메뉴 건너뛰기




Volumn 51, Issue 7, 2011, Pages 1667-1689

RS-predictor: A new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4

Author keywords

[No Author keywords available]

Indexed keywords

FORECASTING; METABOLISM; METABOLITES; QUANTUM CHEMISTRY; REGIOSELECTIVITY; SUBSTRATES;

EID: 79960704005     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci2000488     Document Type: Article
Times cited : (83)

References (47)
  • 1
    • 0033828231 scopus 로고    scopus 로고
    • The Evolution of Drug Metabolism
    • Nebert, D. W.; Dieter, M. Z. The Evolution of Drug Metabolism Pharmacology 2000, 61, 124-135
    • (2000) Pharmacology , vol.61 , pp. 124-135
    • Nebert, D.W.1    Dieter, M.Z.2
  • 2
    • 0037068964 scopus 로고    scopus 로고
    • Clinical importance of the cytochromes P450
    • DOI 10.1016/S0140-6736(02)11203-7
    • Nebert, D. W.; Russell, D. W. Clinical importance of the cytochromes P450 Lancet 2002, 360, 1155-1162 (Pubitemid 35246494)
    • (2002) Lancet , vol.360 , Issue.9340 , pp. 1155-1162
    • Nebert, D.W.1    Russell, D.W.2
  • 3
    • 33645050104 scopus 로고    scopus 로고
    • Cytochrome P450s and other enzymes in drug metabolism and toxicity
    • Guengerich, F. P. Cytochrome P450s and other enzymes in drug metabolism and toxicity AAPS J. 2006, 8, E101-E111
    • (2006) AAPS J. , vol.8
    • Guengerich, F.P.1
  • 6
    • 33646764551 scopus 로고    scopus 로고
    • Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions
    • DOI 10.1124/dmd.105.008631
    • Zhou, D.; Afzelius, L.; Grimm, S. W.; Andersson, T. B.; Zauhar, R. J.; Zamora, I. Comparison of methods for the predictions of the metabolic sites for CYP3A4-mediated metabolic reactions Drug Metab. Dispos. 2006, 34, 976-983 (Pubitemid 43763754)
    • (2006) Drug Metabolism and Disposition , vol.34 , Issue.6 , pp. 976-983
    • Zhou, D.1    Afzelius, L.2    Grimm, S.W.3    Andersson, T.B.4    Zauhar, R.J.5    Zamora, I.6
  • 7
    • 0029083319 scopus 로고
    • Acetaminophen (paracetamol) hepatotoxicity with regular intake of alcohol: Analysis of instances of therapeutic misadventure
    • Zimmerman, H. J.; Maddrey, W. C. Acetaminophen (paracetamol) hepatotoxicity with regular intake of alcohol: Analysis of instances of therapeutic misadventure Hepatology 1995, 22, 767-773
    • (1995) Hepatology , vol.22 , pp. 767-773
    • Zimmerman, H.J.1    Maddrey, W.C.2
  • 8
    • 34547679825 scopus 로고    scopus 로고
    • Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates
    • DOI 10.1021/ci700010t
    • Terfloth, L.; Bienfait, B.; Gasteiger, J. Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates J. Chem. Inf. Model. 2007, 47, 1688-1701 (Pubitemid 47210071)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.4 , pp. 1688-1701
    • Terfloth, L.1    Bienfait, B.2    Gasteiger, J.3
  • 9
    • 23844460948 scopus 로고    scopus 로고
    • Prediction of cytochrome P450 3A4, 2D6, and 2C9 inhibitors and substrates by using support vector machines
    • DOI 10.1021/ci0500536
    • Yap, C. W.; Chen, Y. Z. Prediction of cytochrome P450 3A4, 2D6, and 2C9 inhibitors and substrates by using support vector machines J. Chem. Inf. Model. 2005, 45, 982-992 (Pubitemid 41156697)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.4 , pp. 982-992
    • Yap, C.W.1    Chen, Y.Z.2
  • 10
    • 17444411955 scopus 로고    scopus 로고
    • Cytochrome P450 in silico: An integrative modeling approach
    • DOI 10.1021/jm040180d
    • de Graaf, C.; Vermeulen, N. P. E.; Feenstra, K. A. Cytochrome P450 in silico: an integrative modeling approach J. Med. Chem. 2005, 48, 2725-2755 (Pubitemid 40548088)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.8 , pp. 2725-2755
    • De Graaf, C.1    Vermeulen, N.P.E.2    Feenstra, K.A.3
  • 11
    • 33745741280 scopus 로고    scopus 로고
    • Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs
    • DOI 10.1016/j.ejmech.2006.03.003, PII S0223523406000791
    • Crivori, P.; Poggesi, I. Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs Eur. J. Med. Chem. 2006, 41, 795-808 (Pubitemid 44015977)
    • (2006) European Journal of Medicinal Chemistry , vol.41 , Issue.7 , pp. 795-808
    • Crivori, P.1    Poggesi, I.2
  • 12
    • 33748124863 scopus 로고    scopus 로고
    • Machine learning techniques for in silico modeling of drug metabolism
    • DOI 10.2174/156802606778108915
    • Fox, T.; Kriegl, J. M. Machine learning techniques for in silico modeling of drug metabolism Curr. Top. Med. Chem. 2006, 6, 1579-1591 (Pubitemid 44304616)
    • (2006) Current Topics in Medicinal Chemistry , vol.6 , Issue.15 , pp. 1579-1591
    • Fox, T.1    Kriegl, J.M.2
  • 14
    • 45249121177 scopus 로고    scopus 로고
    • Drugs behave as substrates, inhibitors and inducers of human cytochrome P450 3A4
    • DOI 10.2174/138920008784220664
    • Zhou, S. Drugs behave as substrates, inhibitors and inducers of human cytochrome P450 3A4 Curr. Drug. Metab. 2008, 9, 310-322 (Pubitemid 351836420)
    • (2008) Current Drug Metabolism , vol.9 , Issue.4 , pp. 310-322
    • Zhou, S.-F.1
  • 15
    • 54249099193 scopus 로고    scopus 로고
    • Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors
    • Kontijevskis, A.; Komorowski, J.; Wikberg, J. E. S. Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors J. Chem. Inf. Model. 2008, 48, 1840-1850
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 1840-1850
    • Kontijevskis, A.1    Komorowski, J.2    Wikberg, J.E.S.3
  • 16
    • 33845772311 scopus 로고    scopus 로고
    • Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
    • DOI 10.1021/ci600267k
    • Bazeley, P. S.; Prithivi, S.; Struble, C. A.; Povinelli, R. J.; Sem, D. S. Synergistic use of compound properties and docking scores n neural network modeling of CYP2D6 binding: predicting affinity and conformational sampling J. Chem. Inf. Model. 2006, 46, 2698-2708 (Pubitemid 46008139)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2698-2708
    • Bazeley, P.S.1    Prithivi, S.2    Struble, C.A.3    Povinelli, R.J.4    Sem, D.S.5
  • 17
    • 0036136527 scopus 로고    scopus 로고
    • Computational models for cytochrome P450: A predictive electronic model for aromatic oxidation and hydrogen atom abstraction
    • DOI 10.1124/dmd.30.1.7
    • Jones, J. P.; Mysinger, M.; Korzekwa, K. R. Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction Drug Metab. Dispos. 2002, 30, 7-12 (Pubitemid 34016934)
    • (2002) Drug Metabolism and Disposition , vol.30 , Issue.1 , pp. 7-12
    • Jones, J.P.1    Mysinger, M.2    Korzekwa, K.R.3
  • 18
    • 0037431382 scopus 로고    scopus 로고
    • A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules
    • DOI 10.1021/jm020400s
    • Singh, S. B.; Shen, L. Q.; Walker, M. J.; Sheridan, R. P. A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules J. Med. Chem. 2003, 46, 1330-6 (Pubitemid 36512698)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.8 , pp. 1330-1336
    • Singh, S.B.1    Shen, L.Q.2    Walker, M.J.3    Sheridan, R.P.4
  • 19
    • 34447515639 scopus 로고    scopus 로고
    • Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9
    • DOI 10.1021/jm0613471
    • Sheridan, R. P.; Korzekwa, K. R.; Torres, R. A.; Walker, M. J. Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9 J. Med. Chem. 2007, 50, 3173-3184 (Pubitemid 47065966)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.14 , pp. 3173-3184
    • Sheridan, R.P.1    Korzekwa, K.R.2    Torres, R.A.3    Walker, M.J.4
  • 20
    • 60549087116 scopus 로고    scopus 로고
    • SPORCalc: A development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design
    • Smith, J.; Stein, V. SPORCalc: A development of a database analysis that provides putative metabolic enzyme reactions for ligand-based drug design Comput. Biol. Chem. 2009, 33, 149-159
    • (2009) Comput. Biol. Chem. , vol.33 , pp. 149-159
    • Smith, J.1    Stein, V.2
  • 21
    • 65549103878 scopus 로고    scopus 로고
    • Site of metabolism prediction for six biotransformations mediated by cytochromes P450
    • Zheng, M.; Luo, X.; Shen, Q.; Wang, Y.; Du, Y.; Zhu, W.; Jiang, H. Site of metabolism prediction for six biotransformations mediated by cytochromes P450 Bioinformatics 2009, 25, 1251-1258
    • (2009) Bioinformatics , vol.25 , pp. 1251-1258
    • Zheng, M.1    Luo, X.2    Shen, Q.3    Wang, Y.4    Du, Y.5    Zhu, W.6    Jiang, H.7
  • 22
    • 65549171233 scopus 로고    scopus 로고
    • CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory
    • Hennemann, M.; Friedl, A.; Lobell, M.; Keldenich, J.; Hillisch, A.; Clark, T.; Göller, A. H. CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory ChemMedChem 2009, 4, 657-669
    • (2009) ChemMedChem , vol.4 , pp. 657-669
    • Hennemann, M.1    Friedl, A.2    Lobell, M.3    Keldenich, J.4    Hillisch, A.5    Clark, T.6    Göller, A.H.7
  • 23
  • 24
    • 77953932263 scopus 로고    scopus 로고
    • SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism
    • Rydberg, P.; Gloriam, D. E.; Zaretzki, J.; Breneman, C.; Olsen, L. SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism ACS Med. Chem. Lett. 2010, 1, 96-100
    • (2010) ACS Med. Chem. Lett. , vol.1 , pp. 96-100
    • Rydberg, P.1    Gloriam, D.E.2    Zaretzki, J.3    Breneman, C.4    Olsen, L.5
  • 25
    • 0033533750 scopus 로고    scopus 로고
    • A novel approach to predicting P450 mediated drug metabolism. CYP2D6 catalyzed N-dealkylation reactions and qualitative metabolite predictions using a combined protein and pharmacophore model for CYP2D6
    • DOI 10.1021/jm991058v
    • de Groot, M. J.; Ackland, M. J.; Horne, V. A.; Alex, A. A.; Jones, B. C. A novel approach to predicting P450 mediated drug metabolism. CYP2D6 catalyzed N-Dealkylation reactions and qualitative metabolite predictions using a combined protein and pharmacophore model for CYP2D6 J. Med. Chem. 1999, 42, 4062-4070 (Pubitemid 29483023)
    • (1999) Journal of Medicinal Chemistry , vol.42 , Issue.20 , pp. 4062-4070
    • De Groot, M.J.1    Ackland, M.J.2    Horne, V.A.3    Alex, A.A.4    Jones, B.C.5
  • 26
    • 0037464481 scopus 로고    scopus 로고
    • Construction and assessment of models of CYP2E1: Predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations
    • DOI 10.1021/jm020538a
    • Park, J.; Harris, D. Construction and assessment of models of CYP2E1: predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations J. Med. Chem. 2003, 46, 1645-60 (Pubitemid 36444218)
    • (2003) Journal of Medicinal Chemistry , vol.46 , Issue.9 , pp. 1645-1660
    • Park, J.-Y.1    Harris, D.2
  • 28
    • 42149138057 scopus 로고    scopus 로고
    • New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism
    • DOI 10.1021/ci7003576
    • Oh, W. S.; Kim, D. N.; Jung, J.; Cho, K.; No, K. T. New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism J. Chem. Inf. Model. 2008, 48, 591-601 (Pubitemid 351535427)
    • (2008) Journal of Chemical Information and Modeling , vol.48 , Issue.3 , pp. 591-601
    • Oh, W.S.1    Kim, D.N.2    Jung, J.3    Cho, K.-H.4    No, K.T.5
  • 29
    • 79960745682 scopus 로고    scopus 로고
    • StarDrop, version 4.2.1; Optibrium Ltd.: Cambridge, United Kingdom
    • StarDrop, version 4.2.1; Optibrium Ltd.: Cambridge, United Kingdom, 2009.
    • (2009)
  • 30
    • 79960731486 scopus 로고    scopus 로고
    • MetaSite user manual. (accessed March 23, 2011)
    • MetaSite user manual. http://www.moldiscovery.com/docs/metasite/ background.html (accessed March 23, 2011).
  • 31
    • 56449128429 scopus 로고    scopus 로고
    • In Proceedings of the 25th ICML, Helsinki, Finland, 2008; ACM: New York, NY
    • Bergeron, C.; Zaretzki, J.; Breneman, C.; Bennett, K. P. Multiple instance ranking. In Proceedings of the 25th ICML, Helsinki, Finland, 2008; ACM: New York, NY, 2008; Vol. 307, pp 48-55.
    • (2008) Multiple Instance Ranking , vol.307 , pp. 48-55
    • Bergeron, C.1    Zaretzki, J.2    Breneman, C.3    Bennett, K.P.4
  • 32
    • 0036223831 scopus 로고    scopus 로고
    • Summary of information on human CYP enzymes: Human P450 metabolism data
    • DOI 10.1081/DMR-120001392
    • Rendic, S. Summary of information on human CYP enzymes: human P450 metabolism data Drug Metab. Rev. 2002, 34, 83-448 (Pubitemid 34311090)
    • (2002) Drug Metabolism Reviews , vol.34 , Issue.1-2 , pp. 83-448
    • Rendic, S.1
  • 33
    • 38949204984 scopus 로고    scopus 로고
    • Cytochromes P450: A structure-based summary of biotransformations using representative substrates
    • DOI 10.1080/03602530701836662, PII 790484200
    • Brown, C. M.; Reisfeld, B.; Mayeno, A. N. Cytochromes P450: a structure-based summary of biotransformations using representative substrates Drug Metab. Rev. 2008, 40, 1-100 (Pubitemid 351220646)
    • (2008) Drug Metabolism Reviews , vol.40 , Issue.1 , pp. 1-100
    • Brown, C.M.1    Reisfeld, B.2    Mayeno, A.N.3
  • 35
    • 79960722648 scopus 로고    scopus 로고
    • MOE, version 2009.10; Chemical Computing Group: Montreal, Canada
    • MOE, version 2009.10; Chemical Computing Group: Montreal, Canada, 2009.
    • (2009)
  • 36
    • 0001509942 scopus 로고    scopus 로고
    • Prediction of physicochemical parameters by atomic contributions
    • Wildman, S. A.; Crippen, G. M. Prediction of physicochemical parameters by atomic contributions J. Chem. Inf. Comput. Sci. 1999, 39, 868-873
    • (1999) J. Chem. Inf. Comput. Sci. , vol.39 , pp. 868-873
    • Wildman, S.A.1    Crippen, G.M.2
  • 37
    • 0027662829 scopus 로고
    • PATTY: A programmable atom type and language for automatic classification of atoms in molecular databases
    • Bush, B. L.; Sheridan, R. P. PATTY: A programmable atom type and language for automatic classification of atoms in molecular databases J. Chem. Inf. Comput. Sci. 1993, 33, 756-762
    • (1993) J. Chem. Inf. Comput. Sci. , vol.33 , pp. 756-762
    • Bush, B.L.1    Sheridan, R.P.2
  • 38
    • 0025390935 scopus 로고
    • MOPAC: A semiempirical molecular orbital program
    • Stewart, J. J. P. MOPAC: A semiempirical molecular orbital program J. Comput.-Aided Mol. Des. 1990, 4, 1-103
    • (1990) J. Comput.-Aided Mol. Des. , vol.4 , pp. 1-103
    • Stewart, J.J.P.1
  • 41
    • 78649494564 scopus 로고    scopus 로고
    • Consensus Ranking Approach to Understanding the Underlying Mechanism with QSAR
    • Shao, L.; Wu, L.; Fan, X.; Cheng, Y. Consensus Ranking Approach to Understanding the Underlying Mechanism With QSAR J. Chem. Inf. Model. 2010, 50, 1941-1948
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1941-1948
    • Shao, L.1    Wu, L.2    Fan, X.3    Cheng, Y.4
  • 42
    • 77955622534 scopus 로고    scopus 로고
    • An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data
    • Datta, S.; Pihur, V.; Datta, S. An adaptive optimal ensemble classifier via bagging and rank aggregation with applications to high dimensional data BMC Bioinf. 2010, 11, 427
    • (2010) BMC Bioinf. , vol.11 , pp. 427
    • Datta, S.1    Pihur, V.2    Datta, S.3
  • 43
    • 84880349211 scopus 로고    scopus 로고
    • In Proceedings of the 11th ALENEX, New York, New York, 2009; SIAM: Philadelphia, PA
    • Schalekamp, F.; Zuylen, A. Rank Aggregation: Together We're Strong. In Proceedings of the 11th ALENEX, New York, New York, 2009; SIAM: Philadelphia, PA, 2009; pp 38-51.
    • (2009) Rank Aggregation: Together we'Re Strong , pp. 38-51
    • Schalekamp, F.1    Zuylen, A.2
  • 44
    • 85049919974 scopus 로고    scopus 로고
    • In Proceedings of the 10th International Conference on the WWW. Hong Kong, Hong Kong, 2001; ACM: New York, NY
    • Dwork, C.; Kumar, R.; Naor, M.; Sivakumar, D. Rank Aggregation Methods for the Web. In Proceedings of the 10th International Conference on the WWW. Hong Kong, Hong Kong, 2001; ACM: New York, NY, 2001; pp 613-622.
    • (2001) Rank Aggregation Methods for the Web , pp. 613-622
    • Dwork, C.1    Kumar, R.2    Naor, M.3    Sivakumar, D.4
  • 45
    • 70449119813 scopus 로고    scopus 로고
    • In Proceedings of the Seventh SIAM International Conference on Data Mining. Minneapolis, Minnesota, 2007; SIAM: Philadelphia, PA
    • Sculley, D. Rank Aggregation for Similar Items. In Proceedings of the Seventh SIAM International Conference on Data Mining. Minneapolis, Minnesota, 2007; SIAM: Philadelphia, PA, 2007.
    • (2007) Rank Aggregation for Similar Items
    • Sculley, D.1
  • 47
    • 35348860833 scopus 로고    scopus 로고
    • In Proceedings of the 16th International Conference on WWW, Banff, Alberta, 2007; ACM: New York, NY
    • Liu, Y.; Liu, T.; Qin, T.; Ma, Z.; Li, H. Supervised Rank Aggregation. In Proceedings of the 16th International Conference on WWW, Banff, Alberta, 2007; ACM: New York, NY, 2007; pp 481-490.
    • (2007) Supervised Rank Aggregation , pp. 481-490
    • Liu, Y.1    Liu, T.2    Qin, T.3    Ma, Z.4    Li, H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.