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Volumn 8, Issue 1, 2005, Pages 32-37

Recent uses of topological indices in the development of in silico ADMET models

Author keywords

ADMET; Genotoxicity; Human intestinal absorption; In silico; Mutagenicity; Topological indices

Indexed keywords

CLASTOGEN; CYTOCHROME P450; DRUG;

EID: 12244285670     PISSN: 13676733     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review
Times cited : (17)

References (30)
  • 1
    • 3242885550 scopus 로고    scopus 로고
    • Predictive ADMET studies, the challenges and opportunities
    • Davis AM, Riley RJ: Predictive ADMET studies, the challenges and opportunities. Curr Opin Chem Biol (2004) 8(4):378-386.
    • (2004) Curr Opin Chem Biol , vol.8 , Issue.4 , pp. 378-386
    • Davis, A.M.1    Riley, R.J.2
  • 2
    • 2942620237 scopus 로고    scopus 로고
    • Building predictive ADMET models for early decisions in drug discovery
    • Penzotti JE, Landrum GA, Putta S: Building predictive ADMET models for early decisions in drug discovery. Curr Opin Drug Discovery Dev (2004) 7(1):49-61.
    • (2004) Curr Opin Drug Discovery Dev , vol.7 , Issue.1 , pp. 49-61
    • Penzotti, J.E.1    Landrum, G.A.2    Putta, S.3
  • 4
    • 0037364162 scopus 로고    scopus 로고
    • ADMET in silico modeling towards prediction paradise?
    • Van de Waterbeemd H, Gifford E: ADMET in silico modeling towards prediction paradise? Nat Rev Drug Disc (2003) 2(3):192-204.
    • (2003) Nat Rev Drug Disc , vol.2 , Issue.3 , pp. 192-204
    • Van De Waterbeemd, H.1    Gifford, E.2
  • 5
    • 0004100524 scopus 로고    scopus 로고
    • Academic Press, San Diego, CA, USA
    • Kier LB, Hall LH: Molecular Structure Description: The Electrotopological State. Academic Press, San Diego, CA, USA (1999). An excellent book for readers interested in Kier-Hall topological indices, which includes a CD-ROM giving many numerical examples of the different classes of topological indices and a small computer program to compute many of them.
    • (1999) Molecular Structure Description: The Electrotopological State
    • Kier, L.B.1    Hall, L.H.2
  • 7
    • 0032841864 scopus 로고    scopus 로고
    • The correlation and prediction of the solubility of compounds in water using an amended solvation energy relationship
    • Abraham MH, Le J: The correlation and prediction of the solubility of compounds in water using an amended solvation energy relationship. J Pharm Sci (1999) 88(9):868-880.
    • (1999) J Pharm Sci , vol.88 , Issue.9 , pp. 868-880
    • Abraham, M.H.1    Le, J.2
  • 8
    • 0028974572 scopus 로고
    • AQUAFAC 3: Aqueous functional group activity coefficients; application to the estimation of aqueous solubility
    • Myrdal PB, Manka AM, Yalkowsky SH: AQUAFAC 3: Aqueous functional group activity coefficients; application to the estimation of aqueous solubility. Chemosphere (1995) 30:1619-1637.
    • (1995) Chemosphere , vol.30 , pp. 1619-1637
    • Myrdal, P.B.1    Manka, A.M.2    Yalkowsky, S.H.3
  • 9
    • 3042781869 scopus 로고    scopus 로고
    • In silico ADME predictions: Data, models, facts and myths
    • Lombardo F, Gifford E, Shalaeva MY: In silico ADME predictions: Data, models, facts and myths. Mini Rev Med Chem (2003) 3(8):861-875. A good review of ADME models covering the types and limitations of models, including comments on various published ADME models.
    • (2003) Mini Rev Med Chem , vol.3 , Issue.8 , pp. 861-875
    • Lombardo, F.1    Gifford, E.2    Shalaeva, M.Y.3
  • 10
  • 11
    • 0041731599 scopus 로고    scopus 로고
    • Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships
    • Cheng A, Merz KM Jr: Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships. J Med Chem (2003) 46(17):3572-3580. Paper containing important topological indices that influence aqueous solubility, and provides a breakdown of the functional groups used and gives a comparison of predicted solubilities of drugs to drug-like compounds found in the Comprehensive Medical Chemistry (CMC) database.
    • (2003) J Med Chem , vol.46 , Issue.17 , pp. 3572-3580
    • Cheng, A.1    Merz Jr., K.M.2
  • 13
    • 6444225736 scopus 로고    scopus 로고
    • Prediction of aqueous solubility based on large datasets using several QSPR models utilizing topological structure representation
    • Votano JR, Parham M, Hall LH, Kier LB, Hall LM: Prediction of aqueous solubility based on large datasets using several QSPR models utilizing topological structure representation. Chem Biodivers (2004) 1(11):1829-1841. Paper providing a comprehensive breakdown of compound attributes, relating and describing important topological indices affecting the water solubility of a compound, and comparing results from various QSAR modeling algorithms.
    • (2004) Chem Biodivers , vol.1 , Issue.11 , pp. 1829-1841
    • Votano, J.R.1    Parham, M.2    Hall, L.H.3    Kier, L.B.4    Hall, L.M.5
  • 14
    • 4043112686 scopus 로고    scopus 로고
    • Global and local computational models for aqueous solubility prediction of drug-like molecules
    • Bergstrom CA, Wassvik CM, Norinder U, Luthman K, Artursson P: Global and local computational models for aqueous solubility prediction of drug-like molecules. J Chem Inf Comput Sci (2004) 44(4):1477-1488.
    • (2004) J Chem Inf Comput Sci , vol.44 , Issue.4 , pp. 1477-1488
    • Bergstrom, C.A.1    Wassvik, C.M.2    Norinder, U.3    Luthman, K.4    Artursson, P.5
  • 15
    • 0037208305 scopus 로고    scopus 로고
    • Using general regression and probabilistic neural networks to predict human intestinal absorption with topological descriptors derived from two-dimensional chemical structures
    • 2003
    • Niwa T: Using general regression and probabilistic neural networks to predict human intestinal absorption with topological descriptors derived from two-dimensional chemical structures. (2003) J Chem Inf Comput Sci (2003) 43(1):113-119.
    • (2003) J Chem Inf Comput Sci , vol.43 , Issue.1 , pp. 113-119
    • Niwa, T.1
  • 16
    • 0032811868 scopus 로고    scopus 로고
    • Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 2. Prediction of blood-brain barrier penetration
    • Clark DE: Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 2. Prediction of blood-brain barrier penetration. J Pharm Sci (1999) 88(8):815-821.
    • (1999) J Pharm Sci , vol.88 , Issue.8 , pp. 815-821
    • Clark, D.E.1
  • 17
    • 8544284073 scopus 로고    scopus 로고
    • New predictors for several ADME/Tox properties: Aqueous solubility, human oral absorption and Ames genotoxicity using topological descriptors
    • Votano JR, Parham M, Hall LH, Kier LB: New predictors for several ADME/Tox properties: Aqueous solubility, human oral absorption and Ames genotoxicity using topological descriptors. Mol Divers (2004) 8:385-397. In this study, the large number of compounds used and the trend analysis applied to important topological indices shed light on what types of functional groups enhance or diminish transcellular transport for drugs.
    • (2004) Mol Divers , vol.8 , pp. 385-397
    • Votano, J.R.1    Parham, M.2    Hall, L.H.3    Kier, L.B.4
  • 18
    • 0030914681 scopus 로고    scopus 로고
    • Polar molecular surface properties predict the intestinal absorption of drugs in humans
    • Palm K, Stenberg P, Luthman K, Artursson P: Polar molecular surface properties predict the intestinal absorption of drugs in humans. Pharm Res (1997) 14(5):568-571.
    • (1997) Pharm Res , vol.14 , Issue.5 , pp. 568-571
    • Palm, K.1    Stenberg, P.2    Luthman, K.3    Artursson, P.4
  • 19
    • 0035821601 scopus 로고    scopus 로고
    • Experimental and computational screening models for the prediction of intestinal drug absorption
    • Stenberg P, Norinder U, Luthman K, Artursson P: Experimental and computational screening models for the prediction of intestinal drug absorption. J Med Chem (2001) 44(12):1927-1937.
    • (2001) J Med Chem , vol.44 , Issue.12 , pp. 1927-1937
    • Stenberg, P.1    Norinder, U.2    Luthman, K.3    Artursson, P.4
  • 20
  • 21
    • 0036893593 scopus 로고    scopus 로고
    • Evaluation of cytochrome P450 probe substrates commonly used by the pharmaceutical industry to study in vitro drug interactions
    • Yuan R, Madani S, Wei XX, Reynolds K, Huang SM: Evaluation of cytochrome P450 probe substrates commonly used by the pharmaceutical industry to study in vitro drug interactions. Drug Metab Dispos (2002) 30(12):1311-1319.
    • (2002) Drug Metab Dispos , vol.30 , Issue.12 , pp. 1311-1319
    • Yuan, R.1    Madani, S.2    Wei, X.X.3    Reynolds, K.4    Huang, S.M.5
  • 22
    • 0038121705 scopus 로고    scopus 로고
    • Development and validation of k-nearest-neighbor QSPR models of metabolic stability of drug candidates
    • Shen M, Xiao Y, Golbraikh A, Gombar VJ, Tropsha A: Development and validation of k-nearest-neighbor QSPR models of metabolic stability of drug candidates. J Med Chem (2003) 46(14):3013-3020. A well-documented explanation of the kNN-QSAR methodology employed with topological indices to treat a complex problem.
    • (2003) J Med Chem , vol.46 , Issue.14 , pp. 3013-3020
    • Shen, M.1    Xiao, Y.2    Golbraikh, A.3    Gombar, V.J.4    Tropsha, A.5
  • 23
    • 0141789965 scopus 로고    scopus 로고
    • QSAR analysis of the inhibition of recombinant CYP 3A4 activity by structurally diverse compounds using partial least squares method
    • Wanchanna S, Yamashita F, Hashida M: QSAR analysis of the inhibition of recombinant CYP 3A4 activity by structurally diverse compounds using partial least squares method. Pharm Res (2003) 20(9):1401-1408.
    • (2003) Pharm Res , vol.20 , Issue.9 , pp. 1401-1408
    • Wanchanna, S.1    Yamashita, F.2    Hashida, M.3
  • 24
    • 0037325243 scopus 로고    scopus 로고
    • Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure
    • Serra JR, Thompson ED, Jurs PC: Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure. Chem Res Toxicol (2003) 16(2):153-163. Description of the use of two classification-based models, including a list of compounds. Of importance is the resulting small number of topological indices found to model clastogenicity.
    • (2003) Chem Res Toxicol , vol.16 , Issue.2 , pp. 153-163
    • Serra, J.R.1    Thompson, E.D.2    Jurs, P.C.3
  • 25
    • 0035012857 scopus 로고    scopus 로고
    • A review of the genotoxicity of marketed pharmaceuticals
    • Snyder RD, Green JW: A review of the genotoxicity of marketed pharmaceuticals. Mutat Res (2001) 488(2):151-169.
    • (2001) Mutat Res , vol.488 , Issue.2 , pp. 151-169
    • Snyder, R.D.1    Green, J.W.2
  • 26
    • 2442548465 scopus 로고    scopus 로고
    • Assessment of the sensitivity of the computational programs DEREK, TOPKAT and MCASE in the prediction of genotoxicity of pharmaceutical molecules
    • Snyder RD, Pearl GS, Mandakas G, Choy WN, Goodsaid F, Rosenblum IY: Assessment of the sensitivity of the computational programs DEREK, TOPKAT and MCASE in the prediction of genotoxicity of pharmaceutical molecules. Environ Mol Mutagen (2004) 43(3):143-158. An important review delineating the lack of sensitivity of fragments/alerts to predict genotoxic drugs, and including topological indices used with a regression model.
    • (2004) Environ Mol Mutagen , vol.43 , Issue.3 , pp. 143-158
    • Snyder, R.D.1    Pearl, G.S.2    Mandakas, G.3    Choy, W.N.4    Goodsaid, F.5    Rosenblum, I.Y.6
  • 27
    • 6444224986 scopus 로고    scopus 로고
    • Three new consensus QSAR models for the prediction of Ames genotoxicity
    • Votano JR, Parham M, Hall LH, Kier LB, Oloff S, Tropsha A, Xie Q, Tong W: Three new consensus QSAR models for the prediction of Ames genotoxicity. Mutagenesis (2004) 19(5):365-377. An exhaustive study centered on three unique modeling algorithms, relating topological descriptors to known fragments/alerts and comparing results. An analysis of functional groups is provided, and on-line validation compounds are given with predicted results.
    • (2004) Mutagenesis , vol.19 , Issue.5 , pp. 365-377
    • Votano, J.R.1    Parham, M.2    Hall, L.H.3    Kier, L.B.4    Oloff, S.5    Tropsha, A.6    Xie, Q.7    Tong, W.8
  • 28
    • 0037365123 scopus 로고    scopus 로고
    • Decision Forest: Combining the predictions of multiple independent decision tree models
    • Tong W, Hong H, Fang H, Xie Q, Perkins R: Decision Forest: Combining the predictions of multiple independent decision tree models. J Chem Inf Comput Sci (2003) 43(2):525-531.
    • (2003) J Chem Inf Comput Sci , vol.43 , Issue.2 , pp. 525-531
    • Tong, W.1    Hong, H.2    Fang, H.3    Xie, Q.4    Perkins, R.5
  • 29
    • 0000973407 scopus 로고
    • Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U. S. NTP
    • Ashby J, Tennant RW: Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U. S. NTP. Mutat Res (1991) 257(3):229-306.
    • (1991) Mutat Res , vol.257 , Issue.3 , pp. 229-306
    • Ashby, J.1    Tennant, R.W.2
  • 30
    • 0242624535 scopus 로고    scopus 로고
    • Predicting the carcinogenic potential of pharmaceuticals in rodents using molecular structural similarity and E-state indices
    • Contrera JF, Matthews EJ, Benz RD: Predicting the carcinogenic potential of pharmaceuticals in rodents using molecular structural similarity and E-state indices. Regul Toxicol Pharmcol (2003) 38(3):243-259.
    • (2003) Regul Toxicol Pharmcol , vol.38 , Issue.3 , pp. 243-259
    • Contrera, J.F.1    Matthews, E.J.2    Benz, R.D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.