Structural and chemical basis for enhanced affinity to a series of mycobacterial thymidine monophosphate kinase inhibitors: Fragment-based QSAR and QM/MM docking studies

Journal of Molecular Modeling

Volumn 19, Issue 1, 2013, Pages 179-192

  Bueno, Renata V ^a   Toledo, Ney R ^a   Neves, Bruno J ^a   Braga, Rodolpho C ^a   Andrade, Carolina H ^a  

^a FEDERAL UNIVERSITY OF GOIÁS   (Brazil)

Author keywords

Fragment based; HQSAR; QM MM docking; Thymidine monophosphate kinase; Tuberculosis

Indexed keywords

PHOSPHOTRANSFERASE INHIBITOR; THYMIDINE MONOPHOSPHATE KINASE INHIBITOR; THYMIDINE PHOSPHATE; THYMIDYLATE KINASE; TUBERCULOSTATIC AGENT; UNCLASSIFIED DRUG;

ARTICLE; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR MECHANICS; MOLECULAR MODEL; MOLECULAR RECOGNITION; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; QUANTUM MECHANICS;

ANTITUBERCULAR AGENTS; BINDING SITES; HOLOGRAPHY; MOLECULAR DYNAMICS SIMULATION; MYCOBACTERIUM TUBERCULOSIS; NUCLEOSIDE-PHOSPHATE KINASE; PROTEIN KINASE INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; QUANTUM THEORY;

MYCOBACTERIUM TUBERCULOSIS;

EID: 84872327877     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-012-1527-8     Document Type: Article

References (34)

1. WHO (2010) Global tuberculosis control. WHO/HTM/TB/2010.7.
2. Andrade CH, Salum LDB, Mesquita Pasqualoto KF, Ferreira EI, Andricopulo AD (2008) Three-dimensional quantitative structure-activity relationships for a large series of potent antitubercular agents. Lett Drug Des Discov 5:377-387. doi: 10.2174/157018008785777289
3. Andrade CH, Pasqualoto KFM, Zaim MH, Ferreira EI (2008) Abordagem racional no planejamento de novos tuberculostáticos: inibidores da InhA, enoil-ACP redutase do M. tuberculosis. Rev Bras Cienc Farm 44. doi: 10.1590/S1516-93322008000200002
4. Burki T (2010) Tuberculosis-resistance, funding, and drugs. Lancet Infect Dis 10:297-298
5. Dorman SE, Chaisson RE (2007) From magic bullets back to the magic mountain: the rise of extensively drug-resistant tuberculosis. Nat Med 13:295-298. doi: 10.1038/nm0307-295
6. Munier-Lehmann H, Chaffotte A, Pochet S, Labesse G (2001) Thymidylate kinase of Mycobacterium tuberculosis: a chimera sharing properties common to eukaryotic and bacterial enzymes. Protein Sci 10:1195-1205. doi: 10.1110/ps.45701
7. Ostermann N, Schlichting I, Brundiers R, Konrad M, Reinstein J, Veit T, Goody RS, Lavie A (2000) Insights into the phosphoryltransfer mechanism of human thymidylate kinase gained from crystal structures of enzyme complexes along the reaction coordinate. Structure 8:629-642. doi: 10.1016/S0969-2126(00)00149-0
8. de la Sierra L, Munier-Lehmann H, Gilles AM, Bârzu O, Delarue M (2001) X-ray structure of TMP kinase from Mycobacterium tuberculosis complexed with TMP at 1.95 A resolution. J Mol Biol 311:87-100. doi: 10.1006/jmbi.2001. 4843
9. Familiar O, Munier-Lehmann H, Aínsa JA, Camarasa M-J, Pérez-Pérez M-J (2010) Design, synthesis and inhibitory activity against Mycobacterium tuberculosis thymidine monophosphate kinase of acyclic nucleoside analogues with a distal imidazoquinolinone. Eur J Med Chem 45:5910-5918. doi: 10.1016/j.ejmech.2010.09.056
10. Familiar O, Munier-Lehmann H, Negri A, Gago F, Douguet D, Rigouts L, Hernández A-I, Camarasa M-J, Pérez-Pérez M-J (2008) Exploring acyclic nucleoside analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase. Chem Med Chem 3:1083-1093. doi: 10.1002/cmdc.200800060
11. Van Daele I, Munier-Lehmann H, Froeyen M, Balzarini J, Van Calenbergh S (2007) Rational design of 5′-thiourea-substituted alpha-thymidine analogues as thymidine monophosphate kinase inhibitors capable of inhibiting mycobacterial growth. J Med Chem 50:5281-5292. doi: 10.1021/jm0706158
12. Van Daele I, Munier-Lehmann H, Hendrickx PMS, Marchal G, Chavarot P, Froeyen M, Qing L, Martins JC, Van Calenbergh S (2006) Synthesis and biological evaluation of bicyclic nucleosides as inhibitors of M. tuberculosis thymidylate kinase. Chem Med Chem 1:1081-1090. doi: 10.1002/cmdc.200600028
13. Vanheusden V, Munier-Lehmann H, Froeyen M, Dugué L, Heyerick A, De Keukeleire D, Pochet S, Busson R, Herdewijn P, van Calenbergh S (2003) 3′-C-branched-chain-substituted nucleosides and nucleotides as potent inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase. J Med Chem 46:3811-3821. doi: 10.1021/jm021108n
14. Vanheusden V, Munier-Lehmann H, Pochet S, Herdewijn P, van Calenbergh S (2002) Synthesis and evaluation of thymidine-5′-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase. Bioorg Med Chem Lett 12:2695-2698
15. Vanheusden V, Munier-Lehmann H, Froeyen M, Busson R, Rozenski J, Herdewijn P, Van Calenbergh S (2004) Discovery of bicyclic thymidine analogues as selective and high-affinity inhibitors of Mycobacterium tuberculosis thymidine monophosphate kinase. J Med Chem 47:6187-6194. doi: 10.1021/jm040847w
16. Vanheusden V, Rompaeya PV, Munier-Lehmannb H, Pochetc S, Herdewijnd P, Calenbergh SV (2003) Thymidine and thymidine-5-O-monophosphate analogues as inhibitors of Mycobacterium tuberculosis thymidylate kinase. Bioorg Med Chem Lett 13:3045-3048. doi: 10.1016/S0960-894X(03)00643-7
17. Van Calenbergh S, Pochet S, Munier-Lehmann H (2012) Drug design and identification of potent leads against mycobacterium tuberculosis thymidine monophosphate kinase. Curr Top Med Chem 12:694-705
18. Aparna V, Jeevan J, Ravi M, Desiraju GR, Gopalakrishnan B (2006) 3D-QSAR studies on antitubercular thymidine monophosphate kinase inhibitors based on different alignment methods. Bioorg Med Chem Lett 16:1014-1020. doi: 10.1016/j.bmcl.2005.10.086
19. Andrade CH, Pasqualoto KFM, Ferreira EI, Hopfinger AJ (2009) Rational design and 3D-pharmacophore mapping of 5′-thiourea-substituted alpha-thymidine analogues as mycobacterial TMPK inhibitors. J Chem Inf Model 49:1070-1078. doi: 10.1021/ci8004622
20. Andrade CH, Pasqualoto KFM, Ferreira EI, Hopfinger AJ (2010) 3D-Pharmacophore mapping of thymidine-based inhibitors of TMPK as potential antituberculosis agents. J Comput Aided Mol Des 24:157-172. doi: 10.1007/s10822-010-9323-y
21. Salum LB, Diasb LC, Andricopulo AD (2009) Structural and chemical basis for anticancer activity of a series of beta-Tubulin ligands: molecular modeling and 3D QSAR studies. J Braz Chem Soc 20:693-703
22. Salum LB, Valadares NF (2010) Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example. J Comput Aided Mol Des 24:803-817. doi: 10.1007/s10822-010-9375-z
23. Blondin C, Serina L, Wiesmüller L, Gilles AM, Bârzu O (1994) Improved spectrophotometric assay of nucleoside monophosphate kinase activity using the pyruvate kinase/lactate dehydrogenase coupling system. Anal Biochem 220:219-221. doi: 10.1006/abio.1994.1326
24. Young DC (2009) Computational drug design: a guide for computational and medicinal chemists. Wiley, Hoboken
25. Andrade CH, Pasqualoto KFM, Ferreira EI, Hopfinger AJ (2010) 4D-QSAR: perspectives in drug design. Molecules 15:3281-3294. doi: 10.3390/ molecules15053281
26. Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23:1623-1641. doi: 10.1002/jcc.10128
27. Salum LB, Andricopulo AD (2009) Fragment-based QSAR: perspectives in drug design. Mol Divers 13:277-285. doi: 10.1007/s11030-009-9112-5
28. Cho AE, Guallar V, Berne BJ, Friesner R (2005) Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem 26:915-931. doi: 10.1002/jcc.20222
29. Shelley JC, Cholleti A, Frye LL, Greenwood JR, Timlin MR, Uchimaya M (2007) Epik: a software program for pK(a) prediction and protonation state generation for drug-like molecules. J Comput Aided Mol Des 21:681-691. doi: 10.1007/s10822-007-9133-z
30. Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM (2005) Integrated modeling program, applied chemical theory (IMPACT). J Comput Chem 26:1752-1780. doi: 10.1002/jcc.20292
31. Van Calenbergh S (2006) Structure-aided design of inhibitors of Mycobacterium tuberculosis thymidylate kinase. Verh K Acad Geneeskd Belg 68:223-248
32. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 11:425-445
33. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749. doi: 10.1021/jm0306430
34. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46:3-26