Essential metabolites of mycobacterium tuberculosis and their mimics

mBio

Volumn 2, Issue 1, 2011, Pages

  Lamichhane, Gyanu ^a   Freundlich, Joel S ^b   Ekins, Sean ^c,d,e,f   Wickramaratne, Niluka ^a   Nolan, Scott T ^a   Bishai, William R ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c Collaborative Drug Discovery ^*  (United States)

^d Collaborations in Chemistry ^*  (United States)

^e UNIVERSITY OF MARYLAND   (United States)

^f RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AZASERINE; BLEOMYCIN; CHORISMIC ACID; DIAMINOPIMELIC ACID; GLUTAMIC ACID; METHIONINE SULFOXIMINE; PEPTIDOGLYCAN; PHOTOFRIN; SHIKIMIC ACID DERIVATIVE; TETRAPYRROLE DERIVATIVE; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIUM MUTANT; CONCENTRATION RESPONSE; DRUG STRUCTURE; GENE IDENTIFICATION; GENETIC CODE; GENOTYPE; GROWTH INHIBITION; METABOLITE; MOLECULAR PROBE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHARMACOPHORE; PRIORITY JOURNAL; STRUCTURE ANALYSIS; TRANSPOSON; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

MYCOBACTERIUM TUBERCULOSIS;

BACTERIAL PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; MYCOBACTERIUM TUBERCULOSIS;

EID: 79953700626     PISSN: None     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00301-10     Document Type: Article

References (50)

1. WHO. 2009. Global tuberculosis control, p. 4-5. WHO, Geneva, Switzerland.
2. Corbett, E. L., C. J. Watt, N. Walker, D. Maher, B. G. Williams, M. C. Raviglione, and C. Dye. 2003. The growing burden of tuberculosis: global trends and interactions with the HIV epidemic. Arch. Intern. Med. 163: 1009-1021.
3. Dye, C., S. Scheele, P. Dolin, V. Pathania, and M. C. Raviglione. 1999. Consensus statement. Global burden of tuberculosis: estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project. JAMA 282:677-686.
4. Fauci, A. S. 2008. Multidrug-resistant and extensively drug-resistant tuberculosis: the National Institute of Allergy and Infectious Diseases Research agenda and recommendations for priority research. J. Infect. Dis. 197:1493-1498.
5. Jassal, M., and W. R. Bishai. 2009. Extensively drug-resistant tuberculosis. Lancet Infect. Dis. 9:19-30.
6. Sassetti, C. M., D. H. Boyd, and E. J. Rubin. 2003. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 48:77-84.
7. Lascelles, J., and D. D. Woods. 1952. The synthesis of folic acid by Bacterium coll and Staphylococcus aureus and its inhibition by sulphonamides. Br. J. Exp. Pathol. 33:288-303.
8. Achari, A., D. O. Somers, J. N. Champness, P. K. Bryant, J. Rosemond, and D. K. Stammers. 1997. Crystal structure of the anti-bacterial sulfonamide drug target dihydropteroate synthase. Nat. Struct. Biol. 4:490-497.
9. Tipper, D. J., and J. L. Strominger. 1965. Mechanism of action of penicillins: a proposal based on their structural similarity to acyl-D-alanyl- D-alanine. Proc. Natl. Acad. Sci. U. S. A. 54:1133-1141.
10. Denome, S. A., P. K. Elf, T. A. Henderson, D. E. Nelson, and K. D. Young. 1999. Escherichia coli mutants lacking all possible combinations of eight penicillin binding proteins: viability, characteristics, and implications for peptidoglycan synthesis. J. Bacteriol. 181:3981-3993.
11. Waxman, D. J., and J. L. Strominger. 1983. Penicillin-binding proteins and the mechanism of action of beta-lactam antibiotics. Annu. Rev. Biochem. 52:825-869.
12. Akerley, B. J., E. J. Rubin, A. Camilli, D. J. Lampe, H. M. Robertson, and J. J. Mekalanos. 1998. Systematic identification of essential genes by in vitro mariner mutagenesis. Proc. Natl. Acad. Sci. U. S. A. 95:8927-8932.
13. Murry, J. P., C. M. Sassetti, J. M. Lane, Z. Xie, and E. J. Rubin. 2008. Transposon site hybridization in Mycobacterium tuberculosis. Methods Mol. Biol. 416:45-59.
14. Rubin, E. J., B. J. Akerley, V. N. Novik, D. J. Lampe, R. N. Husson, and J. J. Mekalanos. 1999. In vivo transposition of mariner-based elements in enteric bacteria and mycobacteria. Proc. Natl. Acad. Sci. U. S. A. 96: 1645-1650.
15. Lamichhane, G., M. Zignol, N. J. Blades, D. E. Geiman, A. Dougherty, J. Grosset, K. W. Broman, and W. R. Bishai. 2003. A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U. S. A. 100:7213-7218.
16. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry III, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M. A. Quail, M. A. Rajandream, J. Rogers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J. E. Sulston, K. Taylor, S. Whitehead, and B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
17. Caspi, R., H. Foerster, C. A. Fulcher, P. Kaipa, M. Krummenacker, M. Latendresse, S. Paley, S. Y. Rhee, A. G. Shearer, C. Tissier, T. C. Walk, P. Zhang, and P. D. Karp. 2008. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 36:D623-D631.
18. Parish, T., and N. G. Stoker. 2002. The common aromatic amino acid biosynthesis pathway is essential in Mycobacterium tuberculosis. Microbiology 148:3069-3077.
19. Johnson, M., M. Lajiness, and G. Maggiora. 1989. Molecular similarity: a basis for designing drug screening programs. Prog. Clin. Biol. Res. 291: 167-171.
20. Johnson, M., and G. Maggiora. 1990. Concepts and applications of molecular similarity. Wiley Interscience, Hoboken, NY.
21. Horvath, D., and C. Jeandenans. 2003. Neighborhood behavior of in silico structural spaces with respect to in vitro activity spaces-a benchmark for neighborhood behavior assessment of different in silico similarity metrics. J. Chem. Inf. Comput. Sci. 43:691-698.
22. Kaiser, D., G. Zdrazil, and G. F. Ecker. 2005. Similarity based descriptors (SIBAR)-a tool for safe exchange of chemical information. J. Comput. Aided Mol. Des. 19:687-692.
23. Wang, N., R. K. DeLisle, and D. J. Diller. 2005. Fast small molecule similarity searching with multiple alignment profiles of molecules represented in one-dimension. J. Med. Chem. 48:6980-6990.
24. Willett, P., J. M. Barnard, and G. M. Downs. 1998. Chemical similarity searching. J. Chem. Inf. Comput. Sci. 38:983-996.
25. Krasowski, M. D., M. G. Siam, M. Iyer, A. F. Pizon, S. Giannoutsos, and S. Ekins. 2009. Chemoinformatic methods for predicting interference in drug of abuse/toxicology immunoassays. Clin. Chem. 55:1203-1213.
26. Klein, C., D. Kaiser, S. Kopp, P. Chiba, and G. F. Ecker. 2002. Similarity based SAR (SIBAR) as tool for early ADME profiling. J. Comput. Aided Mol. Des. 16:785-793.
27. Ekins, S., J. Bradford, K. Dole, A. Spektor, K. Gregory, D. Blondeau, M. Hohman, and B. A. Bunin. 2010. A collaborative database and computational models for tuberculosis drug discovery. Mol. Biosyst. 10: 840-851.
28. Hohman, M., K. Gregory, K. Chibale, P. J. Smith, S. Ekins, and B. Bunin. 2009. Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery. Drug Discov. Today 14: 261-270.
29. Kanehisa, M., and S. Goto. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27-30.
30. Karp, P. D., C. A. Ouzounis, C. Moore-Kochlacs, L. Goldovsky, P. Kaipa, D. Ahren, S. Tsoka, N. Darzentas, V. Kunin, and N. Lopez-Bigas. 2005. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res. 33:6083-6089.
31. Sud, M., E. Fahy, D. Cotter, A. Brown, E. A. Dennis, C. K. Glass, A. H. Merrill, Jr., R. C. Murphy, C. R. Raetz, D. W. Russell, and S. Subramaniam. 2007. LMSD: LIPID MAPS structure database. Nucleic Acids Res. 35:D527-D532.
32. Williams, A. J. 2008. A perspective of publicly accessible/open-access chemistry databases. Drug Discov. Today 13:495-501.
33. Irwin, J. J., and B. K. Shoichet. 2005. ZINC-a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 45:177-182.
34. Wiegand, I., K. Hilpert, and R. E. Hancock. 2008. Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances. Nat. Protoc. 3:163-175.
35. Harth, G., and M. A. Horwitz. 1999. An inhibitor of exported Mycobacterium tuberculosis glutamine synthetase selectively blocks the growth of pathogenic mycobacteria in axenic culture and in human monocytes: extracellular proteins as potential novel drug targets. J. Exp. Med. 189: 1425-1436.
36. Ertem, E., K. Yuce, G. Karakartal, O. Onal, and G. Yuce. 1990. The antituberculous effect of bleomycin. J. Antimicrob. Chemother. 26: 862-863.
37. Cho, Y., T. R. Ioerger, and J. C. Sacchettini. 2008. Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. J. Med. Chem. 51:5984-5992.
38. Sacchettini, J. C., E. J. Rubin, and J. S. Freundlich. 2008. Drugs versus bugs: in pursuit of the persistent predator Mycobacterium tuberculosis. Nat. Rev. Microbiol. 6:41-52.
39. Kortagere, S., M. D. Krasowski, and S. Ekins. 2009. The importance of discerning shape in molecular pharmacology. Trends Pharmacol. Sci. 30: 138-147.
40. Andries, K., P. Verhasselt, J. Guillemont, H. W. Gohlmann, J. M. Neefs, H. Winkler, J. Van Gestel, P. Timmerman, M. Zhu, E. Lee, P. Williams, D. de Chaffoy, E. Huitric, S. Hoffner, E. Cambau, C. Truffot-Pernot, N. Lounis, and V. Jarlier. 2005. A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307:223-227.
41. Matsumoto, M., H. Hashizume, T. Tomishige, M. Kawasaki, H. Tsubouchi, H. Sasaki, Y. Shimokawa, and M. Komatsu. 2006. OPC-67683, a nitro-dihydro-imidazooxazole derivative with promising action against tuberculosis in vitro and in mice. PLoS Med. 3:e466.
42. Davis, S. L., N. A. Be, G. Lamichhane, S. Nimmagadda, M. G. Pomper, W. R. Bishai, and S. K. Jain. 2009. Bacterial thymidine kinase as a non-invasive imaging reporter for Mycobacterium tuberculosis in live animals. PLoS One 4:e6297.
43. Larsen, M. H. 2000. Appendix 1. Some common methods in mycobacterial genetics. Electroporation-M. tuberculosis and BCG, p. 320. In Molecular genetics of mycobacteria. ASM Press, Washington, DC.
44. Larsen, M. H. 2000. Appendix 1. Some common methods in mycobacterial genetics. RNA preparation-Trizol, p. 317. In G. F. Hatfull and W. R. Jacobs, Jr. (ed.), Molecular genetics of mycobacteria. ASM Press, Washington, DC.
45. Prathipati, P., N. L. Ma, T. H. Keller. 2008. Global Bayesian models for the prioritization of antitubercular agents. J. Chem. Inf. Model. 48: 2362-2370.
46. Ballell, L., R. A. Field, K. Duncan, and R. J. Young. 2005. New smallmolecule synthetic antimycobacterials. Antimicrob. Agents Chemother. 49:2153-2163.
47. Clement, O. O., and A. T. Mehl. 2000. HipHop: pharmacophore based on multiple common-feature alignments, p. 69-84. In O. F. Guner (ed.), Pharmacophore perception, development, and use in drug design. IUL, San Diego, CA.
48. Ekins, S., C. Chang, S. Mani, M. D. Krasowski, E. J. Reschly, M. Iyer, V. Kholodovych, N. Ai, W. J. Welsh, M. Sinz, P. W. Swaan, R. Patel, and K. Bachmann. 2007. Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sites. Mol. Pharmacol. 72:592- 603.
49. Ekins, S., J. S. Johnston, P. Bahadduri, V. M. D'Souza, A. Ray, C. Chang, and P. W. Swaan. 2005. In vitro and pharmacophore-based discovery of novel hPEPT1 inhibitors. Pharmacol. Res. 22:512-517.
50. Bonnac, L., G. Y. Gao, L. Chen, K. Felczak, E. M. Bennett, H. Xu, T. Kim, N. Liu, H. Oh, P. J. Tonge, and K. W. Pankiewicz. 2007. Synthesis of 4-phenoxybenzamide adenine dinucleotide as NAD analogue with inhibitory activity against enoyl-ACP reductase (InhA) of Mycobacterium tuberculosis. Bioorg. Med. Chem. Lett. 17:4588-4591.