The use of ladder particle swarm optimisation for quantitative structure–activity relationship analysis of human immunodeficiency virus-1 integrase inhibitors

References

• Ribeiro , F.A.L. and Ferreira , M.M.C. 2003 . QSPR models of boiling point, octanol-water partition coefficient and retention time index of polycyclic aromatic hydrocarbons . J. Mol. Struct. Theochem. , 663 : 109 – 126 .
   Web of Science ®Google Scholar
• Jalali-Heravi , M. and Asadollaho-Baboli , M. 2008 . QSAR analysis of platelet-derived growth inhibitors using GA-ANN and shuffling crossvalidation . QSAR Comb. Sci. , 27 : 750 – 757 .
   Google Scholar
• Daszykowski , M. , Walczak , B. and Massart , D.L. 2002 . Representative subset selection . Anal. Chim. Acta , 468 : 91 – 103 .
   Web of Science ®Google Scholar
• Tominaga , Y. 1998 . Representative subset selection using genetic algorithms . Chemom. Intell. Lab. Syst. , 43 : 157 – 163 .
   Web of Science ®Google Scholar
• Sales , F. , Rius , A. , Callao , M.P. and Rius , F.X. 2000 . Standardization of a multivariate calibration model applied to the determination of chromium in tanning sewage . Talanta , 52 : 329 – 336 .
   Google Scholar
• Kennard , R.W. and Stone , L.A. 1969 . Computer aided design of experiments . Technometrics , 11 : 137 – 148 .
   Web of Science ®Google Scholar
• Galvao , R.K.H. , Araujo , M.C.U. , Jose , G.E. , Pontes , M.J.C. , Silva , E.C. and Saldanha , T.C.B. 2005 . A method for calibration and validation subset partitioning . Talanta , 67 : 736 – 740 .
   PubMed Web of Science ®Google Scholar
• United Nations program on HIV/AIDS (UNAIDS), AIDS epidemic update 2008, December 2009. Available at http://www.UNAIDS.org
   Google Scholar
• Gait , M.J. and Karn , J. 1995 . Progress in anti-HIV structure-based drug design . Trends Biotechnol. , 13 : 430 – 438 .
   PubMed Web of Science ®Google Scholar
• Ding , J. , Das , K. , Moereels , H. , Koymans , L. , Andries , K. , Janssen , P.A.J. , Hughes , S.H. and Arnold , E. 1995 . Structure of HIV-1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors . Nat. Struct. Mol. Biol. , 2 : 407 – 415 .
   Google Scholar
• Palmisano , L. 2007 . Role of integrase inhibitors in the treatment of HIV disease . Expert Rev. Anti. Infect. Ther. , 5 : 67 – 75 .
   PubMed Web of Science ®Google Scholar
• Brzozowski , Z. , Saczewski , F. , Slawinski , J. , Sanchez , T. and Neamati , N. 2009 . Synthesis and anti-HIV-1 integrase activities of 3-aroyl-2,3-dihydro-1,1-dioxo-1,4,2-benzodithiazines . Eur. J. Med. Chem. , 44 : 190 – 196 .
   Google Scholar
• Dubey , S. , Satyanarayana , Y.D. and Lavania , H. 2007 . Development of integrase inhibitors for treatment of AIDS: An overview . Eur. J. Med. Chem. , 42 : 1159 – 1168 .
   PubMed Web of Science ®Google Scholar
• Leavitt , A.D. , Shiue , L. and Varmus , H.E. 1993 . Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase functions in vitro . J. Biol. Chem. , 268 : 2113 – 2119 .
   PubMed Web of Science ®Google Scholar
• Cotelle , P. 2006 . Patented HIV-1 integrase inhibitors . Recent Pat. Antiinfect. Drug Discov. , 1 : 1 – 15 .
   PubMedGoogle Scholar
• Lu , P. , Wei , X. and Zhang , R. 2010 . CoMFA and CoMSIA 3D-QSAR studies on quionolone caroxylic acid derivatives inhibitors of HIV-1 integrase . Eur. J. Med. Chem. , 45 : 3413 – 3419 .
   PubMed Web of Science ®Google Scholar
• Ravichandran , V. , Shalini , S. , Sundram , K. and Sokkalingam , A.D. 2010 . QSAR study of substituted 1,3,4-oxadiazole naphthyridines as HIV-1 integrase inhibitors . Eur. J. Med. Chem. , 45 : 2791 – 2797 .
   Google Scholar
• Cheng , Z. , Zhang , Y. and Fu , W. 2010 . QSAR study of carboxylic acid derivatives as HIV-1 integrase inhibitors . Eur. J. Med. Chem. , 45 : 3970 – 3980 .
   PubMed Web of Science ®Google Scholar
• Gupta , P. , Roy , N. and Garg , P. 2009 . Docking-based 3D-QSAR study of HIV-1 integrase inhibitors . Eur. J. Med. Chem. , 44 : 4276 – 4287 .
   PubMed Web of Science ®Google Scholar
• de Melo , E.B. and Ferreira , M.M.C. 2009 . Multivariate QSAR study of 4,5-dihydroxypyrimidine carboxamides as HIV-1 integrase inhibitors . Eur. J. Med. Chem. , 44 : 3577 – 3583 .
   Google Scholar
• Banks , A. , Vincent , J. and Anyakoha , C. 2007 . A review of particle swarm optimisation. Part 1: Background and development . Nat. Comput. , 6 : 467 – 484 .
   Google Scholar
• Kennedy , J. and Eberhart , R. 1995 . A new optimizer using particle swarm theory . Proc. IEEE Int. Conf. Neural Netw. , 4 : 1942 – 1948 .
   Google Scholar
• Chen , D. and Zhao , C. 2009 . Particle swarm optimization with adaptive population size and its application . Appl. Soft Comput. , 9 : 39 – 48 .
   Web of Science ®Google Scholar
• Lazinica , A. 2009 . Particle swarm optimization . In-Tech , Available at http://www.intechweb.org Vienna, Austria
   Google Scholar
• Victoire , T.A.A. and Jeyakumar , A.E. 2004 . Hybrid PSO-SQP for economic dispatch with valve-point effect . Electr. Power Syst. Res. , 71 : 51 – 59 .
   Web of Science ®Google Scholar
• Shayeghi , H. , Pirayeshnegab , A. , Jalili , A. and Shayanfar , H.A. 2009 . Application of PSO technique for GEP in restructured power systems . Energy Convers. Manag. , 50 : 2127 – 2135 .
   Google Scholar
• Boyd , R. and Recharson , P. 1985 . Culture and the evolutionary process , Chicago, IL : University of Chicago Press .
   Google Scholar
• Arumugam , M.S. , Rao , M.V.C. and Tan , A.W.C. 2009 . A novel and effective particle swarm optimization like algorithm with extrapolation technique . Appl. Soft Comput. , 9 : 308 – 320 .
   Web of Science ®Google Scholar
• Shi , Y. and Eberhart , R.C. 1998 . Parameter selection in particle swarm optimization . Lect. Notes Comput. Sci. , 1447 : 591 – 600 .
   Google Scholar
• Zhenya , H. , Chengjian , W. , Luxi , Y. , Xiqi , G. , Susu , Y. , Eberhart , S.C. and Shi , Y. 1998 . Extracting rules from fuzzy neural network by particle swarm optimization . Proc. IEEE Int. Conf. Evol. Comput. ICEC98 , : 74 – 77 . Anchorage, AK, USA
   Google Scholar
• Johns , B.A. , Weatherhead , J.G. , Allen , S.H. , Thompson , J.B. , Garvey , E.P. , Foster , S.A. , Jeffrey , J.L. and Miller , W.H. 2009 . The use of oxadiazole and triazole substituted naphthyridines as HIV-1 integrase inhibitors. Part 1: Establishing the pharmacophore . Bioorg. Med. Chem. Lett. , 19 : 1802 – 1806 .
   PubMed Web of Science ®Google Scholar
• Johns , B.A. , Weatherhead , J.G. , Allen , S.H. , Thompson , J.B. , Garvey , E.P. , Foster , S.A. , Jeffrey , J.L. and Miller , W.H. 2009 . 1,3,4-Oxadiazole substituted naphthyridines as HIV-1 integrase inhibitors. Part 2: SAR of the C5 position . Bioorg. Med. Chem. Lett. , 19 : 1807 – 1810 .
   PubMed Web of Science ®Google Scholar
• HyperChem, Hypercube, Inc. Software available at http://www.hyper.com
   Google Scholar
• R. Todeschini, Milano chemometrics and QSAR group. Available at http://www.disat.unimib.it/chm
   Google Scholar
• Deswal , S. and Roy , N. 2006 . Quantitative structure activity relationship of benzoxazinone derivatives as neuropeptide Y Y5 receptor antagonists . Eur. J. Med. Chem. , 41 : 552 – 557 .
   Google Scholar
• Jalali-Heravi , M. , Shahbazikhah , P. and Ghadiri-Bidhendi , A. 2008 . QSRR study of psychiatric drugs using classification and regression trees combined with adaptive neuro-fuzzy inference system . QSAR Comb. Sci. , 27 : 729 – 739 .
   Google Scholar
• Marengo , E. and Todeschini , R. 1993 . Reference data sets for chemometrical methods testing . Chemom. Intell. Lab. Syst. , 19 : 43 – 51 .
   Google Scholar
• Efron , B. and Gong , G. 1983 . A leisurely look at the bootstrap, the jackknife, and cross-validation . Am. Stat. , 37 : 36 – 48 .
   Web of Science ®Google Scholar
• Xu , Q.S. , Liang , Y.Z. and Du , Y.P. 2004 . Monte Carlo cross-validation for selecting a model and estimating the prediction error in multivariate calibration . J. Chemom. , 18 : 112 – 120 .
   Web of Science ®Google Scholar
• Jalali-Heravi , M. , Ebrahimi-Najafabadi , H. and Khodabandehloo , A. 2009 . Use of Kernel orthogonal projection to latent structure in modelling of retention indices of pesticides . QSAR Comb. Sci. , 28 : 1432 – 1441 .
   Google Scholar
• Golbraikh , A. and Tropsha , A. 2002 . Beware of q2! . J. Mol. Graph. Model. , 20 : 269 – 276 .
   PubMed Web of Science ®Google Scholar
• Roy , P.P. , Paul , S. , Mitra , I. and Roy , K. 2009 . On two novel parameters for validation of predictive QSAR models . Molecules , 14 : 1660 – 1701 .
   PubMed Web of Science ®Google Scholar
• Roy , K. and Roy , P.P. 2009 . Comparative chemometric modeling of cytochrome 3A4 inhibitory activity of structurally diverse compounds using stepwise MLR, FA-MLR, PLS, GFA, G/PLS and ANN techniques . Eur. J. Med. Chem. , 44 : 2913 – 2922 .
   PubMed Web of Science ®Google Scholar
• Roy , P.P. and Roy , K. 2008 . On some aspects of variable selection for partial least squares regression models . QSAR Comb. Sci. , 27 : 302 – 313 .
   Google Scholar
• Mitra , I. , Roy , P.P. , Kar , S. , Ojha , P.K. and Roy , K. 2010 . On further application of as a metric for validation of QSAR models . J. Chemom. , 24 : 22 – 33 .
   Web of Science ®Google Scholar
• Tropsha , A. , Gramatica , P. and Gombar , V.K. 2003 . The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models . QSAR Comb. Sci. , 22 : 69 – 77 .
   Google Scholar
• Massarelli , I. , Imbriani , M. , Coi , A. , Saraceno , M. , Carli , N. and Bianucci , A.M. 2009 . Development of QSAR models for predicting hepatocarcinogenic toxicity of chemicals . Eur. J. Med. Chem. , 44 : 3658 – 3664 .
   Google Scholar
• Mitra , I. , Saha , A. and Roy , K. 2010 . Exploring quantitative structure-activity relationship studies of antioxidant phenolic compounds obtained from traditional Chinese medicinal plants . Mol. Simul. , 36 : 1067 – 1079 .
   Web of Science ®Google Scholar
• Guha , R. and Jurs , P.C. 2005 . Interpreting computational neural network QSAR models: A measure of descriptor importance . J. Chem. Inf. Model. , 45 : 800 – 806 .
   PubMed Web of Science ®Google Scholar
• Gonzalez , M.P. , Teran , C. , Teijeira , M. , Besadac , P. and Gonzalez-Moa , M.J. 2005 . BCUT descriptors to predicting affinity toward A3 adenosine receptors . Bioorg. Med. Chem. Lett. , 15 : 3491 – 3495 .
   Google Scholar
• Todeschini , R. and Consonni , V. 2009 . Molecular Descriptors for Chemoinformatics , 43 Weinheim : Wiley-VCH .
   Google Scholar
• Todeschini , R. and Consonni , V. 2009 . Molecular Descriptors for Chemoinformatics , 109 Weinheim : Wiley-VCH .
   Google Scholar
• Gonzalez , M.P. , Suarez , P.L. , Fall , Y. and Gomez , G. 2005 . Quantitative structure-activity relationship studies of vitamin D receptor affinity for analogues of 1α,25-dihydroxyvitamin D3. 1: WHIM descriptors . Bioorg. Med. Chem. Lett. , 15 : 5165 – 5169 .
   Google Scholar