3D-QSAR study on a series of bcl-2 protein inhibitors using comparative molecular field analysis

Protein and Peptide Letters

Volumn 18, Issue 5, 2011, Pages 440-449

  Hou, Xuben ^a   Du, Jintong ^a   Fang, Hao ^a   Li, Minyong ^a  

^a SHANDONG UNIVERSITY   (China)

Author keywords

3D QSAR; Bcl 2 protein; CoMFA; Inhibitors

Indexed keywords

4 [4 (4' CHLORO 2 BIPHENYLYLMETHYL) 1 PIPERAZINYL] N [4 [3 DIMETHYLAMINO 1 (PHENYLTHIOMETHYL)PROPYLAMINO] 3 NITROBENZENESULFONYL]BENZAMIDE; ABT-737; BIPHENYL DERIVATIVE; ENZYME INHIBITOR; NITROPHENOL; PIPERAZINE DERIVATIVE; PROTEIN BCL 2; SULFONAMIDE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG ANTAGONISM; PROTEIN BINDING; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REPRODUCIBILITY; STATIC ELECTRICITY; STATISTICS;

BIPHENYL COMPOUNDS; ENZYME INHIBITORS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NITROPHENOLS; PIPERAZINES; PROTEIN BINDING; PROTO-ONCOGENE PROTEINS C-BCL-2; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REPRODUCIBILITY OF RESULTS; STATIC ELECTRICITY; STATISTICS AS TOPIC; SULFONAMIDES;

EID: 79952849333     PISSN: 09298665     EISSN: None     Source Type: Journal    
DOI: 10.2174/092986611794927992     Document Type: Article

References (36)

1. Adams, J. M.; Cory, S. The Bcl-2 protein family: Arbiters of cell survival. Science 1998, 281, 1322-1326. (Pubitemid 28406819)
2. Petros, A. M.; Medek, A.; Nettesheim, D. G.; Kim, D. H.; Yoon, H. S.; Swift, K.; Matayoshi, E. D.; Oltersdorf, T.; Fesik, S. W. Solution structure of the antiapoptotic protein Bcl-2. Proc. Natl. Acad. Sci. USA, 2001, 98, 3012-3017. (Pubitemid 32220791)
3. Kirkin, V.; Joos, S.; Zornig, M. The role of Bcl-2 family members in tumorigenesis. BBA- Mol. Cell. Res., 2004, 1644, 229-249. (Pubitemid 38281277)
4. Tzung, S. P.; Kim, K. M.; Basanez, G.; Giedt. C. D.; Simon, J.; Zimmerberg, J.; Zhang, K. Y.; Hockenbery, D. M. Antimycin A mimics a cell-death-inducing Bcl-2 homology domain 3. Nat. Cell. Biol., 2001, 3, 183-191. (Pubitemid 32118372)
5. Porter, J.; Payne, A.; de Candole, B.; Ford, D.; Hutchinson, B.; Trevitt, G.; Turner, J.; Edwards, C.; Watkins, C.; Whitcombe, I.; Davis, J.; Stubberfield, C. Tetrahydroisoquinoline amide substituted phenyl pyrazoles as selective Bcl-2 inhibitors. Bioorg. Med. Chem. Lett., 2009, 19, 230-233 .
6. Bruncko, M.; Oost, T. K.; Belli, B. A.; Ding, H.; Joseph, M. K.; Kunzer, A.; Martineau, D.; McClellan, W. J.; Mitten, M.; Ng, S. C.; Nimmer, P. M.; Oltersdorf, T.; Park, C. M.; Petros, A. M.; Shoemaker, A. R.; Song, X. H.; Wang, X. L.; Wendt, M. D.; Zhang, H. C.; Fesik, S. W.; Rosenberg, S. H.; Elmore, S. W. Studies leading to potent, dual inhibitors of bcl-2 and Bcl-Xl. J. Med. Chem., 2007, 50, 641-662. (Pubitemid 46332978)
7. He, Z. S.; Zhang, J.; Shi, X. H.; Hu, L. L.; Kong, X. G.; Cai, Y. D.; Chou, K. C. Predicting drug-target interaction networks based on functional groups and biological features. PLoS One, 2010, 5, e9603.
8. Xiao, X.; Wang, P.; Chou, K. C. GPCR-CA: A cellular automaton image approach for predicting G-protein-coupled receptor functional classes. J. Comput. Chem., 2009, 30, 1414-1423.
9. Xiao, X.; Wang, P.; Chou, K. C. GPCR-2L: Predicting G proteincoupled receptors and their types by hybridizing two different modes of pseudo amino acid compositions. Mol. BioSyst., 2010, DOI:10.1039/C1030MB00170H.
10. Chou, K. C. Review: Structural bioinformatics and its impact to biomedical science. Curr. Med. Chem., 2004, 11, 2105-2134.
11. Huang, T.; Shi, X. H.; Wang, P.; He, Z.; Feng, K. Y.; Hu, L.; Kong, X.; Li, Y. X.; Cai, Y. D.; Chou, K. C. Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS ONE, 2010, 5, e10972.
12. Chou, K. C.; Wei, D. Q.; Zhong, W. Z. Binding mechanism of coronavirus main proteinase with ligands and its implication to drug design against SARS. (Erratum: ibid., 2003, Vol. 310, 675). Biochem. Biophys. Res. Commun., 2003, 308, 148-151.
13. Chou, K. C.; Wei, D. Q.; Du, Q. S.; Sirois, S.; Zhong, W. Z. Review: Progress in computational approach to drug development against SARS. Curr. Med. Chem, 2006, 13, 3263-3270. (Pubitemid 44669774)
14. Chou, K. C. Prediction of protein cellular attributes using pseudo amino acid composition. Proteins, 2001, 43(3), 246-255.
15. Chou, K. C.; Shen, H. B. Plant-mPLoc: A top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS ONE, 2010, 5, e11335.
16. Chou, K. C.; Shen, H. B. ProtIdent: A web server for identifying proteases and their types by fusing functional domain and sequential evolution information. Biochem. Biophys. Res. Comm., 2008, 376, 321-325.
17. Chou, K. C. A vectorized sequence-coupling model for predicting HIV protease cleavage sites in proteins. J. Biol. Chem., 1993, 268, 16938-16948.
18. Chou, K. C. Review: Prediction of HIV protease cleavage sites in proteins. Anal. Biochem., 1996, 233, 1-14.
19. Chen, L.; Huang, T.; Shi, X. H.; Cai, Y. D.; Chou, K. C. Analysis of protein pathway networks using hybrid properties. Molecules, 2010, 15, 8177-8192 (Openly accessible at www.mdpi.com/journal/molecules).
20. Chou, K. C.; Shen, H. B. Signal-CF: A subsite-coupled and window-fusing approach for predicting signal peptides. Biochem. Biophys. Res. Comm., 2007, 357, 633-640.
21. Chou, K. C.; Shen, H. B. Review: Recent advances in developing web-servers for predicting protein attributes. Natural Science, 2009, 2, 63-92 (openly accessible at http://www.scirp.org/journal/NS/).
22. Sybyl, version 7.3; Tripos Inc.: St. Louis, MO, 2007.
23. Zhang, J.; Wen, R.; Guillaume, D. Three-dimensional quantitative structure-activity relationship (CoMFA and CoMSIA) studies on galardin derivatives as gelatinase A (matrix metalloproteinase 2) inhibitors. J. Enzyme Inhib. Med. Chem., 2008, 23, 445-453.
24. Zhu, Y. Q.; Pei, J. F.; Liu, Z. M.; Lai, L. H.; Cui, J. R.; Li, R. T. 3D-QSAR Studies on Tripeptide Aldehyde Inhibitors of Proteasome using CoMFA and CoMSIA Methods. Bioorg. Med. Chem., 2006, 14, 1483-1496.
25. Collantes, E. R.; Xing, L.; Miller, P. C.; Welsh, W. J.; Profeta, S. Jr. Comparative molecular field analysis as a tool to evaluate modeof action of chemical hybridization agents. J. Agric. Food Chem., 1999, 47, 5245-5251. (Pubitemid 30016969)
26. Puntambekar, D. S.; Giridhar, R.; Yadav, M. R. Understanding the antitumor activity of novel tricyclicpiperazinyl derivatives as farnesyltransferase inhibitors using CoMFA and CoMSIA. Eur. J. Med. Chem., 2006, 41, 1279-1292. (Pubitemid 44666225)
27. Li, Y.; Wei, D. Q.; Gao, W. N.; Gao, H.; Liu, B. N.; Huang, C. J.; Xu, W. R.; Liu, D. K.; Chen, H. F.; Chou, K. C. Computational approach to drug design for oxazolidinones as antibacterial agents. Med. Chem., 2007, 3, 576-582. (Pubitemid 350303073)
28. Du, Q. S.; Huang, R. B.; Wei, Y. T.; Du, L. Q.; Chou, K. C. Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR). J. Comput. Chem., 2008, 29, 211219.
29. Wei, H.; Wang, C. H.; Du, Q. S.; Meng, J.; Chou, K. C. Investigation into adamantane-based M2 inhibitors with FB-QSAR. Med. Chem., 2009, 5, 305-317.
30. Du, Q. S.; Huang, R. B.; Wei, Y. T.; Pang, Z. W.; Du, L. Q.; Chou, K. C. Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design. J. Comput. Chem., 2009, 30, 295-304.
31. Prado-Prado, F. J.; Gonzalez-Diaz, H.; de la Vega, O. M.; Ubeira, F. M.; Chou, K. C. Unified QSAR approach to antimicrobials. Part 3: First multi-tasking QSAR model for Input-Coded prediction, structural back-projection, and complex networks clustering of antiprotozoal compounds. Bioorg. Med. Chem., 2008, 16, 58715880.
32. Prado-Prado, F. J.; de la Vega, O. M.; Uriarte, E.; Ubeira, F. M.; Chou, K. C.; Gonzalez-Diaz, H. Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug-drug complex networks. Bioorg. Med. Chem., 2009, in press.
33. Prado-Prado, F. J.; Martinez de la Vega, O.; Uriarte, E.; Ubeira, F. M.; Chou, K. C.; Gonzalez-Diaz, H. Unified QSAR approach to antimicrobials. 4. Multi-target QSAR modeling and comparative multi-distance study of the giant components of antiviral drug-drug complex networks. Bioorg. Med. Chem., 2009, 17, 569-575.
34. Dea-Ayuela, M. A.; Perez-Castillo, Y.; Meneses-Marcel, A.; Ubeira, F. M.; Bolas-Fernandez, F.; Chou, K. C.; Gonzalez-Diaz, H. HP-Lattice QSAR for dynein proteins: Experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence. Bioorg. Med. Chem., 2008, 16, 7770-7776.
35. Du, Q. S.; Mezey, P. G.; Chou, K. C. Heuristic Molecular Lipophilicity Potential (HMLP): A 2D-QSAR Study to LADH of Molecular Family Pyrazole and Derivatives. J. Comput. Chem., 2005, 26, 461-470. (Pubitemid 40449458)
36. Du, Q. S.; Huang, R. B.; Chou, K. C. Review: Recent advances in QSAR and their applications in predicting the activities of chemical molecules, peptides and proteins for drug design. Curr. Protein Pept. Sci., 2008, 9, 248-259.