Natural products, small molecules, and genetics in tuberculosis drug development

Journal of Medicinal Chemistry

Volumn 51, Issue 9, 2008, Pages 2606-2612

  Gutierrez Lugo, Maria Teresa ^a   Bewley, Carole A ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

1 (6 BROMO 2 METHOXY 3 QUINOLINYL) 4 DIMETHYLAMINO 2 (1 NAPHTHYL) 1 PHENYL 2 BUTANOL; AMIKACIN; AMINOGLYCOSIDE; AMINOSALICYLIC ACID; ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT; CAPREOMYCIN; CIPROFLOXACIN; CYCLOSERINE; ETHAMBUTOL; ETHIONAMIDE; FAS 20013; GATIFLOXACIN; ISONIAZID; KANAMYCIN; LEVOFLOXACIN; MOXIFLOXACIN; NATURAL PRODUCT; NICOTINAMIDE; OFLOXACIN; PYRAZINAMIDE; QUINOLINE DERIVATIVE; QUINOLONE DERIVATIVE; RIFABUTIN; RIFALAZIL; RIFAMPICIN; RIFAMYCIN; RIFAPENTINE; RS 118641; STREPTOMYCIN; SUDOTERB; TUBERCULOSTATIC AGENT; UNINDEXED DRUG;

ANTIBIOTIC RESISTANCE; BIOINFORMATICS; CLINICAL TRIAL; DRUG STRUCTURE; DRUG TARGETING; GENETICS; GENOMICS; HUMAN; REVIEW; STRUCTURE ACTIVITY RELATION; TUBERCULOSIS;

ANTITUBERCULAR AGENTS; BIOLOGICAL PRODUCTS; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; GENOMICS; HUMANS; MYCOBACTERIUM TUBERCULOSIS; SMALL MOLECULE LIBRARIES; TUBERCULOSIS, PULMONARY;

EID: 42949174608     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm070719i     Document Type: Review

References (68)

1. Brock, T. D. Robert Koch: A Life in Medicine and Bacteriology; Science Tech Publishers: Madison, WI, 1988.
2. Corbett, E. L.; Watt, C. J.; Walker, N.; Maher, D.; Williams, B. G.; Raviglione, M. C.; Dye, C. The growing burden of tuberculosis: global trends and interactions with the HIV epidemic. Arch. Intern. Med. 2003, 163 (9), 1009-1021.
3. Frieden, T. R.; Sterling, T. R.; Munsiff, S. S.; Watt, C. J.; Dye, C. Lancet 2003, 362 (9387), 887-899.
4. World Health Organization, Treatment of Tuberculosis Guidelines. http://www.who.int/tb/publications/cds_tb_2003_313/en/index.html and http.y/www.who.int/tb.xdr/faqs/en/ (2007).
5. Fleming, A. On a remarkable bacteriolytic element found in tissues and secretions. Proc. R. Soc. London, Ser. B 1922, 93, 306-317.
6. Demain, A. L. Microbial natural products: alive and well in 1998. Nat. Biotechnol. 1998, 16 (1), 3-4.
7. Woodruff, H. B.; Waksman, S. A. The actinomycins and their importance in the treatment of tumors in animals and man. Historical background. Ann. N.Y. Acad. Sci. 1960, 89, 287-298.
8. Waksman, S. A. Successes and failures in the search for antibiotics. Adv. Appl. Microbiol. 1969, 11, 1-16.
9. Pfuetze, K. H.; Pyle, M. M.; Hinshaw, H. C.; Feldman, W. H. The first clinical trial of streptomycin in human tuberculosis. Am. Rev. Tuberc. 1955, 71 (5), 752-754.
10. Lehmann, J. The treatment of tuberculosis in Sweden with para-aminosalicylic acid; a review. Dis. Chest 1949, 16 (6), 684-703.
11. Domagk, G. Modern methods of chemotherapy of tuberculosis. An. R. Acad. Nac. Med. (Madr.). 1952, 69 (4), 504-513.
12. Dessau, F. I.; Yeager, R. L.; Burger, F. J.; Williams, J. H. Pyrazinamide (aldinamide) in experimental tuberculosis of the guinea pig. Am. Rev. Tuberc. 1952, 65, 519-522.
13. Thomas, J. P.; Baughn, C. O.; Wilkinson, R. G.; Shepherd, R. G. A new synthetic compound with antituberculous activity in mice: ethambutol (dextro-2,2′-(ethylenediimino)-di-1-butanol). Am. Rev. Respir. Dis. 1961, 83, 891-893.
14. Epstein, I. G.; Nair, K. G.; Boyd, L. J. Cycloserine, a new antibiotic, in the treatment of human pulmonary tuberculosis: a preliminary report. Antibiot. Med. Clin. Ther. 1955, 1 (2), 80-93.
15. Floss, H. G.; Yu, T.-W. Rifamycin-mode of action, resistance, and biosynthesis. Chem. Rev. 2005, 105, 621-632.
16. Boshoff, I. M.; Barry, C. E., III. Tuberculosis - Metabolism and respiration in the absence of growth. Nat. Rev. Microbiol. 2005, 3 (1), 70-80.
17. Smith, C. V; Sharma, V.; Sacchettini, J. C. D. TB drug discovery: addressing issues of persistence and resistance. Tuberculosis 2004, 84, 45-55.
18. Bishai, W. R.; Chaisson, R. E. Short-course chemoprophylaxis for tuberculosis. Clin. Chest Med. 1997, 18 (1), 115-122.
19. Gandhi, N. R.; Moll, A.; Sturm, A. W.; Pawinski, R.; Govender, T.; Lalloo, U.; Zeller, K.; Andrews, J.; Friedland, G. Extensively drug-resistant tuberculosis as a cause of death in patients co-infected with tuberculosis and HIV in a rural area of South Africa. Lancet 2006, 368, 1575-1580.
20. Williams, K. J.; Duncan, K. Current strategies for identifying and validating targets for new treatment-shortening drugs for TB. Curr. Mol. Med. 2007, 7 (3), 297-307.
21. Cole, S. T.; Brosch, R.; Parkhill, J.; Garnier, T.; Churcher, C.; Harris, D.; Gordon, S. V.; Eiglmeier, K.; Gas, S.; Barry, C. E., 3rd; et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393, 537-544.
22. Camus, J. C.; Pryor, M. J.; Medigue, C.; Cole, S. T. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 2002, 148, 2967-2973.
23. Duncan, K. Identification and validation of novel drug targets in tuberculosis. Curr. Pharm. Des. 2004, 10, 3185-3194.
24. Sassetti, C. M.; Boyd, D. H.; Rubin, E. J. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003, 48, 77-84.
25. Rengarajan, J.; Bloom, B. R.; Rubin, E. J. Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 8327-8332.
26. Newton, G. L.; Fahey, R. C. Mycothiol biochemistry. Arch. Microbiol. 2002, 178 (6), 388-394.
27. Parish, T.; Stoker, N. G. Use of a flexible cassette method to generate a double unmarked Mycobacterium tuberculosis tlyA plcABC mutant by gene replacement. Microbiology 2000, 146, 1969-1975.
28. Bardarov, S.; Bardarov, S., Jr; Pavelka, M. S.; Sambandamurthy, V.; Larsen, M.; Tufariello, J.; Chan, J.; Hatfull, G.; Jacobs, W. R., Jr. Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis. Microbiology 2002, 148, 3007-3017.
29. Buchmeier, N.; Fahey, R. C. The mshA gene encoding the glycosyltransferase of mycothiol biosynthesis is essential in Mycobacterium tuberculosis Erdman. FEMS Microbiol. Lett. 2006, 264, 74-79.
30. Sareen, D.; Newton, G. L.; Fahey, R. C.; Buchmeier, N. A. Mycothiol is essential for growth of Mycobacterium tuberculosis Erdman. J. Bacteriol. 2003, 185, 6736-6740.
31. Bhatt, A.; Kremer, L; Dai, A. Z.; Sacchettini, J. C.; Jacobs, W. R., Jr. Conditional depletion of KasA, a key enzyme of mycolic acid biosynthesis, leads to mycobacterial cell lysis. J. Bacteriol. 2005, 187, 7596-7606.
32. Warner, D. F.; Mizrahi, V. Mycobacterial genetics in target validation. Drug Discovery Today: Technol. 2004, 1, 93-98.
33. Muttucumaru, N.; Roberts, G.; Hinds, J.; Stabler, R. A.; Parish, T. Gene expression profile of Mycobacterium tuberculosis in a non-replicating state. Tuberculosis 2004, 84, 239-246.
34. Voskuil, M. I. Mycobacterium tuberculosis gene expression during environmental conditions associated with latency. Tuberculosis 2004, 84, 138-143.
35. Voskuil, M. I.; Visconti, K. C.; Schoolnik, G. K. Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis 2004, 84, 218-227.
36. Hampshire, T; Soneji, S.; Bacon, J.; James, B. W.; Hinds, J.; Laing, K.; Stabler, R. A.; Marsh, P. D.; Butcher, P. D. Stationary phase gene expression of Mycobacterium tuberculosis following a progressive nutrient depletion: a model for persistent organisms? Tuberculosis 2004, 84, 228-238.
37. Boshoff, H. I. M.; Myers, T. G.; Copp, B. R.; McNeil, M. R.; Wilson, M. A.; Barry, C. E., III. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 2004, 279, 40174-40184.
38. Cho, S. H.; Goodlett, D.; Franzblau, S. ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis. Tuberculosis 2006, 86, 445-460.
39. Lin, T.-W.; Melgar, M. M.; Kurth, D.; Swamidass, S. J.; Purdon, J.; Tseng, T.; Gago, G.; Baldi, P.; Gramajo, H; Tsai, S.-C. Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 3072-3077.
40. Gopalakrishnan, B.; Aparna, V.; Jeevan, J.; Ravi, M.; Desiraju, G. R. A virtual screening approach for thymidine monophosphate kinase inhibitors as antitubercular agents based on docking and pharmacophore models. J. Chem. Inf. Model. 2005, 45, 1101-1108.
41. Srivastava, S. K.; Tripathi, R. P.; Ramachandran, R. NAD+-dependent DNA ligase (Rv3014c) from Mycobacterium tuberculosis: crystal structure of the adenylation domain and identification of novel inhibitors. J. Biol. Chem. 2005, 280, 30273-30281.
42. Sullivan, T. J.; Truglio, J. J.; Boyne, M. E.; Novichenok, P.; Zhang, X.; Stratton, C. F.; Li, H.-J.; Kaur, T.; Amin, A.; Johnson, F.; Slayden, R. A.; Kisker, C.; Tonge, P. J. High affinity InhA inhibitors with activity against drug-resistant strains of Mycobacterium tuberculosis. ACS Chem. Biol. 2006, 1, 43-53.
43. Kantardjieff, K.; Rupp, B. Structural bioinformatic approaches to the discovery of new antimycobacterial drugs. Curr. Pharm. Des. 2004, 10, 3195-3211.
44. Murillo, A. C.; Li, H. Y.; Alber, T.; Baker, E. N.; Berger, J. M.; Cherney, L. T.; Cherney, M. M.; Cho, Y. S.; Eisenberg, D.; Garen, C. R.; Goulding, C. W.; Hung, L. W.; Ioerger, T. R.; Jacobs, W. R.; James, M. N.; Kim, C.; Krieger, I.; Lott, J. S.; Sankaranarayanan, R.; Segelke, B. W.; Terwilliger, T. C.; Wang, F.; Wang, S.; Sacchettini, J. C. High throughput crystallography of TB drug targets. Infect. Disord. Drug Targets 2007, 7, 127-139.
45. Cole, S. T.; Eiglmeier, K.; Parkhill, J.; James, K. D.; Thomson, N. R.; Wheeler, P. R.; Honore, N.; Garnier, T.; Churcher, C.; Harris, D.;. Massive gene decay in the leprosy bacillus. Nature 2001, 409, 10007-10011.
46. Fleischmann, R. D.; Alland, D.; Eise, J. A.; Carpenter, L.; White, O.; Peterson, J.; DeBoy, R.; Dodson, R.; Gwinn, M.; Haft, D.; et al. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 2002, 184, 5479-5490.
47. Marmiesse, M.; Brodin, P.; Buchrieser, C.; Gutierrez, C.; Simoes, N.; Vincent, V.; Glaser, P.; Cole, S. T.; Brosch, R. Macro-array and bioinformatic analyses reveal mycobacterial "core" genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex. Microbiology 2004, 150, 483-496.
48. Murry, J. P.; Rubin, E. New genetic approaches shed light on TB virulence. Trends Microbiol. 2005, 13, 366-372.
49. Hasan, S.; Daugelat, S.; Rao, P. S. S.; Schreiber, M. Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis. PLoS Comput. Biol. 2006, 2, e61.
50. Murphy, D. J.; Brown, J. R. Identification of gene targets against dormant phase Mycobacterium tuberculosis infections. BMC Infect. Dis. 2007, 7, 84-99.
51. Balganesh, T. S.; Furr, B. J. A. Molecular approaches to target discovery: evaluating targets for antituberculosis drug discovery programmes. Infect. Disord. Drug Targets 2007, 7, 120-126.
52. Stover, C. K.; Warrener, P.; VanDevanter, D. R.; Sherman, D. R.; Arain, T. M.; Langhorne, M. H.; Anderson, S. W.; Towell, J. A.; Yuan, Y.; McMurray, D. N.; Kreiswirth, B. N.; Barry, C. E.; Baker, W. R. A small-molecule nitroimidazopyran drug candidate for the treatment of tuberculosis. Nature 2000, 405, 962-966.
53. Matsumoto, M; Hashizume, H.; Tomishige, T.; Kawasaki, M.; Tsubouchi, H.; Sasaki, H.; Shimokawa, Y.; Komatsu, Y. OPC-67683, a nitro-dihydroimidazooxazole derivative with promising action against tuberculosis in vitro and in mice. PLoS Med. 2006, 3, e466.
54. Manjunatha, U. H.; Boshoff, H.; Dowd, C. S.; Zhang, L.; Albert, T. J.; Norton, J. E.; Daniels, L.; Dick, T.; Pang, S. S.; Barry, C. E., III. Identification of a nitroimidazo oxazine-specific protein involved in PA-824 resistance in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 431-436.
55. Andries, K.; Verhasselt, P.; Guillemont, J.; Göhlmann, H. W. H.; Neefs, J.-M.; Winkler, H.; Gestel, J. V.; Timmerman, P.; Zhu, M.; Lee, E.; Williams, P.; 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.
56. Laurenzi, M.; Ginsberg, A.; Spigelman, M. Challenges associated with current and future TB treatment. Infect. Disord. Drug Targets 2007, 7, 105-119.
57. http://www.tballiance.org/newscenter/view-brief.php?id=726.
58. Arora, S. K.; Sinha, N.; Jain, S.; Upadhayaya, R. S.; Jana, G.; Ajay, S.; Sinha, R. K. Preparation of Pyrrole Derivatives as Antimycobacterial Compounds. WO2004026828, 2004.
59. Ginsberg, A. M.; Spigelman, M. Challenges in tuberculosis drug research and development. Nat. Med. 2007, 13, 290-294.
60. Zhang, Y.; Post-Martens, K.; Denkin, S. New drug candidates and therapeutic targets for tuberculosis therapy. Drug. Discovery Today 2006, 11, 21-27.
61. Rothstein, D. M.; Shalish, C.; Murphy, C. K.; Sternlicht, A.; Campbell, L. A. Development potential of rifalazil and other benzoxazinorifamycins. Expert Opin. Invest. Drugs 2006, 15, 603-623.
62. Portero, J.-L.; Rubio, M. New antituberculisis therapies. Expert Opin. Ther. Pat. 2007, 17, 617-637.
63. Protopopova, M.; Hanrahan, C.; Nikonenko, B.; Samala, R.; Chen, P.; Gearhart, J.; Einck, L.; Nacy, C. A. Identification of a new antitubercular drug candidate, SQ109, from a combinatorial library of 1,2-ethylenediamines. J. Antimicrob. Chemother. 2005, 56, 968-974.
64. Kogal, T; Fukuoka, T.; Dot, N.; Harasaki, T.; Inoue, H.; Hotoda, h.; Kakuta, M.; Muramatsu, Y.; Yamamura, N.; Hoshi, M.; Hirota, T. Activity of capuramycin analogues against Mycobacterium tuberculosis, Mycobacterium avium, and Mycobacterium intracellular in vitro and in vivo. J. Antimicrob. Chemother. 2004, 54, 755-760.
65. Sood, R.; Bhadauriya, R.; Rao, M.; Gautam, R.; Malhotra, S.; Barman, T. K.; Upadhyay, D. J.; Rattan, A. Antimycobacterial activities of oxazolidinones: a review. Infect. Disord. Drug Targets 2006, 6, 343-354.
66. Parrish, N. M.; Houston, T.; Jones, P. B.; Townsend, C.; Dick, J. D. In vitro activity of a novel antimycobacterial compound, N-octane- sulfonylacetamide, and its effects on lipid and mycolic acid synthesis. Antimicrob. Agents Chemother. 2001, 45, 1143-1150.
67. Copp, B. R.; Pearce, A. N. Natural product growth inhibitors of Mycobacterium tuberculosis. Nat. Prod. Rep. 2007, 24, 278-297.
68. Kaufmann, S. H. E.; Parida, S. Changing funding patterns in tuberculosis. Nat. Med. 2007, 13, 299-303.