QSAR Modeling ANTI-HIV-1 Activities by Optimization of Correlation Weights of Local Graph Invariants

References

• Makhija , MT and Kulkarni , VM . 2001 . Eigen value analysis of HIV-1 integrase inhibitors . J. Chem. Inf. Comput. Sci. , 41 : 1569 – 1577 .
   PubMedGoogle Scholar
• Arnold , E , Das , K , Yadav , PNS , Hsiou , Y , Boyer , PL and Hughes , SH . 1996 . Targeting HIV recerse transcriptase for anti-AIDS drug design . Drug Des. Discov. , 13 : 29 – 47 .
   PubMedGoogle Scholar
• De Clercq , E . 1998 . The role of nonnucleoside reverse transcriptase inhibitors (NNRTIs) in the therapy of HIV-1 infection . Antiviral Res. , 38 : 153 – 179 .
   PubMed Web of Science ®Google Scholar
• Jonckheere , H , Anne , J and De Clercq , E . 2000 . The HIV-1 reverse transcription (RT) process as target for RT inhibitors . Med. Res. Rev. , 20 : 129 – 154 .
   PubMed Web of Science ®Google Scholar
• SciFinder Scholar, version 2000.1http://www.cas.org/SCIFINDER/SCHOLAR/index.html
   Google Scholar
• Garg , R , Gupta , SP , Gao , H , Babu , MS , Debnath , AK and Hansch , C . 1999 . Comparative quantitative structure–activity relationship studies on anti-HIV drugs . Chem. Rev. , 99 : 3525 – 3602 .
   PubMed Web of Science ®Google Scholar
• Jalali-Heravi , M and Parastar , F . 2000 . Use of artificial neural networks in a qsar study of anti-HIV activity for a large group of HEPT derivatives . J. Chem. Inf. Comput. Sci. , 40 : 147 – 154 .
   PubMedGoogle Scholar
• Knaggs , MH , McGuigan , C , Harris , SA , Heshmati , P , Cahard , D , Gilbert , IH and Balzarini , J . 2000 . A QSAR study investigating the effect of l-Alanine ester variation on the anti-HIV activity of some phosphoramidate derivatives of d4T . Bioorg. Med. Chem. Lett. , 10 : 2075 – 2078 .
   PubMed Web of Science ®Google Scholar
• Tronchet , JMJ , Grigorov , M , Dolatshahi , N , Moriaud , F and Weber , JA . 1997 . A QSAR study confirming the heterogeneity of the HEPT derivative series regarding their interaction with HIV reverse transcriptase . Eur. J. Med. Chem. , 32 : 279 – 299 .
   Web of Science ®Google Scholar
• Houskonen , J . 2001 . Modeling QSAR with the electrotopological state: TIBO derivatives . J. Chem. Inf. Comput. Sci. , 41 : 425 – 429 .
   PubMedGoogle Scholar
• Maw , HH and Hall , LH . 2002 . E-State modeling of HIV-1 protease inhibitor binding independent of 3D information . J. Chem. Inf. Comput. Sci. , 42 : 190 – 298 .
   Google Scholar
• Gancia , E , Bravi , G , Mascagni , P and Zaliani , A . 2000 . Global 3D-QSAR methods: MS-WHIM and autocorrelation . J. Comput.-Aided Mol. Des. , 14 : 293 – 306 .
   PubMed Web of Science ®Google Scholar
• Klein , CT , Lawtrakul , L , Hannongbua , S and Wolschann , P . 2000 . Accessible charges in structure–activity relationships a study on HEPT-based HIV-1 RT inhibitors . Sci. Pharm. , 68 : 25 – 40 .
   Google Scholar
• Santos-Filho , OA and Hopfinger , AJ . 2002 . The 4D-QSAR paradigm: application to a novel set of Nonpetidic HIV protease inhibitors . Quant. Struct.-Act. Relat. , 21 : 369 – 381 .
   Google Scholar
• Kireev , DB , Chretien , JR and Raevsky , OA . 1995 . Molecular modeling and quantitative structure–activity studies of anti-HIV-1,2-heteroarylquinoline-4-amines . Eur. J. Med. Chem. , 30 : 395 – 402 .
   Web of Science ®Google Scholar
• Hennongbua , S , Nivesanond , K , Lawtrakul , L , Pungpo , P and Wolschann , P . 2001 . 3D-Quantitative structure–activity relationships of HEPT derivatives as HIV-1 reverse transcriptase inhibitors, based on Ab Initio . Chem. Inf. Comput. Sci. , 41 : 848 – 855 .
   PubMedGoogle Scholar
• Jayatilleke , PRN , Nair , AC , Zauhar , R and Welsh , WJ . 2000 . Computational studies on HIV-1 protease inhibitors: influence of calculated inhibitor-enzyme binding affinities on the statistical quality of 3D-QSAR CoMFA models . J. Med. Chem. , 43 : 4446 – 4451 .
   PubMed Web of Science ®Google Scholar
• Debnath , AK . 1999 . Three-dimensional quantitative structure–activity relationhsips study on cyclic urea derivatives as HIV-1 protease inhibitors: application to comparative molecular field analysis . J. Med. Chem. , 42 : 249 – 259 .
   PubMed Web of Science ®Google Scholar
• Buolamwini , JK and Assefa , H . 2002 . CoMFA and CoMSIA 3D QSAR and docking studies on conformationally-restrained cinnamoyl HIV-1 integrase inhibitars: exploration of a binding mode at the active site . J. Med. Chem. , 45 : 841 – 852 .
   PubMed Web of Science ®Google Scholar
• Mickle , T and Nair , V . 2000 . Anti-human immunodeficiency virus activities of nucleosides and nucleotides: correlation with molecular electrostatic potential data . Antimicrob. Agents Chemother. , 44 : 2939 – 2947 .
   PubMed Web of Science ®Google Scholar
• Mickel , T and Nair , V . 2000 . Predictive QSAR analysis of anti-HIV agents . Drugs Future , 25 : 393 – 400 .
   Google Scholar
• Gonzáles OG Murray JS Peralta-Inga Z Politzer P 2001 Computed molecular surface electrostatic potentials of two groups of riverse transcriptase inhibitors: relationships to anti- HIV-1 activities Int. J. Quantum Chem. 83 3–4 115 124
   Web of Science ®Google Scholar
• Firpo , M , Gavernet , L , Castro , EA and Toropov , AA . 2000 . Maximum topological distances based indices as molecular descriptors for QSPR. Part 1. Application to alkyl benzenes boiling points . J. Mol. Struct. (Theochem) , 501–502 : 419 – 425 .
   Web of Science ®Google Scholar
• Castro , EA , Tueros , M and Toropov , AA . 2000 . Maximum topological distances based indices as molecular descriptor for QSPR. 2-Application to Aromatic Hydrocarbons . Comput. Chem. , 24 : 571 – 576 .
   PubMedGoogle Scholar
• Mercader , A , Castro , EA and Toropov , AA . 2001 . Maximum topological distances based indices as molecular descriptors for QSPR. 4-Modeling the enthlpy of formation of hydrocarbons from elements . Int. J. Mol. Sci. , 2 : 121 – 134 .
   Google Scholar
• Toropov , A , Toropova , A , Ismailov , T and Bonchev , D . 1998 . 3D weighting of molecular descriptors for QSPR/QSAR by the method of ideal symmetry (MIS). 1. Application to boiling points of alkanes . J. Mol. Struct. (Theochem) , 424 : 237 – 247 .
   Web of Science ®Google Scholar
• Krenkel , G , Castro , EA and Toropov , AA . 2002 . 3D and 4D Molecular models derived from the ideal symmetry method: prediction of alkanes normal boiling points . Chem. Phys. Lett. , 355 : 517 – 528 .
   Web of Science ®Google Scholar
• Toropov , AA and Toropova , AP . 1997 . Method of ideal symmetry in four-dimensional space: implementation in the QSPR studies on the thermochemistry of complex compounds . Russ. J. Coord. Chem. , 23 : 741 – 747 .
   Web of Science ®Google Scholar
• Toropov , AA and Toropova , AP . 1998 . Optimization of correlation weights of the local graph invariants: use of the enthalpies of formation of complex compounds for the QSPR modeling . Russ. J. Coord. Chem. , 24 : 81 – 85 .
   Web of Science ®Google Scholar
• Toropov , AA and Toropova , AP . 2001 . Modeling QSPR of stability of complexes of adenosine phosphate derivatives with metals absent from the complexes of the teaching access . Russ. J. Coord. Chem. , 27 : 574 – 578 .
   Web of Science ®Google Scholar
• Toropov , AA and Toropova , AP . 2002 . Modeling of acyclic compounds normal boiling points by correlation weighting of nearest neighboring codes . J. Mol. Struct. (Theochem) , 581 : 11 – 15 .
   Web of Science ®Google Scholar
• Toropov , AA and Toropova , AP . 2001 . Prediction of heteroaromatic amine mutagenicity by means of correlation weighting of atomic orbital graph of local invariants . J. Mol. Struct. (Theochem) , 538 : 287 – 293 .
   Web of Science ®Google Scholar
• Toropov AA Toropova AP 2002 QSAR modeling of mutagenicity based on graph of atomic orbitals, internet electron J. Mol. Des. 1 109 113 http://www.biochempress.com.
   Google Scholar
• Toropov , AA and Toropova , AP . 2002 . Modeling QSAR of toxicity on optimization of correlation weights of morgan extended connectivity . J. Mol. Struct. (Theochem) , 578 : 129 – 134 .
   Web of Science ®Google Scholar
• Toropova , AP , Toropov , AA , Ishankhodzhaeva , MM and Parpiev , NA . 2000 . Modeling QSPR of stability constants of coordination compounds by optimization of correlation weights of local graph invariants . Russ. J. Inorg. Chem. , 45 : 1057 – 1059 .
   Google Scholar
• Krenkel , G , Castro , EA and Toropov , AA . 2001 . Improved molecular descriptors to calculate boiling points based on the optimization of correlation weights of local graph invarinats . J. Mol. Struct. (Theochem) , 542 : 107 – 113 .
   Web of Science ®Google Scholar
• Krenkel , G , Castro , EA and Toropov , AA . 2001 . Improved molecular descriptors based on the optimization of correlation weights of local graph invariants . Int. J. Mol. Sci. , 2 : 57 – 65 .
   Google Scholar
• Mercader , A , Castro , EA and Toropov , AA . 2000 . Modeling QSPR of the enthalpy of formation from elements by means of correlation weighting of local invariants of atomic orbital molecular graphs . Chem. Phys. Lett. , 330 : 612 – 623 .
   Web of Science ®Google Scholar
• Duchowicz , PR , Castro , EA and Toropov , AA . 2002 . Improved QSPR analysis of standard entropy of acyclic and aromatic compounds using optimized correlation weights of linear graph invariants . Comput. Chem. , 26 : 327 – 332 .
   PubMedGoogle Scholar
• Peruzzo , PJ , Marino , DJG , Castro , EA and Toropov , AA . 2001 . Calculation of pK values of flavylium salts from the optimization of correlation weights of local graph invariants . J.Mol. Struct. (Theochem) , 572 : 53 – 60 .
   Web of Science ®Google Scholar
• Randic , M . 1991 . On computation of optimal parameters for multivariate analysis of structure–property relationship . J. Comput. Chem. , 12 : 970 – 980 .
   Web of Science ®Google Scholar
• Randic , M . 1991 . Novel graph theoretic approach to heteroatoms in quantitative structure–activity relationships . Chemom. Intell. Lab. Syst. , 10 : 213 – 227 .
   Web of Science ®Google Scholar
• Randic , M . 1991 . Resolution of ambiguities in structure–property studies by use of orthogonal descriptors . J. Chem. Inf. Comput. Sci. , 31 : 311 – 320 .
   Google Scholar
• Ho , W , Kukla , MJ , Breslin , HJ , Ludovici , DW , Grous , PP , Diamond , CJ , Miranda , M , Rodgers , JD , Ho , CY , De Clercq , E , Pauwels , R , Andries , K , Janssen , MAC and Janssen , PAJ . 1995 . J. Med. Chem. , 38 : 794
   PubMed Web of Science ®Google Scholar
• Baba , M , Shigeta , S , Tanaka , H , Miyasaka , T , Ubasawa , M , Umezu , K , Walker , RT , Pauwles , R and De Clerq , E . 1992 . Antiviral Res. , 17 : 245
   PubMed Web of Science ®Google Scholar
• Toropov , AA , Toropova , AP , Voropaeva , NL , Ruban , IN and Rashidova , SSh. 1988 . Generalized zero-order molecular connectivity indez: enthalpies of crystalline aquo and ammino complexes in QSPR modeling . Russ. J. Coord. Chem. , 24 : 525 – 529 .
   Google Scholar
• Toropov , AA , Voropaeva , NL , Ruban , IN and Rashidova , SSh. 1999 . Quantitative structure–property relationships for binary polymer solvent systems: correlation weighting of the local invariants of molecular graphs . Polym. Sci. Ser. A , 41 : 975 – 985 .
   Google Scholar