COMPOUNDS, COMPOSITIONS, AND METHODS FOR INHIBITING

BACTERIAL GROWTH

Cross Reference to Related Applications

This application claims priority to U.S. Provisional Application No. 62/404,492, filed October 5, 2016, the contents of which is incorporated herein by reference in its entirety.

Statement of Government Support

This invention was made with government support under AI105867 awarded by the National Institutes of Health. The government has certain rights in the invention.

Background

Mycobacterium tuberculosis (Mtb) causes tuberculosis (TB) and is responsible for nearly two million deaths annually. In addition, a substantial proportion of the millions of people living with HIV/ AIDS worldwide are co-infected with Mtb. Multi-drug resistant (MDR) tuberculosis as well as extensively drug-resistant (XDR) tuberculosis have evolved, which further restricts treatment options for patients and threatens TB control and prevention efforts. Mtb can persist in the host for decades without causing disease symptoms

(Gengenbacher, M. et al. FEMS Microbiol Rev 36, 514-32 (2012)). Mtb non-replicating persistence (NRP) is characterized by a gradual slowing of metabolic activity upon encountering pressures from the host immune system, including hypoxia, acidic pH or starvation (Boshoff, H.I. et al. Nat Rev Microbiol 3, 70-80 (2005); Wayne, L.G. et al. Annu Rev Microbiol 55, 139-63 (2001); Baker, J.J. et al. Mol Microbiol 94, 56-69 (2014); Betts, J.C. et al. Mol Microbiol 43, 717-31 (2002)). Thus, a fundamental challenge of current TB therapy is the long course of treatment. New drugs that shorten the course of therapy could revolutionize TB control.

Summary

The disclosure is based, at least in part, on the discovery and characterization of new chemical compounds (e.g., anti-virulence compounds or inhibitors) that inhibit a two- component regulatory system (e.g., DosRST two-component regulatory system) signaling and persistence. Said compounds reduce expression of DosRST regulon genes, inhibit Mtb persistence-associated physiologies, and directly inhibit the DosS/T sensor kinases. These observations indicate, among other things, that such inhibitors are useful for treating infections by bacteria in which the two-component regulatory system (e.g., DosRST) is conserved.

One of skill in the art would appreciate that there are several benefits to the use of the instantly-disclosed inhibitors and methods. For example, current treatment schedules for tuberculosis infection involve a regimen of at least four compounds (isoniazid, rifampicin, ethambutol, and pyrazinamide) coadministered over a prolonged period (e.g., 6-9 months). The instantly disclosed compounds and compositins, when used alone or in combination with one or more additional agents (e.g., isoniazid, rifampicin, ethambutol, and pyrazinamide), are believed to effectively treat an infection in a shorter period of time, e.g., less than 8 weeks (e.g., less than 7 weeks, 6 weeks, 5 weeks, 4 weeks, 3 weeks, or 2 weeks) or between 2 to 4 weeks. Thus, the instantly disclosed compounds and compositions offer the opportunity for increased patient compliance. The compounds and compositions are also useful for treating immunocompromised subjects (e.g., subjects afflicted with an HIV infection) and/or subjects with latent bacterial infections. Moreover, the compositions and methods described herein are useful for treating drug-resistant bacterial infections, such as infections with MDR and/or XDR tuberculosis.

One aspect of the invention relates to a method for inhibiting growth of one or more bacterial cells in which an at least two- component regulatory system is conserved, said two- component regulatory system comprises one or more sensor histidine kinase and a cognate response regulator, the method comprising contacting the one or more bacterial cells with an effective amount of a compound that inhibits the at least two component regulatory system to thereby inhibit the growth of the one or more bacterial cells. In some embodiments, the compound that inhibits is selected from any of the compounds set forth in Section II infra.

Another aspect of the invention relates to a method for preventing or reducing the likelihood of a productive bacterial infection in a subject, the method comprising

administering to a subject an effective amount of a compound that inhibits an at least two- component regulatory system, said two-component regulatory system comprises one or more sensor histidine kinase and a cognate response regulator, to thereby prevent or reduce the likelihood of a productive bacterial infection in the subject, wherein the subject has been identified as being at risk of developing an infection with bacterial cells in which the at least two-component regulatory system is conserved. In some embodiments, the compound that inhibits is selected from any of the compounds set forth in Section II infra.

Yet another aspect of the invention relates to a method for treating a subject who is infected with bacterial cells in which an at least two-component regulatory system is conserved, said two-component regulatory system comprises one or more sensor histidine kinase and a cognate response regulator, the method comprising administering to the subject an effective amount of a compound that inhibits the at least two-component regulatory system to thereby treat the infection. In some embodiments, the compound that inhibits is selected from any of the compounds set forth in Section II infra.

Still another aspect of the invention relates to a method for ameliorating the signs or symptoms of an infection of a subject by bacterial cells in which the at least two-component regulatory system is conserved, said two-component regulatory system comprises one or more sensor histidine kinase and a cognate response regulator, the method comprising administering to the subject an effective amount of a compound that inhibits the at least two- component regulatory system to thereby ameliorate the signs and symptoms of the infection. In some embodiments, the compound that inhibits is selected from any of the compounds set forth in Section II infra.

In some embodiments, the at least two-component regulatory system comprises a member of an oxygen sensing pathway. In some embodiments, the at least two-component regulatory system comprises a heme-based oxygen sensor. In some embodiments, the heme- based oxygen sensor is selected from the group consisting of Rhizobium FixL protein, E. coli Dos, Acetobacter AxPDEAl, Halobacterium HemAT, and Azetobacter AvReg. In some embodiments, the at least two-component regulatory system comprises a heme-based redox sensor. In some embodiments, the heme-based redox sensor is selected from the group consisting of Vibrio VF A0071, Clostridium SONO, and Rhodospirillum CooA. In some embodiments, the heme-based histidine sensor kinase is selected from DosS or DosT, both. In some embodiments, the at least two-component regulatory system comprises DosS and DosT. In some embodiments, the cognate response regulator is DosR. In some

embodiments, the at least two-component regulatory system is a DosRST two-component regulatory system. In some embodiments, the at least two-component regulatory system comprises a two-component regulatory system regulon. In some embodiments, the at least two-component regulatory system regulon is a DosRST regulon. In some embodiments, the DosRST regulon comprise a network of at least 50 genes.

In some embodiments, the methods further comprise identifying the subject as having an infection with bacterial cells in which the two component regulatory system is conserved. In some embodiments, the bacteria or bacterial cells are Mycobacterium. In some

embodiments, the Mycobacterium are Mycobacterium tuberculosis. In some embodiments, the Mycobacterium tuberculosis is multi-drug resistant Mycobacterium tuberculosis. In some embodiments, the Mycobacterium tuberculosis is extensively drug resistant Mycobacterium tuberculosis. In some embodiments, the bacteria or bacterial cells are Clostridium or Bacillus. In some embodiments, the bacteria or bacterial cells are C. acetobutylicum or B. subtilis. In some embodiments, the bacteria or bacterial cells are Echerichia coli, Vibrio cholera, or Streptomyces coelicolor. In some embodiments, the bacteria or bacterial cells are Enterobacteriaceae . In some embodiments, the bacteria or bacterial cells are nontuberculosis mycobacterium (NTM). In some embodiments, the NTM are M avium, M. intracellular, M. kansasii, M. abscessus, M. chelonae, M. fortuitum, M. terrae, M. xenopi, or M. simiae. In some embodiments, the NTM areM leprae, M. ulcer ans, or M. marinum. In some embodiments, the compound that inhibits the at least two-component regulatory system is an anti-virulence compound or analogs or derivatives thereof. In some embodiments, the anti- virulence compound is selected from the group consisting of HC101A (artemisinin),

HC101B, HC101C, HC102A, HC103A, HC103B, HC104A, HC105A, and HC106A, or combinations thereof.

In some embodiments, the compound is any of the compounds set forth in Section II infra. In some embodiments, the compound is orally administered to the subject. In some embodiments, the compound is parenterally administered to the subject. In some

embodiments, the compound is administered intravenously. In some embodiments, the compound is administered as an aerosol. In some embodiments, the compound is

administered using a nebulizer or inhaler. In some embodiments, the compound is topically administered. In some embodiments, the compound is administered as an eye drop. In some embodiments, the compound is administered as a cream, an ointment, or a lotion. In some embodiments, the compound is present on a bandage or dressing applied to an infected site. In some embodiments, the subject has a lung infection. In some embodiments, the subject has a skin infection. In some embodiments, the subject has an infection of the eye.

One aspect of the invention relates to a method for treating tuberculosis in a subject, the method comprising administering to the subject a compound that inhibits a DosRST two- component regulatory system and/or DosRST regulon in an amount effective to treat tuberculosis. In some embodiments, the compound is an anti -virulence compound or analog or derivative thereof. In some embodiments, the anti-virulence compound is an anti-malarial compound or analog or derivative thereof. In some embodiments, the compound is selected from the group consisting of HC101A (artemisinin), HC101B, HC101C, HC102A, HC103A, HC103B, HC104A, HC105A, and HC106A, or combinations thereof. In some embodiments, the tuberculosis is multidrug-resistant tuberculosis. In some embodiments, the tuberculosis is extensively multidrug-resistant tuberculosis. In some embodiments, the subject is a human.

Another aspect of the invention relates to a method for eliminating dormant

Mycobacterium tuberculosis cells in a subject afflicted with latent tuberculosis, the method comprising administering to the subject an effective amount of compound that inhibits a DosRST two-component regulatory system and/or DosRST regulon to thereby eliminate dormant Mycobacterium tuberculosis cells in the subject and treat latent tuberculosis. In some embodiments, the method further comprises determining that the subject has latent tuberculosis. In some embodiments, the Mycobacterium tuberculosis is multi-drug resistant Mycobacterium tuberculosis. In some embodiments, the Mycobacterium tuberculosis is extensively drug resistant Mycobacterium tuberculosis. In some embodiments, the compound that inhibits the at least two-component regulatory system is an anti-virulence compound or analogs or derivatives thereof. In some embodiments, the anti-virulence compound is an anti-malarial compound or analogs or derivatives thereof. In some embodiments, the compound is selected from the group consisting of HC101A (artemisinin), HC101B, HC101C, HC102A, HC103A, HC103B, HC104A, HC105A, and HC106A, or combinations thereof. In some embodiments, the compound is an analog or derivative of HC101A (artemisinin), HC101B, HC101C, HC102A, HC103A, HC103B, HC104A,

HC105A, or HC106A. In some embodiments, the effective amount of the compound is between 0.01 and 100 mg/kg body weight of the subject. In some embodiments, the compound is administered in combination with one or more antibiotics. In some embodiments, the compound is administered in combination with one or more of isoniazid, rifampicin, ethambutol, and pyrazinamide. In some embodiments, the compound is administered for less than 6 weeks. In some embodiments, the compound is administered for between 2 to 4 weeks.

Another aspect of the invention relates to a pharmaceutical composition for use in topical treatment of an infection with bacterial cells in which a DosRST two-component regulatory system or DosRST regulon is conserved, wherein the pharmaceutical composition comprises the compounds according to any of the compounds set forth in Section II infra. In some embodiments, the compound is formulated as an eye drop. In some embodiments, the compound is formulated as an ointment, a lotion, a cream, or a gel. In some embodiments, the compound is selected from the group consisting of HC101A (artemisinin), HC101B, HC101C, HC102A, HC103A, HC103B, HC104A, HC105A, and HC106A, or combinations thereof. In some embodiments, the compound is an analog or derivative of HC101A

(artemisinin), HC101B, HC101C, HC102A, HC103A, HC103B, HC104A, HC105A, or HC106A.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains. In case of conflict, the present document, including definitions, will control.

Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the presently disclosed methods and compositions. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety.

Other features and advantages of the present disclosure, e.g., methods for treating bacterial infections, will be apparent from the following description, the examples, the drawings, and from the claims.

Brief Description of the Drawings

Fig. 1 includes three panels, A-C, and depicts identification of inhibitors of the DosRST pathway. Panel A shows scatter plot of primary screening data showing compounds that inhibit CDC1551(fop ': :GFP) reporter GFP fluorescence with limited impact on Mtb growth. Six distinct classes of compounds (HC101-HC106) are highlighted. Panel B shows structures of compounds confirmed to selectively inhibit CDC1551(fop ': :GFP) reporter fluorescence. Panel D shows dose response curves for artemisinin (Art, HCIOIA), HC102A and HC103A inhibition of GFP fluorescence. Dose response curves for other characterized molecules are presented in Fig. 7.

Fig. 2 includes three panels, A-C, and depicts that transcriptional profiling shows that artemisinin, HC102A and HC103A inhibit the core genes of the DosRST regulon during hypoxia. Panel A shows Mtb differential gene expression in response to artemisinin. Genes in red have a p-value <0.05. Indicated gene names include characterized DosR regulated genes. Panel B shows Venn diagram showing genes that are downregulated (>2-fold, p<0.05) in CDC1551 treated with artemisinin, HC102A or HC103A relative to a DMSO treated CDC1551 control. Also shown are genes downregulated (>2-fold, p<0.05) in a DMSO treated CDC1551(zkfosR) mutant strain relative to a DMSO treated CDC 1551 control. Panel C shows Venn diagram showing genes that are downregulated (>2-fold, p<0.05) in a CDC1551(zkfosR) mutant strain treated with artemisinin, HC102A or HC103A relative to a DMSO treated OC\55 l( idosR) control. The limited genes modulated by HC102A and HC103A support that these compounds are highly specific for the DosR regulon.

Fig. 3 includes five panels, A-E, and depicts that Artemisinin, HC102A and HC103A inhibit TAG synthesis, survival and isoniazid tolerance during NRP. Panel A shows inhibition of TAG accumulation. CDC 1551 treated with compounds of interest (at a concentration of 40 μΜ) and the OC\55 l( idosR) mutant were radiolabeled with ¹⁴ C acetate for 6 days and total lipids extracted and analyzed by TLC. The inhibitors reduce TAG accumulation by 60-70% similar to the CDCl55 \(/}dosR) mutant control. The asterisk indicates the position of TAG on the TLC. Panel B shows inhibition of survival during NRP. CDC 1551 and Erdman strains were treated with 40μΜ of the compounds of interest and NRP was induced using the hypoxic shift down persistence model. Following 10 days of treatment, CFUs were determined and percent survival calculated relative to the WT control at day 0. Error bars represent the standard deviation of the mean. Differences between artemisinin, HC102A and HC103A treated samples as compared to the DMSO treated samples, in both strains, are significant with a p-value <0.05 based on a T-test (marked with an asterisk). Panel C shows dose dependent inhibition of Mtb survival during NRP at day 10. Percent viability was calculated relative to viable bacteria in the DMSO control at day 10. Error bars represent the standard deviation of the mean. Panel D shows ten days of treatment with artemisinin, HC102A or HC103A, with or without INH, significantly reduces bacterial survival (p-value <0.05 based on a T-test) during RP relative to the respective DMSO controls. Panel E shows ten days of treatment with artemisinin, HC102A and HC103A reduces isoniazid tolerance during NRP. To quantify INH tolerance, percent viability at 1, 5 and 25 μΜ ΙΝΉ was measured relative to the 0 μΜ ΙΝΉ control (DMSO control). Significant differences (marked with an asterisk, p<0.05 based on a T-test) were calculated relative to the respective DMSO control sample. For example, cells treated with 5 μΜ INH and

artemisinin, HC102A or HC103A are significantly different from the DMSO control treated with 5 μΜ INH. Experiments were repeated at least twice with similar results.

Fig. 4 includes three panels, A-C, and depicts that Artemisinin directly inhibits DosS and DosT by targeting sensor kinase heme. UV- visible spectra of DosS (Panel A) and DosT (Panel B) showing treatment with dithionite (DTN) reduces the heme (the "on" state for the kinases) and that artemisinin oxidizes the heme (the "off state of the kinases). Panel C shows MS spectra showing the presence of peaks at -898 Da that are present in artemisinin treated DosS samples, but absent in DMSO treated samples. This mass is the approximate combined mass of heme (616.487 Da) and artemisinin (282.332 Da) and is consistent with the formation of heme-artemisinin adducts. Experiments were repeated at least twice with similar results.

Fig. 5 includes six panels A-F and depicts amino acid substitutions in DosS or DosT promote resistance to artemisinin. Panel A shows molecular modeling indicates a channel exists in DosS and DosT through which artemisinin may access the heme. In WT DosT, the heme (colored yellow) and iron (green ball) is accessible to artemisinin via a channel. G85L and Gl 15L substitutions are predicted to block this channel and access to the heme. Panel B and C show UV visible spectra show that the DosS (G87L) and DosS (Gl 17L) proteins can be reduced by the addition of dithionite (DTN) but are resistant to oxidation by artemisinin (Art). Panel D and E show WT DosT exhibits a dose-dependent decrease in the amplitude of the Soret peak at 430 nm (left side of Panel D) and a loss of the peak at 560nm (magnified in right side of Panel D). In contrast, DosT (Gl 15L) exhibits resistance to artemisinin because it does not exhibit a dose-dependent decrease in the 430nm peak (left side of Panel E) and the 560 nm peak is maintained at treatments of 50 and 100 μΜ artemisinin (right side of Panel E). DosT (G85L) exhibits spectra similar to WT DosT (Fig. 11, Panel B) Panel F shows overexpression of DosT (G115L) in CDC1551 provides artemisinin resistance. Mtb overexpressing WT DosT or DosT (G85L) exhibit strongly inhibited expression of DosR regulated genes (dosR, hspX and tgsl) in the presence of 1 μΜ artemisinin, while the strain overexpressing DosT (Gl 15L) is resistant. Dose response curves are presented in Fig. 12. Experiments were repeated at least twice with similar results.

Fig. 6 includes two panels, A-B, and depicts that HC103A inhibit DosS and DosT autophosphorylation. Recombinant DosS or DosT was treated with HC103A (Panel A) or HC102A (Panel B) across a dose response curve. The autophosphorylation assay was incubated for 1 hour, the proteins were western blotted and the protein autophosphorylation was assessed by following exposure of the blot to a phosphor screen. HC102A and HC103A inhibit DosS autophosphorylation with ICso of 1.9 μΜ and 0.5 μΜ, respectively. HC102A had limited impact on DosT autophosphorylation, whereas HC103A inhibited DosT autophosphorylation with an ICso of ~5μΜ. Experiments were repeated at least twice with similar results.

Fig. 7 includes three panels, A-C, and depicts statistical analysis of HTS controls. Panel A shows box plots showing the variation of DMSO control wells (negative control) from the screens of the ICCB-Longwood and Molecular Libraries Program (MLP) collections. Boxes show the 25 and 75% quartiles and the whiskers are 1.5x the interquartile range (approximately 3 standard deviations away from the mean). The dots are considered "outliers". Panel B shows table with the means and standard deviations from the DMSO controls. Along with the Z-factor of 0.9, tight clustering of the control wells around 0% inhibition for both fluorescence and optical density support robustness of the screen. Panel C shows FDR p-values plotted vs. the fluorescence inhibition to growth inhibition ratios shows that the chosen 1.5-fold cut-off ratio (red line) is significant (p<0.0003).

Fig. 8 includes four panels, A-D, and depicts identification of inhibitors of the DosRST pathway. Dose response curves of GFP fluorescence inhibition of

CDC1551( 2^p ': :GFP) reporter treated with DosRST regulon inhibitor compounds. Panel A shows Artemisinin analogs, artesunate and dihydroartemisinin (DHA). Panel B shows HC103B and HC104A-HC106A. Panel C shows HC102A generated by organic synthesis (CCG-2323500). Panel D shows HC 103A generated by organic synthesis (CCG-257424). Error bars represent the standard deviation and experiments were repeated at least twice with similar results.

Fig. 9 includes four panels, A-D, and depicts transcriptional profiling shows Artemisinin, HC 102A and HC 103A inhibit the core genes of the DosRST regulon during hypoxia. Panel A shows inhibition of DosR regulon under hypoxic conditions by the DosR regulon inhibitors. Mtb treated with compounds of interest was grown at 37°C without shaking for 6 days, and total RNA was extracted for RT-PCR

quantification. RT-PCR shows three highly induced DosR regulon genes (dosR, hspX and tgsl) under hypoxia were repressed by the DosR regulon inhibitors. Error bars represent the standard deviation. Panel B shows NO and VitaminC assays. Mtb cells were pre-treated with compounds of interest for 24 hours, and total RNA was extracted after inducing with NO or vitamin C for 2 hours. HC 102A and HC 103A inhibited the induction of DosR regulon by NO and vitamin C, but DHA had a little effect. In all cases, the difference in the drug treated samples compared to DMSO treated samples in response to vitamin C or NO is significant with a p-value <0.001 based on T-test, except those marked as non-significant (n.s.). Error bars represent the standard deviation. Mtb differential gene expression in response to HC 102A (Panel C) and HC 103 A (Panel D). Genes in red have a p-value <0.05, and indicated gene names are DosR regulated genes. The transcriptional analysis from different assays collectively support that DosR pathway is the target of artemisinin, HC 102A and HC103A.

Experiments were repeated at least twice with similar results.

Fig. 10 includes four panels, A-D, and depicts Artemisinin, HC 102A and HC 103A inhibit TAG synthesis, survival and isoniazid tolerance during NRP. Panel A shows quantification of TAG accumulation for Mtb treated with compounds of interest shows that DosRST regulon inhibitors repress TAG synthesis to the level similar to AdosR mutant. Error bars represent the standard deviation. Panel B shows dose dependent inhibition of Mtb survival during NRP following 15 days of treatment. Percent viability was calculated relative to the viable bacteria in the DMSO control at Day 15. Error bars represent the standard deviation of the mean. Panel C shows fifteen days of treatment with artemisinin, HC 102A or HC 103A, with or without INH, significantly reduces bacterial survival (p-value <0.05 based on a T-test) during NRP relative to the respective DMSO controls. Panel D shows fifteen days of treatment with artemisinin, HC 102A and HC103A reduces isoniazid tolerance during NRP. To quantify INH tolerance, percent viability at 1, 5 and 25 μΜ INH was measured relative to the 0 μΜ INH control (DMSO control). Significant differences (marked with an asterisks, p<0.05 based on a T-test) were calculated relative to the respective DMSO control sample. For example, cells treated with 5 μΜ INH and artemisinin, HC102A and HC103A are significantly different from the DMSO control treated with 5 μΜ INH. Experiments were repeated at least twice with similar results.

Fig. 11 includes two panels, A-B, and depicts artemisinin directly modulates DosS and DosT (G85L) heme in a dose- dependent manner. UV-visible spectra of DosS (Panel A) and DosT (G85L) (Panel B) treated with different concentrations of artemisinin. Artemisinin modulated DosT heme at a lower concentration (50 μΜ, Fig. 5, Panel D) than DosS heme (400 μΜ), supporting that DosT is more sensitive to artemisinin. DosT (G85L) exhibits a similar profile to WT DosT (Fig. 5, Panel D).

Fig. 12 depicts substitutions in the DosT provide resistance to artemisinin. Mtb was transformed with a replicating plasmid that overexpresses WT dosT, dosT (G85L) or dosT (G115L). Cells were treated with 0.025 μΜ - 20 μΜ artemisinin, and total RNA was extracted after 6 days incubation at 37°C. RT-PCR quantification of DosR- regulated genes (dosR, hspX and tgsl) shows that strains expressing DosT (G1 15L) exhibited EC50 for artemisinin-mediated inhibition of DosR regulon genes of 1.0-1.6 μΜ, which is ~5-fold more resistant than WT DosT or DosT (G85L) with EC50 of 0.2- 0.3 μΜ.

Fig. 13 includes two panels, A-B, and depicts HC102A and HC 103A do not modulate DosS redox. DosS treated with HC 102A (Panel A) or HC 103A (Panel B) shows a similar overall spectrum as DMSO control. This indicates that HC 102A and HC103A has no effect in modulating redox status of DosS, and may inhibit DosR regulon by distinct mechanism.

Fig. 14 depicts GFP fluorescence inhibition and eukaryotic cytotoxicity by DosR regulon inhibitors. Fig. 14 includes EC50 calculation of GFP flourescence inhition and eukaryotic cytotoxicity by DosR regulon inhibitors. For reporter fluorescence EC50 determination, CDC1551( 2^p ': :GFP) reporter was treated with compounds over an 8 point dose response curve ranging from 400 μΜ to 0.65 μΜ. Following 6 days of treatment, GFP florescence and optical density were measured. In all cases, no inhibition of growth was observed at the reported EC50 for inhibition of GFP fluorescence. For eukaryotic cytotoxicity, macrophage cells including bone marrow derived macrophage (BMDM), THP- 1 and J774, were tested with serial dilutions of DosR regulon inhibitors over an 8 point dose response curve ranging from 400 μΜ to 0.65 μΜ. Macrophages were incubated for 3 days and viability was determined using CellTiter-Glo (Promega) luminescent cell viability assay.

Note that for every figure containing a histogram, the bars from left to right for each discreet measurement correspond to the figure boxes from top to bottom in the figure legend as indicated.

Detailed Description

The present disclosure provides, among other things, compounds, compositions, and methods useful for inhibiting bacteria, such as Mycobacterium tuberculosis. These compositions and methods find many uses in medicine and research, e.g., treating subjects afflicted with active or latent bacterial infections. While in no way intended to be limiting, exemplary compositions and methods are elaborated on below.

L Two-component regulatory systems

As used herein, a two-component regulatory system refers to any two-component system that may be involved in oxygen and redox sensing pathways. Such two-component regulatory systems are conserved in many types of bacteria, such as Echerichia coli and M tuberculosis. Such bacteria or bacterial cells are also amenable to treatment with the inhibitors, and analogs or derivatives thereof, described herein. In some embodiments, the two-component regulatory system comprises a heme-based oxygen sensor or kinases (e.g., DosS, DosT, or both). Heme-based oxygen sensors are conserved across all kingdoms of life and fall within six distinct classes of sensors (Fahrana A et al. Antioxid Redox Signal. 17(9): 1232-1245 (2012)). Related bacterial heme-based sensors include: Rhizobium FixL protein, E. coli Dos, Acetobacter AxPDEAl, Halobacterium HemAT, and Azetobacter AvReg.

Heme-based redox sensors include: Vibrio VF A0071, Clostridium SONO and Rhodospirillum CooA. In some embodiments, the two-component regulatory system comprises the DosRST two-component regulatory system or DosRST regulon. Many bacteria have evolved conserved domains in the histidine kinase and response regulator proteins (Capra, EJ et al. Annu Rev Microbiol . 66:325-47 (2012)) and it is possible that inhibitors targeting DosRST may also target domains conserved in other bacterial two-component regulator proteins.

The DosRST two-component regulatory system plays an important role in Mtb RP physiology (Boon, C. et al. J Bacteriol 184, 6760-7 (2002)) and may promote the survival of Mtb during NRP. It is composed of two heme-based histidine sensor kinases, DosS and DosT, and the response regulator DosR, and strongly regulates the expression of

approximately 50 genes known as the DosRST regulon (Roberts, D.M. et al. J Biol Chem 279, 23082-7 (2004); Park, H.D. et al. Mol Microbiol 48, 833-43 (2003); Voskuil, M.I. et al. J Exp Med 198, 705-13 (2003); Galagan, J.E. et al. Nature 499, 178-83 (2013)). Mtb can sense host stimuli, including nitric oxide (NO), carbon monoxide (CO) and oxygen (O2), through DosS and DosT (Ioanoviciu, A. et al. Biochemistry 48, 5839-48 (2009)), with DosS acting as an oxygen and redox sensor and DosT acting as an oxygen sensor (Roberts, D.M. et al. J Biol Chem 279, 23082-7 (2004); Voskuil, M.I. et al. J Exp Med 198, 705-13 (2003); Ioanoviciu, A. et al. Biochemistry 48, 5839-48 (2009); Vos, M.H. et al. Biochemistry 51, 159-66 (2012); Kumar, A. et al. Proc Natl Acad Sci USA 104, 11568-73 (2007); Ohno, H. et al. Cell Microbiol 5, 637-48 (2003)). During hypoxia-driven NRP, DosT is associated with initiating expression of the DosR regulon in response to hypoxia and DosS promotes sustained expression of the DosR regulon (Honaker, R.W. et al. Infect Immun 77, 3258-63 (2009)). dosR mutants have reduced survival during hypoxia in vitro (Leistikow, R.L. et al. J Bacteriol 192, 1662-70 (2010)) and reduced virulence in rabbits, guinea pigs, non-human primates, and C3HeB/FeJ mice (Converse, P.J. et al. Infect Immun 77, 1230-7 (2009);

Gautam, U.S. et al. Am J Respir Cell Mol Biol 52, 708-16 (2015); Mehra, S. et al. Am J Respir Crit Care Med 191, 1185-96 (2015)), animal models that generate hypoxic

granulomas where DosR-dependent persistence is predicted to be required for survival.

Additionally, disruption of a DosR regulated gene, tgsl, results in enhanced sensitivity of Mtb to antibiotics in vitro and during mouse infection (Baek, S.H. et al. PLoS Biol 9, el001065 (2011)). Therefore, chemical inhibition of the DosR regulon may stop the establishment and survival of persistent, drug-tolerant Mtb in the granuloma.

II. Compounds that inhibit two-component regulatory systems and/or their regulon

The disclosure features, among other things, in vitro and in vivo methods for inhibiting the growth or viability of bacteria, such as Mycobacterium tuberculosis, using compounds that inhibit (e.g., inhibitors) a two-component regulatory system and/or its regulon, such as the DosRST two-component regulatory system and/or the DosRST regulon. As used herein, "inhibition of the two-component regulatory system," "inhibition of the DosRST two-component regulatory system," or "inhibition of the DosRST regulon," or similar grammatical terms and phrases, includes direct and indirect inhibition of the DosS, DosT, DosRST regulon, any combination thereof. For example, an inhibitor of the DosRST can be one that directly binds to DosS protein or DosT protein, or both, and inhibits the activity of the protein. In some embodiments, the inhibitor can be one that inhibits the expression or stability of DosS or DosT protein. In some embodiments, the inhibitor inhibits a protein regulator, signaling pathway component, and/or upstream and/or downstream genes of the DosRST regulon. As used herein, the term "inhibiting" and grammatical equivalents thereof refer to a decrease, limiting, and/or blocking of a particular action, function, or interaction. In one embodiment, the term refers to reducing the level of a given output or parameter to a quantity which is at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or less than the quantity in a corresponding control. A reduced level of a given output or parameter need not, although it may, mean an absolute absence of the output or parameter. The disclosure does not require, and is not limited to, methods that wholly eliminate the output or parameter.

In some embodiments, the inhibitors (e.g., artemisinin, HC102A, and HC103A) can inhibit the induction of the core DosRST regulon. In some embodiments, the inhibitors (e.g., HC102A, and HC103A) show strong specificity for the intended target of the DosRST regulon. In some embodiments, the In some embodiments, the inhibitor inhibits the ability of the two component regulatory system, such as DosRST and its regulon, to enhance or repress the expression of a target gene, such as any of those described in the Tables 2-3 provided herein. In some embodiments, the inhibitor can inhibit Mtb persistence associated physiologies, including but not limited to triacylglyerol synthesis, survival, and antibiotic tolerance. In some embodiments, HCIOIA (artemisinin) can disable the hem-based DosS/T sensor kinases by oxidizing ferrous heme and generating heme-artemisinin adducts. In some embodiments, an HC103A inhibitor can inhibit DosS and DosT autophosphorylation activity without targeting the sensor kinase heme.

In certain aspects, provided herein are compounds (e.g., inhibitors) having the structure of Formula I, or a pharmaceutically acceptable salt thereof:

Formula I

wherein

R ¹ and R ² are, independently for each occurrence, H or -OR ³ , or R ¹ and R ² together with the carbon to which they are bound form a carbonyl moiety; and

R ³ is, independently for each occurrence, H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl.

In some embodiments, R ¹ is H and R ² is -OR ³ . In some embodiments,

R ³ is _anc j _n j _{s an mte} g _er f _rom i _g (e.g., 2, 3, 4). In some embodiments,

R ³ i is and n is an integer from 1-6 (e.g., 1, 2, 3, 4). 37. In some embodiments, wherein R ³ is lower alkyl (e.g., methyl, ethyl).

In certain embodiments, the compound is

or a pharmaceutically acceptable salt thereof. In certain aspects, provided herein are compounds (e.g., inhibitors) having the structure of Formula II, or a pharmaceutically acceptable salt thereof:

Formula II

wherein

A ¹ is O, H, or CH ₂ ;

A ² is O, NH, or CH ₂ ;

R ⁴ is H, halo, or optionally substituted alkyl;

R ⁵ and R ⁶ are H or -OR ⁹ , or R ⁵ and R ⁶ together with the carbon to which they are bound form a carbonyl moiety;

R ⁹ is, independently for each occurrence, H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl;

R ⁷ and R ⁸ are H or -OR ¹⁰ , or R ⁵ and R ⁶ together with the carbon to which they are bound form a carbonyl moiety; and

R ¹⁰ is, independently for each occurrence, H or optionally alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl.

In some embodiments, A ¹ is NH. In some embodiments, A ² is NH. In some embodiments, R ⁴ is lower alkyl (e.g., methyl). In some embodiments, R ⁵ and R ⁶ together with the carbon to which they are bound form a carbonyl moiety.

In some embodiments, wherein R ⁷ and R ⁸ together with the carbon to which they are bound form a carbonyl moiety.

In certain embodiments, the compound is

or a pharmaceutically acceptable salt thereof.

In certain aspects, provided herein are compounds (e.g., inhibitors) having the structure of Formula III, or a pharmaceutically acceptable salt thereof:

Formula III

wherein

A ³ is O, NH, or CH ₂ ;

A ⁴ is O, NH, or CH ₂ ;

A ⁵ is O, NH, S or CH ₂ ;

R ¹¹ is H, halo, hydroxyl, or optionally substituted alkyl or alkoxy;

R ¹² and R ¹³ are H or -OR ¹⁶ , or R ¹² and R ¹³ together with the carbon to which they are bound form a carbonyl moiety;

R ¹⁴ and R ¹⁵ are H or -OR ¹⁷ , or R ¹⁴ and R ¹⁵ together with the carbon to which they are bound form a carbonyl moiety; and

R ¹⁶ and R ¹⁷ are, independently for each occurrence, H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl.

In some embodiments, A ³ is NH. In some embodiments, A ⁴ is NH.. In some embodiments, A ⁵ is S. In some embodiments, R ^u is hydroxyl. In some embodiments, R ¹² and R ¹³ together with the carbon to which they are bound form a carbonyl moiety. In some embodiments, R ¹⁴ and R ¹⁵ together with the carbon to which they are bound form a carbonyl moiety.

In certain embodiments, the compound is

or a pharmaceutically acceptable salt thereof.

In certain aspects, provided herein are compounds (e.g., inhibitors) having the structure of Formula IV, or a pharmaceutically acceptable salt thereof:

Formula IV

wherein

A ⁶ is N or CH;

R ¹⁸ is H, halo, or optionally substituted alkyl or alkoxy;

R ²¹ is H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl; R ¹⁹ and R ²⁰ are H or -OR ²⁴ , or R ¹⁹ and R ²⁰ together with the carbon to which they are bound form a carbonyl moiety;

R ²² and R ²³ are H or -OR ²⁵ , or R ²² and R ²³ together with the carbon to which they are bound form a carbonyl moiety; and

R ²⁴ and R ²⁵ are, independently for each occurrence, H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl.

In some embodiments, A ⁶ is NH. In some embodiments, wherein R ¹⁸ is halo (e.g.,

Br).

In some embodiments, R and R together with the carbon to which they are bound form a carbonyl moiety. In some embodiments, R ²² and R ²³ together with the carbon to which they are bound form a carbonyl moiety. In some embodiments, wherein R ²¹ is optionally substituted alkyl. In some embodiments, R ²¹ is aminoalkyl. In some embodiments, R ²¹ is embodiments, the compound is

or a pharmaceutically acceptable salt thereof.

In certain aspects, provided herein are compounds (e.g., inhibitors) having the structure of Formula V, or a pharmaceuticall acceptable salt thereof:

Formula V

wherein

A ⁷ is N or CH;

R ²⁶ is H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl; and R ²⁷ is H or optionally substituted alkyl, cycloalkyl, heterocyclyl, or alkoxy.

In some embodiments,A ⁷ is N. In some embodiments,wherein R ²⁶ is lower alkyl (e.g., ethyl). In some embodiments, R ²⁷ is aminoalkyl. In some embodiments,R ²⁷ is

A ⁸ is N or CH;

A ⁹ is N or CH;

A ¹⁰ is CH ₂ , S0 ₂ , S=0 or S; and

R ²⁸ is optionally substituted alkyl, cycloalkyl, aryl or heteroaryl; In certain embodiments, the compound is

a pharmaceutically acceptable salt thereof. In certain aspects, provided herein are compounds (e.g., inhibitors) having the structure of Formula VI, or a pharmaceutically acceptable salt thereof:

Formula VI

wherein

A ¹¹ is N or CH;

A ¹² is O, NH or CH ₂ ;

A ¹³ is O, NH or CH ₂ ;

A ¹⁴ is O, NH or CH ₂ ;

R ²⁹ is H, halo, or optionally substituted alkyl or alkoxy;

R ³⁰ is H, halo, or optionally substituted alkyl or alkoxy;

R ³¹ and R ³² are H or -OR ³³ , or R ³¹ and R ³² together with the carbon to which they are bound form a carbonyl moiety; and

R ³³ is H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl.

In some embodiments, wherein A ¹¹ is N.

In some embodiments, A ¹² is O. In some embodiments, A ¹³ is NH. In some embodiments,A ¹⁴ is NH. In some embodiments, R ²⁹ is halo. In some embodiments, R ²⁹ is CI. In some embodiments, R ³⁰ is halo (e.g., CI). n embodiments, the compound is

or a pharmaceutically acceptable salt thereof.

In certain aspects, provided herein are compounds (e.g., inhibitors) having the structure of Formula VII, or a pharmaceutically acceptable salt thereof:

Formula VII

wherein

A ¹⁵ is O, NH, or CH ₂ ;

A ¹⁶ is O, NH, or CH ₂ ;

R ³⁴ and R ³⁹ are each, independently for each occurrence H, halo, hydroxyl, or optionally substituted alkyl or alkoxy;

R ³⁵ and R ³⁶ are H or -OR ³⁹ , or R ³⁵ and R ³⁶ together with the carbon to which they are bound form a carbonyl moiety;

R ³⁷ and R ³⁸ are H or -OR ⁴⁰ , or R ³⁷ and R ³⁸ together with the carbon to which they are bound form a carbonyl moiety; and

R ³⁹ and R ⁴⁰ are, independently for each occurrence, H or optionally substituted alkyl, cycloalkyl, heterocyclyl, acyl, aryl, or heteroaryl.

In some embodiments, A ¹⁵ is NH. In some embodiments, A ¹⁶ is NH. In some embodiments, R ³⁴ is hydroxyl. In some embodiments, R ³⁹ is hydroxyl. In some embodiments, R ³⁵ and R ³⁶ together with the carbon to which they are bound form a carbonyl moiety. In some embodiments, R ³⁷ and R ³⁸ together with the carbon to which they are bound form a carbonyl moiety. In certain embodiments, the compound is

or a pharmaceutically acceptable salt thereof.

Exemplary compounds (e.g., inhibitors) of Formula I- VII are depicted in Table 1. The compounds of Table 1 may be depicted as the free base or the conjugate acid.

Compounds may be isolated in either the free base form, as a salt (e.g., a hydrochloride salt) or in both forms. In the chemical structures shown below, standard chemical abbreviations are sometimes used.

Table 1 : Exemplary compounds of Formulas I- VII

Ex. Structure Name

1 HC101A

0

2 HC101B

0

3 HC101C

OH

 HC104A

HC105

HC106

In certain embodiments, compounds of the invention may be racemic. In certain embodiments, compounds of the invention may be enriched in one enantiomer. For example, a compound of the invention may have greater than 30% ee, 40% ee, 50% ee, 60% ee, 70% ee, 80%) ee, 90% ee, or even 95% or greater ee. The compounds of the invention have more than one stereocenter. Consequently, compounds of the invention may be enriched in one or more diastereomer. For example, a compound of the invention may have greater than 30% de, 40% de, 50% de, 60% de, 70% de, 80% de, 90% de, or even 95% or greater de.

1. Pharmaceutical Compositions In certain embodiments, the present invention provides pharmaceutical compositions comprising a compound of one of Formulas I- VII and a pharmaceutically acceptable carrier.

The compositions and methods of the present invention may be utilized to treat an individual in need thereof. In certain embodiments, the individual is a mammal such as a human, or a non-human mammal. When administered to an animal, such as a human, the composition or the compound is preferably administered as a pharmaceutical composition comprising, for example, a compound of the invention and a pharmaceutically acceptable carrier. Pharmaceutically acceptable carriers are well known in the art and include, for example, aqueous solutions such as water or physiologically buffered saline or other solvents or vehicles such as glycols, glycerol, oils such as olive oil, or injectable organic esters. In a preferred embodiment, when such pharmaceutical compositions are for human

administration, particularly for invasive routes of administration (i.e., routes, such as injection or implantation, that circumvent transport or diffusion through an epithelial barrier), the aqueous solution is pyrogen-free, or substantially pyrogen-free. The excipients can be chosen, for example, to effect delayed release of an agent or to selectively target one or more cells, tissues or organs. The pharmaceutical composition can be in dosage unit form such as tablet, capsule (including sprinkle capsule and gelatin capsule), granule, lyophile for reconstitution, powder, solution, syrup, suppository, injection or the like. The composition can also be present in a transdermal delivery system, e.g., a skin patch. The composition can also be present in a solution suitable for topical administration, such as an eye drop.

A pharmaceutically acceptable carrier can contain physiologically acceptable agents that act, for example, to stabilize, increase solubility or to increase the absorption of a compound such as a compound of the invention. Such physiologically acceptable agents include, for example, carbohydrates, such as glucose, sucrose or dextrans, antioxidants, such as ascorbic acid or glutathione, chelating agents, low molecular weight proteins or other stabilizers or excipients. The choice of a pharmaceutically acceptable carrier, including a physiologically acceptable agent, depends, for example, on the route of administration of the composition. The preparation or pharmaceutical composition can be a selfemulsifying drug delivery system or a selfmicroemulsifying drug delivery system. The pharmaceutical composition (preparation) also can be a liposome or other polymer matrix, which can have incorporated therein, for example, a compound of the invention. Liposomes, for example, which comprise phospholipids or other lipids, are nontoxic, physiologically acceptable and metabolizable carriers that are relatively simple to make and administer.

The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

The phrase "pharmaceutically acceptable carrier" as used herein means a

pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material. Each carrier must be "acceptable" in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient. Some examples of materials which can serve as pharmaceutically acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer solutions; and (21) other non-toxic compatible substances employed in pharmaceutical formulations.

A pharmaceutical composition (preparation) can be administered to a subject by any of a number of routes of administration including, for example, orally (for example, drenches as in aqueous or non-aqueous solutions or suspensions, tablets, capsules (including sprinkle capsules and gelatin capsules), boluses, powders, granules, pastes for application to the tongue); absorption through the oral mucosa (e.g., sublingually); anally, rectally or vaginally (for example, as a pessary, cream or foam); parenterally (including intramuscularly, intravenously, subcutaneously or intrathecally as, for example, a sterile solution or suspension); nasally; intraperitoneally; subcutaneously; transdermally (for example as a patch applied to the skin); and topically (for example, as a cream, ointment or spray applied to the skin, or as an eye drop). The compound may also be formulated for inhalation. In certain embodiments, a compound may be simply dissolved or suspended in sterile water. Details of appropriate routes of administration and compositions suitable for same can be found in, for example, U.S. Pat. Nos. 6,110,973, 5,731,000, 5,541,231, 5,427,798, 5,358,970 and

4, 172,896, as well as in patents cited therein.

The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration. The amount of active ingredient that can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect. Generally, out of one hundred percent, this amount will range from about 1 percent to about ninety-nine percent of active ingredient, preferably from about 5 percent to about 70 percent, most preferably from about 10 percent to about 30 percent.

Methods of preparing these formulations or compositions include the step of bringing into association an active compound, such as a compound of the invention, with the carrier and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association a compound of the present invention with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.

Formulations of the invention suitable for oral administration may be in the form of capsules (including sprinkle capsules and gelatin capsules), cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), lyophile, powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in- water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a compound of the present invention as an active ingredient. Compositions or compounds may also be administered as a bolus, electuary or paste. To prepare solid dosage forms for oral administration (capsules (including sprinkle capsules and gelatin capsules), tablets, pills, dragees, powders, granules and the like), the active ingredient is mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as, for example, cetyl alcohol and glycerol monostearate; (8) absorbents, such as kaolin and bentonite clay; (9) lubricants, such a talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof; (10) complexing agents, such as, modified and unmodified cyclodextrins; and (11) coloring agents. In the case of capsules (including sprinkle capsules and gelatin capsules), tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.

A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared using binder (for example, gelatin or hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (for example, sodium starch glycolate or cross-linked sodium carboxymethyl cellulose), surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.

The tablets, and other solid dosage forms of the pharmaceutical compositions, such as dragees, capsules (including sprinkle capsules and gelatin capsules), pills and granules, may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile, other polymer matrices, liposomes and/or microspheres. They may be sterilized by, for example, filtration through a bacteria-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions that can be dissolved in sterile water, or some other sterile injectable medium immediately before use. These compositions may also optionally contain opacifying agents and may be of a composition that they release the active ingredient(s) only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. The active ingredient can also be in microencapsulated form, if appropriate, with one or more of the above-described excipients.

Liquid dosage forms useful for oral administration include pharmaceutically acceptable emulsions, lyophiles for reconstitution, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredient, the liquid dosage forms may contain inert diluents commonly used in the art, such as, for example, water or other solvents, cyclodextrins and derivatives thereof, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.

Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming and preservative agents.

Suspensions, in addition to the active compounds, may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.

Formulations of the pharmaceutical compositions for rectal, vaginal, or urethral administration may be presented as a suppository, which may be prepared by mixing one or more active compounds with one or more suitable nonirritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound. Formulations of the pharmaceutical compositions for administration to the mouth may be presented as a mouthwash, or an oral spray, or an oral ointment.

Alternatively or additionally, compositions can be formulated for delivery via a catheter, stent, wire, or other intraluminal device. Delivery via such devices may be especially useful for delivery to the bladder, urethra, ureter, rectum, or intestine.

Formulations which are suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be appropriate.

Dosage forms for the topical or transdermal administration include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. The active compound may be mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants that may be required.

The ointments, pastes, creams and gels may contain, in addition to an active compound, excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.

Powders and sprays can contain, in addition to an active compound, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.

Transdermal patches have the added advantage of providing controlled delivery of a compound of the present invention to the body. Such dosage forms can be made by dissolving or dispersing the active compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane or dispersing the compound in a polymer matrix or gel.

Ophthalmic formulations, eye ointments, powders, solutions and the like, are also contemplated as being within the scope of this invention. Exemplary ophthalmic

formulations are described in U.S. Publication Nos. 2005/0080056, 2005/0059744,

2005/0031697 and 2005/004074 and U.S. Patent No. 6,583,124, the contents of which are incorporated herein by reference. If desired, liquid ophthalmic formulations have properties similar to that of lacrimal fluids, aqueous humor or vitreous humor or are compatable with such fluids. A preferred route of administration is local administration (e.g., topical administration, such as eye drops, or administration via an implant).

The phrases "parenteral administration" and "administered parenterally" as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion.

Pharmaceutical compositions suitable for parenteral administration comprise one or more active compounds in combination with one or more pharmaceutically acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents.

Examples of suitable aqueous and nonaqueous carriers that may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents that delay absorption such as aluminum monostearate and gelatin. In some cases, in order to prolong the effect of a drug, it is desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be

accomplished by the use of a liquid suspension of crystalline or amorphous material having poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution, which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.

Injectable depot forms are made by forming microencapsulated matrices of the subject compounds in biodegradable polymers such as polylactide-polyglycolide. Depending on the ratio of drug to polymer, and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly (anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions that are compatible with body tissue.

For use in the methods of this invention, active compounds can be given per se or as a pharmaceutical composition containing, for example, 0.1 to 99.5% (more preferably, 0.5 to 90%) of active ingredient in combination with a pharmaceutically acceptable carrier.

Methods of introduction may also be provided by rechargeable or biodegradable devices. Various slow release polymeric devices have been developed and tested in vivo in recent years for the controlled delivery of drugs, including proteinacious biopharmaceuticals. A variety of biocompatible polymers (including hydrogels), including both biodegradable and non-degradable polymers, can be used to form an implant for the sustained release of a compound at a particular target site.

Actual dosage levels of the active ingredients in the pharmaceutical compositions may be varied so as to obtain an amount of the active ingredient that is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of

administration, without being toxic to the patient.

The selected dosage level will depend upon a variety of factors including the activity of the particular compound or combination of compounds employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion of the particular compound(s) being employed, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compound(s) employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts.

A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the therapeutically effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could start doses of the pharmaceutical

composition or compound at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved. By "therapeutically effective amount" is meant the concentration of a compound that is sufficient to elicit the desired therapeutic effect. It is generally understood that the effective amount of the compound will vary according to the weight, sex, age, and medical history of the subject. Other factors which influence the effective amount may include, but are not limited to, the severity of the patient's condition, the disorder being treated, the stability of the compound, and, if desired, another type of therapeutic agent being administered with the compound of the invention. A larger total dose can be delivered by multiple administrations of the agent. Methods to determine efficacy and dosage are known to those skilled in the art (Isselbacher et al. (1996) Harrison's Principles of Internal Medicine 13 ed., 1814-1882, herein incorporated by reference).

In general, a suitable daily dose of an active compound used in the compositions and methods of the invention will be that amount of the compound that is the lowest dose effective to produce a therapeutic effect. Such an effective dose will generally depend upon the factors described above.

If desired, the effective daily dose of the active compound may be administered as one, two, three, four, five, six or more sub-doses administered separately at appropriate intervals throughout the day, optionally, in unit dosage forms. In certain embodiments of the present invention, the active compound may be administered two or three times daily. In preferred embodiments, the active compound will be administered once daily.

The patient receiving this treatment is any animal in need, including primates, in particular humans, and other mammals such as equines, cattle, swine and sheep; and poultry and pets in general. In certain embodiments, compounds of the invention may be used alone or conjointly administered with another type of therapeutic agent. As used herein, the phrase "conjoint administration" refers to any form of administration of two or more different therapeutic compounds such that the second compound is administered while the previously administered therapeutic compound is still effective in the body (e.g., the two compounds are

simultaneously effective in the patient, which may include synergistic effects of the two compounds). For example, the different therapeutic compounds can be administered either in the same formulation or in a separate formulation, either concomitantly or sequentially. In certain embodiments, the different therapeutic compounds can be administered within one hour, 12 hours, 24 hours, 36 hours, 48 hours, 72 hours, or a week of one another. Thus, an individual who receives such treatment can benefit from a combined effect of different therapeutic compounds.

In certain embodiments, conjoint administration of compounds of the invention with one or more additional therapeutic agent(s) (e.g., one or more additional chemotherapeutic agent(s)) provides improved efficacy relative to each individual administration of the compound of the invention (e.g., compound of formula I- VII) or the one or more additional therapeutic agent(s). In certain such embodiments, the conjoint administration provides an additive effect, wherein an additive effect refers to the sum of each of the effects of individual administration of the compound of the invention and the one or more additional therapeutic agent(s).

This invention includes the use of pharmaceutically acceptable salts of compounds of the invention in the compositions and methods of the present invention. The term

"pharmaceutically acceptable salt" as used herein includes salts derived from inorganic or organic acids including, for example, hydrochloric, hydrobromic, sulfuric, nitric, perchloric, phosphoric, formic, acetic, lactic, maleic, fumaric, succinic, tartaric, glycolic, salicylic, citric, methanesulfonic, benzenesulfonic, benzoic, malonic, trifluoroacetic, trichloroacetic, naphthalene-2-sulfonic, and other acids. Pharmaceutically acceptable salt forms can include forms wherein the ratio of molecules comprising the salt is not 1 : 1. For example, the salt may comprise more than one inorganic or organic acid molecule per molecule of base, such as two hydrochloric acid molecules per molecule of compound of Formula I- VII. As another example, the salt may comprise less than one inorganic or organic acid molecule per molecule of base, such as two molecules of compound of Formulas I- VII per molecule of tartaric acid.

In further embodiments, contemplated salts of the invention include, but are not limited to, alkyl, dialkyl, trialkyl or tetra-alkyl ammonium salts. In certain embodiments, contemplated salts of the invention include, but are not limited to, L-arginine, benenthamine, benzathine, betaine, calcium hydroxide, choline, deanol, diethanolamine, diethylamine, 2- (diethylamino)ethanol, ethanolamine, ethylenediamine, N-methylglucamine, hydrabamine, lH-imidazole, lithium, L-lysine, magnesium, 4-(2-hydroxyethyl)morpholine, piperazine, potassium, l-(2-hydroxyethyl)pyrrolidine, sodium, triethanolamine, tromethamine, and zinc salts. In certain embodiments, contemplated salts of the invention include, but are not limited to, Na, Ca, K, Mg, Zn or other metal salts.

The pharmaceutically acceptable acid addition salts can also exist as various solvates, such as with water, methanol, ethanol, dimethylformamide, and the like. Mixtures of such solvates can also be prepared. The source of such solvate can be from the solvent of crystallization, inherent in the solvent of preparation or crystallization, or adventitious to such solvent.

Wetting agents, emulsifiers and lubricants, such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, release agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the compositions.

Examples of pharmaceutically acceptable antioxidants include: (1) water-soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabi sulfite, sodium sulfite and the like; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and (3) metal-chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.

2. Definitions

The term "acyl" is art-recognized and refers to a group represented by the general formula hydrocarbylC(O)-, preferably alkylC(O)- or optionally substituted alkylC(O)-. The term "acylamino" is art-recognized and refers to an amino group substituted with an acyl group and may be represented, for example, by the formula hydrocarbylC(0) H-.

The term "acyloxy" is art-recognized and refers to a group represented by the general formula hydrocarbylC(0)0-, preferably alkylC(0)0-.

The term "alkoxy" refers to an alkyl group, preferably a lower alkyl group, having an oxygen attached thereto. Representative alkoxy groups include methoxy, -OCF3, ethoxy, propoxy, tert-butoxy and the like.

The term "cycloalkyloxy" refers to a cycloakyl group having an oxygen attached thereto.

The term "alkoxyalkyl" refers to an alkyl group substituted with an alkoxy group and may be represented by the general formula alkyl-O-alkyl.

The term "alkylaminoalkyl" refers to an alkyl group substituted with an alkylamino group.

The term "alkenyl", as used herein, refers to an aliphatic group containing at least one double bond and is intended to include both "unsubstituted alkenyls" and "substituted alkenyls", the latter of which refers to alkenyl moieties having substituents replacing a hydrogen on one or more carbons of the alkenyl group. Such substituents may occur on one or more carbons that are included or not included in one or more double bonds. Moreover, such substituents include all those contemplated for alkyl groups, as discussed below, except where stability is prohibitive. For example, substitution of alkenyl groups by one or more alkyl, carbocyclyl, aryl, heterocyclyl, or heteroaryl groups is contemplated.

An "alkyl" group or "alkane" is a straight chained or branched non-aromatic hydrocarbon which is completely saturated. Typically, a straight chained or branched alkyl group has from 1 to about 20 carbon atoms, preferably from 1 to about 10 unless otherwise defined. Examples of straight chained and branched alkyl groups include methyl, ethyl, n- propyl, iso-propyl, n-butyl, sec-butyl, tert-butyl, pentyl, hexyl, pentyl and octyl. A Ci-C ₆ straight chained or branched alkyl group is also referred to as a "lower alkyl" group.

Moreover, the term "alkyl" (or "lower alkyl") as used throughout the specification, examples, and claims is intended to include both "unsubstituted alkyls" and "substituted alkyls", the latter of which refers to alkyl moieties having substituents replacing a hydrogen on one or more carbons of the hydrocarbon backbone. Such substituents, if not otherwise specified, can include, for example, a halogen, a hydroxyl, a carbonyl (such as a carboxyl, an alkoxycarbonyl, a formyl, or an acyl), a thiocarbonyl (such as a thioester, a thioacetate, or a thioformate), an alkoxyl, a phosphoryl, a phosphate, a phosphonate, a phosphinate, an amino, an amido, an amidine, an imine, a cyano, a nitro, an azido, a sulfhydryl, an alkylthio, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a sulfonyl, a heterocyclyl, an aralkyl, or an aromatic or heteroaromatic moiety. It will be understood by those skilled in the art that the moieties substituted on the hydrocarbon chain can themselves be substituted, if appropriate. For instance, the substituents of a substituted alkyl may include substituted and unsubstituted forms of amino, azido, imino, amido, phosphoryl (including phosphonate and phosphinate), sulfonyl (including sulfate, sulfonamido, sulfamoyl and sulfonate), and silyl groups, as well as ethers, alkylthios, carbonyls (including ketones, aldehydes, carboxylates, and esters), -CF ₃ , -CN and the like. Exemplary substituted alkyls are described below. Cycloalkyls can be further substituted with alkyls, alkenyls, alkoxys, alkylthios, aminoalkyls, carbonyl- substituted alkyls, -CF ₃ , -CN, and the like.

The term "Cx- _y " when used in conjunction with a chemical moiety, such as, acyl, acyloxy, alkyl, alkenyl, alkynyl, or alkoxy is meant to include groups that contain from x to y carbons in the chain. For example, the term "Cx- _y alkyl" refers to substituted or unsubstituted saturated hydrocarbon groups, including straight-chain alkyl and branched-chain alkyl groups that contain from x to y carbons in the chain, including haloalkyl groups such as

trifluoromethyl and 2,2,2-trifluoroethyl, etc. Co alkyl indicates a hydrogen where the group is in a terminal position, a bond if internal. The terms "C2- _y alkenyl" and "C2- _y alkynyl" refer to substituted or unsubstituted unsaturated aliphatic groups analogous in length and possible substitution to the alkyls described above, but that contain at least one double or triple bond respectively.

The term "alkylamino", as used herein, refers to an amino group substituted with at least one alkyl group.

The term "alkylthio", as used herein, refers to a thiol group substituted with an alkyl group and may be represented by the general formula alkylS-.

The term "alkynyl", as used herein, refers to an aliphatic group containing at least one triple bond and is intended to include both "unsubstituted alkynyls" and "substituted alkynyls", the latter of which refers to alkynyl moieties having substituents replacing a hydrogen on one or more carbons of the alkynyl group. Such substituents may occur on one or more carbons that are included or not included in one or more triple bonds. Moreover, such substituents include all those contemplated for alkyl groups, as discussed above, except where stability is prohibitive. For example, substitution of alkynyl groups by one or more alkyl, carbocyclyl, aryl, heterocyclyl, or heteroaryl groups is contemplated.

The term "amide", as used herein, refers to a group

wherein each R ¹⁰⁰ independently represent a hydrogen or hydrocarbyl group, or two R ¹⁰⁰ are taken together with the N atom to which they are attached complete a heterocycle having from 4 to 8 atoms in the ring structure.

The terms "amine" and "amino" are art-recognized and refer to both unsubstituted and substituted amines and salts thereof, e.g., a moiety that can be represented by

wherein each R ¹⁰⁰ independently represents a hydrogen or a hydrocarbyl group, or two R ¹⁰ are taken together with the N atom to which they are attached complete a heterocycle having from 4 to 8 atoms in the ring structure.

The term "aminoalkyl", as used herein, refers to an alkyl group substituted with an amino group.

The term "aralkyl", as used herein, refers to an alkyl group substituted with an aryl group.

The term "aryl" as used herein include substituted or unsubstituted single-ring aromatic groups in which each atom of the ring is carbon. Preferably the ring is a 5- to 7- membered ring, more preferably a 6-membered ring. The term "aryl" also includes polycyclic ring systems having two or more cyclic rings in which two or more carbons are common to two adjoining rings wherein at least one of the rings is aromatic, e.g., the other cyclic rings can be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/or heterocyclyls. Aryl groups include benzene, naphthalene, phenanthrene, phenol, aniline, and the like. The term "carbamate" is art-recognized and refers to a group

wherein R ⁹⁰ and R ¹⁰⁰ independently represent hydrogen or a hydrocarbyl group, such as an alkyl group, or R ⁹⁰ and R ¹⁰⁰ taken together with the intervening atom(s) complete a heterocycle having from 4 to 8 atoms in the ring structure.

The terms "carbocycle", and "carbocyclic", as used herein, refers to a saturated or unsaturated ring in which each atom of the ring is carbon. The term carbocycle includes both aromatic carbocycles and non-aromatic carbocycles. Non-aromatic carbocycles include both cycloalkane rings, in which all carbon atoms are saturated, and cycloalkene rings, which contain at least one double bond. "Carbocycle" includes 5-7 membered monocyclic and 8-12 membered bicyclic rings. Each ring of a bicyclic carbocycle may be selected from saturated, unsaturated and aromatic rings. Carbocycle includes bicyclic molecules in which one, two or three or more atoms are shared between the two rings. The term "fused carbocycle" refers to a bicyclic carbocycle in which each of the rings shares two adjacent atoms with the other ring. Each ring of a fused carbocycle may be selected from saturated, unsaturated and aromatic rings. In an exemplary embodiment, an aromatic ring, e.g., phenyl, may be fused to a saturated or unsaturated ring, e.g., cyclohexane, cyclopentane, or cyclohexene. Any combination of saturated, unsaturated and aromatic bicyclic rings, as valence permits, is included in the definition of carbocyclic. Exemplary "carbocycles" include cyclopentane, cyclohexane, bicyclo[2.2.1]heptane, 1,5-cyclooctadiene, 1,2,3,4-tetrahydronaphthalene, bicyclo[4.2.0]oct-3-ene, naphthalene and adamantane. Exemplary fused carbocycles include decalin, naphthalene, 1,2,3,4-tetrahydronaphthalene, bicyclo[4.2.0]octane, 4,5,6,7-tetrahydro- lH-indene and bicyclo[4.1.0]hept-3-ene. "Carbocycles" may be susbstituted at any one or more positions capable of bearing a hydrogen atom.

A "cycloalkyl" group is a cyclic hydrocarbon which is completely saturated.

"Cycloalkyl" includes monocyclic and bicyclic rings. Typically, a monocyclic cycloalkyl group has from 3 to about 10 carbon atoms, more typically 3 to 8 carbon atoms unless otherwise defined. The second ring of a bicyclic cycloalkyl may be selected from saturated, unsaturated and aromatic rings. Cycloalkyl includes bicyclic molecules in which one, two or three or more atoms are shared between the two rings. The term "fused cycloalkyl" refers to a bicyclic cycloalkyl in which each of the rings shares two adjacent atoms with the other ring. The second ring of a fused bicyclic cycloalkyl may be selected from saturated, unsaturated and aromatic rings. A "cycloalkenyl" group is a cyclic hydrocarbon containing one or more double bonds.

The term "carbocyclylalkyl", as used herein, refers to an alkyl group substituted with a carbocycle group.

The term "carbonate" is art-recognized and refers to a group -OCO2-R ¹⁰ , wherein R ¹⁰ represents a hydrocarbyl group.

The term "carboxy", as used herein, refers to a group represented by the

formula -CO2H.

The term "ester", as used herein, refers to a group -C(0)OR ¹⁰ wherein R ¹⁰ represents a hydrocarbyl group.

The term "ether", as used herein, refers to a hydrocarbyl group linked through an oxygen to another hydrocarbyl group. Accordingly, an ether substituent of a hydrocarbyl group may be hydrocarbyl-O-. Ethers may be either symmetrical or unsymmetrical.

Examples of ethers include, but are not limited to, heterocycle-O-heterocycle and aiyl-O- heterocycle. Ethers include "alkoxyalkyl" groups, which may be represented by the general formula alkyl-O-alkyl.

The terms "halo" and "halogen" as used herein means halogen and includes chloro, fluoro, bromo, and iodo.

The terms "hetaralkyl" and "heteroaralkyl", as used herein, refers to an alkyl group substituted with a hetaryl group.

The term "heteroalkyl", as used herein, refers to a saturated or unsaturated chain of carbon atoms and at least one heteroatom, wherein no two heteroatoms are adjacent.

The term "heteroalkylamino", as used herein, refers to an amino group subsituted with a heteralkyl group.

The terms "heteroaryl" and "hetaryl" include substituted or unsubstituted aromatic single ring structures, preferably 5- to 7-membered rings, more preferably 5- to 6-membered rings, whose ring structures include at least one heteroatom, preferably one to four heteroatoms, more preferably one or two heteroatoms. The terms "heteroaryl" and "hetaryl" also include polycyclic ring systems having two or more cyclic rings in which two or more carbons are common to two adjoining rings wherein at least one of the rings is heteroaromatic, e.g., the other cyclic rings can be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/or heterocyclyls. Heteroaryl groups include, for example, pyrrole, furan, thiophene, imidazole, oxazole, thiazole, pyrazole, pyridine, pyrazine, pyridazine, and pyrimidine, and the like.

The term "heteroatom" as used herein means an atom of any element other than carbon or hydrogen. Preferred heteroatoms are nitrogen, oxygen, and sulfur.

The terms "heterocyclyl", "heterocycle", and "heterocyclic" refer to substituted or unsubstituted non-aromatic ring structures, preferably 3- to 10-membered rings, more preferably 3- to 7-membered rings, whose ring structures include at least one heteroatom, preferably one to four heteroatoms, more preferably one or two heteroatoms. The terms "heterocyclyl" and "heterocyclic" also include polycyclic ring systems having two or more cyclic rings in which two or more carbons are common to two adjoining rings wherein at least one of the rings is heterocyclic, e.g., the other cyclic rings can be cycloalkyls, cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/or heterocyclyls. Heterocyclyl groups include, for example, piperidine, piperazine, pyrrolidine, morpholine, lactones, lactams, and the like. Heterocyclyl groups can also be substituted by oxo groups. For example,

"heterocyclyl" encompasses both pyrrolidine and pyrrolidinone.

The term "heterocycloalkyl", as used herein, refers to an alkyl group substituted with a heterocycle group.

The term "heterocycloalkylamino", as used herein refers to an amino group substituted with a heterocycloalkyl group.

The term "hydrocarbyl", as used herein, refers to a group that is bonded through a carbon atom that does not have a =0 or =S substituent, and typically has at least one carbon- hydrogen bond and a primarily carbon backbone, but may optionally include heteroatoms. Thus, groups like methyl, ethoxyethyl, 2-pyridyl, and trifluoromethyl are considered to be hydrocarbyl for the purposes of this application, but substituents such as acetyl (which has a =0 substituent on the linking carbon) and ethoxy (which is linked through oxygen, not carbon) are not. Hydrocarbyl groups include, but are not limited to aryl, heteroaryl, carbocycle, heterocyclyl, alkyl, alkenyl, alkynyl, and combinations thereof.

The term "hydroxyalkyl", as used herein, refers to an alkyl group substituted with a hydroxy group. The term "lower" when used in conjunction with a chemical moiety, such as, acyl, acyloxy, alkyl, alkenyl, alkynyl, or alkoxy is meant to include groups where there are ten or fewer non-hydrogen atoms in the substituent, preferably six or fewer. A "lower alkyl", for example, refers to an alkyl group that contains ten or fewer carbon atoms, preferably six or fewer. In certain embodiments, acyl, acyloxy, alkyl, alkenyl, alkynyl, or alkoxy substituents defined herein are respectively lower acyl, lower acyloxy, lower alkyl, lower alkenyl, lower alkynyl, or lower alkoxy, whether they appear alone or in combination with other

substituents, such as in the recitations hydroxyalkyl and aralkyl (in which case, for example, the atoms within the aryl group are not counted when counting the carbon atoms in the alkyl substituent).

As used herein, the term "oxo" refers to a carbonyl group. When an oxo substituent occurs on an otherwise saturated group, such as with an oxo-substituted cycloalkyl group (e.g., 3-oxo-cyclobutyl), the substituted group is still intended to be a saturated group. When a group is referred to as being substituted by an "oxo" group, this can mean that a carbonyl moiety (i.e., -C(=0)-) replaces a methylene unit (i.e., -CH2-).

The terms "polycyclyl", "polycycle", and "polycyclic" refer to two or more rings (e.g., cycloalkyls, cycloalkenyls, cycloalkynyls, aryls, heteroaryls, and/or heterocyclyls) in which two or more atoms are common to two adjoining rings, e.g., the rings are "fused rings". Each of the rings of the polycycle can be substituted or unsubstituted. In certain embodiments, each ring of the polycycle contains from 3 to 10 atoms in the ring, preferably from 5 to 7.

The term "silyl" refers to a silicon moiety with three hydrocarbyl moieties attached thereto.

The term "substituted" refers to moieties having substituents replacing a hydrogen on one or more carbons of the backbone. It will be understood that "substitution" or "substituted with" includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, e.g., which does not spontaneously undergo transformation such as by

rearrangement, cyclization, elimination, etc. As used herein, the term "substituted" is contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and non-aromatic substituents of organic compounds. The permissible substituents can be one or more and the same or different for appropriate organic compounds. For purposes of this invention, the heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms. Substituents can include any substituents described herein, for example, a halogen, a hydroxyl, a carbonyl (such as a carboxyl, an alkoxycarbonyl, a formyl, or an acyl), a thiocarbonyl (such as a thioester, a thioacetate, or a thioformate), an alkoxyl, a phosphoryl, a phosphate, a phosphonate, a phosphinate, an amino, an amido, an amidine, an imine, a cyano, a nitro, an azido, a sulfhydryl, an alkylthio, a sulfate, a sulfonate, a sulfamoyl, a sulfonamido, a sulfonyl, a heterocyclyl, an aralkyl, or an aromatic or heteroaromatic moiety. It will be understood by those skilled in the art that substituents can themselves be substituted, if appropriate. Unless specifically stated as "unsubstituted," references to chemical moieties herein are understood to include substituted variants. For example, reference to an "aryl" group or moiety implicitly includes both substituted and unsubstituted variants.

The term "sulfate" is art-recognized and refers to the group -OSO3H, or a

pharmaceutically acceptable salt thereof.

The term "sulfonamide" is art-recognized and refers to the group represented by the general formulae

wherein R ⁹ and R ¹⁰ independently represents hydrogen or hydrocarbyl, such as alkyl, or R ⁹ and R ¹⁰ taken together with the intervening atom(s) complete a heterocycle having from 4 to 8 atoms in the ring structure.

The term "sulfoxide" is art-recognized and refers to the group -S(O)-R ¹⁰ °, wherein R ¹⁰⁰ represents a hydrocarbyl.

The term "sulfonate" is art-recognized and refers to the group SO3H, or a

pharmaceutically acceptable salt thereof.

The term "sulfone" is art-recognized and refers to the group -S(0)2-R ¹⁰⁰ , wherein R ¹⁰⁰ represents a hydrocarbyl.

The term "thioalkyl", as used herein, refers to an alkyl group substituted with a thiol group. The term "thioester", as used herein, refers to a group -C(O)SR ¹⁰ ° or -SC(O)R ¹⁰ ° wherein R ¹⁰⁰ represents a hydrocarbyl.

The term "thioether", as used herein, is equivalent to an ether, wherein the oxygen is replaced with a sulfur.

The term "urea" is art-recognized and may be represented by the general formula

wherein R ⁹ and R ¹⁰ independently represent hydrogen or a hydrocarbyl, such as alkyl, or either occurrence of R ⁹ taken together with R ¹⁰ and the intervening atom(s) complete a heterocycle having from 4 to 8 atoms in the ring structure.

"Protecting group" refers to a group of atoms that, when attached to a reactive functional group in a molecule, mask, reduce or prevent the reactivity of the functional group. Typically, a protecting group may be selectively removed as desired during the course of a synthesis. Examples of protecting groups can be found in Greene and Wuts, Protective Groups in Organic Chemistry, 3 ^rd Ed., 1999, John Wiley & Sons, NY and Harrison et al., Compendium of Synthetic Organic Methods, Vols. 1-8, 1971-1996, John Wiley & Sons, NY. Representative nitrogen protecting groups include, but are not limited to, formyl, acetyl, trifluoroacetyl, benzyl, benzyloxycarbonyl ("CBZ"), tert-butoxycarbonyl ("Boc"), trimethylsilyl ("TMS"), 2-trimethylsilyl-ethanesulfonyl ("TES"), trityl and substituted trityl groups, allyloxycarbonyl, 9-fluorenylmethyloxycarbonyl ("FMOC"), nitro- veratryloxycarbonyl ("NVOC") and the like. Representative hydroxylprotecting groups include, but are not limited to, those where the hydroxyl group is either acylated (esterified) or alkylated such as benzyl and trityl ethers, as well as alkyl ethers, tetrahydropyranyl ethers, trialkylsilyl ethers (e.g., TMS or TIPS groups), glycol ethers, such as ethylene glycol and propylene glycol derivatives and allyl ethers.

III. Applications

As elaborated on in more detail below, the compounds (e.g., inhibitors) described herein are useful in a number of in vitro and in vivo applications. For example, the compounds (e.g., inhibitors) described herein can be used to treat bacterial infections, such as Mycobacterium tuberculosis infections. Methods for Treatment

Also featured herein are therapeutic methods for treating subjects with a variety of infections, such as tuberculosis infections. The methods comprise administering to the subject an inhibitor of a two-component regulatory system (e.g., DosRST), such as any of those described herein, in an amount effective to treat the infection. In some embodiments, the bacteria infecting the subject are identified as expressing one or both of DosS or DosT, DosRST, or DosRST regulon.

In some embodiments, the methods include receiving the results of a test determining that the bacteria infecting the subject are identified as bacteria in which the two-component regulatory system (e.g., DosRST) is conserved and, in view of this information, ordering administration of an effective amount of one or more of the inhibitors described herein to the subject. For example, a physician treating a subject can request that a third party (e.g., a CLIA-certified laboratory) to perform a test to determine whether the bacteria infecting the subject are bacteria in which the two-component regulatory system (e.g., DosRST) is conserved. The laboratory may provide such information, or, in some embodiments, provide an expression score or value, or a positive or negative result. If the bacteria have the conserved two-component regulatory system (e.g., DosRST), or if the bacteria are identified as tuberculosis, the physician may then administer to the subject one or more of the inhibitors described herein. Alternatively, the physician may order the administration of the inhibitor to the subject, which administration is performed by another medical professional, e.g., a nurse.

In some embodiments, the method can include: requesting a test, or the results of a test, which determines that the bacteria infecting the subject are Mycobacterium tuberculosis or bacteria in which the two-component regulatory system (e.g., DosRST) is conserved; and administering or ordering administration of an effective amount of an inhibitor described herein to the subject.

A "subject," as used herein, can be any mammal. For example, a subject can be a human, a non-human primate (e.g., monkey, baboon, or chimpanzee), a horse, a cow, a pig, a sheep, a goat, a dog, a cat, a rabbit, a guinea pig, a gerbil, a hamster, a rat, or a mouse. In some embodiments, the subject is an infant (e.g., a human infant). As used herein, a subject "in need of prevention," "in need of treatment," or "in need thereof," refers to one, who by the judgment of an appropriate medical practitioner (e.g., a doctor, a nurse, or a nurse practitioner in the case of humans; a veterinarian in the case of non-human mammals), would reasonably benefit from a given treatment.

The term "preventing" is art-recognized, and when used in relation to a condition, is well understood in the art, and includes administration of a composition which reduces the frequency of, or delays the onset of, symptoms of a medical condition in a subject relative to a subject which does not receive the composition. For example, treatment with an inhibitor described herein may delay the onset of, and/or reduce the severity of symptoms upon onset of, a Myobacterium tuberculosis infection in a subject who has been exposed to

Myobacterium tuberculosis. Exposure to a bacterial infection, such as Myobacterium tuberculosis, can be, e.g., close quarters exposure to an infected individual or exposure to bodily fluids (e.g., sputum, saliva, etc.) from an infected individual.

As used herein, "latent tuberculosis" refers to the presence of ^' Myobacterium tuberculosis in one or more cells of the infected individual (e.g., has a positive tuberculosis skin test), but the individual does not have an active infection (exhibits one or more signs or symptoms of a TB infection, such as cough, fever, night sweats, weight loss, fatigue, flu-like symptoms, chest pain, shortness of breath, blood in the sputum, etc.).

As used herein, "MDR tuberculosis" or "multi-drug resistant tuberculosis" refers to a form of tuberculosis that is resistant to two or more of the primary drugs (isoniazid and rifampicin) used for the treatment of tuberculosis. As used herein, "XDR tuberculosis" or "extensively multi-drug resistant tuberculosis" refers to a form of tuberculosis resistant to at least isoniazid and rifampicin among the first-line anti-TB drugs, is resistant to any fluoroquinolone and at least one of three injectable second-line drugs, such as amikacin, kanamycin or capreomycin.

The inhibitor compositions can be administered to a subject, e.g., a human subject, using a variety of methods that depend, in part, on the route of administration. The route can be, e.g., intravenous injection or infusion (IV), subcutaneous injection (SC), intraperitoneal (IP) injection, or intramuscular injection (IM).

Administration can be achieved by, e.g., local infusion, injection, or by means of an implant. The implant can be of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, or fibers. The implant can be configured for sustained or periodic release of the composition to the subject. See, e.g., U.S. Patent Application Publication No. 20080241223; U.S. Patent Nos. 5,501,856; 4,863,457; and 3,710,795; EP488401; and EP 430539, the disclosures of each of which are incorporated herein by reference in their entirety. The composition can be delivered to the subject by way of an implantable device based on, e.g., diffusive, erodible, or convective systems, e.g., osmotic pumps, biodegradable implants, electrodiffusion systems, electroosmosis systems, vapor pressure pumps, electrolytic pumps, effervescent pumps, piezoelectric pumps, erosion- based systems, or electromechanical systems.

As used herein the term "effective amount" or ''therapeutically effective amount", in an in vivo setting, means a dosage sufficient to treat, inhibit, or alleviate one or more symptoms of the disorder being treated or to otherwise provide a desired pharmacologic and/or physiologic effect (e.g., modulate (e.g., enhance) an immune response to an antigen. The precise dosage will vary according to a variety of factors such as subject-dependent variables (e.g., age, immune system health, etc.), the disease, and the treatment being effected.

Suitable human doses of any of the compounds described herein can further be evaluated in, e.g., Phase I dose escalation studies. See, e.g., van Gurp et al. (2008) Am J Transplantation 8(8): 1711-1718; Hanouska et al. (2007) Clin Cancer Res 13(2, part 1):523- 531; and Hetherington et al. (2006) Antimicrobial Agents and Chemotherapy 50(10): 3499- 3500.

Toxicity and therapeutic efficacy of such compositions can be determined by known pharmaceutical procedures in cell cultures or experimental animals (e.g., animal models of infection). These procedures can be used, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Agents that exhibits a high therapeutic index is preferred. While compositions that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue and to minimize potential damage to normal cells and, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies generally within a range of circulating concentrations of the compounds that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. A therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the inhibitor which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid

chromatography. In some embodiments, e.g., where local administration is desired, cell culture or animal modeling can be used to determine a dose required to achieve a

therapeutically effective concentration within the local site. Suitable dosages are described herein.

In some embodiments of any of the methods described herein, an agent can be administered to a mammal in conjunction with one or more additional therapeutic agents. For example, in some embodiments, it may be advantageous to administer an inhibitor described herein in combination with at least one additional pharmaceutical (or therapeutic) agent (e.g., first-line or second-line antituberculosis drugs, and for patients with HIV or AIDS an HIV/ AIDS drug). The inhibitor may be administered either simultaneously with, or before or after, one or more other therapeutic agent(s). Alternatively, the compound of the present invention may be administered separately, by the same or different route of administration, or together in the same pharmaceutical composition as the other agent(s).

Suitable additional TB agents include first-line drugs (such as isoniazid, rifampicin, pyrazinamide, ethambutol and combinations thereof); second-line drugs (such as

streptomycin, kanamycin, amikacin, capreomycin, ofloxacin, levofioxacin, moxifioxacin, cycloserine, para-aminosaicylic acid, ethioamide, prothionamide, thioacetazone and combinations thereof); and other antituberculosis drugs (such as clofazimine, amoxicilin with clavulanate, imipenem, linezolid, clarithromycin, thioridazine and combinations thereof). Other potential additional TB agents include compounds such as bicyclic nitroimidazoles (e.g., (S)-6,7-dihydro-2-nitro-6-[[4-(trifluoromethoxy)phenyl]metho xy]-5H-imidazo[2, 1 -b][l ,3]oxazine (PA-824) and TBA-354, available from TB Alliance), bedaquiline (TMC-207), delamanid (OPC67683), oxazolidinone, 2-[(2S)-2- methyl- 1 ,4-dioxa-8-azaspiro[4.5]decan-8- yl]-8-nitro-6-trifluoromethyl-4H-l,3- benzothiazin-4-one (BTZ043), imidazopyridines (e.g.,Q201 , available from Quro Science Inc.), and combinations thereof.

Suitable therapeutic agents for adjunct therapy include human immunodeficiency virus (HIV) drugs, immunotherapeutic agents, (e.g., anti-interleukin 4 neutralizing antibodies, high-dose intravenous immunoglobulin, 16a- bromoepiandosterone (HE2000), RUTI® vaccine, DNA vaccine with HSP65, Ag85, MPT-64, and MPT-83, dzherelo (plant extracts from the Ukraine), cytokines (such as Interleukin 2, Interleukin 7, Interleukin 15, Interleukin 27, Interleukin 12, Interferon γ), immunosuppressive agents (such as corticosteroids, thalidomide, and etanercept)), steroids, anti-inflammatory agents (e.g. prednisone), and other agents well-known to those of skill in art for use in improving the quality of care for patients being treated for the diseases, conditions, or disorders described herein.

Suitable HIV/ AIDS drugs include non-nucleoside reverse transcriptase inhibitors (N RTIs), such as efavirenz (Sustiva), etravirine (Intelence) and nevirapine (Viramune); Nucleoside reverse transcriptase inhibitors (NRTIs), such as Abacavir (Ziagen), and the combination drugs emtricitabine and tenofovir (Truvada), and lamivudine and zidovudine (Combivir); Protease inhibitors (Pis), such as atazanavir (Reyataz), darunavir (Prezista), fosamprenavir (Lexiva) and ritonavir (Norvir); Entry or fusion inhibitors, such enfuvirtide (Fuzeon) and maraviroc (Selzentry); and Integrase inhibitors, such as Raltegravir (Isentress).

Methods for diagnosing a subject has having tuberculosis are well known in the art and include, e.g., chest x-ray, testing of a sputum sample, tuberculin skin test, or a blood test (e.g., to test for the presence of microbial DNA or circulating anti-TB antibodies).

Likewise, methods for determining whether bacteria express DosS, DosT, DosRST, and/or DosRST regulon are known in the art and include, e.g., protein (e.g., Western blot, dot blot, or other immunoassays) and nucleic acid (e.g., RT-PCR) detection techniques.

The International Standards for Tuberculosis Care describes a widely accepted level of care that all practitioners, public and private, should follow in dealing with people who have, or are suspected of having, tuberculosis. The Standards are intended to facilitate the effective engagement of all care providers in delivering high-quality care for patients of all ages, including those with sputum smear-positive, sputum smear- negative, and

extrapulmonary tuberculosis; tuberculosis caused by drug resistant Mycobacterium tuberculosis complex (M tuberculosis) organisms; and tuberculosis combined with human immunodeficiency virus (HIV) infection, all of which are amenable to treatment using one or more of the inhibitors described herein.

Another aspect of the disclosure is a product comprising an inhibitor described herein and at least one other therapeutic agent (or pharmaceutical agent) as a combined preparation for simultaneous, separate or sequential use in therapy to treat a subject having sputum smear-positive, sputum smear-negative, and extrapulmonary tuberculosis; tuberculosis caused by drug resistant Mycobacterium tuberculosis complex (M tuberculosis) organisms; or tuberculosis combined with human immunodeficiency virus (HIV) infection.

Embodiments of the present invention are illustrated by the following Examples. It is to be understood, however, that the embodiments of the invention are not limited to the specific details of these Examples, as other variations thereof will be known, or apparent in light of the instant disclosure, to one of ordinary skill in the art.

Examples

Example 1. Materials and Methods

Bacterial strains and growth conditions

Mtb strains CDC 1551 and Erdman were used as indicated. DC\55 \{AdosR) and Erdman^dasR) mutants were constructed using gene replacement by homologous recombination (Sander, P., B, S. & Bottger, E. Gene Replacement in Mycobacterium tuberculosis and Mycobacterium bovis BCG Using rpsL as a Dominant Negative Selectable Marker, 93-104 (Humana Press, Totowa, NJ, 2001)) using methods as previously described (Abramovitch, R.B. et al. Mol Microbiol 80, 678-94 (2011)). Deletions were confirmed by PCR and transcriptional profiling. All strains were cultured at 37°C and 5% CO2 in standing, vented tissue culture flasks in 7H9 Middlebrook medium supplemented with 10% OADC and 0.05% Tween-80. For ifos overexpression strains, the dosT gene was cloned under the control of the strong hsp60 promoter in the pVV16 vector and transformed into CDC 1551. dosT (G85L) and and dosT(G115L) mutants were generated using the QuickChange site directed mutagenesis approach (Agilent) in pVV16 and confirmed by sequencing. High-throughput screening assay and data analysis

The HTS was conducted against two compound collections, the 211,655 compound ICCB-Longwood collection and the 328,633 compound NIH Molecular Libraries Program (MLP) collection, both provided by the ICCB at Harvard Medical School. The compounds were arrayed in 384-well clear bottom, black sided microtiter plates (Corning) at a final screening concentration of ~ 10 μΜ. Two columns of each plate were left blank for positive and negative controls of 0.3 μΜ rifampicin and DMSO alone, respectively. The M

tuberculosis CDC 1551 (hspX ': :GFP) fluorescent reporter was grown to mid- to late-log phase in vented T-150 standing flasks in Middlebrook 7H9 (OADC) medium (buffered to pH 7.0 with 100 mM MOPS). The cultures were then re-suspended in 7H9 (OADC) pH 7.0 medium and dispensed into the 384-well assay plates utilizing a Cy-Bio Selma liquid handler robot to an OD595 of 0.05. The plates were then placed in a Ziploc bag with a moistened paper towel (to limit evaporation) and incubated for 6 days at 37°C. Fluorescence and optical density (OD) readings were made on an EnSpire plate reader (Perkin Elmer, Inc.) at excitation and emission wavelengths of 488 and 509 nm as a top read, with the OD being taken at 595 nm as a bottom read.

Data analysis was performed utilizing an in-house developed computational tool written in Python. Raw fluorescence and optical density measurements were exported from the EnSpire plate reader (Perkin Elmer, Inc.) in plate format as comma-separated files.

Measurements were then normalized as a function of percent inhibition compared to the negative (DMSO) control (see equation below).

The normalized percent inhibition (NPI) for fluorescence or optical density was calculated by subtracting the overall mean of the negative controls within the run fi _nk ) from the measured value (β), divided by the dynamic range and multiplied by 100. The overall means for the positive and negative controls within the run fi _nk , Ji _pk ) are determined if there exists at least one plate in the run with a Z' greater than or equal to 0.5 ⁶⁰ . ijk represents the z ^' th value in the y ^' th plate within the Ath run. σ represents the standard deviation. Potential inhibitors of the DosRST regulon were defined as compounds with greater than 35% fluorescence inhibition, limited growth inhibition, and at least 1.5-fold selectivity in the fluorescence to growth inhibition ratio. To determine the statistical significance of the 1.5 fold selectivity cutoff, Z- scores were calculated for each experimental compound fluorescence inhibition:growth inhibition ratio relative to the negative controls and P-values were derived by testing against the null distribution. Due to the high number of tests, each P-value was false-discovery rate corrected (Fig. 7, Panel C). These "class 1" compounds may be directly or indirectly inhibiting DosRST signaling. The Z-factors of the screens were 0.90 and 0.89 for the ICCB-L and MLP library screens, respectively (Zhang, J.H. et al. J Biomol Screen 4, 67-73 (1999)).

For GFP quenching assays, the CDC 1551 (hspX ': :GFP) reporter was grown under GFP-inducing conditions, aliquoted into 96 well plates, treated with a dose response of HC101 A- HC106A and then the plates were immediately read for GFP fluorescence. GFP quenchers cause an inhibition of GFP fluorescence and none of the compounds exhibited GFP quenching activity. Cytotoxicity assays were conducted against three eukaryotic cells, primary C57B1/6 murine derived macrophages (BMDMs), TFQ and J774 cells.

Macrophages were prepared as previously described (Johnson, B.K. et al. Methods Mol Biol 1285, 329-41 (2015)) and seeded in white, opaque, 96 well plates (Corning) and treated for three days with the compounds treated with a 8-point dose response curve ranging from 400 μΜ to 0.65 μΜ. Following 3 days, viability was determined using the CellTiter-glo luminescent cell viability assay (Promega). Percent inhibition was normalized to a triton X- 100 positive control and a DMSO negative control. EC50s were calculated using the GraphPad Prism software package (version 6). Each experiment included two technical replicates per plate and two biological replicates and error bars represent the standard deviation of the biological replicates. The experiment was repeated at least twice.

EC50 determinations for HC101 A-HC106 compounds were performed in clear bottom, black, 96 well plates (Corning), following methods similar to those described above for the HTS. Briefly, 200 μΐ, of the CDC1551( ? '::GFPj reporter was inoculated into each well at an initial OD of 0.05. The cells were treated for 6 days with compounds using an 8- point dose response curve ranging from 400 μΜ to 0.65 μΜ. The plates were then read for GFP fluorescence and optical density and percent inhibition was normalized to a rifampin positive control and DMSO negative control. EC50s were calculated using the GraphPad Prism software package (version 6). Each experiment included two technical replicates per plate and two biological replicates and error bars represent the standard deviation of the biological replicates. The experiment was repeated at least twice.

Transcriptional profiling and data analysis

CDC 1551 or DC\55 l(AdosR) cultures were treated with 40 μΜ artemisinin, HC102A, HC103A or DMSO (as a negative control) and grown at 37°C without shaking in T-25 vented, standing tissue culture flasks in 8 mL of 7H9 medium seeded at an initial OD of 0.1. The experiments were performed with two biological replicates. Following 6 days of incubation, total bacterial RNA was extracted and sequenced as described by Baker, Johnson and Abramovitch (Baker, J.J. et al. Mol Microbiol 94, 56-69 (2014). RNA-seq data was analyzed using the SPARTA software package (Johnson, B.K. et al. BMC Bioinformatics 17, 66 (2016)v). The transcriptional profiling data have been submitted to the NCBI GEO database (accession no. GSE76566).

Real Time PCR assays

For the NO and vitamin C sensitivity assays, CDC 1551 was seeded at an initial density of 0.6 OD and treated with 80 μΜ DHA, HC102A, or HC103A for 24 hours, and then induced with 50 μΜ DETA-NONOate or 2 mM vitamin C for 2 hours. After treatment, total bacterial RNA was extracted as previously described (Rohde, K.H. et al. Cell Host Microbe 2, 352-64 (2007)). Transcripts of representative genes from the dosR regulon, including dosR, hspX, and tgsl, were quantified by RT-PCR using gene-specific primers as previously described (Abramovitch, R.B. et al. Mol Microbiol 80, 678-94 (2011)). The experiment included three biological replicates and error bars represent the standard deviation from the mean. The experiment was repeated twice with similar results. For the artemisinin resistance assays, CDC 1551 was seeded at an initial density of 0.1 and treated with 0.025 μΜ - 20 μΜ artemisinin for six days at 37 °C. Total RNA was extracted and RT-PCR quantification of DosR-regulated genes (dosR, hspX and tgsl) was conducted as described above. The experiment was repeated with three biological replicates with similar results. EC50s were calculated using the GraphPad Prism software package (version 6).

Triacylglycerol accumulation analysis

CDC 1551 cultures were seeded at a density of 0.1 OD in 8 mL of 7H9 medium and treated with 40 μΜ of artemisinin, HC102A, HC103A or DMSO. The cultures were radiolabeled by addition of 80 μθ of [! ,2- ¹⁴ C] sodium acetate to the culture, which was then grown at 37°C in vented, standing, T-25 tissue culture flasks. Total lipid was extracted after 6 days incubation and analyzed in thin-layer chromatography (TLC), as previously described (Abramovitch, R.B. et al. Mol Microbiol SO, 678-94 (2011)). Total extractable lipid ⁱ⁴ C incorporation was determined in scintillation counter, and 20,000 cpm was loaded for analysis in a 100-cm ² high-performance TLC silica gel 60 aluminum sheet. To analyze triacylglycerol (TAG), the lipids were resolved in hexane-diethyl ether-acetic acid (80:20: 1 [vol/vol/vol]} solvent system. The TLC was exposed to a phosphor screen for three days, imaged on a Typhoon imager and quantified by ImageJ (Schneider, C. A. et al. Nat Methods 9, 671-5 (2012)). The experiment was repeated with two biological replicates with similar results.

NRP survival and antibiotic tolerance assays

The hypoxic shift down assay was used as a model for NRP and performed as previously described (Mak, P.A. et al. ACS Chem Biol 7, 1190-7 (2012)). CDC1551 or Erdman cultures were pelleted and resuspended in Dubos medium at OD of 0.25, and inoculated in 24-well plates (1 mL/well). In the experiments presented in Fig. 3, Panel B, cells were treated with 40 μΜ artemisinin, HC102A or HC103A or equal volume of DMSO, and incubated in an anaerobic chamber (BD GasPak™) for 12 days. Cultures become anaerobic within 48 hours incubation as indicated by methylene blue turning to colorless, and consequently day 0 is considered after 48 hours of incubation. Bacteria were plated on solid medium to enumerate CFUs at day 0 and day 10. Percent viability was determined by comparing surviving bacteria at day 10 relative to day 0. Experimental conditions were examined with three biological replicates and error bars represent the standard deviation from the mean. The dose response experiments (Fig. 3, Panel C and Fig. 10, Panel B) were performed as described above with Mtb CDC 1551 using an 8-point dose response covering 1-100 μΜ and a DMSO control. CFUs were enumerated at day 10 and day 15 and percent viability was determined relative to the DMSO control at day 10 or day 15. The INH tolerance assays (Fig. 3, Panel D and Fig. 10, Panel C) were performed as described above with the following modifications. Mtb Erdman was pretreated with 20 or 40 μΜ artemisinin, HC102A or HC103A for 2 days in the hypoxic shift down assay and then the anaerobic chamber was opened and the cells were treated again with 20 or 40 μΜ artemisinin, HC102A or HC103A (for a total treatment of 40 or 80 μΜ). The cells were also treated with 1, 5 or 25 μΜ INH or a DMSO control. The cells were incubated in the anaerobic chamber for 10 or 15 days and CFUs were enumerated by plating on solid medium. To quantify INH tolerance, percent viability at 1, 5 and 25 μΜ INH was measured relative to the 0 μΜ INH control (DMSO control). These experiments were repeated at least twice with similar results.

DosS and DosT protein purification

The dosS (Rv3132c) and dosT (Rv2027c) genes were amplified from Mtb genomic DNA by PCR and cloned into the expression vector pET15b (Novagen Darmstadt, Germany). The DosS E87L and Gl 17L substitutions and DosT G85L and Gl 15L mutants were generated using the QuickChange site directed mutagenesis approach (Agilent) and confirmed by sequencing. The resulting constructs were confirmed by DNA sequencing. DosS/T protein expression in E. coli BL21(DE3) and purification via Co ²⁺ column were performed as previously described (Podust, L.M. et al. Biochemistry 47, 12523-31 (2008)). Briefly, the His ₆ -DosS or His ₆ -DosT were expressed in E. coli BL21(DE3) supplemented with hemin (30 mg/L) and induced by isopropyl l-thio-P-D-galactopyranoside (IPTG, 1 mM) at 18°C for 20 h. Cell pellet was suspended in lysis buffer (50 mM sodium phosphate (pH 7.6), 10% glycerol, 200 mM sodium chloride, 1% Triton X-100, 0.5 mg/mL lysozyme, 0.1 mg/mL PMSF). The cell suspension was incubated with shaking at 37°C for 0.5 h and then sonicated. Soluble extract was applied to a Co ²⁺ column (Clontech) and washed with washing buffers (with or without 20 mM imidazole in 50 mM sodium phosphate (pH 7.6), 10% glycerol, 500 mM sodium chloride). The recombinant proteins were eluted with 200 mM imidazole in the same buffer. The fractions containing the purified proteins were pooled together and dialyzed in 20 mM Tris-HCl, pH 7.5.

UV- Visible spectroscopy assay and mass spectrometry

The absorption spectra of DosS (7.5 μΜ) and DosT (7.5 μΜ or 16.9 μΜ) were analyzed in a stoppered quartz cuvette by a DU800 spectrophotometer (Beckman Coulter). All reagents were degassed with argon in a sealed cuvette or vial prior to use. Proteins were also degassed, and then treated with 400 μΜ dithionite (DTN). The UV- Visible spectra were recorded before and after DTN treatment. Lastly, different concentration of artemisinin or equal volume of DMSO was added to the reaction. The kinetic changes in the absorption spectra were recorded for 2 h. For mass spectroscopy (MS) analysis, the proteins were subjected to pepsin digestion at 37°C for 30 min after the assay, and then analyzed by liquid chromatography MS (LC-MS). Sample analysis was carried out on Waters Xevo G2-XS QTof mass spectrometer (Milford, MA, USA) with an electrospray ionization positive mode. The parameters were: capillary voltage, 3 kV; sampling cone, 40 V; source temperature, 100 °C; desolvation temperature, 350 °C; cone gas flow, 25 L/Hr; desolvation gas flow, 600 L/Hr. Chromatographic separation was done in Waters ultra-performance liquid

chromatograph (ACQUITY UPLC) system equipped with a Waters BEH C18 column (1.7 μΜ, 100x2.1 mm). The column temperature was kept at 30 °C. Solvents were (A) 0.1% (vol) folic acid in water, and (B) acetonitrile. The flow rate was 0.2 mL/min with following gradient: A/B = 99/1 to A/B = 70/30 in 8 minutes, then A/B = 1/99 for 10 minutes, and A/B = 99/1 for last 2 minutes. The acquisition mass range was 200-2,000 Da. The retention time for heme and heme-artemisinin adducts was between 10-11 min. The experiment was repeated with at least two biological replicates with similar results.

DosS and DosT autophosphorylation assay

The in vitro phosphorylation assays were performed as previously described (Roberts, D M. et al. J Biol Chem 279, 23082-7 (2004)). Briefly, 4 μΐ. reaction contained 0.2 μg/μL purified DosS or DosT protein, 100 mM Tris-HCl, pH 8.0, 50 μΜ KC1 ₂ , 5 μΜ MgCl ₂ and 2.5 μθ/μί [γ- ³² Ρ] ATP (6000 Ci/mmol, PerkinElmer Life Science). The proteins were treated with a 9 or 10 point dose response curve of HC102A or HC103A and the reaction was incubated at RT for 1 hour. All aliquots were analyzed in 4-12% gradient SDS-PAGE (Bio- Rad), and blotted to PVDF membrane. The blot was exposed to phosphor screen overnight and quantified by ImageJ (Schneider, C.A. et al. Nat Methods 9, 671-5 (2012)). The experiment was repeated with three biological replicates with similar results.

Chemical Synthesis of HC102A (CCG-232500) andHC103A (CCG-257424)

Powdered samples of commercially sourced HC102A and HC103A were analyzed by mass spectroscopic and combustion analysis and found to have a molecular formula consistent with the reported structures. 2D- MR analysis confirmed HC102A to be the racemic (5S,9R)-7,7,9-trimethyl-l,3-diazaspiro[4.5]decane-2,4-dione (alpha) isomer. For HC102A synthesis (generating a compound designated CCG-232500), a mixture of 3,3,5- trimethylcyclohexan-l-one (1.1 g, 7.6 mmol) was treated with sodium cyanide (0.92 g, 18.8 mmol), and carbonic acid, diammonia salt (3.6 g, 37.5 mmol). EtOH (lOmL) and water (lOmL) were added and the resulting mixture was heated to 55 °C for 6 hours. The mixture was cooled and then diluted with cold water, treated with cone. HCl (2mL) and filtered. The collected solid was washed with water (2x) and triturated in hot methanol. The resulting solid was collected by filtration anddried under high vacuum overnight at room temp.

(5S,9R)-7,7,9-trimethyl-l,3-diazaspiro[4.5]decane-2,4-dio ne was obtained as a white solid (0.53g, 2.5 mmol, 32%). HPLC system A (t _R = 5.6 min). ¹ H MR (400 MHz, DMSO-d6) δ 10.63 (s, 1H), 8.09 (s, 1H), 1.83 (d, J= 9.3 Hz, 1H), 1.44 (dd, J= 13.3, 7.1 Hz, 2H), 1.32 (dd, J= 32.7, 13.7 Hz, 2H), 1.14 (t, J= 12.9 Hz, 1H), 0.96 (s, 3H), 0.92 - 0.62 (m, 7H). ESI-MS m/z 209.1 (M-H+). For HC103A synthesis (generating a compound designated CCG- 257424), first 3-amino-N-(3-hydroxyphenyl)benzamide was synthesized. To a solution of 3- aminobenzoic acid (1 g, 7.3 mmol), 3-aminophenol (0.88 g, 8.0 mmol) and HOBT (1.3 g, 8.7 mmol) in dry DMF cooled to 0 °C was added EDC (1.6 g, 8.75 mmol). The resulting solution was allowed to warm to room temperature and stirred overnight. The reaction was diluted with water and washed with satd. NaHCC>3, satd. NaCl solution and dried over MgS04. After filtration, the organic layer was concentrated in vacuo and purified by flash chromatography. (CombiFlash, QH^C^ MeOH gradient). 3-amino-N-(3-hydroxyphenyl)benzamide was obtained as an amorphous solid (0.24 g, 7.29 mmol, 14.4 % yield). ¾ NMR (400 MHz, DMSO-d6) (Rotomers) δ 10.18 (m, J= 51.4, 10.6 Hz, 1H), 9.90 (s, 1H), 9.35 (m, 2H), 8.25 (s, 1H), 7.95 (m, 1H), 7.83 - 7.34 (m, 2H), 6.82 - 6.32 (m, 2H). 5.2 (s, 2H). To synthesize CGC257424, to a solution of 3-amino-N-(3-hydroxyphenyl)benzamide (0.2 g, 0.87 mmol), EDC (0.20 g, 1.1 mmol), and HOBT (0.16 g, 1.0 mmol) in dry DMF cooled to 0 °C was added thiophene-2-carboxylic acid (0.12 g, 0.96 mmol) followed by catalytic DMAP. The resulting solution was allowed to warm to room temperature and stir overnight. The reaction was diluted with water and washed with satd. NaHCC>3, satd. NaCl solution and dried,

MgS04. The organic layer was filtered and concentrated in vacuo. Flash chromatography

(CH2Cl2/MeOH) was used to obtain N-(3-((3-hydroxyphenyl)carbamoyl)phenyl)thiophene-

2-carboxamide as a white solid (0.06 g, 0.17 mmol, 20.2 % yield). HPLC system A (t _R = 5.8 min). ¾ NMR (400 MHz, DMSO-d6) δ 10.04 (s, 1H), 9.62 (s, 1H), 8.91 (s, 1H), 8.13 (t, J = 1.9 Hz, 1H), 8.02 - 7.90 (m, 2H), 7.59 (d, J= 17.2 Hz, 2H), 7.50 (dd, J= 4.9, 1.2 Hz, 1H), 7.38 - 7.29 (m, 2H), 7.11 - 6.97 (m, 2H), 6.47 (dt, J= 8.3, 1.4 Hz, 1H). ESI-MS m/z 339.0 (M+H+). Starting materials were purchased from Fisher, Sigma-Aldrich Lancaster, Fluka or TCI-America and were used without purification. All reaction solvents were purchased from Fisher and used as received. Reactions were monitored by TLC using precoated silica gel 60 F254 plates. Silica gel chromatography was performed by flash chromatography using silica gel (220-240 mesh) obtained from Silicycle or via MPLC on a CombiFlash instrument. MR spectra were recorded on a Varian 400 MHz spectrometer. Chemical shifts are reported in δ (parts per million), by reference to the hydrogenated residues of deuterated solvent as internal standard CDCL3: δ = 7.28 (¾ NMR). Mass spectra were recorded on a Micromass LCT time-of-flight instrument utilizing the electrospray ionization mode. The purity of the compounds was assessed via analytical rpHPLC with a gradient of 10% acetonitrile/water to 90% acetonitrile/water over 6 minutes ("System A", C18 column, 3.5 um, 4.6x100mm, 254 nm μ).

Structural modeling of DosT and the G85L and G115L substituted proteins

Modeling of DosT was performed using the Molecular Operating Environment (MOE) software (Montreal, Canada). The structure for DosT (2VZW) was downloaded from the RCSB protein data bank. For DosT images, all of Chain B and its associated water molecules were deleted. For Chain A, all water molecules and the acetic acid were deleted. Heavy atoms were fixed and hydrogen atoms relaxed with energy minimization to a gradient of 0.001. Good parameters do not exist for the heme group. Sets were defined for the protein, heme, iron, and oxygen (O2 ligand). Carbon atoms making up the heme were colored yellow. The iron atom of the heme was colored green as a large sphere. The oxygen atoms of the oxygen group were hidden from view in all of the remaining MOE files and pictures.

Residues 85 and 115 were labeled and colored purple with heavy bonds. A "Molecular Surface" was created on the protein only. The surface was colored by electrostatics using Posson-Boltzmann to compute the electrostatic field. The iron atom of the heme can be seen down the narrow gorge.

Example 2. Results

Identification and validation of DosRST regulon inhibitors

A whole-cell phenotypic high throughput screen was conducted to identify small molecule inhibitors of DosRST. The COC\55 l(hspX'::GFP) fluorescent reporter strain was previously reported to exhibit DosR-dependent GFP fluorescence that is induced by hypoxia and NO (Tan, S. et al. PLoS Pathog 9, el003282 (2013)). Notably, the reporter is strongly induced under conditions of mild hypoxia {e.g. 2% O2) where Mtb is capable of robust growth (Tan, S. et al. PLoS Pathog 9, el003282 (2013)). dosR mutant strains grow well in rich medium until oxygen is almost fully consumed (Boon, C. et al. J Bacteriol 184, 6760-7 (2002); Leistikow, R.L. et al. J Bacteriol 192, 1662-70 (2010)), therefore, discovery of compounds that inhibit hypoxia-inducible reporter fluorescence, but leave growth unaffected, may be inhibitors of the DosRST pathway. To discover inhibitors of the DosRST regulon, the DC\55 \{hspX' : :GFP) reporter strain was used to screen a 540,288 compound library. The reporter strain was grown in rich medium with individual compounds (at a screening concentration of -10 μΜ) in 384-well plates and incubated for 6 days. Growth of Mtb causes the consumption of oxygen and promotes hypoxic conditions at the bottom of the well. GFP fluorescence and growth (as measured by optical density) were measured after 6 days incubation. For analysis of hits, fluorescence and growth inhibition were normalized at 100% or 0% inhibition based on rifampin and DMSO controls, respectively. The Z-factor for the screen was 0.9 and the variation of controls was limited (Fig. 7, Panels A and B) supporting that the screen was robust. Hits were then distinguished based on their ability to specifically inhibit reporter fluorescence or as general inhibitors of Mtb growth. Putative DosRST pathway inhibitors were defined as compounds that exhibit >1.5 fold higher fluorescence inhibition as compared to growth inhibition (p<0.0003, Fig. 7, Panel C) with at least 35% fluorescence inhibition (Class 1 inhibitors, Fig. 1, Panel A). Fresh powders of several putative DosRST inhibitors were obtained and tested in secondary assays to confirm activity, and exclude compounds with GFP quenching activity and eukaryotic cytotoxicity. Six distinct scaffolds named HC101-HC106 (Fig. 1, Panel B) were confirmed as inhibitors of reporter fluorescence, while exhibiting no GFP quenching activity and limited eukaryotic cytotoxicity {e.g. EC50 >70 μΜ for eukaryotic cytotoxicity in murine bone marrow derived macrophages, Fig. 14).

The most frequently identified scaffold from the primary screen was the first-line antimalarial natural product artemisinin (HCIOIA) and its analogs artemether, artesunate and dihydroartemisinin (DHA, Fig. 1, Panel A). This scaffold was identified as nine independent hits in the screen. Artemisinin and its analogs inhibit CDC1551(fop ': :GFP) reporter fluorescence with an EC50 ranging from 1.2-3.7 μΜ (Fig. 1, Panel C; Fig. 8, Panel A; and Fig. 14), while the growth inhibition EC50 is >80 μΜ, indicating a limited impact on growth. HC102A (diazospiro[4.5]decane small molecule (7,7,9-trimethyl-l,3-diazaspiro[4.5]decane- 2,4-dione)) was isolated as a singleton and inhibits dasR-dependent GFP fluorescence with an EC50 of 12.4 μΜ, while not inhibiting Mtb growth (e.g. a growth inhibition EC50 >80μΜ). HC103A (N-[3~[(3-hydroxyphenyl)carbamoyi]phenyl]ihiopheiUi-2-carbox ainide) and the analog HC103B inhibit dasR-dependent GFP fluorescence with an EC50 of 2.7 μΜ and 5.0 μΜ, respectively (Fig. 1, Fig. 8, Panel B) while not inhibiting growth (e.g. a growth inhibition EC5o >80μM). HC104A (6-bromo-2-[3-

(dimethylamino)propyl]benzo[de]isoqi!inoline-l,3-dione), HC105A (9-ethyl~3-[(4- propylsu] onylpiperazin-I-yl)rneihy].]carbazole,oxalic acid) and HC106A ( 1 -(2,4- dichlorophenyl)-3"( L2"Oxazol-5-yl)urea) inhibit dasR-dependent GFP fluorescence with EC50 of 2.8 μΜ, 12.7 μΜ and 6.9 μΜ respectively, while not inhibiting Mtb growth (e.g. a growth inhibition EC50 >80 μΜ; Fig. 8, Panel B; Fig. 14). Artemisinin, HC102A and HC103A were selected for proof-of-concept follow-up experiments characterizing their ability to inhibit dosRST signaling. Both HC102A and HC103A were regenerated by organic synthesis and confirmed to have the activity of the commercially sourced compounds, thus confirming the assigned structures as the active structures (Fig. 8, Panels C and D).

The DosRST regulon is strongly induced by hypoxia and nitric oxide and composed of -50 genes that are directly regulated by DosR (Park, H.D. et al. Mol Microbiol 48, 833-43 (2003)). An additional >100 genes are also differentially expressed in a dosR mutant, possibly due to weak binding by DosR or indirect consequences of misregulated DosR regulon genes (Galagan, J.E. et al. Nature 499, 178-83 (2013)). To investigate the inhibitory mechanism of the compounds, RNAseq-based transcriptional profiling was undertaken on CDC1551 treated with 40 μΜ artemisinin, HC102A, HC103A or a DMSO control. The cultures were grown in standing flasks where growth causes the consumption of oxygen, and following six days of treatment RNA was isolated, sequenced and analyzed (Johnson, B.K. et al. BMC Bioinformatics 17, 66 (2016)) (Tables 2-4; Tables 2-4 are provided here; Table 4 is not provided).

Table 2 A depicts downregulated gene expression tables of DMSO treated DosR mutant compared to DMSO treated WT (>2 fold, p<0.05). Table 2B depicts upregulated gene expression tables of DMSO treated DosR mutant compared to DMSO treated WT (>2 fold, p<0.05). Table 2C depicts downregulated gene expression tables of WT Mtb treated with HC101A compared to DMSO (>2 fold, p<0.05). Table 2D depicts upregulated gene expression tables of WT Mtb treated with HC101A compared to DMSO (>2 fold, p<0.05). Table 2E depicts downregulated gene expression tables of WT Mtb treated with HC102A compared to DMSO (>2 fold, p<0.05). Table 2F depicts upregulated gene expression tables of WT Mtb treated with HC102A compared to DMSO (>2 fold, p<0.05). Table 3A depicts downregulated gene expression tables of DosR mutant treated with HC101 A compared to DMSO (>2 fold, p<0.05). Table 3B depicts upregulated gene expression tables of DosR mutant treated with HC101A compared to DMSO (>2 fold, p<0.05). Table 3C depicts downregulated gene expression tables of DosR mutant treated with HC 102 A compared to DMSO (>2 fold, p<0.05). Table 3D depicts upregulated gene expression tables of DosR mutant treated with HC102A compared to DMSO (>2 fold, p<0.05). Table 3E depicts downregulated gene expression tables of DosR mutant treated with HC 103 A compared to DMSO (>2 fold, p<0.05). Table 2F depicts upregulated gene expression tables of DosR mutant treated with HC103A compared to DMSO (>2 fold, p<0.05).

Artemisinin caused the strong downregulation of well-characterized DosR regulon genes, including hspX,fdxA, tgsl, and dosRS (Park, H.D. et al. Mol Microbiol 48, 833-43 (2003)) (Fig. 2, Panel A). Real-time PCR confirms the RNA-seq data with hspX, tgsl and dosRS showing 51-, 166-, and 37-fold inhibition by artemisinin, respectively (Fig. 9, Panel A). Artemisinin inhibited 85 genes (>2-fold, p<0.05) that are also repressed in the

OC\55 l(AdosR) mutant, accounting for greater than two-thirds of the 125 downregulated genes in the COC\55 l(AdosR) mutant (Fig. 2, Panel B, Table 2). Notably, artemisinin also inhibited 157 genes that are not modulated in the OC\55 l(AdosR) mutant, suggesting the drug is also impacting DosRST-independent targets. HC102A and HC103A also inhibited DosRST regulon genes, however, in contrast to artemisinin, HC102A and HC103A showed greater specificity for inhibition of the DosRST regulon; for example, 48 out of 55 genes downregulated by HC102A and 76 out of 90 genes downregulated by HC103A are also downregulated in the OC\55 l(AdosR) mutant (Fig. 2, Panels B and C, Fig. 9, Panels C and D, Table 2). These transcriptional profiles demonstrate that artemisinin, HC102A and HC103A inhibit induction of the core DosRST regulon. To further assess the specificity of the compounds for inhibition of the DosRST pathway, a OC\55 l(AdosR) mutant was treated with the compounds of interest, with the hypothesis that compounds specific for the DosRST pathway will not modulate gene expression in the COCl55 \(AdosR) mutant. The COC\55 \(AdosR) mutant treated with HC102A or HC 103 A, exhibited only 0 and 13 downregulated genes, respectively, confirming the on-target specificity of HC102A and HC103A (Fig. 2, Panel C, Table 3). In contrast, the OC\55 l(AdosR) mutant treated with artemisinin exhibited 69 downregulated genes (Fig. 2, Panel C, Table 3), confirming substantial off-target activity for artemisinin. Overall, these data further support that artemisinin, HC102A and HC103A function to inhibit the core DosRST regulon, with HC102A and HC103A showing strong specificity for the intended target of the DosRST regulon.

The DosRST pathway is also induced by NO and vitamin C (Voskuil, M.I. et al. J Exp Med 198, 705-13 (2003); Kumar, A. et al. Proc Natl Acad Sci USA 104, 11568-73 (2007); Taneja, N.K. et al. PLoS One 5, el0860 (2010)) and it was examined if the inhibitors could suppress induction of the DosR pathway by these stimuli. CDC 1551 was pre-treated with DHA, HC102A or HC103A for 1 day prior to induction with NO or vitamin C. As markers for the DosR regulon, the expression of three strongly DosR regulated genes (dosR, tgsl and hspX) was monitored by real-time PCR. dosR, hspXand tgsl, were strongly up- regulated when Mtb was treated with vitamin C or DETA-NONOate (Fig. 9, Panel B). For example vitamin C caused a 4-, 14- and 52-fold induction of dosR, hspX and tgsl, respectively, and NO caused an 491-, 373-, and 47-fold induction of dosR, hspX and tgsl, respectively. Pre-treatment with HC102A or HC103A strongly inhibited the induction of dosR, hspX and tgsl transcripts in response to both vitamin C and DETA-NONOate. For example, in HC102A and HC103A pretreated cells the tgsl transcript following treatment with DETA-NONOate is repressed 3-fold and 50-fold, respectively, whereas tgsl is induced >47-fold in the DMSO pretreated cells. Similarly, in vitamin C treated cells, the tgsl transcript is repressed 2-fold and 3-fold and in HC102A and HC103A pretreated cells, respectively, while induced >50 fold in the DMSO treated cells. Notably, DHA only weakly inhibited the induction of the DosR regulated genes by NO or vitamin C. In DHA pretreated cells, the dosR, hspX and tgsl transcripts remain induced by both Vitamin C and DETA- NONOate treatments. Notably, the magnitude of the induction of the transcripts in response to DETA-NONOate is significantly reduced ~2-fold in DHA pretreated cells compared to the DMSO treatment, demonstrating partial inhibition of NO-dependent DosRST signaling by DHA. These data support that HC102A and HC103A act as broad inhibitors of the DosRST regulon in response to both hypoxia and redox environmental cues. In contrast, artemisinin likely acts by a mechanism that is distinct from HC102A and HC103A, given its limited effectiveness to inhibit redox-mediated stimulation of the DosRST regulon.

Artemisinin, HC102A and HC103A disrupt persistence-associated physiologies

DosRST is required for several persistence-associated physiologies during hypoxia, including triacylglycerol (TAG) synthesis (Wayne, L.G. et al. Annu Rev Microbiol 55, 139- 63 (2001); Mehra, S. et al. Am J Respir Crit Care Med 191, 1185-96 (2015); Johnson, B.K. et al. BMC Bioinformatics 17, 66 (2016)) and survival (Leistikow, R.L. et al. J Bacteriol 192, 1662-70 (2010)). It was hypothesized that artemisinin, HC102A or HC103A may target these physiologies and compared the activity of the inhibitors to a COC\55 l(AdosR) mutant.

Transcriptional profiling data in CDC 1551 showed that the tgsl gene, which encodes for the TAG synthase involved in last step of TAG synthesis, is downregulated -100 fold by artemisinin and -20 and -180 fold by HC102A and HC103A, respectively (Fig. 2; Fig. 8, Panel A; Table 2). Therefore, it was hypothesized that CDC1551 treated with artemisinin, HC102A or HC103A would be defective in TAG accumulation. To test this hypothesis, ^R elabeled lipids were isolated from DC\55 \{AdosR) mutant and WT CDC1551 treated with inhibitors or equal volume of DMSO. The lipids were analyzed by thin layer chromatography and quantified. TAG accumulated in the DMSO-treated cells, whereas it was reduced 82% in the CT)C\55 l(AdosR) mutant (Fig. 3, Panel A; Fig. 10, Panel A). Treatment with artemisinin, HC102A and HC103A caused a 74%, 67% and 56% reduction in TAG accumulation, respectively (Fig. 3, Panel A; Fig. 10, Panel A), thus providing functional evidence that the inhibitors are impacting persistence-associated lipid metabolism.

During RP, the AdosR mutant has previously been shown to exhibit reduced intracellular survival as compared to WT bacteria (Leistikow, R.L. et al. J Bacteriol 192, 1662-70 (2010)). Using the hypoxic shift down model of NRP (Mak, P.A. et al. ACS Chem Biol 7, 1190-7 (2012)), the impact of DHA, HC102A or HC103A on survival during NRP was examined. Following 10 days of incubation in the hypoxic shift down assay, CDC 1551 treated with 40 μΜ DHA, HC102A or HC103A, exhibited significantly reduced survival (70-80%) reduction) as compared to the DMSO control (Fig. 3, Panel B). This reduction in survival is comparable to the COCl55 l(AdosR) mutant relative to the DMSO treated WT control. The survival defect of the COC\55 l(AdosR) mutant was partially complemented in the OC\55 l(AdosR) complemented strain, indicating that the observed survival defect is dasR-dependent. The impact of the inhibitors in the Mtb Erdman strain was also examined, to ensure the observed physiologies are not unique to CDC1551 strain. Although minor differences between CDC 1551 and Erdman existed, it was observed that the inhibitors also significantly inhibited survival during RP in the Erdman strain (Fig. 3, Panel B). The function of the inhibitors was examined in the hypoxic shift down assay in a 8 point dose response covering 1 μΜ -100 μΜ and percent viability relative to the DMSO treated control was examined following 10 days and 15 days treatment. Artemisinin, HC102A and HC103A exhibited dose dependent inhibition of viability in the hypoxic shift down model with all three compounds causing an -50% reduction of viability at 10 μΜ following 10 or 15 days of incubation (Fig. 3, Panel C and Fig. 10, Panel B). Together, these data support that treatment of Mtb with these inhibitors copies the Mtb AdosR mutant phenotypes and reduces survival during NRP.

The DosR regulated gene tgsl has previously been shown to be required for Mtb tolerance to isoniazid (INH) during hypoxia (Baek, S.H. et al. PLoS Biol 9, el001065 (2011)). Because artemisinin, HC102A and HC103A strongly inhibit tgsl gene expression, it was hypothesized these compounds may sensitize Mtb to ΙΝΉ. Using the hypoxic shift down assay, Mtb Erdman was pretreated with either 20 μΜ or 40 μΜ of artemisinin, HC102A or HC103A and following two days, the cells were treated again with the experimental inhibitors (for a combined treatment of 40 μΜ or 80 μΜ) in addition to ΙΝΉ over a dose response (1 μΜ, 5 μΜ, 25 μΜ ΙΝΉ or a DMSO control). Following 10 and 15 days of INH treatment in the hypoxic shift down assay surviving bacteria were enumerated (Fig. 3, Panel D and Fig. 10, Panel C). At day 10, treatment with artemisinin, HC102A or HC103A alone at 40 μΜ or 80 μΜ causes a significant reduction of survival ranging from a 3 -fold to 30-fold decrease in surviving bacteria (Fig. 3, Panel D). Ten days post INH treatment, INH alone had minimal impact on Mtb survival, with -100% viability at 1 μΜ and 5 μΜ INH and -75% viability at 25 μΜ INH (Fig. 3, Panel E), supporting that Mtb is tolerant to INH in the hypoxic shift down assay. Treatment with 40 μΜ artemisinin, HC102A or HC103A caused a significant -30% reduction of Mtb viability in the presence of 5 μΜ INH (Fig. 3, Panel E) relative to cultures not treated with INH, supporting that the inhibitors inhibit INH tolerance. At day 15, similar trends were observed in reduction of Mtb survival and antibiotic tolerance in cultures treated with artemisinin, HC102A or HC103A (Fig. 10, Panels C and D). Notably, at day 15, treatment with 40 μΜ artemisinin or HC103A caused a -50% reduction of Mtb viability when treated with 5 μΜ INH (Fig. 10, Panel D), suggesting that the function of artemisinin and HC103A may be enhanced during longer periods of NRP. These data support that artemisinin, HC102A and HC103A reduce survival and INH tolerance during NRP.

Artemisinin directly modulates DosS/T activity by targeting sensor kinase heme

Artemisinin is a first-line drug for treating malaria (O'Neill, P.M. et al. Molecules 15, 1705-21 (2010); Krishna, S. et al. Trends Pharmacol Sci 29, 520-7 (2008)) and the mechanism of action has been extensively studied (Taneja, N.K. et al. PLoS One 5, el0860 (2010); Mak, P.A. et al. ACS Chem Biol 7, 1190-7 (2012)). Evidence suggests that reductive cleavage of the artemisinin endoperoxide bridge is initiated by ferrous iron (Fe ²⁺ ) under reduced conditions, and generates a C4-centered radical (Meshnick, S.R. et al. Microbiol Rev 60, 301-15 (1996)). The radical form of artemisinin can alkylate heme and results in artemisinin-heme adduct formation (Selmeczi, K. et al. FEBS Lett 556, 245-8 (2004); Robert, A. et al. Acc Chem Res 35, 167-74 (2002)). Thus, it has been suggested that heme is both the trigger and target of artemisinin (Zhang, S. et al. Bioorg Med Chem 16, 7853-61 (2008); Meunier, B. et al. Acc Chem Res 43, 1444-51 (2010)). Because DosS/T are also heme- containing proteins, it was hypothesized that artemisinin interacts similarly with the heme in DosS/T leading to artemisinin-mediated inhibition of the DosRST regulon. Biochemical data suggests DosS is a redox sensor that autoxidizes quickly under aerobic conditions

(Ioanoviciu, A. et al. Biochemistry 46, 4250-60 (2007)), whereas, DosT is a hypoxia sensor and has high affinity and sensitivity to O2 (Cho, H.Y. et al. FEBS Lett 585, 1873-8 (2011)). Both kinases sense environmental cues via heme, and are inactive when the heme group exists as either the Met (Fe ³⁺ ) form (in the case of DosS) or the oxy (Fe ²⁺ -0 ₂ ) form (in the case of DosT) in the presence of O2; the kinases are activated when DosS is in ferrous form and DosT is in the deoxy form (Kumar, A. et al. Proc Natl Acad Sci USA 104, 11568-73 (2007); Ioanoviciu, A. et al. Biochemistry 46, 4250-60 (2007); Podust, L.M. et al.

Biochemistry 47, 12523-31 (2008); Cho, H.Y. et al. J Biol Chem 284, 13057-67 (2009); Sousa, E H. et al. Protein Sci 16, 1708-19 (2007)). A UV- Visible spectroscopy assay was employed to determine the interaction between DosS/T and artemisinin (Kumar, A. et al. Proc Natl Acad Sci USA 104, 11568-73 (2007)). DosS and DosT, purified under aerobic conditions, have Soret peaks at 409 nm and 412 nm, respectively (Kumar, A. et al. Proc Natl Acad Sci USA 104, 11568-73 (2007)) (Fig. 4, Panels A and B). Reduction of the heme by dithionite (DTN) shifts the DosS/T Soret peaks to 430 nm. Treatment of DosS with artemisinin (purged of O2) causes the Soret peak of DosS to gradually shift back to the original oxidized Soret peak. This supports that artemisinin can function to modulate DosS redox status. Notably, treatment of DosT with artemisinin reduces the amplitude of the Soret peak, a response that has previously been shown to be associated with artemisinin-mediated degradation of heme (Zhang, S. et al. Bioorg Med Chem 16, 7853- 61 (2008); Messori, L. et al. Bioorg Med Chem 14, 2972-7 (2006)). The position of the peaks did not shift to the oxidized state in the DMSO treated proteins. Dose-response studies further show that artemisinin inhibits DosT at 50 μΜ (Fig. 5, Panel D), whereas artemisinin only causes the shift of the reduced Soret peak of DosS at a much higher concentration of 400 μΜ (Fig. 11, Panel A). This suggests that DosT is more sensitive to artemisinin than DosS and may explain why the artemisinins had weaker activity for the inhibition of the DosR pathway when stimulated by NO or vitamin C. Because the DosS/T kinases are active in the reduced form and inactive in the oxidized form (Kumar, A. et al. Proc Natl Acad Sci USA 104, 11568-73 (2007)), these data are consistent with artemisinin inhibiting DosS/T kinases by modulating their redox status {e.g. DosS at high concentrations) or causing degradation of the heme {e.g. DosT). To test the hypothesis that artemisinin can alkylate heme carried by the sensor kinase, DosS reaction samples treated with artemisinin or DMSO were subjected to LC-MS analysis. Molecules with masses of -898 Da were identified in the artemisinin treated sample that are absent in the DMSO treated sample (Fig. 4, Panel C). This molecular weight corresponds to the sum of the masses of artemisinin (282 Da) and heme (616 Da), supporting that artemisinin alkylates the sensor kinase heme to form heme-artemisinin adducts (Robert, A. et al. Chem Commun (Camb), 414-5 (2002); Kannan, R. et al. Chem Biol 9, 321-32 (2002)). In a previous study, a structure of the artemisinin-alkylated heme with a mass of 898.3 was shown to involve alkylation of the heme at the α, β, or δ positions with the iron in the ferric state (Robert, A. et al. Chem Commun (Camb), 414-5 (2002)). The molecules observed in this study with a mass of 838 Da were also previously shown to be heme- artemisinin adducts that have lost an acetic acid molecule during mass spectrometry (Robert, A. et al. Chem Commun (Camb), 414-5 (2002)). Notably, adducts of DosS peptides were not observed. Together, these findings support a mechanism of action where artemisinin directly targets the heme to inactivate the DosS and DosT sensor kinases. The UV-visible spectra and mass spectrometry data support differing mechanisms for DosS and DosT inactivation by artemisinin, with DosS alkylated-heme remaining intact but in the ferric state (Robert, A. et al. Chem Commun (Camb), 414-5 (2002)) and the DosT heme being degraded by artemisinin (Zhang, S. et al. Bioorg Med Chem 16, 7853-61 (2008); Messori, L. et al. Bioorg Med Chem 14, 2972-7 (2006)). In both cases, these heme-artemisinin interactions would result in disabling the sensor functions of DosS/T.

Molecular modeling of DosS and DosT structures (Podust, L.M. et al. Biochemistry 47, 12523-31 (2008); Cho, H.Y. et al. JBiol Chem 284, 13057-67 (2009)) shows that the kinases have a channel through which the artemisinin may access and dock to the heme (Fig. 5, Panel A). To test this model, amino acid substitutions were generated along the channel in DosS/T, including E87L and Gl 17L in DosS or G85L and Gl 15L in DosT, that are predicted to limit the ability of artemisinin to access the heme based on modeling conducted in this study and published studies (Cho, H.Y. et al. FEBS Lett 585, 1873-8 (2011)). In the UV-visible spectroscopy assay, DosS (E87L) and DosS (Gl 17L) exhibited similar overall spectra as WT DosS under aerobic conditions and treatment with DTN caused the Soret peak to shift to the reduced position (Fig. 5, Panels B and C); thus, the heme in both mutant proteins retains the ability to respond to reduction by DTN. Notably, the DosS (E87L) and DosS (Gl 17L) proteins were resistant to oxidation by 400 μΜ artemisinin and the major Soret peak (430 nm) did not shift to the oxidized position following 60 minutes of treatment (Fig. 5, Panels B and C). The analogous mutations of DosT, G85L and Gl 15L, also exhibited similar overall spectrum as WT DosT under aerobic conditions, as well as in responding to DTN treatment (Fig. 5, Panels D and E and Fig. 11, Panel B). However, the lower peak at 560 nm of deoxy- DosT (Gl 15L) was maintained when treated with 100 μΜ artemisinin as compared to WT DosT and DosT (G85L) (Fig. 5, Panels D and E and Fig. 11, Panel B). The 560 nm peak is generated by merging two lower peaks at 538 nm and 575 nm together after DTN treatment, and is another signature of reduced penta-coordinated high-spin heme (Sivaramakrishnan, S. et al. Biosensors (Basel) 3, 259-282 (2013)). This peak is highly sensitive to oxygen or artemisinin treatment and disappears immediately upon exposure to oxygen or artemisinin (Kumar, A. et al. Proc Natl Acad Sci USA 104, 11568-73 (2007); Zhang, S. et al. Bioorg Med Chem 16, 7853-61 (2008); Messori, L. et al. Bioorg Med Chem 14, 2972-7 (2006)). Additionally, the Soret peak in the Gl 15L mutant is not reduced in a dose-dependent manner, as compared to the WT and G85L mutants (Fig 5, Panels D and E and Fig. 11, Panel B), further supporting the DosT (Gl 15L) protein exhibits artemisinin resistance.

The UV- visible spectroscopy data collectively support that DosS E87L and Gl 17L and DosT Gl 15L substitutions may limit artemisinin from fully accessing the heme, thereby providing resistance to artemisinin. To test this hypothesis in whole cells of Mtb, CDC 1551 was transformed with a replicating plasmid overexpressing the WT dosT, dosT (G85L) or dosT (G115L) genes and determined if artemisinin resistance is observed. The strains were grown in standing flasks to stimulate the DosRST regulon and expression of DosRST regulon genes (dosR, hspX, tgsl) was examined by real-time PCR following 6 days of treatment with artemisinin over a dose response curve (Fig. 12). Strains expressing WT dosT or dosT (G85L) exhibited ECso for artemisinin-mediated inhibition of DosR regulon genes of 0.2-0.3 μΜ whereas, dosT (G115L) exhibited ECso of 1.0-1.6 μΜ. (Fig. 5, Panel F and Fig. 12). Therefore, the DosT (Gl 15L) protein provides ~5 fold resistance to artemisinin and nearly full resistance at 1 μΜ artemisinin (Fig. 5F). These biochemical and biological data support that artemisinin modulates the DosRST signaling by directly targeting the heme sensor carried by DosS and DosT histidine kinases.

HC103A inhibits DosS and DosT autophosphorylation

UV- Visible spectroscopy studies showed that HC102A and HC103A have no impact on the redox status of DosS or DosT heme (Fig. 13), suggesting these compounds function by a mechanism that is distinct from artemisinin. Given the strong specificity with which these compounds inhibit the DosRST regulon, it was hypothesized that HC102A and HC103A may directly inhibit DosS/T autophosphorylation activity. To test this hypothesis, in vitro phosphorylation assays were performed as previously described (Roberts, D.M. et al. J Biol Chem 279, 23082-7 (2004)). DosS and DosT were quickly phosphoiylated within 30 seconds of initiating the assay by adding [γ- ³² Ρ] ATP. The amount of phosphoiylated protein increased over time consistent with previous reports (Roberts, D.M. et al. J Biol Chem 279, 23082-7 (2004); Saini, D.K. et al. Microbiology 150, 865-75 (2004); Saini, D.K. et al. FEBS Lett 565, 75-80 (2004)). DosS treated with HC102A and HC103A showed decreased autophosphorylation activity (Fig. 6). Inhibition of DosS autophosphorylation activity increased in a dose-dependent manner with ICsos of 1.9 μΜ and 0.5 μΜ for HC102A and HC103A, respectively. Notably, differences in maximal inhibition were observed, with -60% and -90% for HC102A and HC103A, respectively. DosT treated with HC103A also showed a dose-dependent inhibition of autophosphorylation and an ICso of -5 μΜ (Fig. 6). These findings support that HC103A functions by directly modulating DosS and DosT kinase activity.

Discussion

In this study a CDC1551(fop ': :GFP) fluorescent reporter strain was used as a synthetic phenotype for the targeted discovery of several compounds that inhibit the DosRST pathway. Biochemical studies of three prioritized compounds revealed distinct mechanisms of action, with artemisinin oxidizing and alkylating the heme group in the sensor kinases, and HC103A inhibiting sensor kinase autophosphorylation activity, without modulating heme redox status. Treatment of Mtb with these compounds copies several phenotypes of a

OC\55 l(AdosR) mutant, including: downregulation of the core DosRST regulon, reduced TAG synthesis, and decreased survival during NRP. These findings provide proof-of-concept data that the high throughput screen successfully identified inhibitors of the DosRST regulon and support further studies characterizing additional putative DosRST regulon inhibitors, including HC104-HC106, as well as uncharacterized putative hits from the primary screen. Several new chemical inhibitors of Mtb during NRP have been recently described. One promising target is the direct inhibition of ATP homeostasis by targeting the components of the electron transport chain or ATP synthase (Mak, P. A. et al. ACS Chem Biol 7, 1190-7 (2012); Koul, A. et al. J Biol Chem 283, 25273-80 (2008); Pethe, K. et al. Nat Med 19, 1157- 60 (2013); Li, W. et al. Antimicrob Agents Chemother 58, 6413-23 (2014)). However, the approach of targeting the DosRST top-level regulators has the potential to inhibit multiple physiologies required for establishing or maintaining NRP and this multifactorial approach may broadly limit persistence in heterogeneous NRP-inducing environments. Using homology modeling, Gupta et al. reported the discovery of a DosR regulon inhibitor that specifically inhibits DosR binding to target DNA (Gupta, R.K. et al. J Med Chem 52, 6324- 34 (2009)). Additionally, a screen for small molecules that modulate Esx-1 export, identified inhibitors that indirectly modulate the DosR regulon (Rybniker, J. et al. Cell Host & Microbe 16, 538-548 (2014)). However, the newly discovered compounds represent novel inhibitors of the DosRST regulon with distinct mechanisms of action.

Both HC102A and HC103A appear to be remarkably specific for inhibiting the DosRST pathway. Indeed, no genes were downregulated (>2-fold, p<0.05) in the

OC\55 l(AdosR) mutant treated with HC102A, supporting that only DosR controlled pathways are targeted by HC102A. HC103A treatment of the COC\55 l(AdosR) caused downregulation (>2-fold, p<0.05) of 13 genes. Several genes fell into related classes including: four arginine biosynthesis genes (argC, argB, argj and argF), two acyl-(ACP) desaturases (desAl and desA ), two ferroredoxins (fdxC and JprB), three PE-PPE genes (Rv0160c, Rvl386 and Rvl387), and an orphan response regulator (Rv0260c). This finding suggests that although HC103A is highly specific for the DosRST pathway other targets likely exist. It is notable that no inhibitors that target multiple two component regulatory pathways were identified. For example, HC101-HC106 were not identified in a similar screen aimed at finding inhibitors of the PhoPR regulon (Johnson, B.K. et al. Antimicrob Agents Chemother 59, 4436-45 (2015)). Inhibitors targeting all sensor histidine kinases would not be identified from this screen because at least one, MtrAB, is essential for growth (Zahrt, T.C. et al. JBacteriol 182, 3832-8 (2000)).

In contrast to HC102A and HC103A, artemisinin exhibits significant off-target activities, with 69 genes differentially regulated in the OC\55 l(AdosR) mutant treated with artemisinin. Given that artemisinin has a reactive endoperoxide bridge, it is perhaps surprising that there are not a greater number of genes that are differentially regulated, as one might expect artemisinin to react with any proteins carrying reduced iron. The downregulated genes do not match genes regulated by ROS (Boshoff, H.I. et al. J Biol Chem 279, 40174-84 (2004)), suggesting that artemisinin is not promoting Fenton reactions and acting as an indiscriminate oxidant. Miller and colleagues have shown that when artemisinin is delivered into Mtb as a mycobactin-artemisinin conjugate it causes an intracellular burst of reactive oxygen via Fenton reactions that kills Mtb (Miller, M.J. et al. J Am Chem Soc 133, 2076-9 (2011)). Based on this finding, it is tempting to speculate that artemisinin alone cannot fully access the Mtb cytoplasm and is thus modulating membrane-associated proteins, such as DosS/T. Other membrane proteins that may interact with artemisinin (e.g. heme-bearing cytochromes) may be resistant to artemisinin if the heme is buried in the protein and not accessible to artemisinin. Structural analysis of the heme-embedded GAF domain of DosST shows that DosT has a wider channel than DosS that could potentially provide greater accessibility to artemisinin (Podust, L.M. et al. Biochemistry 47, 12523-31 (2008); Cho, H.Y. et al. J Biol Chem 284, 13057-67 (2009)). This is supported by the data herein that DosT is more sensitive to artemisinin than DosS and is consistent with artemisinins having limited ability to inhibit NO-mediated stimulation of the DosR regulon. Alternatively, DosS may be less sensitive to artemisinin than DosT due to differences in autooxidation rates, where DosS is more quickly oxidized to the ferric state in the presence of oxygen (Kim, M.J. et al. J Bacteriol 192, 4868-75 (2010)). Autooxidized DosS in the ferric form would not react with artemisinin, resulting in the observed insensitivity. Collectively, it was shown herein that this channel is susceptible to drugs with artemisinin as a proof-of-concept, therefore structure- based synthesis of compounds that block the heme-bearing channel of DosS and DosT may promote the development of additional novel inhibitors of Mtb persistence. The discovery that artemisinin inhibits Mtb persistence raises interesting questions about the use of artemisinin to treat malaria in individuals co-infected with malaria and Mtb.

Incorporation by Reference

The contents of all references, patent applications, patents, and published patent applications, as well as the Figures, cited throughout this application are hereby incorporated by reference.

Equivalents

While the present disclosure has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the disclosure. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present disclosure. All such modifications are intended to be within the scope of the disclosure. Table 2A: Downregulated gene expression tables of DMSO treated DosR mutant compared to DMSO treated WT

Gene Counts per million (CPM) WT DMSO/DosR DMSO

WT_DMS01 WT_DMS02 Dos _DMS01 DosR_DMS02 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0038 22.1279311 12.8686451 3.512558319 5.150881219 0.250393046 -1.997733597 3.38036778 0.009459706 Rv0033 Rv0033 possible acyl carrier protein

MT0040 92.32688494 82.9955313 27.09687846 33.27469268 0.344561457 -1.537166766 5.87336991 0.001819859 Rv0035 fadD34 acyl-CoA synthase

MT0075 45.01889431 42.6544978 20.43018614 12.6711678 0.379012439 -1.399682898 4.90648668 0.034764592

MT0086 1,308.98 2,581.54 9.032292821 4.120704975 0.003412235 -8.195067471 9.93012145 4.85E-33 Rv0079 Rv0079 hypothetical protein

MT0087 357.0990261 867.404516 2.652339955 1.442246741 0.003414974 -8.193909753 8.26182025 4.86E-32 Rv0080 Rv0080 hypothetical protein

MT0091 130.8600063 129.987775 71.11138475 45.01870186 0.445691448 -1.165882815 6.55623613 0.04586184 Rv0084 hycD formate hydrogenlyase subunit 4

MT0175 278.8882351 151.387319 70.8246453 68.30068497 0.3240725 -1.625611493 7.14732831 0.004118518 Rv0166 fadD5 acyl-CoA synthase

MT0176 259.8124324 253.179748 87.74227312 73.03949569 0.31357103 -1.673135816 7.3935147 0.000781511

MT0178 564.2622431 404.422476 144.9467943 189.9644994 0.345884196 -1.531638997 8.34634202 0.006937962 Rv0169 mcel cell invasion protein

MT0179 438.3619455 306.967792 107.1688712 144.6367446 0.33804041 -1.564732377 7.95899111 0.004663194 Rv0170 Rv0170 part of mcel operon

MT0180 462.0159408 361.189612 116.8463278 166.7855339 0.344642164 -1.53682888 8.11016007 0.005838808 Rv0171 Rv0171 part of mcel operon

MT0181 579.1413692 479.031699 156.9181666 257.0289728 0.391221237 -1.353943409 8.52243103 0.034099178 Rv0172 Rv0172 part of mcel operon

MT0182 311.3170996 282.676417 76.84617384 122.590973 0.335714585 -1.57469288 7.62955686 0.004118518 RV0173 IprK part of mcel operon

MT0475 28.23218796 26.3156563 9.964196049 8.550462824 0.340744223 -1.553238897 4.1725818 0.025007583 RV0459 Rv0459 conserved hypothetical protein

MT0595 285.7555241 177.124609 20.00007696 15.96773178 0.077988598 -3.680592977 6.9516389 6.61E-15 Rv0569 Rv0569 conserved hypothetical protein

MT0596 2,911.35 1,704.88 39.92846906 37.1893624 0.016717814 -5.902469967 10.195018 2.73 E-28 Rv0570 nrdZ ribonucleotide reductase, class II

MT0597 248.3669508 416.423572 36.55928047 28.84493483 0.098381097 -3.345475053 7.50990205 9.20E-12 Rv0571c Rv0571c conserved hypothetical protein

MT0598 202.5850244 342.681897 10.03588091 8.962533322 0.034883115 -4.841327312 7.13641696 3.27E-22

MT0599 568.4589197 773.130846 17.41942187 27.09363521 0.033130208 -4.915708918 8.43464209 1.32E-21 Rv0572c Rv0572c hypothetical protein

MT0600 973.2474525 1,312.17 2.15054591 1.030176244 0.001438969 -9.44074926 9.15876849 7.94E-50

MT0601 94.23446521 88.4900089 7.813650139 7.932357078 0.086361819 -3.533462557 5.61425504 4.41E-16 Rv0573c Rv0573c conserved hypothetical protein

MT0602 380.3715053 345.718319 13.76349382 14.01039692 0.038294812 -4.706707252 7.55221244 2.87E-24 Rv0574c Rv0574c conserved hypothetical protein

MT1095 466.5941334 486.116683 238.0654322 156.9988596 0.414753404 -1.269674273 8.39570064 0.039405387 RV1065 RV1065 conserved hypothetical protein

MT1296 330.3929023 458.21052 177.4200376 115.8948274 0.371841482 -1.427240372 8.07907409 0.017194468 RV1257C RV1257C similar to many dehydrogenases

MT1297 207.163217 217.899417 43.94282142 42.95834937 0.20446722 -2.290058522 6.99533809 1.70E-07 Rvl258c Rvl258c probable multidrug resistance pump

MT1635 1,021.32 525.156393 345.3776731 224.3723859 0.368667553 -1.439607648 9.04576691 0.036001439 Rvl599 hisD histidinol dehydrogenase

MT1657 644.7621304 536.434531 284.0871147 171.3183094 0.38572261 -1.374364378 8.67544048 0.033703938 Rvl621c cydD ABC transporter

MT1773 155.2770338 225.562768 89.67776444 57.48383441 0.386124805 -1.372860856 7.04421147 0.022935127 Rvl732c Rvl732c conserved hypothetical protein

MT1774 1,426.87 1,750.86 4.372776683 2.678458234 0.002250709 -8.795404644 9.63579929 6.49E-49 Rvl733c Rvl733c possible membrane protein

MT1775 566.1698234 649.505098 52.04321102 11.43495631 0.052343645 -4.255841806 8.3182942 3.18E-09

MT1776 20.22035084 16.3388415 5.161310184 3.193546356 0.231999244 -2.107807993 3.44026242 0.003118061 Rvl735c Rvl735c hypothetical protein

MT1777 107.206011 191.872944 0.286739455 0.721123371 0.003281004 -8.251646766 6.22188263 1.05E-37

MT1778 5,668.95 3,546.69 10.75272955 5.665969341 0.001795059 -9.121752773 11.1717362 1.05 E-44 Rvl736c narX fused nitrate reductase

MT1779 2,028.90 1,469.34 6.738377184 5.562951717 0.003534852 -8.144134574 9.77581156 3.51E-46 RV1737C narK2 nitrite extrusion protein

MT1780 3,772.05 4,986.96 4.157722092 2.472422985 0.000768719 -10.34525576 11.0972462 4.44E-59 Rvl738 Rvl738 conserved hypothetical protein

MT1823 659.6412565 359.309922 211.7570873 154.0113485 0.359315519 -1.476676847 8.43312551 0.022917062 Rvl773c Rvl773c transcriptional regulator (IcIR family)

MT1860 242.64421 163.099232 62.7242557 48.93337158 0.275812553 -1.858239976 7.00905311 0.000243876 R l812c Rvl812c probable dehydrogenase

MT1861 2,999.86 1,583.42 10.53767496 7.726321829 0.004002567 -7.964858879 10.1663707 2.92E-38 Rvl813c Rvl813c conserved hypothetical protein

MT1882 80.11837123 75.9105469 33.04672215 33.68676317 0.428062862 -1.224105421 5.7946528 0.021630684 Rvl834 Rvl834 conserved hypothetical protein

MT1987 385.7127301 97.1655 74.7673128 59.54418689 0.278840296 -1.842489033 7.26040158 0.025007583 Rvl937 R«1937 similar to ring-hydroxylating dioxygenases

MT1988 152.2249053 35.7141049 29.03236978 20.08843676 0.263136796 -1.926115091 5.86465135 0.021403294 Rvl938 ephB probable epoxide hydrolase

MT2016 368.1629916 168.159935 83.79960562 65.82826198 0.279600125 -1.838563087 7.41576938 0.002724711 Rvl964 Rvl964 part of mce3 operon

MT2017 303.3052625 91.2372478 40.00015392 49.55147733 0.227583638 -2.135531255 6.90708944 0.002246518

MT2018 337.6417073 108.443638 53.69196288 58.41099303 0.251926888 -1.988922984 7.11488281 0.004118518 RV1966 mce3 cell invasion protein

MT2019 349.0871889 97.5992746 62.36583138 47.69716009 0.247093802 -2.016869274 7.11054156 0.007217261 Rvl967 Rvl967 part of mce3 operon

MT2020 398.6842759 112.781384 80.21536244 41.10403213 0.237814764 -2.072089814 7.29639671 0.009603969 Rvl968 Rvl968 part of mce3 operon

MT2021 101.4832702 40.0518505 27.31193305 12.87720305 0.286477895 -1.803504271 5.48197442 0.016676652 Rvl969 Rvl969 part of mce3 operon

MT2022 234.6323729 74.3200402 37.06107451 31.11132256 0.22160796 -2.173918395 6.54376541 0.000935379 Rvl970 IprM part of mce3 operon

MT2023 317.0398405 90.3696987 50.53782888 46.77000147 0.239555542 -2.061567906 6.9678295 0.004118518 Rvl971 Rvl971 part of mce3 operon

MT2048 2,083.08 798.434362 501.077197 316.5731597 0.283876924 -1.816662515 9.85171079 0.011300679 Rvl992c ctpG probable cation transport ATPase

MT2052 40,500.98 9,131.10 62.65257084 89.62533322 0.003068089 -8.34844373 13.6032098 7.05 E-24 Rvl996 Rvl996 conserved hypothetical protein

MT2053 3,166.58 1,679.72 29.10405465 26.16647659 0.011416583 -6.452725332 10.2576158 3.48E-30 R 1997 ctpF probable cation transport ATPase

MT2059 538.7006675 897.190368 68.74578425 49.55147733 0.082406364 -3.601100429 8.60078438 3.27E-12 Rv2003c Rv2003c conserved hypothetical protein

MT2060 2,717.54 2,771.24 163.4414891 230.656461 0.071792403 -3.800025009 10.5216697 1.07E-15 Rv2004c Rv2004c hypothetical protein

MT2061 2,440.18 2,227.00 91.25483144 124.9603784 0.046320465 -4.432206465 10.2527586 2.61E-20 Rv2005c Rv2005c conserved hypothetical protein

MT2062 602.7953645 816.508301 94.4806503 134.3349822 0.16113863 -2.633625696 8.68544794 1.81E-07 Rv2006 otsB trehalose-6-phosphate phosphatase

MT2063 7,680.30 9,830.05 47.45537974 62.32566275 0.006267929 -7.317795385 12.1047351 1.13E-41 Rv2007c fdxA ferredoxin

MT2086 332.3004826 194.620183 54.69555097 59.64720452 0.217342141 -2.201960166 7.31831837 1.34E-05 Rv2027c Rv2027c sensor histidine kinase

MT2087 792.4088431 718.909027 4.014352365 2.678458234 0.004488188 -7.799651114 8.5647231 2.00E-42 Rv2028c Rv2028c conserved hypothetical protein

MT2088 4,892.94 2,628.82 6.236583138 5.87200459 0.001615214 -9.274058907 10.8782427 1.82E-48

MT2089 14,539.96 14,668.81 6.451637729 3.914669727 0.000358657 -11.4451059 12.8344686 2.19E-69 Rv2030c Rv2030c conserved hypothetical protein

MT2090 46,354.20 44,251.51 9.032292821 10.91986818 0.000220144 -12.14926404 14.4675784 3.64E-80

MT2091 3,999.05 5,966.42 7.383540957 5.356916468 0.001286705 -9.602102615 11.2842649 4.29E-55 RV2032 RV2032 conserved hypothetical protein

MT2445.1 74.01411438 109.600371 18.85311914 39.76480301 0.317771865 -1.653936698 5.91799559 0.006970954

MT2446 80.88140334 101.069471 32.04313406 46.8730191 0.432413961 -1.209514992 6.02582456 0.035645827 Rv2378c mbtG mycobactin/exochelin synthesis (lysine hydroxyla

MT2447 228.1466 293.231598 121.5775288 103.8417654 0.432103481 -1.21055124 7.54425616 0.040809265 Rv2379c mbtF mycobactin/exochelin synthesis (lysine ligation)

MT2448 633.6981648 578.799846 213.2624694 222.3120334 0.359288996 -1.476783345 8.68553436 0.008161223 Rv2380c mbtE mycobactin/exochelin synthesis (lysine ligation)

MT2449 201.4404762 170.762583 80.71715648 33.17167505 0.306584243 -1.705644545 6.92070866 0.007058523 Rv2381c mbtD mycobactin/exochelin synthesis (polyketide

MT2489 207.163217 308.413708 62.86762543 62.9437685 0.243761345 -2.036458729 7.32357418 3.52E-05 Rv2416c Rv2416c conserved hypothetical protein

MT2556 807.2879692 426.255795 185.3770574 243.4306464 0.34782334 -1.52357335 8.69697564 0.02170976 Rv2483c Rv2483c possible transferase

MT2557 1,231.53 615.3815 271.9006879 344.4909359 0.33388514 -1.582576209 9.26490002 0.014560858 Rv2484c Rv2484c conserved hypothetical protein

MT2576 1,467.31 658.180589 394.7685442 396.9269068 0.372649095 -1.424110338 9.50913273 0.042258365

MT2577 473.0799063 238.865188 134.5524891 107.5503999 0.340574739 -1.553956663 7.89427969 0.011759403 RV2502C accDl acetyl/propionyl-CoA carboxylase, [beta] subunit

MT2579 611.1887177 294.243739 140.6457025 153.0841898 0.324744749 -1.622621899 8.22465824 0.009371108 Rv2504c scoA 3-oxo acid:CoA transferase, [alpha] subunit

MT2600 59,719.47 11,091.04 7,787.77 4,178.60 0.168994642 -2.564950587 14.3368479 0.004674557 Rv2524c fas fatty acid synthase

MT2684 186.9428662 175.24492 76.98954357 79.11753553 0.431182006 -1.213631121 7.01544962 0.028172861 Rv2609c Rv2609c conserved hypothetical protein

MT2686 241.8811779 186.956833 86.38026071 86.43178686 0.403439086 -1.309577233 7.22971648 0.01939155 Rv2611c Rv2611c conserved hypothetical protein

MT2687 217.0826344 190.427029 86.52363044 80.14771177 0.409326843 -1.288674814 7.16285946 0.018562405 Rv2612c pgsA CDP-diacylglycerol-glycerol-3-phosphate

MT2695 364.3478311 225.418176 134.1940648 78.29339453 0.360880071 -1.470408621 7.64454318 0.021403294

MT2698 43,651.54 22,787.33 92.68852871 59.64720452 0.002294397 -8.76766896 14.0229365 1.13E-41 Rv2623 Rv2623 conserved hypothetical protein

MT2699 2,493.21 1,896.75 8.960607958 7.417268956 0.003745743 -8.060532534 10.10408 1.10E-46 Rv2624c Rv2624c conserved hypothetical protein

MT2700 5,930.29 3,801.89 12.40148141 8.4474452 0.002152157 -8.86000071 11.250982 1.85 E-48 Rv2625c Rv2625c conserved hypothetical protein

MT2701 13,330.55 10,898.30 8.315444185 9.683656692 0.000742957 -10.39443406 12.5652855 4.67E-66 RV2626C RV2626C conserved hypothetical protein

MT2702 8,011.07 5,842.22 21.36208937 28.84493483 0.003622325 -8.108868104 11.7627405 2.04E-46 Rv2627c Rv2627c conserved hypothetical protein

MT2703 716.4871485 928.711319 33.19009187 31.21434019 0.039162393 -4.674387255 8.73761123 2.20E-21 Rv2628 Rv2628 hypothetical protein

MT2704 7,924.47 5,007.78 327.5998269 429.0684056 0.058511346 -4.095139792 11.7403054 2.59E-16 Rv2629 Rv2629 hypothetical protein

MT2705 781.7263936 580.679536 40.57363283 39.97083826 0.059162822 -4.079165319 8.49131437 1.04E-17 Rv2630 Rv2630 hypothetical protein

MT2707 1,151.80 503.323074 75.19742198 74.89381293 0.090752608 -3.461917083 8.81435422 2.85 E-10 Rv2631 Rv2631 conserved hypothetical protein

MT2797 738.6150796 774.142987 373.1914002 265.3734004 0.422157177 -1.244147853 9.07061229 0.042657862 Rv2725c hfIX GTP-binding protein

MT3004 1,541.71 986.981701 211.3986629 180.0748074 0.154875364 -2.690820423 9.51028601 5.23E-08 Rv2934 ppsD phenolpthiocerol synthesis (pksE)

MT3210 8.393353177 6.07284375 0.215054591 0.206035249 0.031757839 -4.976743426 1.7015464 4.50E-09

MT3212 16,224.35 10,456.71 28.6022606 30.39019919 0.00221177 -8.820582855 12.7064774 9.85 E-51 Rv3127 Rv3127 conserved hypothetical protein

MT3216 33,572.27 28,005.50 9.749141458 9.683656692 0.000316093 -11.6273646 13.9104897 2.79E-76 conserved hypothetical protein

MT3217 19,054.06 10,491.71 7.813650139 6.593127961 0.000489538 -10.99629141 12.8511309 8.37E-60 Rv3131 Rv3131 conserved hypothetical protein

MT3218 5,329.40 3,268.20 1,468.11 1,110.12 0.299909861 -1.737399134 11.4477977 0.002445427 Rv3132c Rv3132c sensor histidine kinase

MT3219 3,862.85 2,091.66 0.071684864 0.206035249 4.81962E-05 -14.34072209 10.5386559 1.04E-64 Rv3133c Rv3133c two-component response regulator

MT3220 6,333.93 3,965.28 80.71715648 43.67947274 0.012091382 -6.369877033 11.3469612 8.94E-28 Rv3134c Rv3134c conserved hypothetical protein

MT3233 146.8836806 228.165415 73.04687607 46.8730191 0.319475008 -1.64622502 6.95060923 0.003280598 Rv3145 nuoA NADH dehydrogenase chain A

MT3234 203.7295726 202.717308 60.78876438 79.0145179 0.343871913 -1.540056812 7.09060659 0.002953587 Rv3146 nuoB NADH dehydrogenase chain B

MT3235 149.554293 161.219542 58.27979416 57.38081678 0.372063645 -1.426378665 6.73366611 0.003086323 Rv3147 nuoC NADH dehydrogenase chain C

MT3236 410.8927896 352.224938 118.4950796 141.6492335 0.340987349 -1.552209882 7.99699076 0.003086323 RV3148 nuoD NADH dehydrogenase chain D

MT3237 188.0874144 216.019728 63.72784379 45.01870186 0.269191984 -1.893292643 6.99941876 9.87E-05 Rv3149 nuoE NADH dehydrogenase chain E

MT3238 327.3407739 314.920326 132.6169978 134.0259293 0.415231564 -1.268011979 7.82669393 0.021630684 Rv3150 nuoF NADH dehydrogenase chain F

MT3239 718.7762448 598.175109 264.3737772 262.2828717 0.400013299 -1.321880129 8.84739698 0.02186282 Rv3151 nuoG NADH dehydrogenase chain G

MT3240 507.4163511 394.590252 124.8750325 206.8593898 0.367838093 -1.442857202 8.26706742 0.018637339 Rv3152 nuoH NADH dehydrogenase chain H

MT3241 237.6845013 191.872944 62.86762543 102.0904658 0.38413039 -1.38033199 7.21234636 0.020937675 Rv3153 nuol NADH dehydrogenase chain I

MT3244 308.2649712 401.819828 139.7854841 167.1976044 0.432021639 -1.210824519 7.98994584 0.043964462 Rv3156 nuoL NADH dehydrogenase chain L

MT3290.1 94.99749732 134.903886 62.93931029 33.27469268 0.418167093 -1.257848558 6.34941027 0.049623816

MT3370 4,292.44 2,498.83 1,575.49 563.1973525 0.314961629 -1.666752016 11.1240739 0.034099178 Rv3270 ctpC cation transport ATPasc

MT3402 1,123.56 907.167183 178.0652013 186.5649178 0.179594079 -2.477188306 9.22456494 1.39E-07 Rv3303c IpdA dihydrolipoamide dehydrogenase

MT3427 239.5920816 243.925891 66.16512916 89.11024509 0.32102187 -1.639256507 7.31665292 0.001570229

MT3444 1,122.04 664.976391 304.5889857 232.6137959 0.300775754 -1.733239819 9.18107601 0.002930145 RV3341 metA homoserine o-acetyltransferase

MT3581 263.2460769 206.332096 96.41614162 72.21535469 0.359592374 -1.475565671 7.31465472 0.007151511 Rv3477 PE PE-family protein

MT3582 157.9476461 113.938116 69.67768748 46.97603672 0.430319871 -1.216518632 6.59737042 0.036554628 Rvl361c PPE PPE-family protein

MT3634 231.5802445 93.1169375 50.8962532 67.68257922 0.366329269 -1.448787122 6.78337768 0.033703938 Rv3531c Rv3531c hypothetical protein

MT3653 340.6938358 209.946884 120.3588861 113.2163692 0.424820904 -1.235073338 7.6121441 0.046356345 Rv3549c Rv3549c short-chain alcohol dehydrogenase fai

MT3655 235.395405 124.204114 63.44110434 56.35064054 0.334121422 -1.581555612 6.89802833 0.005251593 Rv3551 Rv3551 possible glutaconate CoA-transferase

MT3656 475.7505187 197.512013 94.6957049 128.6690129 0.332209831 -1.589833329 7.80377476 0.020864159 Rv3552 Rv3552 hypothetical protein

MT3657 127.4263619 89.068375 45.30483383 34.92297467 0.37199042 -1.426662628 6.20542704 0.007639252

MT3716 3,343.61 2,173.79 623.1565198 659.0037432 0.232414502 -2.105228004 10.7306738 3.65E-05 Rv3614c Rv3614c conserved hypothetical protein

MT3717 1,445.18 1,052.92 243.6568516 257.7500962 0.200760238 -2.316454534 9.54928945 1.96E-06 Rv3615c Rv3615c conserved hypothetical protein

MT3718 4,661.36 3,470.05 922.7992499 692.8965416 0.198719299 -2.331196103 11.2503906 2.00E-06 conserved hypothetical protein

MT3907 14,047.04 4,046.54 3,073.85 2,453.88 0.305527197 -1.710627283 12.5275801 0.03595872 Rv3800c pksl3 polyketide synthase

MT3947 91.94536889 62.4635357 30.32269733 13.70134404 0.286990675 -1.800924236 5.61822685 0.003113511 Rv3839 Rv3839 hypothetical protein

MT3953 57.99044013 42.2207232 19.35491319 20.19145438 0.396619289 -1.334173252 5.1133998 0.028946617

Table 2B: Upregulated gene expression tables of DMSO treated DosR mutant compared to DMSO treated WT

Gene Counts per mi Won (CPM) WT DMSO/DosR DMSO

WT_DMS01 WT_DMS02 Dos _DMS01 DosR_DMS02 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0160 38.9146375 40.6302165 81.57737485 108.6835937 2.388163199 1.255901429 6.08932008 0.021630684

MT0169 4.9597087 8.82008259 54.48049638 68.30068497 8.551198149 3.096126577 5.13510505 2.74E-09 Rv0160c PE PE-family protein

MT0258 635.987261 642.130931 1,818.64 1,416.29 2.530986008 1.339699532 10.1407928 0.02186282 RV0244C fadE5 acyl-CoA dehydrogenase

MT0273 11.0639656 4.91611161 42.36575442 25.13630035 4.39162198 2.134753876 4.43365706 0.005768789 Rv0260c Rv0260c two-component response regulator

MT0342 4.19667659 3.32560491 14.33697273 11.12590343 3.451503664 1.787225016 3.15003122 0.036554628 Rv0327c Rv0327c cytochrome P-450 monooxygenasemonoxygenase

MT0468 36.2440251 52.0529464 153.548978 79.0145179 2.619991667 1.389562223 6.34004103 0.025437098 Rv0452 Rv0452 putative transcriptional regulator

MT0483 486.814484 522.698337 1,914.85 1,420.61 3.303653028 1.724062173 10.0862308 0.001203906 Rv0467 aceA isocitrate lyase

MT0484 113.310268 124.78248 379.7864077 271.5544579 2.733913604 1.450967652 7.80164398 0.007217261

MT0491 62.5686328 62.6081272 206.3090376 185.8437944 3.132456858 1.64729464 7.02350646 0.000800955 Rv0474 Rv0474 transcriptional regulator (PbsX/Xre family)

MT0493 546.330989 416.857346 1,555.35 1,455.33 3.127103411 1.644826929 9.95739247 0.002139976 Rv0475 Rv0475 possible exported protein

MT0542 21.7464151 30.2196272 67.74219616 111.0529991 3.406562009 1.768316468 5.86990244 0.000894459 Rv0520 Rv0520 similar to methyltransferases

MT0738 236.921469 148.929263 554.4107355 442.1516439 2.587204776 1.371394247 8.43557051 0.028172861

MT0908 925.17643 216.019728 3,657.22 4,034.17 6.745474828 2.753920001 11.1092014 0.000244637 RV0885 RV0885 unknown transmembrane protein

MT0909 135.438199 34.2681897 701.8665001 443.1818201 6.784841686 2.762315153 8.36467109 0.000211208 Rv0886 fprB ferredoxin, ferredoxin-NADP reductase

MT1087 113.310268 195.053958 515.772594 324.2994816 2.718228635 1.442666809 8.16969686 0.027414181 Rvl057 Rvl057 conserved hypothetical protein

MT1168 70.5804699 69.1147455 131.3266702 198.2059093 2.358565228 1.2379095 6.88173624 0.032709004 Rvll35c PPE PPE-family protein

MT1213 31.2843164 31.5209509 86.30857585 76.33605967 2.588866752 1.372320712 5.83404475 0.007245332 Rvll76c Rvll76c conserved hypothetical protein

MT1232 44.2558622 29.7858527 97.20467512 103.0176244 2.727487557 1.447572615 6.11246536 0.006669465

MT1252 15.2606421 23.7130089 64.73143189 39.97083826 2.652043806 1.407104606 5.19750573 0.034099178

MT1259 814.155258 804.362614 1,720.15 2,174.70 2.406403224 1.266878405 10.4294001 0.033703938 Rvl221 sigE ECF subfamily sigma subunit

MT1555.1 2.67061237 1.15673214 11.039469 5.665969341 4.800819214 2.263280609 2.52401764 0.031759562

MT1567 30.5212843 57.2582411 183.0831418 183.9894772 4.139077099 2.049309122 6.84109591 5.81E-05 Rvl517 Rvl517 conserved hypothetical protein

MT1568 15.6421582 11.4227299 65.01817134 76.85114779 5.31907376 2.411175043 5.42891369 9.37E-07 RV1518 RV1518 involved in exopolysaccharide synthesis

MT1577 24.0355114 18.6523058 102.4376702 91.27361521 4.580236438 2.195422074 5.90555169 1.24E-06 RV1526C RV1526C possible rhamnosyl/glycosyl transferase

MT1580 101.48327 114.082708 250.0368044 428.4502998 3.144100998 1.652647562 7.80907092 0.002953587 Rvl529 fadD24 acyl-CoA synthase

MT1905 38.1516054 45.2571451 96.12940217 113.6284397 2.504745813 1.324664203 6.20907615 0.011661834 Rvl857 modA molybdate binding protein

MT1922 6.86728896 8.38630804 29.60584869 28.63889958 3.766893019 1.913375061 4.25903931 0.003118061 Rvl873 Rvl873 hypothetical protein

MT2040 55.3198278 32.2439085 570.3247753 79.32357078 7.442851069 2.895855368 7.53450033 0.002953587 Rvl986 Rvl986 membrane protein, LYSE/YGGA family

MT2417 8.01183712 6.07284375 15.84235487 28.7419172 3.205618031 1.68060253 3.93265985 0.041840399

MT2526 114.454816 182.763679 1,809.18 337.2797022 7.214264063 2.850852231 9.25760852 0.000876027 Rv2450c Rv2450c conserved hypothetical protein

MT2593.2 2.67061237 3.61478795 12.75990573 14.01039692 4.120891771 2.042956574 3.16550579 0.008030283

MT2792 11.0639656 22.9900513 58.63821847 39.76480301 2.828958129 1.500270824 5.08509452 0.03351671 Rv2719c Rv2719c conserved hypothetical protein

MT2804 37.0070572 32.9668661 69.2475783 95.29130256 2.356319316 1.236535059 5.88806015 0.028860259 Rv2735c Rv2735c hypothetical protein

MT2805 23.6539953 32.099317 83.08275698 52.84804131 2.419830115 1.274905766 5.60439534 0.035645827 RV2736C recX regulatory protein for RecA

MT2849 22.8909632 7.95253348 61.29055843 40.38290876 3.392796632 1.762474956 5.0773488 0.026850503 Rv2779c Rv2779c transcriptional regulator (Lrp/AsnC family)

MT3010 1,991.13 718.619844 6,831.93 2,972.47 3.619282173 1.85570359 11.6116154 0.022912631 Rv2940c mas mycocerosic acid synthase

MT3110 4.9597087 3.75937947 20.14344669 10.71383294 3.614771479 1.853904445 3.40249143 0.034099178 Rv3026c Rv3026c some similarity to acyltransferase Q59601

MT3111 45.0188943 34.4127813 126.8822087 86.12273399 2.696689768 1.431189561 6.20517185 0.009371108 Rv3027c Rv3027c hypothetical protein

MT3132 32.0473485 29.4966697 94.55233517 78.19037691 2.813307288 1.492267142 5.88937727 0.003086323

MT3133 306.357391 226.7195 761.3649369 867.5114149 3.058158084 1.612662985 9.07999842 0.003086323 Rv3048c nrdG ribonucleoside-diphosphate small subunit

MT3134 877.868439 237.419272 1,977.00 2,032.74 3.598450575 1.847375843 10.3240757 0.02186282 Rv3049c Rv3049c Probable monooxygenase

MT3140 1.90758027 2.4580558 25.37644174 10.40478006 7.960462609 2.992852273 3.45187296 0.000200867 Rv3054c Rv3054c conserved hypothetical protein

MT3247 25.1800595 18.2185313 57.34789093 58.10194015 2.687723222 1.426384579 5.33378974 0.016676652 Rv3159c PPE PPE-family protein

MT3248 78.210791 66.8012813 144.3016305 213.2464825 2.469112207 1.3039924 6.98017178 0.024272786

MT3441 83.1704997 67.8134219 317.4922612 207.2714603 3.482898672 1.800288501 7.4071827 0.000694534 Rv3338 RV3338 conserved hypothetical protein

MT3513 28.613704 27.6169799 133.2621615 43.57645512 3.148339387 1.65459107 5.88456794 0.024335692

MT3514 63.7131809 49.3057076 572.6186909 314.2037544 7.869912383 2.976347574 7.97166866 4.79E-09 Rv3406 Rv3406 putative dioxygenasediooxygenase

MT3515 64.476213 46.4138772 217.9936704 178.9416136 3.596611544 1.846638348 6.99698457 0.000198777 Rv3407 Rv3407 conserved hypothetical protein

MT3532.2 32.4288646 13.5916027 89.82113417 73.34854856 3.624643162 1.857838972 5.72742878 0.002445427 Rv3424c Rv3424c hypothetical protein

MT3533 109.113591 55.9569174 238.1371171 197.0727154 2.650734927 1.406392408 7.23515869 0.028172861 Rv3429 PPE PPE-family protein

MT3941 27.4691559 31.3763594 91.25483144 72.73044282 2.776179349 1.473100773 5.81881977 0.003842811 Rv3833 Rv3833 transcriptional regulator (AraC/Xyl5 far

MT3976 96.9050776 37.3046116 593.5506711 79.4265884 5.030707226 2.330761231 7.6634557 0.041661275 Rv3862c hypothetical protein

Table 2C: Downregulated gene expression tables of WT tb treated with HC101A compared to DMSO

Gene Counts per million (CPM) WT DMSO/WT HC101A

WT_DMS01 WT_DMS02 WT_HC101A1 WT_HC101A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0037 105.768758 87.457548 35.2352806 27.75295477 0.326829649 -1.613389228 5.98129424 1.29E-05 Rv0032 bioF2 C-terminal similar to B. subtilis BioF

MT0038 22.6368559 13.1260064 2.484119968 3.490937707 0.17223375 -2.537560218 3.2080193 1.17E-07 Rv0033 Rv0033 possible acyl carrier protein

MT0040 94.4503296 84.6553669 24.97194284 29.55660592 0.305148266 -1.712417701 5.84685602 1.36E-06 RV0035 fadD34 acyl-CoA synthase

MT0062 243.541346 182.87919 104.594525 99.66627154 0.479854072 -1.05933236 7.29458933 0.011192668 Rv0056 rpll 505 ribosomal protein L9

MT0065 97.9629451 59.8781863 35.16990902 29.03296526 0.409633748 -1.287593517 5.77070182 0.002536411

MT0086 1,339.09 2,633.17 496.301021 1,101.39 0.40214484 -1.314212885 10.4433477 0.044203618 Rv0079 Rv0079 hypothetical protein

MT0105 21.0756934 27.5793617 8.62904831 7.796427546 0.333840825 -1.582767706 3.98651137 0.000151741 Rv0096 PPE PPE-family protein

MT0106 76.4969611 67.5473136 24.38359863 21.52744919 0.319546938 -1.645900232 5.54431417 3.96E-06 Rv0097 Rv0097 conserved hypothetical protein

MT0107 37.85819 30.529026 11.70151248 9.89099017 0.318098281 -1.652455521 4.43829409 4.04E-05 Rv0098 Rv0098 hypothetical protein

MT0108 78.0581236 71.9718102 39.35369002 32.64026756 0.480564612 -1.057197681 5.78167989 0.007028674 Rv0099 fadDIO acyl-CoA synthase

MT0117 383.265387 341.423649 157.5455032 202.6489339 0.497275233 -1.007883515 8.08053967 0.019433804

MT0122 80.7901579 47.0471464 36.47734058 25.54202756 0.489225714 -1.03142786 5.54483179 0.0338307 Rv0113 gmhA phosphoheptose isomerase

MT0124 28.1009245 8.70150984 5.295097827 3.898213773 0.258135559 -1.953799204 3.34212895 0.002071634

MT0175 285.302442 154.414929 67.07123914 45.73128396 0.257182706 -1.959134461 7.09489141 1.29E-05 RV0166 fadD5 acyl-CoA synthase

MT0176 265.787911 258.243114 118.5186711 96.69897448 0.410752586 -1.283658436 7.52510923 0.000964269

MT0178 577.239824 412.51056 178.4644082 133.5865496 0.315521154 -1.664191363 8.34152685 4.81E-05 Rv0169 mcel cell invasion protein

MT0179 448.44392 313.106871 123.1600532 102.1681102 0.296206916 -1.755322771 7.94008087 1.25E-05 Rv0170 Rv0170 part of mcel operon

MT0180 472.641938 368.413077 138.5877456 130.0374296 0.31964589 -1.64545355 8.11077899 1.61E-05 Rv0171 Rv0171 part of mcel operon

MT0181 592.461158 488.6119 183.5633913 197.8198034 0.35295154 -1.502457979 8.51074265 0.000198389 Rv0172 Rv0172 part of mcel operon

MT0182 318.477144 288.32969 87.14031361 107.6954283 0.321272367 -1.638131198 7.64065981 1.66E-05 Rv0173 IprK part of mcel operon

MT0183 971.823639 854.960212 348.9534839 411.6979202 0.416464694 -1.263733899 9.3357677 0.004816418 Rv0174 Rv0174 part of mcel operon

MT0241 149.871597 167.098486 59.55350765 72.37877513 0.415933405 -1.265575537 6.80398903 0.000935573 Rv0231 fadE4 acyl-CoA dehydrogenase

MT0244 127.625032 68.2847297 37.26179952 30.02206428 0.345666501 -1.5325473 6.01420461 0.000493148 Rv0233 nrdB ribonucleoside-diphosphate reductase B2

MT0329 252.127739 246.59194 70.60130435 95.12805252 0.332425853 -1.588895508 7.36939005 2.91E-05 RV0315 RV0315 probable [beta]-l,3-glucanase

MT0417 71.0328925 58.4033542 28.9596091 22.92382428 0.402402748 -1.313287937 5.47978443 0.000697909

MT0423 2,729.30 844.931353 514.0820902 411.8724671 0.259149552 -1.948143194 10.1333761 0.002195753 Rv0410c pknG serine-threonine protein kinase

MT0424 1,285.23 391.862909 282.7320753 249.9511398 0.317858952 -1.653541373 9.10526088 0.009921952 Rv0411c glnH putative glutamine binding protein

MT0425 1,440.17 508.227168 385.4961961 301.2679241 0.352693195 -1.503514353 9.3603738 0.015307302 Rv0412c Rv0412c unknown probable membrane protein

MT0429 18.7339497 13.1260064 5.818070451 5.876411807 0.375236657 -1.414127321 3.35475139 0.002553491 Rv0416 Rv0416 conserved hypothetical protein

MT0434 71.4231831 34.9535226 27.78292069 21.99290755 0.47351635 -1.078513853 5.25314311 0.037382435

MT0524 472.251648 436.107874 188.6623744 239.3619621 0.471342152 -1.085153389 8.3817664 0.010449641

MT0595 292.327673 180.666942 36.08511111 36.48029904 0.153815128 -2.700730692 7.07431352 2.35E-12 Rv0569 Rv0569 conserved hypothetical protein

MT0596 2,978.31 1,738.97 90.4742641 115.6664027 0.04371453 -4.515743287 10.2629631 5.00E-21 Rv0570 nrdZ ribonucleotide reductase, class II

MT0597 254.079192 424.751667 81.5183579 88.37890628 0.249911923 -2.00050836 7.72578327 9.86E-07 RV0571C RV0571C conserved hypothetical protein

MT0598 207.244318 349.535226 19.08850081 37.46939806 0.101519613 -3.300169619 7.25271008 9.14E-13

MT0599 581.533021 788.592764 38.43848793 70.86603545 0.0797843 -3.647751302 8.52648178 5.13E-16 Rv0572c Rv0572c hypothetical protein

MT0600 995.631367 1,338.41 30.4631554 87.62253645 0.050609577 -4.304445781 9.25695819 2.64E-14

MT0601 96.4017827 90.2597291 10.19796618 13.26556329 0.126045785 -2.987980224 5.67982926 1.06E-17 Rv0573c Rv0573c conserved hypothetical protein

MT0602 389.119746 352.632373 28.89423752 33.92027805 0.084759226 -3.560485768 7.6412979 1.93E-22 Rv0574c Rv0574c conserved hypothetical protein

MT0637 62.8367895 53.2414415 30.13629751 24.84384001 0.47540372 -1.072774903 5.3997676 0.007860746 Rv0608 Rv0608 conserved hypothetical protein

MT0735 197.877343 95.569125 74.26211273 58.88048256 0.455739016 -1.133720209 6.7228957 0.025765689 Rv0708 rpIP 50S ribosomal protein L16

MT0736 288.034476 135.094627 109.6935081 91.92802628 0.477963365 -1.065028053 7.27785554 0.044117567 Rv0709 rpmC 50S ribosomal protein L29

MT0741 355.945044 244.232208 127.4745773 136.8447581 0.441087078 -1.1808646 7.75023671 0.005505017

MT0741.1 335.259641 201.904525 117.603469 110.9536368 0.426391462 -1.229749545 7.57354669 0.005083875 Rv0715 rplX 50S ribosomal protein L24

MT0742.1 168.215256 111.054863 74.78508535 58.99684725 0.480685353 -1.05683525 6.67961107 0.017145527 Rv0717 rpsN 30S ribosomal protein S14

MT0747 157.67741 79.345971 51.70891828 38.1094033 0.380875532 -1.392608485 6.33217258 0.004200151 Rv0722 rpmD 50S ribosomal protein L30

MT0845 2,819.46 2,651.60 1,309.20 1,158.35 0.451029246 -1.148707111 10.9542494 0.019433804 Rv0823c Rv0823c transcriptional regulator (NifR3/Smml

MT0846 8,232.01 7,693.31 2,534.91 2,497.59 0.316010048 -1.661957664 12.3549648 0.000214157 Rv0824c desAl acyl-[ACP] desaturase

MT0877 79.2289955 76.8387563 32.03207327 42.41489314 0.477500297 -1.066426464 5.83714388 0.007303548 Rv0854 Rv0854 conserved hypothetical protein

MT0908 945.454749 220.339927 115.5769501 190.5470165 0.26263688 -1.92885858 8.51659222 0.007969339 Rv0885 Rv0885 unknown transmembrane protein

MT0909 138.553169 34.9535226 22.29170813 38.69122625 0.354064311 -1.497916665 5.83382041 0.037486354 Rv0886 fprB ferredoxin, ferredoxin-NADP reductase

MT0911 39.4193524 31.1189589 8.106075685 5.527318036 0.194605368 -2.361376587 4.31727681 6.29E RV0888 RV0888 possible membrane protein

MT1002 1,675.13 581.526327 418.3127283 235.2892015 0.28976904 -1.787024636 9.50355257 0.005414793 accD2 acetyl/propionyl-CoA carboxylase, [bet

MT1019 92.8891671 82.7380851 34.58156482 43.40399216 0.445023322 -1.168047152 5.97317663 0.002584789 Rv0990c Rv0990c hypothetical protein

MT1020 1,013.19 948.317089 343.0046703 416.0615924 0.387022077 -1.369512232 9.40821284 0.001896362

MT1066 1,408.95 630.933205 451.979091 332.8609104 0.384956024 -1.377234448 9.46130025 0.016187653 Rvl037c Rvl037c conserved hypothetical protein

MT1095 477.325426 495.838577 232.5920749 199.4489077 0.443913856 -1.171648353 8.45447392 0.004923309 Rvl065 Rvl065 conserved hypothetical protein

MT1106 157.67741 161.936573 66.48289493 91.17165645 0.493273578 -1.019540082 6.89364645 0.015307302 Rvl076 lipU probable esterase

MT1126 7,609.50 5,962.16 2,656.44 2,736.08 0.397351627 -1.331511844 12.210737 0.005787145 Rvl094 desA2 acyl-[ACP] desaturase

MT1214 1,812.90 2,122.28 754.7148692 847.8905867 0.407223683 -1.296106627 10.4345882 0.00593149 Rvll77 fdxC ferredoxin 4Fe-4S

MT1233 751.69973 233.7609 121.1989058 83.31704661 0.207804107 -2.266703925 8.20692286 0.000103204 Rvll95 PE PE-family protein

MT1234 798.144314 248.361738 155.7804706 129.2810597 0.272740166 -1.874400914 8.37107001 0.001548013 Rvll96 PPE PPE-family protein

MT1235 435.95462 181.256874 117.8649553 84.42251021 0.328412061 -1.606420982 7.66840469 0.002536411

MT1236 386.778003 113.857044 78.31515057 44.97491413 0.246852707 -2.018277629 7.26756526 0.001410479

MT1314 458.201186 368.560561 209.2544215 172.8014165 0.462415968 -1.112736877 8.23619081 0.007536006 Rvl277 Rvl277 hypothetical protein

MT1322 613.536852 648.631191 175.0650862 138.7647739 0.248620268 -2.00798418 8.61874959 4.05E Rvl284 Rvl284 conserved hypothetical protein

MT1385 149.871597 118.72399 26.14863124 81.16430169 0.400178018 -1.321286172 6.54248787 0.033990726

MT1414.1 19.5145309 15.7807043 7.648474638 6.865510824 0.416439762 -1.263820269 3.57480341 0.005205549

MT1430 70.2523112 140.109057 44.64878785 57.71683676 0.483835603 -1.047411161 6.2892869 0.039370591 Rvl386 PE PE-family protein

MT1431 606.12133 560.731193 210.3657383 246.3438375 0.391483328 -1.352977226 8.66246816 0.001641323 Rvl387 PPE PPE-family protein

MT1484 12.8795904 7.37416088 4.118409421 4.7709482 0.458242826 -1.1258158 2.75702763 0.045909218 Rvl439c Rvl439c hypothetical protein

MT1585.1 1,469.44 796.261892 142.6407834 232.7873628 0.165785388 -2.592611235 9.36314818 1.36E

MT1586 217.782165 67.5473136 48.50571095 45.14946101 0.329836934 -1.600175139 6.54160975 0.007230989 RV1535 RV1535 hypothetical protein

MT1600 28.4912151 17.4030197 9.740365138 9.134620333 0.420024644 -1.251454118 3.94969202 0.008075386 RV1550 fadDll acyl-CoA synthase, N-term

MT1627 53.8601053 19.6152679 14.6432335 15.5346728 0.418123259 -1.257999797 4.63177606 0.038713875

MT1638 569.824302 231.253685 205.0052689 158.6049365 0.454639521 -1.137204993 8.17997361 0.047745648 Rvl602 hisH amidotransferase

MT1692 624.464989 234.20335 192.0616965 153.5430768 0.403109649 -1.310755778 8.22756611 0.02413631 Rvl654 argB acetylglutamate kinase

MT1693 520.647684 197.922478 174.4113704 139.2302322 0.437297282 -1.193313713 8.00459605 0.039763779 Rvl655 argD acetylornithine aminotransferase

MT1694 564.360234 168.130868 117.5380974 85.87706759 0.278189896 -1.845858074 7.8590386 0.002584789 Rvl656 argF ornithine carbamoyltransferase

MT1725 37.4678993 26.9894288 12.48597142 11.63645902 0.378651434 -1.401057704 4.41802284 0.000897781 Rvl685c Rvl685c conserved hypothetical protein

MT1726 99.5241076 64.3026829 24.7758281 27.98568395 0.324307005 -1.624567907 5.73029344 3.15E Rvl686c Rvl686c probable transmembrane protein

MT1727 73.7649268 54.2738241 20.06907448 22.45836592 0.334373509 -1.58046754 5.38275784 3.48E Rvl687c Rvl687c probable ABC transporter

MT1736 284.521861 300.128348 131.2661288 161.0485929 0.499910619 -1.000257923 7.77378636 0.017572545

MT1774 1,459.69 1,785.87 39.4190616 105.1354073 0.044553172 -4.488328032 9.72484599 4.34E possible membrane protein

MT1775 579.191277 662.494613 38.24237319 49.68768003 0.070829072 -3.819514543 8.37108749 1.03E

MT1776 20.6854028 16.6656036 2.810977859 3.781849183 0.179446818 -2.478371755 3.32331401 9.89E Rvl735c Rvl735c hypothetical protein

MT1777 109.671664 195.71023 2.810977859 8.610979677 0.037504115 -4.736807275 6.29019257 1.56E

MT1778 5,799.33 3,617.62 80.0148116 197.1797982 0.029443155 -5.085923898 11.2416403 2.20E-18 Rvl736c narX fused nitrate reductase

MT1779 2,075.57 1,498.72 39.61517633 104.7863135 0.040420307 -4.62877591 9.85761264 1.76E Rvl737c narK2 nitrite extrusion protein

MT1780 3,858.80 5,086.70 117.0804964 274.2131569 0.043746244 -4.514697042 11.1879313 8 Rvl738 Rvl738 conserved hypothetical protein

MT1797 58.5435927 48.5219786 11.30928301 15.5346728 0.252153196 -1.987627585 5.02178996 2.38E

MT1809 133.869682 74.4790249 57.13475926 39.44759609 0.466037561 -1.101481858 6.23546713 0.025279872 Rvl760 Rvl760 conserved hypothetical protein

MT1822 26.9300526 15.7807043 12.15911353 7.27278689 0.463755812 -1.108562733 3.89280495 0.043686606

MT1823 674.812479 366.495796 189.5775765 111.2445483 0.289154101 -1..790089532 8.3844375 0.000266213 Rvl773c Rvl773c transcriptional regulator (IcIR family)

MT1840 382.094515 306.027676 169.3777589 147.3757535 0.46069087 -1. .118129088 7.96894214 0.007433984 Rvl791 PE PE-family protein

MT1860 248.224833 166.361069 69.35924437 114.0954807 0.443450499 -1. .173155026 7.21617316 0.014375115 Rvl812c Rvl812c probable dehydrogenase

MT1851 3,068.86 1,615.09 65.63306442 173.7323332 0.051121904 -4 .289914622 10.262847 8.10E-13 Rvl813c Rvl813c conserved hypothetical protein

MT1882 81.9610298 77.4286892 28.50200805 25.48384526 0.339094111 -1. .560242365 5.71719585 9.58E-06 Rvl834 Rvl834 conserved hypothetical protein

MT1932 497.620538 648.926157 219.8446172 285.675069 0.440721541 -1. .182060681 8.68887422 0.011431961

MT1942 142.846366 155.152345 74.52359904 69.70238955 0.483622049 -1. .048048074 6.78351419 0.00717373

MT1943 127.625032 133.914762 65.43694968 61.14959217 0.483777053 -1. .047585756 6.59421867 0.007208548

MT1955 220.514199 167.983385 88.57848833 104.4372197 0.497762522 -1. .006470485 7.17743577 0.01939937 R 1904 RV1904 conserved hypothetical protein

MT1969 153.384213 126.393117 62.82208656 65.5132643 0.459643027 -1. .121414242 6.66386585 0.004050835 R l918c PPE PPE-family protein

MT1986 313.403366 78.4610717 47.52513728 27.86931936 0.192984535 -2. .373442854 6.84111617 0.000324511 Rvl936 Rvl936 similar alkanal monooxygenase alpha chain

MT1987 394.583815 99.1087222 66.35215178 34.03664264 0.203799426 -2. .294778105 7.19360922 0.000883361 Rvl937 Rvl937 similar to ring-hydroxylating dioxygenases

MT1988 155.725957 36.4283547 24.12211232 13.49829247 0.196974749 -2. .343917397 5.7897951 0.000642266 Rvl938 ephB probable epoxide hydrolase

MT1989 67.9105675 20.0577176 13.66265982 7.38915148 0.242339546 -2. .044898243 4.67516663 0.002071634 Rvl939 Rvl939 similar nitrilotriacetate monooxygenase component

MT2007 62.8367895 25.5145966 22.22633656 14.60375607 0.422513495 -1. .242930672 4.91685218 0.037265682

MT2016 376.630446 171.522982 104.4637818 57.77501905 0.29655925 -1. .753607723 7.46055446 0.000941593 Rvl964 Rvl964 part of mce3 operon

MT2017 310.281041 93.0619103 43.40672786 25.54202756 0.171463905 -2. .544023187 6.85729679 2.29E-05

MT2018 345.407197 110.612413 50.33611514 26.88022034 0.169759242 -2. .558437974 7.03575458 1.87E-05 Rvl966 mce3 cell invasion protein

MT2019 357.115916 99.5511719 52.88560669 27.86931936 0.177281435 -2. .495886634 7.04650222 9.97E-05 RV1967 RV1967 part of mce3 operon

MT2020 407.853696 115.03691 57.9192182 26.88022034 0.162506529 -2. .621430414 7.2259919 7.31E-05 Rvl968 Rvl968 part of mce3 operon

MT2021 103.817304 40.8528513 23.72988285 17.45468854 0.287327416 -1. .799232438 5.49093853 0.000564397 Rvl969 Rvl969 part of mce3 operon

MT2022 240.02873 75.8063738 37.39254268 24.43656395 0.196559328 -2. .346963263 6.53023751 5.05E-05 Rvl970 IprM part of mce3 operon

MT2023 324.331504 92.177011 53.53932247 31.18571018 0.204009759 -2.29328993 6.94552809 0.000231201 Rvl971 Rvl971 part of mce3 operon

MT2024 36.2970275 22.4174491 16.14677979 10.41463083 0.458782172 -1.124118764 4.36505888 0.031292773 Rvl972 Rvl972 conserved hypothetical protein

MT2042.1 64.7882426 78.0186221 19.87295974 29.96388199 0.348200966 -1.522007888 5.57400375 0.000113121

MT2052 41,432.47 9,313.71 177.9414356 195.376147 0.007357233 -7.086621003 13.6412361 1.73E-20 Rvl996 Rvl996 conserved hypothetical protein

MT2053 3,239.41 1,713.31 70.20907489 92.04439087 0.032773923 -4.931307818 10.3179607 1.93E-22 Rvl997 ctpF probable cation transport ATPasc

MT2059 551.090353 915.133365 101.8489187 119.9137102 0.151170782 -2.72574877 8.71859637 2.61E-10 Rv2003c Rv2003c conserved hypothetical protein

MT2060 2,780.04 2,826.66 233.964878 227.90005 0.082380416 -3. .601554787 10.5658011 1.13E-17 hypothetical protein

MT20B1 2,496.30 2,271.54 149.3086844 179.2596513 0.068923173 -3. .858867071 10.3134888 1.08E-19 RV2005C RV2005C conserved hypothetical protein

MT2062 616.659177 832.83773 122.7678237 137.4847634 0.179486125 -2. .478055772 8.7367092 7.32E-10 Rv2006 otsB trehalose-6-phosphate phosphatase

MT2063 7,856.94 10,026.65 580.1727557 1,435.65 0.112720075 -3. .149183619 12.2801231 7.51E-09 Rv2007c fdxA ferredoxin

MT2079 37.0776087 31.5614086 11.24391143 12.85828722 0.353465499 -1. .500358692 4.49040228 0.000186055 Rv2023c Rv2023c hypothetical protein

MT2080 100.304689 79.0510046 28.30589332 33.92027805 0.348344663 -1. .521412636 5.895632 4.81E-05

MT2086 339.943128 198.512411 56.35030033 58.93866495 0.214609111 -2. .220216767 7.33935177 3.20E-08 Rv2027c Rv2027c sensor histidine kinase

MT2087 810.633614 733.286558 41.77243841 89.71709907 0.085211169 -3 .552813642 8.70509527 8.52E-14 Rv2028c Rv2028c conserved hypothetical protein

MT2088 5,005.48 2,681.39 91.91243882 170.4159424 0.034136438 -4. .872543662 10.9549642 6.68E-19

MT2089 14,874.37 14,962.17 490.6136937 1,178.54 0.055945122 -4. .159843853 12.9430482 8.64E-15 Rv2030c Rv2030c conserved hypothetical protein

MT2090 47,420.31 45,136.50 697.7762247 1,736.45 0.026300434 -5. .248769581 14.5354016 1.86E-20

MT2091 4,091.03 6,085.75 87.33642835 255.0711818 0.03364996 -4. .893251407 11.3600939 8.47E-16 RV2032 RV2032 conserved hypothetical protein

MT2166 57.7630115 43.5075492 20.06907448 13.38192788 0.332234462 -1. .589726364 5.0353742 0.000149414 Rv2107 PE PE-family protein

MT2278 1,279.76 1,006.57 436.2245407 385.9231635 0.359672237 -1. .475245294 9.60032212 0.000981117 Rv2220 glnAl glutamine synthase class 1

MT2304 5,107.73 2,123.46 626.6519477 987.3535481 0.223236286 -2. .163356548 11.1095232 0.00018736 Rv2244 acp acyl carrier protein (meromycolate extension)

MT2305 5,019.92 2,531.55 854.7987553 1,424.88 0.301926853 -1. .727729022 11.2623262 0.00211661 Rv2245 kasA [beta]-ketoacyl-ACP synthase (meromycolate

MT2306 2,614.56 1,561.26 581.8070451 834.8577526 0.339328292 -1. .559246371 10.4480685 0.002554128

MT2307 2,316.37 2,024.21 817.0793547 1,179.12 0.459925909 -1 .120526623 10.6289766 0.03235796 Rv2247 accD6 acetyl/propionyl CoA carboxylase [beta] subunit

MT2329 57.3727209 62.9753339 24.25285548 26.99658493 0.425135813 -1. .234004299 5.4076728 0.00126386 Rv2267c Rv2267c hypothetical protein

MT2391 137.772588 53.6838912 43.01449839 32.23299149 0.395827325 -1. .337056885 6.03162931 0.015331014 Rv2329c narKl probable nitrite extrusion protein

MT2399 61.6659177 60.0256695 23.01079549 25.0183869 0.395100831 -1. .339707215 5.38685136 0.000296028 Rv2336 Rv2336 hypothetical protein

MT2412 2,673.88 1,182.23 901.6048052 586.0702587 0..385898205 -1.373707762 10.3822627

MT2455 365.702309 179.634559 119.2377585 92.27712006 0. .388745837 -1.36310087 7.5548903 0.005505017

MT2504 293.888835 410.888244 119.2377585 223.4200132 0. .485828522 -1.041480905 8.03149708 0.043287009 Rv2429 ahpD member of AhpC/TSA family

MT2556 825.854948 434.780525 303.2587508 203.6962152 0. 402456138 -1.313096535 8.78394075 0.015218202 Rv2483c Rv2483c possible transferase

MT2559 33.1747025 29.4966435 9.478878825 10.00735476 0. .312652244 -1.677369221 4.30714999 1.68E-05 Rv2485c lipQ probable carboxlyesterase

MT2574 537.820472 208.688753 176.9608619 105.2517719 0. .378646869 -1.401075095 7.99895112 0.017713159 Rv2499c Rv2499c putative aldehyde dehydrogenase

MT2575 1,805.09 827.675817 668.6205009 432.5271819 0. .418407288 -1.257020115 9.86465534 0.03821673 Rv2500c fadE19 acyl-CoA dehydrogenase (aka mmgC)

MT2577 483.960366 243.642275 133.6848772 116.1900433 0. .344012239 -1.539468203 7.92540501 0.001133528 accDl acetyl/propionyl-CoA carboxylase, [beta] subunit

MT2578 621.342664 260.455362 124.1406268 102.2844748 D. .257166758 -1.959223924 8.10544747 8.35E-05 3-oxo acid:CoA transferase, [beta] subunit

MT2579 625.24557 300.128348 157.0225306 129.0483306 0. .309567309 -1.691674968 8.23583645 0.000358942 Rv2504c scoA 3-oxo acid:CoA transferase, [alpha] subunit

MT2600 61,092.97 11,312.85 13,005.68 8,330.13 0. .294673885 -1.762808886 14.5162761 0.040131693 Rv2524c fas fatty acid synthase

MT2603 23.0271465 24.4822141 9.086649357 11.8691882 0. .440534032 -1.182674621 4.06514809 0.00717373 Rv2528c mrr restriction system protein

MT2634 895.326678 721.045451 293.6491288 273.6895162 0. .351103372 -1.510032242 9.09019171 0.000438489 Rv2557 Rv2557 conserved hypothetical protein

MT2698 44,655.49 23,243.06 425.7650882 779.933666 0. .017758251 -5.815366693 14.0762905 6.52E-24 Rv2623 Rv2623 conserved hypothetical protein

MT2699 2,550.55 1,934.68 49.48628463 78.89519218 0.02863648 -5.126002039 10.1692966 3.90E-26 Rv2624c Rv2624c conserved hypothetical protein

MT2700 6,066.68 3,877.92 78.90349477 150.6339621 0.023088062 -5.436709124 11.3114209 9.02E-24 Rv2625c Rv2625c conserved hypothetical protein

MT2701 13,637.14 11,116.25 153.8846949 330.6499831 0.019576871 -5.674706025 12.6228786 8.20E-25 Rv2626c Rv2626c conserved hypothetical protein

MT2702 8,195.32 5,959.06 62.56060025 108.7427096 0.012106337 -6.368093763 11.805502 2.43E-32 Rv2627c Rv2627c conserved hypothetical protein

MT2703 732.965781 947.284706 18.30404187 29.03296526 0.02819297 -5.14852072 8.75010527 5.02E-29 RV2628 RV2628 hypothetical protein

MT2704 8,106.73 5,107.93 492.2479831 567.801018 0. .080224587 -3.639811732 11.8004038 2.16E-15 Rv2629 Rv2629 hypothetical protein

MT2705 799.705476 592.292602 73.86988326 67.49146234 0. 101612565 -3.298849289 8.57624072 5.23E-17 Rv2630 Rv2630 hypothetical protein

MT2707 1,178.29 513.38908 99.10331241 69.52784266 0. .099752969 -3.325496402 8.85461609 5.72E-11 Rv2631 Rv2631 conserved hypothetical protein

MT2708 112.403698 75.5114074 38.17700161 35.49120002 0. .394162385 -1.343137987 6.01133739 0.000703663 Rv2632c Rv2632c conserved hypothetical protein

MT2709 254.079192 135.389594 56.80790137 62.89506102 0. .308403524 -1.697108846 6.9772474 8.84E-05 Rv2633c Rv2633c hypothetical protein

MT2795 174.069616 142.763755 77.85754952 74.24060857 0. 480905382 -1.056175023 6.86581617 0.008117818 Rv2723 Rv2723 probable membrane protein, tellurium resistance

MT2850 1,480.76 447.759049 463.0922593 163.3758847 0. .324986539 -1.621548134 9.31529438 0.043100188 Rv2780 aid L-alanine dehydrogenase

MT2876 78.4484142 58.5508374 33.56636272 31.0111633 0. .474839031 -1.074489567 5.63734483 0.007298242 Rv2809 Rv2809 hypothetical protein

MT2889 19.5145309 10.9137581 6.994758857 5.352771151 0. .418240594 -1.257595 3.32082922 0.019433804

MT2985 65.5688238 50.7342268 28.30589332 21.4692669 0. .430254567 -1.216737588 5.35157405 0.002845529 RV2917 RV2917 conserved hypothetical protein

MT3056 782.142399 661.314748 256.0604714 203.05621 D. .318147403 -1.652232748 8.89090713 0.000106318 transposase

MT3057 236.516115 211.7859 109.1705354 89.42618759 0. .443281521 -1.173704873 7.33191161 0.003205018 Rv2979c Rv2979c resolvase

MT3085 506.597222 529.907201 240.6981506 239.536509 0. .463285117 -1.110027758 8.56497446 0.010203936 Rv3005c Rv3005c conserved hypothetical protein

MT3118 32.7844119 50.4392604 10.98242512 21.87654296 0. .392203413 -1.350326006 4.84630937 0.010866027 Rv3033 Rv3033 hypothetical protein

MT3132 32.7844119 30.0865764 11.37465459 6.807328529 0.28977082 -1.787015774 4.28496567 3.56E-05

MT3133 313.403366 231.253685 113.3543164 79.70974431 0. .354909645 -1.494476313 7.5195057 0.000269814 Rv3048c nrdG ribonucleoside-diphosphate small subunit

MT3165 979.629451 373.280024 290.2498068 251.5802441 0. 400856616 -1.31884181 8.88372585 0.030312812 Rv3080c pknK serine-threonine protein kinase

MT3168 323.160632 313.549321 112.8313438 148.4230348 0. .410422716 -1.284817513 7.80655801 0.0014B9159 Rv3083 Rv3083 probable monooxygenase

MT3171 701.742531 435.665425 192.3231828 192.8743083 0. .338959558 -1.560814942 8.56803889 0.000446334 Rv3086 adhD zinc-containing alcohol dehydrogenase

MT3172 370.385797 255.145966 136.2997403 149.5284985 0. .457608238 -1.127815072 7.82690262 0.00904192 Rv3087 Rv3087 conserved hypothetical protein

MT3173 249.005414 212.080867 98.5149682 104.9026781 0. .441629354 -1.179092026 7.37045764 0.002530467

MT3175 64.397952 66.5149311 23.07616707 28.33477772 0. .392688129 -1.348544109 5.49273373 0.000307474 Rv3090 Rv3090 hypothetical protein

MT3210 8.5863936 6.19429514 0.130743156 0.349093771 0. .035772197 -4.805017477 1.52086904 3.48E-14

MT3212 16,597.50 10,665.84 231.7422444 409.079717 0. .023507189 -5.410754173 12.7677567 3.08E-24 Rv3127 Rv3127 conserved hypothetical protein

MT3216 34,344.40 28,565.58 221.1520487 476.1639032 0. .011085249 -6.49521497 13.9567337 5.67E-30 Rv3130c Rv3130c conserved hypothetical protein

MT3217 19,492.28 10,701.53 147.5436518 329.9517956 0. .015816395 -5.982435365 12.904169 3.95E-23 Rv3131 Rv3131 conserved hypothetical protein

MT3218 5,451.97 3,333.56 240.8288937 318.5480658 0. 063680094 -3.973013716 11.1887328 4.71E-17 Rv3132c Rv3132c sensor histidine kinase

MT3219 3,951.69 2,133.49 109.9549944 149.5866807 0. .042663798 -4.550843798 10.6293405 1.65E-19 Rv3133c Rv3133c two-component response regulator

MT3220 6,479.60 4,044.58 145.9093623 248.5547647 0. .037488517 -4.737407446 11.4134083 2.23E-20 Rv3134c Rv3134c conserved hypothetical protein

MT3223 32.3941213 5.30939583 6.929387279 3.549120002 0. .285283537 -1.809531602 3.39081696 0.043997396

MT3227 2,351.11 1,444.89 910.3645967 765.5626391 0.441594486 -1.179205936 10.4168658 0.026876437 Rv3140 fadE23 acyl-CoA dehydrogenase

MT3257 61.6659177 34.0686233 21.96485024 19.89834493 0.442794803 -1.175289804 5.06730841 0.012325698

MT3261 55.0309771 44.3924485 23.99136916 24.84384001 0.494113328 -1.017086125 5.19091987 0.013593095

MT3292 45.6640023 47.3421128 13.98951771 21.4692669 0.381393779 -1.390646785 4.98044788 0.00095557

MT3295 244.321927 179.487076 90.34352094 70.80785316 0.380903791 -1.392501447 7.18341883 0.000617173 Rv3201c Rv3201c probable ATP-dependent DNA helicase

MT3296 277.496629 221.814759 96.68456402 84.36432792 0.36303142 -1.461833676 7.40282326 0.000134878 Rv3202c Rv3202c similar to UvrD proteins

MT3344 857.078197 811.747629 414.6519199 352.8174376 0.459919873 -1.120545557 9.24916061 0.015218202 Rv3246c mtrA two-component response regulator

MT3409 113.964861 87.1625816 35.2352806 51.66587806 0.433638273 -1.205436001 6.1556138 0.004366979 RV3310 RV3310 probable acid phosphatase

MT3413 11.7087185 6.34177836 3.203207327 2.676385575 0.341627838 -1.549502556 2.41021594 0.006054645

MT3424 83.9124829 60.320636 29.48258173 27.4620433 0.397242447 -1.331908306 5.62866332 0.000582996 Rv3323c gphA phosphoglycolate phosphatase

MT3425 81.5707392 61.5005017 25.6910302 25.60020985 0.360521927 -1.471841086 5.57695963 7.88E-05 Rv3324c moaC3 molybdenum cofactor biosynthesis, protein C

MT3426 47.6154554 51.7666094 17.65032609 20.36380329 0.381929641 -1.388621205 5.08021868 0.0002669

MT3427 245.102508 248.804188 54.32378141 69.35329578 0.2504605 -1.997344998 7.26192473 3.37E-08

MT3443 2,028.34 1,018.81 499.4388567 496.7604357 0.327045269 -1.612437752 9.97943634 0.001896362 Rv3340 metC cystathionine [beta]-lyase

MT3444 1,147.84 678.275318 300.447773 343.7991818 0.352988491 -1.502306948 9.26784854 0.00182937 Rv3341 metA homoserine o-acetyltransferase

MT3449.2 7.80581236 6.93171123 3.726179952 2.792750166 0.447241796 -1.160873076 2.33003806 0.040866137

MT3491 92.4988765 46.1622471 33.60099115 20.77107936 0.395346484 -1.3388105 5.56024252 0.008340803 Rv3383c idsB transfergeranyl, similar geranyl pyrophosphate

MT3497 149.481307 126.245634 57.85384662 60.7423161 0.430920606 -1.214506008 6.61345577 0.001470284 Rv3390 IpqD lipoprotein

MT3580 61.6659177 76.3963067 28.04440701 34.5602833 0.45181394 -1.146199311 5.6392313 0.003820169

MT3581 269.300526 210.458551 30.26704066 41.48397642 0.149833433 -2.738568522 7.09230371 1.63E-13 Rv3477 PE PE-family protein

MT3582 161.580316 116.216775 42.29541103 54.51681052 0.349621428 -1.516134485 6.53450558 0.000142385 Rvl361c PPE PPE-family protein

MT3583 213.098677 161.051674 100.3453724 79.76792661 0.48227584 -1.052069555 7.10750292 0.013635153 Rv3479 Rv3479 hypothetical protein

MT3591 117.087185 34.8060393 12.15911353 12.45101115 0.163599442 -2.611760268 5.39463971 4.00E-06 Rv3487c lipF probable esterase

MT3608 164.702641 88.9323802 69.62073068 44.50945576 0.451872395 -1.146012671 6.5077355 0.025926815 Rv3504 fadE26 acyl-CoA dehydrogenase

MT3629 264.226748 252.491268 111.9815133 124.5101115 0.457832033 -1.127109688 7.55278186 0.004274618 Rv3528c Rv3528c hypothetical protein

MT3634 236.906405 94.9791921 83.08727577 41.13488265 0.375502968 -1.413103785 6.81635547 0.021245859 Rv3531c Rv3531c hypothetical protein

MT3640 599.096099 239.365262 221.0213056 125.3246637 0.413634417 -1.273571864 8.20425666 0.037209726 Rv3536c Rv3536c aromatic hydrocarbon degradation

MT3649 218.172456 148.368117 73.54302537 59.22957643 0.363144104 -1.46138594 6.95243011 0.000269435 Rv3545c Rv3545c cytochrome p450

MT3653 348.529522 214.145632 154.2115528 107.9863397 0.466776412 -1.099196436 7.68206379 0.023308096 short-chain alcohol dehydrogenase family

MT3656 485.692401 201.462075 154.1461812 82.96795284 0.345106745 -1.534885423 7.84492555 0.008659974 RV3552 RV3552 hypothetical protein

MT3715 114.355151 41.1478177 36.15048269 17.33832394 0.346402328 -1.529479471 5.66792251 0.016066587 Rv3612c Rv3612c hypothetical protein

MT3716 3,420.51 2,217.26 563.3722601 375.7412619 0.166595834 -2.585575773 10.6818002 6.27E-08 Rv3614c Rv3614c conserved hypothetical protein

MT3717 1,478.42 1,073.97 308.0962476 205.4416841 0.201242953 -2.312989833 9.57953024 2.60E-07 Rv3615c Rv3615c conserved hypothetical protein

MT3718 4,768.57 3,539.45 1,098.37 739.7878824 0.221264778 -2.17615428 11.3079104 3.59E-06 Rv3616c Rv3616c conserved hypothetical protein

MT3722 659.591145 306.470126 217.0336393 163.7249785 0.394629365 -1.341429782 8.39014392 0.010704637

MT3750.1 3,039.58 2,447.19 1,243.69 1,392.01 0.480413824 -1.057650429 10.9872494 0.039159881 Rv3648c cspA cold shock protein, transcriptional regulator

MT3838 87.0348078 84.9503333 37.98088688 41.60034101 0.463029946 -1.110822594 5.96360915 0.003563541 Rv3733c Rv3733c hypothetical protein

MT3839 313.013076 293.786569 116.6882669 125.790122 0.399746804 -1.322841597 7.72558479 0.000623369 Rv3734c Rv3734c conserved hypothetical protein

MT3867 41.7610961 29.3491603 18.56552818 14.77830296 0.47377179 -1.077735798 4.67142562 0.021245859 Rv3760 Rv3760 conserved hypothetical protein

MT3870 299.352904 369.150494 106.0980713 166.8086401 0.408019558 -1.293289786 7.87602759 0.003232032 RV3763 IpqH 19 kDKD

MT3907 14,370.11 4,127.47 2,825.10 2,333.05 0.278872845 -1.842320637 12.5294487 0.006363538 Rv3800c pksl3 polyketide synthase

MT3908 4,858.34 1,777.17 1,423.79 1,165.10 0.390224236 -1.357624713 11.1703676 0.036285309 Rv3801c fadD32 acyl-CoA synthase

MT3932 87.8153891 36.575838 20.91890499 22.6329128 0.354143925 -1.497592299 5.3476356 0.003424009 Rv3824c papAl PKS-associated protein, unknown function

MT3939 16.392206 21.3850666 8.498305154 10.24008394 0.489918288 -1.029386947 3.80251024 0.033759492 Rv3831 Rv3831 hypothetical protein

MT3953 59.3241739 43.0650995 21.89947867 20.94562624 0.421809953 -1.245334956 5.15268502 0.00207743

MT3963 489.424435 315.024153 131.5929867 130.910164 0.326744 -1.61376735 8.05317994 7.13E-05 Rv3848 Rv3848 probable membrane proteinprot

MT3969 1,650.93 1,190.34 200.8868595 159.0122126 0.126698983 -2.980523155 9.64148554 2.87E-12 Rv3854c Rv3854c probable monooxygenase

MT3970 186.949206 169.310734 55.04286876 47.94221118 0.289310529 -1.789309267 6.83158774 5.84E-07 Rv3855 Rv3855 putative transcriptional regulator

MT3972 17.1727872 9.73389236 7.060130435 4.538219019 0.444260982 -1.170520655 3.16995054 0.040466515 Rv3857c Rv3857c hypothetical protein

MT3988 3,168.38 2,112.11 1,252.52 1,278.56 0.4793938 -1.060716843 10.9308176 0.044973745 Rv3874 Rv3874 conserved hypothetical protein

MT4005 180.704556 188.483552 72.23559381 97.04806825 0.458491225 -1.125033971 7.06774704 0.005886986 Rv3890c Rv3890c hypothetical protein

Table 2D: Upregulated gene expression tables of WT tb treated with HC101A compared to DMSO

Gene Counts per million (CPM) DMSO WT/HC101A WT

WT_DMS01 WT_DMS02 WT_HC101A1 WT_HC101A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0153 196.316181 299.685898 654.8924695 893.5055061 3. 116888797 1.540106684 9.00107705 0.000436841 Rv0145 Rv0145 conserved hypothetical protein

MT0154 206.854028 336.556703 857.3482469 1,090.63 3. .578987361 1.839551449 9.28592322 7.32E-05 Rv0146 Rv0146 conserved hypothetical protein

MT0213 25.3688902 52.0615758 66.94049598 102.9826624 2. 152396313 1.112630957 5.975215 0.033071525 RV0203 RV0203 hypothetical protein

MT0236 16.7824966 34.3635897 47.7866236 71.15694693 2. .275753662 1.186344402 5.44602791 0.019109561 Rv0226c Rv0226c probable membrane protein

MT0247 68.6911488 75.3639242 188.9238607 166.9250047 2. .465713077 1.30200493 6.97691654 0.00058961 Rv0236c Rv0236c possible membrane protein

MT0265 53.0795241 43.360066 401.9698338 182.9251358 6. .083941323 2.605006239 7.42456039 1.65 E-08 Rv0251c hsp possible heat shock protein

MT0270.2 1.95145309 4.57197974 9.544250403 10.7055423 2. .806463025 1.488753052 2.91633916 0.005185649

MT0298 19.9048215 26.3994959 30.98612802 96.98988596 2. .744589875 1.456590583 5.48068753 0.019260881

MT0342 4.2931968 3.392114 11.37465459 8.785526563 2. 700598296 1.43327906 2.9303237 0.011192668 Rv0327c Rv0327c cytochrome P-450 monooxygenasemonoxygenase

MT0382 1.95145309 2.21224826 17.12735345 12.04373509 6. .830401583 2.771970402 3.23386343 6.59E-08 Rv0366c Rv0366c conserved hypothetical protein

MT0384 1.17087185 2.80218113 5.295097827 6.516417053 2.635271 1.39795133 2.2172623 0.02336732 Rv0368c Rv0368c conserved hypothetical protein

MT0398 24.1980183 47.9320457 76.28863165 92.33530235 2. .298631885 1.200775444 5.93736923 0.010449641 Rv0385 Rv0385 similar to oxidoreductases

MT0426 37.85819 55.1587234 83.80636313 112.3500119 2. .089943741 1.063464107 6.19468928 0.014262803 RV0413 mutT3 utT homologue

MT0435 11.7087185 14.4533553 33.40487641 33.3966374 2. .514673933 1.330371344 4.594804 0.001805253 Rv0421c RV0421C hypothetical protein

MT0453 18.3436591 31.5614086 42.29541103 62.66233184 2. .063842714 1.045333027 5.3100483 0.033252288 Rv0437c psd putative phosphatidylserine decarboxylase

MT0465 16.7824966 19.3203015 34.84305113 39.91305445 2. .053885116 1.038355487 4.83349715 0.019433804 Rv0449c Rv0449c putative dehydrogenase

MT0468 37.0776087 53.0939583 320.9090769 348.9774061 7. .362190895 2.880135158 7.58244365 6.44E-15 Rv0452 Rv0452 putative transcriptional regulator

MT0469 12.4892998 12.6835567 35.43139533 28.50932461 2. .535063932 1.342022131 4.5325702 0.001864605 Rv0453 PPE PPE-family protein

MT0502 32.0038307 63.5652668 85.83288205 112.1172827 2. .045184861 1.032231252 6.21751778 0.039159881 Rv0484c Rv0484c oxidoreductase

MT0511 8.19610298 14.4533553 26.14863124 31.94208002 2. .471160841 1.305188915 4.40401589 0.005083875 Rv0492c Rv0492c gmc-type oxidoreductase

MT0519 12.4892998 24.1872477 38.89608897 39.21486691 2. .059191924 1.049067456 4.88996359 0.034688101 Rv0499 Rv0499 hypothetical protein

MT0535 2.34174371 7.07919444 19.51147343 18.15287608 3. .631988279 1.860759547 3.69041987 0.000201488 Rv0514 Rv0514 possible membrane protein

MT0556 12.8795904 10.3238252 29.94018277 25.77475674 2. .441383492 1.287698931 4.35709052 0.004070146 Rv0532 PE_PGRS PE_PGRS-family protein

MT0564 8.5863936 14.1583889 26.54086071 30.54570494 2. .424711819 1.277813291 4.38651639 0.004895033

MT0566 30.4426682 46.75218 87.85940097 78.13882234 2. 123534911 1.086467827 5.94863123 0.010221912 Rv0541c Rv0541c unknown membrane protein

MT0569 10.5378467 15.4857378 23.86062601 30.72025182 2. .046125087 1.032894345 4.3914378 0.031559747

MT0574 28.1009245 21.9749994 57.00401611 45.14946101 2. .061778861 1.043889603 5.27598414 0.017572545

MT0586 28.1009245 30.2340596 201.4752037 136.2629352 5. .771647481 2.528983186 6.65079751 1.50E-11 Rv0560c Rv0560c methyl transferase

MT0589 96.011492 120.346306 425.8304598 287.0132618 3. .286878746 1.716718236 7.86749244 2.80E-05 Rv0563 htpX probable (transmembrane) heat shock protein

MT0651 1.17087185 3.392114 6.341043075 8.087339021 2. 772796626 1.471341804 2.46807479 0.013593095

MT0654 9.36697483 19.6152679 38.76534582 51.14223741 2. .992689934 1.581442812 4.94947852 0.000812298 Rv0626 Rv0626 conserved hypothetical protein

MT0679 0.39029062 2.35973148 4.510638889 5.178224265 2. .851715697 1.511830159 1.93584468 0.018356424

MT0689 19.9048215 24.9246638 70.01296015 83.54977579 3. .386082932 1.759617308 5.66632135 1.59E-06 Rv0660c Rv0660c conserved hypothetical protein

MT0706.1 137.772588 69.7595619 521.7305649 291.7260277 3. .938996402 1.977828099 8.00218591 6.45 E-05 RV0678 RV0678 hypothetical protein

MT0738 242.370474 151.907714 816.1641526 730.3623506 3. .930874669 1.974850356 8.92602148 9.76E-06

MT0739 158.457991 119.16644 344.442845 284.3368762 2. .270233353 1.182840597 7.8291977 0.005158165 Rv0712 Rv0712 conserved hypothetical protein

MT0754 10.9281373 21.9749994 31.37835749 47.06947675 2. .315280291 1.211186859 4.85133483 0.02108558 Rv0729 xylB xylulose kinase

MT0772.1 1.17087185 5.8993287 12.87820089 25.89112133 4. .880196579 2.286939262 3.6666453 0.000208725

MT0808 27.7106339 41.2953009 265.4739787 172.3941404 6. .273762007 2.649330802 7.00317008 3.30E-11 Rv0784 Rv0784 conserved hypothetical protein

MT0851 67.5202769 79.6409375 251.7459473 276.0749903 3. .576123611 1.838396605 7.40955711 4.19E-07 Rv0830 Rv0830 conserved hypothetical protein

MT0854 11.7087185 20.9426169 39.22294686 39.04032002 2. 327104893 1.218536241 4.84420804 0.008203865 Rv0832 PE_PGRS PE_PGRS-family protein

MT0860 13.6601716 34.9535226 55.17361192 56.90228462 2. .244046651 1.166102658 5.3672368 0.028070721 Rv0838 IpqR lipoprotein

MT0885 35.9067369 63.71275 98.71108294 116.0154965 2. 131607785 1.091942007 6.31498285 0.020363606 Rv0862c Rv0862c conserved hypothetical protein

MT1021 3.90290618 9.29144271 15.16620612 27.52022559 3. .044793671 1.506344458 3.91105566 0.003989351 Rv0992c Rv0992c conserved hypothetical protein

MT1034 30.4426682 33.4786904 67.65958334 66.32781643 2.087643477 1.061875353 5.65277661 0.006175481 Rvl005c pabB p-aminobenzoate synthase

MT1054 8.19610298 11.6511742 27.12920491 25.30929838 2.565416889 1.359193288 4.24831867 0.001734138

MT1073 39.809643 37.9031869 245.6010189 98.38626104 4.42899315 2.146978766 6.73779954 1.46E-05 Rvl043c Rvl043c hypothetical protein

MT1087 115.916314 198.954861 368.8918152 553.4299912 2.919948846 1.545943095 8.27875796 0.000827668 Rvl057 Rvl057 conserved hypothetical protein

MT1112 9.75726545 11.3562078 22.61856602 22.98200657 2.131270014 1.091713382 4.12486106 0.015850829 Rvl081c Rvl081c hypothetical protein

MT1123 19.5145309 20.0577176 41.77243841 45.2658256 2.195533216 1.134571361 5.02104076 0.005787145 Rvl091 PE_PGRS PE_PGRS-family protein

MT1178 67.5202769 134.504694 231.0885286 239.6528736 2.315538464 1.211347722 7.40373555 0.011657439

MT1186 17.9533684 18.8778519 38.37311635 38.98213773 2.093484779 1.065906429 4.87422501 0.01294452 RV1152 RV1152 transcriptional regulator (GntR family)

MT1247 7.80581236 28.1692946 35.2352806 61.20777446 2.596957451 1.376822377 5.10147795 0.034766654 RV1209 RV1209 conserved hypothetical protein

MT1303 88.2056797 89.3748298 336.5982557 191.827027 2.97476628 1.572776324 7.47251288 0.000231662 Rvl265 Rvl265 hypothetical protein

MT1379 62.0562083 59.2882535 141.5948382 101.1208289 2.001623231 1.001170439 6.52020231 0.021193865 Rvl338 murl glutamate racemase

MT1429 26.1494714 34.5110729 78.77275162 83.49159349 2.645457172 1.403517062 5.82759285 0.00020113 Rvl385 pyrF orotidine 5'-phosphate decarboxylase

MT1446 9.75726545 9.43892592 20.33056079 18.38560526 2.021213343 1.015221609 3.92042063 0.034281244

MT1514.1 19.1242403 33.92114 43.99507206 74.58970234 2.197094946 1.135597216 5.45687431 0.025203737 Rvl468c PE_PGR5 PE_PGRS-family protein

MT1613 33.5649932 47.6370793 93.1544988 79.12792136 2.099880584 1.070307287 6.00681164 0.009738412 Rvl562c glgZ maltooligosyltrehalose trehalohydrolase

MT1619 23.4174371 42.3276834 74.32748431 99.14263088 2.595110077 1.375795735 5.92945404 0.00197997 Rvl568 bioA adenosylmethionine-8-amino-7-oxononanoate

MT1620 13.6601716 38.9355694 44.32192996 92.9753076 2.557940633 1.354982781 5.60579953 0.033675427 Rvl569 bioF 8-amino-7-oxononanoate synthase

MT1621 4.68348742 9.14395949 21.18039131 33.3384551 3.736178549 1.901563402 4.19000449 8.41E-05 Rvl570 bioD dethiobiotin synthase

MT1622 1.56116247 2.65469792 5.818070451 11.63645902 3.85016715 1.94492108 2.65113909 0.001896362 RV1571 RV1571 conserved hypothetical protein

MT1645 19.1242403 41.0003345 69.48998753 88.32072399 2.570978984 1.362317817 5.79841313 0.003964587 Rvl610 Rvl610 possible membrane protein

MT1719 80.0095767 70.2020116 162.1215137 144.4084565 2.045124255 1.032188499 6.84491956 0.010919028 Rvl679 fadE16 acyl-CoA dehydrogenase

MT1746 4.68348742 5.75184549 14.6432335 10.7637246 2.37444345 1.247589397 3.277647 0.017967173 Rvl706c PPE PPE-family protein

MT1753 62.0562083 77.8711389 170.9466767 129.6883358 2.139692787 1.097403672 6.79526578 0.007969339 Rvl713 Rvl713 conserved hypothetical protein

MT1758 7.02523112 7.07919444 12.94357246 15.65103739 2.024987774 1.017913198 3.5006925 0.049024614

MT1836 51.5183616 33.3312072 118.2571848 69.99330103 2.239540405 1.163202695 6.1083948 0.017688136 Rvl787 PPE PPE-family protein

MT1837 3.51261556 3.68708044 18.17329871 7.38915148 3.518866315 1.815110706 3.17552499 0.004627557 Rvl788 PE PE-family protein

MT1888 15.2213341 14.3058721 38.04625846 31.94208002 2.378402695 1.249993003 4.68344445 0.004200151 Rvl840c PE_PGRS PE_PGRS-family protein

MT1893 61.6659177 127.278017 230.8924139 298.0678979 2.781237859 1.475727133 7.49782011 0.002014733 Rvl845c Rvl845c hypothetical protein

MT1960 53.0795241 49.8493275 131.9198446 75.0551607 2.012848292 1.009238441 6.2897503 0.033134083

MT2055 7.41552174 9.73389236 25.56028704 19.72379804 2.575174209 1.364670033 4.04417813 0.002584789

MT2084 27.3203433 18.4354022 52.03577617 50.50223216 2.28278274 1.19079356 5.24020568 0.00578763 Rv2025c Rv2025c possible membrane protein

MT2094 1.95145309 5.8993287 10.78631039 14.72012066 2.928455963 1.5501402 3.2171278 0.005008925

MT2112 41.3708055 53.8313744 246.5815926 122.4737312 3.857035592 1.947492459 6.87489784 1.94E-05 Rv2052c Rv2052c hypothetical protein

MT2126 17.1727872 25.9570463 42.75301208 62.72051414 2.402614999 1.264605486 5.25402506 0.004366979 Rv2066 cobl Cobl-CobJ fusion protein

MT2159 7.80581236 9.43892592 19.54610185 15.88376657 2.017464249 1.012543108 3.79490609 0.03961407 Rv2098c PE_PGR5 PE_PGRS-family protein

MT2164 7.80581236 15.3382546 26.21400282 23.68019411 2.067517442 1.0478995 4.25968596 0.037189219 Rv2104c Rv2104c conserved hypothetical protein

MT2182.1 2.73203433 7.5216441 11.24391143 23.15655346 3.11673293 1.640034537 3.61040594 0.007028674

MT2220 309.11017 447.316599 815.183579 804.1375008 2.138629257 1.096686405 9.21660886 0.02413631 Rv2162c PE_PGRS PE_PGRS-family protein

MT2264 7.80581236 16.0756707 39.68054791 67.08418627 4.302885731 2.105304528 5.08799787 9.81E-06 Rv2208 cobS cobalamin (5'-phosphate) synthase

MT2310 22.2465652 20.2052008 36.93494163 49.80404462 2.052978984 1.037718859 5.04586575 0.021255562 putative transcriptional regulator

MT2311 161.580316 216.35788 395.8249054 613.532302 2.666528778 1.414962898 8.4428077 0.001734138 Rv2251 Rv2251 conserved hypothetical protein

MT2334 8.5863936 17.8454693 32.16281643 45.09127872 2.817302962 1.494314714 4.75744434 0.002409597

MT2389 115.916314 121.378688 252.4650346 271.7695005 2.207966094 1.142718018 7.57962372 0.003671666 Rv2327 Rv2327 conserved hypothetical protein

MT2434 1.95145309 5.0144294 12.09374195 9.367349514 2.77776241 1.473923207 2.99599504 0.006298485

MT2515 8.19610298 16.3706372 36.47734058 45.44037249 3.206324692 1.680920529 4.79717304 0.0002669 Rv2439c proB glutamate 5-kinase

MT2526 117.087185 186.418787 295.5449046 339.493692 2.085449997 1.060358721 7.8805006 0.021295236 Rv2450c Rv2450c conserved hypothetical protein

MT2533 8.97668421 21.680033 29.61332488 43.05489839 2.289470441 1.195013939 4.74870605 0.0338307 Rv2458 Rv2458 conserved hypothetical protein

MT2540 25.3688902 59.2882535 78.5112653 119.3318873 2.303713508 1.203961313 6.16545003 0.027194856 Rv2465c rpi phosphopcntosc isomcrasc

MT2608 78.0581236 110.46493 212.0000278 258.5039372 2.484956519 1.313220608 7.37372216 0.001365742 Rv2533c nusB N-utilisation substance protein B

MT2615.1 1.56116247 4.86694618 6.733272545 12.80010493 2.731778008 1.449840251 2.88124352 0.023378291

MT2628 0.78058124 5.45687905 12.15911353 11.8691882 3.321507788 1.731838297 3.10280927 0.003668674

MT2631 21.8562746 31.2664421 57.85384662 50.38586757 2.007268018 1.005233264 5.3651424 0.019433804

MT2657 597.144546 619.282031 1,613.24 1,665.93 2.695545894 1.430577473 10.1356765 0.001486586 Rv2590 fadD9 acyl-CoA synthase

MT2668.1 33.9552838 39.0830527 114.661748 87.62253645 2.75598679 1.462568973 6.12689548 0.000134878 Rv2591 PE_PGRS PE_PGRS-family protein

MT2690 12.0990092 20.9426169 37.3271711 79.12792136 3.448774073 1.786083622 5.27128487 0.000453302 Rv2615c PE_PGRS PE-family protein

MT2693 17.5630778 19.3203015 39.09220371 41.94943478 2.184547265 1.127334321 4.92172818 0.007175485

MT2718 8.19610298 12.9785231 31.83595854 47.24402363 3.620228381 1.856080712 4.71432411 3.62E-05

MT2729 12.0990092 14.7483218 31.83595854 26.53112657 2.143221757 1.099781132 4.46680489 0.014408261 Rv2652c phiRV2 phage related protein

MT2736.1 2.73203433 3.53959722 11.44002617 8.029156726 2.987385962 1.578883642 2.84973253 0.003964587

MT2739 23.8077277 40.1154352 97.86125242 97.57170891 3.005875284 1.587785152 6.04543073 7.49E-05

MT2793 232.613208 269.894288 538.0080878 493.3276803 2.050915155 1.03626781 8.58628718 0.021245859 RV2720 lexA LexA, SOS repressor protein

MT2805 24.1980183 32.7412743 59.03053503 60.27685774 2.069316609 1.049154397 5.49025089 0.010374701 Rv2736c recX regulatory protein for RecA

MT2808.1 16.392206 29.4966435 39.28831844 64.87325906 2.224804255 1.153678409 5.26775839 0.023378291 Rv2739c Rv2739c glycosyltransferase

MT2814 76.4969511 98.0763397 202.2596627 164.1322545 2.091313814 1.064409563 7.08920106 0.011470854 Rv2743c Rv2743c conserved hypothetical protein

MT2816 59.3241739 75.5114074 296.3293635 188.8015477 3.583855095 1.841512307 7.28787865 7.54E-06 Rv2745c Rv2745c putative transcriptional regulator

MT2832 2.73203433 6.63674479 16.56975242 14.13829771 3.015345533 1.592323332 3.46285068 0.001697979 Rv2762c Rv2762c hypothetical protein

MT2902 28.8815057 28.464261 75.11194324 64.3496184 2.432653335 1.282530744 5.6469077 0.000718899 Rv2836c dinF DNA-damage-inducible protein F

MT2914 50.3474897 41.4427841 106.9479018 81.74612464 2.055793601 1.046696118 6.14685145 0.013851196 cobB cobyrinic acid a,c-diamide synthase

MT3002 817.268554 569.28522 1,831.19 1,332.20 2.282482861 1.190604027 10.1526528 0.022139378

MT3003 2,070.49 1,694.29 4,461.74 4,282.33 2.322828008 1.215882335 11.6110682 0.012801313 RV2933 ppsC phenolpthiocerol synthesis (pksD)

MT3018 366.873181 292.754187 895.8521064 876.7490051 2.689153979 1.427152365 9.25040831 0.001196406 Rv2946c pksl polyketide synthase

MT3021.1 86.6445172 67.8422801 202.5865205 158.0812958 2.343337999 1.228565061 7.01827515 0.002584789 Rv2947c pksl5 polyketide synthase

MT3044 5.46406865 9.73389236 20.85353342 19.84016263 2.545482494 1.347939144 3.89808912 0.003953304

MT3050 6.63494051 6.48926157 16.01603664 12.33464656 2.161716242 1.11217716 3.46325515 0.034443851 Rv2972c Rv2972c hypothetical protein

MT3110 5.07377803 3.83456366 30.39778382 18.15287608 5.618510293 2.490187661 3.95181228 4.26E-07 Rv3026c Rv3026c some similarity to acyltransferase Q59601

MT3122 7.80581236 12.9785231 33.56636272 38.98213773 3.369485613 1.752528366 4.61506366 5.05E-05 Rv3037c Rv3037c hypothetical protein

MT3124 23.0271465 42.1802002 63.34505918 72.7278689 2.04970793 1.03541835 5.68107454 0.025279872 Rv3039c echA17 enoyl-CoA hydratase/isomerase superfamil

MT3140 1.95145309 2.5072147 26.21400282 9.076438038 7.635770088 2.932773654 3.47069402 7.46E-06 conserved hypothetical protein

MT3151 14.0504523 13.8634225 39.4190615 31.94208002 2.556879158 1.354383978 4.68339085 0.001656726 RV3066 RV3066 putative transcriptional regulator

MT3176.1 94.0600389 97.1914404 246.6469642 215.681768 2.416055519 1.272653607 7.36071869 0.000935573

MT3256 4.2931968 4.71946296 10.98242512 8.843708858 2.169478554 1.117348325 2.97180107 0.046428091 Rv3167c Rv3167c putative transcriptional regulator

MT3271 11.3184279 11.9461406 22.74930918 24.96020461 2.041154612 1.029385467 4.20673149 0.02515022 Rv3180c Rv3180c hypothetical protein

MT3276 38.2484806 44.2449653 99.49554188 72.6696866 2.07755312 1.054885365 6.01162539 0.011192668

MT3293 41.7610961 66.5149311 106.294186 124.5682938 2.112502714 1.078953195 6.42254074 0.015069945 Rv3199c Rv3199c conserved hypothetical protein

MT3340 8.19610298 7.96409375 18.5001565 18.85106362 2.316064787 1.21167561 3.81930887 0.008660259 Rv3242c Rv3242c conserved hypothetical protein

MT3345 7.02523112 12.2411071 29.35183857 31.59298625 3.032604843 1.600557523 4.40147904 0.0002669 Rv3247c tmk thymidylate kinase

MT3369 418.781833 351.010058 1,077.85 1,295.49 3.084469984 1.525022607 9.6200301 0.000214157 Rv3269 Rv3269 probable heat shock protein

MT3406 38.2484806 61.7954682 94.59267352 147.4921181 2.398262855 1.26198979 6.43662874 0.006797906 Rv3307 deoD probable purine nucleoside phosphorylase

MT3407 22.6368559 24.9246638 49.22479831 63.53506627 2.359735275 1.238625022 5.35725334 0.00202223 RV3308 pmmB phosphomannomutase

MT3492 4.2931968 10.7662749 32.29355958 30.48752264 3.897635134 1.962599043 4.37117375 2.90E-05 Rv3384c Rv3384c conserved hypothetical protein

MT3495 4.2931968 1.62231539 10.39408092 9.309167219 3.815297509 1.93179556 2.82408928 0.00223136 Rv3388 PE_PGR5 PE_PGRS-family protein

MT3514 65.1785332 50.2917772 303.5202371 96.05896924 3.469025162 1.794530305 7.02099715 0.002407018 Rv3406 Rv3406 putative dioxygenasediooxygenase

MT3524 2.34174371 3.09714757 6.341043076 11.8691882 3.223784028 1.688755096 2.74715203 0.005505017 Rv3415c Rv3415c conserved hypothetical protein

MT3539 12.0990092 16.8130868 32.94727537 32.23299149 2.2076827 1.142532835 4.60893403 0.010732372 Rv3433c Rv3433c conserved hypothetical protein

MT3548 247.834542 367.380695 589.8477492 693.8238693 2.083917608 1.059298239 8.89396797 0.033604484 Rv3443c rplM 50S ribosomal protein L13

MT3592 2.73203433 9.43892592 12.551343 17.74560001 2.296121357 1.199198895 3.53183797 0.04811238

MT3612 15.6116247 24.1872477 51.97040459 50.44404987 2.517241207 1.331843465 5.19319801 0.001223163 Rv3507 PE_PGRS PE_PGRS-family protein

MT3666 19.1242403 31.7088918 54.32378141 56.72773774 2.141453364 1.098590259 5.37285514 0.012098186

MT3696 6.24464989 11.3562078 21.76873551 31.65116854 2.905364083 1.538718965 4.23330711 0.001340758 Rv3590c PE_PGR5 PE_PGRS-family protein

MT3756 6.24464989 12.2411071 22.29170813 19.89834493 2.172874227 1.119604669 4.00548733 0.024333502

MT3758 3.90290618 6.78422801 9.740365138 16.00013116 2.287001502 1.193457313 3.30955767 0.034876382 Rv3658c Rv3658c probable transmembrane protein

MT37S3 3.90290518 6.63674479 11.37465459 11.81100591 2.078813776 1.055760525 3.19706184 0.048817793 Rv3662c Rv3662c hypothetical protein

MT3831 6.63494051 9.29144271 24.90657125 26.06566821 3.098585585 1.631609817 4.14886482 0.000110601 Rv3728 Rv3728 possible sugar transporter

MT3880 5.07377803 3.98204687 9.217392513 11.17100066 2.319941604 1.214088491 2.99383814 0.034220816 Rv3771c Rv3771c conserved hypothetical protein

MT3914 71.0328925 109.874997 201.9328048 221.4999975 2.32789127 1.219023675 7.24939738 0.004133928 Rv3807c Rv3807c possible membrane protein

MT3921 5.07377803 2.94966435 10.32870934 13.0910164 3.128576963 1.645506595 3.09822964 0.003794215

MT3998 121.380382 111.497313 412.7561442 272.1767766 2.94323293 1.557401723 7.8488052 0.000176222 RV3883C RV3883C probable secreted protease

MT4025 10.5378467 19.9102344 35.69288165 38.63304396 2.363203499 1.240743867 4.76582909 0.008706425 Rv3906c Rv3906c conserved hypothetical protein

as

Table 2E: Downregulated gene expression tables of WT Mtb treated with HC102A compared to DMSO

Gene Counts per million (CPM) WT D SO/WT HC102A

WT_DMS01 WT_DMS02 WT_HC102A1 WT_HC102A2 Fold change log2 Fold change logCP Adjusted p-value Rv number Gene name Annotated function

MT0595 268.86154 166.489022 21.37579586 25.91548951 0.10889336 -3.199012103 6.90534438 6.46E-10 Rv0569 Rv0569 conserved hypothetical protein

MT0596 2,739.23 1,602.51 102.6525862 94.10488838 0.045326402 -4.46350456 10.1467857 1.17E-11 Rv0570 nrdZ ribonucleotide reductase, class II

MT0597 233.683395 391.419089 94.1998 81.32304061 0.280536264 -1.833740818 7.64431228 0.007274158 Rv0571c Rv0571c conserved hypothetical protein

MT0598 190.608115 322.105292 57.70652114 66.54769365 0.242120414 -2.046203369 7.313962 0.000631144

MT0599 534.851395 726.707593 127.4420072 180.587574 0.244148489 -2.034169248 8.61536498 0.003135948 Rv0572c Rv0572c hypothetical protein

MT0600 915.708663 1,233.38 129.5552038 211.3109145 0.158620436 -2.656349443 9.28114862 6.40E-05

MT0601 88.6632849 83.1765564 13.81705436 19.29003631 0.193202634 -2.371813334 5.66671759 4.53E-07 Rv0573c Rv0573c conserved hypothetical protein

MT0602 357.883786 324.95939 45.10861864 51.53781737 0.141618201 -2.819921397 7.602328 9.79E-08 Rv0574c Rv0574c conserved hypothetical protein

MT109S 16.5121907 20.6582297 9.103000518 3.811101398 0.343643905 -1.541013723 3.63229664 0.153219639

MT1385 137.840896 109.407072 56.64992286 35.06213287 0.371217878 -1.429661902 6.3994683 0.031837186

MT1774 1,342.51 1,645.73 109.6423902 115.9747472 0.075506286 -3.727259433 9.64920275 9.78E-10 Rvl733c Rvl733c possible membrane protein

MT1775 532.697631 610.505051 172.1442419 61.79847498 0.20456776 -2.289349304 8.42595935 0.004239872

MT1776 19.0249154 15.3577629 5.201714582 4.162895374 0.274235718 -1.866511608 3.40676192 0.00225844 Rvl735c Rvl735c hypothetical protein

MT1777 100.867948 180.351782 11.46002744 24.0978873 0.126516464 -2.982602952 6.30334017 1.38E-07

MT1778 5,333.80 3,333.72 234.4835401 246.0798857 0.055450253 -4.172662152 11.1586863 6.00E-11 Rvl736c narX fused nitrate reductase

MT1779 1,908.95 1,381.11 72.41762019 91.9354922 0.049973376 -4.322696514 9.75284262 1.17E-11 Rvl737c narK2 nitrite extrusion protein

MT1780 3,549.04 4,687.52 337.7863406 628.9489954 0.117377012 -3.090778204 11.1676891 4.29E-06 Rvl738 Rvl738 conserved hypothetical protein

MT1839 62.1001955 42.9473723 29.82858205 18.93824233 0.466011498 -1.101562543 5.25494611 0.49861605 RV1790 PPE PPE-family protein

MT1860 228.298985 153.30581 54.94311027 65.8441057 0.317076728 -1.657096103 6.96750601 0.007760235 Rvl812c Rvl812c probable dehydrogenase

00 MT1861 2,822.51 1,488.34 121.346248 147.2257786 0.062318769 -4.004189449 10.1597254 1.18E-09 Rvl813c Rvl813c conserved hypothetical protein

MT1882 75.3817402 71.3524381 37.79370751 31.48556078 0.47231284 -1.082185339 5.75107316 0.275155648 Rvl834 Rvl834 conserved hypothetical protein

MT2052 38,106.55 8,582.81 561.6226212 277.3309171 0.017968834 -5.798359383 13.536324 2.50E-10 Rvl996 Rvl996 conserved hypothetical protein

MT2053 2,979.37 1,578.86 105.0908899 117.3819231 0.048820109 -4.356380684 10.2218042 5.28E-11 Rvl997 ctpF probable cation transport ATPase

MT2059 506.852463 843.317864 203.5983598 97.1537695 0.222651698 -2.16713948 8.68849175 0.006801091 Rv2003c Rv2003c conserved hypothetical protein

MT2060 2,556.88 2,604.84 661.1866894 393.8919876 0.204398455 -2.290543807 10.6015696 0.001198816 Rv2004c Rv2004c hypothetical protein

MT2061 2,295.91 2,093.28 308.4454193 262.8487318 0.130163441 -2.9416038 10.2756004 1.66E-06 Rv2005c Rv2005c conserved hypothetical protein

MT2062 567.157855 767.480415 140.7714009 181.0566326 0.241112783 -2.052219957 8.69310712 0.002861277 Rv2006 otsB trehalose-6-phosphate phosphatase

MT2063 7,226.24 9,239.80 1,505.73 2,151.57 0.222112178 -2.170639598 12.2965031 0.00225844 Rv2007c fdxA ferredoxin

MT2086 312.654741 182.93406 90.78617481 84.3132894 0.353776498 -1.499089886 7.38546279 0.065748479 Rv2027c Rv2027c sensor histidine kinase

MT2087 745.561307 675.741566 62.09546782 56.16977138 0.083223857 -3.586859038 8.5858908 3.60E-10 Rv2028c Rv2028c conserved hypothetical protein

MT2088 4,603.67 2,470.97 254.0712466 225.5585705 0.067802631 -3.882514936 10.8823475 2.73E-09

MT2089 13,680.35 13,788.01 1,125.52 784.7350941 0.069543418 -3.845942215 12.8423576 4.93E-10 Rv2030c Rv2030c conserved hypothetical protein

MT2090 43,613.72 41,594.39 3,874.46 5,782.55 0.113335288 -3.141330972 14.5335551 4.53E-07

MT2091 3,762.63 5,608.17 270.570435 336.8427313 0.064822017 -3.947372269 11.28433 4.32E-10 Rv2032 Rv2032 conserved hypothetical protein

MT2698 41,070.84 21,419.05 903.5540782 611.3592966 0.024242603 -5.366311566 13.9657966 2.87E-14 Rv2623 Rv2623 conserved hypothetical protein

MT2699 2,345.81 1,782.86 106.228765 108.4111767 0.051997333 -4.26541855 10.0835172 1.38E-11 Rv2624c Rv2624c conserved hypothetical protein

MT2700 5,579.68 3,573.60 146.135669 111.8704841 0.028188487 -5.148750164 11.1996004 1.76E-14 Rv2625c Rv2625c conserved hypothetical protein

MT2701 12,542.44 10,243.90 447.5100076 554.4859373 0.043975931 -4.507142079 12.5377788 5.37E-13 Rv2626c Rv2626c conserved hypothetical protein

MT2702 7,537.46 5,491.42 101.2708808 156.724216 0.01980729 -5.6578247 11.6973292 6.57E-17 Rv2627c Rv2627c conserved hypothetical protein

MT2703 674.128134 872.946114 20.64430475 33.42042765 0.034986572 -4.837054871 8.64298969 2.96E-14 Rv2628 Rv2628 hypothetical protein

MT2704 7,455.97 4,707.09 540.5719325 660.1413945 0.098725003 -3.340440678 11.7056884 1.12E-07 Rv2629 Rv2629 hypothetical protein

MT2705 735.510408 545.812174 71.27974513 56.05250672 0..099397816 -3.33064204 8.45712957 1.63E-08 Rv2630 Rv2630 hypothetical protein

MT2707 1,083.70 473.100642 110.861542 72.58682356 0. .117877549 -3.084639128 8.76191316 1.10E-05 Rv2631 Rv2631 conserved hypothetical protein

MT3168 297.219433 288.943397 100.2955593 66.8408553 0. .285100254 -1.81045877 7.55451932 0.005587532 Rv3083 Rv3083 probable monooxygenase

MT3169 45.5880048 49.3351143 16.74301881 9.205275685 0. .272400211 -1.876200276 4.90417444 0.001146198 Rv3084 lipR probable acetyl-hydrolase

MT3170 28.7168534 34.2491703 11.7851346 8.618952393 0. .322380984 -1.633161448 4.3696841 0.007955648 Rv3085 Rv3085 short chain alcohol dehydrogenase

MT3209 12.5636234 14.9500347 5.689375324 5.394174287 0. .400042658 -1.321774248 3.25998407 0.179392401

MT3210 7.89713469 5.70819505 0.568937532 0.117264658 0. .049489681 -4.336728438 1.63692637 7.67E-09

MT3212 15,265.16 9,828.83 690.1212267 898.1886511 0. .063297395 -3.981710068 12.7034075 3.82E-10 Rv3127 Rv3127 conserved hypothetical protein

MT3216 31,587.46 26,323.89 1,395.93 1,787.99 0. .054980252 -4.184942683 13.8987023 1.54E-11 Rv3130c Rv3130c conserved hypothetical protein

MT3217 17,927.57 9,861.72 415.6495058 421.6837117 0. .030133008 -5.05251151 12.8048644 3.98E-14 Rv3131 Rv3131 conserved hypothetical protein

MT3218 5,014.32 3,071.96 438.9759446 364.75172 0. .099400131 -3.330608443 11.1174312 1.84E-07 Rv3132c Rv3132c sensor histidine kinase

MT3219 3,634.48 1,966.07 233.8333258 174.0207531 0. .072830384 -3.779315735 10.5518606 8.64E-09 Rv3133c Rv3133c two-component response regulator

MT3220 5,959.47 3,727.18 264.5559525 171.7927246 0. .045046862 -4.472429565 11.3048235 1.54E-11 Rv3134c Rv3134c conserved hypothetical protein

MT3947 86.5095209 58.7128633 25.92729612 7.680835126 0. .231430045 -2.111351925 5.46470098 0.006563585 Rv3839 Rv3839 hypothetical protein

Table 2F: Upregulated gene expression tables of WT Mtb treated with HC102A compared to DMSO

Gene Counts per million (CPM) WT DMSO/WT HC102A

WT_DMS01 WT_DMS02 WT_HC102A1 WT_HC102A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT3514 59.9464315 46.3451074 494.4067156 167.9816232 6.242013606 2.642011502 7.59224185 0.000317734 Rv3406 Rv3406 putative dioxygenasediooxygenase MT3515 60.6643528 43.6269193 191.0817341 103.1342671 2.83052096 1.501067607 6.64659687 0.059101187 Rv3407 Rv3407 conserved hypothetical protein

00

Table 2G: Down regulated gene expression tables of WT Mtb treated with HC103A compared to DMSO

Gene Counts per million (CPM) WT DMSO /WT HC103A

WT_DMS01 WT_DMS02 WT_HC103A1 WT_HC103A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0086 1,344.34 2,642.07 612.5276035 320.9822393 0.234129998 -2.094618305 10.2641608 0.002403546 Rv0079 Rv0079 hypothetical protein

MT0087 366.745783 887.742741 224.6690753 124.678515 0.278271737 -1.845433709 8.64718864 0.011177019 Rv0080 Rv0080 hypothetical protein

MT0595 293.474991 181.277689 28.43338011 30.13064112 0.123647827 -3.015691208 7.04534272 4.00E-12 RV0569 RV0569 conserved hypothetical protein

MT0596 2,990.00 1,744.85 73.80579518 59.09242116 0.028074924 -5.154574088 10.2471594 7.73E-20 Rv0570 nrdZ ribonucleotide reductase, class 1

MT0597 255.076394 426.187547 71.15907097 45.13102495 0.170484289 -2.552289305 7.63637259 1.57E-07 Rv0571c Rv0571c conserved hypothetical protein

MT0598 208.057704 350.716836 38.26407004 19.74076487 0.103640123 -3.27034546 7.26356337 9.61E-11

MT0599 583.815402 791.258616 49.6827945 34.61127525 0.061279748 -4.028445826 8.50796164 9.17E-17 Rv0572c Rv0572c hypothetical protein

MT0600 999.538986 1,342.93 44.69182885 9.22101517 0.023006121 -5.441838415 9.22447285 2.48E-12

MT0601 96.780137 90.5648538 11.49434515 9.545698803 0.112430302 -3.152897175 5.6772449 1.09E-16 Rv0573c Rv0573c conserved hypothetical protein

MT0602 390.64595 353.824453 26.39162143 16.68873872 0.057867557 -4.111101441 7.61294181 1.23E-19 Rv0574c Rv0574c conserved hypothetical protein

MT0846 8,264.32 7,719.32 2,581.69 3,416.39 0.375267691 -1.414008011 12.4238902 0.049685627 Rv0824c desAl acyl-[ACP] desaturase

MT1095 479.198816 497.514769 198.5043159 168.5757421 0.37580797 -1.411932431 8.39033385 0.008693841 Rvl065 Rvl065 conserved hypothetical protein

MT1126 7,639.36 5,982.31 2,249.03 2,771.69 0.368594808 -1.439892344 12.1861135 0.042853699 RV1094 desA2 acyl-[ACP] desaturase

MT1322 615.94484 650.8239 223.6860063 205.2649926 0.338601401 -1.562340153 8.72613001 0.003978725 RV1284 RV1284 conserved hypothetical protein

MT1692 626.915868 234.995078 176.2718326 60.13140879 0.274508805 -1.865075672 8.09465786 0.032145592 Rvl654 argB acetylglutamate kinase

MT1693 522.691105 198.591558 135.0585555 51.68963433 0.259191794 -1.947908054 7.81868454 0.014293698 Rvl655 argD acetylornithine aminotransferase

MT1694 566.575215 168.699237 115.1703136 42.01406208 0.214013541 -2.224226011 7.79205039 0.008693841 Rvl656 argF ornithine carbamoyltransferase

MT1774 1,465.42 1,791.91 40.60831149 8.961268264 0.015211976 -6.038648635 9.68951437 5.69E-15 Rvl733c Rvl733c possible membrane protein

MT1775 581.464467 664.734188 101.9366925 24.15646228 0.101154341 -3.305369861 8.41880625 2.26E-06

MT1776 20.7665881 16.721942 4.990965658 2.922152695 0.212549883 -2.234126628 3.41909127 3.64E-05 Rvl735c Rvl735c hypothetical protein

MT1777 110.102099 196.371832 5.142207042 2.013038523 0.023219994 -5.42848851 6.28084269 1.09E-22

MT1778 5,822.09 3,629.85 122.2786585 26.1695008 0.01570476 -5.992654328 11.2279303 4.16E-13 Rvl736c narX fused nitrate reductase

MT1779 2,083.71 1,503.79 36.90289759 14.54582675 0.01433855 -6.123957096 9.82700111 7.71E-21 Rvl737c narK2 nitrite extrusion protein

MT1780 3,873.95 5,103.89 133.470521 33.11773054 0.018553396 -5.752172919 11.1580888 5.71E-14 RV1738 RV1738 conserved hypothetical protein

MT1823 677.460959 367.734741 222.7029373 163.7054876 0.369999624 -1.434404289 8.48011424 0.030780306 Rvl773c Rvl773c transcriptional regulator (IcIR family)

MT1860 249.199057 166.923456 78.19179531 78.70331258 0.377784471 -1.404364695 7.15571214 0.006966211 Rvl812c Rvl812c probable dehydrogenase

MT1861 3,080.90 1,620.55 58.53041544 24.74089282 0.017712284 -5.819105922 10.222168 6.26E-18 Rvl813c Rvl813c conserved hypothetical protein

MT1882 82.2827076 77.6904383 28.35775942 29.22152695 0.360385832 -1.4723858 5.75296114 0.000318876 Rvl834 Rvl834 conserved hypothetical protein

MT1986 314.633401 78.7263108 72.29338135 31.5592491 0.264644172 -1.917874211 6.94117308 0.036540371 Rvl936 Rvl936 similar alkanal monooxygenase alpha chain

MT1987 396.132464 99.443761 83.71210581 36.75418723 0.243540613 -2.037765716 7.2530058 0.021838157 Rvl937 Rvl937 similar to ring-hydroxylating dioxygenases

MT1988 156.337145 36.5515014 32.13879401 15.97443473 0.250792275 -1.995435178 5.87799594 0.019514616 Rvl938 ephB probable epoxide hydrolase

MT1989 68.1771006 20.1255231 16.33406943 8.831394811 0.288272345 -1.794495652 4.76511612 0.032145592 Rvl939 Rvl939 similar nitrilotriacctatc monooxygenase component

MT2016 378.108633 172.102819 93.31593367 56.94950919 0.273586323 -1.869931983 7.44310485 0.002131279 Rvl964 Rvl964 part of mce3 operon

MT2017 311.498822 93.3765077 44.46496677 29.87089421 0.184132813 -2.441181356 6.88594958 0.000176184

MT2018 346.762839 110.98634 54.82500155 33.76709781 0.194002689 -2.365851444 7.07797394 0.000318876 RV1966 mce3 cell invasion protein

MT2019 358.517512 99.8877063 58.15231198 26.29937425 0.184609615 -2.437450404 7.06759573 0.001388491 Rvl967 Rvl967 part of mce3 operon

MT2020 409.454426 115.425794 72.36900204 31.88393274 0.19897433 -2.329345774 7.28307276 0.00283279 Rvl968 Rvl968 part of mce3 operon

MT2021 104.224763 40.9909551 29.34082841 13.89645948 0.299724448 -1.738291327 5.52495651 0.014293698 Rvl969 Rvl969 part of mce3 operon

MT2022 240.970787 76.0626386 41.74262187 24.09152555 0.208386864 -2.262663756 6.55893009 0.000614941 Rvl970 IprM part of mce3 operon

MT2023 325.604429 92.488617 53.3882084 33.31254072 0.207923107 -2.265877997 6.96231439 0.001404244 Rvl971 Rvl971 part of mce3 operon

MT2024 36.4394848 22.4932317 12.77989691 9.285951897 0.379139962 -1.399197566 4.29593002 0.022895927 Rvl972 Rvl972 conserved hypothetical protein

MT2048 2,139.35 817.155429 531.3866012 326.761608 0.290344505 -1.784162363 9.89554944 0.02467178 Rvl992c ctpG probable cation transport ATPase

MT2052 41,595.08 9,345.20 107.0788995 83.44369362 0.003740545 -8.062535237 13.6416439 2.73 E-20 Rvl996 Rvl996 conserved hypothetical protein

MT2053 3,252.13 1,719.10 57.84982922 33.11773054 0.018301247 -5.771914204 10.3036166 4.69E-20 Rvl997 ctpF probable cation transport ATPase

MT2059 553.253253 918.226989 93.54279574 62.92368803 0.106281917 -3.234031939 8.66688637 2.99E-10 Rv2003c Rv2003c conserved hypothetical protein

MT2060 2,790.95 2,836.22 219.6781096 144.3543431 0.064691641 -3.950276881 10.5476363 6.06E-14 Rv2004c Rv2004c hypothetical protein

MT2061 2,506.10 2,279.22 138.385866 91.75559462 0.04809474 -4.377977065 10.2908234 1.17E-16 Rv2005c Rv2005c conserved hypothetical protein

MT2052 619.079419 835.653152 107.457003 97.40508983 0.140787855 -2.828405205 8.69441052 1.78E-09 Rv2006 otsB trehalose-6-phosphate phosphatase

MT2063 7,887.78 10,060.54 527.756808 132.3410487 0.036776485 -4.765072593 12.1833835 1.97E-10 Rv2007c fdxA ferredoxin

MT2086 341.277325 199.183486 73.20082965 62.79381457 0.252079115 -1.988051492 7.39337895 2.99E-05 Rv2027c Rv2027c sensor histidine kinase

MT2087 813.815161 735.765446 35.9198286 8.701521358 0.028784019 -5.118588124 8.63420694 2.36E-13 Rv2028c Rv2028c conserved hypothetical protein

MT2088 5,025.12 2,690.46 84.09020927 21.29924631 0.01365854 -6.194052864 10.9318764 1.20E-14

MT2089 14,932.74 15,012.75 451.0774265 80.39166747 0.017747447 -5.816244714 12.8952105 1.30E-11 Rv2030c conserved hypothetical protein

MT2090 47,606.42 45,289.09 1,309.90 213.7067671 0.016401187 -5.930055975 14.5267165 2.25E-11

MT2091 4,107.08 6,106.32 93.24031297 24.61101936 0.011537183 -6.437565232 11.3342536 1.17E-16 Rv2032 Rv2032 conserved hypothetical protein

MT2445.1 76.0135489 112.170195 33.65120785 43.89722715 0.410508589 -1.284515686 6.05094956 0.010996717

MT2556 829.096235 436.250309 246.1453518 207.9923351 0.359152376 -1.477332034 8.74488432 0.029194771 Rv2483c Rv2483c possible transferase

MT2557 1,264.80 629.810486 325.1689747 280.0721016 0.319604679 -1.645639566 9.28539783 0.014293698 Rv2484c Rv2484c conserved hypothetical protein

MT2574 539.931291 209.394229 131.6556244 99.22331817 0.308582331 -1.696272638 7.93033342 0.011019471 Rv2499c Rv2499c putative aldehyde dehydrogenase

MT2576 1,506.95 573.613095 381.7332521 270.2666559 0.299127429 -1.741167888 9.46570666 0.014355782

MT2577 485.859797 244.465912 138.3102453 104.8078767 0.333354395 -1.584871345 7.92145921 0.007362242 Rv2502c accDl acetyl/propionyl-CoA carboxylase, [beta] subunit

MT2578 623.781288 261.335836 136.9490728 114.223702 0.284132026 -1.815366642 8.14436233 0.003492974 Rv2503c scoB 3-oxo acid:CoA transferase, [beta] subunit

MT2579 627.699512 301.142937 149.7289697 111.0418024 0.281045175 -1.83112605 8.21112326 0.002131279 Rv2504c scoA 3-oxo acid:CoA transferase, [alpha] subunit

MT2698 44,830.75 23,321.63 323.5809402 153.3156114 0.006997504 -7.158943883 14.0663893 1.55E-23 Rv2623 Rv2623 conserved hypothetical protein

MT2699 2,560.56 1,941.23 46.27986337 12.98734531 0.013162362 -6.24743783 10.153358 1.61E-17 Rv2624c Rv2624c conserved hypothetical protein

MT2700 6,090.49 3,891.03 65.10941563 13.96139621 0.007920691 -6.980157945 11.2955224 2.53E-16 Rv2625c Rv2625c conserved hypothetical protein

MT2701 13,690.67 11,153.83 174.8350394 34.87102216 0.008440262 -6.888496456 12.6124486 1.24E-15 Rv2626c Rv2626c conserved hypothetical protein

MT2702 8,227.49 5,979.20 50.96834626 24.87076627 0.005337923 -7.549505876 11.8013664 8.53E-29 Rv2627c Rv2627c conserved hypothetical protein

MT2703 735.8425 950.487019 26.46724213 22.33823393 0.028942941 -5.110644648 8.75778035 3.83E-24 Rv2628 Rv2628 hypothetical protein

MT2704 8,138.54 5,125.20 413.1914599 339.4242697 0.056745847 -4.13934138 11.7742307 6.87E-14 Rv2629 Rv2629 hypothetical protein

MT2705 802.844133 594.294857 59.8159672 43.0530497 0.073654982 -3.763073086 8.54591318 3.82E-15 Rv2630 Rv2630 hypothetical protein

MT2707 1,182.91 515.124601 74.71324349 51.81950779 0.074561034 -3.745434328 8.82811081 7.33E-11 Rv2631 Rv2631 conserved hypothetical protein

MT3171 704.496706 437.138199 246.825938 214.6158813 0.404459787 -1.305931823 8.64417435 0.048905958 ad D zinc-containing alcohol dehydrogenase

MT3210 8.62009318 6.21523506 0.226862075 0 0.016401029 -5.930069827 1.59138092 6.06E-13

MT3212 16,662.64 10,701.89 251.2875588 90.32698663 0.012483603 -6.323821761 12.7575933 1.09E-18 Rv3127 RV3127 conserved hypothetical protein

MT3216 34,479.20 28,662.15 290.8371806 74.09280499 0.00577936 -7.434874628 13.9544872 6.82E-20 Rv3130c Rv3130c conserved hypothetical protein

MT3217 19,568.79 10,737.71 118.8001068 25.13051318 0.004748874 -7.718198819 12.8938498 1.61E-17 Rv3131 Rv3131 conserved hypothetical protein

MT3218 5,473.37 3,344.83 237.9026964 168.7056156 0.046114017 -4.438650848 11.1703676 4.05E-15 Rv3132c Rv3132c sensor histidine kinase

MT3219 3,967.20 2,140.70 112.5235894 67.0147018 0.029397765 -5.088149713 10.6167498 5.91E-17 Rv3133c Rv3133c two-component response regulator

MT3220 6,505.04 4,058.25 155.1736595 61.75482695 0.020535938 -5.605705377 11.3952646 8.05E-17 Rv3134c Rv3134c conserved hypothetical protein

MT3427 246.064478 249.645275 112.372348 107.4702824 0.443484319 -1.173045002 7.48030878 0.030125275

MT3443 2,036.30 1,022.26 593.2443271 359.1000978 0.31144493 -1.B82951008 9.96829767 0.022475051 Rv3340 metC cystathionine [beta]-lyase

MT3444 1,152.35 680.568239 307.3981121 175.4590351 0.263523562 -1.923996132 9.17484404 .00228429 Rv3341 metA homoserine o-acetyltransferase

MT3608 165.34906 89.2330177 48.09475998 42.0789988 0.355796739 -1.490874807 6.41567229 0.004050376 RV3504 fadE26 acyl-CoA dehydrogenase

MT3634 237.836207 95.3002709 55.2787257 43.57254352 0.297808555 -1.747542899 6.7400196 0.004050376 Rv3531c Rv3531c hypothetical protein

MT3655 241.754431 127.116355 77.96493323 70.71609521 0.404241247 -1.306711559 7.00706704 0.033246082 Rv3551 Rv3551 possible glutaconate CoA-transferase

MT3656 488.602554 202.143121 108.5156927 106.3663581 0.311623713 -1.682123076 7.81591006 0.007764831 Rv3552 Rv3552 hypothetical protein

MT3716 3,433.93 2,224.76 1,189.74 540.013818 0.305702713 -1.709798739 10.8503981 0.026274113 Rv3614c Rv3614c conserved hypothetical protein

MT3717 1,484.22 1,077.60 538.7218083 261.0456407 0.312225946 -1.679337665 9.71363719 0.016305758 Rv3615c Rv3615c conserved hypothetical protein

MT3718 4,787.29 3,551.41 1,818.45 821.5145276 0.316601944 -1.659257979 11.422029 0.032145592 Rv3616c Rv3616c conserved hypothetical protein

Table 2H: Upregulated gene expression tables of WT Mtb treated with HC103A compared to DMSO

Gene Counts per mi llion (CPM) WT DMSO /WT HC103A

WT_DMS01 WT_DM502 WT_HC103A1 WT_HC103A2 Fold change log >2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0169 5.09369142 9.02688902 19.66137986 19.54595469 2.65424121 1.408299485 3.82188565 0.024220713 Rv0160c PE PE-family protein

MT0206 29.7785037 29.1524121 145.1917282 138.3152276 4.812769415 2.266867304 6.43805492 2.94E-09 Rv0196 Rv0196 transcriptional regulator (TetR/AcrR family)

MT0207 106.183875 77.8384201 324.1859057 345.528322 3.650489315 1.868089857 7.74407444 4.88 E-05 Rv0197 Rv0197 conserved hypothetical protein

MT0337 24.6848123 23.0851588 71.00782959 46.2349493 2.459102365 1.298131791 5.39177723 0.014293698 Rv0322 udgA UDP-glucose dehydrogenase/GDP-mannose

MT0468 37.2231296 53.2734434 128.9332795 95.91154512 2.464713661 1.301420051 6.31646908 0.010802249 Rv0452 Rv0452 putative transcriptional regulator

MT0491 64.2588764 64.0761138 167.575453 130.5877571 2.322964768 1.215967273 6.74652129 0.017604747 Rv0474 Rv0474 transcriptional regulator (PbsX/Xre family)

MT0585 516.813768 721.559194 2,729.98 4,689.54 5.989313531 2.582390657 11.0806573 8.14E-06 Rv0559c Rv0559c possible exported

MT0586 28.211214 30.3362664 6,038.01 10,500.79 281.967054 8.139382793 12.0192376 4.69E-35 Rv0560c Rv0560c methyl transferase

MT0808 27.8193916 41.4349004 168.9366255 139.873709 4.409357079 2.140558314 6.57959735 2.49 E-07 RV0784 RV0784 conserved hypothetical protein

MT0910 12.1464949 13.0223973 40.68393218 23.63696846 2.542787418 1.346410855 4.53042946 0.035131938 Rv0887c Rv0887c hypothetical protein

MT1294 5.87733626 5.7712897 27.37469043 11.94835769 3.371255322 1.753285894 3.75644833 0.01541127 Rvl255c Rvl255c transcriptional regulator (TetR/AcrR family)

MT1608 47.4105125 34.6277382 306.7931466 411.3741627 8.810245489 3.139182219 7.65359653 7.95E-13 Rvl557 mmpL6 conserved large membrane protein

MT1924 28.211214 49.5738987 139.9739005 72.46938683 2.701976395 1.434015071 6.19955069 0.019618016 Rvl875 Rvl875 conserved hypothetical protein

MT2526 117.546725 187.048979 565.3402918 307.6702104 2.859869289 1.51594921 8.20640952 0.019618016 Rv2450c Rv2450c conserved hypothetical protein

MT2792 11.3628501 23.5291042 54.3712774 41.55950499 2.673772219 1.418876566 5.07183172 0.018868454 Rv2719c Rv2719c conserved hypothetical protein

MT2805 24.2929899 32.8519568 90.29110599 59.15735789 2.588825705 1.372297838 5.71429378 0.00721086 Rv2736c recX regulatory protein for RecA

MT3110 5.09369142 3.84752647 19.13203502 14.80557365 3.905613947 1.965549352 3.52262207 0.001035498 Rv3026c Rv3026c some similarity to acyltransferase Q59601

MT3140 1.95911209 2.51569038 40.68393218 10.90937006 11.16441708 3.480836022 3.91758447 3.76E-06 Rv3054c Rv3054c conserved hypothetical protein

MT3345 7.05280351 12.2824883 32.74375954 20.58494232 2.667096434 1.415269989 4.24792745 0.031354665 Rv3247c tmk thymidylate kinase

MT3513 29.3866813 28.2645214 104.8858995 49.09216527 2.671952469 1.417894344 5.74663856 0.016305758

MT3514 65.4343437 50.4617894 685.0478469 289.7476739 8.432726886 3.07599923 8.09771066 1.14E-08 Rv/3406 Rv/3406 putative dioxygenasediooxygenase

MT3515 66.2179885 47.5021537 276.7717319 112.9249675 3.438630065 1.781833916 6.9856793 0.004813941 Rv3407 Rv3407 conserved hypothetical protein

MT3723 9.0119156 5.91927149 40.45707011 11.42886387 3.541646992 1.824420421 4.12573872 0.049772943 Rv3621c PPE PPE-family protein

MT3724 3.52640176 2.95963574 20.2663454 6.363799202 4.15388209 2.054460265 3.17403054 0.02286752 Rv3622c PE PE-family protein

MT3846 16.8483639 21.4573591 53.3882084 59.48204152 2.911687207 1.54185538 5.27373589 0.000789768

Table 3A: Downregulated gene expression tables of DosR mutant treated with HCIOIA compared to DMSO

Gene Counts per million (CPM) DosR D SO/DosR HCIOIA

DosR_DMS01 DosR_DMS02 DosR_HC101Al DosR_HC101A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0169 64.58870928 84.06373882 26.44202932 29.07142071 0.3768729 -1.407850038 5.67432191 1.79E -11 Rv0160c PE PE-family protein

MT0258 2,155.07 1,743.15 759.8536329 1,123.31 0.476497164 -1.069460467 10.4975482 3.12E -06 Rv0244c fadE5 acyl-CoA dehydrogenase

MT0273 50.22521998 30.93748458 15.80072484 7.243384284 0.276685089 -1.853683197 4.71135163 3.79E -15 Rv0260c Rv0260c two-component response regulator

MT0292 87.78965353 32.83937912 31.79492794 16.54232357 0.421264317 -1.247202377 5.40852797 6.32E -08 Rv0280 PPE PPE-family protein

MT0329 315.2948835 381.9004243 113.2492768 189.11106 0.421745609 -1.245555046 7.96529685 7.73E -11 Rv0315 Rv0315 probable [beta]-l,3-glucanase

MT0456 13,997.90 10,939.82 5,842.91 4,666.11 0.42194445 -1.244875019 13.1133853 9.01E -08 Rv0440 groEL2 60 kD chaperonin 2

MT0483 2,270.12 1,748.48 884.5181272 561.0686313 0.353704674 -1.499382811 10.4159166 1.78E -19 Rv0467 aceA isocitrate lyase

MT0484 450.2512918 334.2262678 179.3543501 142.8121307 0.41241961 -1.277815164 8.11264396 7.22E -14

MT0493 1,843.92 1,791.20 790.810155 938.1161484 0.473889687 -1.077376829 10.3891973 1.91E -10 Rv0475 Rv0475 possible exported protein

MT0901 34.24901295 28.65521112 18.57391328 12.13756285 0.48399995 -1.046921195 4.55743969 1.50E- -05 Rv0878c PPE PPE-family protein

MT0908 4,335.77 4,965.21 437.9058027 441.3570235 0.094762148 -3.399545287 11.313454 6.23E -73 RV0885 RV0885 unknown transmembrane protein

MT0909 832.0895428 545.4633551 103.5753636 55.40210142 0.112773205 -3.148503776 8.58572063 4.33E -77 RV0886 fprB ferredoxin, ferredoxin-NADP reductase

MT0911 34.41898323 21.6815978 9.415942149 8.907404998 0.330101989 -1.599016264 4.22765557 1.31E -10 RV0888 RV0888 possible membrane protein

MT0915.1 27.62017173 17.37063683 9.86739143 9.494706427 0.434673077 -1.201997355 4.02121398 5.15E -06

MT1019 184.0778214 157.3500752 62.68695732 83.49468641 0.424443557 -1.23635538 6.9306166 5.19E -09 Rv0990c Rv0990c hypothetical protein

MT1020 1,742.62 1,801.09 529.4210213 1,032.48 0.417341957 -1.260698129 10.3179161 3.64E -08

MT1224 101.1323211 61.49459024 50.04637745 29.85448928 0.490463134 -1.027783396 5.92646369 5.03E -07 Rvll87 rocA pyrrol ine-5-carboxylate dehydrogenase

MT1233 1,072.43 189.5554895 282.5427572 86.52907713 0.344705898 -1.536562112 8.67267356 1.73E -13 Rvll95 PE PE-family protein

MT1385 164.3612681 49.82963704 26.31304381 28.67988642 0.300795667 -1.733144309 6.0767996 1.15E- -05

MT1430 211.5280229 69.22896139 77.39130534 47.86506642 0.498258307 -1.005034237 6.66893887 7.89E -05 Rvl386 PE PE-family protein

MT1431 686.6799618 1,329.93 317.6913084 543.6453556 0.434847868 -1.201417334 9.49074034 1.16E- -15 Rvl387 PPE PPE-family protein

MT1484 22.26610767 16.99025792 6.96521748 6.851849999 0.351511648 -1.5083556 3.74179423 2.06E -09 Rvl439c Rvl439c hypothetical protein

MT1585.1 1,611.23 1,599.87 293.5065255 393.6877242 0.211686853 -2.23999642 9.92864322 1.01E -41

MT1586 245.6070655 107.5204382 44.69347883 38.95766142 0.255009473 -1.971377256 6.77287532 1.22E -15 Rvl535 Rvl535 hypothetical protein

MT1627 65.77850129 40.70054323 22.44347855 21.43650214 0.420349715 -1.250337999 5.23787941 3.25E -07

MT1628 830.5598102 715.2391413 334.3304391 332.3147249 0.432331395 -1.20979049 9.11168696 4.83E -15 Rvl592c Rvl592c conserved hypothetical protein

MT1736 339.4306643 676.5672856 181.2891328 300.2089135 0.486736165 -1.038788124 8.54821507 8.49E -10

MT1775 61.69921439 14.07401962 17.80000023 12.82274785 0.495705695 -1.012444261 4.7475838 0.01098138

MT1854 34.75892381 34.61448069 12.83405814 20.45766642 0.466148949 -1.101137082 4.68590074 2.84E -05 Rvl804c Rvl804c conserved hypothetical protein

MT1922 35.09886438 35.24844554 11.35072478 17.71692643 0.402336506 -1.313525449 4.63891402 2.55E -07 Rvl873 Rvl873 hypothetical protein

MT1969 184.2477917 195.3879661 90.22536347 98.56875641 0.496989464 -1.008712826 7.15166692 1.59E -08 Rvl918c PPE PPE-family protein

MT2040 676.141804 97.63058657 79.06811695 31.42062642 0.191586675 -2.383930874 7.79016121 1.24E -14 Rvl986 Rvl986 membrane protein, LYSE/YGGA family

MT2166 118.809231 106.2525085 25.86159453 35.23808571 0.268141469 -1.898933742 6.16160663 7.06E -19 Rv2107 PE PE-family protein

MT2167 117.7894093 105.1113718 31.60144968 38.76189428 0.313858093 -1.671815685 6.19725282 1.57E -16 Rv2108 PPE PPE-family protein

MT2168 25.83548371 22.18876967 9.544927658 9.201055713 0.390066405 -1.358208345 4.06987805 1.54E- -08

MT2278 1,659.42 1,394.85 635.8985589 701.140022 0.438790291 -1.188396492 10.100566 1.97E -12 RV2220 glnAl glutamine synthase class 1

MT2284 394.7559929 430.0817528 197.4768141 213.4840692 0.498334104 -1.004814785 8.27159151 4.03E -09 RV2225 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase

MT2304 2,882.27 3,978.89 831.7630541 1,835.61 0.364903403 -1.454413488 11.2180288 1.93E -11 Rv2244 acpM acyl carrier protein (meromycolate extension)

MT2305 3,048.08 4,168.70 1,175.19 2,060.94 0.436596286 -1.195628236 11.3516205 1.14E- -09 Rv2245 kasA [beta]-ketoacyl-ACP synthase (meromycolate

MT2306 1,735.23 2,051.26 704.1318931 1,234.02 0.494085354 -1.017167804 10.4830102 1.77E -07

MT2391 194.1060684 118.1710476 72.03840672 73.99997999 0.48031748 -1.057939782 6.84214371 3.49E -06 Rv2329c narKl probable nitrite extrusion protein

MT2417 18.78171678 35.37523851 8.835507359 16.05290571 0.462050215 -1.113878445 4.30360189 1.78E -06

MT2503 1,013.70 1,679.12 372.703628 897.8860005 0.443527623 -1.172904135 9.95248823 5.58E -11 Rv2428 ahpC alkyl hydroperoxide reductase

MT2504 416.8521303 612.663629 163.8760891 315.7724014 0.450251864 -1.151195845 8.55953127 4.66E- -11 Rv2429 ahpD member of AhpC/TSA family

MT2506 448.9765146 464.8230264 236.2369595 203.0105271 0.479671999 -1.05987987 8.40239452 1.00E- -09

MT2526 2,144.86 415.1201824 892.3862433 239.7168664 0.489117101 -1.031748189 9.85074083 2.90E -09 Rv2450c Rv2450c conserved hypothetical protein

MT2698 109.8857909 73.41312938 41.08188458 44.83067571 0.475570384 -1.07226922 6.07558838 5.65E -06 Rv2623 Rv2623 conserved hypothetical protein

MT2778 93.05373245 111.7046062 45.20942087 56.67458785 0.496425032 1.010352231 6.26154043 1.54E-07 Rv2705c Rv2705c hypothetical protein

MT2849 72.66229794 49.70284407 26.8934786 12.92063143 0.314626742 1.668286794 5.34642958 1.82E-13 Rv2779c Rv2779c transcriptional regulator (Lrp/AsnC family)

MT2850 3,452.35 1,786.13 1,263.03 369.1189478 0.275243597 1.861219091 10.7463868 1.63E-17 Rv2780 aid L-alanine dehydrogenase

MT3065 409.9683336 29.54276191 140.2072482 20.16401571 0.468314386 1.094450737 7.23227791 2.39E-05 Rv2987c leuD 3-isopropylmalate dehydratase small subunit

MT3118 48.27156167 75.56860986 22.05652202 33.57406499 0.450654957 1.149904836 5.48777325 4.92E-08 Rv3033 Rv3033 hypothetical protein

MT3132 112.0954047 96.2358639 35.5355077 21.04496785 0.265633497 -1.91249101 6.0511335 1.78E-19

MT3133 902.6272122 1,067.72 232.5608725 256.0634228 0.248616092 2.008008413 9.26383339 1.84E-42 Rv3048c nrdG ribonucleoside-diphosphate small subunit

MT3134 2,343.81 2,501.88 487.3717454 585.0501063 0.220501526 .181139458 10.5309216 .93E-41 Rv3049c Rv3049c Probable monooxygenase

MT3178 110.3957018 41.58809402 44.69347883 16.44444 0.400684732 1.319460558 5.74220275 1.57E-10 Rv3094c Rv3094c conserved hypothetical protein

MT3441 376.3992018 255.1074548 119.763045 82.41796713 0.320596258 1.641170509 7.70423005 7.19E-21 Rv3338 Rv3338 conserved hypothetical protein

MT3481 167.1657778 70.75047702 86.74275473 29.16930428 0.466099048 1.101291528 6.47109453 2.40E-08 Rv3371 Rv3371 conserved hypothetical protein

MT3498 157.0525457 92.68566076 73.1992763 47.47353213 0.487784668 1.035683682 6.53587331 4.31E-08 Rv3391 acrAl fatty acyl-CoA reductase

MT3581 114.3050184 88.88187167 30.05362357 39.25131214 0.339690806 1.557705924 6.09187099 1.76E-11 Rv3477 PE PE-family protein

MT3591 85.91998037 32.33220724 22.95942058 20.55555 0.40596188 -1.30058383 5.34500007 4.34E-05 Rv3487c lipF probable esterase

MT3947 35.94871582 16.86346495 12.44710161 10.47354214 0.45262101 1.143624541 4.2572301 4.84E-05 Rv3839 Rv3839 hypothetical protein

MT3963 553.0833158 592.2499609 225.5311623 354.9258299 0.494260436 1.016656668 8.7532464 6.07E-08 RV3848 RV3848 probable membrane proteinprot

MT3969 918.2644786 1,935.62 246.4913075 439.3993521 0.246822495 -2.01845421 9.78925838 1.31E-40 Rv3854c probable monooxygenase

MT3970 182.7180591 232.0311343 59.4623196 89.17193355 0.353628242 1.499694597 7.1380532 5.25E-17 Rv3855 RV3855 putative transcriptional regulator

MT3S76 703.6769906 97.75737954 184.2557995 55.69575213 0.382440282 1.386693606 8.0260941 1.78E-07 Rv3862c hypothetical protein

MT3978 1,992.82 1,049.21 526.4543546 634.3834263 0.399484534 1.323788446 10.0373647 5.50E-07 Rv3864 Rv3864 conserved hypothetical protein

MT3988 3,617.31 2,423.90 1,214.01 1,648.46 0.477698917 -1.06582649 11.120268 5.37E-05 Rv3874 Rv3874 conserved hypothetical protein

MT3989 4,163.17 5,549.60 1,889.51 2,881.50 0.48544579 1.042617896 11.8221611 2.87E-07 Rv3875 esat6 early secretory antigen target

Table 3B: Upregulated gene expression tables of DosR mutant treated with HCIOIA compared to DMSO

Gene Counts per million (CPM) DosR DMSO/DosR HCIOIA

DosR_DMS01 DosR_DMS02 DosR_HC101Al DosR_HC101A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0468 182.038178 97.25020766 461.5101508 261.5449028 2.609307907 1.383667197 7.97137994 7.91E-16 Rv0452 Rv0452 putative transcriptional regulator

MT0530 571.4676211 626.6108556 ,704 1,028.46 2.042497809 1.030334531 .97755494 7.38E-08 Rv0509 hemA glutamyl-tRNA reductase

MT0531 272.6323413 206.7993334 794.6152275 398.3861356 2.373685343 1.247128703 8.70902983 3.03E-11 /0510 heme porphobilinogen deaminase

MT0532 568.3806417 442.5074638 1,631.80 832.7934256 2.326476251 1.21814646 .76361083 2.56E-11 Rv0511 cysG uroporphyrin c-methyltransferase

MT0533 234.049086 160.3931065 601.201457 365.6930228 2.421877135 1.276125677 8.41233028 .47E-14 Rv0512 hemB [delta]-aminolevulinic acid dehydratase

MT0583 136.8260815 132.8790321 376.895657 224.6427964 2.162414792 1.112643286 7.76911036 3.39E-07 Rv0557 Rv0557 conserved hypothetical protein

MT0586 25.92046886 .00460168 106.1550738 65.09257499 3.862908971 1.949687681 5.75984128 .26E-21 Rv0560c Rv0560c methyl transferase

MT0658 25.92046886 24.85142204 75.58550821 34.25924999 2.029015455 1.020779854 5.33989547 0.000692083 Rv0630c recB exodeoxyribonuclease V

MT0705 912.8254294 1,004.71 3,503.44 3,550.24 3.682762206 1.880788246 11.1312868 7.94E-27 Rv0676c mmpL5 conserved large membrane protein

MT0706 374.4445435 389.1276236 1,184.86 1,231.08 3.163944842 1.661724449 9.63513029 2.79E-30 Rv0677c mm S5 conserved small membrane protein

MT0706.1 82.26561919 76.07578174 272.4818875 202.4232257 2.973758576 1.572287527 7.30970488 9.70E-18 RV0678 RV0678 hypothetical protein

MT0772.5 59.00793676 40.70054323 199.9920315 58.24072499 2.060267909 1.042831952 6.53007235 0.000102935 RV0747 PE_PGRS PE_PGRS-family protein

MT0808 121.6987259 62.38214103 811.834793 173.351805 4.335232504 .116109369 8.19408205 .26E-14 RV0784 RV0784 conserved hypothetical protein

MT0956 154.4180063 202.8687513 370.5108743 355.6110149 2.051794886 1.036886515 8.0826697 7.77E-08 Rv0929 pstC2 membrane-bound component of phosphate transport

MT1073 70.28271391 115.5083953 209.4079737 170.4152978 2.097730541 1.068829372 7.14621936 3.97E-05 Rvl043c Rvl043c hypothetical protein

MT1123 30.0847409 12.04533211 76.29492851 18.20634428 2.020723749 1.014872106 5.11304295 0.000164604 Rvl091 PE_PGRS PE_PGRS-family protein

MT1296 210.3382309 142.6420908 517.1029052 305.0052085 2.294968556 1.198474387 8.20030973 6.21E-12 Rvl257c Rvl257c similar to many dehydrogenases

MT1297 52.09589314 52.87266831 201.7333359 152.3068371 3.348797584 1.743643176 6.84667558 4.42E-20 Rvl258c Rvl258c probable multidrug resistance pump

MT1303 138.1008587 104.6041999 292.6036269 237.2697771 2.190933348 1.131545596 7.59584057 .97E-10 Rvl265 Rvl265 hypothetical protein

MT1424 103.5119051 62.76251994 370.4463815 97.00261927 2.36979857 1.244764437 7.3118985 .28E-05 Rvl380 pyrB aspartate carbamoyltransferase

MT1425 255.2953719 158.491212 782.684068 262.425855 2.259917715 1.176270244 8.51235533 2.69E-07 Rvl381 pyrC dihydroorotase

MT1426 45.97696279 30.81069161 173.5500022 47.37564856 2.442760358 1.288512338 6.22648987 2.70E-05

MT1427 248.0716347 170.4097511 572.8891378 296.3914542 2.007479995 1.005385611 8.33225518 7.72E-08 Rvl383 carA carbamoyl-phosphate synthase subunit

MT1428 538.8058116 442.7610497 1,369.37 816.1532184 2.165978513 1.115018931 9.62956458 4.94E-11 Rvl384 carB carbamoyl-phosphate synthase subunit

MT1429 35.69376039 18.25818762 136.9826104 37.58729142 2.871304664 1.521706418 5.84806679 3.05E-09 Rvl385 pyrF orotidine 5'-phosphate decarboxylase

MT1620 36.79856726 .763058657 87.71014605 20.65343357 2.269157962 1.182157042 5.29300694 .55E-07 Rvl569 bioF 8-amino-7-oxononanoate synthase

MT1836 60.84936295 40.32016432 284.6710181 109.7274836 3.598432437 1.847368571 6.95820103 6.83E-17 /1787 PPE PPE-family protein

MT1893 140.3104724 34.48768772 347.744932 58.82802642 2.083536209 1.059034172 7.18838382 3.55E-07 Rvl845c Rvl845c hypothetical protein

MT2126 24.6456917 .13139465 68.03985594 27.11374928 2.068388446 1.048507151 5.12347158 0.000180441 Rv2066 cobl Cobl-CobJ fusion protein

MT2264 22.69103339 7.607578174 65.13768199 14.09523428 2.402237549 1.264378821 4.8000351 .25E-06 Rv2208 cobs cobalamin (5'-phosphate) synthase

MT2615 185.012658 26.37293767 668.7253709 48.55025142 2.641782364 1.401511619 7.8627379 .24E-08 Rv2540c aroF chorismate synthase

MT2631 46.91179937 7.987957083 100.8021752 15.95502214 2.089072285 1.062862413 5.4403404 4.03E-06

MT2863 54.47547717 68.72178951 147.5239149 103.8544693 2.029218701 1.020924361 6.55383074 2.88E-05 Rv2794c Rv2794c conserved hypothetical protein

MT3110 23.8808254 .18646884 98.60942155 28.28835214 3.057275312 1.612246475 5.37357044 2.51E-09 Rv3026c Rv3026c some similarity to acyltransferase Q59601

MT3293 56.60010576 70.62368405 141.5905815 118.6348885 2.054631858 1.03887992 6.60216128 .16E-06 conserved hypothetical protein

MT3327 811.4381529 430.7157176 1,566.59 1,092.38 2.211109757 1.144770641 9.93018834 5.56E-12 similar to various oxygenases

MT3492 23.54088483 4.691339874 51.14275428 8.907404998 2.072623049 1.051457755 4.49525699 6.11E-05 conserved hypothetical protein

MT3539 17.67690991 5.452097692 60.36521816 7.341267856 2.349607525 1.232419791 4.53755458 0.000295271 Rv3433c Rv3433c conserved hypothetical protein

MT3696 24.73067684 4.057375026 89.00000114 5.481479999 2.528782815 1.338443136 4.9723221 8.07E-05 Rv3590c PE_PGRS PE_PGRS-family protein

Table 3C: Downregulated gene expression tables of DosR mutant treated with HC102A compared to DMSO

Gene Counts per million (CPM) DosR DMSO/DosR HC102A

DosR DMSOl DosR D S02 DosR HC102A1 DosR HC102A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

Table 3D: Upregulated gene expression tables of DosR mutant treated with HC102A compared to DMSO

Gene Counts per million (CPM) DosR DMSO/DosR HC102A

DosR_DMS01 DosR_DMS02 DosR_HC102Al DosR_HC102A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

Table 3E: Downregulated gene expression tables of DosR mutant treated with HC103A compared to DMSO

Gene Counts per mill ion (CPM) DosR DMSO/DosR HC103A

Dos _DMS01 DosR_DMS02 DosR_HC103Al DosR_HC103A2 Fold change log2 Fold change logCPM Adjusted p-value Rv number Gene name Annotated function

MT0169 65.85191614 84.53368756 32.4008011 38.88882855 0.475892173 -1.071293369 5.79145216 3.88E-05 Rv0160c PE PE-family protein

MT0273 51.20852953 31.11043705 19.06256394 17.9486901 0.460945483 -1.117331966 4.9019279 0.002130737 Rv0260c Rv0260c two-component response regulator

MT0846 4,560.33 12,066.90 2,264.39 5,375.06 0.470288699 -1.088381431 12.5666524 7.66E-07 Rv0824c desAl acyl-[ACP] desaturase

MT0908 4,420.57 4,992.97 2,165.30 1,401.92 0.370895088 -1.430916935 11.6640643 1.43E-08 Rv0885 Rv0885 unknown transmembrane protein

MT0909 848.3633039 548.5127057 412.6517122 231.1962225 0.453003864 -1.14240474 8.99505899 3.98E-10 RV0886 fprB ferredoxin, ferredoxin-NADP reductase

MT1214 1,358.72 2,946.95 704.925834 1,378.70 0.492649453 -1.02136664 10.6413369 1.77E-07 Rvll77 fdxC ferredoxin 4Fe-4S

MT1430 215.6650254 69.61597799 63.30105053 54.48709495 0.476492293 -1.069475216 6.6566741 0.010220947 Rvl386 PE PE-family protein

MT1690 411.2278869 71.65600665 130.6035722 56.83751865 0.497858635 -1.006191942 7.39031805 0.010220947 Ryl652 argC l\l-acetyl-[gamma]-glutamyl-phosphate reductase

MT1691 265.3139043 42.45809647 81.47439866 33.33328161 0.484648036 -1.04499069 6.72563835 0.01108789

MT1692 339.1373681 84.0236804 128.7695646 55.27056951 0.496487803 -1.010169819 7.2476763 0.000384713 RV1654 argB acetylglutamate kinase

MT1694 240.8793775 71.14599949 79.75154302 39.5298532 0.425890365 -1.231446004 6.75437876 5.96E-06 Ryl656 argF ornithine carbamoyltransferase

MT3134 2,389.64 2,515.87 1,202.50 892.6624326 0.422609861 -1.242601664 10.7732604 3.66E-09 Ry3049c Rv3049c Probable monooxygenase

MT3573.12 587.5550571 755.95812 280.9921962 281.5522697 0.422123825 -1.244261836 8.89619806 1.03E-10

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