Pharmacophore and docking based virtual screening of validated Mycobacterium tuberculosis targets

Combinatorial Chemistry and High Throughput Screening

Volumn 18, Issue 7, 2015, Pages 624-637

  Vyas, Renu ^a   Karthikeyan, Muthukumarasamy ^a   Nainaru, Ganesh ^a   Muthukrishnan, Murugan ^a  

^a NATIONAL CHEMICAL LABORATORY   (India)

Author keywords

Binding energy; Docking; Mycobacterium tuberculosis; Open source drug discovery (OSDD); Pharmacophore; Structure based drug design (SBDD)

Indexed keywords

3 DEHYDROQUINATE DEHYDRATASE; BACTERIAL PROTEIN; HYDROGEN; LUMAZINE; PHOSPHOTRANSFERASE; THYMIDINE PHOSPHATE; TUBERCULOSTATIC AGENT; LIGAND;

ANTIBACTERIAL ACTIVITY; ARTICLE; BINDING AFFINITY; CLUSTER ANALYSIS; DRUG DESIGN; DRUG SCREENING; DRUG TARGETING; ENZYME ACTIVE SITE; HIGH THROUGHPUT SCREENING; HYDROGEN BOND; HYDROPHOBICITY; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR MODEL; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHARMACOPHORE; PRIORITY JOURNAL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; COMPUTER SIMULATION; DRUG DATABASE; DRUG EFFECTS; PRECLINICAL STUDY;

ANTITUBERCULAR AGENTS; CLUSTER ANALYSIS; COMPUTER SIMULATION; DATABASES, PHARMACEUTICAL; DRUG EVALUATION, PRECLINICAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MYCOBACTERIUM TUBERCULOSIS; USER-COMPUTER INTERFACE;

EID: 84942113405     PISSN: 13862073     EISSN: 18755402     Source Type: Journal    
DOI: 10.2174/1386207318666150703112759     Document Type: Article

References (40)

1. Marrone T.J.; Briggs, J.M.; Mc Cammon, J.A. Structure based drug design: Computational Advances. Anu. Rev. Pharmacol. Toxicol., 1997, 37, 71-90.
2. Marrone, T.J.; Luty, B.A.; Rose, P.W. Discovering high-affinity ligands from the computationally predicted structures and affinities of small molecules bound to a target: a virtual screening approach. Perspect Drug Discov., 2000, 20, 209-230.
3. Jordi, M.; Knegtel, R.M.A. Similarity versus docking in 3D virtual screening. Perspect Drug Discov., 2000, 20, 191-207.
4. Karthikeyan, M; Vyas, R. Docking and pharmacophore modeling for virtual screening. In Practical Chemoinformatics, Springer, 2014, pp. 195-267.
5. Fitzgerald, D.W.; Sterling, T.R.; Haas, D.W. M. tuberculosis. In:Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 7th ed. Mandell GL, Bennett JE, Dolan R, Eds. Saunders Elsevier: Orlando, FL, 2009.
6. http://www.who.int/tb/publications/factsheets/en/index.html (accessed on February 2014).
7. Banerjee A.; Dubnau, E.; Quemard A.; Balasubramanian, V.; Um, K.S.; Wilson, T.; Collins, D.; de L.G.; Jacobs, W.R. Jr. A gene encoding a target for isoniazid and ethionamide in M. tuberculosis. Science, 1994, 263, 227-230.
8. Lyne, P.D.; Kenny, P.W.; Cosgrove, D.A.; Deng, C.; Zabludoff, S.; Wendoloski, J.J.; Ashwell, S. Identification of compounds with nanomolar binding affinity for checkpoint kinase-1 using knowledge-based virtual screening. J. Med. Chem., 2004, 47, 1962-1968.
9. Mdbuli, K.; Spigelman, M. Novel targets for tuberculosis drug discovery. Curr. Opin. Pharmacol., 2006, 6, 459-467.
10. Zhiyong L.; Zhang, X. Protein targets for structure based anti-M. tuberculosis drug discovery. Protein Cell, 2010, 1, 435-442.
11. Lamichahane G. Novel targets in M Tuberculosis search for new drugs. Trends Mol. Med., 2011, 1, 25-33.
12. Anurag, M.; Dash, D. Unraveling the potential of intrinsically disordered proteins as drug targets: applications to M. tuberculosis. Mol. Biosyst., 2009, 5, 1752-1757.
13. Munier, L.H.; Chaffotte, A.; Pochet, S.; Labesse, G. Thymidylate kinase of Mycobacterium tuberculosis: a chimera sharing properties common to eukaryotic and bacterial enzymes. Protein Sci., 2001, 10 (6), 1195-1205.
14. Li de la, S.I.; Munier, L.H.; Gilles, A.M.; Barzu, O.; Delarue, M. X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution. J. Mol. Biol., 2001, 311 (1), 87-100.
15. Talukdar, A.; Illarionov, B.; Bacher, A.; Fischer, M.; Cushman, M. Synthesis and enzyme inhibitory activity of the S nucleoside analogue of the Ribitylaminopyrimidine substrate of lumazine synthase and product of riboflavin synthase. J. Org. Chem., 2007, 72, 7167-7175.
16. Morgunova, E.; Meining, W.; Illarionov, B. Crystal structure of lumazine synthase from Mycobacterium tuberculosis as a target for rational drug design: binding mode of a new class of purinetrione inhibitors. Biochemistry, 2005, 44(8), 2746-2758.
17. Oliveira, J.S.; Pereira, J.H.; Canduri, F.; Rodrigues, N.C.; de Souza, O.N.; de Azevedo Jr, W.F.; Basso, L.A.; Santos, D.S. Crystallographic and pre steady state kinetic studies on binding of NADH to wild type and isoniazid resistant enoyl-ACP CoA reductase enzymes from M. tuberculosis. J. Mol. Biol., 2006, 359, 646-666.
18. Schroeder, E.K.; de Souza, N.; Santos, D.S.; Blanchard, J.S.; Basso, L.A. Drugs that inhibit mycolic acid biosynthesis in M. tuberculosis. Curr. Pharm. Biotechnol., 2002, 3, 197-225.
19. Oliveira, J.S.; Pereira, J.H.; Canduri, F. Crystallographic and presteady-state kinetics studies on binding of NADH to wild-type and isoniazid-resistant enoyl-ACP(CoA) reductase enzymes from Mycobacterium tuberculosis. J. Mol. Biol., 2006, 359(3), 646-666.
20. Zhao, Y.; Bacher, A.; Illarionov, B.; Fischer, M.; Georg, G.; Ye Q.Z.; Fanwick, P.E.; Franzblau S.G.; Wan, B.; Cushman, M. Discovery and development of the covalent hydrates of trifluoromethylated pyrazoles as riboflavin synthase inhibitors with antibiotic activity against M. tuberculosis. J. Org. Chem., 2009, 7(74), 5297-5303.
21. Tizon, L.; Otero, J.M.; Prazeres, V.F.; Llamas-Saiz, A.L.; Fox, G.C.; van Raaij M.J.; Lamb, H.; Hawkins, A.R.; Ainsa, J.A.; Castedo, L.; González-Bello, C.A. A prodrug approach for improving anti-tuberculosis activity of potent M. tuberculosis type II dehydroquinase inhibitors. J. Med. Chem., 2011, 8(54), 6063-6084.
22. Zheng, R.; Dam, T.K.; Brewer, C.F.; Blanchard, J.S. Active site residues in Mycobacterium tuberculosis pantothenate synthetase required in the formation and stabilization of the adenylate intermediate. Biochemistry, 2004, 43(22), 7171-7178.
23. Shen, L.; Huang, H.; Makriyannis, A.; Fisher, L.S. Integrated ligand based pharmacophore model derived from FAAH covalent ligands classes. Curr. Comput. Aided Drug Des., 2012, 8(4), 330-334.
24. 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.
25. Wermuth, C.G.; Ganellin, C.R.; Lindberg, P.; Mitscher, L.A. Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure and Applied Chemistry, 1998, 70, 1129-1143.
26. Hu, Q.; Huang, J.X.; Hu, X. Modeling and mining term association for improving biomedical information retrieval performance, BMC Bioinformatics, 2012, 13 (Suppl 9), S2.
27. www.chemaxon.com/jchem/(Accessed 10 October 2014).
28. www.chemcomp.com/software.htm (Accessed 10 October 2014).
29. Good, A.C.; Cho, S.J.; Mason, J.S. Descriptors you can count on? Normalized and filtered pharmacophore descriptors for virtual screening. J. Comput. Aided Mol. Des., 2004, 18, 523-527.
30. Chemical Computing Group Inc., Molecular Operating Environment Software, Montreal, 2010.
31. Schrödinger Drug-Like Ligands Decoy Set (2008) Schrödinger, Inc. http://www.schrodinger.com/glide-decoy-set
32. LigPrep, version 2.5, Schrödinger, LLC, New York, NY, 2012.
33. Glide, version 5.8, Schr?inger, LLC, New York, NY, 2012.
34. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracy. J. Med. Chem,. 2004, 47, 1739-1749.
35. http://www.chemaxon.com/products/jklustor/ (Accessed 10 October 2014).
36. Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv Rev., 1997, 23(1-3), 3-25.
37. Binkowski, T.A.; Naghibzadeh, S; Liang J. Computed atals of surface topography of proteins. Nucleic Acid Res., 2003, 31, 3352-3355.
38. Prathipati P.; Ngai M.; Manjunatha, U.; Bender, A. Fishing the target of antitubercular compounds: Insilico target deconvolution model development and validation. J. Proteome Res., 2009, 8(6), 2788-2798.
39. Muthukrishnan, M.; Mujahid, M.; Yogeshwari, P.; Sriram, D. Synthesis and biological evaluation of new triazole-spirochromone conjugates as inhibitors of M. tuberculosis. Tetrahedron Lett., 2011, 52, 2387-2389.
40. moltable.ncl.res.in/ (Accessed 10 October 2014).