Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of some benzimidazole derivatives with trichomonicidal activity

European Journal of Medicinal Chemistry

Volumn 46, Issue 8, 2011, Pages 3499-3508

  Pérez Villanueva, Jaime ^a   Medina Franco, José L ^b   Caulfield, Thomas R ^b   Hernández Campos, Alicia ^a   Hernández Luis, Francisco ^a   Yépez Mulia, Lilián ^c   Castillo, Rafael ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^b TORREY PINES INSTITUTE FOR MOLECULAR STUDIES   (United States)

^c INSTITUTO MEXICANO DEL SEGURO SOCIAL   (Mexico)

Author keywords

3D QSAR; Benzimidazole; CoMFA; CoMSIA; Structure activity relationships; Trichomonas vaginalis

Indexed keywords

BENZIMIDAZOLE DERIVATIVE;

ARTICLE; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; DRUG ACTIVITY; DRUG STRUCTURE; HYDROGEN BOND; NONHUMAN; QUANTITATIVE STRUCTURE ACTIVITY RELATION; TRICHOMONAS VAGINALIS;

ALGORITHMS; ANTITRICHOMONAL AGENTS; BENZIMIDAZOLES; BINDING SITES; DRUG DESIGN; ELECTRONS; HUMANS; MATHEMATICAL COMPUTING; MODELS, MOLECULAR; MOLECULAR CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; STEREOISOMERISM; THERMODYNAMICS; TRICHOMONAS INFECTIONS; TRICHOMONAS VAGINALIS;

EID: 79958252481     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2011.05.016     Document Type: Article

References (49)

1. Global Prevalence and Incidence of Selected Curable Sexually Transmitted Infections: Overview and Estimates 2001 World Health Organization Geneva
2. J.R. Schwebke Update of trichomoniasis Sex. Transm. Infect. 78 2002 378 379 (Pubitemid 35177069)
3. P. Upcroft, and J.A. Upcroft Drug targets and mechanisms of resistance in the anaerobic protozoa Clin. Microbiol. Rev. 14 2001 150 164 (Pubitemid 32096211)
4. S.L. Cudmore, K.L. Delgaty, S.F. Hayward-McClelland, D.P. Petrin, and G.E. Garber Treatment of infections caused by metronidazole-resistant Trichomonas vaginalis Clin. Microbiol. Rev. 17 2004 783 793 (Pubitemid 39372517)
5. M. Boiani, and M. Gonzalez Imidazole and benzimidazole derivatives as chemotherapeutic agents Mini Rev. Med. Chem. 5 2005 409 424 (Pubitemid 40476050)
6. G. Navarrete-Vázquez, R. Cedillo, A. Hernández-Campos, L. Yépez, F. Hernández-Luis, J. Valdez, R. Morales, R. Cortés, M. Hernández, and R. Castillo Synthesis and antiparasitic activity of 2-(trifluoromethyl)-benzimidazole derivatives Bioorg. Med. Chem. Lett. 11 2001 187 190 (Pubitemid 32099636)
7. J. Valdez, R. Cedillo, A. Hernández-Campos, L. Yépez, F. Hernández-Luis, G. Navarrete-Vázquez, A. Tapia, R. Cortés, M. Hernández, and R. Castillo Synthesis and antiparasitic activity of 1H-benzimidazole derivatives Bioorg. Med. Chem. Lett. 12 2002 2221 2224 (Pubitemid 34804404)
8. G. Navarrete-Vázquez, L. Yépez, A. Hernández-Campos, A. Tapia, F. Hernández-Luis, R. Cedillo, J. González, A. Martínez-Fernández, M. Martínez-Grueiro, and R. Castillo Synthesis and antiparasitic activity of albendazole and mebendazole analogues Bioorg. Med. Chem. 11 2003 4615 4622 (Pubitemid 37194266)
9. G. Navarrete-Vázquez, M.D. Rojano-Vilchis, L. Yépez-Mulia, V. Meléndez, L. Gerena, A. Hernández-Campos, R. Castillo, and F. Hernández-Luis Synthesis and antiprotozoal activity of some 2-(trifluoromethyl)-1H-benzimidazole bioisosteres Eur. J. Med. Chem. 41 2006 135 141 (Pubitemid 43276069)
10. D. Valdez-Padilla, S. Rodríguez-Morales, A. Hernández- Campos, F. Hernández-Luis, L. Yépez-Mulia, A. Tapia-Contreras, and R. Castillo Synthesis and antiprotozoal activity of novel 1-methylbenzimidazole derivatives Bioorg. Med. Chem. 17 2009 1724 1730
11. M. Andrzejewska, L. Yépez-Mulia, R. Cedillo-Rivera, A. Tapia, L. Vilpo, J. Vilpo, and Z. Kazimierczuk Synthesis, antiprotozoal and anticancer activity of substituted 2-trifluoromethyl- and 2-pentafluoroethylbenzimidazoles Eur. J. Med. Chem. 37 2002 973 978 (Pubitemid 36349006)
12. M. Andrzejewska, L. Yépez-Mulia, A. Tapia, R. Cedillo-Rivera, A.E. Laudy, B.J. Starosciak, and Z. Kazimierczuk Synthesis, and antiprotozoal and antibacterial activities of S-substituted 4,6-dibromo- and 4,6-dichloro-2- mercaptobenzimidazoles Eur. J. Pharm. Sci. 21 2004 323 329 (Pubitemid 38156169)
13. F. Ooms Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry Curr. Med. Chem. 7 2000 141 158 (Pubitemid 30396444)
14. W.L. Jorgensen The many roles of computation in drug discovery Science 303 2004 1813 1818 (Pubitemid 38374866)
15. J.L. Medina-Franco, F. López-Vallejo, and R. Castillo Diseño de fármacos asistido por computadora Educ. Quím 17 2006 452 457
16. W.L. Jorgensen Efficient drug Lead discovery and Optimization Acc. Chem. Res. 42 2009 724 733
17. R.D. Cramer, D.E. Patterson, and J.D. Bunce Comparative molecular field analysis. 1. Effect of shape on binding of steroids to carrier proteins J. Am. Chem. Soc. 110 1988 5959 5967
18. H. Kubinyi Comparative molecular field analysis (CoMFA) P.v.R. Schleyer, N.L. Allinger, T. Clark, J. Gasteiger, P.A. Kollman, H.F. SchaeferIII, P.R. Schreiner, The Encyclopedia of Computational Chemistry 1998 John Wiley & Sons Chichester 448 460
19. G. Klebe, and U. Abraham Comparative Molecular Similarity Index Analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries J. Comput. Aided Mol. Des 13 1999 1 10 (Pubitemid 29098938)
20. O. Temiz-Arpaci, B. Tekiner-Gulbas, I. Yildiz, E. Aki-Sener, and I. Yalcin 3D-QSAR analysis on benzazole derivatives as eukaryotic topoisomerase II inhibitors by using comparative molecular field analysis method Bioorg. Med. Chem. 13 2005 6354 6359 (Pubitemid 41539299)
21. P.D. Patel, M.R. Patel, N. Kaushik-Basu, and T.T. Talele 3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors J. Chem. Inf. Model. 48 2008 42 55 (Pubitemid 351271049)
22. M.L. López-Rodríguez, M. Murcia, B. Benhamú, A. Viso, M. Campillo, and L. Pardo Benzimidazole derivatives. 3. 3D-QSAR/CoMFA model and computational simulation for the recognition of 5-HT4 receptor antagonists J. Med. Chem. 45 2002 4806 4815 (Pubitemid 35192770)
23. F. López-Vallejo, J.L. Medina-Franco, A. Hernández-Campos, S. Rodríguez-Morales, L. Yépez, R. Cedillo, and R. Castillo Molecular modeling of some 1H-benzimidazole derivatives with biological activity against Entamoeba histolytica: a comparative molecular field analysis study Bioorg. Med. Chem. 15 2007 1117 1126 (Pubitemid 44880700)
24. A. Golbraikh, and A. Tropsha Beware of q(2)! J. Mol. Graph. Model. 20 2002 269 276
25. A. Golbraikh, and A. Tropsha Predictive QSAR modeling based on diversity sampling of experimental datasets for the training and test set selection J. Comput.-Aided Mol. Des 16 2002 357 369 (Pubitemid 35414668)
26. Spartan, Version 02, Wavefunction Inc., Irvine, CA.
27. R.S. Mulliken Electronic population analysis on LCAO-MO molecular wave functions J. Chem. Phys. 23 1955 1833 1840
28. S.R. Cox, and D.E. Williams Representation of the molecular electrostatic potential by a net atomic charge model J. Comput. Chem. 2 1981 304 323
29. J.J.P. Stewart Optimization of parameters for semiempirical methods I. Method J. Comput. Chem. 10 1989 209 220
30. J. Gasteiger, and M. Marsili Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges Tetrahedron 36 1980 3219 3228
31. Sybyl, Version 7.3, Tripos Inc., St. Louis, MO.
32. Rocs, Version 2.3.1, OpenEye Scientific Software Inc., Santa Fe, NM.
33. P. Willett, J.M. Barnard, and G.M. Downs Chemical similarity searching J. Chem. Inform. Comput. Sci. 38 1998 983 996 (Pubitemid 128591261)
34. T.S. Rush, J.A. Grant, L. Mosyak, and A. Nicholls A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction J. Med. Chem. 48 2005 1489 1495 (Pubitemid 40364556)
35. M.J. Sykes, M.J. Sorich, and J.O. Miners Molecular modeling approaches for the prediction of the nonspecific binding of drugs to hepatic microsomes J. Chem. Inf. Model. 46 2006 2661 2673 (Pubitemid 46008135)
36. V.N. Viswanadhan, A.K. Ghose, G.R. Revankar, and R.K. Robins Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics J. Chem. Inf. Comput. Sci. 29 1989 163 172
37. S.S. Kulkarni, A.H. Newman, and W.J. Houlihan Three-dimensional quantitative structure-activity relationships of Mazindol analogues at the dopamine transporter J. Med. Chem. 45 2002 4119 4127 (Pubitemid 35025563)
38. V. Ravichandran, and R.K. Agrawal Predicting anti-HIV activity of PETT derivatives: CoMFA approach Bioorg. Med. Chem. Lett. 17 2007 2197 2202 (Pubitemid 46484318)
39. A.K. Chakraborti, B. Gopalakrishnan, M.E. Sobhia, and A. Malde Comparative molecular field analysis (CoMFA) of phthalazine derivatives as phosphodiesterase IV inhibitors Bioorg. Med. Chem. Lett. 13 2003 2473 2479 (Pubitemid 36830753)
40. G. Klebe Recent developments in structure-based drug design J. Mol. Med. 78 2000 269 281 (Pubitemid 30489711)
41. Y.C. Martin Let's not forget tautomers J. Comput.-Aided Mol. Des 23 2009 693 704
42. A.R. Katritzky, C.D. Hall, B. El-Dien, M. El-Gendy, and B. Draghici Tautomerism in drug discovery J. Comput.-Aided Mol. Des 24 2010 475 484
43. F. Milletti, and A. Vulpetti Tautomer preference in PDB complexes and its impact on structure-based drug discovery J. Chem. Inf. Model. 50 2010 1062 1074
44. K.H. Kim Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers? J. Comput.-Aided Mol. Des 21 2007 63 86 (Pubitemid 46416667)
45. K.H. Kim Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers? J. Comput.-Aided Mol. Des 21 2007 421 435 (Pubitemid 47423276)
46. M.T. Sisay, L. Peltason, and J. Bajorath Structural interpretation of activity cliffs revealed by systematic analysis of structure-activity relationships in analog series J. Chem. Inf. Model. 49 2009 2179 2189
47. G.M. Maggiora On outliers and activity cliffs - Why QSAR often disappoints J. Chem. Inf. Model. 46 2006 1535 (Pubitemid 44185680)
48. J.L. Medina-Franco, K. Martínez-Mayorga, A. Bender, R.M. Marin, M.A. Giulianotti, C. Pinilla, and R.A. Houghten Characterization of activity Landscapes using 2D and 3D similarity methods: consensus activity cliffs J. Chem. Inf. Model. 49 2009 477 491
49. J. Pérez-Villanueva, R. Santos, A. Hernández-Campos, M.A. Giulianotti, R. Castillo, and J.L. Medina-Franco Towards a systematic characterization of the antiprotozoal activity landscape of benzimidazole derivatives Bioorg. Med. Chem. 18 2010 7380 7391