QSAR study of curcumine derivatives as HIV-1 integrase inhibitors

Current Computer-Aided Drug Design

Volumn 9, Issue 1, 2013, Pages 141-150

  Gupta, Pawan ^a   Sharma, Anju ^a   Garg, Prabha ^a   Roy, Nilanjan ^a  

^a NATIONAL INSTITUTE OF PHARMACEUTICAL EDUCATION AND RESEARCH NIPER   (India)

Author keywords

2D QSAR; Applicability domain; Curcumine derivatives; Descriptors; HIV 1 integrase

Indexed keywords

COMPUTATIONAL CHEMISTRY; MULTIPLE LINEAR REGRESSION; RELIABILITY ANALYSIS;

2D-QSAR; APPLICABILITY DOMAIN; CURCUMINE DERIVATIVE; DESCRIPTORS; DEVELOPED MODEL; HIV-1 INTEGRASE; MULTIPLE LINEAR REGRESSIONS; QSAR STUDIES; SQUARED CORRELATION COEFFICIENTS; STATISTICALLY SIGNIFICANT MODELS;

MOLECULES;

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; CURCUMIN; INTEGRASE INHIBITOR;

ARTICLE; CHEMICAL STRUCTURE; COMPARATIVE MOLECULAR FIELD ANALYSIS; ELECTRON DIFFRACTION; GEOMETRY; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROPHILICITY; IC 50; MOLECULAR DOCKING; MULTIPLE LINEAR REGRESSION ANALYSIS; PARSIMONY ANALYSIS; PHARMACOPHORE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; X RAY DIFFRACTION;

EID: 84876875727     PISSN: 15734099     EISSN: 18756697     Source Type: Journal    
DOI: 10.2174/157340913804998793     Document Type: Article

References (54)

1. Mehellou, Y.; De Clercq, E. Twenty-six years of anti-HIV drug discovery: where do we stand and where do we go? J. Med. Chem., 2010, 53, 521-538.
2. Hicks, C.; Gulick, R.M. Raltegravir: the first HIV type 1 integrase inhibitor. Clin. Infect. Dis., 2009, 48, 931-939.
3. Shimura, K.; Kodama, E.; Sakagami, Y.; Matsuzaki, Y.; Watanabe, W.; Yamataka, K.; Watanabe, Y.; Ohata, Y.; Doi, S.; Sato, M. Broad antiretroviral activity and resistance profile of the novel human immunodeficiency virus integrase inhibitor elvitegravir (JTK-303/GS-9137). J. Virol., 2008, 82, 764-774.
4. Dayam, R.; Al-Mawsawi, L.Q.; Neamati, N. HIV-1 integrase inhibitors: an emerging clinical reality. Drugs R. D., 2007, 8, 155-168.
5. De Clercq, E. Anti-HIV drugs: 25 compounds approved within 25 years after the discovery of HIV. Int. J. Antimicrob. Agents, 2009, 33, 307-320.
6. McColl, D.J.; Chen, X. Strand transfer inhibitors of HIV-1 integrase: bringing IN a new era of antiretroviral therapy. Antiviral Res., 2010, 85, 101-118.
7. Hu, L.; Zhang, S.; He, X.; Luo, Z.; Wang, X.; Liu, W.; Qin, X. Design and synthesis of novel β-diketo derivatives as HIV-1 integrase inhibitors. Bioorg. Med. Chem., 2012, 20, 177-182.
8. Vandurm, P.; Guiguen, A.; Cauvin, C.; Georges, B.; Le Van, K.; Michaux, C.; Cardona, C.; Mbemba, G.; Mouscadet, J.F.; Hevesi, L. Synthesis, biological evaluation and molecular modeling studies of quinolonyl diketo acid derivatives: New structural insight into the HIV-1 integrase inhibition. Eur. J. Med. Chem., 2011, 46, 1749-1756.
9. Brzozowski, Z.; Slawinski, J.; Saczewski, F.; Sanchez, T.; Neamati, N. Synthesis, anti-HIV-1 integrase, and cytotoxic activities of 4-chloro-N-(4-oxopyrimidin-2-yl)-2-mercaptobenzen-esulfonamide derivatives. Eur. J. Med. Chem., 2008, 43, 1188-1198.
10. Bodiwala, H.S.; Sabde, S.; Gupta, P.; Mukherjee, R.; Kumar, R.; Garg, P.; Bhutani, K.K.; Mitra, D.; Singh, I.P. Design and synthesis of caffeoyl-anilides as portmanteau inhibitors of HIV-1 integrase and CCR5. Bioorg. Med. Chem., 2010, 19, 1256-1263.
11. Zouhiri, F.; Mouscadet, J.F.; Mekouar, K.; Desmaele, D.; Savoure, D.; Leh, H.; Subra, F.; Le Bret, M.; Auclair, C.; d'Angelo, J. Structure-activity relationships and binding mode of styrylquinolines as potent inhibitors of HIV-1 integrase and replication of HIV-1 in cell culture. J. Med. Chem., 2000, 43, 1533-1540.
12. Sechi, M.; Rizzi, G.; Bacchi, A.; Carcelli, M.; Rogolino, D.; Pala, N.; Sanchez, T.W.; Taheri, L.; Dayam, R.; Neamati, N. Design and synthesis of novel dihydroquinoline-3-carboxylic acids as HIV-1 integrase inhibitors. Bioorg. Med. Chem., 2009, 17, 2925-2935.
13. Jin, H.; Metobo, S.; Jabri, S.; Mish, M.; Lansdown, R.; Chen, X.; Tsiang, M.; Wright, M.; Kim, C.U. Tricyclic HIV integrase inhibitors V. SAR studies on the benzyl moiety. Bioorg. Med. Chem. Lett., 2009, 19, 2263-2265.
14. Donghi, M.; Kinzel, O.D.; Summa, V. 3-Hydroxy-4-oxo-4H-pyrido [1, 2-a] pyrimidine-2-carboxylates-A new class of HIV-1 integrase inhibitors. Bioorg. Med. Chem. Lett., 2009, 19, 1930-1934.
15. Lin, Z.; Neamati, N.; Zhao, H.; Kiryu, Y.; Turpin, J.A.; Aberham, C.; Strebel, K.; Kohn, K.; Witvrouw, M.; Pannecouque, C. Chicoric acid analogs as HIV-1 integrase inhibitors. J. Med. Chem., 1999, 42, 1401-1414.
16. Yu, S.; Zhang, L.; Yan, S.; Wang, P.; Sanchez, T.; Christ, F.; Debyser, Z.; Neamati, N.; Zhao, G. Nitrogen-containing polyhydroxylated aromatics as HIV-1 integrase inhibitors: synthesis, structure-activity relationship analysis, and biological activity. J. Enzyme Inhib. Med. Chem., 2012, 27,628-640.
17. Sharma, H.; Patil, S.; Sanchez, T.W.; Neamati, N.; Schinazi, R.F.; Buolamwini, J.K. Synthesis, biological evaluation and 3D-QSAR studies of 3-keto salicylic acid chalcones and related amides as novel HIV-1 integrase inhibitors. Bioorg. Med. Chem., 2011, 19, 2030-2045.
18. De Luca, L.; Barreca, M.L.; Ferro, S.; Christ, F.; Iraci, N.; Gitto, R.; Monforte, A.M.; Debyser, Z.; Chimirri, A. Pharmacophore-based discovery of small-molecule inhibitors of protein-protein interactions between HIV-1 integrase and cellular cofactor LEDGF/p75. ChemMedChem, 2009, 4, 1311-1316.
19. De Luca, L.; De Grazia, S.; Ferro, S.; Gitto, R.; Christ, F.; Debyser, Z.; Chimirri, A. HIV-1 integrase strand-transfer inhibitors: design, synthesis and molecular modeling investigation. Eur. J. Med. Chem., 2011, 46, 756-764.
20. Liao, C.; Nicklaus, M.C. Computer tools in the discovery of HIV-1 integrase inhibitors. Future Med. Chem., 2011, 2, 1123-1140.
21. Almerico, A.M.; Tutone, M.; Ippolito, M.; Lauria, A. Molecular modelling and QSAR in the discovery of HIV-1 integrase inhibitors. Curr. Comput. Aided Drug Des., 2007, 3, 214-233.
22. Cheng, Z.; Zhang, Y.; Fu, W. QSAR study of carboxylic acid derivatives as HIV-1 Integrase inhibitors. Eur. J. Med. Chem., 2010, 45, 3970-3980.
23. Ravichandran, V.; Shalini, S.; Sundram, K.; Sokkalingam, A.D. QSAR study of substituted 1,3,4-oxadiazole naphthyridines as HIV-1 integrase inhibitors. Eur. J. Med. Chem., 2010, 45, 2791-2797.
24. Ghasemi, G.; Nirouei, M.; Shariati, S.; Abdolmaleki, P.; Rastgoo, Z. A quantitative structure-activity relationship study on HIV-1 integrase inhibitors using genetic algorithm, artificial neural networks and different statistical methods. Arab. J. Chem., 2011, http://dx.doi.org/10.1016/j.arabjc.2011.1003.1006.
25. Leonard, J.T.; Roy, K. Exploring molecular shape analysis of styrylquinoline derivatives as HIV-1 integrase inhibitors. Eur. J. Med. Chem., 2008, 43, 81-92.
26. Toropova, A.P.; Toropov, A.A.; Benfenati, E.; Gini, G. Simplified Molecular Input-Line Entry System and International Chemical Identifier in the QSAR Analysis of Styrylquinoline Derivatives as HIV-1 Integrase Inhibitors. Chem. Biol. Drug Des., 2011, 77, 343-360.
27. Vengurlekar, S.; Sharma, R.; Trivedi, P. Two-and three-dimensional QSAR studies on benzyl amide-ketoacid inhibitors ofHIV integrase and their reduced analogs. Med. Chem. Res., 2010, 19, 1106-1120.
28. Gupta, P.; Garg, P.; Roy, N. Comparative docking and CoMFA analysis of curcumine derivatives as HIV-1 integrase inhibitors. Mol. Divers., 2011, 15, 733-750.
29. Costi, R.; Santo, R.D.; Artico, M.; Massa, S.; Ragno, R.; Loddo, R.; La Colla, M.; Tramontano, E.; La Colla, P.; Pani, A. 2, 6-Bis (3, 4, 5-trihydroxybenzylydene) derivatives of cyclohexanone novel potent HIV-1 integrase inhibitors that prevent HIV-1 multiplication in cell-based assays. Bioorg. Med. Chem., 2004, 12, 199-215.
30. Hawkins, D.M. The problem of overfitting. J. Chem. Inf. Comput. Sci., 2004, 44, 1-12.
31. Gupta, P.; Garg, P.; Roy, N. Identification of novel HIV-1 Integrase inhibitors using shape-based screening, QSAR, and docking approach. Chem. Biol. Drug Des., 2012, 79, 835-849.
32. Chernick, M.R.; Friis, R.H. Introductory biostatistics for the health sciences:Modern applications including the bootstrap, John Wiley & Sons: NJ, USA, 2003.
33. Van Belle, G.; Fisher, L. Biostatistics: a methodology for the health sciences, John Wiley & Sons, Inc.,: Hoboken, New Jersey, 2004.
34. Randic, M. Comparative regression analysis. Regressions based on a single descriptor. Croat. Chem. Acta, 1993, 66, 289-289.
35. Randić, M. Fitting of nonlinear regressions by orthogonalized power series. J. Comput. Chem., 1993, 14, 363-370.
36. Tropsha, A.; Gramatica, P.; Gombar, V.K. The importance of being earnest: validation is the absolute essential for successful application and interpretation of QSPR models. QSAR Comb. Sci., 2003, 22, 69-77.
37. Kiralj, R.; Ferreira, M.M.C. Basic validation procedures for regression models in QSAR and QSPR studies: theory and application. J. Braz. Chem. Soc., 2009, 20, 770-787.
38. Aptula, A.O.; Jeliazkova, N.G.; Schultz, T.W.; Cronin, M.T.D. The better predictive model: High q2 for the training set or low root mean square error of prediction for the test set? QSAR Comb. Sci., 2005, 24, 385-396.
39. Hall, M.; Frank, E.; Holmes, G.; Pfahringer, B.; Reutemann, P.; Witten, I.H. The WEKA data mining software: an update. ACM SIGKDD Explorations Newsletter, 2009, 11, 10-18.
40. Hall, M.A., Ph. D. Thesis, The University of Waikato, Hamilton, NewZealand, 1999.
41. Witten, I.H.; Frank, E. Data Mining: Practical machine learning tools and techniques, Morgan Kaufmann, San Francisco, CA 94111: 2005.
42. Todeschini, R.; Consonni, V.; Mauri, A.; Pavan, M. Detecting "bad" regression models: multicriteria fitness functions in Regression analysis. Anal. Chim. Acta, 2004, 515, 199-208.
43. Afantitis, A.; Melagraki, G.; Sarimveis, H.; Igglessi-Markopoulou, O.; Kollias, G. A novel QSAR model for predicting the inhibition of CXCR3 receptor by 4-N-aryl-[1,4] diazepane ureas. Eur. J. Med. Chem., 2009, 44, 877-884.
44. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors, Wiley-VCH: Weinheim, 2000.
45. Golbraikh, A.; Tropsha, A. Beware of q2! J. Mol. Graph. Model., 2002, 20, 269-276.
46. Roy, P.P.; Roy, K. On some aspects of variable selection for partial least squares regression models. QSAR Comb. Sci., 2008, 27, 302-313.
47. Atkinson, A.C. Plots, Transformations and Regression, 1985, Clarendon Press, Oxford.
48. Stanforth, R.W.; Kolossov, E.; Mirkin, B. A measure of domain of applicability for QSAR modelling based on intelligent K means clustering. QSAR Comb. Sci., 2007, 26, 837-844.
49. Hawkins, D.M.; Kraker, J. Deterministic fallacies and model validation. J. Chemometr., 2010, 24, 188-193.
50. Schuur, J.H.; Selzer, P.; Gasteiger, J. The coding of the three-dimensional structure of molecules by molecular transforms and its application to structure-spectra correlations and studies of biological activity. J. Chem. Info. Compt. Sci., 1996, 36, 334-344.
51. Consonni, V.; Todeschini, R.; Pavan, M. Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 1. Theory of the novel 3D molecular descriptors. J. Chem. Info. Comp. Sci., 2002, 42, 682-692.
52. Kier, L.B.; Hall, L.H.; Frazer, J.W. An index of electrotopological state for atoms in molecules. J. Med. Chem., 1991, 7, 229-241.
53. Magnuson, V.R.; Harriss, D.K.; Basak, S.C. Topological Indices Based on Neighborhood Symmetry: Chemical and Biological Applications in Studies in Physical and Theoretical Chemistry, Elsevier: Amsterdam, Netherlands, 1983.
54. Todeschini, R.; Vighi, M.; Finizio, A.; Gramatica, P. 30-Modelling and prediction by WHIM descriptors. Part 8. Toxicity and physico-chemical properties of environmental priority chemicals by 2D-TI and 3D-WHIM Descriptors. SAR QSAR Environ. Res., 1997, 7, 173-193.