In some embodiments, R₉ is -SRD- In certain embodiments, R₉ is alkylthiol. In certain embodiments, R₉ is C_1-6 alkylthiol. In certain embodiments, R₉ is methanethiol. In certain embodiments, R₉ is ethanethiol. In certain embodiments, R₉ is propanethiol. In certain embodiments, R₉ is butanethiol. In certain embodiments, R₉ is -SH. In certain embodiments, R₉ is hydrogen. In some embodiments, R₉ is cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic. In some embodiments, R₉ is alkyl. In some embodiments, R₉ is C_1-6 alkyl. In certain embodiments, R₉ is methyl. In certain embodiments, R₉ is ethyl. In certain embodiments, R₉ is propyl. In certain embodiments, R₉ is butyl. In some embodiments, R₉ is halogen. In certain embodiments, R₉ is fluorine. In other embodiments, R₉ is -N(RD)₂ or -NH(RD). In certain embodiments, R₉ is alkylamino or dialkylamino. In some embodiments, R₉ is a protected hydroxyl group. In certain embodiments, the R₉ hydroxyl group is protected with a silyl group. In certain embodiments, R₉ is -OTBS. In some embodiments, R₉ is a fluoroalkyl group. In certain embodiments, R₉ is -CF₃, -CHF₂, or -CH₂F.

[00119] In some embodiments, Rio is substituted or unsubstituted alkyl. In other embodiments, R₁₀ is -ORD- In some embodiments, R₁₀ is -ORD or -CH₂ORD, wherein R_D is an oxygen protecting group. In certain embodiments, R₁₀ is alkoxy. In certain embodiments, R₁₀ is Ci-6 alkoxy. In certain embodiments, Rio is -CH₂OH, In certain embodients, Rio is - CH₂OCH₃. In certain embodients, Rio is -CH₂N₃. In certain embodiments, Rio is hydroxyl, methoxy, or trifluoromethoxy. In some embodiments, Rio is -N(RD)₂. In some

embodiments, R₁₀ is -SRD- In certain embodiments, R₁₀ is alkylthiol. In certain

embodiments, R₁₀ is Ci_₆ alkylthiol. In certain embodiments, R₁₀ is methanethiol. In certain embodiments, Rio is ethanethiol. In certain embodiments, Rio is propanethiol. In certain embodiments, Rio is butanethiol. In certain embodiments, Rio is -SH. In certain

embodiments, R₁₀ is hydroxyl. In certain embodiments, R₁₀ is halogen. In other

embodiments, R₁₀ is fluorine. In some embodiments, R₁₀ is Ci_₆ alkyl. In certain

embodiments, Rio is methyl. In certain embodiments, Rio is ethyl In certain embodiments, Rio is propyl. In certain embodiments, Rio is butyl. In certain other embodiments, Rio is - CF₃, -CHF₂, or -CH₂F. In certain embodiments, R₁₀ is hydrogen. In other embodiments, R₁₀ is not hydrogen.

[00120] In certain embodiments, Rn is substituted or unsubstituted aliphatic. In some embodiments, Rn is substituted or unsubstituted alkyl. In other embodiments, Rn is -OR_D. In yet other embodiments, Rn is -N(R_D)₂. In other embodiments, Rn is -OR_D- In some embodiments, Rn is -OR_D or -CH₂OR_D, wherein R_D is an oxygen protecting group. In certain embodiments, R is alkoxy. In certain embodiments, Rn is C_1-6 alkoxy. In certain embodiments, Rn is hydroxyl, methoxy, or trifluoromethoxy. In certain embodiments, Rn is alkylthiol. In certain embodiments, Rn is C_1-6 alkylthiol. In certain embodiments, Rn is methanethiol. In certain embodiments, Rn is ethanethiol. In certain embodiments, Rn is propanethiol. In certain embodiments, Rn is butanethiol. In certain embodiments, R is thiol. In certain embodiments, Rn is hydroxyl, methoxy, or trifluoromethoxy. In certain embodiments, Rn is hydroxyl. In certain embodiments, Rn is halogen. In other

embodiments, Rn is fluorine. In some embodiments, R is C_1-6 alkyl. In certain

embodiments, Rn is methyl. In certain embodiments, R is ethyl. In certain embodiments, Rn is propyl. In certain embodiments, Rn is butyl. In certain other embodiments, Rn is - CF₃, -CHF₂, or -CH₂F. In certain embodiments, Rn is hydrogen.

[00121] As generally described above, R₆ and R₈ are absent if the dashed line between the carbon atoms to which R₆ and Rg are attached represents a bond, or are each selected independently from the group consisting of hydrogen, halogen, substituted or unsubstitued aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, substituted or unsubstituted alkoxy, -OH, -CN, -SCN, -SH, alkylthio, -N₃; -N0₂, amino, alkyl amino, and dialkyl amino groups. In certain embodiments, both R₆ and Rg are absent. In other embodiments, R₆ or Rg is absent. In some embodiments, R₆ and Rg are each hydrogen.

[00122] The variable n is an integer in the range of 0 to 8, inclusive. As will be appreciated by one of skill in the art, when the D-ring is aromatic n is an integer between 0 and 4. In some embodiments, n is an integer between 1 and 3. In certain embodiments, n is an integer between 1 and 2. In certain embodiments, n is 1, In certain embodiments, n is 2. In certaine embodiments, n is 3. In certain embodiments, n is 4.

[00123] In certain embodiments, when n is 2, the substituents R₇ are ortho to each other. In other embodiments, when n is 2, the substituents R₇ are para to each other. In yet other embodiments, when n is 2, the substituents R₇ are meta to each other.

[00124] In certain embodiments, each represents a double bond, R₆ and Rg are absent and n is an integer in the range of 0 to 4, inclusive.

[00125] In certain embodiments, R₇ is independently selected from lower alkyl, lower alkenyl, lower alkynyl, halogen, -OR_c, -SR_C, -N(R_C)₂, -NR_CC(0)R_c; -NR_cS0₂R_c; - NRcC(0)CH₂Rc; or -C(Rc)₃. In certain embodiments, R₇ is independently selected from halogen, -OH, -N(R_C)₂, -NR_cC(0)R_c; -NR_cS0₂R_c; or -NR_cC(0)CH₂R_c. In certain embodiments, R₇ is independently selected from -CI, -F, -OH, -NH₂, -N(CH )₂, - NHC(0)R_c; -NHS0₂R_c; and -NHC(0)CH₂R_c, wherein R_c is amide, carbamate, amino (e.g., -NH₂), alkylamino (e.g. , -NH(CH₃), -NH(Et), -NH(iPr), -NH(nPr), -NH(tBu)) or

dialkylamino (e.g. -N(CH )_2> cyclic diaminoalkyl groups selected from aziridinyl, pyrrolidinyl, piperidinyl, morpholinyl, pyrrolyl, imidazolyl, 1,3,4-trianolyl, and tetrazolyl). In certain embodiments, R₇ is selected from -OH. In certain embodiments, R₇ is selected from -CI and -OH. In certain embodiments, R₇ is selected from -F and -OH. In certain embodiments, R₇ is selected from -OH and -N(CH )₂. In certain embodiments, R₇ is selected from -F, -OH, -NH₂, -N(CH₃)₂ and -NHC(0)CH₂R_c. In certain embodiments, R₇ is selected from -OH, -N(CH₃)₂ and -NHC(0)CH₂Rc. In certain embodiments, R₇ is selected from -OH, -NH₂ and -N(CH₃)₂. In certain embodiments, R₇ is selected from -F, - OH and -NHC(0)CH₂R_c. In certain embodiments, at least one R₇ is -OH.

[00126] In certain embodiments, wherein each = represents a double bond, R₆ and

Rg are absent and n is an integer in the range of 0 to 4, inclusive (i.e. , wherein the D ring of the compound is aromatic), the present invention provides compounds of the formula (I-a):

(I-a)

and pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, R_{1 ;} R₂, R₃, R₄, R₅, R₇, Rg, Rio and Rn are as defined herein.

[00127] In certain further embodiments, wherein R₉ is -ORD, the present invention provides compounds of the formula I-b):

(I-b) and pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, Ri, R₂, R₃, R4, R5, R₇, RD, RIO and Rn are as defined herein.

[00128] In certain further embodiments, wherein R⁵ is -N(CH )₂, the present invention provides compounds of the formula I-c):

(I-c)

and pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, Ri, R₂, R₃, R₄, R₇, RD, RIO and Rn are as defined herein.

[00129] In certain further embodiments, wherein R₁₀ and Rn are hydrogen, the present invention provides com ounds of the formula (I-d):

(I-d)

and pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, Ri, R₂, R₃, R₄, R₇, and R_D, are as defined herein.

[00130] In certain further embodiments, wherein Ri and R₂ are hydrogen, the present invention provides com ounds of the formula (I-e):

(I-e) and pharmaceutically acceptable salts thereof, wherein n, Rp_1; Rp₂, Rp₃,R₃, R₄, R₇, and R_D, are as defined herein.

[00131] Various substitution patterns are contemplated for Ring D, wherein n is 1, 2, 3 or 4. For example, in certain further embodiments, wherein n is 1, the present invention rovides compounds of the formulae (I-f), (I-g), (I-h) and (I-i):

and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, R₃, R₄, R₇, and R_D, are as defined herein.

[00132] In certain further embodiments, wherein n is 2, the present invention provides com ounds of the formulae (I-j), (I-k), (1-1), (I-m), (I-n) and (I-o):

(i-j) (I-k)

(I-n) (!-°) and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, R₃, R₄, R₇, and R_D, are as defined herein.

[00133] In certain further embodiments, wherein n is 3, the present invention provides com ounds of the formulae (I-p), (I-q), (I-r) and (I-s):

and pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, R₃, R₄, R₇, and RD, are as defined herein. [00134] In certain embodiments, wherein at least one R₇ is -OH, the present invention provides compounds of the formula (I-t):

(i-t)

and pharmaceutically acceptable salts thereof, wherein R₃, R₄ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from hydrogen, halogen, -N(Rc)₂, - NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, one of R₃ and R₄ is hydrogen and the other is halogen (e.g., fluoro). In certain embodiments, one of R and R₄ is hydrogen and the other is -OR_B- In certain embodiments, one of R and R₄ is hydrogen and the other is -N(R_B)₂ group. In certain embodiments, one of R₃ and R₄ is hydrogen and the other is -N_3. In certain embodiments, one of R₃ and R₄ is hydrogen and the other is - CH₂N(R_B)_2. hi certain embodiments, one of R and R₄ is hydrogen and the other is -CH₂OR_B. In certain embodiments, one of R and R₄ is hydrogen and the other is -CH₂F. In certain embodiments, one of R₃ and R₄ is hydrogen and the other is -CH₂N_3. In certain

embodiments, one of R₃ and R₄ is hydrogen and the other is -C(0)R_B. In certain

embodiments, one of R and R₄ is hydrogen and the other is -C(R_B)₃.

[00135] As generally defined above, the present invention is specifically directed to

C5-tetracycline analogs. C5-tetracycline analogs can be referred to as either "alpha" or "beta" depending upon the nature of the groups R₃ and R₄. alpha C5-tetracycline analogs

[00136] Alternatively, in certain embodiments, wherein R₄ is hydrogen and R₃ is a group other than hydrogen, the present invention provides alpha C5-tetracycline analogs of the formula (I-bl):

(I-bl) or pharmaceutically acceptable salts thereof, wherein n, Rpi, Rp₂, Rp₃, Ri, R₂, R₃, R5, R₇, R9, Rio and Rn are as defined herein. In certain embodiments, each represents a double bond, R₆ and R₈ are absent and n is an integer in the range of 0 to 4. In certain embodiments, R9 is -ORD- In certain embodiments, R⁵ is -N(CH₃)₂. In certain

embodiments, Rio and Rn are hydrogen. In certain embodiments, Ri and R₂ are hydrogen.

[00137] For example, in certain embodiments, provided are alpha C5-tetracycline analogs of formula (I-b2):

(I-b2)

and pharmaceutically acceptable salts thereof, wherein n, Rpi, Rp₂, Rp₃, RD, RI, R₂, R₃ and R₇ are as defined herein. In certain embodiments, Ri and R₂ are hydrogen. In certain embodiments, R₇ is independently selected from halogen, -OH, -N(Rc)₂, -NRcC(0)Rc; - NRcS0₂Rc; or -NRcC(0)CH₂Rc- In certain embodiments, R is halogen (e.g. , fluoro). In certain embodiments, R₃ is -ORB. In certain embodiments, R₃ is -N(RB)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R₃ is -CH₂N(RB)_2. In certain embodiments, R₃ is -CH₂ORB_. In certain embodiments, R is -CH₂F. In certain embodiments, R is - CH₂N₃. In certain embodiments, R is -C(0)RB_. In certain embodiments, R is -C(R_B)₃.

However, in certain embodiments, R₃ is not -OH.

[00138] In certain embodiments, provided are alpha C5-tetracycline analogs of formula (I-b3):

(I-b3)

and pharmaceutically acceptable salts thereof, wherein n, Rpi, Rp₂, Rp₃, Rc, R₃ and R₇ defined herein. In certain embodiments, R₇ is independently selected from halogen, N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R₃ is -ORB- In certain embodiments, R is - N(RB)₂ group. In certain embodiments, R is -N₃. In certain embodiments, R is - CH₂N(RB)_2. In certain embodiments, R₃ is -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R IS -C(RB)₃. However, in certain embodiments, R is not -OH.

[00139] In certain embodiments, wherein n is 1 , provided are alpha C5-tetracycline analo s of formulae (I-b4), (I-b5), (I-b6) and (I-b7):

(I-b6) _(I._b7) and pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, R_P , R_D, R and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₇ is - OH. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R₃ is - ORB- In certain embodiments, R is -N(RB)₂ group. In certain embodiments, R is -N₃. In certain embodiments, R is -CH₂N(RB)_2. In certain embodiments, R is -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R₃ IS -C(RB)₃. However, in certain embodiments, R₃ is not -OH.

[00140] In certain embodiments, wherein n is 2, provided are alpha C5-tetracycline analogs of formulae (I-b8), (I-b9), (I-bl0), (I-bll), (I-bl2) and (I-bl3):

(I-b8) (I-b9)

(I-blO) I-bll)

(I-bl2) (I-bl3)

and pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, Rp₃, RD, R₃ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R is -ORB- In certain embodiments, R is - N(RB)₂ group. In certain embodiments, R is -N₃. In certain embodiments, R is - CH₂N(RB)_2. In certain embodiments, R₃ is -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R IS -C(RB)₃. However, in certain embodiments, R is not -OH.

[00141] In certain further embodiments, wherein n is 3, the present invention provides alpha C5-tetracycline analogs of formulae (I-bl4), (I-bl5), (I-bl6) and (I-bl7):

(I-bl6) (I-bl7)

and pharmaceutically acceptable salts thereof, wherein n, Rp_1; Rp₂, Rp₃, R_D, R₃ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_cC(0)R_c; -NR_CS0₂R_c; or -NR_cC(0)CH₂R_c. In certain embodiments, R₃ is halogen (e.g., fluoro). In certain embodiments, R is -OR_B- In certain embodiments, R is - N(R_B)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R₃ is - CH₂N(R_B)₂. In certain embodiments, R₃ is -CH₂OR_B. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R is -CH₂N_3. In certain embodiments, R is -C(0)R_B. In certain embodiments, R IS -C(R_B)₃. However, in certain embodiments, R is not -OH.

[00142] Certain alpha C5-tetracycline analogs are preferred, for example, wherein

Ring D has a specific substitution pattern.

[00143] For example, in certain embodiments, wherein n is 1 and R₇ is -OH, the present invention provides al ha C5-tetracycline analogs of formula (I-bl8):

(I-bl8) and pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, RD and R₃ are as defined herein. In certain embodiments, R is halogen (e.g. , fluoro). In certain embodiments, R₃ is -ORB- In certain embodiments, R is -N(RB)₂ group. In certain embodiments, R is - N₃. In certain embodiments, R₃ is -CH₂N(RB)_2. In certain embodiments, R₃ is -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R is -C(0)RB_. In certain embodiments, R IS -C(RB)₃. However, in certain embodiments, R is not -OH.

[00144] For example, in certain embodiments, wherein n is 1, R₇ is -OH, and R₃ is -F,

-N(RB)₂, or -ORB_, the present invention provides alpha C5-tetracycline analogs of formula:

(I-bl8-iii)

and pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, RD and RB are as defined herein.

[00145] In certain embodiments, wherein n is 2 and R₇ is selected from -OH and -

N(CH₃)₂, the present invention provides alpha C5-tetracycline analogs of formula (I-bl9):

and pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, RD and R₃ are as defined herein. In certain embodiments, R is halogen (e.g. , fluoro). In certain embodiments, R₃ is -ORB- In certain embodiments, R is -N(RB)₂ group. In certain embodiments, R is - N₃. In certain embodiments, R₃ is -CH₂N(RB)_2. In certain embodiments, R₃ is -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R is -C(0)RB_. In certain embodiments, R IS -C(RB)₃. However, in certain embodiments, R is not -OH.

[00146] For example, in certain embodiments, wherein n is 2, R₇ is selected from -OH and -N(CH₃)₂, and R₃ is -F, -N(RB)₂, or -ORB, the present invention provides alpha C5- tetracycline analogs of formula:

(I-bl9-iii)

[00147] In certain embodiments, wherein n is 2 and R₇ is selected from -OH and -F, the present invention provides alpha C5-tetracycline analogs of formula (I-b24):

(I-b24) and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, R_D and R₄ are as defined herein. In certain embodiments, R₃ is halogen (e.g., fluoro). In certain embodiments, R₃ is -OR_B- In certain embodiments, R is -N(R_B)₂ group. In certain embodiments, R is - N_3. In certain embodiments, R₃ is -CH₂N(R_B)₂. In certain embodiments, R₃ is -CH₂OR_B. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N_3. In certain embodiments, R is -C(0)R_B. In certain embodiments, R IS -C(R_B)₃. However, in certain embodiments, R is not -OH.

[00148] For example, in certain embodiments, wherein n is 2, R₇ is selected from -OH and -F, and R₃ is -F, -N(R_B)₂, or -OR_B, the present invention provides alpha C5-tetracycline analogs of formula:

(I-b24-iii)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, R_D and R_B are as defined herein.

[00149] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -NH₂, and -NHC(0)CH₂Rc, the present invention provides alpha C5-tetracycline analogs of formula (I-b20):

(I-b20) and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, R_D and R₃ are as defined herein. In certain embodiments, R is halogen (e.g., fluoro). In certain embodiments, R₃ is -OR_B- In certain embodiments, R is -N(R_B)₂ group. In certain embodiments, R is - N_3. In certain embodiments, R₃ is -CH₂N(R_B)₂. In certain embodiments, R₃ is -CH₂OR_B. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N_3. In certain embodiments, R is -C(0)R_B. In certain embodiments, R IS -C(R_B)₃. However, in certain embodiments, R is not -OH.

[00150] For example, in certain embodiments, wherein n is 3, R₇ is selected from -OH,

-NH₂, and -N(CH₃)₂, and R₃ is -F, -N(R_B)₂, or -OR_B, the present invention provides alpha -tetracycline analogs of formula:

(I-b20-iii)

and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, R_B, and R_D are as defined herein.

[00151] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -

N(CH )₂, and -NHC(0)CH₂Rc, the present invention provides alpha C5-tetracycline analogs of formula (I-b21):

(I-b21) and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, Rc, R_D and R₃ are as defined herein. In certain embodiments, R_C is dialkylamino. In certain embodiments, R_C is alkylamino. In certain embodiments, R is halogen (e.g., fhioro). In certain embodiments, R is -OR_B. In certain embodiments, R₃ is -N(R_B)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R₃ is -CH₂N(R_B)₂. In certain embodiments, R₃ is -CH₂OR_B. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N_3. In certain embodiments, R is -C(0)R_B. In certain embodiments, R IS -C(R_B)₃. However, in certain embodiments, R₃ is not -OH.

[00152] For example, in certain embodiments, wherein n is 3, R₇ is selected from -OH,

-N(CH₃)₂, and -NHC(0)CH₂R_C, and R₃ is -F, -N(R_B)₂, or -OR_B, the present invention provides alpha C5-tetracycline analogs of formula:

(I-b21-iii)

and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, Rc, R_D and R_B are as defined herein.

[00153] In yet other embodiments, wherein n is 3 and R₇ is selected from -F, -OH, and -NHC(0)CH₂R_c, the present invention provides alpha C5-tetracycline analogs of formula (I-b22):

(I-b22) and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, Rc, R_D and R₃ are as defined herein. In certain embodiments, R_c is dialkylamino. In certain embodiments, R_c is alkylamino. In certain embodiments, R is halogen (e.g., fluoro). In certain embodiments, R is -OR_B. In certain embodiments, R₃ is -N(R_B)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R₃ is -CH₂N(R_B)₂. In certain embodiments, R₃ is -CH₂OR_B. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N_3. In certain embodiments, R is -C(0)R_B. In certain embodiments, R IS -C(R_B)₃. However, in certain embodiments, R₃ is not -OH.

[00154] For example, in certain embodiments, wherein n is 3, R₇ is selected from -OH,

-NH₂, and -NHC(0)CH₂R_c, and R₃ is -F, -N(R_B)₂, or -OR_B, the present invention provides alpha C5-tetracycline analogs of formula:

(I-b22-iii)

[00155] Moreover, as described above, in certain embodiments, at least one R₇ group is -OH. For example, in certain embodiments, the present invention provides alpha C5- tetracycline analogs of formula (I-b23):

(I-b23) and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, Rc and R₄ are as defined herein, and n is 0, 1, 2 or 3. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -OR_B- In certain embodiments, R₄ is -N(R_B)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R^ is -CH₂N(R_B)₂. In certain embodiments, R₄ is-CH₂OR_B. In certain embodiments, R^ is-CH₂F. In certain embodiments, R₃ is - CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ IS -C(R_B)₃.

However, in certain embodiments, R^ is not -OH.

[00156] For example, in certain embodiments, when at least one R₇ group is -OH and

R₃ is -F, -N(R_B)₂, or -OR_B, the present invention provides alpha C5-tetracycline analogs of formula:

(I-b23-iii)

(I-b23-vi)

(I-b23-ix)

and pharmaceutically acceptable salts thereof, wherein R₇, R_P1, R_P2, Rp₃, RD and R_B are as defined herein.

[00157] In certain embodiments, the compound is selected from any one of the following alpha C5-tetracycline analogs:

₅ and pharmaceutically acceptable salts thereof.

[00158] However, in certain embodiments, any one or more of the following compounds are specifically excluded:

and pharmaceutically acceptable salts thereof. beta C5-tetracycline analogs

[00159] In certain embodiments, wherein R₃ is hydrogen, and R₄ is a group other than hydrogen, the present invention provides beta C5-tetracycline analogs of the formula (I-al):

(I-al)

and pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, Ri, R₂, R₄, R5, R7, R9, Rio and Rn are as defined herein. In certain embodiments, each = represents a double bond, R₆ and R₈ are absent and n is an integer in the range of 0 to 4. In certain embodiments, R9 is -OR_D- In certain embodiments, R⁵ is -N(CH )₂. In certain embodiments, R₁₀ and Rn are hydrogen. In certain embodiments, Ri and R₂ are hydrogen.

[00160] For example, in certain embodiments, provided are beta C5-tetracycline analogs of formula (I-a2):

(I-a2) and pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, RD, RI, R₂, R4 and R₇ are as defined herein. In certain embodiments, Ri and R₂ are hydrogen. In certain embodiments, R₇ is independently selected from halogen, -OH, -N(Rc)₂, -NRcC(0)Rc; - NRcS0₂Rc; or -NRcC(0)CH₂Rc- In certain embodiments, R4 is halogen (e.g., fluoro). In certain embodiments, R₄ is -ORB. In certain embodiments, R^ is -N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, Rj is -CH₂N(RB)_2. In certain embodiments, R₄ IS -CH₂ORB_. In certain embodiments, Rj is -CH₂F. In certain embodiments, R₄ is - CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃.

However, in certain embodiments, R^ is not -OH.

[00161] In certain embodiments, provided are beta C5-tetracycline analogs of formula

(I-a3):

(I-a3)

and pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, Rp₃, RD, R₄ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB. In certain embodiments, R₄ is - N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, R₄ is - CH₂N(RB)_2. hi certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00162] In certain embodiments, wherein n is 1 , provided are beta C5-tetracycline analogs of formulae I-a3), (I-a4), (I-a5) and (I-a6):

(I-a4) (I-a5)

(I-a6) _(I._a7) and pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, RD, R4 and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₇ is - OH. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is - ORB. In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00163] In certain embodiments, wherein n is 2, provided are beta C5-tetracycline analo s of formulae (I-a8), (I-a9), (I-al0), (I-all), (I-al2) and (I-al3):

(I-al0) (I-all)

(I-al2) (!-^a13)

and pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, R_P3, RD, R4 and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB- In certain embodiments, R₄ is - N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, R₄ is - CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00164] In certain further embodiments, wherein n is 3, the present invention provides beta C5-tetrac cline analogs of formulae (I-al4), (I-al5), (I-al6) and (I-al7):

(I-al6) _(I._al7)

and pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, R_P , R_D, R₄ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_cC(0)R_c; -NR_cS0₂R_c; or -NR_cC(0)CH₂R_c. In certain embodiments, R₄ is halogen (e.g., fluoro). In certain embodiments, R4 is -OR_B. In certain embodiments, R₄ is - N(R_B)₂ group. In certain embodiments, R₄ is -N_3. In certain embodiments, R^ is - CH₂N(R_B)_2. In certain embodiments, R^ is -CH₂OR_B. In certain embodiments, R^ is -CH₂F. In certain embodiments, R^ is -CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ IS -C(R_B)₃. However, in certain embodiments, R₄ is not -OH.

[00165] Certain beta C5-tetracycline analogs are preferred, for example, wherein Ring

D has a specific substitution pattern. For example, in certain embodiments, wherein n is 1 and R₇ is -OH, the present invention provides beta C5-tetracycline analogs of formula (I- al8):

(I-al8)

and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, R_D and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g., fluoro). In certain embodiments, R₄ is -OR_B- In certain embodiments, R₄ is -N(R_B)₂ group. In certain embodiments, R₄ is - N_3. In certain embodiments, R₄ is -CH₂N(R_B)₂. In certain embodiments, R₄ is -CH₂OR_B. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ is -C(R_B)₃. However, in certain embodiments, R₄ is not -OH.

[00166] For example, in certain embodiments, wherein n is 1, R₇ is -OH, and R₄ is -F,

-OR or -N(R_B)₂, the present invention provides beta C5 -tetracycline analogs of formula:

(I-al8-i) (I-al8-ii)

(I-al8-iii)

[00167] In certain embodiments, wherein n is 2 and R₇ is selected from -OH and -

N(CH₃)₂, the present invention rovides beta C5 -tetracycline analogs of formula (I-al9):

(I-al9)

and pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, RD and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB- In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₄ is - N₃. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ is -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00168] For example, in certain embodiments, wherein n is 2, R₇ is selected from -OH and -N(CH₃)₂, and R₄ is -F, -ORB, or -N(RB)₂, the present invention provides beta C5- tetracycline analogs of formula:

(I-al9-i) (I-al9-ii)

(I-al9-iii)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, R_P3, R_D and R_B are as defined herein.

[00169] In certain embodiments, wherein n is 2 and R₇ is selected from -OH and -F, the present invention provides beta C5-tetrac cline analogs of formula (I-a24):

(I-a24)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, R_P , R_D and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g., fluoro). In certain embodiments, R₄ is -OR_B. In certain embodiments, R₄ is -N(R_B)₂ group. In certain embodiments, R₄ is - N_3. In certain embodiments, R₄ is -CH₂N(R_B)₂. In certain embodiments, R₄ is -CH₂OR_B. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ is -C(R_B)₃. However, in certain embodiments, R₄ is not -OH.

[00170] For example, in certain embodiments, wherein n is 2, R₇ is selected from -OH and -F, and R₄ is -F, -OR_B, or -N(R_B)₂, the present invention provides beta C5 -tetracycline analogs of formula:

(I-a24-i) (I-a24-ii)

(I-a24-iii)

[00171] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -NH₂, and -N(CH₃)₂, the present invention provides beta C5-tetracycline analogs of formula (I- a20):

(I-a20)

and pharmaceutically acceptable salts thereof, wherein Rp_1; Rp₂, Rp₃, R_D and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g., fluoro). In certain embodiments, R₄ is -OR_B- In certain embodiments, R₄ is -N(R_B)₂ group. In certain embodiments, R₄ is - N₃. In certain embodiments, R₄ is -CH₂N(R_B)₂. In certain embodiments, R₄ is -CH₂OR_B. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ is -C(R_B)₃. However, in certain embodiments, R₄ is not -OH.

[00172] For example, in certain embodiments, wherein n is 3, R₇ is selected from -OH,

-NH₂, and -NH(CH₃)₂, and R₄ is -F, -OR_B, or -N(R_B)₂, the present invention provides beta C5-tetracycline analogs of formula:

(l-a20-i) (I-a20-ii)

(I-a20-iii)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, R_B and R_D are as defined herein.

[00173] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -

N(CH₃)₂, and -NHC(0)CH₂Rc, the present invention provides beta C5-tetracycline analogs of formula (I-a21):

(I-a21)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, Rc, R_D and R₄ are as defined herein. In certain embodiments, Rc is dialkylamino. In certain embodiments, Rc is alkylamino. In certain embodiments, R₄ is halogen (e.g., fluoro). In certain embodiments, R₄ is -OR_B- In certain embodiments, R₄ is -N(R_B)₂ group. In certain embodiments, R₄ is -N_3. In certain embodiments, R₄ is -CH₂N(R_B)₂. In certain embodiments, R₄ is -CH₂OR_B. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₃ is -CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ is -C(R_B)₃. However, in certain embodiments, R₄ is not -OH.

[00174] For example, in certain embodiments, wherein n is 3, R₇ is selected from -OH,

-N(CH₃)₂, and -NHC(0)CH₂R_C, and R₄ is -F, -N(R_B)₂, or—OR_B, the present invention provides beta C5-tetracycline analogs of formula:

(I-a21-iii)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, Rc, RD and R_B are as defined herein.

[00175] In yet other embodiments, wherein n is 3 and R₇ is selected from -F, -OH, and -NHC(0)CH₂Rc, the present invention provides beta C5-tetracycline analogs of formula (I-a22):

(I-a22)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, Rc, RD and R₄ are as defined herein. In certain embodiments, Rc is dialkylamino. In certain embodiments, Rc is alkylamino. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB. In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ is -C(RB)₃. However, in certain embodiments, R₄ is not -OH. [00176] For example, in certain embodiments, wherein n is 3, R₇ is selected from -OH,

-F, and -NHC(0)CH₂Rc, and R4 is -F, -N(R_B)₂, or -OR_B, the present invention provides beta C5-tetracycline analogs of formula:

(I-a22-iii)

[00177] Moreover, as described above, in certain embodiments, at least one R₇ group is -OH. For example, in certain embodiments, the present invention provides beta C5- tetracycline analogs of formula (I-a23):

(I-a23)

and pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, R_P3, R_D and R₄ are as defined herein, and n is 0, 1, 2 or 3. In certain embodiments, R₄ is halogen (e.g., fluoro). In certain embodiments, R₄ is -OR_B- In certain embodiments, R₄ is -N(R_B)₂ group. In certain embodiments, R₄ is -N_3. In certain embodiments, R₄ is -CH₂N(R_B)_2. In certain embodiments, R₄ is -CH₂OR_B. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is - CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ IS -C(R_B)₃.

However, in certain embodiments, R₄ is not -OH. [00178] For example, in certain embodiments, when at least one R₇ group is -OH and

R4 is -F, -N(RB)₂, or -ORB, the present invention provides beta C5-tetracycline analogs of formula:

(I-a23-iii)

(I-a23-vi)

(I-a23-ix)

and pharmaceutically acceptable salts thereof, wherein R₇, R_P1, R_P2, R_P3, R_D and R_B are as defined herein.

[00179] In certain embodiments, the compound is selected from any one or more of the following beta C5-tetracycline analogs:

armaceutically acceptable salts thereof.

Compounds of Formula (II)

[00180] The preparation of tetracyclines (I) and (IV) from enones is well-described, wherein an enone comprising the A and B rings of the tetracycline core is joined with another molecule to form the C and D rings of the tetracycline core; see, e.g., for example, US 2005/0282787; WO 2005/112985; WO 2007/117639; US 2009/0093640; and WO

2008/127361; each of which is incorporated herein by reference). This convergent methodology also allows for the synthesis of pentacyclines, hexacyclines, or higher ring systems as well as the incorporation of heterocycles into the ring system. [00181] The preparation of compounds of formula (III) has also been described in

PCT Application No. PCT/US2010/001284, filed April 30, 2010, incorporated herein by reference in its entirety. One new feature, which is the subject of this present application, is the preparation of enones containing substituents at the C5 position and their use in the preparation of new tetracycline analogs. Thus, in one aspect, the present invention provides methods for the preparation of C5-substituted enones of the formula (II) from a compound of formula (III). C5-substituted enones of the formula (II) may be accessed, for example, by reacting a compound of formula (III) with various electrophiles.

[00182] For example, in certain embodiments, the present invention provides a C5- substituted enone of the formula (II):

or a pharmaceutically acceptable salt thereof,

wherein:

Rp4, P3, P4, P5, P9, Rio, and Rn are as defined herein, and

each Rp4 and Rp₅ is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

[00183] In certain embodiments, the present invention provides a method for preparing a C5-substituted enone of the formula (II):

(Π)

or a pharmaceutically acceptable salt thereof, from a compound of formula (III):

(III)

or a pharmaceutically acceptable salt thereof, the method comprising reacting an electrophile with a compound of formula (III) to provide a compound of formula (II), wherein R₃, R₄, R₅, R9, Rio, Rn Rp₄ and R_P5 are as defined herein.

[00184] In certain embodiments, R_P4 is substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, an oxygen protecting group, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In certaine embodiments, Rp₄ is substituted aliphatic (e.g. , aralkyl). In certain embodiments, In certaine embodiments, R_P4 is substituted or unsubstituted benzyl. In other embodiments, R_P4 is hydrogen. In yet other embodiments, R_P4 is acyl. In yet other embodiments, R_P4 is silyl.

[00185] In certain embodiments, R_P5 is a substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, an oxygen protecting group, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl. In certain embodiments, R_P5 is a silyl group. In certain embodiments, R_P5 is a tert-butyl dimethyl silyl group (TBS,

TBDMS).

[00186] In certain embodiments, a compound of formula (II) is an alpha C5- substituted enone of the formula -x):

(II-x)

or a pharmaceutically acceptable salt thereof, wherein R , R5, R₉, R₁₀ and R_P4 are as defined herein.

[00187] For example, in certain embodiments, wherein Rio and Rn are hydrogen, R5 is

-N(CH )₂, and R₉ is -ORD, provided is an alpha C5- substituted enone of the formula (II-x-i):

(ΙΙ-χ-i)

or a pharmaceutically acceptable salt thereof, wherein R₃, R_D and R_P4 are as defined herein.

[00188] In certaine embodiments, a compound of formula (II) is a beta C5- substituted enone of the formula (Il-y):

(ii-y)

or a pharmaceutically acceptable salt thereof, wherein R₄, R5, R₉, R₁₀ and R_P4 are as defined herein.

[00189] For example, in certain embodiments, wherein Rio and Rn are hydrogen, R5 is

-N(CH₃)₂, and R9 is -OR_D, provided is an beta C5- substituted enone of the formula (II-y-i):

(II-y-i)

or a pharmaceutically acceptable salt thereof, wherein R , R_D and R_P4 are as defined herein.

[00190] It was unexpectedly discovered that electrophilic attack of the double bond favors formation of the alpha C5-substituted enone. For example, reaction of (III) with a halogenating reagent as electrophile (e.g., a brominating, chlorinating or iodinating reagent, e.g., Br₂, N-bromosuccinimide, I₂, N-iodosuccinimide; an electrophilic fluorinating agent, e.g., F-TEDA-BF4, Accufluor® NFSi) provides the alpha C5-substituted enone (Il-a) as the preferred product, wherein R₃ is "Hal" selected from bromo, chloro, iodo, and fluoro, and R₄ is hydrogen (Scheme 1). In certain embodiments, the reaction provides the alpha C5- substituted enone (Il-a) as a diastereomerically enriched alpha C5-substituted enone. In certain embodiments, the reaction provides the alpha C5-substituted enone (Il-a) as a diastereomerically pure alpha C5-substituted enone.

Scheme 1.

(Ill) (U-^a)

[00191] Utilizing the halogen C5 group of (Il-a) as a synthetic handle, a wide variety of other diastereomerically enriched C5-substituted enones are contemplated (Schemes 2-3). For example, nucleophilic displacement of bromine, chlorine, or iodine with a hydroxide reagent (e.g., AgOCOCF₃) provides an inverted beta C5- substituted enone (Il-b) wherein R₃ is hydrogen and R₄ is -OR_B, wherein R_B is hydrogen. Substitution/protection of the hydroxyl group of (Il-b) is straightforward, and can provide enones wherein R_B is a group other than hydrogen. Nucleophilic displacement of the beta hydroxyl group of (Il-b) (e.g., under Mitsunobu conditions (e.g., PPh₃, DEAD)) provides the alpha-C5 substitited enones (Il-d) or (Il-f), wherein R₃ is, respectively, either N₃ or -OR_B, R₄ is hydrogen, and R_B is as defined herein. Alpha C5-fluoro substituted enone (II-c) is accessed from beta hydroxy enone (Il-b) upon reaction with nucleophilic fluorine reagent (e.g., DAST), wherein R is fluoro and R₄ is hydrogen. Alternatively, the beta C5-fluoro substituted enone (Il-t) is accessed from alpha hydroxy enone (Il-f) (i.e., wherein R_B is -OH) upon reaction with nucleophilic fluorine reagent (e.g., DAST), wherein R₄ is fluoro and R is hydrogen. Other beta C5 halogen substituted enones (II-u) can be accessed from (Il-t) using nucleophilic reagents, wherein "Hal" is bromo, iodo and chloro. Azido enone (Il-d), upon reduction and optional substitution of the amino group, provides alpha-C5 amino-substituted enones (Il-e), wherein R is -N(R_B)₂, R₄ is hydrogen and R_B is as defined herein. Scheme 2.

(II-e)

[00192] Alternatively, beta C5 amino-substituted enones can be accessed from displacement of the R₃ "Hal" group of (Il-a) with an azido reagent to provide a beta C5 azido-substituted enone (Il-g), wherein R₃ is hydrogen and R₄ is -N₃. Reduction of enone (Il-g) and optional substitution of the amino group provides beta C5 amino-substituted enones (Il-h) wherein R₃ is hydrogen and R₄ is -N(R_B)₂ (Scheme 3).

Sche

(II-a) (Il-g) (II-h)

[00193] Reaction of the compound of formula (III) with an activated imine, e.g.,

CH₂=N(R_B)₂ ⁺X , wherein X is a counterion (e.g., Eschenmoser's salt, CH₂=N(CH₃)₂ ⁺ ; CH₂=N(allyl)₂ ⁺TFA^") provides alpha-C5 substituted enone (II-i), wherein R₃ is -CH₂N(R_B)₂ (e.g., -CH₂N(CH₃)₂ or -CH₂N(allyl)₂) and R₄ is hydrogen (Scheme 4). In certain embodiments, the reaction provides the alpha C5- substituted enone (Il-i) as a diastereomerically enriched alpha C5-substituted enone. In certain embodiments, the reaction provides the alpha C5- substituted enone (Il-i) as a diastereomerically pure alpha C5- substituted enone. In certain further embodiments, when one or both of R is an amino protecting group, such as allyl, the protecting group may be removed to provide the free amine -CH₂NH₂ which may then futher be synthetically manipulated.

Scheme 4.

[00194] Reaction of the compound of formula (III) with activated formaldehyde as an electrophile {e.g., such as formaldehyde-TiCl₄) provides alpha-C5 substituted enone (II-j), wherein R₃ is -CH₂OR_B, and R₄ and R_B are hydrogen. The hydroxyl group of enone (II-j), in turn, can be used as a synthetic handle to provide a variety of functionalized alpha-C5 substituted enones (Schemes 5-7).

[00195] For example, nucleophilic displacement of the hydroxyl group of (Il-b) {e.g., under Mitsunobu conditions {e.g., PPh₃, DEAD)) provides the alpha-C5 substitited enones (Il-k) and (Il-m) wherein R is, respectively, either -CH₂OR_B or -CH₂N₃, R₄ is hydrogen, and R_B is as defined herein (Scheme 5). Reaction of the hydroxyl group of (Il-b) with a nucleophilic fluorine reagent {e.g., DAST) provides alpha-C5 substitited enone (II-l), wherein R₃ is -CH₂F and R₄ is hydrogen. Selective oxidation of the hydroxyl group of (Il-b) provides either the aldehyde enone (Il-n) or the acid enone (II-o), wherein R₃ is an acyl group selected from -CHO or -C0₂H, respectively, and R₄ is hydrogen. Scheme 5.

[00196] The acyl enones (Il-n) and (II-o), in turn, can be further synthetically manipulated. For example, the aldehyde of enone (Il-n) can be reacted with fluorinating reagents (e.g., Deoxofluor™, Ruppert's reagent (CF₃SiMe₃)) to provide fluorinated alpha- substitited enones (II-p) and (Il-q), e.g., wherein R₃ is -C(R_B)₃, R_B is selected from hydrog and fluoro, wherein at least one of R_B are fluoro, and R₄ is hydrogen. Alternatively, the aldehyde of enone (Il-n) can be reductively aminated to alpha-C5 substitited enone (II-i) wherein R₃ is -CH₂N(R_B)₂, R₄ is hydrogen, and R_B is as defined herein.

Scheme 6.

[00197] Furthermore, the carboxylic acid group of enone (II-o) can be converted to wide variety of groups, for example, ester enone (Il-r) and amide enone (II-s), wherein R₃ -C(0)OR_B and -C(0)N(R_B)₂, respectively, R4 is hydrogen and R_B is as defined herein. Scheme 7.

[00198] However, in certain embodiments, alpha C5-substituted enones of the formula

(II), or subgenera thereof, wherein R₃ is -Br and R₄ is hydrogen are excluded. In certain embodiments, beta C5- substituted enones of the formula (II), or subgenera thereof, wherein R₄ is -Br and R₃ is hydrogen are excluded.

[00199] In certain embodiments, alpha C5-substituted enones of the formula (II), or subgenera thereof, wherein R is -N₃ and R₄ is hydrogen are excluded. In certain

embodiments, beta C5- substituted enones of the formula (II), or subgenera thereof, wherein R₄ is -N₃ and R₃ is hydrogen are excluded.

[00200] In certain embodiments, alpha C5-substituted enones of the formula (II), or subgenera thereof, wherein R is -CH₂N(CH )₂ and R₄ is hydrogen are excluded. In certain embodiments, beta C5- substituted enones of the formula (II), or subgenera thereof, wherein R₄ is -CH₂N(CH )₂ and R is hydrogen are excluded.

[00201] However, in certain embodiments, any one of the following compounds of formula II) are specifically excluded:

Compounds of Formula (IV)

[00202] The present invention also provides C5-pentacycline isoxazoles of the formula

(IV):

(IV)

or pharmaceutically acceptable salts thereof; wherein each of =-=-=, n, R_P1, R_P4, R_{1 ;} R₂, R₃, R₄, R₅, R₆, R7, R8, R₉, Rio, and Rn are as defined herein.

[00203] Preferred embodiments of all of the variables (e.g., n, Rp_{1 ;} Rp₂, Rp₃, Ri, R₂, R₃,

R₅, R₆, R₇, R₈, R₉, Rio and Rn as discussed above and herein) are also contemplated for compounds of formula (IV).

[00204] In certain embodiments, wherein =-=-= represents a double bond, R₆ and Rg are absent and n is an integer in the range of 0 to 4, inclusive, the present invention provides compounds of formula (I -a):

(IV-a)

and pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, Rp₄, Ri, R₂, R₃, R₄, R₅, R₇, R9, Rio, and R_{11 ;} are as described herein. [00205] Compounds of formula (IV-a) are provided upon treatment of a C5- substituted enone of the formula (II) with a compound of formula (V), (VI), (VII) or (VIII):

and pharmaceutically acceptable salts thereof, wherein n, Rp_1; Rp₂, Rp₃, Rp₄, Ri, R₂, R₃, R₄, R₅, R₆, R7, R8, R9, Rio, and R_{11 ;} are as described herein, Hal is chloro, bromo or iodo; M is a metal selected from lithium, potassium, or sodium; and R₁₂ is selected from substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

[00206] In certain further embodiments, wherein R₉ is -OR_D, the present invention provides compounds of the formula (IV-b):

(IV-b)

and pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, R_P , R_1; R₂, R , R₄, R5, R₇, R_D, RI_O and Rn are as defined herein.

[00207] In certain further embodiments, wherein R⁵ is -N(CH₃)₂, the present invention provides compounds of the formula (IV-c):

(IV-c)

and pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, Rp₃, R_1; R₂, R₃, R₄, R7, R_D, RI_O and Rn are as defined herein.

[00208] In certain further embodiments, wherein and Rn are hydrogen, the present invention provides compounds of the formula (IV-d):

(IV-d)

or pharmaceutically acceptable salts thereof, wherein n, Rp_1; Rp₂, Rp₃, Ri, R₂, R₃, R*, R7, and R_D, are as defined herein.

[00209] In certain further embodiments, wherein Ri and R₂ are hydrogen, the present invention provides compounds of the formula (IV-e):

(IV-e)

or pharmaceutically acceptable salts thereof, wherein n, Rp_1; Rp₂, Rp₃,R₃, R₄, R₇, and R_D, are as defined herein.

[00210] As generally defined above, the present invention provides C5-pentacycline isoxazoles of the formula (IV). C5-pentacycline isoxazoles can be referred to as either "alpha" or "beta" depending upon the nature of the groups R and R₄.

[00211] For example, wherein R₃ is hydrogen, and R⁴ is a group other than hydrogen, the present invention provides beta C5-pentacycline isoxazoles of the formula (IV-al):

(IV-al)

or pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, Rp₃, Ri, R₂, R₃, R5, R7, R9, R₁₀ and Rn are as defined herein. In certain embodiments, R₉ is -ORc- In certain

embodiments, R5 is -N(CH₃)₂. In certain embodiments, Rio and Rn are hydrogen. In certain embodiments, Ri and R₂ are hydrogen.

[00212] For example, in certain embodiments, wherein R5 is -N(CH )₂, provided are beta C5-pentacycline isoxazoles of the formula (IV-a2):

(IV-a2)

or pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, Rp₃, Rc, Ri, R₂, R4 and R₇ are as defined herein. In certain embodiments, Ri and R₂ are hydrogen. In certain embodiments, R₇ is independently selected from halogen, -OH, -N(Rc)₂, -NRcC(0)Rc; - NRcS0₂Rc; or -NRcC(0)CH₂Rc- In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB- In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₄ is -N_3. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is - CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃.

However, in certain embodiments, R₄ is not -OH.

[00213] In certain further embodiments, wherein Ri and R₂ are hydrogen, provided are beta C5-pentacycline isoxazoles of formula (IV-a3):

(IV-a3)

or pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, RD, R4 and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB- In certain embodiments, R₄ is - N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, R₄ is - CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00214] In certain embodiments, wherein n is 1 , provided are beta C5-pentacycline isoxazoles of formulae (IV-a4), (IV-a5), (IV-a6) and (IV-a7):

(IV-a6) (IV-a7)

or pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, RD, R₄ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_cC(0)R_c; -NR_cS0₂R_c; or -NR_cC(0)CH₂R_c. In certain embodiments, R₇ is - OH. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is - ORB. In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, R₄ is -CH₂N(RB)2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00215] In certain embodiments, wherein n is 2, provided are beta C5-pentacycline isoxazoles of formulae (IV-a8), (IV-a9), (IV-alO), (IV-all), (IV-al2) and (IV-al3):

(IV-al2) (IV-al3)

or pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, Rp₃, RD, R₄ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB. In certain embodiments, R₄ is - N(RB)₂ group. In certain embodiments, R₄ is -N₃. In certain embodiments, R₄ is - CH₂N(RB)_2. hi certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R4 is -CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ IS -C(R_B)₃. However, in certain embodiments, R₄ is not -OH.

[00216] In certain further embodiments, wherein n is 3, the present invention provides beta C5-pentacycline isoxazoles of formulae (IV-al4), (IV-al5), (IV-al6) and (IV-al7):

(IV-al6) (IV-al7)

or pharmaceutically acceptable salts thereof, wherein n, Rp_1; Rp₂, Rp₃, R_D, R₄ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_cC(0)R_c; -NR_CS0₂R_c; or -NR_cC(0)CH₂R_c. In certain embodiments, R₄ is halogen {e.g., fluoro). In certain embodiments, R₄ is -OR_B. In certain embodiments, R₄ is - N(R_B)₂ group. In certain embodiments, R₄ is -N_3. In certain embodiments, R₄ is - CH₂N(R_B)_2. In certain embodiments, R₄ is -CH₂OR_B. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₄ is -CH₂N_3. In certain embodiments, R₄ is -C(0)R_B. In certain embodiments, R₄ IS -C(R_B)₃. However, in certain embodiments, R₄ is not -OH.

[00217] Certain beta C5-pentacycline isoxazoles are preferred, for example, wherein

Ring D has a specific substitution pattern.

[00218] For example, in certain embodiments, wherein n is 1 and R₇ is -OH, the present invention provides beta C5-pentacycline isoxazoles of formula (IV-al8):

(IV-al8)

or pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, Rc and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is - ORB. In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R is -CH₂N_3. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00219] In certain embodiments, wherein n is 2 and R₇ is selected from -OH and -

N(CH₃)₂, the present invention provides beta C5-pentacycline isoxazoles of formula (IV- a!9):

(IV-al9)

or pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, RD and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is - ORB- In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R is -N₃. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00220] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -NMe₂, and -NH₂, the present invention provides beta C5-pentacycline isoxazoles of formula (IV- a20):

(IV-a20)

or pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, RD and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is - ORB. In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R is -CH₂N_3. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00221] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -

N(CH₃)₂, and -NHC(0)CH₂Rc, the present invention provides beta C5-pentacycline isoxazoles of formula -a21):

(IV-a21)

or pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, Rc and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is - ORB- In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R is -N_3. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00222] In yet other embodiments, wherein n is 3 and R₇ is selected from -F, -OH, and -NHC(0)CH₂Rc, the present invention provides beta C5-pentacycline isoxazoles of formula (IV-a22):

(IV-a22)

or pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, RD and R₄ are as defined herein. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is - ORB. In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R is -CH₂N_3. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃. However, in certain embodiments, R₄ is not -OH.

[00223] Moreover, as described above, in certain embodiments, at least one R₇ group is -OH. For example, in certain embodiments, the present invention provides beta C5- pentacycline isoxazoles of formula (IV-a23):

(IV-a23)

or pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, Rc and R₄ are as defined herein, and n is 0, 1, 2 or 3. In certain embodiments, R₄ is halogen (e.g. , fluoro). In certain embodiments, R₄ is -ORB. In certain embodiments, R₄ is -N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R₄ is -CH₂N(RB)_2. In certain embodiments, R₄ is -CH₂ORB_. In certain embodiments, R₄ is -CH₂F. In certain embodiments, R is - CH₂N₃. In certain embodiments, R₄ is -C(0)RB_. In certain embodiments, R₄ IS -C(RB)₃.

However, in certain embodiments, R₄ is not -OH.

[00224] Alternatively, in certain embodiments, the present invention provides for alpha C5-pentacycline isoxazoles of the formula (IV-bl):

(IV-bl)

or pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, Rp₃, Ri, R₂, R₃, R5, R6, R7, Rg, R9, Rio and Rn are as defined herein.

[00225] In certain embodiments, wherein R₄ is hydrogen, and R₃ is a group other than hydrogen, the present invention provides alpha C5-pentacycline isoxazoles of the formula (IV-bl):

(IV-bl)

or pharmaceutically acceptable salts thereof, wherein n, Rpi, Rp₂, Rp₃, Ri, R₂, R₃, R5, R7, R9, R₁₀ and Rn are as defined herein. In certain embodiments, R₉ is -ORc- In certain embodiments, R5 is -N(CH )₂. In certain embodiments, R₁₀ and Rn are hydrogen. In certain embodiments, Ri and R₂ are hydrogen.

[00226] For example, in certain embodiments, wherein R5 is -N(CH₃)₂, provided are alpha C5-pentacycline isoxazoles of the formula (IV-b2):

(IV-b2)

or pharmaceutically acceptable salts thereof, wherein n, Rpi, Rp₂, Rp₃, Rc, Ri, R₂, R₄ and R₇ are as defined herein. In certain embodiments, Ri and R₂ are hydrogen. In certain embodiments, R₇ is independently selected from halogen, -OH, -N(Rc)₂, -NRcC(0)Rc; - NRcS0₂Rc; or -NRcC(0)CH₂Rc- In certain embodiments, R₃ is halogen (e.g., fluoro). In certain embodiments, R₃ is -ORB- In certain embodiments, R is -N(RB)₂ group. In certain embodiments, R is -N₃. In certain embodiments, R is -CH₂N(RB)_2. In certain embodiments, R₃ IS -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is - CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R₃ IS -C(RB)₃.

However, in certain embodiments, R is not -OH.

[00227] In certain further embodiments, wherein Ri and R₂ are hydrogen, provided are alpha C5-pentacycline isoxazoles of formula IV-b3):

(IV-b3)

or pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, RD, R4 and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R₃ is -ORB. In certain embodiments, R₃ is - N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R₃ is - CH₂N(RB)_2. In certain embodiments, R is -CH₂ORB_. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N₃. In certain embodiments, R is -C(0)RB_. In certain embodiments, R₃ IS -C(RB)₃. However, in certain embodiments, R₃ is not -OH.

[00228] In certain embodiments, wherein n is 1 , provided are alpha C5-pentacycline isoxazoles of formulae (IV-b4), (IV-b5), (IV-b6) and (IV-b7):

(IV-b4) (IV-b5)

(IV-b6) (IV-b7)

or pharmaceutically acceptable salts thereof, wherein n, Rp_{1 ;} Rp₂, Rp₃, RD, R4 and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_cS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₇ is - OH. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R₃ is - ORB. In certain embodiments, R₃ is -N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R is -CH₂N(RB)_2. In certain embodiments, R is -CH₂ORB_. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R₃ IS -C(RB)₃. However, in certain embodiments, R₃ is not -OH.

[00229] In certain embodiments, wherein n is 2, provided are alpha C5-pentacycline isoxazoles of formulae (IV-b8), (IV-b9), (IV-blO), (IV-bll), (IV-bl2) and (IV-bl3):

(IV-blO) (IV-bll)

(IV-bl2) (IV-bl3)

or pharmaceutically acceptable salts thereof, wherein n, R_P1, Rp₂, R_P3, RD, R4 and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_CC(0)R_C; -NR_CS0₂R_C; or -NR_CC(0)CH₂R_C. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R₃ is -ORB. In certain embodiments, R₃ is - N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R₃ is - CH₂N(RB)_2. In certain embodiments, R is -CH₂ORB_. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N₃. In certain embodiments, R is -C(0)RB_. In certain embodiments, R₃ IS -C(RB)₃. However, in certain embodiments, R₃ is not -OH.

[00230] In certain further embodiments, wherein n is 3, the present invention provides alpha C5-pentacycline isoxazoles of formulae (IV-bl4), (IV-bl5), (IV-bl6) and (IV-bl7):

(IV-bl6) (IV-bl7)

or pharmaceutically acceptable salts thereof, wherein n, R_P1, R_P2, R_P , R_D, R₄ and R₇ are as defined herein. In certain embodiments, R₇ is independently selected from halogen, -OH, - N(R_C)₂, -NR_cC(0)R_c; -NR_CS0₂R_c; or -NR_cC(0)CH₂R_c. In certain embodiments, R₃ is halogen (e.g., fluoro). In certain embodiments, R₃ is -OR_B. In certain embodiments, R₃ is - N(R_B)₂ group. In certain embodiments, R is -N_3. In certain embodiments, R is - CH₂N(R_B)_2. In certain embodiments, R is -CH₂OR_B. In certain embodiments, R is -CH₂F. In certain embodiments, R₃ is -CH₂N_3. In certain embodiments, R₃ is -C(0)R_B. In certain embodiments, R₃ IS -C(R_B)₃. However, in certain embodiments, R₃ is not -OH.

[00231] Certain alpha C5-pentacycline isoxazoles are preferred, for example, wherein

Ring D has a specific substitution pattern.

[00232] For example, in certain embodiments, wherein n is 1 and R₇ is -OH, the present invention provides al ha C5-pentacycline isoxazoles of formula (IV-bl8):

(IV-bl8)

or pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, R_P , R_D and R₄ are as defined herein. In certain embodiments, R is halogen (e.g., fluoro). In certain embodiments, R is - OR_B. In certain embodiments, R₃ is -N(R_B)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R₃ is -CH₂N(R_B)₂. In certain embodiments, R₃ is -CH₂OR_B. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N_3. In certain embodiments, R₃ is -C(0)R_B. In certain embodiments, R IS -C(R_B)₃. However, in certain embodiments, R is not -OH.

[00233] In certain embodiments, wherein n is 2 and R₇ is selected from -OH and -

N(CH )₂, the present invention provides alpha C5-pentacycline isoxazoles of formula (IV- b!9):

(IV-bl9) or pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, RD and R4 are as defined herein. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R is - ORB- In certain embodiments, R is -N(RB)₂ group. In certain embodiments, R is -N₃. In certain embodiments, R₃ is -CH₂N(RB)_2. In certain embodiments, R₃ is -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R IS -C(RB)₃. However, in certain embodiments, R is not -OH.

[00234] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -NMe₂, and -NH₂, the present invention provides alpha C5-pentacycline isoxazoles of formula (IV- b20):

(IV-b20)

or pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, RD and R₄ are as defined herein. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R₃ is - ORB. In certain embodiments, R₃ is -N(RB)₂ group. In certain embodiments, R₃ is -N_3. In certain embodiments, R is -CH₂N(RB)_2. In certain embodiments, R is -CH₂ORB_. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R₃ IS -C(RB)₃. However, in certain embodiments, R₃ is not -OH.

[00235] In certain embodiments, wherein n is 3 and R₇ is selected from -OH, -

N(CH )₂, and -NHC(0)CH₂Rc, the present invention provides alpha C5-pentacycline isoxazoles of formula -b21):

(IV-b21) or pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, Rc and R4 are as defined herein. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R is - ORB- In certain embodiments, R is -N(RB)₂ group. In certain embodiments, R is -N_3. In certain embodiments, R₃ is -CH₂N(RB)_2. In certain embodiments, R₃ is -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is -CH₂N_3. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R IS -C(RB)₃. However, in certain embodiments, R is not -OH.

[00236] In yet other embodiments, wherein n is 3 and R₇ is selected from -F, -OH, and -NHC(0)CH₂Rc, the present invention provides alpha C5-pentacycline isoxazoles of formula (IV-b22):

(IV-b22)

or pharmaceutically acceptable salts thereof, wherein R_P1, R_P2, Rp₃, RD and R₄ are as defined herein. In certain embodiments, R₃ is halogen (e.g. , fluoro). In certain embodiments, R₃ is - ORB. In certain embodiments, R₃ is -N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R is -CH₂N(RB)_2. In certain embodiments, R is -CH₂ORB_. In certain embodiments, R is -CH₂F. In certain embodiments, R is -CH₂N₃. In certain embodiments, R₃ is -C(0)RB_. In certain embodiments, R₃ IS -C(RB)₃. However, in certain embodiments, R₃ is not -OH.

[00237] Moreover, as described above, in certain embodiments, at least one R₇ group is -OH. For example, in certain embodiments, the present invention provides alpha C5- pentacycline isoxazoles of formula (IV-b23):

(IV-b23) or pharmaceutically acceptable salts thereof, wherein Rp_{1 ;} Rp₂, Rp₃, RD and R4 are as defined herein, and n is 0, 1, 2 or 3. In certain embodiments, R is halogen (e.g. , fluoro). In certain embodiments, R is -ORB- In certain embodiments, R is -N(RB)₂ group. In certain embodiments, R₃ is -N₃. In certain embodiments, R₃ is -CH₂N(RB)_2. In certain embodiments, R₃ IS -CH₂ORB_. In certain embodiments, R₃ is -CH₂F. In certain embodiments, R₃ is - CH₂N_3. In certain embodiments, R is -C(0)RB_. In certain embodiments, R IS -C(RB)₃.

However, in certain embodiments, R is not -OH.

[00238] However, certain embodiments, any one of the following compounds are specifically excluded:

and pharmaceutically acceptable salts thereof. Pharmaceutical Compositions

[00239] In certain embodiments, the present invention provides a pharmaceutical composition comprising a compound of the present invention (e.g., a compound of formula (I)) or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

[00240] Pharmaceutically acceptable excipients include any and all solvents, diluents or other liquid vehicles, dispersion or suspension aids, surface active agents, isotonic agents, thickening or emulsifying agents, preservatives, solid binders, lubricants and the like, as suited to the particular dosage form desired. General considerations in the formulation and/or manufacture of pharmaceutical compositions agents can be found, for example, in Remington's Pharmaceutical Sciences, Sixteenth Edition, E. W. Martin (Mack Publishing Co., Easton, Pa., 1980), and Remington: The Science and Practice of Pharmacy, 21^s Edition (Lippincott Williams & Wilkins, 2005).

[00241] Except insofar as any conventional carrier medium is incompatible with the anti-cancer compounds of the invention, such as by producing any undesirable biological effect or otherwise interacting in a deleterious manner with any other component(s) of the pharmaceutical composition, its use is contemplated to be within the scope of this invention. Some examples of materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; Cremophor; Solutol; excipients such as cocoa butter and suppository waxes; oils such as peanut oil, cottonseed oil; safflower oil; sesame oil; olive oil; corn oil and soybean oil;

glycols; such a propylene glycol; esters such as ethyl oleate and ethyl laurate; agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.

[00242] Liquid dosage forms for oral and parenteral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents. In certain embodiments for parenteral administration, the compounds of the invention are mixed with solubilizing agents such an Cremophor, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and combinations thereof.

[00243] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S. P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

[00244] The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

[00245] In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide- polyglycolide. Depending upon the ratio of drug to polymer and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other

biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissues.

[00246] Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.

[00247] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar— agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.

[00248] Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.

[00249] The active compounds can also be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes.

[00250] Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, ear drops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms can be made by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.

[00251] It will also be appreciated that the compounds and pharmaceutical

compositions of the present invention can be employed in combination therapies, that is, the compounds and pharmaceutical compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of the desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, an inventive compound may be administered concurrently with another anticancer agent), or they may achieve different effects (e.g. , control of any adverse effects).

[00252] In still another aspect, the present invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention, and in certain embodiments, includes an additional approved therapeutic agent for use as a combination therapy. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceutical products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

[00253] Although the descriptions of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and/or perform such modification with ordinary experimentation. General considerations in the formulation and/or manufacture of pharmaceutical compositions can be found, for example, in Remington: The Science and Practice of Pharmacy 21^st ed., Lippincott Williams & Wilkins, 2005.

Methods of Use and Treatment

[00254] The present invention further provides methods of treating microbial infections and hyperproliferative diseases.

[00255] For example, in one aspect, provided is a method of treating a microbial infection comprising administering a therapeutically effective amount of a compound of the present invention {e.g., a compound of formula (I)) or pharmaceutically acceptable salt thereof to a subject in need thereof.

[00256] As used herein, a "microbial infection" refers to an infection with a

microorganism, such as a fungus, bacteria or virus. In certain embodiments, the "microbial infection is an infection with a bacteria, i.e., a "bacterial infection". In certain embodiments, the compounds of the invention exhibit antibacterial activity. For example, in certain embodiments, the compound has a mean inhibitory concentration, with respect to a particular bacteria, of less than 50 μg/mL, preferably less than 25 μg/mL, more preferably less than 5 μg/mL, and most preferably less than 1 μg/mL. Various microbial infections include, but are not limited to, skin infections, GI infections, urinary tract infections, genito-urinary infections, systemic infections.

[00257] Exemplary bacteria include, but are not limited to, gram positive bacteria {e.g.,

Staphylocococcus aureus, Streptococcus Group A, Streptococcus viridans and Streptococcus pneumoniae), and gram-negative bacteria {e.g., Neisseria meningitidis, Neisseria

gonorrhoeae, Haemophilus influenzae, Escherichia coli, Bacteroides fragilis, other

Bacteroides) and other bacteria {e.g., Mycoplasma pneumoniae, Treponema pallidum, Rickettsia, and Chlamydia.

[00258] In certain embodiments, a compound of the present invention {e.g., a compound of formula (I)) inhibits the growth of or kill microorganisms, and, in certain embodiments, inhibit the growth of or kill tetracycline-resistant organisms including chlortetracycline-resistant organisms, oxytetracycline-resistant organisms, demeclocycline- resistant organisms, doxycycline-resistant organisms, minocycline-resistant organisms, or any organisms resistant to antibiotics of the tetracycline class used in human or veterinary medicine. Thus, in certain embodiments of the present invention, a "therapeutically effective amount" of a compound of the present invention or pharmaceutically acceptable derivative thereof is that amount sufficient in killing or inhibiting the growth of bacteria.

[00259] In other embodiments, a compound of the present invention (e.g., a compound of formula (I)) shows cytostatic or cytotoxic activity against neoplastic cells such as cancer cells. Thus, in another aspect, provided is a method of treating a proliferative disease (e.g., cancer) comprising administering a therapeutically effective amount of a compound of the present invention or pharmaceutically acceptable salt thereof to a subject in need thereof.

[00260] In yet other embodiments, a compound of the present invention (e.g., a compound of formula (I)) inhibits the growth of or kill rapidly dividing cells such as stimulated inflammatory cells. Thus, in yet another aspect, provided is a method of treating an autoimmune disease (e.g. , inflammatory diseases, rheumatoid arthritis, lupus) comprising administering a therapeutically effective amount of a compound of the present invention or pharmaceutically acceptable salt thereof to a subject in need thereof.

[00261] Other conditions which are contemplated for treatment include inflammatory diseases and diabetic retinopathy.

[00262] The compound of the present invention can be administered using any amount and any route of administration effective for treatment. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular composition, its mode of administration, its mode of activity, and the like.

[00263] Compounds provided herein are typically formulated in dosage unit form for ease of administration and uniformity of dosage. It will be understood, however, that the total daily usage of the compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject or organism will depend upon a variety of factors including the disease, disorder, or condition being treated and the severity of the disorder; the activity of the specific active ingredient employed; the specific composition employed; the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific active ingredient employed; the duration of the treatment; drugs used in combination or coincidental with the specific active ingredient employed; and like factors well known in the medical arts.

[00264] The compounds and compositions provided herein can be administered by any route, including oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal, interdermal, rectal, intravaginal, intraperitoneal, topical (as by powders, ointments, creams, and/or drops), mucosal, nasal, bucal, enteral, sublingual; by intratracheal instillation, bronchial instillation, and/or inhalation; and/or as an oral spray, nasal spray, and/or aerosol. In general the most appropriate route of administration will depend upon a variety of factors including the nature of the agent (e.g. , its stability in the environment of the gastrointestinal tract), the condition of the subject (e.g. , whether the subject is able to tolerate oral administration), etc. In certain embodiments, the compound or pharmaceutical composition is administered orally. In other embodiments, the compound or pharmaceutical composition is administered parenterally.

[00265] In certain embodiments, the compounds of the invention may be administered orally or parenterally at dosage levels sufficient to deliver from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, preferably from about 0.1 mg/kg to about 40 mg/kg, preferably from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, and more preferably from about 1 mg/kg to about 25 mg/kg, of a subject' s body weight per day, one or more times a day, to obtain the desired therapeutic effect. The desired dosage may be delivered three times a day, two times a day, once a day, every other day, every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage may be delivered using multiple administrations (e.g. , two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations). It will be appreciated that dose ranges as described herein provide guidance for the administration of provided pharmaceutical compositions to an adult. The amount to be administered to, for example, a child or an adolescent can be determined by a medical practitioner or person skilled in the art and can be lower or the same as that administered to an adult.

[00266] It will be also appreciated that a compound or composition, as described herein, can be administered in combination with one or more additional therapeutically active agents. The compound or composition can be administered concurrently with, prior to, or subsequent to, one or more additional therapeutically active agents. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In will further be appreciated that the additional therapeutically active agent utilized in this combination can be administered together in a single composition or administered separately in different compositions. The particular combination to employ in a regimen will take into account compatibility of the inventive compound with the additional therapeutically active agent and/or the desired therapeutic effect to be achieved. In general, it is expected that additional therapeutically active agents utilized in combination be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually.

[00267] The compounds or compositions can be administered in combination with other agents that improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body. It will also be appreciated that therapy employed may achieve a desired effect for the same disorder (for example, a compound can be administered in combination with an anti-inflammatory, anti-anxiety and/or anti-depressive agent, etc.), and/or it may achieve different effects (e.g., control of adverse side-effects). Exemplary therapeutically active agents include, but are not limited to, antimicrobial agents, antiproliferative agents and antiinflammatory agents (e.g. aspirin, ibuprofen, acetaminophen, etc., pain reliever) and anti-pyretic agents.

Examples

[00268] These and other aspects of the present invention will be further appreciated upon consideration of the following Examples, which are intended to illustrate certain particular embodiments of the invention but are not intended to limit its scope, as defined by the claims.

Materials and Methods

[00269] General Procedures. All reactions were performed in flame-dried round bottomed or modified Schlenk (Kjeldahl shape) flasks fitted with rubber septa under a positive pressure of argon, unless otherwise noted. Air- and moisture-sensitive liquids and solutions were transferred via syringe or stainless steel cannula. Where necessary (so noted), solutions were deoxygenated by alternative freeze (liquid nitrogen)/evacuation/ thaw cycles (> three iterations). Organic solutions were concentrated by rotary evaporation at -25 Torr

(house vacuum). Flash column chromatography was performed on silica gel (60 A, standard grade) as described by Still et al. (Still, W. C; Kahn, M.; Mitra, A. J. Org. Chem. 1978, 43, 2923-2925; incorporated herein by reference). Analytical thin-layer chromatography was performed using glass plates pre-coated with 0.25 mm 230-400 mesh silica gel impregnated with a fluorescent indicator (254 nm). Thin layer chromatography plates were visualized by exposure to ultraviolet light and/or exposure to eerie ammonium molybdate or an acidic solution of /7-anisaldehyde followed by heating on a hot plate.

[00270] Materials. Commercial reagents and solvents were used as received with the following exceptions. Chlorotrimethylsilane, triethylamine, diisopropylamine, 2,2,6,6- tetramethylpiperidine, N,N, N',N'-tetramethylethylenediamine, DMPU, HMPA, and N,N- diisopropylethylamine were distilled from calcium hydride under dinitrogen atmosphere. Benzene, dichloromethane, ethyl ether, methanol, pyridine, tetrahydrofuran, hexane, acetonitrile, N,N-dimethylformamide, and toluene were purified by the method of Pangborn et al. (Pangborn, A. B.; Giardello, M. A.; Grubbs, R. H.; Rosen, R. K.; Timmers, F. J. Organometallics 1996, 15, 1518-1520; incorporated herein by reference). The molarity of n- butyllithium, s-butyllithium, and i-butyllithium were determined by titration with a tetrahydrofuran solution of 2-butanol using triphenylmethane as an indicator (Duhamel, L.; Palquevent, J.-C. /. Org. Chem. 1979, 44, 3404-3405; incorporated herein by reference).

[00271] Instrumentation. Proton nuclear magnetic resonance (1H NMR) spectra a+nd carbon nuclear magnetic resonance ( 13 C NMR) were recorded with Varian Unity/Inova 600 (600 MHz), Varian Unity/Inova 500 (500 MHz/125 MHz), or Varian Mercury 400 (400 MHz/100 MHz) NMR spectrometers. Chemical shifts for protons are reported in parts per million scale (δ scale) downfield from tetramethylsilane and are referenced to residual protium in the NMR solvents (CHC1₃: δ 7.26, C₆D₅H: δ 7.15, D₂HCOD: δ 3.31, CDHC1₂: δ 5.32, (CD₂H)CD₃SO: δ 2.49). Chemical shifts for carbon are reported in parts per million (δ scale) downfield from tetramethylsilane and are referenced to the carbon resonances of the solvent (CDC1₃: δ 77.0, C₆D₆: δ 128.0, D₃COD: δ 44.9, CD₂C1₂: δ 53.8, (CD₃)₂SO: δ 39.5). Data are represented as follows: chemical shift, multiplicity (s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet, br = broad), integration, coupling constant in Hz, and assignment. Infrared (IR) spectra were obtained using a Perkin-Elmer 1600 FT-IR spectrophotometer referenced to a polystyrene standard. Data are represented as follows: frequency of the absorption (cm^-1), intensity of absorption (s = strong, sb = strong broad, m = medium, w = weak, br =broad), and assignment (where appropriate). Optical rotations were determined on a JASCO DIP-370 digital polarimeter equipped with a sodium lamp source using a 200-μΙ. or 2-mL solution cell. High resolution mass spectra were obtained at the Harvard University Mass Spectrometry Facilities. [00272] The syntheses of enones (1) and (2) and (3) have been described in PCT Application No. PCT/US2010/001284, filed April 30, 2010, incorporated herein by reference in its entirety.

Exemplary Syntheses of C5-Substituted Enones

Example 1A

[00273] Synthe - substituted Enone 4.

3 4

[00274] To a stirred solution of 3 (3.048 g, 5.11 mmol) in THF (40 mL) with H₂0 (10 mL) was added N-bromosuccinimide (1.09 g, 6.13 mmol, 1.2 eq.) which dissolved over approximately two minutes, at which point the reaction was determined to be complete (TLC monitoring). The reaction mixture was poured over NaHC0₃ sat. aq. (100 mL) and extracted with ethyl acetate (2 x 120 mL). The combined organics were washed with brine (100 mL), dried (Na₂S0₄), and concentrated in vacuo. Only a single diastereomeric product was observed by NMR of the crude residue. Flash column chromatography (Si0₂, 20% ethyl acetate in hexanes) of the residue provided the alpha-C5 bromo enone 4 as a yellow solid

(2.456 g, 86%).

[00275] Characterization of 4: R_f = 0.50 (20% ethyl acetate in hexanes); IR (neat) 2935, 1722, 1688, 1616, 1514, 1473 cm^"1; 1H NMR (500 MHz, CDC1₃) δ 7.50 (d, J = 6.8 Hz, 2H), 7.37 (m, 3H), 6.88 (m, 1H), 6.10 (d, J = 10.2 Hz, 1H), 5.37 (s, 2H), 5.34 (d, J = 4.4 Hz, 1H), 3.55 (d, J = 10.7 Hz, 1H), 3.22 (d, J = 10.7 Hz, 1H), 2.52 (s, 6H), 0.94 (s, 9H), 0.22 (s, 3H), 0.06 (s, 3H); ¹³C NMR (500 MHz, CDC1₃) δ 193.3, 186.3, 179.4, 167.4, 145.1, 134.9, 128.6, 128.6, 128.4, 127.3, 82.7, 72.7, 60.8, 53.0, 42.0, 38.2, 26.4, 19.3, 17.8, 12.3, -2.4, -2.7; HRMS for CaeHssNaOsSiBr [MH+] m/z calc. 561.14149, found 561.14899.

[00276] Single crystal X-ray Diffraction confirmed the stereochemistry of 4 as the above- depicted alpha C5-isomer (see Figure 1 depicting an ORTEP for 4).

Example

[00277] Synthesis of C5- substituted Enone 5.

[00278] To a stirred solution of the 4 (790 mg, 1.41 mmol) in dry acetonitrile (12 mL) under an atmosphere of Ar at room temperature was added tetramethylguanidinium azide (660 mg, 5.64 mmol, 4.0 eq.). After 30 min, the mixture was added dropwise via cannula to methyl i-butyl ether (200 mL). The mixture was dried (Na₂S0₄), filtered over Celite, and the filtrate was concentrated in vacuo. Flash column chromatography (Si0₂, 10% ethyl acetate in hexanes) of the residue provided the beta C5 azido enone 5 as a pink powder, which was recrystallized from hot hexanes (412 mg, 60%) to off-white needles. Only a single diastereomeric product was observed by NMR of the crude residue.

[00279] Characterization of 5: R_f = 0.68 (20% ethyl acetate in hexanes); ¹H NMR (500 MHz, CDC1₃) δ 7.49 (d, J = 7.0 Hz, 2H), 7.37 (m, 3H), 6.72 (dd, J = 8.0, 6.5 Hz, 1H), 6.10 (dd, J = 10.5, 3.0 Hz, 1H), 5.34 (s, 2H), 5.18 (m, 1H), 4.04 (d, J = 8.5 Hz, 1H), 3.12 (m, 1H), 2.44 (s, 6H), 0.86 (s, 9H), 0.30 (s, 3H), 0.05 (s, 3H); ¹³C NMR (500 MHz, CDC1₃) δ 190.9, 185.6, 179.8, 166.9, 147.9, 134.8, 128.6, 128.5, 128.5, 128.4, 108.9, 83.4, 72.6, 58.0, 57.9, 51.5, 41.2, 31.2, 29.7, 26.0, 18.9, 1.0, -2.4, -3.9; HRMS for C^HssNsOsSi [MH+] m/z calc. 524.23237, found 524.23489. Example 3A

- substituted Enones 6 and 7.

3 6 7

[00281] To a stirred solution of 3 (362 mg, 0.652 mmol) in 1,2-dichloroethane (10 mL) was added Eschenmoser's salt (150 mg, 0.80 mmol, 1.2 eq.). The mixture was heated to reflux and stirred 14 h. After cooling to room temperature, the solution was diluted in

CH₂CI₂ (25 mL) and washed with sat. aq. NaHC0₃ (2 x 25 mL), the organic layer was dried

(Na₂S0₄) and concentrated in vacuo. Flash column chromatography of the residue (S1O₂,

20% ethyl acetate in hexanes to elute enone 7, and flushing with ethyl acetate to elute enone

6) provided the alpha-C5 (dimethylamino)methyl enone 6 (139 mg, 40%) as a bright yellow oil and the methylene enone 7 (154 mg, 48%) as an orange solid. Only a single diastereomeric product corresponding to 6 was observed by NMR of the crude residue. The stereochemistry of the (dimethylamino)methyl group at the C5 position of 6 was determined by 1D-NOESY NMR.

[00282] Characterization of 6: R_f = 0.05 (20% ethyl acetate in hexanes); ¹H NMR (500 MHz, CDC1₃) δ 7.52 (d, J = 6.9 Hz, 2H), 7.41 (dd, J = 7.8, 6.8 Hz, 2H), 7.36 (d, J = 7.3 Hz, 1H), 6.92 (m, 1H), 6.10 (dd, J = 10.2 , 1.9 Hz, 1H), 5.38 (s, 2H), 3.59 (d, J = 11.3 Hz, 1H), 3.21 (m, 1H), 2.92 (d, J = 12.2 Hz, 1H), 2.80 (dd, J = 11.7, 8.8 Hz, 1H), 2.56 (dd, J = 12.2, 6.3 Hz, 1H), 2.50 (s, 6H), 2.28 (s, 6H), 0.90 (s, 9H), 0.26 (s, 3H), 0.03 (s, 3H);

[00283] Characterization of 7: R_f = 0.52 (20% ethyl acetate in hexanes); 1H NMR (500 MHz, CDC1₃) δ 7.52 (d, J = 7.4 Hz, 2H), 7.41 (dd, J = 7.4, 5.9 Hz, 2H), 7.37 (d, J = 5.9 Hz, 1H), 7.13 (d, J = 10.3 Hz, 1H), 6.00 (d, J = 10.3 Hz, 1H), 5.64 (s, 1H), 5.52 (s, 1H), 5.38 (s, 2H), 3.74 (d, J = 10.3 Hz, 1H), 3.27 (d, J = 10.3 Hz, 1H), 2.48 (s, 6H), 0.80 (s, 9H), 0.24 (s, 3H), 0.07 (s, 3H). Example 4A

[00284] Synthesis of C5- substituted Enone 8.

[00285] Light was excluded during the reaction, work-up and purification. N- Iodosuccinimide (646 mg, 2.81 mmol, 1.05 equiv) was added in one portion to a solution of 3 (1.60 g, 2.68 mmol, 1 equiv) in acetonitrile-water (20 mL, 19: 1) at -10 °C (ice-salt bath). The reaction mixture was allowed to warm to 0 °C and then was stirred at this temperature for 4 1/2 h, whereupon saturated aqueous sodium thiosulfate solution and ethyl acetate (80 mL each) were added in sequence. The phases were separated and the aqueous phase was further extracted with ethyl acetate (80 mL). The combined organic extracts were dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. Only a single diastereomeric product was observed by NMR of the crude residue. The crude iodination product was purified by flash-column chromatography (12% ethyl acetate- hexanes, grading to 15%), affording the alpha-C5 iodo enone 8 as a yellow solid (1.55 g, 95%).

Example 5A

Synthesis of C5- substituted Enone 9.

4

[00287] Method 1: Silver trifluoroacetate (556 mg, 2.465 mmol, 1 equiv) was added to a solution of 8 (1.50 g, 2.465 mmol, 1 equiv) in dioxane-water (5: 1, 30 mL) at 23 °C. The resulting mixture was heated to 40 °C. After stirring at this temperature for 13 h, the reaction mixture was allowed to cool to 23 °C. Saturated aqueous sodium thiosulfate solution and ethyl acetate (150 mL each) were added in sequence to the cooled solution. The phases were separated and the organic phase was washed with saturated aqueous sodium bicarbonate solution (75 mL). The aqueous phases were combined and the combined solution was extracted with ethyl acetate (150 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (20% ethyl acetate-hexanes, grading to 25%), affording the beta C5 hydroxy enone 9 as an off-white solid (723 mg, 59%).

[00288] Method 2: Silver trifluoroacetate (75 mg, 0.339 mmol, 1.5 equiv) was added to a solution of bromo enone 4 (127 mg, 0.226 mmol, 1 equiv) in dioxane-water (5: 1, 6 mL) at 23 °C. The resulting mixture was heated to 60 °C. After stirring at this temperature for 16 h, the reaction mixture was allowed to cool to 23 °C. The mixture was diluted with methyl tert- butyl ether (20 mL) and then washed with saturated aqueous sodium bicarbonate solution. The phases were separated and the organic phase was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (20% ethyl acetate-hexanes, grading to 25%), affording the beta C5 hydroxy enone 9 as an off-white solid (56 mg, 50%). [00289] Characterization of 9: R/ = 0.40 (30% ethyl acetate-hexanes); 1H NMR (500 MHz, CDC1₃) δ 7.50 (d, 2H, J = 6.5 Hz), 7.41-7.35 (m, 3H), 7.30 (1H, bs), 7.08 (1H, d, J = 11.0 Hz), 6.07 (dd, 1H, J = 10.5, 2.5 Hz), 5.36 (s, 2H), 5.21 (m, 1H), 4.37 (d, 1H, J = 11.0 Hz), 3.26 (m, 1H), 2.56 (bs, 6H), 0.84 (s, 9H), 0.27 (s, 3H), 0.04 (s, 3H); HRMS-ESI (m z): [M+H]⁺ calcd for C26H34N2O6S1, 499.2259; found, 499.2278.

Example 6A

[00290] Synthes - substituted Enone 10.

9 10

[00291] Diethyl azodicarboxylate (434 μΐ., 40% solution in toluene, 0.953 mmol, 1.25 equiv) was added dropwise to a solution of 9 (380 mg, 0.762 mmol, 1 equiv) and triphenylphosphine (250 mg, 0.953 mmol, 1.25 equiv) in anhydrous dichloromethane (13.0 mL) at 23 °C. The resulting mixture was stirred at this temperature for 2 min, whereupon diphenyl phosphoryl azide (212 μί, 0.953 mmol, 1.25 equiv) was added. The reaction mixture was stirred at 23 °C for 2 h, then was concentrated. The crude product was purified by flash-column chromatography (13% ethyl acetate-hexanes), affording alpha-C5 hydroxy enone 9 (287 mg, 72%).

Example

[00292] Synthesis of C5- substituted Enone 11.

11

[00293] Diethylamino sulfur trifluoride (DAST) (74 μΐ,, 0.562 mmol, 1.1 equiv) was added dropwise to a solution of 9 (255 mg, 0.511 mmol, 1 equiv) in anhydrous dichloromethane (10.0 mL) at 0 °C. The resulting mixture was allowed to warm to 23 °C. After stirring at this temperature for 15 min, the reaction mixture was diluted with dichloromethane (10 mL) and washed with saturated aqueous sodium bicarbonate solution (20 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (20 mL). The organic extracted were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (20% ethyl acetate-hexanes, grading to 50%), affording alpha-C5 fluoro enone 11 as a yellow solid (171 mg, 67%).

Example 8A

[00294] Synthesis of C5- substituted Enone 12.

[00295] A solution of titanium tetrachloride in dichloromethane (1.0 M, 80 μί, 0.080 mmol, 1.25 equiv) was added dropwise to a solution of 3 (38 mg, 0.064 mmol, 1 equiv) and paraformaldehyde (9.6 mg, 0.318 mmol, 5 equiv) in dichloromethane (1.5 mL) at 0 °C. The resulting mixture was allowed to warm to 23 °C, then was stirred at this temperature for 11 h. The resulting mixture was diluted with dichloromethane (10 mL) and then washed with saturated aqueous sodium bicarbonate solution (10 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (15% ethyl acetate-hexanes, grading to 50%), affording the alpha-C5 hydroxymethyl enone 12 shown as a yellow solid (4.0 mg, 12 %).

[00296] Characterization of 12: 1H NMR (500 MHz, CDC1₃) δ 7.50 (d, 2H, J = 7.5 Hz), 7.40-7.34 (m, 3H), 6.96 (ddd, 1H, J = 10.0, 5.0, 1.5 Hz), 6.13 (dd, 1H, J = 10.0, 2.0 Hz), 5.37 (s, 2H), 4.05-3.97 (m, 2H), 3.59 (d, 1H, J = 10.5 Hz), 3.26-3.23 (m, 1H), 2.77 (d, 1H, J = 10.5 Hz), 2.49 (s, 6H), 0.88 (s, 9H), 0.24 (s, 3H), 0.01 (s, 3H).

Example 9A

[00297] Synthesis of C5- substituted Enone 13.

9 13

[00298] A solution of diethyl azodicarboxylate (40% in toluene, 364 μΐ,, 0.928 mmol, 1.25 equiv) was added dropwise to a solution of 9 (370 mg, 1 equiv), triphenylphosphine (243 mg, 1.25 equiv) and formic acid (35 μί, 1.25 equiv) in tetrahydrofuran at 0 °C. The resulting mixture was allowed to warm to 23 °C, then was stirred at this temperature for 4 h. The reaction mixture was diluted with dichloromethane and washed with saturated aqueous sodium bicarbonate solution. The phases were separated and the organic phase was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (15% ethyl acetate-hexanes), affording the alpha-C5 formate ester enone 13 (260 mg, 67%). Example

[00299] Synthesis of C5- substituted Enone 14.

13 14

[00300] An aqueous solution of hydrochloric acid (2.0 M, 1.0 mL) was added to a cooled solution of 13 (210 mg) in methanol (5.0 mL). After stirring at 23 °C for 4 h, the reaction mixture was carefully poured into saturated aqueous sodium bicarbonate solution (20 mL), then extracted with dichloromethane (2 x 20 mL). The combined organic extracts were dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (15% ethyl acetate-hexanes, grading to 25%), affording the alpha-C5 hydroxy enone 14 as an off-white solid (80 mg, 40%).

Example 11A

[00301] Synthe - substituted Enone 15.

14 15

[00302] Diethylamino sulfur trifluoride (DAST) (31 μί, 1.2 equiv) was added dropwise to a solution of 14 (97 mg, 1 equiv) in dichloromethane (2.0 mL) at 0 °C. The resulting mixture was allowed to warm to 23 °C, then was stirred at this temperature for 1 ½ h. The reaction mixture was diluted with dichloromethane and washed with saturated aqueous sodium bicarbonate solution. The phases were separated and the organic phase was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (12% ethyl acetate- hexanes), affording beta C5 fluoro enone 15 (29 mg, 30%). Example 12A

- substituted Enones 16 and 17

[00304] To a stirred suspension of 5 (345 mg, 0.659 mmol) in methanol (10 mL) was added anhydrous stannous chloride (375 mg, 1.97 mmol, 3.0 eq.). The mixture was stirred 12 h at 23 °C and concentrated in vacuo. The residue was suspended between methyl i-butyl ether (10 mL) and 0.5 M NaOH aq. (15 mL) and stirred vigorously until both layers were clear. The organic layer was collected and the aqueous layer was further extracted with methyl i-butyl ether (3 x 10 mL). The combined organics were dried (Na₂S0₄) and concentrated to provide the beta C5 amino enone 16 as a gray solid, pure by 1H NMR.

[00305] 16 was dissolved in dry acetonitrile (4 mL) under an atmosphere of Ar. To this was added triethylamine (450 μί, 3.23 mmol, 5.0 eq.) and i-butyldiphenylsilyl chloride (339 μί, 1.30 mmol, 2.02 eq.) and the mixture stirred lh. The reaction mixture was diluted in methyl t-butyl ether (25 mL) and washed with 0.5M NaOH aq. (2 x 20 mL), brine (20 mL), dried (Na₂S0₄) and concentrated in vacuo to the beta C5 TBDPS protected amino enone 17 as a brown oil, pure by 1H NMR, and was used without further purification.

Example 13A

[00306] Synthes - substituted enones 43 and 46.

[00307] Synthesis of enone 43 was accomplished from 9 using a standard protection protocols; see Protective Groups in Organic Synthesis, Fourth Ed. Greene, T.W. and Wuts, P.G., Eds., John Wiley & Sons, New York: 2007, the entire contents of which are hereby incorporated by reference. Enone 46 may be synthesized from enone 9 following standard reaction with methyl iodide. Enone 46 was synthesized from the iodo enone 8 by displacement with methanol.

Example 14A

- substituted enones 100 to 104 from enone 12

104

[00309] Based on the above-described Examples, the above depicted reactions are envisioned. These new enones may be useful in the synthesis of new C5-tetracycline analogs.

Example 15A

[00310] Synthesis of C5- substituted enone 105b from enone 9

105a: phenol; R = H

105b: 4-bromophenol; R = 4-Br

R = hydrogen, halogen, alkyl, aryl, heteroaryl, etc. [00311] Diethyl azodicarboxylate (40% solution in toluene, 228 μί, 0.501 mmol, 1.25 equiv) was added dropwise to a solution of enone 9 (200 mg, 0.401 mmol, 1 equiv), 4- bromophenol (76 mg, 0.441 mmol, 1.1 equiv) and triphenylphosphine (131 mg, 0.501 mmol, 1.25 equiv) in THF at 0 °C. The resulting mixture was allowed to warm to 23 °C. After stirring at this temperature for 3 h, the reaction mixture was partitioned between dichloromethane (20 mL) and pH7 buffer (20 mL). The phases were separated and the aqueous phase was extracted with dichloromethane (20 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (10% ethyl acetate-hexanes), providing enone 105b (187 mg, 71%).

[00312] Characterization of 105: 1H NMR (500 MHz, CDC1₃) δ 7.50 (d, 2H, J = 6.8 Hz), 7.41-7.35 (m, 5H), 7.06 (d, 2H, J = 8.8 Hz), 6.92 (ddd, 1H, J = 10.3, 4.7, 1.7 Hz), 6.20 (d, 1H, J = 10.3 Hz), 5.37 (2H, AB quartet), 5.26 (d, 1H, J = 4.9 Hz), 3.61 (d, 1H, J = 11.2 Hz), 2.98 (d, 1H, J = 10.7 Hz), 2.52 (s, 6H), 0.91 (s, 9H), 0.24 (s, 3H), 0.05 (s, 3H).

[00313] Enone 105 can be used, for example, in the synthesis of 5-(phenoxy)tigecyclines of the formula:

Example 16A

[00314] Synthesis of C5- substituted enone 106 from enone 10

10 106

[00315] Triphenylphosphine (176 mg, 0.672 mmol, 1 equiv) was added to a solution of enone 10 in tetrahydrofuran (10 mL) and water (2 mL) at 23 °C. The reaction solution was stirred at 23 °C for 18 h, then was concentrated. The crude γ-amino enone intermediate was divided into six equal portions. Aqueous formaldehyde (37% solution, 36 μί, 0.480 mmol, 4 equiv) was added to an ice-cold solution of crude γ- amino enone (0.12 mmol, 1 equiv), sodium cyanoborohydride (19 mg, 0.300 mmol, 2.5 equiv) and glacial acetic acid (9 μί, 0.15 mmol, 1.25 equiv) in methanol (1.5 mL) and acetonitrile (0.5 mL). The reaction mixture was allowed to warm to 23 °C. After stirring at this temperature for 4 h, saturated aqueous sodium bicarbonate solution (10 mL), ethyl acetate (10 mL) and water (5 mL) were added in sequence. The phases separated. The aqueous phase was extracted with ethyl acetate (10 mL). The organic extracts were combined and the combined solution was dried over sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (12% ethyl acetate-hexanes, grading to 15% ethyl acetate), providing enone 106 (24 mg, 38%, 2 steps).

[00316] Characterization of 106: 1H NMR (500 MHz, CDC1₃) δ 7.47 (d, 2H, J = 6.8 Hz), 7.39-7.33 (m, 3H), 6.84 (dd, 1H, J = 10.2, 2.4 Hz), 6.22 (dd, 1H, J = 10.2, 2.4 Hz), 5.37 (AB quartet, 2H), 4.07 (d, 1H, J = 2.0 Hz), 2.94-2.91 (m, 1H), 2.85 (dd, 1H, J = 9.8, 2.0 Hz), 2.43 (s, 6H), 2.32 (s, 6H), 0.80 (s, 9H), 0.18 (s, 3H), -0.09 (s, 3H).

Example 17A

[00317 - substituted enone 107 from enone 3

[00318] A freshly prepared solution of immonium trifluoroacetate salt (see Millot et ah, Synthesis 2000, 7, 941-948) in anhydrous 1,2-dichloroethane (0.6 M, 4.3 mL, 2.58 mmol, 1.5 equiv) was added dropwise to a solution of ie/t-butyldimethylsilyl dienol ether 3 (1.01 g, 1.69 mmol, 1 equiv) in anhydrous 1,2-dichloroethane (10 mL) at 23 °C. The reaction mixture was heated to 60-65 °C. After stirring at this temperature for 1 h, a second portion of immonium trifluoroacetate solution (0.6 M, 4.3 mL, 2.58 mmol, 1.5 equiv) was added dropwise to the reaction solution. The resulting solution was stirred at 60-65 °C for 1 h, whereupon a final portion of immonium trifluoroacetate (0.6 M, 2.8 mL, 1.68 mmol, 1 equiv) was added dropwise. After stirring at 60-65 °C for a further 30 min, the reaction solution was allowed to cool to 23 °C. The cooled solution was poured into saturated aqueous sodium bicarbonate solution (60 mL). Dichloromethane (60 mL) was added and the phases were separated. The aqueous phase was extracted with dichloromethane (60 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated, affording a brown oil. The crude product was purified by flash-column chromatography (dichloromethane flush, then 1% ether-dichloromethane, grading to 3% ether-dichloromethane), affording the -( )-N,N- diallylaminomethyl- substituted AB enone 107 (699 mg, 70%).

[00319] Characterization of 107: 1H NMR (500 MHz, CDC1₃) δ 7.50 (d, 2H, J = 6.8 Hz), 7.40-7.34 (m, 3H), 6.94 (ddd, 1H, J = 10.3, 4.9, 1.5 Hz), 6.06 (dd, 1H, J = 10.3, 2.0 Hz), 5.87-5.79 (m, 2H), 5.36 (2H, AB quartet), 5.18-5.13 (m, 4H), 3.57 (d, 1H, J = 11.2 Hz), 3.21- 3.16 (m, 5H), 2.89 (dd, 1H, J = 12.7, 7.3 Hz), 2.83 (dd, 12.7, 7.3 Hz), 2.76 (d, 1H, J = 11.2 Hz), 2.48 (s, 9H), 0.86 (s, 9H), 0.24 (s, 3H), 0.01 (s, 3H); ¹³C NMR (125 MHz, CDC1₃) δ ; FTIR (neat film), cm^-1 ; HRMS-ESI (m/z): [M+H]⁺ calcd for C₃₃H₄₆N₃0₅Si, 592.3201 ; found, 592.3212. Exemplary Syntheses of C5-Substituted Tetracyclines from C5-Substituted Enones

Example IB

[00320] Synthesis of C5-amino-6-deoxytetracycline 21

[00321] A solution of lithium diisopropylamide (LDA, 0.5M in THF) was prepared immediately prior to its use and kept under an atmosphere of Ar (g). To a stirred solution of 18 (880 mg, 2.58 mmol, 4.0 eq.) in dry THF (12 mL) with dry TMEDA (distilled from CaH₂, 423 2.84 mmol, 4.4 eq.) under an atmosphere of Ar (g) at -78 °C was added LDA (5.7 mL, 2.84 mmol, 4.4 eq.). After allowing to stir 30 min at -78 °C, during which time the solution became a deep red color, the crude reaction mixture (0.645 mmol, 1.0 eq.) was added as a solution in dry THF (4 mL) and the mixture was stirred an additional 40 min. The reaction was slowly warmed to -10 °C over 2 hrs, at which point it was quenched by the addition of pH = 7 buffer. The aqueous layer was adjusted to pH = 7, then extracted with dichloromethane (2x 20 mL) and the organic layer dried (Na₂S0₄) and concentrated. Flash column chromatography (Si0₂, 20% ethyl acetate in hexanes) of the residue provided the Michael-Claisen product 19 (411 mg, 65% for three steps) as a bright yellow foam.

[00322] Characterization of 19: R_f= 0.57 (30% ethyl acetate in hexanes); IR (neat) 2929, 1759, 1716, 1604, 1510, 1147 cm^"1; 1H NMR (500 MHz, CDC1₃) δ 17.33 (s, 1H), 7.28 - 7.54 (m, 16H), 7.05 (dd, J = 7.8, 6.4 Hz, 2H), 5.44 (q, J = 8.2 Hz, 2H), 3.60 (s, 1H), 3.35 (d, J = 12.2 Hz, 1H), 3.16 (m, 1H), 2.75 (dd, J = 8.3, 3.0 Hz, 1H)2.35 (s, 1H), 2.21 (s, 6H), 1.60 (m ,1H), 1.58 (s, 9H), 0.81 (s, 9H), 0.70 (bs, 3H), 0.60 (s, 3H), -0.10 (s, 3H); ¹³C NMR (500 MHz, CDC1₃) δ 193.4, 188.2, 184.3, 180.7, 167.8, 151.6, 150.4, 147.7, 146.8, 136.3, 136.3, 135.2, 134.9, 134.0, 133.7, 129.9, 129.3, 128.4, 128.4, 127.9, 127.3, 124.0, 122.7, 121.9, 114.3, 108.3, 105.6, 97.4, 83.4, 72.1, 61.3, 54.2, 52.6, 45.1, 42.2, 31.9, 27.7, 27.2, 25.7, 18.9, 18.8, 17.0, -3.1, -3.2; HRMS for C₅₆H₆₉N₃O₉S1₂ [MH+] m/z calc.

984.46451, found 984.46680.

[00323] Concentrated aqueous hydrofluoric acid solution (48 wt%, 1.5 mL) was degassed with bubbling Ar and added to a degassed (Ar) solution of 19 (9.1 mg, 0.0089 mmol) in acetonitrile (1.5 mL) in a polypropylene reaction vessel at 23 °C. The reaction solution was stirred vigorously under an atmosphere of Ar at 23 °C for 36 h. To this mixture was added a suspension of palladium on activated carbon (10 wt%, 22 mg) in methanol (degassed with bubbling Ar) in one portion at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The yellow reaction mixture was stirred at 23 °C for 1 h, then was cooled in a 4 °C bath and quenched by the dropwise addition of methoxytrimethylsilane until bubbling ceased. The mixture was filtered through a syringe filter and the filtrate concentrated, providing a yellow solid. The product was purified by preparatory HPLC using an Agilent C18 column [10 μΜ, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: 0.1% TFA aq., Solvent B: acetonitrile, isochratic elution 15% B, flow rate: 15 mL/min] . Fractions eluting at 39 min were collected and concentrated, affording C5-amino-6-deoxycycline 21, trifluoracetate (TFA) salt as a pale yellow powder (2.2 mg, 57% for two steps).

[00324] Characterization of 21: ¹H NMR (500 MHz, CD₃OD) δ 7.47 (t, J = 8.0, 7.5 Hz, 1H), 7.00 (d, J = 7.5 Hz, 1H), 6.82 (d, J = 8.0 Hz, 1H), 4.49 (s, 1H), 4.18 (d, J = 10.0 Hz, 1H), 2.8 - 3.12 (m, 3H), 3.10 (s, 6H), 1.49 (d, J = 6.0 Hz, 3H); HRMS for C₂₂H₂₅N₃O₇ [MH+] m/z calc. 444.17653, found 444.17616.

Example 2B

-dimethylaminomethyl-minocycline 25

C5-dimethylaminomethyl minocycline, 25 24

[00326] A solution of lithium diisopropylamide (LDA, 0.5M in THF) was prepared immediately prior to its use and kept under an atmosphere of Ar (g). To a stirred solution of phenylester 22 (59 mg, 0.160 mmol, 4.0 eq.) in dry THF (3 mL) with dry TMEDA (distilled from CaH₂, 26 μί, 0.176 mmol, 4.4 eq.) under an atmosphere of Ar (g) at -78°C was added LDA (352 jxL, 0.176 mmol, 4.4 eq.). After allowing to stir 30 min at -78°C, during which time the solution became a deep red color, 6 (22 mg, 0.040 mmol, 1.0 eq.) was added as a solution in dry THF (1 mL) and the mixture was stirred an additional 40 min. The reaction was slowly warmed to -10°C over 1.5 hrs, at which point it was quenched by the addition of pH 7 buffer. The pH of the aqueous layer was adjusted to 7, which was then extracted with dichloromethane (3 x 25 mL) and the organic layer dried (Na₂S0₄) and concentrated. Flash column chromatography (Si0₂, 20% ethyl acetate in hexanes, then 50% ethyl acetate in hexanes) of the residue provided the Michael-Claisen product 23 (25.0 mg, 78%) as a bright yellow oil.

[00327] Characterization of 23: R_f= 0.55 (50% ethyl acetate in hexanes); 1H NMR (500 MHz, CDC1₃) δ 15.69 (s, 1H), 7.52 (d, J = 6.9 Hz, 2H), 7.42 (dd, J = 7.4, 6.9 Hz, 2H), 7.38 (d, J = 1.4 Hz, 1H), 7.25 (d, J = 8.8 Hz, 1H), 7.03 (d, J = 8.8 Hz, 1H), 5.39 (s, 2H), 3.71 (d, J = 11.2 Hz, 1H), 3.54 (dd, J = 15.1, 5.4 Hz, 1H), 2.99 (d, J = 11.2 Hz, 1H), 2.82 (d, J = 10.7 Hz, 1H), 2.71 (s, 6H), 2.67 (m, 1H), 2.51 (s, 6H), 2.38 (m, 1H), 2.29 (t, J = 5.4 Hz, 1H), 2.26 (s, 6H), 1.55 (s, 9H), 0.91 (s, 9H), 0.25 (s, 3H), -0.01 (s, 3H).

[00328] Concentrated aqueous hydrofluoric acid solution (48 wt%, 1.5 mL) was added to a solution of 23 (25 mg, 0.031 mmol) in acetonitrile (1.5 mL) in a polypropylene reaction vessel at 23 °C. The reaction solution was stirred vigorously at 23 °C for 30 h, then was poured into aq. K₂HP0₄ and adjusted to pH = 7. The resulting mixture was extracted with ethyl acetate (3 x 25 mL). The organic extracts were combined and the combined solution was dried (Na₂S0₄) and concentrated, affording a yellow solid.

Methanol (4 mL) was added to the crude product, forming a yellow solution. Palladium on activated carbon (10 wt%, 22 mg) was added in one portion at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The yellow reaction mixture was stirred at 23 °C for 20 min, then was filtered through a syringe filter plug. The filtrate was concentrated, providing a yellow solid. The product was purified by preparatory HPLC in using an Agilent CI 8 column [10 μΜ, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: 0.1% TFA aq., Solvent B:

acetonitrile, gradient elution 5-35% B over 40 min, flow rate: 10 niL/min] . Fractions eluting at 30-32 min were collected and concentrated, affording 5-dimethylaminomethyl minocycline 25, trifluoracetate salt, as a pale yellow powder (13.7 mg, 70% for two steps).

[00329] Characterization of 25: 1H NMR (500 MHz, CD₃OD) δ 7.86 (d, J = 9.3 Hz, 1H), 7.04 (d, J = 9.3 Hz, 1H), 5.62 (bs, 1H), 5.45 (bs, 1H),4.65 (bs, 1H), 3.74 (dd, J = 11.2, 10.7 Hz, 1H), 3.65 (d, J = 10.7 Hz, 1H), 3.60 (dd, J = 11.3, 6.9 Hz, 1H), 3.39 (dd, J = 13.2, 4.9 Hz, 1H), 3.23 (s, 6H), 3.00 (bs, 6H), 2.89 (m, 1H), 2.62 (s, 6H), 2.61 (m, 1H), 2.32 (m, 1H); HRMS for C₂₆H₃₄N₄0₇ [MH+] m/z calc. 515.25003, found 515.24919.

Example 3B

00330] Synthesis of C5-amino tigecycline analogs (31, 33, 35, 37, 39, and 40)

HCIO4, THF

[00331] A freshly-prepared solution of lithium diisopropylamide in tetrahydrofuran (1.0 M, 430 μί, 0.430 mmol, 3.0 equiv) was added dropwise via syringe to a solution of the 26 (239 mg, 0.430 mmol, 3.0 equiv) and N,N,N',N'-tetramethylethylenediamine (129 μL·, 0.859 mmol, 6.0 equiv) in tetrahydrofuran (4.5 mL) at -78 °C, forming a bright red solution. After stirring at -78 °C for 45 min, a solution of 10 (75 mg, 0.143 mmol, 1 equiv) in tetrahydrofuran (0.8 mL) was added dropwise via syringe to the reaction solution. The resulting mixture was allowed to warm slowly to -10 °C over 90 min, then was partitioned between aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 20 mL) and dichloromethane (20 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (2 x 20 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by flash-column chromatography (10% ethyl acetate-hexanes, grading to 15%), providing the Michael-Claisen cyclization product 27 as a yellow solid (62 mg, 44%). [00332] Concentrated aqueous hydrofluoric acid solution (48 wt%, 1.5 mL) was added to a solution of the Michael-Claisen cyclization product 27 (116 mg, 0.118 mmol, 1 equiv) in acetonitrile (3.0 mL) in a polypropylene reaction vessel at 23 °C. The reaction mixture was stirred vigorously at 23 °C for 13 h, then was poured into water (50 mL) containing dipotassium hydrogenphosphate trihydrate (20.0 g). The resulting mixture was extracted with ethyl acetate (2 x 50 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product 28 was purified by preparatory HPLC on an Agilent Prep C-18 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: water, Solvent B: acetonitrile, injection volume: 8 mL (CH₃CN-H₂0, 85: 15), gradient elution with 85— >100% B over 40 min, flow rate: 15 mL/min]. Fractions eluting at 24-26 min were collected and concentrated, affording 28 as a yellow solid (90 mg, 88%).

[00333] A solution of trimethylphosphine in toluene (1.0 M, 91 μΐ,, 0.091 mmol, 1.1 equiv) was added dropwise to a solution of 28 (72.0 mg, 0.083 mmol, 1 equiv) in benzene (3.5 mL) at 23 °C. After stirring at this temperature for 20 min, a solution of 2-(tert- butoxycarbonyloxyimino)-2-phenylacetonitrile (50.8 mg, 0.206 mmol, 2.5 equiv) in benzene (1.0 mL) was added dropwise. The resulting mixture was stirred at 23 °C for 2 h, then was partitioned between dichloromethane (40 mL) and aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 40 mL). The phases were separated and the aqueous phase was extracted with dichloromethane (20 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product mixture was purified by preparatory HPLC on an Agilent Prep C-18 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: water, Solvent B: acetonitrile, injection volume: 8 mL (CH CN-H₂0, 85: 15), gradient elution with 85— > 100% B over 40 min, flow rate: 15 mL/min]. Fractions eluting at 22-24 min were collected and concentrated, affording product 29 as a yellow solid (22 mg, 28%). Fractions eluting at 17-21 min were collected and concentrated, affording product 30 as a yellow solid (8.5 mg, 12 %). 29 can be deprotected to provide 30 using, for example, HCIO₄ as a reagent.

33

[00334] Palladium black (6 mg, 0.056 mmol, 6.7 equiv) was added in one portion to a solution of 29 (8 mg, 8.5 μιηοΐ, 1 equiv) in methanol (1.5 mL) and dioxane (1.5 mL) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23 °C for 3 h, then was filtered through a plug of Celite. The filtrate was concentrated to provide 31.

[00335] Sodium carbonate (7.7 mg, 0.128 mmol, 15 equiv) was added to a solution of the crude hydrogenation product 31 in l,3-dimethyl-3,4,5,6-tetrahydro-2(lH)-pyrimidinone (DMPU, 250 μ¾ and acetonitrile (50 μί) at 23 °C. After stirring at 23 °C for 5 min, 2- (dimethylamino)acetyl chloride hydrochloride 32 (6.7 mg, 0.043 mmol, 5 equiv) was added. The reaction mixture was stirred at 23 °C for 1 ½ h, whereupon methanol (250 μί) and an aqueous solution of trifluoroacetic acid (0.1 %, 6.0 mL) were added in sequence. The resulting mixture was filtered, then purified by preparatory HPLC on an Agilent Prep C-18 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, gradient elution with 5— >40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 28-30 min were collected and concentrated, affording the product 33 as a yellow solid.

[00336] Triethylamine (3.5 μί, 0.025 mmol, 3.0 equiv) and trifluoroacetic anhydride (2.3 μί, 0.017 mmol, 2.0 equiv) were added in sequence to a solution of 30 (7.0 mg, 8.3 μιηοΐ, 1 equiv) in dichloromethane (0.3 mL) at 23 °C. After stirring at this temperature for 1 h, the reaction mixture was diluted with dichloromethane (10 mL) and then washed with saturated aqueous sodium bicarbonate solution (10 mL). The layers were separated and the aqueous phase was extracted with dichloromethane (10 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude acylation product 34 was purified by preparatory HPLC on an Agilent Prep C-18 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: water, Solvent B: acetonitrile, injection volume: 8 mL (CH₃CN-H₂0, 85: 15), gradient elution with 85— > 100% B over 40 min, flow rate: 15 mL/min]. Fractions eluting at 18-21 min were collected and concentrated, affording the purified product 34 (7.0 mg, 90%).

[00337] Palladium black (7 mg) was added in one portion to a solution of 34 in methanol (1.5 mL) and dioxane (1.5 mL) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23 °C for 3 ½ h, then was filtered through a plug of Celite. The filtrate was concentrated to provide 35.

[00338] 2-(ie/t-Butylamino)acetyl chloride hydrochloride 36 (5.5 mg, 0.030 mmol, 4 equiv) was added to a solution of the crude hydrogenation product 35 in 1,3-dimethyl- 3,4,5,6-tetrahydro-2(lH)-pyrimidinone (DMPU, 250 μί) and acetonitrile (50 μί) at 23 °C. The reaction mixture was stirred at 23 °C for 2 ½ h, whereupon methanol (250 μί) and an aqueous solution of trifluoroacetic acid (0.1 %, 6.0 mL) were added in sequence. The resulting mixture was filtered, then purified by preparatory HPLC on an Agilent Prep C-18 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, gradient elution with 5— >40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 26-28 min were collected and concentrated, affording the product 37 as a yellow solid (3.0 mg, 39% over 3 steps).

[00339] Triethylamine and methane sulfonic anhydride were added in sequence to a solution of the 30 in dichloromethane (0.4 mL) at 23 °C. The reaction mixture was stirred at this temperature for 2 h, then was partitioned between dichloromethane (10 mL) and aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 10 mL). The phases were separated and the organic phase was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by preparatory HPLC on an Agilent Prep C-18 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: water, Solvent B: acetonitrile, injection volume: 8 mL (CH₃CN-H₂0, 85: 15), gradient elution with 85— >100% B over 40 min, flow rate: 15 mL/min]. Fractions eluting at 14-16 min were collected and concentrated, affording the desired sulfonamide product 38 (4.0 mg, 4.3 μιηοΐ, 52%).

[00340] Palladium black (5.3 mg) was added in one portion to a solution of 38 in methanol (1.5 mL) and dioxane (1.5 mL) at 23 °C. An atmosphere of hydrogen was introduced by briefly evacuating the flask, then flushing with pure hydrogen (1 atm). The reaction mixture was stirred at 23 °C for 3 h, then was filtered through a plug of Celite. The filtrate was concentrated to provide 39.

[00341] Sodium carbonate (6.9 mg, 15 equiv) was added to a solution of the crude hydrogenation product 39 in l,3-dimethyl-3,4,5,6-tetrahydro-2(lH)-pyrimidinone (DMPU, 250 μΙ_) and acetonitrile (50 μΙ_) at 23 °C. After stirring at 23 °C for 5 min, 2- (dimethylamino)acetyl chloride hydrochloride 32 (3.4 mg, 5 equiv) was added. The reaction mixture was stirred at 23 °C for 1 ½ h, whereupon methanol (250 μί) and an aqueous solution of trifluoroacetic acid (0.1 , 6.0 mL) were added in sequence. The resulting mixture was filtered, then purified by preparatory HPLC on an Agilent Prep C-18 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: 0.1% trifluoroacetic acid in water, Solvent B: acetonitrile, gradient elution with 5— >40% B over 50 min, flow rate: 7.5 mL/min]. Fractions eluting at 21-23 min were collected and concentrated, affording the product 40 as a yellow solid.

[00342] Based on the above-described reactions, the following synthesis of tetracycline 102 is also contemplated from 30:

[00343] Based on the above-described reactions, the following synthesis of tetracyclines 203, 204 and 205 is also contemplated from enone 106:

204 205

Example 4B

[00344] Synthesis of 5-beta-Fluorotigecycline 42

5- -Fluorotigecycline, 42

[00345] The synthesis of 5-beta-fluorotigecycline (42) from enone 15 was accomplished following the procedure of Example 3B.

Example 5B

[00346] Synthesis of 5-Hydroxyminocycline 44

44

43 40%

(i) HF (aq), CH₃CN, 40 °C

(ii) H₂, Pd black

CH₃OH-dioxane

5-Hydroxyminocycline, 45 [00347] The synthesis of 5-Hydroxyminocycline 45 from enone 43 was accomplished following the procedure of Example 3B.

Example 6B

[00348] Synthesis of 5-Methoxyminocycline 45

5-Methoxyminocycline, 48

[00349] The synthesis of 5-Methoxyminocycline 45 from enone 43 was accomplished following the procedure of Example 3B.

Example 7B

50] Synthesis of C5-amino substituted tetracycline analogs

The above depicted reactions are all envisioned in providing new C5-tetracycline

Example 8B

[00352] Synthesis of isoxazole tetracyclines and tetracycline analogs from enone 12

X = any group, e.g. , halogen, aliphatic, heteroaliphatic, aryl, heteroaryl, etc.

[00353] The above depicted reactions are all envisioned in providing new C5-isoxazole tetracyclines and C5-tetracycline analogs.

Example 9B

354] Synthesis of isoxazole tetracyclines and tetracycline analogs from enone 100

[00355] The above depicted reactions are all envisioned in providing new C5-isoxazole tetracyclines and C5-tetracycline analogs.

Example 10B

[00356] Synthesis of isoxazole tetracyclines and tetracycline analogs from enone 107

[00357] A freshly prepared solution of lithium diisopropylamide (1.0 M, 4.91 mL, 4.91 mmol, 3.0 equiv) was added drop wise via syringe to a solution of the phenyl ester D-ring precursor 22 (1.82 g, 4.91 mmol, 3.0 equiv) and N,N,N',N'-tetramethylethylenediamine (1.48 mL, 9.82 mmol, 6.0 equiv) in tetrahydrofuran (35 mL) at -78 °C, forming a dark red solution. After stirring at -78 °C for 40 min, a solution of AB enone 107 (969 mg, 1.64 mmol, 1 equiv) in tetrahydrofuran (5 mL) was added dropwise via syringe to the reaction solution. The resulting mixture was allowed to warm slowly to -10 °C over 90 min, then was partitioned between aqueous potassium phosphate buffer solution (pH 7.0, 0.2 M, 80 mL) and dichloromethane (100 mL). The phases were separated and the aqueous phase was further extracted with dichloromethane (2 x 50 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The product was purified by preparative HPLC on an Agilent Prep CI 8 column [10 μιη, 250 x 21.2 mm, UV detection at 350 nm, Solvent A: water, Solvent B: methanol, 5 batches, injection volume: 8.0 mL (7.5 mL methanol, 0.5 mL water), gradient elution with 95— >100 B over 50 min, flow rate: 15 mL/min] . Fractions eluting at 22-28 min were collected and concentrated, providing the Michael-Claisen cyclization product 300 (1.00 g, 70%). [00358] Characterization of 300: 1H NMR (500 MHz, CDC1₃) δ 15.62 (s, 1H), 7.53-7.51 (m, 2H), 7.41-7.35 (m, 3H), 7.23 (d, 1H, J = 8.8 Hz), 7.01 (d, 1H, J = 8.8 Hz), 5.90-5.82 (m, 2H), 5.38 (AB quartet, 2H), 5.18 (dd, 2H, J = 17.1, 2.0 Hz), 5.15-5.12 (m, 2H), 3.70 (d, 1H, J = 10.7 Hz), 3.65 (dd, 1H, J = 15.1, 5.4 Hz), 3.23-3.15 (m, 4H), 2.82-2.77 (m, 1H), 2.76 (d, 1H, J = 10.7 Hz), 2.73-2.65 (m, 2H), 2.68 (s, 6H), 2.51 (s, 6H), 2.41-2.38 (m, 1H), 2.19 (dd, 1H, J = 15.1, 14.6 Hz), 1.53 (s, 9H), 0.86 (s, 9H), 0.24 (s, 3H), -0.01 (s, 3H).

[00359] Michael-Claisen cyclization product 300 (815 mg, 0.938 mmol, 1 equiv) was dissolved in 1,2-dichloroethane (10 mL) and argon was bubbled through the resulting solution for 2 min. The solution was then transferred to a round-bottomed flask containing tetrakis(triphenylphosphine)palladium (108 mg, 0.094 mmol, 0.1 equiv) and 1,3- dimethylbarbituric acid (878 mg, 5.63 mmol, 6.0 equiv). The yellow homogeneous reaction solution was heated to 35 °C. After stirring at this temperature for 80 min, the reaction solution was allowed to cool to 23 °C. The cooled solution was diluted with ethyl acetate (50 mL) and the resulting solution was poured into saturated aqueous sodium bicarbonate solution (50 mL). The phases were separated and the aqueous phase was further extracted with ethyl acetate (2 x 50 mL). The organic extracts were combined and the combined solution was dried over anhydrous sodium sulfate. The dried solution was filtered and the filtrate was concentrated. The crude product was purified by flash-column chromatography (1.5% methanol-dichloromethane, grading to 5% methanol-dichloromethane), affording amine 301 as a golden brown solid (571 mg, 77%).

[00360] Characterization of 301: 1H NMR (500 MHz, CDC1₃) δ 7.50 (d, 2H, J = 6.8 Hz), 7.39-7.32 (m, 3H), 7.23 (d, 1H, J = 8.8 Hz), 7.01 (d, 1H, J = 8.3 Hz), 5.37 (AB quartet, 2H), 3.71 (d, 1H, J = 10.7 Hz), 3.60 (dd, 1H, J = 15.4, 5.2 Hz), 3.09-3.00 (m, 2H), 2.77 (d, 1H, J = 10.3 Hz), 2.75-2.70 (m, 1H), 2.66 (s, 6H), 2.50 (s, 6H), 2.29 (dd, 1H, J = 15.2, 15.1 Hz), 2.22-2.18 (m, 1H), 1.52 (s, 9H), 0.87 (s, 9H), 0.24 (s, 3H), -0.03 (s, 3H); ¹³C NMR (125 MHz, CDC1₃) δ 187.3, 187.2, 181.0, 180.1, 167.3, 152.0, 149.4, 145.1, 136.3, 135.0, 128.4, 128.4, 128.3, 124.1, 123.2, 122.1, 108.5, 107.4, 83.6, 83.5, 72.4, 62.6, 53.4, 48.4, 47.7, 44.4, 43.0, 41.8, 33.7, 33.5, 27.6, 26.4, 19.1, -2.5, -2.6; HRMS-ESI (m z): [M+H]⁺ calcd for C₄₂H₅₇N₄O₉S1, 789.3889; found, 789.3920.

R_F = aliphatic, heteroaliphatic, aryl, heteroaryl

R = H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, amino protecting group

R = H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, amino protecting group

R = H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, hydroxyl protecting group

R = H, alkyl, alkenyl, alkynyl, aryl, heteroaryl, hydroxyl protecting group

[00361] The above depicted reactions are all envisioned in providing new C5-isoxazole tetracyclines and C5-tetracycline analogs.

Example 1C. Antibacterial Activity

[00362] The antibacterial activities for the compounds of the invention were studied according to the following protocols, and are shown in Figures 2-4.

Minimum Inhibitory Concentration (MIC) Assay

[00363] MICs were determined according to the Clinical and Laboratory Standards Institute (CLSI) guidances (e.g., CLSI. Performance standards for antimicrobial susceptibility testing; nineteenth information supplement. CLSI document M100-S19, CLSI, 940 West Valley Road, Suite 1400, Wayne, Pennsylvania 19087-1898, USA, 2009). Briefly, frozen bacterial strains were thawed and subcultured onto Mueller Hinton Broth (MHB) or other appropriate media {Streptococcus requires blood and Haemophilus requires hemin and NAD). Following incubation overnight, the strains were subcultured onto Mueller Hinton Agar and again incubated overnight. Colonies were observed for appropriate colony morphology and lack of contamination. Isolated colonies were selected to prepare a starting inoculum equivalent to a 0.5 McFarland standard. The starting inoculum was diluted 1: 125 using MHB for further use. Test compounds were prepared by dilution in sterile water to a final concentration of 5.128 mg/mL. Antibiotics (stored frozen, thawed and used within 3 hours of thawing) and compounds were further diluted to the desired working concentrations.

[00364] The assays were run as follows. Fifty

of MHB was added to wells 2 - 12 of a 96-well plate. One hundred

of appropriately diluted antibiotics was added to well 1. Fifty of antibiotics was removed from well 1 and added to well 2 and the contents of well 2 mixed by pipetting up and down five times. Fifty

of the mixture in well 2 was removed and added to well 3 and mixed as above. Serial dilutions were continued in the same manner through well 12. Fifty

was removed from well 12 so that all contained 50 of the working inoculum was then added to all test wells. A growth control well was prepared by adding 50

of working inoculum and 50 of MHB to an empty well. The plates were then incubated at 37 °C overnight, removed from the incubator and each well was read on a plate reading mirror. The lowest concentration (MIC) of test compound that inhibited the growth of the bacteria was recorded. Example:

[abt] = antibiotic concentration in the well

Grow = bacterial growth (cloudiness)

Interpretation: MIC = 2 μg/mL

Protocol for Determining Inoculum Concentration (Viable Count)

[00365] Ninety μΐ of sterile 0.9% NaCl was pipetted into wells 2-6 of a 96-well microtiter plate. Fifty 50 μΐ_^ of the inoculum was pipetted into well 1. Ten μL· from was removed from well 1 and added it to well 2 followed by mixing. Ten μL· was removed from well two and mixed with the contents of well 3 and so on creating serial dilutions through well 6. Ten μL· was removed from each well and spotted onto an appropriate agar plate. The plate was placed into an incubator overnight. The colonies in spots that contain distinct colonies were counted. Viable count was calculated by multiplying the number of colonies by the dilution factor.

Bacterial Strains

[00366] One or more of the following bacterial strains, listed below and in Figures 2-4, were examined in minimum inhibitory concentration (MIC) assays.

STRAIN

ORGANISM DESIGNATION KEY PROPERTIES

Haemophilus influenzae H I262 Tetracycline-resistant, ampicillin-resistant

Moraxella catarrhalis MC205 ATCC 8176, CLSI quality control strain

Escherichia coli EC107 ATCC 25922, CLSI quality control strain

Escherichia coli EC155 Tetracycline-resistant, tet(A)

Escherichia coli EC878 MG1655 tolC::kan

Escherichia coli EC880 IpxA

Escherichia coli EC882 impA

MDR uropathogenic; serotype 017:K52:H 18; UMN

Escherichia coli EC200

026; trimeth/sulfa-R; BAA-1 161

Enterobacter cloacae EC108 ATCC 13047, wt

Enterobacter cloacae EC603 Urine isolate (Spain)

Klebsiella pneumoniae KP109 ATCC 13883, wt

Klebsiella pneumoniae KP153 Tetracycline-resistant, fef(A), MDR, ESBL⁺

Klebsiella pneumoniae KP457 2009 ESBL⁺, CTX-M, OXA

Proteus mirabilis PM1 12 ATCC 35659

Proteus mirabilis PM385 Urine ESBL⁺ isolate

Pseudomonas aeruginosa PA1 1 1 ATCC 27853, wt, control strain

Pseudomonas aeruginosa PA169 Wt, parent of PA170-173

PA170 AmexX; MexXY-(missing a functional efflux

Pseudomonas aeruginosa PA173 pump)

Pseudomonas aeruginosa PA555 ATCC BAA-47, wild type strain PA01

Pseudomonas aeruginosa PA556 Multiple-Mex efflux pump knockout strain

Pseudomonas aeruginosa PA689 Blood isolate (US)

Acinetobacter baumannii AB1 10 ATCC 19606, wt

Acinetobacter baumannii AB250 Cystic fibrosis isolate, MDR

Stenotrophomonas maltophilia SM256 Cystic fibrosis isolate, MDR

Burkholderia cenocepacia BC240 Cystic fibrosis isolate, MDR

*MDR, multidrug-resistant; MRSA, methicillin-resistant S. aureus; MSSA, methicillin-sensitive S. aureus; HA-MRSA, hospital-associated MRSA; tet(K), major gram-positive tetracycline efflux mechanism; tet(M), major gram-positive tetracycline ribosome-protection mechanism; ESBL⁺, extended spectrum β-lactamase

Other Embodiments

[00367] The foregoing has been a description of certain non-limiting preferred embodiments of the invention. Those of ordinary skill in the art will appreciate that various changes and modifications to this description may be made without departing from the spirit or scope of the present invention, as defined in the following claims.

Claims

What is claimed is:

(I-b23)

or a pharmaceutically acceptable salt thereof;

wherein:

R₃ is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched

heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_B; -CH₂OR_B; -CH₂R_B; -CH₂N(R_B)₂; -C(0)R_B; -C0₂R_B; -C(0)N(R_B)₂; -CN; -SCN; -SR_B; - SOR_B; -S0₂R_B; -N0₂; -N₃; -N(R_B)₂; or -C(R_B)₃; wherein each occurrence of R_B is

independently hydrogen, halogen, azido, a protecting group, sulfonyl, sulfinyl, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or

heteroarylthio; or two R_B groups, when attached to a nitrogen atom, are joined to form a heterocyclic ring;

R_D is hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, amide, carbamate, silyl, aryl, and heteroaryl;

each R₇ is independently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_c; -CH₂OR_c; -CH₂R_C; -CH₂N(R_C)₂; -C(=0)R_c; -C0₂R_c; -CN; -SCN; - SR_C; -SORc; -S0₂R_c; -N₃; -N0₂; -N(R_C)₂; -NR_C C(0)R_c; -NR_cS0₂R_c; -NR_cC(0)CH₂R_c; or -C(Rc)₃; wherein each occurrence of Rc is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; each Rpi and Rp₂ is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, pernuoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

each Rp3 is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, a nitrogen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and

n is an integer in the range of 0 to 3, inclusive,

provided the following compound is specifically excluded:

2. The compound of claim 1, wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof.

3. The compound of claim 1, wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof. The compound of claim 1, wherein the compound is of the formula:

(I-b24) _{or a} ph_armaCeutically acceptable salt thereof.

5. The compound of claim 1, wherein the compound is of the formula:

(I-b20) or a pharmaceutically acceptable salt thereof.

6. The compound of claim 1, wherein the compound is of the formula:

(I-b21)

or a pharmaceutically acceptable salt thereof.

The compound of claim 1, wherein the compound is of the formula:

(I-b23-i) or a pharmaceutically acceptable salt thereof.

8. The compound of claim 1, wherein the compound is of the formula:

(I-b23-ii) or a pharmaceutically acceptable salt thereof.

The compound of claim 1, wherein the compound is of the formula:

(I-b23-iii) or a pharmaceutically acceptable salt thereof.

10. The compound of claim 1, wherein the compound is selected from the group consisting of:

and pharmaceutically acceptable salts thereof.

(I-a23)

or a pharmaceutically acceptable salt thereof;

wherein:

R₄ is halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched

each R₇ is indepedently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_c; -CH₂OR_c; -CH₂R_C; -CH₂N(R_C)₂; -C(=0)R_c; -C0₂R_c; -CN; -SCN; - SR_C; -SORc; -S0₂R_c; -N₃; -N0₂; -N(R_C)₂; -NR_C C(0)R_c; -NR_cS0₂R_c; -NR_cC(0)CH₂R_c; or -C(Rc)₃; wherein each occurrence of R_c is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; each Rpi and Rp₂ is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, pernuoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

n is an integer in the range of 0 to 3, inclusive;

provided the following compound is specifically excluded:

The compound of claim 11, wherein the compound is of the formula:

(I-al8) or a pharmaceutically acceptable salt thereof.

The compound of claim 11, wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof. The compound of claim 11, wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof.

The compound of claim 11, wherein the compound is of the formula:

or a pharmaceutically acceptable salt thereof.

The com ound of claim 11, wherein the compound is of the formula:

(I-a21)

or a pharmaceutically acceptable salt thereof.

The compound of claim 11, wherein the compound is of the formula:

(I-a23-i) _{or a} pharmaceutically acceptable salt thereof. The compound of claim 11, wherein the compound is of the formula:

(I-a23-ii) _{or a} pharmaceutically acceptable salt thereof.

The compound of claim 11, wherein the compound is of the formula:

(I-a23-iii) or a pharmaceutically acceptable salt thereof.

20. The compound of claim 11, wherein the compound is selected from the group consisting

and pharmaceutically acceptable salts thereof.

21. A pharmaceutical composition comprising a compound of claim 1 or 11 or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable excipient.

22. A method of treating a microbial infection comprising administering a therapeutically effective amount of a compound of claim 1 or 11 or pharmaceutically acceptable salt thereof to a subject in need thereof.

23. A method of treating cancer comprising administering a therapeutically effective amount of a compound of claim 1 or 11 or pharmaceutically acceptable salt thereof to a subject in need thereof.

24. A compound of the formula (II-x-i

(II-x-i)

or a pharmaceutically acceptable salt thereof,

wherein:

R_D is hydrogen, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, amide, carbamate, silyl, aryl and heteroaryl; and

R_P4 is hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; provided the following compounds are specifically excluded:

(II-y-i)

or a pharmaceutically acceptable salt thereof,

wherein:

Rp₄ is hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; provided the following compounds are specifically excluded:

A compound of the formula (IV-b23):

(IV-b23)

or a pharmaceutically acceptable salt thereof,

wherein:

heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_B; -CH₂OR_B; -CH₂R_B; -CH₂N(R_B)₂; -C(0)R_B; -C0₂R_B; -C(0)N(R_B)₂; -CN; -SCN; -SR_B; - SOR_B; -S0₂R_B; -N0₂; -N ; -N(R_B)₂; or -C(R_B) ; wherein each occurrence of R_B is

each R₇ is indepedently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_c; -CH₂OR_c; -CH₂R_C; -CH₂N(R_C)₂; -C(=0)R_c; -C0₂R_c; -CN; -SCN; - SR_C; -SORc; -S0₂R_c; -N₃; -N0₂; -N(R_C)₂; -NR_C C(0)R_c; -NR_cS0₂R_c; -NR_cC(0)CH₂R_c; or -C(Rc)₃; wherein each occurrence of Rc is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

Rpi is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

R_P4 is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

n is an integer in the range of 0 to 3, inclusive;

provided the following compounds are specifically excluded:

(IV-a23)

or a pharmaceutically acceptable salt thereof,

wherein:

heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_B; -CH₂OR_B; -CH₂R_B; -CH₂N(R_B)₂; -C(0)R_B; -C0₂R_B; -C(0)N(R_B)₂; -CN; -SCN; -SR_B; - SOR_B; -S0₂R_B; -N0₂; -N₃; -N(R_B)₂; or -C(R_B)₃; wherein each occurrence of R_B is independently hydrogen, halogen, azido, a protecting group, sulfonyl, sulfinyl, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or

each R₇ is indepedently halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_c; -CH₂OR_c; -CH₂R_C; -CH₂N(R_C)₂; -C(=0)R_c; -C0₂R_c; -CN; -SCN; - SR_C; -SORc; -S0₂R_c; -N₃; -N0₂; -N(R_C)₂; -NR_C C(0)R_c; -NR_cS0₂R_c; -NR_cC(0)CH₂R_c; or -C(Rc)₃; wherein each occurrence of R_c is independently hydrogen, halogen, azido, a protecting group, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate, aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio;

R_P1 is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, silyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

n is an integer in the range of 0 to 3, inclusive;

provided the following compounds are specifically excluded:

A method of preparing a compound of formula (II):

(III)

or a salt thereof,

the method comprising reacting an electrophile with a compound of formula (III) to provide a compound of formula (II),

wherein:

R5, R9, R₁₀, and Rn are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_D; -CH₂OR_D; -CH₂R_D; -CH₂N(R_D)₂; -C(=0) R_D; -C0₂ R_D; -CN; -SCN; -S R_D; -SO R_D; -S0₂R_D; -N0₂; -N₃; -N(R_D)₂; -NHC(0)R_D; or - C(R_D)₃; wherein each occurrence of R_D is independently hydrogen, halogen, azido, a protecting group, silyl, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate,aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and

each Rp₄ and Rp₅ is independently hydrogen, substituted or unsubstituted aliphatic, substituted or unsubstituted heteroaliphatic, perfluoroalkyl, an oxygen protecting group, acyl, amide, carbamate, sulfonyl, sulfinyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;

provi

29. The method according to claim 28, wherein the electrophile is an activated imine and R₃ is -CH₂N(R_B)₂.

30. The method according to claim 28, wherein the electrophile is an activated formaldehyde, R₃ is -CH₂OR_B, and R_B is hydrogen.

31. The method according to claim 28, wherein the electrophile is an electrophilic halogenating reagent, and R is bromo, chloro, iodo, or fluoro.

32. A method of preparing a compound of the formula (II-c):

(ll-c)

or a pharmaceutically acceptable salt thereof,

from a compound of formula (III):

(III)

or a pharmaceutically acceptable salt thereof,

the method comprising:

(Il-a)

or a pharmaceutically acceptable salt thereof, wherein Hal is bromine, iodine, or chlorine;

(li b)

or a pharmaceutically acceptable salt thereof, wherein R_B is hydrogen; and

(iii) reacting a compound of formula (Il-b) with a nucleophilic fluorinating reagent to provide a compound of formula (II-c);

wherein:

R₅, R9, Rio, and Rn are each independently hydrogen; halogen; cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic; cyclic or acyclic, substituted or unsubstituted, branched or unbranched heteroaliphatic; substituted or unsubstituted aryl; substituted or unsubstituted heteroaryl; acyl; -OR_D; -CH₂OR_D; -CH₂R_D; -CH₂N(R_D)₂; -C(=0) R_D; -C0₂ R_D; -CN; -SCN; -S R_D; -SO R_D; -S0₂R_D; -N0₂; -N₃; -N(R_D)₂; -NHC(0)R_D; or - C(R_D)₃; wherein each occurrence of R_D is independently hydrogen, halogen, azido, a protecting group, silyl, aliphatic, heteroaliphatic, perfluoroalkyl, acyl, acyloxy, amide, carbamate,aryl, heteroaryl, alkoxy, aryloxy, alkylthio, arylthio, amino, alkylamino, dialkylamino, heteroaryloxy, or heteroarylthio; and