WO2009039102A1

WO2009039102A1 - Inhibitors of copn (cpn) for the treatment of bacterial infections

Info

Publication number: WO2009039102A1
Application number: PCT/US2008/076538
Authority: WO
Inventors: Jin Huang; Stephen Lory; Cammie F. Lesser
Original assignee: President And Fellows Of Harvard College; The General Hospital Corporation
Priority date: 2007-09-17
Filing date: 2008-09-16
Publication date: 2009-03-26
Also published as: WO2009039102A8

Abstract

This invention features compounds which are inhibitors of CopN(Cpn) and their use for treating bacterial infections in humans and animals.

Description

Inhibitors of CopN(Cpn) for the Treatment of Bacterial Infections

RELATED APPLICATIONS

This application claims priority to US Provisional Application No. 60/994,105, filed on September 17, 2007, the entire contents of which are hereby incorporated herein by reference.

BACKGROUND OF THE INVENTION

Bacterial virulence determinants can be identified, according to the molecular Koch's postulates (Falkow, S. Rev. Infect. Dis. 10:Suppl 2, S274 (1988)), if specific inactivation of the gene(s) associated with a suspected virulence trait results in a measurable loss in pathogenicity or virulence. This reverse genetic approach is commonly used to determine the role of specific proteins in virulence of a pathogen. However, the current lack of genetic tools for targeted gene disruptions in obligate intracellular bacteria, including Chlamydia species, has seriously hampered the identification of their virulence determinants and the development of target- specific antibiotics.

Chlamydia pneumoniae is primarily a human respiratory pathogen and is associated with atherosclerosis and related clinical manifestations including coronary heart disease (Campbell et al., Nat. Rev. Microbiol. 2:23 (2004)). If left untreated Chlamydia infections may become chronic with severe complications such as sterility, blindness and potentially thrombosis. Chlamydia pneumoniae is an obligate intracellular bacterial pathogen that resides within vacuoles (inclusions) inside host cells (Hackstadt, T. Cell biology. In Chlamydia: Intracellular Biology, Pathogenesis, and Immunity, R. S. Stephens, ed. (Washington, DC: ASM Press), pp. 101-138 (1999)). Although entirely sequestered within inclusions, the bacteria interact with various cellular processes and manipulate functions of the infected host cell (Crocker et al., /. Infect. Dis. 115: 105 (1965); Hackstadt et al., Proc. Natl. Acad. ScL USA. 92:4877 (1995); Fan et al., /. Exp. Med. 187:487 (1998); Carabeo et al., Infect. Immun. 70:3793 (2002); Carabeo et al., Proc. Natl. Acad. ScL USA. 100:6771 (2003); and Su et al., /. Biol. Chem. 279:9409 (2004)), presumably through the activity of chlamydial proteins secreted directly into the host cell cytosol or inserted into the inclusion membrane (Hsia et al., MoI. Microbiol. 25:351 (1997); Fields et al., MoI. Microbiol. 48:671 (2003); Peters et al., Trends Microbiol 15:241 (2007)). Due to the intracellular developmental cycle persistent Chlamydia infections may cause an aberrant immune response, which fails to clear the organisms. Association of these secreted proteins with chlamydial virulence phenotypes remains to be established in order to fully understand the pathogenesis of the chlamydial infections.

SUMMARY OF THE INVENTION

The present invention addresses the need for new anti-infective therapies and therapeutic targets by identifying compounds that inhibit CopN(Cpw), an essential virulence factor of Chlamydia pneumoniae, and are useful for treating infections where this organism is the etiological or exacerbating agent.

Disclosed herein are compounds which inhibit CopN(Cpn) activity and are useful for the treatment of bacterial infections.

In a first aspect, the invention features a method of treating a bacterial infection in a subject by administering to the subject a CopN(Cpra) inhibitor in an amount effective to treat the infection. In certain embodiments, the bacterial infection is selected from community-acquired pneumonia, upper and lower respiratory tract infection, skin and soft tissue infection, acute bacterial otitis media, bacterial pneumonia, complicated infection, pyelonephritis, intra-abdominal infection, bacterial sepsis, central nervous system infection, bacteremia, wound infection, peritonitis, meningitis, infections after burn, urogenital tract infection, pelvic inflammatory disease, endocarditis, and intravascular infection. In still other embodiments, the CopN(Cpra) inhibitor is a compound of formulas (Ia), (Ib), (Ha), or (lib), or a salt thereof.

The methods of the present invention can also be used to treat diseases associated with Chlamydia pneumoniae infections. For example, infections with these bacteria can produce inflammation, resulting in the pathogenesis of atherosclerosis, multiple sclerosis, rheumatoid arthritis, diabetes, Alzheimer's disease, asthma, cirrhosis of the liver, psoriasis, meningitis, cystic fibrosis, cancer, or osteoporosis. Accordingly, the present invention also features a method of treating the diseases associated with bacterial infection listed above.

In a related aspect, the invention features a method of treating, preventing, or reducing the development of an atherosclerosis-associated disease in a subject in need thereof by administering to the subject a CopN(Cpra) inhibitor in an amount effective to treat, prevent, or reduce the development of the atherosclerosis-associated disease in the subject. In certain embodiments, the atherosclerosis-associated disease is coronary artery disease, myocardial infarction, angina pectoris, stroke, cerebral ischemia, intermittent claudication, gangrene, mesenteric ischemia, temporal arteritis, or renal artery stenosis.

In another related aspect, the invention features a method for reducing Chlamydia pneumoniae replication in macrophages or foam cells in a subject in need thereof by administering a CopN(Cpra) inhibitor to said subject in an amount effective to reduce Chlamydia pneumoniae replication in macrophages or foam cells in the subject.

In still another related aspect, the invention features a method of treating a subject diagnosed as having a chronic disease associated with a bacterial infection by administering to the subject a CopN(Cpra) inhibitor, wherein the administering is for a duration and in an amount effective to treat the subject. In certain embodiments, the chronic disease is an inflammatory disease, such as asthma, coronary artery disease, arthritis, conjunctivitis, lymphogranuloma venerum, cervicitis, or salpingitis. In other embodiments, the chronic disease is an autoimmune disease, such as systemic lupus erythematosus, diabetes mellitus, or graft versus host disease. In one particular embodiment, the chronic disease is atherosclerosis.

In yet another aspect, the present invention provides a method for inhibiting CopN(Cpra) mediated microtubule disruption in a cell by contacting said cell with an effective amount of CopN(Cpra) inhibitor, thereby inhibiting CopN(Cpn) mediated microtubule disruption in the cell. In one embodiment of this aspect of the invention, the CopN(Cpn) inhibitor is a compound of formula Ia, Ib, Ha, and/or lib.

In a further aspect, the present invention provides a method for inhibiting CopN(Cpra) mediated cell cycle arrest by contacting a cell with an effective amount of a CopN(Cpra) inhibitor, thereby inhibiting CopN(Cpra) mediated cell cycle arrest. In one embodiment of this aspect of the invention, the CopN(Cpn) inhibitor is a compound of formula Ia, Ib, Ha, or lib.

In yet another aspect, the present invention provides a method for reducing or preventing the multiplication of bacteria in a subject by administering to the subject a CopN(Cpra) inhibitor, in an amount effective to reduce or prevent the multiplication of bacteria in the subject, thereby reducing or preventing the multiplication of bacteria in the subject. In one embodiment of this aspect of the invention, the bacteria are Chlamydia pneumoniae. In other embodiments of this aspect of the invention, the CopN(Cpra) inhibitor is a compound of formula Ia, Ib, Ha, or lib. In another aspect, the invention features a pharmaceutical composition including a compound of formula (Ia), or a salt thereof, and a pharmaceutically acceptable excipient.

In formula (Ia), X¹ is C or N; each of X² and X³ are independently selected from C, O, S, or N; R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(O)R^1N, NHC(S)R¹⁰, NHC(O)OR^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_6 heterocyclyl, C₆-_I2 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl; and wherein the dotted lines represent single or double bonds, optionally selected such that the dotted lines represent bonds which form an aromatic ring. In a further embodiment, each of X¹, X², and X³ are nitrogen.

In another aspect, the invention features a pharmaceutical composition including a compound of formula (Ib), or a salt thereof, and a pharmaceutically acceptable excipient.

In formula (Ib) each of R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(O)R^1N, NHC(S)R¹⁰, NHC(O)OR^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V,

C(O)OR , i¹w ^w, and C(0)NHR 1 I¹X^Λ; and each of R I¹J^J, r ^M r R> I¹N^1N _, r R> lⁱ r> l

R> I¹M θ^υ RⁱP^r r R> IⁱQ^y r R> I¹R^K r R> I¹S⁵ _, _R ⁱτ _R ⁱu _R ⁱv _R ⁱw _{and R} ⁱx _{are^ independently;} selected from H, C_i_₄ alkyl, C₂-₄ alkenyl,

C₂-₄ alkynyl, C₂-₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl.

In certain embodiments, R^1A, R^1B, R^1C and R^1D are H; each of R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, 0C(0)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(0)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ _, R^1P _R ^IQ _R ^iR _R ⁱs _R ⁱτ _R ⁱu _R ⁱv _R ⁱw _{and R} ⁱx ^ independently, selected from H, C_i_₄ alkyl,

C₂-₄ alkenyl, C₂-₄ alkynyl, C₂.₆ heterocyclyl, C₆_₁₂ aryl, Cγ_₁₄ alkaryl, C_3-10 alkheterocyclyl, and Ci_₄ heteroalkyl.

In certain embodiments, R^1A, R^1B, R^1C and R^1D are H; each of R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, 0C(0)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)0R^1Q, NHC(0)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M _, R^1N _, R¹⁰ _, R^1P _R ^IQ _R ^iR _R ⁱs _R ⁱτ _R ⁱu _R ⁱv _R ⁱw _{and R} ⁱx ^ _independently, selected from H, C_i_₄ alkyl,

C₂-₄ alkenyl, C₂-₄ alkynyl, and C_1-4 heteroalkyl.

In a further embodiment, each of R^1A, R^1B, R^1C R^1D, R^1F, R^1G, R^1H, and R¹¹ are H; and R^1E is C^₄ alkyl, e.g., alkyl.

In another embodiment, the compound of formula (Ib) is CP0433YC1, e.g.,

In still another aspect, the invention features a pharmaceutical composition including a compound of formula (Ha), or a salt thereof, and a pharmaceutically acceptable excipient.

In formula (Ha), X⁴ is N or C; each of Y, X⁵, and X⁶ are, independently, selected from O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(O)OR^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R R^2S _, R^2T, R^2U, R^2V, and R^2W, are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl. In a further embodiment, X⁴ is N, X⁵ is S, and X⁶ is O.

In still another aspect, the invention features a pharmaceutical composition including a compound of formula (lib), or a salt thereof, and a pharmaceutically acceptable excipient.

In formula (lib), Y is O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(O)OR^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R _R ²s _R ²τ _R ²u _R ²v _{and R} ²w ^ independently, selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl.

In certain embodiments, R^2E and R^2F are H; R^2A, R^2B, R^2C, and R^2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R _R ²s _R ²τ _R ²u _R ²v _{and R} ²w ^ independently, selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C₇_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

In still other embodiments, Y is NH; R^2E and R^2F are H; R^2A, R^2B, R^2C, and R^2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, 0C(0)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)0R^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(0)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(0)NHR^2W; and each of R^2G R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R R^2S _, R²¹, R^2U, R^2V, and R^2W is, independently, selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C₆.₁₂ aryl, C₇_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

In a further embodiment, Y is NH; R^2G is C_1-4 alkyl, e.g., cyclopropyl; R^2A, R^2B, R^2D, R^2E, and R^2F are H; and R^2C is C₁-C₄ heteroalkyl (e.g., CH₃-O-).

In another embodiment, the compound of formula (lib) is CP0433YC2.

The invention also pertains, at least in part, to compounds of formulae (Ia), (Ib), (Ha) and/or (lib), as described herein.

The invention also relates to derivatives of the compounds of formula (Ia), (Ib), (Ha), and (lib) which are inhibitors of CopN homologues in all organisms that express a CopN homologue, including other Chlamydia. In another embodiment, the present invention relates to derivatives of the compounds CP0433YC1 and CP0433YC2 which are inhibitors of CopN homologues in all organisms that express a CopN homologue, including other Chlamydia.

The invention further features a kit including: (i) a pharmaceutical composition including a CopN(Cpn) inhibitor and (ii) instructions for administering the composition to a subject for the treatment of a bacterial infection. In certain embodiments, the CopN(Cpra) inhibitor is a compound of formula (Ia), (Ib), (Ha), (lib) or a salt thereof. In still other embodiments, the bacterial infection is selected from community-acquired pneumonia, upper and lower respiratory tract infection, skin and soft tissue infection, acute bacterial otitis media, bacterial pneumonia, complicated infection, pyelonephritis, intra-abdominal infection, bacterial sepsis, central nervous system infection, bacteremia, wound infection, peritonitis, meningitis, infections after burn, urogenital tract infection, pelvic inflammatory disease, endocarditis, and intravascular infection.

In still another related aspect, the invention features a kit including (i) a pharmaceutical composition comprising a CopN(Cpn) inhibitor and (ii) instructions for administering the composition to a subject for the treatment of a chronic disease associated with a bacterial infection. In certain embodiments, the chronic disease is an inflammatory disease, such as asthma, coronary artery disease, arthritis, conjunctivitis, lymphogranuloma venerum, cervicitis, or salpingitis. In other embodiments, the chronic disease is an autoimmune disease, such as systemic lupus erythematosus, diabetes mellitus, or graft versus host disease. In one particular embodiment, the chronic disease is atherosclerosis.

In any of the kits and methods of the invention, the bacterial infection can be, for example, an infection caused by Chlamydia pneumoniae, Chlamydia trachomatis, Chlamydia psittaci, or any other Chlamydia spp. Other features and advantages of the invention will be apparent from the following Detailed Description, the Drawings, and the Claims.

BRIEF DESCRIPTION OF THE DRAWINGS

Figures Ia-Ic are pictures depicting CopN( Cp n) -induced yeast growth inhibition due to cell cycle arrest. Figure Ia depicts yeast (W303a) that conditionally express the designated proteins. The yeast were grown overnight in non-inducing selective media, cultures were normalized to OD_60O = 1.0 and serial 10-fold dilutions were spotted onto inducing media. Protein expression at relatively high or low levels was achieved by using high-copy, low-copy or integrative plasmids. Photos were taken after incubation for 48 hours at 30⁰C. Figure Ib depicts exponentially growing yeast that express relatively high-levels of GFP-CopN(Cpw) and GFP (vector control). The yeast were examined by fluorescence microscopy, six hours after induction of expression of GFP- CopN(Cpw), the yeast accumulated as large-budded cells (top panel) as compared to those that express GFP (bottom panel). Figure Ic depicts the large-budded GFP- CopN(Cpra) expressing yeast which arrested at 6 hours and carry a single un-elongated nucleus (blue).

Figure 2a is a series of histograms and Figure 2b is a series of pictures showing that expression of CopN(Cpra) in yeast results in a G2/M cell cycle arrest associated with disruption of the mitotic spindle. Figure 2a depicts yeast that express a chromosomal copy of GFP-CopN(Cpra) or GFP, the yeast were synchronized at Gl with alpha factor and then released. The DNA content of the cells was monitored via FACS analysis of Pi-stained cells at 0.5-hour interval for 4.5 hours. The distribution of fluorescence intensity from individual cells is presented as histograms corresponding to 3 to 4.5 hour time points. The x-axis shows fluorescence intensity while the y-axis shows cell number. The arrows labeling the peaks of IN and 2N indicate the positions of cells containing pre-S phase (Gl) and post-S phase (G2/M) DNA contents, respectively. Figure 2b depicts yeast six hours after the induction of expression, yeast expressing relatively high levels of GFP-CopN(Cpw) or GFP were fixed and stained with rat anti-α- tubulin antibody and Texas Red dye-conjugated donkey anti-rat IgG.

Figure 3a is a series of pictures and Figure 3b is a series of histograms showing that CopN( Cp n) -induced microtubule disruption and cell cycle arrest in mammalian cells. Figure 3a depicts PtK2 cells that transiently express GFP-CopN(Cpra) (top panel) and GFP (bottom panel) for 20 hours, the yeast were then fixed and stained with mouse anti-α- tubulin monoclonal antibody and Alexa Fluor 594-conjugated goat anti-mouse IgG and DAPI. The diffused GFP green fluorescence identifies positively transfected cells. Networks of interphase microtubules are labeled red. The nuclei are labeled blue. Figure 3b depicts stably transfected 293 cell lines that conditionally express CopN(Cpra) and GFP. The transfected cell lines were synchronized at Gl, then released and allowed for expression of GFP-CopN(Cpra) (top panel) and GFP (bottom panel). The DNA content of the cells was monitored with FACS analysis of propidium iodine (PI)- stained cells at 1-hour interval for 18 hours. The distribution of fluorescence intensity from individual cells is presented as histograms corresponding to 12 to 18 hour time points. The x-axis shows fluorescence intensity while the y-axis shows cell number. The arrows labeling the peaks of 2N and 4N indicate the positions of cells containing pre-S phase (Gl) and post-S phase (G2/M) DNA contents, respectively. Figure 3c depicts HeLa cells 12h post-transfection for transient expression of GFP- CopN(Cpra) or GFP, cells were fixed and stained with anti-α-tubulin antibodies (red). Figure 3d depicts FACS analysis of the DNA content of HeLa cells expressing GFP- CopN(Cpra) or GFP at the designated time points. The peaks labeled as 2N or 4N indicate the DNA content.

Figure 4a is a graph depicting yeast growth and Figure 4b depicts the structure two compounds that inhibit CopN(Cpn) activity in yeast and identified in a high throughput growth screen. Figure 4a depicts yeast strains that conditionally express GFP, a mutant allele of CopN(Cpra) R268H, and wild type CopN(Cpra) in the presence and absence of a small molecule library were grown in inducing media. Growth was monitored by measuring the OD_60O 40 hours after incubation at 30⁰C in the presence of the compound. Only two compounds, CP0433YC1 and CP0433YC2, restored growth when present in the media at a concentration of 12.5 μg/ml. Figure 4b depicts structures of compounds CP0433YC1 and CP0433YC2.

Figure 5 shows that CP0433YC1 and CP0433YC2 inhibit Chlamydia pneumoniae growth in mammalian cells. Figure 5a is a graph depicting transcription of Chlamydia pneumoniae dnaK in infected BGMK cells (MOI=IO) in the presence and absence of CP0433YC1 and CP0433YC2 and quantified by a real-time PCR 72 hours after addition of the compounds. Chloramphenicol (Cm) (10 μg/ml), a known inhibitor of Chlamydia growth, was included as a positive control. This method (measurement of dnaK transcript number) is an indirect measurement of Chlamydia pneumoniae growth in infected cells. Figure 5b depicts Hep-2 cells treated with CP0433YC2 (P=0.0016) at 10 μg ml^"1. Figure 5c is a graph depicting dose-dependent reduction of dnaK gene transcripts of Chlamydia pneumoniae in the BGMK cells as determined by a real-time PCR in the infected BGMK cell cultures (MOI=IO) treated with compounds CP0433YC1 and CP0433YC2 for 72 hours at various concentrations: 20, 10, 5, 2.5, 1.25, 0.625, and 0.3125 μg/ml. Figure 5d depicts BGMK cells that were first treated with CP0433YC2 for 72h. The compounds were then removed and dnaK levels were determined after an additional 48 hours. Figure 5e is a series of pictures showing the development of Chlamydia pneumoniae inclusions (green) was inhibited by 72h treatment of the infected BGMK cell cultures (MOI=IO) with the compounds CP0433YC1, CP0433YC2, positive control (chloramphenicol, Cm) at the concentration of 10 μg/ml, and negative control (media plus 2% DMSO), and shown in the immunofluorescence images acquired after staining the infected BGMK cells with the FITC-conjugated monoclonal antibody against chlamydial LPS.

Figure 6 is a graph depicting the accumulation of large-budded cells in yeast expressing GFP-CopN(Cpw). Exponentially growing yeast carrying high-copy plasmid constructs pYl(0433) and pFUS were induced for expression of GFP-CopN(Cpw) and GFP (vector control). At 2, 4, and 6 hours post-induction, the proportions of cells with different budding morphology were determined by fluorescence microscopy. Each percentage is based on a count of 300 cells.

Figure 7 is a graph showing no inhibitory effect of compounds CP0433YC1 and CP0433YC2 on C. trachomatis growth. Transcription of C. trachomatis dnaK in infected BGMK cells (MOI=2) in the presence and absence of CP0433YC1 and CP0433YC2 was quantified by a real-time PCR 48 hours after addition of the compounds. Chloramphenicol (Cm) (10 μg/ml), a known inhibitor of Chlamydia growth, was included as a positive control. Data are presented as an average of total copy number of dnaK gene transcripts per well of 24-well plate (-250, 000 cells) with standard error.

Figure 8 is a picture depicting the aligned amino acid sequences of the CopN homologs. Multi- alignment of amino acid sequences was carried out using the program CLUSTALW Alignment for the CopN homologs in six chlamydial species and Y. enterocolotica with genome sequences available in the GeneBank. Identical residues are shown with dark shading and similar residues shown with light shading. Percentage identity refers to the CopN of Chlamydia pneumoniae strain AR-39. The GeneBank ID number gill6752714 is for the CopN of Chlamydia pneumoniae AR39 (In certain publications, CopN is also referred to as SctW)), gil29840220 for the CopN of C. caviae GPIC, gil89898356 for the LcrE of C. felis Fe/C-56, gil62185073 for the hypothetical protein CAB444 of C. abortus S26/3, gill5834983 for the CopN of C muridarum Nigg, gill5604808 for the CopN of C. trachomatis serovar D, and gill239131 for the YopN of Y. enterocolotica.

DETAILED DESCRIPTION OF THE INVENTION

/. Definitions

The term "infection" refers to the invasion of a host by bacteria (e.g., by Chlamydia pneumoniae, Chlamydia trachomatis, or Chlamydia psittacϊ). For example, the infection may include the excessive growth of bacteria that are normally present in or on the body of a mammal or growth of bacteria that are not normally present in or on a mammal. More generally, a bacterial infection can be any situation in which the presence of a bacterial population is damaging to a host body. In some instances, bacterial growth may be modest, but the damage is caused by production of various toxic constituents by the bacteria. In rare cases, bacteria grow outside of the host, produce toxins that are ingested and the damage is entirely the result of the activity of this bacterial toxin. Thus, a mammal is "suffering" from an infection when an excessive amount of a bacterial population is present in or on the mammal's body, or when the presence of a bacterial population is damaging the cells or other tissue of the mammal.

The term "effective" amount refers to the amount of a pharmaceutical composition of the invention required to treat or prevent an infection or a disease associated with an infection. The term "effective amount" also refers to that amount effective to inhibit a CopN(Cpra) mediated microtubule disruption in a cell and/or that amount effective to inhibit CopN(Cpra) mediated cell cycle arrest in a cell. The effective amount of a pharmaceutical composition of the invention used to practice the invention for therapeutic or prophylactic treatment of conditions caused by or contributed to by an infection varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an "effective" amount.

As used herein, the term "CopN(Cpw) inhibitor" refers to a compound that reduces the ability of CopN(Cpra) to interfere with cell growth. CopN(Cpn) inhibitors of the invention are able to restore growth by 5, %, 10%, 15%, 20%, 25%, 30%, 35%, or 40% in comparison to cell growth observed under the same conditions but in the absence of CopN(Cpn). Methods for determining whether a compound is a CopN(Cpra) inhibitor are described herein.

The term "pharmaceutical composition" is defined as a composition containing a compound of the invention formulated with one or more pharmaceutical-grade excipients in a manner that conforms with the requirements of a governmental agency regulating the manufacture and sale of pharmaceuticals as part of a therapeutic regimen for the treatment or prevention of disease in a mammal (e.g., manufactured according to GMP regulations and suitable for administration to a human). Pharmaceutical compositions can be formulated, for example, for oral administration in unit dosage form (e.g., a tablet, capsule, caplet, gelcap, or syrup); for topical administration (e.g., as a cream, gel, lotion, or ointment); for intravenous administration (e.g., as a sterile solution free of particulate emboli and in a solvent system suitable for intravenous use); or any other formulation described herein. Desirably, the pharmaceutical composition does not contain DMSO.

As used herein, the term "treating" refers to administering a pharmaceutical composition for prophylactic and/or therapeutic purposes. To "prevent disease" refers to prophylactic treatment of a subject who is not yet ill, but who is susceptible to, or otherwise at risk of, a particular disease. To "treat disease" or use for "therapeutic treatment" refers to administering treatment to a subject already suffering from a disease to improve or stabilize the subject's condition. Thus, in the claims and embodiments, treating is the administration to a subject either for therapeutic or prophylactic purposes.

The term "atherosclerosis" refers to the progressive accumulation of smooth muscle cells, immune cells (e.g., lymphocytes, macrophages, or monocytes), lipid products (e.g., lipoproteins, or cholesterol), cellular waste products, calcium, or other substances within the inner lining of an artery, resulting in the narrowing or obstruction of the blood vessel and the development of atherosclerosis-associated diseases. Atherosclerosis is typically manifested within large and medium-sized arteries, and is often characterized by a state of chronic inflammation within the arteries.

The term "atherosclerosis-associated disease" is defined as any disorder that is caused by or is associated with atherosclerosis. Typically, atherosclerosis of the coronary arteries commonly causes coronary artery disease, myocardial infarction, coronary thrombosis, and angina pectoris. Atherosclerosis of the arteries supplying the central nervous system frequently provokes strokes and transient cerebral ischemia. In the peripheral circulation, atherosclerosis causes intermittent claudication and gangrene and can jeopardize limb viability. Atherosclerosis of an artery of the splanchnic circulation can cause mesenteric ischemia. Atherosclerosis can also affect the kidneys directly (e.g., renal artery stenosis).

A subject who is being treated for an atherosclerosis-associated disease is one who a medical practitioner has diagnosed as having such a disease. Diagnosis may be done by any suitable means. Methods for diagnosing atherosclerosis by measuring systemic inflammatory markers are described, for example, in U.S. Patent No. 6,040,147, hereby incorporated by reference. Diagnosis and monitoring may employ an electrocardiogram, chest X-ray, echocardiogram, cardiac catheterization, ultrasound (for the measurement of vessel wall thickness), or measurement of blood levels of CPK, CPK-MB, myoglobin, troponin, homocysteine, or C-reactive protein. A subject in whom the development of an atherosclerosis-associated disease is being prevented is one who has not received such a diagnosis. One in the art will understand that these subjects may have been subjected to the same tests (electrocardiogram, chest X-ray, etc.) or may have been identified, without examination, as one at high risk due to the presence of one or more risk factors (e.g., family history, hypertension, diabetes mellitus, high cholesterol levels). Thus, prophylactic administration of a CopN(Cpra) inhibitor is considered to be preventing the development of an atherosclerosis- associated disease.

An atherosclerosis-associated disease has been treated or prevented when one or more tests of the disease (e.g., any of those described above) indicate that the subject's condition has improved or the subject's risk reduced. In one example, a reduction in C-reactive protein to normal levels indicates that an atherosclerosis- associated disease has been treated or prevented.

An alternative means by which treatment or prevention is assessed includes determination of the presence of an infection of Chlamydia pneumoniae. Any suitable method may be employed (e.g., determination of Chlamydia pneumoniae in blood monocytes or in the atheroma itself (e.g., in macrophages or foam cells present in the fatty streak), or detection of Chlamydia pneumoniae DNA, Chlamydia pneumoniae RNA, or antibodies to Chlamydia pneumoniae in a biological sample from the subject).

The term "subject" includes humans, and non-human animals amenable to therapy, e.g., preferably mammals and animals susceptible to bacterial infections, such as non-human primates, transgenic animals, mice, rats, dogs, cats, rabbits, pigs, chickens, sheep, horses, and cows. The term "subject" also includes the term "patient". In the generic descriptions of compounds of this invention, the number of atoms of a particular type in a substituent group is generally given as a range, e.g., an alkyl group containing from 1 to 4 carbon atoms or C_1-4 alkyl. Reference to such a range is intended to include specific references to groups having each of the integer number of atoms within the specified range. For example, an alkyl group from 1 to 4 carbon atoms includes each of C₁, C₂, C₃, and C₄. A C_1-4 heteroalkyl, for example, includes from 1 to 3 carbon atoms in addition to one or more heteroatoms. Other numbers of atoms and other types of atoms may be indicated in a similar manner.

As used herein, the terms "alkyl" and the prefix "alk-" are inclusive of both straight chain and branched chain groups and of cyclic groups, i.e., cycloalkyl. Exemplary cyclic groups include cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl groups. The C_1-4 alkyl group may be substituted or unsubstituted. Exemplary substituents include alkoxy, aryloxy, sulfhydryl, alkylthio, arylthio, halide, hydroxyl, fluoroalkyl, perfluoralkyl, amino, aminoalkyl, disubstituted amino, quaternary amino, hydroxyalkyl, carboxyalkyl, and carboxyl groups. C_1-4 alkyls include, without limitation, methyl; ethyl; n-propyl; isopropyl; cyclopropyl; cyclopropylmethyl; cyclopropylethyl; n- butyl; iso-butyl; sec -butyl; tert-butyl; and cyclobutyl.

The term "C₂_₄ alkenyl" refers to a branched or unbranched hydrocarbon group containing one or more double bonds and having from 2 to 4 carbon atoms. The C₂-₄ alkenyl group may be substituted or unsubstituted. Exemplary substituents include alkoxy, aryloxy, sulfhydryl, alkylthio, arylthio, halide, hydroxyl, fluoroalkyl, perfluoralkyl, amino, aminoalkyl, disubstituted amino, quaternary amino, hydroxyalkyl, carboxyalkyl, and carboxyl groups. C₂_₄ alkenyls include, without limitation, vinyl; allyl; 2-cyclopropyl-l-ethenyl; 1-propenyl; 1-butenyl; 2-butenyl; 3-butenyl; 2-methyl-l- propenyl; and 2-methyl-2-propenyl.

The term "C₂_₄ alkynyl" refers to a branched or unbranched hydrocarbon group containing one or more triple bonds and having from 2 to 4 carbon atoms. The C₂_₄ alkynyl group may be substituted or unsubstituted. Exemplary substituents include alkoxy, aryloxy, sulfhydryl, alkylthio, arylthio, halide, hydroxy, fluoroalkyl, perfluoralkyl, amino, aminoalkyl, disubstituted amino, quaternary amino, hydroxyalkyl, carboxyalkyl, and carboxyl groups. C₂_₄ alkynyls include, without limitation, ethynyl, 1- propynyl, 2-propynyl, 1-butynyl, 2-butynyl, and 3-butynyl.

The term "C_1-4 heteroalkyl" refers to a branched or unbranched alkyl, alkenyl, or alkynyl group having from 1 to 4 carbon atoms in addition to 1, 2, or 3 heteroatoms independently selected from the group consisting of N, O, S, and P. Heteroalkyls include, without limitation, tertiary amines, secondary amines, ethers, thioethers, amides, thioamides, carbamates, thiocarbamates, hydrazones, imines, phosphodiesters, phosphoramidates, sulfonamides, and disulfides. A heteroalkyl may optionally include monocyclic, bicyclic, or tricyclic rings, in which each ring desirably has three to six members. The heteroalkyl group may be substituted or unsubstituted. Exemplary substituents include alkoxy, aryloxy, sulfhydryl, alkylthio, arylthio, halide, hydroxyl, fluoroalkyl, perfluoralkyl, amino, aminoalkyl, disubstituted amino, quaternary amino, hydroxyalkyl, hydroxyalkyl, carboxyalkyl, and carboxyl groups.

The term "acyl" is defined as a chemical moiety with the formula R-C(O)-, wherein R is selected from C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, or C_1-4 heteroalkyl.

The term "halide" is defined as bromine, chlorine, iodine, or fluorine.

The term "fluoroalkyl" is defined as an alkyl group that is substituted with fluorine.

The term "perfluoroalkyl" refers to an alkyl group consisting of only carbon and fluorine atoms.

The term "carboxyalkyl" refers to i a chemical moiety with the formula -(R)- COOH, wherein R is selected from C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, or C_1-4 heteroalkyl.

The term "hydroxyalkyl" is defined as a chemical moiety with the formula -(R)- OH, wherein R is selected from C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, or C_1-4 heteroalkyl.

The term "alkoxy" is defined as a chemical substituent of the formula -OR, wherein R is selected from C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, or C_1-4 heteroalkyl.

The term "alkylthio" refers to a chemical substituent of the formula -SR, wherein R is selected from C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, or C_1-4 heteroalkyl.

The term "quaternary amino" refers to a chemical substituent of the formula - (R)-N(R' )(R")(R'")⁺, wherein R, R', R", and R'" are each independently an alkyl, alkenyl, alkynyl, or aryl group. R may be an alkyl group linking the quaternary amino nitrogen atom, as a substituent, to another moiety. The nitrogen atom, N, is covalently attached to four carbon atoms of alkyl and/or aryl groups, resulting in a positive charge at the nitrogen atom.

//. CopN(Cpn) Inhibitors

The genomes of pathogenic bacteria are rapidly being sequenced and annotated resulting in the in silico identification of proteins potentially involved in the manipulation of eukaryotic host cells. The study of the role of these proteins during infection is particularly difficult in genetically intractable organisms like Chlamydia pneumoniae where it is currently not possible to generate targeted gene disruptions.

The instant invention provides a functional assay that monitors the activity of the protein of interest outside of its natural setting and then exploits this assay to identify compounds that inhibit the activity of the protein. The ability of a compound to interfere with virulence of the organism in a relevant model effectively substitutes for a virulence phenotype of a mutant in the corresponding gene.

A. Virulence Proteins

Virulence proteins of the present invention include the Chlamydia pneumoniae proteins encoded by CP0433, CP1062, CP0833, CP0679 and CP0358. In one embodiment CopN is the CP0433 gene product and a putative substrate of the Chlamydia, pneumoniae type HI system that localizes in the inclusion membrane and possibly host cell cytosol (In certain publications, CopN is also referred to as SctW). In another embodiment, CP1062 and CP0833 encode two putative type in effectors that localize to the host cell cytosol. In another embodiment, CP0679 encodes a putative serine/threonine kinase. In a further embodiment, CP0358 encodes a putative serine/threonine protein phosphatase.

In one aspect of the instant invention, expression of a virulence protein in yeast inhibits the growth of yeast. In a preferred embodiment of this aspect, the inhibition of yeast growth results from microtubule disruption. In another preferred embodiment of this aspect, the inhibition of yeast growth results from G2/M cell cycle arrest. In a further preferred embodiment of this aspect, the inhibition of yeast growth results from G2/M cell cycle arrest due to the disruption of microtubules. In one embodiment of this aspect, the virulence protein is selected from the group comprising the Chlamydia pneumoniae proteins encoded by CP0433, CP1062, CP0833, CP0679 and CP0358. In another embodiment of this aspect, the virulence protein is the CP0433 gene product. In a preferred embodiment of this aspect, the virulence protein is CopN.

In another aspect, expression of a Chlamydia pneumoniae virulence protein in yeast results in cell cycle G2/M cell cycle arrest, which thereby benefits the multiplication of Chlamydia pneumoniae. In one embodiment, CopN induced cell cycle arrest allows for the diversion of resources of the infected cell to favor the multiplication of Chlamydia pneumoniae.

In one aspect of the instant invention, expression of a virulence protein in mammalian cells inhibits the growth of the mammalian cells. In a preferred embodiment of this aspect, the inhibition of mammalian cell growth results from microtubule disruption. In another preferred embodiment of this aspect, the inhibition of mammalian cell growth results from G2/M cell cycle arrest. In a further preferred embodiment of this aspect, the inhibition of mammalian cell growth results from G2/M cell cycle arrest due to the disruption of microtubules. In one embodiment of this aspect, the virulence protein is selected from the group comprising the Chlamydia pneumoniae proteins encoded by CP0433, CP1062, CP0833, CP0679 and CP0358. In another embodiment of this aspect, the virulence protein is the CP0433 gene product. In a preferred embodiment of this aspect, the virulence protein is CopN. In a further embodiment of this aspect, the mammalian cells are macrophages or foam cells.

In another aspect, expression of a Chlamydia pneumoniae virulence protein in mammalian cells results in cell cycle G2/M cell cycle arrest, which thereby benefits the multiplication of Chlamydia pneumoniae

B. Small Molecule Inhibitors

The instant invention provides small molecule inhibitors of CopN(Cpra) activity. Two of these compounds were identified in a chemical library screen for inhibiting the CopN(Cpw)-mediated yeast growth effect. These compounds were used to essentially generate "functional knockouts" of CopN(Cpra) in a mammalian cell culture model of infection and demonstrate that CopN(Cpra) is required to support the intracellular growth of Chlamydia pneumoniae. Thus, CopN(Cpw), plays a virulence role in the cell culture model of Chlamydia, pneumoniae infection. This novel strategy can be extended to all Chlamydia spp. including Chlamydia trachomatis where over thirty proteins have recently been identified that inhibit yeast growth (Sisko et al., MoI. Microbiol. 60:51 (2006)).

Small molecule compounds were identified in the yeast screen and used to validate the importance of the targeted protein for Chlamydia, pneumoniae during intracellular replication by creating a "functional knockout", substituting treatment with an inhibitor for a genetic disruption that is not possible in this group of organisms. Although it is likely that the target of the compounds is CopN(Cpra) itself, it is equally conceivable that the compounds interact with a cellular target of CopN( Cp n), blocking its interaction with the secreted chlamydial protein. Nevertheless, the instant invention teaches that small molecule-centered chemical genetics can be used to mimic classical reverse genetic strategies for examining virulence function of genes in an intracellular bacterial system through essentially generating a "loss of function" mutation in a protein apparently essential for pathogenicity of a genetically intractable obligate intracellular bacterium.

The cellular effects induced by CopN(Cpra) on microtubules and cell cycle progression taught in the instant specification provide valuable insights into potential mechanisms by which CopN(Cpra) affects host cells. Mammalian microtubules form network structures (interphase) or spindles (mitosis/meiosis) essential for a variety of cellular functions, including maintenance of cell shape, cell polarity, intracellular transport, cell mitosis, and meiosis. Dynamic instability is believed to be central to the biological functions of microtubules (Desai et a\., Annu. Rev. Cell Dev. Biol. 13:83 (1997)).

CopN(Cpw)-induced cell cycle arrest at G2/M stage may contribute to the overall suppression of the host cell division. This cell cycle G2/M cell division block could potentially benefit the multiplication of Chlamydia, pneumoniae. Therefore, the microtubule-dependent cell cycle arrest represents a novel mechanism for bacterial manipulation of host cell division (Oswald et al., Curr. Opin. Microbiol. 8:83 (2005); Shafikhani et al., Proc. Natl. Acad. ScL USA 103:15605 (2006)).

In one aspect of the instant invention, expression of CopN(Cpra) is required to support the intracellular growth of Chlamydia, pneumoniae. In one embodiment of this aspect, the expression of CopN(Cpra) supports the intracellular growth of Chlamydia pneumoniae by disrupting the microtubules of the cell. In another embodiment of this aspect, the expression of CopN(Cpn) supports the intracellular growth of Chlamydia pneumoniae by mediating G2/M cell cycle arrest. In a further preferred embodiment of this aspect, the expression of CopN(Cpra) supports the intracellular growth of Chlamydia, pneumoniae by mediating G2/M cell cycle arrest due to microtubule disruption.

In another embodiment of this aspect, CopN(Cpra) is required to support the intracellular growth of Chlamydia, pneumoniae in mammalian cells. In a further embodiment of this aspect, the mammalian cells are macrophages or foam cells.

In another aspect of the present invention, expression of CopN(Cpn) in a host cell allows for bacterial manipulation of the host cell. In one embodiment of this aspect, the bacteria are Chlamydia pneumoniae. In a further embodiment of this aspect, expression of CopN(Cpn) in a host cell allows for bacterial manipulation of the host cell by mediating cell cycle arrest. In another embodiment of this aspect, expression of CopN(Cpn) in a host cell allows for bacterial manipulation of the host cell by mediating G2/M phase cell cycle arrest. In a further embodiment of this aspect, expression of CopN(Cpn) in a host cell allows for bacterial manipulation of the host cell by disrupting microtubules of the host cell. In a further preferred embodiment of this aspect, expression of CopN(Cpn) in a host cell allows for bacterial manipulation of the host cell by mediating cell cycle arrest due to microtubule disruption.

In another aspect of the present invention, administration of CopN(Cpn) inhibitors to a subject inhibits bacterial manipulation of the host cell. In one embodiment of this aspect, the bacteria are Chlamydia pneumoniae. In an additional embodiment of this aspect, administration of CopN(Cpn) inhibitors to a subject inhibits the disruption of the microtubules of the host cell. In an additional embodiment of this aspect, administration of CopN(Cpn) inhibitors to a subject inhibits bacterial manipulation of the host cell by inhibiting cell cycle arrest of the host cell. In a further embodiment of this aspect, administration of CopN(Cpn) inhibitors to a subject inhibits bacterial manipulation of the host cell by inhibiting cell cycle arrest at G2/M phase. In an additional embodiment of this aspect, administration of CopN(Cpn) inhibitors to a subject inhibits bacterial manipulation of the host cell by inhibiting cell cycle arrest due to microtubule disruption. In one embodiment of this aspect, the CopN(Cpn) inhibitors comprise the compounds of formula Ia, Ib, Ha, lib, CP0433YC1 and/or CP0433YC2.

In one aspect of the present invention, administration of CopN(Cpra) inhibitors to a subject inhibits CopN(Cpra) mediated microtubule disruption. In an additional aspect, administration of CopN(Cpn) inhibitors to a subject inhibits CopN(Cpn) mediated cell cycle arrest. In a further aspect, administration of CopN(Cpra) inhibitors to a subject inhibits CopN(Cpra) mediated cell cycle arrest at G2/M phase. In another aspect of the present invention, administration of CopN(Cpra) inhibitors to a subject inhibits CopN(Cpra) cell cycle arrest due to the disruption of microtubules. In one embodiment of these aspects, the CopN(Cpra) inhibitors comprise the compounds of formula Ia, Ib, Ha, lib, CP0433YC1 and/or CP0433YC2.

In another aspect of the present invention, administration of CopN(Cpn) inhibitors to a subject inhibits bacterial infection of the host cell. In another aspect of the present invention, administration of CopN(Cpra) inhibitors to a subject treats a bacterial infection in the subject. In one embodiment of these aspects, the CopN(Cpra) inhibitors comprise the compounds of formula Ia, Ib, Ha, lib, CP0433YC1 and/or CP0433YC2.

///. Compounds of the Invention

CopN(Cpn) inhibitors of the invention include compounds of formula (Ia), (Ib), (Ha) and (lid). Other CopN(Cpra) inhibitors can be identified using the methods provided in the examples.

Compounds of Formula (Ia) and (Ib)

Compounds of the invention include compounds of formula (Ia).

In formula (Ia), X¹ is C or N; each of X² and X³ are independently selected from C, O, S, or N; R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(O)R^1N, NHC(S)R¹⁰, NHC(O)OR^1P, NHC(S)OR^1Q, NHC(0)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_6 heterocyclyl, C₆-I₂ aryl, C_7-14 alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl; and wherein the dotted lines represent single or double bonds, optionally selected such that the ring is aryl. In a further embodiment, the compounds of formula (Ia) do not include CP0433YC1, e.g., compounds wherein X¹, X², and X³ are each N; R^1A, R^1B, R^1C, R^1D, R^1F, R^1G, R^1H, and R¹¹ are each hydrogen, R^1E is not lower alkyl (e.g., methyl or ethyl). In a further embodiment, each of X¹, X², and X³ are nitrogen.

In another aspect, the compounds of the invention include compounds of formula

(Ib):

C(O)OR , i¹w ^w, and C(0)NHR 1 I¹X^Λ; and each of R I¹J^J, r R> l¹K^K r> I ⁱθ^υ r R>

R¹M^M r R> I¹N^1N _, r R> l lⁱP^r r R> IⁱQ^y r R> I¹R^K r R> I¹S⁵ _, _R ⁱτ _R ⁱu _R ⁱv _R ⁱw _{and R} ⁱx _{are^ independently;} selected from H, C_i_₄ alkyl, C₂-₄ alkenyl,

C₂-₄ alkynyl, C₂-₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C₃_io alkheterocyclyl, and C_1-4 heteroalkyl. In a further embodiment, the compounds of formula (Ib) do not include CP0433YC1, e.g., compounds wherein R^1A, R^1B, R^1C, R^1D, R^1F, R^1G, R^1H, and R¹¹ are each hydrogen, R^1E is not lower alkyl (e.g., methyl or ethyl).

In a further embodiment, each of R^1A, R^1B, R^1C R^1D, R^1F, R^1G, R^1H, and R¹¹ are H; and R^1E is C_1-4 alkyl, e.g., alkyl. In another embodiment, the compound of formula (Ib) is

Compounds of Formula (Ia) and (Ib) can be prepared by methods known in the art. In particular, compounds of formula (Ib) can be prepared, for example, using the combination of an arylpropiolate ester and an aryl azide in a Huisgen cycloaddition reaction (see Scheme 1) as described in Bock et al., Eur. J. Org. Chem.: 51 (2006). The substituent X is a reacting group for C-C bond forming reactions and can include, but is not limited to: I, Br, Cl, OSO₂CF₃, OSO₂(CF₂)_nCF₃ where n = 1-3, and OSO₂(^- CH₃C₆H₄). In a manner analogous to Chuprakov et al., Org. Lett. 12: 2333 (2007), an intramolecular arylation of the resultant triazole can afford the desired product.

Scheme 1

Compounds of Formula (Ha) and (lib)

Compounds of the invention include compounds of formula (Ha).

In formula (Ha), X⁴ is N or C; each of Y, X⁵, and X⁶ are, independently, selected from O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)0R^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(0)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R R^2S _, R^2T, R^2U, R^2V, and R^2W, are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl. In a further embodiment, the compounds of formula (Ha) do not include CP0433YC2, e.g., compounds wherein X⁴ is N; X⁵ is S; X⁶ is O; Y is NH; R^2A, R^2B, R^2D, R^2E, and R^2F are H; R^2G is not cyclopropyl. In a further embodiment, X⁴ is N, X⁵ is S, and X⁶ is O.

In still another aspect, the invention includes compounds of formula (lib).

In formula (lib), Y is O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(O)OR^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R _R ²s _R ²τ _R ²u _R ²v _{and R} ²w ^ independently, selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl. In a further embodiment, the compounds of formula (lib) do not include CP0433YC2, e.g., compounds wherein Y is NH; R^2A, R^2B, R^2D, R^2E, and R^2F are each H; R^2G is not cyclopropyl.

Compounds of formula (Ha) and (lib) can be prepared according to art recognized methods. In addition, certain compounds of formula (lib) can be prepared by the procedure outlined in Scheme 2. The thienoquinoline can be synthesized from acetylated aniline starting materials according to the procedure outlined by Srivastava et al., Indian J. Chem., Sect B AA: 2077 (2005). The product can be de-aminated using a protocol of diazotization followed by reducing conditions. Such transformations are comprehensively discussed in "S. Patai: Amino, Nitroso, Nitro, and Related Groups" (1996, John Wiley & Sons). Nitrile hydrolysis can then afford a carboxylic acid intermediate. Following activation of the acid moiety using standard peptide coupling protocols (reviewed in Han et al., Tetrahedron 60:2447 (2004)), the desired product can be obtained upon treatment with the selected nucleophile. Scheme 2

Y=O, S, NR^2H

The synthesis of the compounds of the invention may involve selective protection and deprotection of alcohols, amines, sulfhydryls and carboxylic acid functional groups in one or more reactants. For example, commonly used protecting groups for amines include carbamates, such as tert-butyl, benzyl, 2,2,2 -trichloroethyl, 2-trimethylsilylethyl, 9-fluorenylmethyl, allyl, and m-nitrophenyl. Other commonly used protecting groups for amines include amides, such as formamides, acetamides, trifluoroacetamides, sulfonamides, trifluoromethanesulfonyl amides, trimethylsilylethanesulfonamides, and te/t-butylsulfonyl amides. Examples of commonly used protecting groups for carboxylic acids include esters, such as methyl, ethyl, tert-butyl, 9-fluorenylmethyl, 2-(trimethylsilyl)ethoxy methyl, benzyl, diphenylmethyl, O-nitrobenzyl, ortho-esters, and halo-esters. Examples of commonly used protecting groups for alcohols include ethers, such as methyl, methoxymethyl, methoxyethoxymethyl, methylthiomethyl, benzyloxymethyl, tetrahydropyranyl, ethoxyethyl, benzyl, 2-napthylmethyl, O-nitrobenzyl, P-nitrobenzyl, P-methoxybenzyl, 9-phenylxanthyl, trityl (including methoxy-trityls), and silyl ethers. Examples of commonly used protecting groups for sulfhydryls include many of the same protecting groups used for hydroxyls. In addition, sulfhydryls can be protected in a reduced form (e.g., as disulfides) or an oxidized form (e.g., as sulfonic acids, sulfonic esters, or sulfonic amides). Protecting groups can be chosen such that selective conditions (e.g., acidic conditions, basic conditions, catalysis by a nucleophile, catalysis by a lewis acid, or hydrogenation) are required to remove each, exclusive of other protecting groups in a molecule. The conditions required for the addition of protecting groups to amine, alcohol, sulfhydryl, and carboxylic acid functionalities and the conditions required for their removal are provided in detail in "T.W. Green and P.G.M. Wuts: Protective Groups in Organic Synthesis" (2^nd ed., 1991, John Wiley & Sons) and "PJ. Kocienski: Protecting Groups" (1994 Georg Thieme Verlag); each of which is hereby incorporated by reference.

IV. Therapy

The invention features methods for treating bacterial infections and diseases associated with such infections by administering a CopN(Cpra) inhibitor.

Therapy according to the invention may be performed alone or in conjunction with another therapy and may be provided at home, the doctor's office, a clinic, a hospital's outpatient department, or a hospital. The duration of the therapy depends on the type of disease or disorder being treated, the age and condition of the subject, the stage and type of the subject's disease, and how the subject responds to the treatment.

Bacterial infections

The methods and compositions of the present invention can be used to treat, for example, respiratory tract infections, acute bacterial otitis media, bacterial pneumonia, urinary tract infections, complicated infections, pyelonephritis, intra-abdominal infections, bacterial sepsis, skin and skin structure infections, soft tissue infections, central nervous system infections, bacteremia, wound infections, peritonitis, meningitis, infections after burn, urogenital tract infections, pelvic inflammatory disease, endocarditis, intravascular infections, and any other infections described herein.

Diseases associated with infections

Diseases associated with bacterial infections include, but are not limited to, multiple sclerosis (MS), rheumatoid arthritis (RA), inflammatory bowel disease (IBD), interstitial cystitis (IC), fibromyalgia (FM), autonomic nervous dysfunction (AND, neural-mediated hypotension); pyoderma gangrenosum (PG), chronic fatigue (CF) and chronic fatigue syndrome (CFS).

Several lines of evidence have led to the establishment of a link between bacterial infections and a broad set of inflammatory, autoimmune, and immune deficiency diseases. Thus, the present invention describes methods for treating chronic diseases associated with a persistent infection, such as autoimmune diseases, inflammatory diseases and diseases that occur in immuno-compromised individuals by administering a CopN(Cpra) inhibitor. Progress of the treatment can be evaluated, using the diagnostic tests known in the art, to determine the presence or absence of the bacteria. Physical improvement in the conditions and symptoms typically associated with the disease to be treated can also be evaluated. Based upon these evaluating factors, the physician can maintain or modify the anti-bacterial therapy accordingly.

The therapies described herein can be used for the treatment of chronic immune and autoimmune diseases when subjects are demonstrated to have a bacterial infection. These diseases include, but are not limited to, systemic lupus erythematosus, arthritis, thyroidosis, scleroderma, diabetes mellitus, Graves' disease, Beschet's disease, and graft versus host disease (graft rejection). The therapies of this invention can also be used to treat any disorders in which a bacterial infection is a factor or co-factor.

Thus, the present invention can be used to treat a range of disorders in addition to the above immune and autoimmune diseases when demonstrated to be associated with chlamydial infection by the methods of detection described herein; for example, various infections, many of which produce inflammation as primary or secondary symptoms, including, but not limited to, sepsis syndrome, cachexia, circulatory collapse and shock resulting from acute or chronic bacterial infection, acute and chronic parasitic and/or infectious diseases from bacterial, viral or fungal sources, such as a HIV, AIDS (including symptoms of cachexia, autoimmune disorders, AIDS dementia complex and infections) can be treated..

Among the various inflammatory diseases, there are certain features that are generally agreed to be characteristic of the inflammatory process. These include fenestration of the microvasculature, leakage of the elements of blood into the interstitial spaces, and migration of leukocytes into the inflamed tissue. On a macroscopic level, this is usually accompanied by the familiar clinical signs of erythema, edema, tenderness (hyperalgesia), and pain. Inflammatory diseases, such as chronic inflammatory pathologies and vascular inflammatory pathologies, including chronic inflammatory pathologies such as aneurysms, hemorrhoids, sarcoidosis, chronic inflammatory bowel disease, ulcerative colitis, and Crohn's disease and vascular inflammatory pathologies, such as, but not limited to, disseminated intravascular coagulation, atherosclerosis, and Kawasaki's pathology are also suitable for treatment by methods described herein. The invention can also be used to treat inflammatory diseases such as coronary artery disease, hypertension, stroke, asthma, chronic hepatitis, multiple sclerosis, peripheral neuropathy, chronic or recurrent sore throat, laryngitis, tracheobronchitis, chronic vascular headaches (including migraines, cluster headaches and tension headaches) and pneumonia when demonstrated to be pathogenically related to a bacterial infection.

Treatable disorders when associated with a bacterial infection also include, but are not limited to, neurodegenerative diseases, including, but not limited to, demyelinating diseases, such as multiple sclerosis and acute transverse myelitis; extrapyramidal and cerebellar disorders, such as lesions of the corticospinal system; disorders of the basal ganglia or cerebellar disorders; hyperkinetic movement disorders such as Huntington's Chorea and senile chorea; drug-induced movement disorders, such as those induced by drugs which block CNS dopamine receptors; hypokinetic movement disorders, such as Parkinson's disease; progressive supranucleo palsy; cerebellar and spinocerebellar disorders, such as astructural lesions of the cerebellum; spinocerebellar degenerations (spinal ataxia, Friedreich's ataxia, cerebellar cortical degenerations, multiple systems degenerations (Mencel, Dejerine-Thomas, Shi-Drager, and Machado Joseph)); and systemic disorders (Refsum's disease, abetalipoprotemia, ataxia, telangiectasia, and mitochondrial multi- system disorder); demyelinating core disorders, such as multiple sclerosis, acute transverse myelitis; disorders of the motor unit, such as neurogenic muscular atrophies (anterior horn cell degeneration, such as amyotrophic lateral sclerosis, infantile spinal muscular atrophy and juvenile spinal muscular atrophy); Alzheimer's disease; Down's Syndrome in middle age; Diffuse Lewy body disease; senile dementia of Lewy body type; Wernicke-Korsakoff syndrome; chronic alcoholism; Creutzfeldt-Jakob disease; subacute sclerosing panencephalitis, Hallerrorden-Spatz disease; and dementia pugilistica.

It is also recognized that malignant pathologies involving tumors or other malignancies, such as, but not limited to leukemias (acute, chronic myelocytic, chronic lymphocytic and/or myelodyspastic syndrome); lymphomas (Hodgkin's and non-Hodgkin's lymphomas, such as malignant lymphomas (Burkitt's lymphoma or mycosis fungoides)); carcinomas (such as colon carcinoma) and metastases thereof; cancer-related angiogenesis; infantile hemangiomas; and alcohol-induced hepatitis. Ocular neovascularization, psoriasis, duodenal ulcers, angiogenesis of the female reproductive tract, can also be treated when demonstrated by the diagnostic procedures described herein to be associated with a bacterial infection.

V. Pharmaceutical Compositions

The invention features compositions, kits, and methods for treating or preventing a disease or condition associated with a bacterial infection by administering a compound of the invention (i.e., a CopN(Cpra) inhibitor). Compounds of the present invention may be administered by any appropriate route for treatment or prevention of a disease or condition associated with a microbial or viral infection. These may be administered to humans, domestic pets, livestock, or other animals with a pharmaceutically acceptable diluent, carrier, or excipient, in unit dosage form. Administration may be topical, parenteral, intravenous, intra-arterial, subcutaneous, intramuscular, intracranial, intraorbital, ophthalmic, intraventricular, intracapsular, intraspinal, intracisternal, intraperitoneal, intranasal, aerosol, by suppositories, or oral administration.

Therapeutic formulations may be in the form of liquid solutions or suspensions; for oral administration, formulations may be in the form of tablets or capsules; and for intranasal formulations, in the form of powders, nasal drops, ear drops, or aerosols.

Methods well known in the art for making formulations are found, for example, in "Remington: The Science and Practice of Pharmacy" (20th ed., ed. A.R. Gennaro, 2000, Lippincott Williams & Wilkins). Formulations for parenteral administration may, for example, contain excipients, sterile water, or saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated napthalenes. Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds. Nanoparticulate formulations (e.g., biodegradable nanoparticles, solid lipid nanoparticles, liposomes) may be used to control the biodistribution of the compounds. Other potentially useful parenteral delivery systems include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes. Formulations for inhalation may contain excipients, for example, lactose, or may be aqueous solutions containing, for example, polyoxyethylene-9-lauryl ether, glycholate and deoxycholate, or may be oily solutions for administration in the form of nasal drops, or as a gel. The concentration of the compound in the formulation will vary depending upon a number of factors, including the dosage of the drug to be administered, and the route of administration.

The compound may be optionally administered as a pharmaceutically acceptable salt, such as a non-toxic acid addition salts or metal complexes that are commonly used in the pharmaceutical industry. Examples of acid addition salts include organic acids such as acetic, lactic, pamoic, maleic, citric, malic, ascorbic, succinic, benzoic, palmitic, suberic, salicylic, tartaric, methanesulfonic, toluenesulfonic, or trifluoroacetic acids or the like; polymeric acids such as tannic acid, carboxymethyl cellulose, or the like; and inorganic acid such as hydrochloric acid, hydrobromic acid, sulfuric acid phosphoric acid, or the like. Metal complexes include zinc, iron, and the like. Administration of compounds in controlled release formulations is useful where the compound of formula Ia, Ib, Ha, and/or lib has (i) a narrow therapeutic index (e.g., the difference between the plasma concentration leading to harmful side effects or toxic reactions and the plasma concentration leading to a therapeutic effect is small; generally, the therapeutic index, TI, is defined as the ratio of median lethal dose (LD₅₀) to median effective dose (ED₅₀)); (ii) a narrow absorption window in the gastro-intestinal tract; or (iii) a short biological half-life, so that frequent dosing during a day is required in order to sustain the plasma level at a therapeutic level.

Many strategies can be pursued to obtain controlled release in which the rate of release outweighs the rate of metabolism of the therapeutic compound. For example, controlled release can be obtained by the appropriate selection of formulation parameters and ingredients, including, e.g., appropriate controlled release compositions and coatings. Examples include single or multiple unit tablet or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, nanoparticles, patches, and liposomes.

Formulations for oral use include tablets containing the active ingredient(s) in a mixture with non-toxic pharmaceutically acceptable excipients. These excipients may be, for example, inert diluents or fillers (e.g., sucrose and sorbitol), lubricating agents, glidants, and antiadhesives (e.g., magnesium stearate, zinc stearate, stearic acid, silicas, hydrogenated vegetable oils, or talc).

Formulations for oral use may also be provided in unit dosage form as chewable tablets, tablets, caplets, or capsules (i.e., as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium).

The formulations can be administered to human subjects in therapeutically effective amounts. Typical dose ranges are from about 0.01 μg/kg to about 2 mg/kg of body weight per day. The preferred dosage of drug to be administered is likely to depend on such variables as the type and extent of the disorder, the overall health status of the particular subject, the specific compound being administered, the excipients used to formulate the compound, and its route of administration. Standard clinical trials maybe used to optimize the dose and dosing frequency for any particular compound.

In one embodiment, the CopN(Cpra) inhibitor is administered at a concentration in the range from about 0.001 μg/kg to greater than about 500 mg/kg. For example, the concentration may be 0.001 μg/kg , 0.01 μg/kg , 0.05 μg/kg , 0.1 μg/kg , 0.5 μg/kg, 1.0 μg/kg, 10.0 μg/kg, 50.0 μg/kg, 100.0 μg/kg, 500 μg/kg, 1.0 mg/kg, 5.0 mg/kg, 10.0 mg/kg, 15.0 mg/kg, 20.0 mg/kg, 25.0 mg/kg, 30.0 mg/kg, 35.0 mg/kg, 40.0 mg/kg, 45.0 mg/kg, 50.0 mg/kg, 60.0 mg/kg, 70.0 mg/kg, 80.0 mg/kg, 90.0 mg/kg, 100.0 mg/kg, 150.0 mg/kg, 200.0 mg/kg, 250.0 mg/kg, 300.0 mg/kg, 350.0 mg/kg, 400.0 mg/kg, 450.0 mg/kg, to greater than about 500.0 mg/kg or any incremental value thereof. It is to be understood that all values and ranges between these values and ranges are meant to be encompassed by the present invention.

In another embodiment, the CopN(Cpra) inhibitor is administered in doses that range from 1.0 μM to greater than or equal to 500 μM. For example, the dose may be 1.0 μM, 5.0 μM, 10.0 μM, 15.0 μM, 20.0 μM, 25.0 μM, 30.0 μM, 35.0 μM, 40.0 μM, 45.0 μM, 50.0 μM, 60.0 μM, 70.0 μM, 80.0 μM, 90.0 μM, 100.0 μM, 150.0 μM, 200.0 μM, 250.0 μM, 300.0 μM, 350.0 μM, 400.0 μM, 450.0 μM, to greater than about 500.0 μM or any incremental value thereof. It is to be understood that all values and ranges between these values and ranges are meant to be encompassed by the present invention.

In yet another embodiment, the CopN(Cpra) inhibitor is administered at concentrations that range from 0.10 μg/ml to 500.0 μg/ml. For example, the concentration may be 0.10 μg/ml, 0.50 μg/ml, 1 μg/ml, 2.0 μg/ml, 5.0 μg/ml, 10.0 μg/ml, 20 μg/ml, 25 μg/ml. 30 μg/ml, 35 μg/ml, 40 μg/ml, 45 μg/ml, 50 μg/ml, 60.0 μg/ml, 70.0 μg/ml, 80.0 μg/ml, 90.0 μg/ml, 100.0 μg/ml, 150.0 μg/ml, 200.0 μg/ml, 250.0 μg/ml, 300.0 μg/ml, 350.0 μg/ml, 400.0 μg/ml, 450.0 μg/ml, to greater than about 500.0 μg/ml or any incremental value thereof. It is to be understood that all values and ranges between these values and ranges are meant to be encompassed by the present invention.

In a preferred exemplary embodiment, the CopN(Cpra) inhibitor is the compound of formula Ia or Ib. In another preferred exemplary embodiment, the CopN(Cpn) inhibitor is the compound of formula Ha or lib.

VI. Kits of the Invention

In one aspect, the present invention comprises a kit including: (i) a pharmaceutical composition comprising a CopN(Cpra) inhibitor and (ii) instructions for administering the composition to a subject for the treatment of a bacterial infection.

In another aspect, the present invention comprises a kit including: (i) a pharmaceutical composition comprising a compound of formula Ia, Ib, Ha, or lib and (ii) instructions for administering the composition to a subject for the treatment of a bacterial infection.

In one embodiment of these aspects, the bacterial infection is selected from community-acquired pneumonia, upper and lower respiratory tract infection, skin and soft tissue infection, acute bacterial otitis media, bacterial pneumonia, complicated infection, pyelonephritis, intra-abdominal infection, bacterial sepsis, central nervous system infection, bacteremia, wound infection, peritonitis, meningitis, infections after burn, urogenital tract infection, pelvic inflammatory disease, endocarditis, and intravascular infection. In another embodiment of these aspects, said bacterial infection is by Chlamydia pneumoniae, Chlamydia trachomatis, or Chlamydia psittaci.

In a further aspect, the present invention comprises a kit including: (i) a pharmaceutical composition comprising a CopN(Cpra) inhibitor and (ii) instructions for administering the composition to a subject for the treatment of a chronic disease associated with a bacterial infection.

In one embodiment of this aspect, said chronic disease is an inflammatory disease. In another embodiment of this aspect, said inflammatory disease is selected from the group consisting of asthma, coronary artery disease, arthritis, conjunctivitis, lymphogranuloma venerum, cervicitis, and salpingitis.

In a further embodiment of this aspect, said chronic disease is an autoimmune disease. In another embodiment of this aspect, said autoimmune disease is selected from the group consisting of systemic lupus erythematosus, diabetes mellitus, and graft versus host disease.

In a preferred embodiment of this aspect, said chronic disease is atherosclerosis.

In one aspect, the present invention comprises a kit including: (i) a pharmaceutical composition comprising a CopN(Cpn) inhibitor and (ii) instructions for administering the composition to a subject, thereby inhibiting microtubule disruption of a host cell.

In one aspect, the present invention comprises a kit including: (i) a pharmaceutical composition comprising a CopN(Cpn) inhibitor and (ii) instructions for administering the composition to a subject, thereby inhibiting the cell cycle arrest.

In one embodiment of these aspects, the CopN(Cpn) inhibitor comprises a compound of formula Ia, Ib, Ha, or lib.

The present invention is further illustrated by the following examples, which should not be construed as further limiting. The contents of all figures and all references, patents and published patent applications cited throughout this application, as well as the Figures, are expressly incorporated herein by reference in their entirety.

EXAMPLES

Example 1. Methods

The effect of heterologous expression of chlamydial proteins on yeast growth was conducted following growth of yeast in non-inducing selective synthetic media plating aliquots (5μl) from serial 1:10 dilutions onto a selective medium plate supplemented with either 2% glucose (non-inducing media) or 2% galactose (inducing media). The plates were incubated at 3O⁰C and photographs of the plates were taken 48 hours after plating. The high-throughput screen of a 40,000 compound chemical library utilized S. cervisiae strain RDY0433, lacking the major efflux pumps PDRl and PDR3 and expressing GFP-CopN(Cpw). The effect of compounds on growth of Chlamydia pneumoniae following infection of BGMK cells with Chlamydia pneumoniae strain AR39 was determined by immunflurescence staining and by measurements of copies of dnaK transcripts using RT-PCR.

Plasmids and expression constructs. Original plasmid vectors and derived expression constructs are summarized in Table 1. For yeast expression, the open reading frames of the Chlamydia pneumoniae genes (CP0358, CP0433, CP0679, CP0833, and CP1062) were PCR amplified from Chlamydia pneumoniae AR39 chromosomal DNA prepared as described (Huang et al., Proc. Natl. Acad. ScL USA 99:3914 (2002)), and cloned by the gateway technology (Invitrogen) into the yeast high-copy plasmid pDSTYl, a gateway-adapted 2μ-based pFUS (Lesser, C. F., Miller, S. I. EMBO J. 20:1840 (2001)), which created expression constructs pYl(CP0358), pYl(CP0433), pYl(CP0679), pYl(CP0833) and pYl(CP1062). The same strategy was used for the cloning of CopN from C. trachomatis L2 genomic DNA (provided by Dr. Zarine R. Balsara, Harvard Medical School), YopN from Y. entercolitica pYVe227 plasmid DNA (provided by Dr. Vince T. Lee currently at University of Maryland), and PopN from P. aeruginosa PAOl genomic DNA. This cloning allows for generation of N-terminal GFP fusion proteins under the control of the GALlO promoter. The fragments containing the GaIlO promoter, GFP fusion gene and the ADH terminator from pFUS, pYl(CP0433) and pYl(CP1062) constructs were subcloned into the centromere-based (cen) pRS313 (Lesser, C. F., Miller, S. I. EMBO J. 20:1840 (2001); Mumberg et al., Gene 156:119 (1995)) through homologous recombination-mediated DNA replacement to make low- copy versions of GALlO-GFP-CopN(Cpra) and GAL10-GFP-CP1062 expression constructs pRS(0433) and pRS(1062). Integrating versions of the of GALlO-GFP (vector control) and GALlO-GFP-CopN(Cpra) were made by deleting the 2μ replication origin from the backbone of pFUS and pYl(0433) constructs which then gave rise to pYGFP/int and pY0433/int to target integration at the yeast chromosomal LEU2 locus. The high-copy (2μ) plasmid vector pDSTY3 is the non-GFP version of pDSTYl modified by deleting the GFP open reading frame, and was used to create pY3(0433) construct for expressing pure CopN(Cpra) protein in the yeast. For transient mammalian expression, the CP0433 open reading frame was cloned by the gateway technology into the vector pDEST53 (Invitrogen) to create pM53(CP0433) where expression of the GFP- CopN(Cpra) fusion protein is driven from a constitutive CMV promoter. The GFP expression construct pM53(GFP) was made by the removal of the att cassette containing the chloramphenicol resistance gene and ccdB gene from pDEST53 following restriction digestion with Notl and Pad, blunt-end treatment, and self-ligation. For integration and "stably" regulated mammalian expression, the genes for GFP and GFP-CopN(Cpw) fusion protein were PCR amplified from the pM53(CP0433), and inserted into the EcoRV and Notl sites of the pcDNA5/FRT/TO (Invitrogen) to create pM5to(GFP) and pM5to(0433) for targeted chromosomal integration thereafter expression of the GFP or GFP-CopN(Cpra) is regulated by a tetracycline-inducible CMV promoter. The pOG44 vector (Invitrogen) was used for the FIp recombinase expression in mammalian cells.

Table 1. Plasmids and constructs

Sources: 1. this study; 2. Invitrogen; 3. Lesser, C. F., Miller, S. I. EMBO J. 20:1840 (2001); 4. Mumberg et al., Gene 156:119 (1995).

Random mutagenesis. Mutagenesis of the gene CP0433 was carried out with the GeneMorph II Random Mutagenesis kit following the manufacture's instruction (Stratagene). The target DNA was pYl(0433) and primers were the universal attB primers (Invitrogen). The pool of mutagenized PCR products and the BgIII and BsiWI (within the CP0433 insert)-linearized pYl(0433) were used to co-transform the yeast wherein the mutagenized CP0433 gene fragments were incorporated into the yeast expression vector pDSTYl through in vivo homologous recombination and gap repair. The growth of resulting yeast transformants was selected on inducing selective medium plate supplemented with 2% galactose, and the plasmids were recovered for sequencing analysis.

Yeast strains and growth assay. The yeast strains for episomal and integrative expression of bacterial genes were created by transforming the yeast strains W303a with different plasmid expression constructs (Table 1) using a lithium acetate method (Gietz et al., Methods Enzymol. 350:87 (2002)). Yeast growth assays were conducted and the yeast growth rates of individual strains were compared as described (Lesser, C. F., Miller, S. I. EMBO J. 20:1840 (2001)). Briefly, saturated overnight cultures of the strains of interest were grown in non-inducing selective synthetic media supplemented with 2% raffinose. Each culture was normalized to OD_60O = 1 and then serial 10-fold dilutions (5μl) were spotted onto inducing media. The plates were incubated at 3O⁰C and photographs of the plates were taken 48 hours after plating.

Yeast microscopy and immunofluorescence. Yeast strains carrying the plasmid constructs of interest were grown overnight in non-inducing selective synthetic media supplemented with 2% raffinose. Yeast cells were diluted to OD_60O = 0.5-0.6 and grown for an additional 1 hour. Then 2% galactose was added to induce expression of the fusion protein. For examination of budding morphology and nuclear division, yeast cells sampled at the designated time points were re-suspended in mounting media containing DAPI (Sigma). For immunofluorescence observation of microtubules, yeast cells were fixed in 3.7% formaldehyde, and stained with rat anti-α- tubulin antibody YOL1/34 (SeroTec) and the secondary antibody Texas Red dye-conjugated donkey anti-rat IgG (H+L, Jackson ImmunoResearch Laboratory) followed by DAPI (Sigma) staining of DNA as described (Miller, R. K. Methods MoL Biol. 241:341 (2004)). All microscopic observations were performed on an inverted Nikon Eclipse TE2000-U microscope. Images were generated by using MetaMorph software, converted to Tiff format, and then transferred into Adobe Photoshop CS2 Version 9.0.2 (Adobe Microsystems) where they were re-sized, contrast-enhanced, pseudocolored, and/or merged.

Yeast cell synchronization and flow cytometry. The yeast strains Y0433 and YGFP, derivatives of W303a carrying integrating versions of GFP-CP0433 fusion gene and GFP gene for integrative expression of the GFP-CopN(Cpra) fusion protein and GFP, were grown to early-log phase in non-inducing selective synthetic media supplemented with 2% raffinose at 3O⁰C. Then α-factor (10 μg/ml, Zymo Research) was added to synchronize the yeast cells at Gl phase for a total of 3 hours as described (Day et al., Methods MoL Biol. 241:55 (2004)). At 1.5 hour after addition of the α-factor, 2 % galactose was added to induce protein expression. The yeast cells were released from OC- factor-arrest 1.5 hours after the galactose was added where designated as "0 hour" point, and continued to grow in inducing selective synthetic media supplemented with 2% galactose at 3O⁰C. Yeast were harvested at 30 min intervals and fixed in 70% ethanol. For flow cytometric analysis of DNA contents, DNA of the fixed yeast cells was stained using the fluorescence propidium iodide (PI, Sigma) as previously described (Zhang et al., Methods MoL Biol. 241:77 (2004)). Samples were analyzed on the FACscan flow cytometer using ModFit software.

Mammalian cell transection and immunofluorescence. HeLa cells were grown in DMEM medium supplemented with 10% fetal bovine serum (Inviirogen) in an incubator at 37°C, 5% CO2. Chemical iranstecdon of HeLa cells was performed with GeneJiiice transfection reagent according to the manufacturer^'s instruction (Novagen). Transfected HeLa cells were cultured for 12 h. All imrnunostaining procedures were performed at room temperature according to the online protocol of the Mitchison lab authored by A. Desai at Harvard Medical School (mitchison.med.harvard.edu/protocols). Cells were rinsed in BRB80 (8OmM PIPES, ImM EGTA, and ImM MgC12. pH 6.8) and fixed for 10 min in 0,5% glutaradehyde in BRBSO. Cell membranes were permeabilized for J 5 min with a solution of 1 % Triton X-100 in PBS { l2mM phosphate, J 37mM NaCl, and 3ml\'1 KC 3, pH 7.4). Free aldehydes were quenched three times with NaBFI4 (1 mg ml^"1. Sigma) in PBS for 10 min each. Fixed cells were rinsed three times with PBST (PBS + 0.1% Triton X-100) and blocked in 1% bovine serum albumin (BSA) in PBST for 20 min. AU subsequent rinses between antibody incubations were performed using PBST. All antibodies were diluted in 1 % BSA in PBST. For immunofluorescence of microtubules, cells were incubated for 60 min in 1/8.000 mouse anti-α-tubulin primary antibody (B-5-1-2. Sigma) followed by a 60-min incubation in 1/2,000 Alexa Fluor 594- conjugated goat anti-mouse IgG (H1 L) secondary antibody (mvitrogen). For labelling DNA, cells were incubated in DAPI (10 mg rnl21, Sigma) for 20 min. After the coverslips had been washed three times with PBS and once with deionized water, they were mounted and observed on an inverted Nikon Eclipse TE2000-U microscope. Images were generated by using MetaMorph software, converted to ,tif format, and then transferred into Adobe Photoshop CS2 Version 9.0.2 (Adobe Microsystems) where they were rc-sized. contrast-enhanced, pseudocoloured, and/or overlaid,

Transient transfection and Ptk2 cell immunofluorescence. PtK2 cells were grown DMEM medium (low glucose, Invitrogen) supplemented with 10% fetal bovine serum (Invitrogen) in an incubator at 37⁰C, 5% CO2. For transient transfection by electroporation, an aliquot of 5x10⁶ cells in 250 μl of serum- free DMEM was mixed with 20 μg of plasmid DNA of pM53(0433) or pDEST53 vector control in a 4mm gap gene pulser cuvette (BioRad), and pulsed at 960 μF and 250 V using Gene Pulser II (BioRad). Cells were then transferred into 10 ml of pre- warmed DMEM medium supplemented with 10% FBS, plated on 18 mm coverslips, and cultured for 20 hours before immunofluorescence staining. All immunostaining procedures were performed at room temperature according to the online protocol of the Mitchison lab authored by Dr. Arshad Desai at Harvard Medical School (mitchison.med.harvard.edu/protocols). Cells were rinsed in BRB80 (80 mM PIPES, 1 mM EGTA, and 1 mM MgC12, pH 6.8] and fixed for 10 min in 0.5% glutaradehyde in BRB80. Cell membranes were permeabilized for 15 min with a solution of 1% Triton X-100 in PBS (12 mM phosphate, 137 mM NaCl, and 3 mM KCl, pH 7.4). Free aldehydes were quenched three times with NaBH4 (1 mg/ml, Sigma) in PBS for 10 min each. Fixed cells were rinsed three times with PBST (PBS + 0.1% Triton X-100) and blocked in 1% bovine serum albumin (BSA) in PBST for 20 min. All subsequent rinses between antibody incubations were performed using PBST. All antibodies were diluted in 1% BSA in PBST. For immunofluorescence of microtubules, cells were incubated for 60 min in 1/8000 mouse anti-α-tubulin primary antibody (B-5-1-2, Sigma) followed by a 60-min incubation in 1/2000 Alexa Fluor 594- conjugated goat anti-mouse IgG (H+L) secondary antibody (Invitrogen). For labeling DNA, cells were incubated in DAPI (lOmg/ml, Sigma) for 20 min. After the coverslips had been washed three times with PBS and once with deionized water, they were mounted and observed on an inverted Nikon Eclipse TE2000-U microscope. Images were generated by using MetaMorph software, converted to Tiff format, and then transferred into Adobe Photoshop CS2 Version 9.0.2 (Adobe Microsystems) where they were re-sized, contrast-enhanced, pseudocolored, and/or overlaid.

Stable cell lines and mammalian cell flow cytometry. Using the Lipofectamine 2000 (Invitrogen), the FIp-In T-REx 293 cells (Invitrogen) were co-transfected with the plasmid construct pM5to(0433) or pM5to(GFP) along with the FIp recombinase- expressing plasmid pOG44 according to the manufacturer's instructions (Invitrogen). Being selected in the presence of hygromycin (100 μg/ml) and blasticidin (15μg/ml), individual colonies were tested for tetracycline (1 μg/ml) -regulatable expression of the relevant constructs by fluorescence microscopy and western blotting. The resulting stable cell lines TR293-CopN(Q?«) and TR293-GFP capable of expressing CopN(Cpra) and GFP, respectively, were maintained in the constant selection of hygromycin (50 μg/ml) and blasticidin (15μg/ml). For flow cytometric analysis of DNA contents, 5- 10x10⁵ cells were seeded in individual T-25 cell culture flasks. Following a 24-hour incubation, the semi-confluent cells were synchronized in the Gl stage with amphidicolin (5 μg/ml) for a total of 20 hours. Upon removal of amphidicolin, it was designated "0 hour" time point. To ensure the presence of the protein at work immediately after release of the Gl synchronization, tetracycline (1 μg/ml) was added to the cultures to initiate the protein expression at -12 hour point, and the post- synchronization induction continued for 18 hours. Cells in one flask from each different cell lines were collected at 1-hour intervals starting at the 0-hour point, and then fixed and permeabilized in 4 ml of 75% ethanol in PBS at -2O⁰C for at least 16 hours. After 1 wash with PBS containing 1% (BSA), the cell pellets were resuspended in 1 ml of solution containing propidium iodide (50 μg/ml; Sigma), RNase (240 μg/ml; Sigma) and Triton X-100 (0.01% v/v; Sigma). Cells were stained for at least 30 min in the dark before cell cycle analysis. The distribution of cells in the various phases of the cell cycle was analyzed on a Becton-Dickinson FACScan flow cytometer using ModFit software.

Chemical library and high-throughput screen. The screening was performed at the Institute of Chemistry and Cell Biology (ICCB) at Harvard Medical School. The isogenic yeast strain RDY0433 capable of integratively expressing GFP-CopN(Cpw) was screened in the CopN(Cpra)-based yeast growth interference assay against a pilot library of 40,000 small-molecule compounds representing a diverse portion of the ICCB collection from multiple sources. The assay strains were constructed from the drug- sensitive strain RDY84 (Mat a, pdrlDKAN, pdr3DHIS5+, ade2, trpl, his3, Ieu2, ura3, canl), derivative of S. cerevisiae W303a lacking the major efflux pumps PDRl and PDR3 (Dorer et al., Curr. Biol. 15:1070 (2005)). The screen assay was validated by a genetically introduced point mutation to create the mutant CopN(Cpra) R268H that completely eliminated the inhibitory growth effect of the wild type CopN(Cpn). All primary screening was done in duplicate in 384-well plates (COSTAR™, Corning). DMSO stock compounds were pin-transferred from a stock solution of 5 mg/ml to the wells, each of which was pre-filled with 30 μl of inducing synthetic selective media containing 2% galactose. Then 10 μl of RDY0433 cells diluted to an OD_60O of 0.16 in inducing synthetic media containing 2% galactose were added immediately to 384-well plates. The final volume in each well was 40 μl that contained DMSO at a final concentration of 2% and compounds at a final concentration of about 12.5 mg/ml. As a positive control, cells of the strain RDY0433(R268H) carrying integrated CopN(Cpra) R268H were similarly constructed, grown, and diluted to the same OD_60O and then inoculated. The negative control was the assay strain RDY0433 without compounds. All plates were incubated at 3O⁰C for 40-42 h, and OD₆₀₀ was read with a microtiter plate reader (Molecular Device, Menlo Park, CA). The effect of compounds was measured as a percentage of growth restoration using the following equation: percentage of growth restoration = [(ODt - ODn) / (ODp - ODn)] x 100, where ODt is OD₆₀₀ of the well with the assay strain RDY0433 and test compounds, ODn is the median value of OD₆₀₀ of the RDY0433 cells without compounds, and ODp is the median value of OD₆₀₀ of RDY0433(R268H) cells without compounds. Compounds showing >=10% of growth restoration in duplicate tests were scored as hits. Hit compounds identified from the primary screening were confirmed by repeating the growth restoration assay in 96-well plates (COSTAR™, Corning). The compounds were tested against other isogenic strains expressing different proteins that also elicit lethal phenotypes but are not related to CopN(Cpn).

Chlamydia pneumoniae infection and immunofluorescence. Chlamydia pneumoniae strain AR39 (53592; ATCC) was cultured in buffalo green monkey kidney (BGMK) cells and the inclusion forming units (IFUs ) of partially purified EBs were determined as previously described (Huang et al., Proc. Natl. Acad. ScL USA 99:3914 (2002)). Test of small molecule compounds on Chlamydia pneumoniae growth was performed in the BGMK cell culture in 24- well cell culture plates (COSTAR™, Corning) in 5% CO2 at 37⁰C, each well containing 1 ml of growth medium. The confluent monolayer BGMK cells were infected with EBs at a multiplicity of infection (MOI) of 10 by centrifugation at 35⁰C with 1,200 x g for 1 h, washed twice with Hanks' balanced salt solution, and incubated in the fresh medium plus 2% DMSO, with or without compounds, for up to 72 h. Except in the dose-dependence experiment, all compounds were used at a final concentration of 10 μg/ml. Chloramphenicol (10 μg/ml)- treated and untreated BGMK cells were also prepared as the positive and negative control cultures, respectively. Cells from three wells for each concentration of compounds and from the positive and negative control wells were harvested for RNA extraction and subsequent RT-PCR. For visualization of chlamydial inclusions, the chlamydial infection and compound-treatments were carried out following the same procedures in the BGMK cells cultured on coverslips in wells of 24-well plates. After incubation for 72 hours, cells were washed with PBS, fixed with 100% methanol, and stained with FITC-conjugated mAb against chlamydial LPS of the Chlamydia Culture Confirmation System (Pathfinder, BIO-RAD). Hep-2 cells were grown and treated with the same procedures as used for BGMK cells.

RNA extraction and real-time RT-PCR. Total RNA was extracted from single inoculated wells by using the RNAqueous-Micro kit (Ambion) in accordance with the manufacturer's instructions. The extracted RNAs were treated with DNase I included in the kit to eliminate the contaminating DNA. The DNA-free RNAs were confirmed by PCR without RT. Reverse Transcription (RT) was performed using the reverse primer specific for Chlamydia pneumoniae dnaK gene with the Superscript HI reverse transcriptase (Invitrogen) according to the manufacturer's instructions. The resulting cDNAs were then subjected to the real-time PCR with primers specific for Chlamydia pneumoniae dnaK gene and with the use of the Platinum SYBR Green qPCR SuperMix- UDG kit (Invitrogen) following the manufacturer's instructions on the ABI PRISM 7700 Sequence Detection System.

Example 2. Results

CopN of Chlamydia pneumoniae inhibits yeast growth by causing cell cycle arrest. To identify candidate Chlamydia pneumoniae virulence proteins amenable to analysis in yeast, five prospective virulence proteins of the strain AR39 were screened for those whose expression results in yeast growth inhibition. CopN is the CP0433 gene product and a putative substrate of the Chlamydia pneumoniae type in system that localizes in the inclusion membrane and possibly host cell cytosol (Lugert et al., Med. Microbiol. Immunol. (Bed). 193:163 (2004)). CP1062 and CP0833 encode two putative type HI effectors that localize in the host cell cytosol (Lugert et al., Med. Microbiol. Immunol. (Bed). 193:163 (2004)). CP0679 encodes a putative serine/threonine kinase (Verma et al., Infect. Immun. 71:5772 (2003)) and CP0358 encodes a putative serine/threonine protein phosphatase. Each of the Chlamydia pneumoniae proteins was conditionally expressed in yeast as a GFP fusion protein. As shown in Figure Ia, expression of GFP-CopN and GFP- CP 1062 resulted in marked growth inhibition when the proteins were expressed at relatively high-levels in yeast. However, only low-level expression of GFP-CopN resulted in growth inhibition. Furthermore, CopN expression resulted in severe yeast growth inhibition in the absence of GFP. This inhibitory activity was also observed with expression of CopN from Chlamydia psittaci B577 (Chlamydia abortus). The expression of distally related CopN homologs, including CopN of Chlamydia trachomatis, YopN of Yersinia enterocolitica and PopN of Pseudomonas aeruginosa did not result in yeast growth inhibition. For the emphasis of its unique cellular activity the CopN of Chlamydia, pneumoniae, this protein will be referred to as CopN(Cpra) throughout the instant specification.

Notably, yeast expressing GFP-CopN(Cpw) accumulated progressively as large- budded cells after the induction of the GFP-CopN(Cpra) expression (Figure Ib, top panel). Six hours after the induction of GFP-CopN(Cpra) expression, 90% of the yeast cells in this population had arrested as large-budded cells compared to 22% of those expressing GFP (Figureό). The majority (91%) of large-budded GFP-CopN(Cpw) expressing cells observed at 6 hour contained only a single un-elongated nucleus present in one of the two buds (Figure Ic). Thus, the cell cycle arrest resulting from expression of CopN(Cpra) takes place prior to nuclear division and cytokinesis.

To determine if the large-budded cells had undergone DNA replication, we quantified the DNA content of the cells using flow cytometry (FACS). Exponentially growing yeast expressing either GFP-CopN(Cpw) or GFP were synchronized at Gl and then allowed to progress through the cell cycle. DNA content was monitored (Figure 2a) every thirty minutes. Yeast expressing either GFP or GFP-CopN(Cpra) underwent DNA replication and by 3 hours a significant proportion of the cells had a 2N content of DNA indicating that the majority of the cells have progressed through the S phase and completed DNA replication. Subsequently, haploid yeast cells expressing GFP- CopN(Cpra) accumulated with a 2N DNA peak characteristic of cell cycle arrest at G2/M phase while the GFP-expressing cells continued to cycle and traversed the G2/M (Zhang et al., Methods MoI. Biol. 241:77 (2004)).

In order to identify the underlying mechanism responsible for the block of cell division at mitosis, the yeast microtubule cytoskeleton was analyzed by examining the integrity of the spindle apparatus that is formed essentially by microtubules and functions to segregate chromosomes (Botstein et al., The yeast cytoskeleton. In The Molecular and Cellular Biology of the Yeast Saccharomyces cerevisiae, Cell cycle and cell biology, Vol. 3, J. R. Pringle, J. R. Broach & E. W. Jones, ed. (New York: Cold Spring Harbor Laboratory Press), pp. 1-90 (1997); Winey et al., Nat. Cell Biol. 3:E23 (2001)). Complete disruption of yeast microtubules prevents formation of the spindle and interferes with mitosis (Schatz et al., Genetics 120:681 (1988); Huffaker et al., /. Cell Biol. 106:1997 (1988); Jacobs et al., /. Cell Biol. 107:1409 (1988); Stearns et al., Genetics 124:251 (1990); Li et al., Cell 66:519 (1991)), resulting in the arrest of cell cycle progression at the G2/M phase (Botstein et al., The yeast cytoskeleton. In The Molecular and Cellular Biology of the Yeast Saccharomyces cerevisiae, Cell cycle and cell biology, Vol. 3, J. R. Pringle, J. R. Broach & E. W. Jones, ed. (New York: Cold Spring Harbor Laboratory Press), pp. 1-90 (1997); Li et al., Cell 66:519 (1991); Hoyt et al., Cell 66:507 (1991)). Morphologically, these haploid cells accumulate as large budded cells with an undivided nucleus located randomly in the mother cell and 2N DNA content (Botstein et al., The yeast cytoskeleton. In The Molecular and Cellular Biology of the Yeast Saccharomyces cerevisiae, Cell cycle and cell biology, Vol. 3, J. R. Pringle, J. R. Broach & E. W. Jones, ed. (New York: Cold Spring Harbor Laboratory Press), pp. 1-90 (1997); Hoyt et al., Cell 66:507 (1991); Day et al., Methods MoI. Biol. 241:55 (2004)). The spindles of yeast expressing either GFP-CopN(Cpn) or GFP at 6 hours were examined using indirect immunofluorescence microscopy. No spindles were detected in cells expressing GFP-CopN(Cpra) (Figure 2b, top panel) suggesting that microtubules were disrupted in these cells. In contrast, the GFP-expressing cells displayed normal short or elongated microtubule spindles (Figure 2b, bottom panel). Thus, CopN(Cpra) expression results in a G2/M cell cycle arrest in yeast due to the disruption of microtubules.

Effect of ^'CopN(Cpn) on mammalian cell cycle progression.

The integrity of microtubules in epithelial cells (PtK2 cells) transiently expressing GFP-CopN(Cpra) (Figure 3a, upper cell in top panel) was compared with PtK2 cells transiently expressing GFP (Figure 3a, bottom panel). The GFP-CopN(Cpw) expressing cells were rounded in shape and the radial interphase array of microtubule network was disrupted although cytoplasmic microtubules were still detectable. In contrast, characteristic interphase microtubule networks were detected in the GFP- expressing cells, which were morphologically indistinguishable from those of non- transfected cells (Figure 3a, lower cell in top panel).

As in yeast, disruption of mammalian microtubules results in a G2/M cell cycle arrest (Rieder et al., Curr. Biol. 10:1067 (2000): Hang et al., Methods MoL Biol. 241:23 (2004)). In order to test if CopN(Cpn) confers a cell cycle phenotype when expressed in mammalian cells, we created stable cell lines TR293-CopN(Cpra) and TR293-GFP that conditionally express GFP-CopN(Cpra) and GFP, respectively, transcribed from the tetracycline inducible promoter. FACS analysis was performed to evaluate DNA contents and cell cycle progression over a period of 18 hours after release from Gl synchronization. The TR293-CopN(Cpra) cells started to accumulate at the G2/M transition at 12 hour, and more prominent and progressive accumulation at G2/M transition was observed at later time points through 18 hour. In contrast, the TR293- GFP cells continued to progress through the cell cycle with no G2/M accumulation after 13 hours.

In addition, the structural integrity of the microtubule network in GFP- CopN(Cpw)-expressing HeLa cells and GFP expressing HeLa cells was examined 12- hours post-transfection (Figure 3c). Microtubule networks were disrupted in GFP- CopN(Cpw)-expressing cells. In contrast, a characteristic radial array of microtubules was observed in GFP-expressing HeLa cells.

HeLa cells expressing GFP-CopN(Cpw) or GFP alone were also examined by FACS analysis (Figure 3d). Delay of cell cycle progression in CopN(Cpw)-expressing HeLa cells was first observed 12 hours after release from Gl synchronization when the cells started to accumulate at the G2/M transition. The 4N peak continued to accumulate over the next four hours. However, GFP-expressing HeLa cells continued to progress through the cell cycle. These results demonstrate that expression of CopN(Cpn) was able to induce G2/M cell cycle arrest in mammalian cells.

Small molecule inhibitors ofCopN(Cpn) activity in yeast. Since genetic tools are currently unavailable to create a Chlamydia pneumoniae strain that does not express CopN, we undertook a chemical genetic approach to identify specific small molecules that inhibit CopN(Cpra) activity in yeast. These molecules could then be used to create a functional "knock out" of CopN during Chlamydia pneumoniae infection of mammalian cells. The severe growth inhibition phenotype conferred in yeast by CopN(Cpn) provided a positive selection mechanism to identify small molecules that inhibit CopN(Cpra) activity. Thus, a high throughput yeast growth assay to screen for compounds that inhibit CopN(Cpra) yeast toxicity was developed. Yeast expressing mutant CopN, CopN(Cpra) R268H, were used as a control for full restoration of yeast growth, which was identified by its inability to interfere with yeast growth. In a screen of -40,000 small molecules, two compounds, referred to as CP0433YC1 and CP0433YC2, were found to reproducibly restore the growth of the yeast expressing CopN(Cpra) to levels 40% and 29%, respectively, with reference to the yeast expressing the mutant CopN(Cpra) R268H. The growth of CopN(Cpw)-expressing yeast treated with these two compounds and their structures are shown in Figure 4. Notably, neither of these compounds affects growth of wild type yeast harboring vector control at concentrations used in the screen (data not shown).

CopN(Cpn) is a Chlamydia pneumoniae virulence determinant. To investigate the potential virulence function of CopN(Cpn) produced during Chlamydia pneumoniae infection, a reverse chemical genetic approach was used to examine whether CopN(Cpra) is required to support the intracellular chlamydial growth, a virulence associated phenotype (Moulder, J. W. Infection 10:Suppl 1, S10-8 (1982)). The two inhibitors of CopN(Qw) activity, CP0433YC1 and CP0433YC2, were used to inactivate CopN(Cpra) function (create a functional knockout) during Chlamydia pneumoniae infection in buffalo green monkey kidney (BGMK) cell culture. The two compounds did not have a toxic effect on the BGMK monolayer cells when assessed in a mitochondrial dehydrogenase activity-based cell proliferation assay (Lee et al., Infect. Immun. 75:1089 (2007)) as well as by microscopic examination of the morphology after the cell culture was incubated in the presence of the compounds at concentrations up to 20 μg/ml (data not shown). A real-time RT-PCR assay was used to monitor the active intracellular multiplication of Chlamydia pneumoniae by quantifying transcription of dnaK (Khan et al., /. Antimicrob. Chemother. 37:677 (1996); Cross et al., Antimicrob Agents Chemother. 43:2311 (1999); and Huang et al., Proc. Natl. Acad. ScL USA 99:3914 (2002)). Functional knockout of the CopN(Cpra) protein by these two compounds resulted in a significant reduction in the dnaK gene transcripts of Chlamydia, pneumoniae in the infected cell culture (Figure 5). Treatment with compounds CP0433YC1 at a final concentration of 10 μg/ml led to a decrease of dnaK gene transcripts by -50% compared to the control (DMSO media). Higher potency was observed with CP0433YC2 treatment which caused a decrease of dnaK gene transcripts by -75% (Figure 5a). Similarly, the addition of CP0433YC2 inhibited replication in Hep-2 cells (Figure 5b). Thus, the presence of the compounds in the media led to a decrease in dnaK transcription by 68-84% as compared to dnaK levels present in host cells grown in untreated media. Furthermore, the two CopN(Cpra) inhibitors interfered with the intracellular replication of Chlamydia pneumoniae in a dose-dependent manner (Figure 5c). A toxic effect was not observed on BGMK cells was observed when either compound was added at 20 μg ml^"1 as assayed by monitoring mitochondrial dehydrogenase activity or by microscopic examination of cell morphology. Removal of CP0433YC2 from the media of infected BGMK cells after 72 hours of treatment did not lead to an immediate recovery of Chlamydia pneumoniae growth (Figure 5d). In agreement with the real-time RT-PCR analysis, the immunofluorescence microscopy using FITC-conjugated the monoclonal antibody against chlamydial LPS also revealed an inhibition of development of the Chlamydia pneumoniae inclusions in a second set of infected BGMK cell culture treated with the compounds; with essentially no large inclusions observed in the CP0433YC2 treated culture (Figure 5e). Thus, the instant invention teaches that CopN(Cpra) is required to support the intracellular growth of Chlamydia pneumoniae and therefore plays an essential virulence role in the cell culture infection model. This work represents the first demonstration of the role of a specific chlamydial protein in virulence of this obligate intracellular organism.

EQUIVALENTS

While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.

Other embodiments are within the claims.

Claims

1. A method of treating a bacterial infection in a subject, said method comprising administering to said subject a CopN(Cpn) inhibitor in an amount effective to treat said infection, thereby treating said infection in said subject.

2. The method of claim 1, wherein said bacterial infection is selected from community- acquired pneumonia, upper and lower respiratory tract infection, skin and soft tissue infection, acute bacterial otitis media, bacterial pneumonia, complicated infection, pyelonephritis, intra-abdominal infection, bacterial sepsis, central nervous system infection, bacteremia, wound infection, peritonitis, meningitis, infections after burn, urogenital tract infection, pelvic inflammatory disease, endocarditis, and intravascular infection.

3. The method of claim 2, wherein said bacterial infection is caused by Chlamydia pneumoniae, Chlamydia trachomatis, or Chlamydia psittaci.

4. The method of claim 1, wherein said CopN(Cpn) inhibitor is a compound of formula (Ia) or a salt thereof,:

wherein X¹ is C or N; each of X² and X³ are independently selected from C, O, S, or N; R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl; and wherein the dotted lines represent single or double bonds, optionally selected such that the dotted lines represent bonds which form an aromatic ring.

5. The method of claim 4, wherein said compound is a compound of formula (Ib) or a salt thereof:

wherein each of R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(O)R^1N, NHC(S)R¹⁰, NHC(O)OR^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl.

6. The method of claim 5, wherein R^1A, R^1B, R^1C and R^1D are H; each of

R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(0)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L

_R1M _R1N _R1O _R1P _R1Q _R1R _R1S _R1T _R1U _R1V _R1W ^ _R1X ^ _{independently; selected} from H, Ci_₄ alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆_₁₂ aryl, Cγ_₁₄ alkaryl, C₃_io alkheterocyclyl, and C_1-4 heteroalkyl.

7. The method of claim 6, wherein R^1A, R^1B, R^1C and R^1D are H; each of

R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂.₄ alkenyl, C₂.₄ alkynyl, OR^1J, 0C(0)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(0)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(0)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L _R1M _R1N _R1O _R1P _R1Q _R1R _R1S _R1T _R1U _R1V _R1W ^ _R1X ^ _{independently; selected} from H, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C₆-_I2 aryl, C_7-14 alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl.

8. The method of claim 7, wherein each of R^1A, R^1B, R^1C R^1D, R^1F, R^1G, R^1H, and R¹¹ are H; and R^1E is Ci_₄ alkyl.

9. The method of claim 5, wherein said compound is CP0433YC1.

10. The method of claim 1, wherein said CopN(Cpra) inhibitor is a compound of formula (Ha) or a salt thereof:

wherein: X⁴ is N or C; each of Y, X⁵, and X° are, independently, selected from O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R R^2S _, R^2T, R^2U, R^2V, and R^2W, are, independently, selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C₆.₁₂ aryl, C₇_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl.

11. The method of claim 10, wherein said compound is a compound of formula (lib):

wherein: Y is O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(O)OR^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R _R ²s _R ²τ _R ²u _R ²v _{and R} ²w ^ independently, selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl.

12. The method of claim 11 , wherein R^2E and R^2F are H; R^2A, R^2B, R^2C, and

R , 2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, 0C(0)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)0R^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(0)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(O)NHR^2W; and each of R^2G R^2H R²¹ _, R^2J _, R^2K R^2L R^2M _R ^2N _R ²o _R ^2P _R ^2Q _R ^2R _R ²s _R ²τ _R ²u _R ²v _{and R} ²w ^ _indep_endently, _sel_ected from H,

Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C₇_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

13. The method of claim 12, wherein Y is NH; R^2E and R^2F are H; R^2A, R^2B, R^2C, and R^2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂.₄ alkynyl, OR²¹, 0C(0)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)0R^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(0)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(O)NHR^2W; and each of R^2G R²¹ _, R^2J _, R^2K R^2L R^2M R^2N

R , 2^zO^υ _p R2^zP^r _p R2^zQ^y _p R2^zR^κ _p

R2^ZT¹, _p R2^zU^u, R , 2^zV^v, and R j 2^zW^w i •s, independently, selected from H, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C₆.₁₂ aryl, C₇_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

14. The method of claim 13, wherein Y is NH; R^2Gis Ci_₄ alkyl; R^2A, R^2B,

R^2D, R^2E, and R^2F are H; and R^2C is C₁-C₄ heteroalkyl.

15. The method of claim 11, wherein said compound is CP0433YC2.

16. A pharmaceutical composition comprising a compound of formula (Ia) or a salt thereof, and a pharmaceutically acceptable excipient, wherein said compound of formula (Ia) is:

wherein X¹ is C or N; each of X² and X³ are independently selected from C, O, S, or N; R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(O)R^1N, NHC(S)R¹⁰, NHC(O)OR^1P, NHC(S)OR^1Q, NHC(0)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-I₂ aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl; and wherein the dotted lines represent single or double bonds, optionally selected such that the dotted lines represent bonds which form an aromatic ring.

17. The pharmaceutical composition of claim 16, wherein said compound is a compound of formula (Ib):

wherein each of R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C₃_io alkheterocyclyl, and C_1-4 heteroalkyl.

18. The pharmaceutical composition of claim 17, wherein R^1A, R^1B, R^1C and

R^1D are H; each of R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂.₄ alkenyl, C₂.₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂__<5 heterocyclyl, C₆_₁₂ aryl, Cγ_₁₄ alkaryl, C₃_io alkheterocyclyl, and C_1-4 heteroalkyl.

19. The pharmaceutical composition of claim 18, wherein R^1A, R^1B, R^1C and

R^1D are H; each of R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂.₄ alkenyl, C₂.₄ alkynyl, OR^1J, 0C(0)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R¹¹ R^1U R¹ IV ^v _, R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkyn C₂_₆ heterocyclyl, C₆_₁₂ aryl, Cγ_₁₄ alkaryl, C₃_io alkheterocyclyl, and C_1-4 heteroalkyl.

20. The pharmaceutical composition of claim 19, wherein each of R^1A, R^1B,

_R1C _R1D^ _R1F _R1G^ _R1H^ ^ _R1I ^ _R. _{and R}1E ^ _Q^ ^j

21. The pharmaceutical composition of claim 17, wherein said compound is CP0433YC1.

22. A pharmaceutical composition comprising a compound of formula (Ha) or a salt thereof, and a pharmaceutically acceptable excipient, wherein said compound of formula (Ha) is:

wherein: X⁴ is N or C; each of Y, X⁵, and X° are, independently, selected from O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂.₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(O)OR^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R R^2S _, R^2T, R^2U, R^2V, and R^2W, are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl.

23. The pharmaceutical composition of claim 22, wherein said compound is a compound of formula (lib):

wherein: Y is O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(O)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(O)OR^2V, and C(O)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R _R ²s _R ²τ _R ²u _R ²v _{and R} ²w ^ independently, selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl.

24. The pharmaceutical composition of claim 23, wherein R^2E and R^2F are H; R^2A, R^2B, R^2C, and R^2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(O)NHR^2W; and each of R^2G R^2H R²¹ _, R^2J _,

_R2K _R2L _R2M _R2N _R2O _R2P _R2Q _R2R _R2S _R2T _R2U _R2V ^ _R2W ^ _{independently;} selected from H, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C₇_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

25. The pharmaceutical composition of claim 24, wherein Y is NH; R^2E and R^2F are H; R^2A, R^2B, R^2C, and R^2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR²¹, 0C(0)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)0R^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(0)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(O)NHR^2W; and each of R^2G R²¹ _, R^2J _, R^2K

_R2L _R2M _R2N _R2O _R2P _R2Q _R2R _R2S _R2T _R2U _R2V ^ _R2W ^ _{independently; selected} from H, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, C₂-₆ heterocyclyl, C_6-12 aryl, C₇_₁₄ alkaryl, C₃_₁₀ alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

26. The pharmaceutical composition of claim 25, wherein Y is NH; R^2G is C_1- ₄ alkyl; R^2A, R^2B, R^2D, R^2E, and R^2F are H; and R^2C is C₁-C₄ heteroalkyl.

27. The pharmaceutical composition of claim 23, wherein said compound is CP0433YC2.

28. A kit comprising: (i) a pharmaceutical composition comprising a CopN(Cpra) inhibitor and (ii) instructions for administering the composition to a subject for the treatment of a bacterial infection.

29. A kit comprising: (i) a pharmaceutical composition of any one of claims 16-27 and (ii) instructions for administering the composition to a subject for the treatment of a bacterial infection.

30. The kit of any of claims 28-29, wherein said bacterial infection is selected from community-acquired pneumonia, upper and lower respiratory tract infection, skin and soft tissue infection, acute bacterial otitis media, bacterial pneumonia, complicated infection, pyelonephritis, intra-abdominal infection, bacterial sepsis, central nervous system infection, bacteremia, wound infection, peritonitis, meningitis, infections after burn, urogenital tract infection, pelvic inflammatory disease, endocarditis, and intravascular infection.

31. The kit of claim 30, wherein said bacterial infection is caused by Chlamydia pneumoniae, Chlamydia trachomatis, or Chlamydia psittaci.

32. A method of treating, preventing, or reducing the development of an atherosclerosis-associated disease in a subject in need thereof, said method comprising administering to said subject a CopN(Cpra) inhibitor in an amount effective to treat, prevent, or reduce the development of said atherosclerosis-associated disease in said subject, thereby treating, preventing, or reducing the development of an atherosclerosis- associated disease in said subject.

33. The method of claim 32, wherein said atherosclerosis-associated disease is coronary artery disease, myocardial infarction, angina pectoris, stroke, cerebral ischemia, intermittent claudication, gangrene, mesenteric ischemia, temporal arteritis, or renal artery stenosis.

34. A method for reducing Chlamydia pneumoniae replication in macrophages or foam cells in a subject in need thereof, said method comprising administering a CopN(Cpra) inhibitor to said subject in an amount effective to reduce Chlamydia pneumoniae replication in macrophages or foam cells in said subject, thereby reducing Chlamydia pneumoniae replication in macrophages or foam cells in said subject.

35. A method of treating a subject diagnosed as having a chronic disease associated with a bacterial infection, said method comprising the step of administering to said subject a CopN(Cpra) inhibitor, wherein said administering is for a duration and in an amount effective to treat said subject, thereby treating said subject.

36. The method of claim 35, wherein said chronic disease is an inflammatory disease.

37. The method of claim 36, wherein said inflammatory disease is selected from the group consisting of asthma, coronary artery disease, arthritis, conjunctivitis, lymphogranuloma venerum, cervicitis, and salpingitis.

38. The method of claim 35, wherein said chronic disease is an autoimmune disease.

39. The method of claim 38, wherein said autoimmune disease is selected from the group consisting of systemic lupus erythematosus, diabetes mellitus, and graft versus host disease.

40. The method of claim 35, wherein said chronic disease is atherosclerosis.

41. A kit comprising: (i) a pharmaceutical composition comprising a CopN(Cpra) inhibitor and (ii) instructions for administering the composition to a subject for the treatment of a chronic disease associated with a bacterial infection.

42. The kit of claim 41, wherein said chronic disease is an inflammatory disease.

43. The kit of claim 42, wherein said inflammatory disease is selected from the group consisting of asthma, coronary artery disease, arthritis, conjunctivitis, lymphogranuloma venerum, cervicitis, and salpingitis.

44. The kit of claim 41, wherein said chronic disease is an autoimmune disease.

45. The kit of claim 44, wherein said autoimmune disease is selected from the group consisting of systemic lupus erythematosus, diabetes mellitus, and graft versus host disease.

46. The kit of claim 41, wherein said chronic disease is atherosclerosis.

47. A compound of formula (Ia) or a salt thereof,:

wherein X¹ is C or N; each of X² and X³ are independently selected from C, O, S, or N; R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(0)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, C_7-14 alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl; and wherein the dotted lines represent single or double bonds, optionally selected such that the dotted lines represent bonds which form an aromatic ring.

48. The compound of claim 47, wherein said compound is a compound of formula (Ib) or a salt thereof:

wherein each of R^1A, R^1B, R^1C, R^1D, R^1E, R^1F, R^1G, R^1H, and R¹¹ are independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L R^1M R^1N R¹⁰ R^1P R^1Q R^1R R^1S _, R^1T R^1U R^1V R^1W and R^1X are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl.

49. The compound of claim 48, wherein R^1A, R^1B, R^1C and R^1D are H; each of

R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂-₄ alkenyl, C₂-₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L

50. The compound of claim 49, wherein R^1A, R^1B, R^1C and R^1D are H; each of

R^1E, R^1F, R^1G, R^1H, and R¹¹ are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂.₄ alkenyl, C₂.₄ alkynyl, OR^1J, OC(O)R^1K, NR^1LR^1M, NHC(0)R^1N, NHC(S)R¹⁰, NHC(0)0R^1P, NHC(S)OR^1Q, NHC(O)NHR^1R, NHC(S)NHR^1S, NHC(O)SR¹¹, NHC(S)SR^1U, NHS(O)₂R^1V, C(O)OR^1W, and C(O)NHR^1X; and each of R^1J, R^1K R^1L

_R1M _R1N _R1O _R1P _R1Q _R1R _R1S _R1T _R1U _R1V _R1W ^ _R1X ^ _{independently}^ ^^ from H, Ci_₄ alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆_₁₂ aryl, Cγ_₁₄ alkaryl, C₃_io alkheterocyclyl, and C_1-4 heteroalkyl.

51. The compound of claim 50, wherein each of R^1A, R^1B, R^1C R^1D, R^1F, R^1G, R^1H, and R¹¹ are H; and R^1E is Ci_₄ alkyl.

52. A compound of formula (Ha) or a salt thereof:

wherein: X⁴ is N or C; each of Y, X⁵, and X⁶ are, independently, selected from O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, Ci_₄ alkyl, C₂.₄ alkenyl, C₂.₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(O)OR^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R R^2S _, R^2T, R^2U, R^2V, and R^2W, are, independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, Cγ_₁₄ alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl.

53. The compound of claim 52, wherein said compound is a compound of formula (lib):

wherein: Y is O, S, or NR^2H; each of R^2A, R^2B, R^2C, R^2D, R^2E, and R^2F are, independently, selected from H, halide, nitro, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(0)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ R^2J _, R^2K R^2L R^2M R^2N R²° R^2P R^2Q R^2R _R2 ^S _R2 ^T _R2 ^U _R2 ^V _{and R2} ^W _are^ independently, selected from H, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆-_I2 aryl, C_7-14 alkaryl, C_3-10 alkheterocyclyl, and C_1-4 heteroalkyl.

54. The compound of claim 53, wherein R^2E and R^2F are H; R^2A, R^2B, R^2C, and R^2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, OR²¹, OC(O)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)OR^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(O)SR^2S, NHC(S)SR²¹,

NHS(O)₂R^2U, C(O)OR^2V, and C(0)NHR^2W; and each of R^2G R^2H R²¹ _, R^2J _, R^2K R^2L R^2M _R2N _R2O _R2P _R2Q _R2R _R2S _R2T _R2U _R2V _{and R2}W _{is> independently; selected from H;}

Ci_₄ alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆_₁₂ aryl, C₇_₁₄ alkaryl, C₃_₁₀ alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

55. The compound of claim 54, wherein Y is NH; R^2E and R^2F are H; R^2A, R^2B, R^2C, and R^2D are, selected independently from H, halide, nitro, C_1-4 alkyl, C₂_₄ alkenyl, C₂-₄ alkynyl, OR²¹, 0C(0)R^2J, NR^2KR^2L, NHC(O)R^2M, NHC(S)R^2N, NHC(O)OR²⁰, NHC(S)0R^2P, NHC(0)NHR^2Q, NHC(S)NHR^2R, NHC(0)SR^2S, NHC(S)SR²¹, NHS(O)₂R^2U, C(0)0R^2V, and C(O)NHR^2W; and each of R^2G R²¹ _, R^2J _, R^2K _{R2L R2}M _R2N _R2O _R2P _R2Q _R2R _R2S _R2T _R2U _R2V _{and R2}W _iS) independently, selected from H, Ci_₄ alkyl, C₂_₄ alkenyl, C₂_₄ alkynyl, C₂_₆ heterocyclyl, C₆_₁₂ aryl, C₇_₁₄ alkaryl, C₃^o alkheterocyclyl, and C_1-4 heteroalkyl, provided that at least three of R^2A, R^2B, R^2C and R^2D are H.

56. The compound of claim 55, wherein Y is NH; R^2G is Ci_₄ alkyl; R^2A, R^2B, R^2D, R^2E, and R^2F are H; and R^2C is C₁-C₄ heteroalkyl.

57. A method for inhibiting CopN(Cpra) mediated microtubule disruption in a cell, said method comprising contacting said cell with an effective amount of a CopN(Cpra) inhibitor, thereby inhibiting said microtubule disruption in said cell.

58. The method of claim 57, wherein said CopN(Cpra) inhibitor is a compound of any one of claims 47-56.

59. The method of claim 57, wherein said cell is a foam cell or a macrophage.

60. A method for inhibiting CopN(Cpra) mediated cell cycle arrest in a cell, said method comprising contacting said cell with an effective amount of a CopN(Cpn) inhibitor, thereby inhibiting cell cycle arrest in said cell.

61. The method of claim 60, wherein said CopN(Cpra) inhibitor is a compound of any one of claims 47-56.

62. The method of claim 60, wherein said cell is a foam cell or a macrophage.

63. The method of claim 60, wherein cell cycle arrest is inhibited at the G2/M phase.

64. A method for inhibiting CopN(Cpra) mediated cell cycle arrest due to microtubule disruption in a subject, said method comprising administering to said subject a CopN(Cpra) inhibitor in an amount effective to inhibit CopN(Cpra) mediated cell cycle arrest due to microtubule disruption, thereby inhibiting said cell cycle arrest due to microtubule disruption in said subject.

65. The method of claim 64, wherein said CopN(Cpra) inhibitor is a compound of any one of claims 47-56.

66. The method of claim 64 , wherein CopN(Cpn) mediated cell cycle arrest due to microtubule disruption is inhibited in the foam cells or macrophages of the subject.

67. The method of claim 64, wherein cell cycle arrest is inhibited at the G2/M phase.

68. A method for reducing or preventing the multiplication of bacteria in a subject, said method comprising administering to said subject a CopN(Cpra) inhibitor, in an amount effective to reduce or prevent the multiplication of bacteria in said subject, thereby reducing or preventing the multiplication of bacteria in said subject.

69. The method of claim 68, wherein the bacteria is Chlamydia pneumoniae .

70. The method of claim 68, wherein said CopN(Cpra) inhibitor is a compound of any one of claims 47-56.

71. The method of claim 68, wherein bacteria multiplication is reduced or prevented in the foam cells or macrophages of the subject.