Consensus features of CP-MLR and GA in modeling HIV-1 RT inhibitory activity of 4-benzyl/benzoylpyridin-2-one analogues

Journal of Enzyme Inhibition and Medicinal Chemistry

Volumn 26, Issue 5, 2011, Pages 696-705

  Deshpande, Shreekant ^a   Singh, Rinki ^a   Goodarzi, Mohammad ^b   Katti, Seturam B ^a   Prabhakar, Yenamandra S ^a  

^a CENTRAL DRUG RESEARCH INSTITUTE   (India)

^b ISLAMIC AZAD UNIVERSITY   (Iran)

Author keywords

ANN; Benzyl benzoylpyridinones; CPMLR; GA; HIV 1 RT inhibitors; QSAR

Indexed keywords

PYRIDONE DERIVATIVE; RNA DIRECTED DNA POLYMERASE;

ARTICLE; ARTIFICIAL NEURAL NETWORK; BACK PROPAGATION; CHEMICAL MODEL; COMBINATORIAL CHEMISTRY; CONTROLLED STUDY; ENZYME ACTIVITY; GENETIC ALGORITHM; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; HYDROPHILICITY; MULTIPLE LINEAR REGRESSION ANALYSIS; NONHUMAN; PRIORITY JOURNAL;

ALGORITHMS; ANTIVIRAL AGENTS; ENZYME ACTIVATION; ENZYME INHIBITORS; HIV REVERSE TRANSCRIPTASE; HIV-1; HUMANS; MODELS, BIOLOGICAL; PYRIDONES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REGRESSION ANALYSIS;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 80052854752     PISSN: 14756366     EISSN: 14756374     Source Type: Journal    
DOI: 10.3109/14756366.2010.548328     Document Type: Article

References (38)

1. Pauwels R. New non-nucleoside reverse transcriptase inhibitors (NNRTIs) in development for the treatment of HIV infections. Curr Opin Pharmacol 2004;4:437-446. (Pubitemid 40533003)
2. Clercq ED. Te design of drugs for HIV and HCV. Nat Rev Drug Discov 2007;6:1001-1018.
3. Safadi YE, Boudou VV, Marquet R. HIV-1 reverse transcriptase inhibitors. Appl Microbiol Biotechnol 2007;75:723-737. (Pubitemid 47164912)
4. Clercq ED. Non-nucleoside reverse transcriptase inhibitors (NNRTIs): past, present and future. Chem Biodivers 2004;1:44-64.
5. Prajapati DG, Ramajayam R, Yadav MR, Giridhar R. Te search for potent, small molecule NNRTIs: A review. Bioorg Med Chem 2009;17:5744-5762.
6. Esnouf R, Ren J, Ross C, Jones Y, Stammers D, Stuart D. Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors. Nat Struct Biol 1995;2:303-308.
7. Ragno R, Frasca S, Manetti F, Brizzi A, Massa S. HIV-reverse transcriptase inhibition: inclusion of ligand-induced ft by cross-docking studies. J Med Chem 2005;48:200-212. (Pubitemid 40109511)
8. Clercq ED. Emerging antiHIV drugs. Expert Opin Emerg Drugs 2005;10: 241-274.
9. Buckheit RW, Fliakas-Boltz V, Yeagy-Bargo S, Weislow O, Mayers DL, Boyer PL, Hughes SH, Pan BC, Chu SH, Bader JP. Resistance to 1-[(2-hydroxyethoxy) methyl]-6-(phenylthio)thymine derivatives is generated by mutations at multiple sites in the HIV-1 reverse transcriptase. Virology 1995;210:186-193.
10. Richman D, Shih CK, Lowy I, Rose J, Prodanovich P, Gof S, Grifn J. Human immunodefciency virus type 1 mutants resistant to nonnucleoside inhibitors of reverse transcriptase arise in tissue culture. Proc Natl Acad Sci (USA) 1991;88: 11241-11245. (Pubitemid 21916016)
11. Franco JLM, Mayorga KM, Gordiano CJ, Castillo R. Pyridin-2(1H)-ones: a promising class of HIV-1 non-nucleoside reverse transcriptase inhibitors. Chem Med Chem 2007;2:1141-1147.
12. Prabhakar YS, Solomon VR, Rawal RK, Gupta MK, Katti SB. CP-MLR/PLS Directed Structure-Activity Modeling of the HIV-1 RT Inhibitory Activity of 2,3-Diaryl-1,3-thiazolidin-4-ones. QSAR Comb Sci 2004;23:234-244. (Pubitemid 39490415)
13. Prabhakar YS, Rawal RK, Gupta MK, Solomon VR, Katti SB. Topological descriptors in modeling the HIV inhibitory activity of 2-aryl-3-pyridyl- thiazolidin-4-ones. Comb Chem High T Scr 2005;5:431-437. (Pubitemid 41008790)
14. Rawal RK, Prabhakar YS, Katti SB. Molecular surface features in modeling the HIV-1 RT inhibitory activity of 2-(2,6-disubstituted phenyl)-3-(substituted pyrimidin-2-yl)-thiazolidin-4-ones. QSAR Comb Sci 2007;26:398-406. (Pubitemid 46932866)
15. Sharma BK, Kumar R, Singh P. Quantitative structure-activity relationship study of 2-arylsulfonyl-6-substituted benzonitriles as non-nucleoside reverse transcriptase inhibitors of HIV-1. J Enzyme Inhib Med Chem 2002;17:219-225. (Pubitemid 35175258)
16. Benjahad A, Croisy M, Monneret C, Bisagni E, Mabire D, Coupa S et al. 4-Benzyl and 4-benzoyl-3-dimethylaminopyridin-2(1H)-ones: in vitro evaluation of new C-3-amino-substituted and C-5,6-alkyl-substituted analogues against clinically important HIV mutant strains. J Med Chem 2005;48:1948-1964 (Pubitemid 40396325)
17. DRAGON software version 5.0-2005. By Todeschini R, Consonni V, Mauri A, Pavan M. Milano, Italy. Error! Hyperlink reference not valid.
18. Reddy AS, Kumar S, Garg R. Hybrid-genetic algorithm based descriptor optimization and QSAR models for predicting the biological activity of Tipranavir analogs for HIV protease inhibition. J Mol Graph Model 2010;28:852-862.
19. Guha R, Stanton DT, Jurs PC. Interpreting computational neural network quantitative structure-activity relationship models: a detailed interpretation of the weights and biases. J Chem Inf Model 2005;45:1109-1121. (Pubitemid 41156711)
20. Prabhakar YS. A combinatorial approach to the variable selection in multiple linear regression analysis of Selwood et al. data set-a case study. QSAR Comb Sci 2003;22:583-595. (Pubitemid 37010625)
21. Prabhakar YS, Gupta MK, Roy N, Venkateswarlu Y. A high dimensional QSAR study on the aldose reductase inhibitory activity of some favones: topological descriptors in modeling the activity. J Chem Inf Model 2006;46:86-92. (Pubitemid 43282102)
22. Saquib M, Gupta MK, Sagar R, Prabhakar YS, Shaw AK, Kumar R, Maulik PR, Gaikwad AN, Sinha S, Srivastava AK, Chaturvedi V, Srivastava R, Srivastava BS. C-3 Alkyl/Arylalkyl-2,3-dideoxy Hex-2-enopyranosides as antitubercular agents: synthesis, biological evaluation, and QSAR study. J Med Chem 2007;50:2942-2950.
23. Pavan M, Mauri A, Todeschini R. Total ranking models by the genetic algorithm variable subset selection (GA-VSS) approach for environmental priority settings. Anal Bioanal Chem 2004;380:430-444.
24. Deshpande S, Gupta MK, Prabhakar YS. Multi-model environment as a rational approach for drug design: an experience with CP-MLR. IUP J Chem 2010; 3:1-33.
25. Rumelhart DE, Hinton GE, Williams RJ. Learning representations by backpropagating errors. Nature, 1986;323:533-536.
26. Gasteiger J, Zupan J. Neural networks in chemistry. Angew Chem Intl Ed Engl 1993;32:503-527.
27. Bishop CM. Neural Networks for Pattern Recognition. Clarendon Press: Oxford, 1995. P 116-163 and 253-294.
28. Graupe D. Principles of Artifcial Neural Networks, 2nd ed. World Scientifc Publishing Co.: Singapore; 2007. P 59-111.
29. Wold S. Cross validatory estimation of the number of components in factor and principal components analysis. Technometrics 1978;20:397-406.
30. Stahle L, Wold S, in: Eillis GP, West WB. ggEds., Progress in Medicinal Chemistry, vol. 25, Elsevier Science Publishers, B.V. Amsterdam, 1988. P 291-338 (Chapter 6).
31. So SS, Karplus M. Tree-dimensional quantitative structure-activity relationships from molecular similarity matrices and genetic neural networks. 1. Method and validations. J Med Chem 1997;40:4347-4359. (Pubitemid 28042314)
32. Todeschini R, Consonni V, Pavan M. MOBYDIGS software (Version 1.2) for Windows, Talete Srl, Milan, Italy, 2002. http://www.talete. mi.it/mobydigs.htm.
33. Marini F, Bucci R, Magrì AL, Magrì AD. Artifcial neural networks in chemometrics: History, examples and perspectives. Microchem J 2008;88:178-185.
34. Marquardt DW. An algorithm for leastsquares estimation of nonlinear parameters. J Soc Ind Appl Math 1963;11:431-441.
35. Hagan MT, Menhaj MB. Training Feedforward Networks with the Marquardt Algorithm. IEEE T Neural Net 1994;5:989-993.
36. MATLAB, Version 7.6: http://www.mathworks.com/products/matlab/.
37. Carlsson J, Boukharta L, Aqvist J. Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and afnities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. J Med Chem 2008;51:2648-2656. (Pubitemid 351620786)
38. Goodarzi M, Deshpande S, Murugesan V, Katti SB, Prabhakar YS. Is Feature Selection Essential for ANN Modeling? QSAR Comb Sci 2009; 28: 1487-1499.