Structure-based design of DevR inhibitor active against nonreplicating Mycobacterium tuberculosis

Journal of Medicinal Chemistry

Volumn 52, Issue 20, 2009, Pages 6324-6334

  Gupta, Rajesh Kumar ^a   Thakur, Tejender S ^b   Desiraju, Gautam R ^b   Tyagi, Jaya Sivaswami ^a  

^a ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

^b UNIVERSITY OF HYDERABAD   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; COUMARIN DERIVATIVE; PHENYLCOUMARIN DERIVATIVE; PROTEIN DEVR; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; DRUG DESIGN; DRUG DNA BINDING; DRUG IDENTIFICATION; DRUG PROTEIN BINDING; DRUG STRUCTURE; MOLECULAR MODEL; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHARMACOPHORE; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STRUCTURE;

AEROBIOSIS; ANOXIA; ANTITUBERCULAR AGENTS; BACTERIAL PROTEINS; BINDING SITES; COMPUTATIONAL BIOLOGY; DNA, BACTERIAL; DRUG DESIGN; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; PROTAMINE KINASE; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY; TRANSCRIPTION, GENETIC;

EID: 70350048603     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm900358q     Document Type: Article

References (41)

1. Parrish, N. M.; Dick, J. D.; Bishai, W. R. Mechanisms of latency in Mycobacterium tuberculosis. Trends Microbiol. 1998, 6, 107-112.
2. Grange, J. M. The mystery of the mycobacterial "persistor". Tuberculosis Lung Dis. 1992, 73, 249-251.
3. Mitchison, D. A. Basic mechanisms of chemotherapy. Chest 1979, 76, 771-781.
4. Young, D. B. A post-genomic perspective. Nat. Med. 2001, 7, 11-13.
5. Macielag, M. J.; Goldschmidt, R. Inhibitors of bacterial twocomponent signalling systems. Expert Opin. Investig. Drugs 2000, 9, 2351-2369.
6. Stephenson, K.; Hoch, J. A. Two-component and phosphorelay signal-transduction systems as therapeutic targets. Curr. Opin. Pharmacol. 2002, 2, 507-512.
7. Tyagi, J. S.; Sharma, D. Signal transduction systems of mycobacteria with special reference to M. tuberculosis. Curr. Sci. 2004, 86, 93-102.
8. Dasgupta, N.; Kapur, V.; Singh, K. K.; Das, T. K.; Sachdeva, S.; Jyothisri, K.; Tyagi, J. S. Characterization of a two-component system, devR-devS, of Mycobacterium tuberculosis. Tuberculosis Lung Dis. 2000, 80, 141-159. (Pubitemid 30728777)
9. Park, H. D.; Guinn, K. M.; Harrell, M. I.; Liao, R.; Voskuil, M. I.; Tompa, M.; Schoolnik, G. K.; Sherman, D. R. Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Mol. Microbiol. 2003, 48, 833-843.
10. Ohno, H.; Zhu, G.; Mohan, V. P.; Chu, D.; Kohno, S.; Jacobs, W. R., Jr.; Chan, J. The effects of reactive nitrogen intermediates on gene expression in Mycobacterium tuberculosis. Cell. Microbiol. 2003, 5, 637-648.
11. Voskuil, M. I.; Schnappinger, D.; Visconti, K. C.; Harrell, M. I.; Dolganov, G. M.; Sherman, D. R.; Schoolnik, G. K. Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J. Exp. Med. 2003, 198, 705-713.
12. Kumar, A.; Deshane, J. S.; Crossman, D. K.; Bolisetty, S.; Yan, B. S.; Kramnik, I.; Agarwal, A.; Steyn, A. J. Heme oxygenase- 1-derived carbon monoxide induces the Mycobacterium tuberculosis dormancy regulon. J. Biol. Chem. 2008, 283, 18032-18039.
13. Shiloh, M. U.; Manzanillo, P.; Cox, J. S. Mycobacterium tuberculosis senses host-derived carbon monoxide during macrophage infection. Cell Host Microbe 2008, 3, 323-330. (Pubitemid 351635997)
14. Wayne, L. G.; Sohaskey, C. D. Nonreplicating persistence ofMycobacterium tuberculosis. Annu. Rev. Microbiol. 2001, 55, 139-163.
15. Gomez, J. E.; McKinney, J. D. M. Tuberculosis persistence, latency, and drug tolerance. Tuberculosis (Edinburgh) 2004, 84, 29-44.
16. Murphy, D. J.; Brown, J. R. Identification of gene targets against dormant phase Mycobacterium tuberculosis infections. BMC Infect. Dis. 2007, 7, 84.
17. Boon, C.; Dick, T. Mycobacterium bovis BCG response regulator essential for hypoxic dormancy. J. Bacteriol. 2002, 184, 6760-6767. (Pubitemid 36356110)
18. Saini, D. K.; Tyagi, J. S. High-throughput microplate phosphorylation assays based on DevR-DevS/Rv2027c 2-component signal transduction pathway to screen for novel anti-tubercular compounds. J. Biomol. Screening 2005, 10, 215-224.
19. Wisedchaisri, G.; Wu, M.; Rice, A. E.; Roberts, D. M.; Sherman, D. R.; Hol, W. G. Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency. J. Mol. Biol. 2005, 354, 630-641.
20. Wisedchaisri, G.; Wu, M.; Sherman, D. R.; Hol, W. G. Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation. J. Mol. Biol. 2008, 378, 227-242.
21. Gao, R.; Mack, T. R.; Stock, A. M. Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem. Sci. 2007, 32, 225-234.
22. Irwin, J. J.; Shoichet, B. K.ZINC - a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45, 177-182.
23. Baikalov, I.; Schroder, I.; Kaczor-Grzeskowiak, M.; Cascio, D.; Gunsalus, R. P.; Dickerson, R. E. dimerization? Suggestive evidence from a new crystal form. Biochemistry 1998, 37, 3665-3676. (Pubitemid 28162921)
24. Chauhan, S.; Tyagi, J. S. Cooperative binding of phosphorylated DevR to upstream sites is necessary and sufficient for activation of the Rv3134c-devRS operon in Mycobacterium tuberculosis: implication in the induction of DevR target genes. J. Bacteriol. 2008, 190, 4301-4312.
25. Betts, J. C.; Lukey, P. T.; Robb, L. C.; McAdam,R. A.; Duncan, K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol. 2002, 43, 717-731.
26. Sharma, D.; Bose, A.; Shakila, H.; Das, T. K.; Tyagi, J. S.; Ramanathan, V. D. Expression of mycobacterial cell division protein, FtsZ, and dormancy proteins, DevR and Acr, within lung granulomas throughout guinea pig infection. FEMS Immunol. Med. Microbiol. 2006, 48, 329-336.
27. Schnappinger, D.; Ehrt, S.; Voskuil, M. I.; Liu, Y.; Mangan, J. A.; Monahan, I. M.; Dolganov, G.; Efron, B.; Butcher, P. D.; Nathan, C.; Schoolnik, G. K. Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment. J. Exp. Med. 2003, 198, 693-704.
28. Karakousis, P. C.; Yoshimatsu, T.; Lamichhane, G.; Woolwine, S. C.; Nuermberger, E. L.; Grosset, J.; Bishai, W. R. Dormancy phenotype displayed by extracellular Mycobacterium tuberculosis within artificial granulomas in mice. J. Exp. Med. 2004, 200, 647-657.
29. Rustad, T. R.; Harrell, M. I.; Liao, R.; Sherman, D. R. The enduring hypoxic response of Mycobacterium tuberculosis. PLoS One 2008, 3, e1502.
30. Mitchison, D. A. The action of antituberculosis drugs in shortcourse chemotherapy. Tubercle 1985, 66, 219-225.
31. Zhang, Y.; Wade, M. M.; Scorpio, A.; Zhang, H.; Sun, Z. Mode of action of pyrazinamide: disruption of Mycobacterium tuberculosis membrane transport and energetics by pyrazinoic acid. J. Antimicrob. Chemother. 2003, 52, 790-795.
32. Koul, A.; Vranckx, L.; Dendouga, N.; Balemans, W.; Van den Wyngaert, I.; Vergauwen, K.; Gohlmann, H. W.; Willebrords, R.; Poncelet, A.; Guillemont, J.; Bald, D.; Andries, K. Diarylquinolines are bactericidal for dormant mycobacteria as a result of disturbed ATP homeostasis. J. Biol. Chem. 2008, 283, 25273-25280.
33. Andries, K.; Verhasselt, P.; Guillemont, J.; Gohlmann, H. W.; Neefs, J. M.; Winkler, H.; Van Gestel, J.; Timmerman, P.; Zhu, M.; Lee, E.; Williams, P.; de Chaffoy, D.; Huitric, E.; Hoffner, S.; Cambau, E.; Truffot-Pernot, C.; Lounis, N.; Jarlier, V. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 2005, 307, 223-227. (Pubitemid 40116230)
34. Stock, A. M.; Mottonen, J. M.; Stock, J. B.; Schutt, C. E. Threedimensional structure of CheY, the response regulator of bacterial chemotaxis. Nature 1989, 337, 745-749. (Pubitemid 19064730)
35. Boehr, D. D.; Wright, P. E. Biochemistry. How do proteins interact? Science 2008, 320, 1429-1430.
36. Marti-Renom, M. A.; Stuart, A. C.; Fiser, A.; Sanchez, R.; Melo, F.; Sali, A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 291-325.
37. Thompson, J. D.; Higgins, D. G.; Gibson, T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22, 4673-4680.
38. Liang, J.; Edelsbrunner, H.; Woodward, C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 1998, 7, 1884-1897. (Pubitemid 28432430)
39. Tiwari, A.; Panigrahi, S. K. HBAT: a complete package for analysing strong and weak hydrogen bonds in macromolecular crystal structures. In Silico Biol. 2007, 7, 651-661.
40. Bagchi, G.; Chauhan, S.; Sharma, D.; Tyagi, J. S. Transcription and autoregulation of the Rv3134c-devR-devS operon of Mycobacterium tuberculosis. Microbiology 2005, 151, 4045-4053.
41. Taneja, N. K.; Tyagi, J. S. Resazurin reduction assays for screening of antitubercular compounds against dormant and actively growing Mycobacterium tuberculosis, Mycobacterium bovis BCG and Mycobacterium smegmatis. J. Antimicrob. Chemother. 2007, 60, 288-293.