QSAR Modeling Based on Structure-Information for Properties of Interest in Human Health

References

• Dearden , JC . 2003 . In silico prediction of drug toxicity . J. Comp. Aided Mol. Des. , 16 : 1 – 9 .
   Google Scholar
• van de Waterbeemd , H . 2003 . ADMET in silico modeling: towards prediction paradise? . Nat. Rev. Drug Dis. , 2 : 192 – 204 .
   PubMed Web of Science ®Google Scholar
• Charifson P Kuntz ID 1997 Recent successes and continuing limitations in computer-aided drug design Charifson P Practical Application of Computer-Aided Drug Design, Marcel-Dekker New York 1 37
   Google Scholar
• Hall , LH . 2004 . A structure-information approach to the prediction of biological activities and properties . Chem. Biodivers. , 1 : 183 – 201 .
   PubMed Web of Science ®Google Scholar
• Kier LB Hall LH 1999 Molecular Structure Description: The Electrotopological State, Academic Press San Diego, CA 13 74
   Google Scholar
• Kier LB Hall LH 1986 Molecular Connectivity in Structure–Activity Analysis, Research Studies Press, John Wiley & Sons 1 101
   Google Scholar
• Kier LB Hall LH 1999 The electrotopological state: structure modeling for QSAR and database analysis Devillers J Balaban AT Topological Indices and Related Descriptors in QSAR and QSPR, Gordon and Breach Reading, UK 307 360
   Google Scholar
• Kier LB Hall LH 1999 Molecular connectivity chi indices for database analysis and structure-property modeling Devillers J Balaban AT Topological Indices and Related Descriptors in QSAR and QSPR, Gordon and Breach Reading, UK 455 490
   Google Scholar
• Kier , LB , Hall , LH , Boyd , D and Lipkowitz , K . 1991 . The molecular connectivity chi indexes and kappa shape indexes in structure-property relations . Reviews of Computational Chemistry, VCH Publishers, Inc. , 2 : 367 – 422 .
   Google Scholar
• Silverman RB 1992 The Organic Chemistry of Drug Design and Drug Action, Academic Press San Diego, CA 83 86
   Google Scholar
• Waes , WHJ , Ramos , EU , Verhaar , HLM and Hermens , JLM . 1998 . Acute toxicity of nonpolar versus polar narcosis: is there a difference? . Environ. Toxicol. Chem. , 17 : 1380 – 1384 .
   Web of Science ®Google Scholar
• Dearden , JC , Cronin , MTD , Zhao , Y-H and Raevsky , OA . 2000 . QSAR studies of compounds acting by polar and non-polar narcosis: an examination of the role of polarizability and hydrogen bonding . Quant. Struct. Act. Relat. , 19 : 3 – 9 .
   Google Scholar
• Kier , LB and Hall , LH . 1997 . Introductory Editorial . Med. Chem. Res. , 7 : 335 – 339 .
   Google Scholar
• Adamson , GW and Bawden , D . 1976 . An empirical method for structure–activity correlation for polycyclic compounds using Wiswesser Line Notation . J. Chem. Inf. Comput. Sci. , 16 : 161 – 169 .
   Google Scholar
• Huuskonen , JJ , Villa , AEP and Tetko , IV . 1999 . Prediction of partition coefficient based on atom-type electrotopological state indices . J. Pharm. Sci. , 88 : 229 – 233 .
   PubMed Web of Science ®Google Scholar
• Basak , SC , Gute , BD and Grunwald , G . 1996 . A comparative study of topological and geometric parameters in estimating normal boiling point and octanol/water partition coefficient . J. Chem. Inf. Comput. Sci. , 36 : 1054 – 1060 .
   Google Scholar
• Tetko , IV , Tanchuk , VY and Villa , AEP . 2001 . Prediction of n-octanol/water partition coefficients from PHYSPROP database using artificial neural networks and E-state indices . J. Chem. Inf. Comput. Sci. , 41 : 1407 – 1421 .
   PubMedGoogle Scholar
• Huuskonen , J . 2000 . Neural network modeling for estimation of partition coefficient based on atom-type electrotopological state indices . J. Chem. Inf. Comput. Sci. , 40 : 947 – 955 .
   PubMedGoogle Scholar
• Hall , LH and Kier , LB . 1995 . Electrotopological state indices for atom types: a novel combination of electronic, topological and valence state information . J. Chem. Inf. Comput. Sci. , 35 : 1039 – 1045 .
   Google Scholar
• Kier , LB and Hall , LH . 1981 . Derivation and significance of valence molecular connectivity . J. Pharm. Sci. , 70 : 583 – 589 .
   PubMed Web of Science ®Google Scholar
• Hall , LH , Mohney , BK and Kier , LB . 1993 . Comparison of electrotopological state indexes with molecular orbital parameters: inhibition of MAO by hydrazides . Quant. Struct. Act. Relat. , 12 : 44 – 48 .
   Google Scholar
• Kier , LB and Hall , LH . 1990 . An electrotopological state index for atoms in molecules . Pharm. Res. , 7 : 801 – 807 .
   PubMed Web of Science ®Google Scholar
• Hall , LH , Mohney , BM and Kier , LB . 1991 . The electrotopological state: structure information at the atomic level for molecular graphs . J. Chem. Inf. Comput. Sci. , 31 : 76 – 82 .
   Google Scholar
• Kier LB Hall LH 1992 An atom-centered index for drug QSAR models Testa B Advances in Drug Design, Academic Press London 2 38
   Google Scholar
• Hall , LH , Mohney , BM and Kier , LB . 1993 . Comparison of electrotopological state indexes with molecular orbital parameters: inhibition of MAO by hydrazides . Quant. Struct.-Act. Relat. , 12 : 44 – 48 .
   Web of Science ®Google Scholar
• Gough , JD and Hall , LH . 1999 . Modeling the toxicity of amide herbicides using the electrotopological state . Environ. Toxicol. Chem. , 18 : 1069 – 1075 .
   Web of Science ®Google Scholar
• Roy , K , Pal , DK and Sengupta , C . 2001 . QSAR of antineoplastics V: exploration of receptor interaction sites of antitumor N-(7-indoyl) benzenesulfonamides targeting G1 phase using electrotopological state atom index . Drug Design Discov. , 17 : 207 – 218 .
   PubMedGoogle Scholar
• Maw , HH and Hall , LH . 2000 . E-state modeling of dopamine transporter binding: validation of model for small data set . J. Chem. Inf. Comput. Sci. , 40 : 1270 – 1275 .
   PubMedGoogle Scholar
• Maw , HH and Hall , LH . 2001 . E-state modeling of corticosteroids binding affinity: validation of model for small data set . J. Chem. Inf. Comput. Sci. , 41 : 1248 – 1254 .
   PubMedGoogle Scholar
• Kier , LB and Hall , LH . 1992 . Inhibition of salicylamide binding: an electrotopological state analysis . Med. Chem. Res. , 2 : 497 – 502 .
   Google Scholar
• Boulamnwini , JK , Raghaven , K , Fresen , M , Pommier , Y , Kohn , K and Weinstein , J . 1995 . Application of the electrotopological state index to QSAR analysis of flavone derivatives as HIV-1 integrase inhibitors . Pharm. Res. , 13 : 1892 – 1895 .
   Google Scholar
• Gozalbes , R , Galvez , J , Garcia-Domenech , R and Derouin , F . 1999 . Molecular search of new active drugs against Toxoplasma gondii . SAR QSAR Environ. Res. , 10 : 47 – 60 .
   PubMed Web of Science ®Google Scholar
• Hall , LH and Kier , LB . 2000 . The E-state as the basis for molecular structure space definition and structure similarity . J. Chem. Inf. Comput. Sci. , 40 : 784 – 791 .
   PubMedGoogle Scholar
• Kier , LB and Hall , LH . 2001 . E-state indices for database organization and molecular similarity . SAR QSAR Environ. Res. , 12 : 55 – 74 .
   PubMed Web of Science ®Google Scholar
• Hall , LH , Kier , LB and Brown , BB . 1995 . Molecular similarity based on novel atom type electrotopological state indices . J. Chem. Inf. Comput. Sci. , 35 : 1074 – 1080 .
   Google Scholar
• Hall , LH and Kier , LB . 2001 . Issues in the representation of molecular structure: the development of molecular connectivity . J. Mol. Model. Graphics , 20 : 4 – 18 .
   Google Scholar
• Shen , MS , LeTiran , A , Xiao , Y , Kohn , H and Tropsha , A . 2002 . QSAR analysis of functionalized amino acid anticonvulsant agents using k-nearest neighbor and simulated annealing-PLS methods . J. Med. Chem. , 45 : 2811 – 2823 .
   PubMed Web of Science ®Google Scholar
• Golbraikh , A , Bonchev , D and Tropsha , A . 2002 . Novel Z/E-isomerism descriptors derived from molecular topology and their application to QSAR analysis . J. Chem. Inf. Comput. Sci. , 42 : 769 – 787 .
   PubMedGoogle Scholar
• Hall LH Kier LB 1999 The Kappa indices for modeling molecular shape and flexibility Devillers J Balaban AT Topological Indices and Related Descriptors in QSAR and QSPR, Gordon and Breach Reading, UK 491 562
   Google Scholar
• Kier LB Hall LH 2001 Database organization and similarity searching with E-state indices Carbo-Dorca R Symposium on Computer Methods for Structure Representation, Kluwer Academic Publishing Co. New York 33 49
   Google Scholar
• Kier , LB and Hall , LH . 2000 . Intermolecular accessibility: the meaning of molecular connectivity . J. Chem. Inf. Comput. Sci. , 40 : 792 – 795 .
   PubMedGoogle Scholar
• Kier , LB and Hall , LH . 2001 . Molecular connectivity: intermolecular accessibility and encounter simulation . J. Mol. Model. Graphics , 20 : 76 – 83 .
   Google Scholar
• Kier , LB . 1980 . Structural information from molecular connectivity 4χPC index . J. Pharm. Sci. , 69 : 1034 – 1039 .
   PubMedGoogle Scholar
• Votano , JR , Parham , M , Hall , LH , Kier , LB and Hall , LM . New predictors for several ADME/Tox properties: aqueous solubility, human oral absorption, and Ames genotoxicity using topological descriptors . J. Mol. Divers. , 8 385 – 397 .
   Google Scholar
• Huuskonen , J , Salo , M and Taskinen , J . 1997 . Neural network modeling for estimation of the aqueous solubility of structurally related drugs . J. Pharm. Sci. , 86 : 450 – 454 .
   PubMed Web of Science ®Google Scholar
• Huuskonen , J , Salo , M and Taskinen , J . 1998 . Aqueous solubility prediction of drugs based on molecular topology and neural network modeling . J. Chem. Inf. Comput. Sci. , 38 : 450 – 456 .
   PubMedGoogle Scholar
• Huuskonen , J . 2000 . Estimation of aqueous solubility for a diverse set of organic compounds based on molecular topology . J. Chem. Inf. Comput. Sci. , 40 : 773 – 777 .
   PubMedGoogle Scholar
• Lobell , M and Sivarajah , V . 2003 . In silico prediction of aqueous solubility, human plasma protein binding, and volume distribution from calculated pKa and AlogP98 values . J. Mol. Divers. , 7 : 69 – 87 .
   PubMed Web of Science ®Google Scholar
• Ertl , P , Rohde , B and Selzer , P . 2000 . Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of transport properties . J. Med. Chem. , 43 : 3714 – 3717 .
   PubMed Web of Science ®Google Scholar
• Winiwarter , SF , Lennernas , H , Hallberg , A , Pettersson , C and Karlen , A . 2003 . Hydrogen bonding descriptors in the prediction of human in vivo intestinal permeability . J. Mol. Graph , 21 : 273 – 287 .
   Google Scholar
• Wessel , D , Jurs , P , Tolan , J and Muskal , S . 1998 . Prediction of human intestinal absorption of drug compounds from molecular structure . J. Chem. Inf. Comput. Sci. , 38 : 726 – 735 .
   PubMedGoogle Scholar
• Derety , E , Feher , M and Schmidt , J . 2000 . Rapid prediction of human intestinal absorption . Quant. Struct. Act. Relat. , 21 : 493 – 505 .
   Google Scholar
• Raevsky , O , Fetisov , V , Trepalina , E , McFarland , J and Schaper , K . 2000 . Quantitative estimation of drug absorption in humans for passively transported compounds and the basis of their physico-chemical parameters . Quant. Struct. Act. Relat. , 19 : 366 – 374 .
   Google Scholar
• Mattioni , BE , Kauffman , GW and Jurs , PC . 2003 . Predicting the genotoxicity of secondary and aromatic amines using data subsetting to generate a model ensemble . J. Chem. Inf. Comput. Sci. , 43 : 949 – 963 .
   PubMedGoogle Scholar
• Votano , JR , Parham , M , Hall , HH , Kier , LB , Oloff , S , Tropsha , A , Tonga , W and Xie , Q . 2004 . Three new QSAR consensus models for prediction of Ames mutagenicity . Mutagenesis , 19 : 365 – 378 .
   PubMed Web of Science ®Google Scholar
• Robert , D and Carbo-Dorca , R . 1999 . Aromatic compounds aquatic toxicity QSAR using molecular quantum similarity measures . SAR QSAR Environ. Res. , 10 : 401 – 422 .
   Web of Science ®Google Scholar
• Verhaar, H.J.M., Mulder, W., Hermens, J.L.M., Rorije, E., Langenberg, J.H., Peijnenberg, W.J.G.M., Sabljic, A., Gusten, H., Eriksson, L., Sjostrom, M., Hansen, B., Nouwen, J. and Karcher, W. (1995) Overview of Structure–Activity Relationships for Environmental Endpoints. Part 1: General Outline and Procedure. Report of the EU-DG-XII Project QSAR for Predicting Fate and Effects of Chemicals in the Environment. (Contract #EV3V-CT92-0211)
   Google Scholar
• Rose , K and Hall , LH . 2002 . E-state modeling of fish toxicity independent of 3D structure information . J. Chem. Inf. Comput. Sci. , 42 : 651 – 666 .
   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 : 290 – 298 .
   PubMedGoogle Scholar
• Holloway , MK , Wai , JM , Halgren , TA , Fitzgerald , PMD , Vacca , JP , Dorsey , BD , Levin , RB , Thompsom , WJ , Chen , J , deSolms , SJ , Gaffin , N , Ghosh , AK , Giuliani , EA , Graham , SL , Guare , JP , Hungate , RW , Lyle , TA , Sanders , WM , Tucker , TJ , Wiggins , M , Wiscount , CM , Woltersdorf , OW , Young , SD , Darke , PL and Zugay , J . 1995 . A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site . J. Med. Chem. , 38 : 305 – 317 .
   PubMed Web of Science ®Google Scholar
• Kellogg , GE , Kier , LB , Gaillard , P and Hall , LH . 1996 . The E-state fields. Application to QSAR . J. Comp. Aid. Mol. Des. , 10 : 513 – 520 .
   PubMed Web of Science ®Google Scholar