A support vector machine approach to classify human cytochrome P450 3A4 inhibitors

Journal of Computer-Aided Molecular Design

Volumn 19, Issue 3, 2005, Pages 189-201

  Kriegl, Jan M ^a   Arnhold, Thomas ^a   Beck, Bernd ^a   Fox, Thomas ^a  

^a BOEHRINGER INGELHEIM PHARMA GMBH AND CO KG   (Germany)

Author keywords

ADME; CytochromeP450; In silico filter; Molecular descriptor; QSAR; Support vector machine

Indexed keywords

BANDPASS FILTERS; COMPUTATIONAL CHEMISTRY; DRUG INTERACTIONS; ENZYME INHIBITION; STATISTICAL TESTS;

ADME; CYTOCHROMEP450; DESCRIPTORS; IN SILICO FILTER; IN-SILICO; KERNEL FUNCTION; MOLECULAR DESCRIPTORS; QSAR; SUPPORT VECTORS MACHINE; TEST SETS;

SUPPORT VECTOR MACHINES;

CYTOCHROME P450 3A4; CYTOCHROME P450 INHIBITOR;

ARTICLE; COMPUTER AIDED DESIGN; COMPUTER MODEL; COMPUTER PROGRAM; DISCRIMINANT ANALYSIS; ENZYME INHIBITION; MULTIVARIATE ANALYSIS; PRIORITY JOURNAL; QUANTUM MECHANICS; REGRESSION ANALYSIS;

EID: 22144466197     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-005-3785-3     Document Type: Article

References (54)

1. D.F. Lewis 2003 Curr. Med. Chem. 10 195510.2174/0929867033456855 1:CAS:528:DC%2BD3sXnslyqtbo%3D 12871098
2. P.B. Danielson 2002 Curr. Drug Metab. 3 56110.2174/1389200023337054 1:CAS:528:DC%2BD38XoslKiu7s%3D 12369887
3. S. Rendic and F.J. Di Carlo 1997 Drug Metab. Rev. 29 4131:CAS:528:DyaK2sXkt1Onur8%3D 9187528
4. S.A. Wrighton E.G. Schuetz K.E. Thummel D.D. Shen K.R. Korzekwa and P.B. Watkins 2000 Drug Metab. Rev. 32 33910.1081/DMR-100102338 1:CAS:528:DC%2BD3MXjsFCmsw%3D%3D 11139133
5. V.P. Miller D.M. Stresser A.P. Blanchard S. Turner and C.L. Crespi 2000 Ann. NewYork Acad. Sci. 919 261:CAS:528:DC%2BD3cXosFSktL0%3D
6. K.M. Jenkins R. Angeles M.T. Quintos R. Xu D.B. Kassel and R.A. Rourick 2004 J. Pharm. Biomed. Anal. 34 98910.1016/j.jpba.2003.08.001 1:CAS:528:DC%2BD2cXhslWmtro%3D 15019033
7. H.-J. Böhm and G. Schneider 2000 Virtual Screening for Bioactive Molecules Wiley-VCH New York
8. G.A. Schoch J.K. Yano M.R. Wester K.J. Griffin C.D. Stout and E.F. Johnson 2004 J. Biol. Chem. 279 949710.1074/jbc.M312516200 1:CAS:528:DC%2BD2cXhs1Omt78%3D 14676196
9. G.D. Szklarz and J.R. Halpert 1998 Drug Metab Dispos. 26 11791:CAS:528:DyaK1MXhvFCqtg%3D%3D 9860924
10. M.R. Wester E.F. Johnson C. Marques-Soares P.M. Dansette D. Mansuy and C.D. Stout 2003 Biochemistry 42 637010.1021/bi0273922 1:CAS:528:DC%2BD3sXjsVOhurs%3D 12767218
11. P.A. Williams J. Cosme A. Ward H.C. Angove D.M. Vinković and H. Jhoti 2003 Nature 424 46410.1038/nature01862 1:CAS:528:DC%2BD3sXls1aqtrk%3D 12861225
12. P.A. Williams J. Cosme D.M. Vinković A. Ward H.C. Angove P.J. Day C. Vonrhein I.J. Tickle and H. Jhoti 2004 Science 305 68310.1126/ science.1099736 1:CAS:528:DC%2BD2cXmtFWqsrY%3D 15256616
13. M.R. Wester J.K. Yano G.A. Schoch C. Yang K.J. Griffin C.D. Stout and E.F. Johnson 2004 J. Biol. Chem. 279 3563010.1074/jbc.M405427200 1:CAS:528:DC%2BD2cXmsl2hsLs%3D 15181000
14. J.K. Yano M.R. Wester G.A. Schoch K.J. Griffin C.D. Stout and E.F. Johnson 2004 J. Biol. Chem. 279 3809110.1074/jbc.C400293200 1:CAS:528:DC%2BD2cXnt1Oqs7c%3D 15258162
15. S. Ekins G. Bravi J.H. Wikel and S.A. Wrighton 1999 J. Pharmacol. Exp. Ther. 291 4241:CAS:528:DyaK1MXmtlaktrc%3D 10490933
16. S. Ekins D.M. Stresser and J.A. Williams 2003 Trends Pharmacol. Sci. 24 16110.1016/S0165-6147(03)00049-X 1:CAS:528:DC%2BD3sXjtFeqt7c%3D 12707001
17. S. Ekins G. Bravi S. Binkley J.S. Gillespie B.J. Ring J.H. Wikel and S.A. Wrighton 1999 J. Pharmacol. Exp. Ther. 290 4291:CAS:528:DyaK1MXktFKit7s%3D 10381809
18. G.N. Kumar and Surapaneni 2001 Med. Res. Rev. 21 39710.1002/med.1016 1:CAS:528:DC%2BD3MXmsFCmtbg%3D 11579440
19. G.D. Szklarz and J.R. Halpert 1997 J. Comput.-Aided Mol. Des. 11 26510.1023/A:1007956612081 1:CAS:528:DyaK2sXlsVCrsr0%3D 9263853
20. M.L. Schrag and L.C. Wienkers 2001 Arch. Biochem. Biophys. 391 4910.1006/ abbi.2001.2401 1:CAS:528:DC%2BD3MXksVKjsb4%3D 11414684
21. J. Zuegge U. Fechner O. Roche N.J. Parrott O. Engkvist and G. Schneider 2002 Quant. Struct. Act. Relat. 21 24910.1002/ 1521-3838(200208)21:3<249::AID-QSAR249>3.0.CO;2-S 1:CAS:528:DC%2BD38XmvFCqsb4%3D
22. L. Molnár and G.M. Keseru 2002 Bioorg. Med. Chem. Lett. 12 41910.1016/S0960-894X(01)00771-5 11814811
23. S. Ekins J. Berbaum and R.K. Harrison 2003 Drug Metab. Dispos. 31 107710.1124/dmd.31.9.1077 1:CAS:528:DC%2BD3sXmslKlurw%3D 12920160
24. C. Merkwirth H. Mauser T. Schulz-Gasch O. Roche M. Stahl and T. Lengauer 2004 J. Chem. Inf. Comput. Sci. 44 197110.1021/ci049850e 1:CAS:528:DC%2BD2cXotlalsro%3D 15554666
25. V. Vapnik 1995 The Nature of Statistical Learning Theory Springer New York
26. Y. Lee and C.K. Lee 2003 Bioinformatics 19 113210.1093/bioinformatics/ btg102 1:CAS:528:DC%2BD3sXks1Wrtbo%3D 12801874
27. E. Byvatov U. Fechner J. Sadowski and G. Schneider 2003 J. Chem. Inf. Comput. Sci. 43 188210.1021/ci0341161 1:CAS:528:DC%2BD3sXns1Wmt74%3D 14632437
28. M.K. Warmuth J. Liao G. Rätsch M. Mathieson S. Putta and C. Lemmen 2003 J. Chem. Inf. Comput. Sci. 43 66710.1021/ci025620t 1:CAS:528:DC%2BD3sXhtVOjtbk%3D 12653536
29. M.W.B. Trotter and S.B. Holden 2003 Quant. Struct. Act. Relat. 22 5331:CAS:528:DC%2BD3sXmtFeksbw%3D
30. V.V. Zernov K.V. Balakin A.A. Ivaschenko N.P. Savchuk and I.V. Pletnev 2003 J. Chem. Inf. Comput. Sci. 43 204810.1021/ci0340916 1:CAS:528:DC%2BD3sXotFSht7w%3D 14632457
31. P. Lind and T. Maltseva 2003 J. Chem. Inf. Comput. Sci. 43 185510.1021/ ci034107s 1:CAS:528:DC%2BD3sXotFCgt70%3D 14632433
32. M.J. Sorich J.O. Miners R.A. McKinnon D.A. Winkler F.R. Burden and P.A. Smith 2003 J. Chem. Inf. Comput. Sci. 43 201910.1021/ci034108k 1:CAS:528:DC%2BD3sXnt1Ohsbs%3D 14632453
33. C. Cortes and V. Vapnik 1995 Mach. Learn. 20 273
34. C.-W. Hsu and C.-J. Lin 2002 IEEE Transactions on Neural Networks 13 41510.1109/TNN.2002.1000139
35. G.C. Moody S.J. Griffin A.N. Mather D.F. McGinnity and R.J. Riley 1999 Xenobiotica 29 5310.1080/004982599238812 1:CAS:528:DyaK1MXotlOjsg%3D%3D 10078840
36. These descriptors are calculated by a Boehringer Ingelheim in-house software package (propty, developed by K.M. Hasselbach)
37. Molecular Operating Environment Release 2003.2, Chemical Computing Group, Montreal, Canada, 2003
38. VolSurf 3.0.11, Molecular Discovery Ltd., London, UK, 2004
39. G. Cruciani M. Pastor and W. Guba 2000 Eur. J. Pharm. Sci. 11 Suppl 2 S2910.1016/S0928-0987(00)00162-7 1:CAS:528:DC%2BD3cXntF2gtbo%3D 11033425
40. CORINA 3.1, Molecular Networks GmbH, Erlangen, Germany, 2004
41. M.J.S. Dewar E.G. Zoebisch E.F. Healy and J.J.P. Stewart 1985 J. Am. Chem. Soc. 107 390210.1021/ja00299a024
42. VAMP 8.1, University of Erlangen, Erlangen, Germany (This version is provided as part of Materials Studio 2.2.1 by Accelrys, Inc.), 2003
43. A. Golbraikh M. Shen Z. Xiao Y.D. Xiao K.H. Lee and A. Tropsha 2003 J. Comput.-Aided Mol. Des. 17 24110.1023/A:1025386326946 1:CAS:528:DC%2BD3sXmsVGnsL0%3D 13677490
44. R.W. Kennard and L.A. Stone 1969 Technometrics 11 137
45. L. Eriksson E. Johansson F. Lindgren M. Sjøstrøm and S. Wold 2002 J. Comput.-Aided Mol. Des. 16 71110.1023/A:1022450725545 1:CAS:528:DC%2BD3sXht1WksbY%3D 12650589
46. L. Eriksson T. Arnhold B. Beck T. Fox E. Johansson and J.M. Kriegl 2004 J. Chemometrics 18 18810.1002/cem.854 1:CAS:528:DC%2BD2cXnt1WgtrY%3D
47. SIMCA-P+ 10, Umetrics AB, Umeå, Sweden, 2004
48. S. Wold 1978 Technometrics 20 397
49. LIBSVM 2.5 National Taiwan University, 2003; http://www.csie.ntu.edu.tw/~cjlin/libsvm/index.html
50. S.S. Keerthi and C.-J. Lin 2003 Neural Comput. 15 166710.1162/ 089976603321891855 12816571
51. P. Baldi S. Brunak Y. Chauvin C.A. Andersen and H. Nielsen 2000 Bioinformatics 16 41210.1093/bioinformatics/16.5.412 1:CAS:528:DC%2BD3cXlvVKqt74%3D 10871264
52. B.W. Matthews 1975 Biochim. Biophys. Acta 405 4421:CAS:528:DyaE2MXlslCksbk%3D 1180967
53. C.M. Bishop 2004 Br. J. Clin. Pharmacol. 57 473 10.1111/j.1365-2125.2003.02041.x 15025746
54. E. Byvatov and G. Schneider 2004 J. Chem. Inf. Comput. Sci. 44 99310.1021/ci0342876 1:CAS:528:DC%2BD2cXhslajtrs%3D 15154767