Virtual screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis

BMC Bioinformatics

Volumn 11, Issue SUPPLL.1, 2010, Pages

  Garg, Aarti ^a,b   Tewari, Rupinder ^b   Raghava, Gajendra P S ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

^b PANJAB UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ANTITUBERCULAR AGENTS; BIOSYNTHETIC PATHWAY; COMBINATORIAL LIBRARY; INHIBITORY ACTIVITY; MULTIDRUG RESISTANTS; MYCOBACTERIUM TUBERCULOSIS; POTENTIAL INHIBITORS; SIMILARITY SEARCH; FAVORABLE INTERACTIONS;

AMINO ACIDS; BIOCHEMISTRY; BIOSYNTHESIS; ENZYME INHIBITION; BIOINFORMATICS;

MOLECULES;

MYCOBACTERIUM TUBERCULOSIS;

DIAMINOPIMELIC ACID; DIHYDRODIPICOLINATE SYNTHASE; HYDROLYASE; LYSINE; PYRUVIC ACID; TUBERCULOSTATIC AGENT;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; DRUG DESIGN; DRUG EFFECT; ENZYME ACTIVE SITE; ENZYMOLOGY; FACTUAL DATABASE; METABOLISM; MULTIDRUG RESISTANT TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS; STRUCTURE ACTIVITY RELATION;

ANTITUBERCULAR AGENTS; BINDING SITES; CATALYTIC DOMAIN; DATABASES, FACTUAL; DIAMINOPIMELIC ACID; DRUG DESIGN; HYDRO-LYASES; LYSINE; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; PYRUVIC ACID; STRUCTURE-ACTIVITY RELATIONSHIP; TUBERCULOSIS, MULTIDRUG-RESISTANT;

EID: 75149192318     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-S1-S53     Document Type: Article

References (32)

1. Bloom BR, Murray CJ. Tuberculosis: commentary on a reemergent killer. Science 1992, 257:1055-64. 10.1126/science.257.5073.1055, 1509256.
2. LoBue P. Extensively drug-resistant tuberculosis. Curr Opin Infect Dis 2009, 22:167-173. 10.1097/QCO.0b013e3283229fab, 19283912.
3. Jain A, Dixit P. Multidrug-resistant to extensively drug resistant tuberculosis: what is next?. J Biosci 2008, 33:605-616. 10.1007/s12038-008-0078-8, 19208985.
4. Rattan A, Kalia A, Ahmad N. Multidrug-resistant Mycobacterium tuberculosis: molecular perspectives. Emerg Infect Dis 1998, 4:195-209. 10.3201/eid0402.980207, 2640153, 9621190.
5. WHO Report. , http://www.who.int/tb/publications/global_report/2008/summary/en/index.h tml
6. Hutton CA, Perugini MA, Gerrard JA. Inhibition of lysine biosynthesis: an evolving antibiotic strategy. Mol BioSyst 2007, 3:458-465. 10.1039/b705624a, 17579770.
7. Cox RJ, Sutherland A, Vederas JC. Bacterial diaminopimelate metabolism as a target for antibiotic design. Bioorg Med Chem 2000, 8:843-871. 10.1016/S0968-0896(00)00044-4, 10881998.
8. Hutton CA, Southwood TJ, Turner JJ. Inhibitors of lysine biosynthesis as antibacterial agents. Mini Rev Med Chem 2003, 3:115-127. 10.2174/1389557033405359, 12570844.
9. Pavelka MS, Jacobs WR. Biosynthesis of diaminopimelate, the precursor of lysine and a component of peptidoglycan, is an essential function of Mycobacterium smegmatis. J Bacteriol 1996, 178:6496-507. 178536, 8932306.
10. Shedlarski JG, Gilvarg C. The pyruvate-aspartic semialdehyde condensing enzyme of Escherichia coli. J Biol Chem 1970, 245:1362-1373.
11. Laber B, Gomis-Rüth FX, Romão MJ, Huber R. Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization. Biochem J 1992, 288:691-695. 1132066, 1463470.
12. Blickling S, Renner C, Laber B, Pohlenz H, Holak T, Huber R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochem J 1997, 36:24-33.
13. Karsten WE. Dihydrodipicolinate Synthase from Escherichia coli: pH dependent changes in the kinetic mechanism and kinetic mechanism of allosteric inhibition by L-Lysine. Biochem J 1997, 36:1730-1739.
14. Blagova E, Levdikov V, Milioti N, Fogg MJ, Kalliomaa AK, Brannigan JA, Wilson KS, Wilkinson AJ. Crystal structure of dihydrodipicolinate synthase (BA3935) from Bacillus anthracis at 1.94 A resolution. Proteins 2006, 62:297. 10.1002/prot.20684, 16287120.
15. Burgess BR, Dobson RC, Dogovski C, Jameson GB, Parker MW, Perugini MA. Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008, 64:659-61. 10.1107/S1744309108016746, 18607102.
16. Pearce FG, Perugini MA, McKerchar HJ, Gerrard JA. Dihydrodipicolinate synthase from Thermotoga maritima. Biochem J 2006, 400:359-66. 10.1042/BJ20060771, 1652817, 16872276.
17. Dobson RCJ, Valegard K, Gerrard JA. The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad. J Mol Biol 2004, 338:329-339. 10.1016/j.jmb.2004.02.060, 15066435.
18. Blickling S, Beisel HG, Bozic D, Knablein J, Laber B, Huber R. Structure of dihydrodipicolinate synthase of Nicotiana sylvestris reveals novel quaternary structure. J Mol Biol 1997, 274:608-621. 10.1006/jmbi.1997.1393, 9417939.
19. Mirwaldt C, Korndorfer I, Huber R. The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 resolution. J Mol Biol 1995, 246:227-239. 10.1006/jmbi.1994.0078, 7853400.
20. Kefala G, Evans GL, Griffin MD, Devenish SR, Pearce FG, Perugini MA, Gerrard JA, Weiss MS, Dobson RC. Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis. Biochem J 2008, 411:351-60. 10.1042/BJ20071360, 18062777.
21. Kefala G, Weiss MS. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapA (Rv2753c) from Mycobacterium tuberculosis. Acta Crystallograph Sect F Struct Biol Crystal Commun 2006, 62:1116-1119.
22. Turner JJ, Gerrard JA, Hutton CA. Heterocyclic inhibitors of dihydrodipicolinate synthase are not competitive. Bioorg Med Chem 2005, 13:2133-40. 10.1016/j.bmc.2005.01.001, 15727866.
23. Turner JJ, Healy JP, Dobson RC, Gerrard JA, Hutton CA. Two new irreversible inhibitors of dihydrodipicolinate synthase: diethyl (E,E)-4-oxo-2,5-heptadienedioate and diethyl (E)-4-oxo-2-heptenedioate. Bioorg Med Chem Lett 2005, 15:995-8. 10.1016/j.bmcl.2004.12.043, 15686899.
24. Turner JJ, Gerrard JA, Hutton CA. Conformationally constrained diketopimelic acid analogues as inhibitors of dihydrodipicolinate synthase. Bioorg Med Chem 2005, 13:2133-40. 10.1016/j.bmc.2005.01.001, 15727866.
25. Mitsakos V, Dobson RCJ, Pearce FG, Devenish SR, Evans GL, Burgess BR, Perugini MA, Gerrard JA, Hutton CA. Inhibiting dihydrodipicolinate synthase across species: towards specificity for pathogens?. Bioorg Med Chem Lett 2008, 18:842-844. 10.1016/j.bmcl.2007.11.026, 18054225.
26. VLife Sciences technologies MDS 2.0 Molecular Design Suite. 2003, Pvt Ltd, Pune, India, VLife Sciences technologies.
27. Lipinski CA. Drug-like properties and the causes of poor solubility and poor permeability. J Pharmacol Toxicol Methods 2000, 44:235-249. 10.1016/S1056-8719(00)00107-6, 11274893.
28. Muegge I, Oloff S. Advances in virtual screening. Drug Discov Today 2006, 3:405-411.
29. Lyne PD. Structure-based virtual screening: an overview. Drug Discov Today 2002, 7:1047-1055. 10.1016/S1359-6446(02)02483-2, 12546894.
30. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian Genetic algorithm and empirical binding free energy function. J Computational Chemistry 1998, 19:1639-1662.
31. PUB475318. , http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=475318&loc=e c_rcs
32. Anti-infective. , http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=1332&loc=ea_ras