Predictive QSAR modeling of CCR5 antagonist piperidine derivatives using chemometric tools

Journal of Enzyme Inhibition and Medicinal Chemistry

Volumn 24, Issue 1, 2009, Pages 205-223

  Roy, Kunal ^a   Mandal, Asim Sattwa ^a  

^a JADAVPUR UNIVERSITY   (India)

Author keywords

CCR5 antagonist piperidines; QSAR

Indexed keywords

CHEMOKINE RECEPTOR CCR5 ANTAGONIST; PIPERIDINE DERIVATIVE;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CHEMOMETRIC ANALYSIS; CORRELATION COEFFICIENT; EXTERNAL VALIDITY; FACTORIAL ANALYSIS; GENETIC ALGORITHM; INTERNAL VALIDITY; MULTIPLE LINEAR REGRESSION ANALYSIS; PARTIAL LEAST SQUARES REGRESSION; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICAL ANALYSIS; STATISTICAL MODEL; STEP WISE MULTIPLE REGRESSION;

ARTIFICIAL INTELLIGENCE; HUMANS; MOLECULAR CONFORMATION; PIPERIDINES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTORS, CCR5;

EID: 58949103064     PISSN: 14756366     EISSN: 14756374     Source Type: Journal    
DOI: 10.1080/14756360802051297     Document Type: Article

References (43)

1. Carrington, M., Dean, M., Martin, MP and O'Brien, SJ (1990) Genetics of HIV-1 infection: Chemokine receptor CCR5 polymorphism and its consequences. Hum Mol Genet, 8:10, pp. 1939-1945.
2. Mack, M., Pfirstinger, J., Haas, J., Nelson, PJ, Kufer, P., Riethmuller, G. and Schlondorff, D. (2005) Preferential targeting of CD4-CCR5 complexes with bifunctional inhibitors: A novel approach to block HIV-1 infection. Immunology, 175, pp. 7586-7593.
3. Berchanski, A. and Lapidot, A. (2007) Prediction of HIV-1 entry inhibitors neomycin-arginine conjugates interaction with the CD4-gp120 binding site by molecular modeling and multistep docking procedure. Biochim Biophys Acta, 1768:9, pp. 2107-2119.
4. Liu, S., Fan, S. and Sun, Z. (2003) Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies. J Mol Model, 9:5, pp. 329-336.
5. Roy, K. and Leonard, JT (2005) QSAR analyses of 3-(4-Benzylpiperidin-1-yl)-N-phenylpropylamine derivatives as potent CCR5 antagonists. J Chem Inf Model, 45, pp. 1352-1368.
6. Aher, YD, Agrawal, A., Bharatam, PV and Garg, P. (2007) 3D-QSAR studies of substituted 1-(3,3-diphenylpropyl)-piperidinyl amides and ureas as CCR5 receptor antagonists. J Mol Model, 13:4, pp. 519-529.
7. Xu, Y., Liu, H., Niu, C., Luo, C., Luo, X., Shen, J., Chen, K. and Jiang, H. (2004) Molecular docking and 3D QSAR studies on 1-amino-2-phenyl-4-(piperidin-1-yl)-butanes based on the structural modeling of human CCR5 receptor. Bioorg Med Chem, 12:3, pp. 6193-6208.
8. Song, M., Breneman, CM and Sukumar, N. (2004) Three-dimensional quantitative structure-activity relationship analyses of piperidine-based CCR5 receptor antagonists. Bioorg Med Chem, 12:2, pp. 489-499.
9. Afantitis, A., Melagraki, G., Sarimveis, H., Koutentis, PA, Markopoulos, J. and Igglessi-Markopoulou, O. (2006) Investigation of substituent effect of 1-(3,3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques. J Comput Aided Mol Des, 20, pp. 83-95.
10. Roy, K. and Leonard, JT (2004) QSAR modeling of HIV-1 reverse transcriptase inhibitor 2-amino-6- arylsulfonylbenzonitriles and congeners using molecular connectivity and E-state parameters. Bioorg Med Chem, 12, pp. 745-754.
11. Leonard, JT, Roy, K. and Classical, QSAR (2004) modeling of HIV-1 reverse transcriptase inhibitor 2-amino-6-arylsulfonylbenzonitriles and congener. QSAR Comb Sci, 23, pp. 23-35.
12. Leonard, JT and Roy, K. (2003) QSAR modeling of anti-HIV activities of alkenyldiarylmethanes using topological and physicochemical descriptors. Drug Des Discov, 18, pp. 165-180.
13. Leonard, JT, Roy, K. and Classical, QSAR (2004) modeling of CCR5 receptor binding affinity of substituted benzylpyrazoles. QSAR Comb Sci, 23, pp. 387-398.
14. Roy, K. and Leonard, JT (2005) Classical QSAR modeling of anti-HIV 2,3-diaryl-1,3-thiazolidin-4-ones. QSAR Comb Sci, 24, pp. 579-592.
15. Roy, K. and Leonard, JT (2005) QSAR by LFER model of cytotoxicity data of anti-HIV 5-phenyl-1-phenylamino-1H-imidazole derivatives using principal component factor analysis and genetic function approximation. Bioorg Med Chem, 13, pp. 2967-2973.
16. Roy, K. and Leonard, JT (2006) Topological QSAR modeling of cytotoxicity data of anti-HIV5-phenyl-1-phenylamino-imidazole derivatives using GFA, G/PLS, FA and PCRA techniques. Indian J Chem, 45, pp. 126-137.
17. Leonard, JT and Roy, K. (2006) QSAR by LFER model of HIV protease inhibitor mannitol derivatives using FA-MLR, PCRA, and PLS techniques. Bioorg Med Chem, 14, pp. 1039-1046.
18. Leonard, JT and Roy, K. (2006) Comparative QSAR modeling of CCR5 receptor binding affinities of substituted 1-(3,3-diphenylpropyl)-piperidinyl amides and ureas. Bioorg Med Chem Lett, 16, pp. 4467-4474.
19. Dorn, CP, Finke, PE, Oates, B., Budhu, RJ, Mills, SG, MacCoss, M., Malkowitz, L., Springer, MS, Daugherty, BL, Gould, SL, DeMartino, JA, Siciliano, SJ, Carella, A., Carver, G., Holmes, K., Danzeisen, R., Hazuda, D., Kessler, J., Lineberger, J., Miller, M., Schleif, WA and Emini, EA (2001) Antagonists of the human CCR5 receptor as anti-HIV-1 agents. Part 1: Discovery and initial structure-activity relationships for 1-amino-2-phenyl-4-(piperidin-1-yl) butanes. Bioorg Med Chem Lett, 11, pp. 259-264.
20. Finke, PE, Meurer, LC, Oates, B., Mills, SG, MacCoss, M., Malkowitz, L., Springer, MS, Daugherty, BL, Gould, SL, DeMartino, JA, Sicilino, SJ, Carella, A., Carver, G., Holmes, K., Danzeisen, R., Hazuda, D., Kessler, J., Lineberger, J., Miller, M., Schleif, WA and Emini, EA (2001) Antagonists of the human CCR5 receptor as anti-HIV-1 agents. Part 2: Structure-activity relationships for substituted 2-aryl-1-[N-(methyl)-N-(phenylsulfonyl) amino]-4-(piperidin-1-yl) butanes. Bioorg Med Chem Lett, 11, pp. 265-270.
21. Finke, PE, Meurer, LC, Oates, B., Shah, SK, Loebach, JL, Mills, SG, MacCoss, M., Castonguay, L., Malkowitz, L., Springer, MS, Gould, SL and DeMartino, JL (2001) Antagonists of the human CCR5 receptor as anti-HIV-1 agents. Part 3: A proposed pharmacophore model for 1-[N-(methyl)-N-(phenylsulfonyl) amino]-2-(phenyl)-4-[4-(substituted)piperidin-1-yl] butanes. Bioorg Med Chem Lett, 11, pp. 2469-2473.
22. Finke, PE, Oates, B., Mills, SG, MacCoss, M., Malkowitz, L., Springer, MS, Gould, SL, DeMartino, JA, Carella, A., Carver, G., Holmes, K., Danzeisen, R., Hazuda, D., Kessle, J., Lineberger, J., Miller, M., Schleif, WA and Emini, EA (2001) Antagonists of the human CCR5 receptor as anti-HIV-1 agents. Part 4: Synthesis and structure-activity relationships for 1-[N-(methyl)-N-(phenylsulfonyl)amino]-2-(phenyl) -4-(4-(N-(alkyl)-N-(benzyloxycarbonyl)amino)piperidin-1-yl)butanes.
23. Roy, K. and Mandal, AS (2007) Development of linear and nonlinear predictive QSAR models and their external validation using molecular similarity principle for anti-HIV indolyl aryl sulfones. J Enz Inhib Med Chem
24. Eriksson, L., Jaworska, J., Worth, AP, Cronin, MTD, McDowell, RM and Gramatica, P. (2003) Methods for reliability and uncertainty assessment and for applicability evaluations of classification and regression-based QSARs. Environ Health Perspect, 111, pp. 1361-1375.
25. Guha, R. and Jurs, PC (2005) Determining the validity of a QSAR model - A classification approach. J Chem Inf Model, 45, pp. 65-73.
26. Leonard, JT and Roy, K. (2006) On selection of training and test sets for the development of predictive QSAR models. QSAR Comb Sci, 253, pp. 235-251.
27. Roy, K. (2007) On some aspects of validations of predictive QSAR models. Expert Opin Drug Discov, 2, pp. 1567-1577.
28. Everitt, B., Landau, S. and Leese, M. (2001) Cluster analysis, Arnold, London
29. Dougherty, ER, Barrera, J., Brun, M., Kim, S., Cesar, RM, Chen, Y., Bittner, M. and Trent, JM (2002) Inference from clustering with application to gene-expression microarrays. J Comput Biol, 9, pp. 105-126.
30. Darlington, RB (1990) Regression and linear models, McGraw-Hill, New York
31. Wold, S. (1995) PLS for multivariate linear modeling. Chemometric methods in molecular design, pp. 195-218. VCH, Weinheim
32. Franke, R. (1984) Theoretical drug design methods, Elsevier, Amsterdam
33. Franke, R. and Gruska, A. (1995) Principal component and factor analysis. Chemometric methods in molecular design, pp. 113-163. VCH, Weinheim
34. Hopfinger, AJ and Tokarsi, JS (1997) Three dimensional quantitative structure-activity relationship analysis. Practical applications of computer-aided drug design, pp. 105-164. Marcel Dekker, New York
35. Rogers, D. and Hopfinger, AJ (1994) Application of genetic function approximation to quantitative structure-activity relationships and quantitative structure-property relationships. J Chem Inf Comput Sci, 34, pp. 854-866.
36. Zupan, J. and Gasteiger, J. (1999) Neural networks in chemistry and drug design, Wiley-VCH, Weinheim
37. Tang, Y., Jiang, HL, Chen, KX and Ji, RY (1996) QSAR study of artemisinin (Qinghaosu) derivatives using neural network method. Indian J Chem, 35, pp. 325-332.
38. Snedecor, GW and Cochran, WG (1967) Statistical methods, p. 381. Oxford and IBH, New Delhi
39. Wold, S. and Eriksson, L. (1995) Chemometric methods in molecular design, p. 312. VCH, Weinheim
40. Debnath, AK (2001) Combinatorial library design and evaluation, p. 73. Marcel Dekker Inc., New York
41. Livingstone, DJ and Salt, DW (2005) Judging the significance of multiple linear regression models. J Med Chem, 48, pp. 661-663.
42. 2!. J Mol Graphics Mod, 20, pp. 269-276.
43. Roy, P. and Roy, K. (2008) On some aspects of variable selection for partial least squares regression models. QSAR Comb Sci, 27