QSAR analysis of the inhibition of recombinant CYP 3A4 activity by structurally diverse compounds using a genetic algorithm-combined partial least squares method

Pharmaceutical Research

Volumn 20, Issue 9, 2003, Pages 1401-1408

  Wanchana, Suchada ^a   Yamashita, Fumiyoshi ^a   Hashida, Mitsuru ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

CYP 3A4; Genetic algorithm; Molconn Z; Partial least squares; Quantitative structure activity relationship

Indexed keywords

7 BENZYLOXY 4 TRIFLUOROMETHYL COUMARIN; ALPRAZOLAM; AMIODARONE; ASTEMIZOLE; BENZO[A]PYRENE; BUSPIRONE; CAFFEINE; CARBAMAZEPINE; CHLORPHENIRAMINE MALEATE; CLONAZEPAM; CLOTRIMAZOLE; CLOZAPINE; COLCHICINE DERIVATIVE; CORTISONE; COUMARIN DERIVATIVE; CYCLOPHOSPHAMIDE; CYCLOSPORIN A; CYTOCHROME P450 3A4; DAPSONE; DEXAMETHASONE; DIAZEPAM; DILTIAZEM; ERYTHROMYCIN; ESTRADIOL; ESTRIOL; ETHINYLESTRADIOL; FLUTAMIDE; HALOPERIDOL; PARACETAMOL; UNCLASSIFIED DRUG; UNINDEXED DRUG;

ANALYTIC METHOD; ARTICLE; DRUG ACTIVITY; DRUG METABOLISM; DRUG STRUCTURE; ENZYME ACTIVITY; ENZYME INHIBITION; GENETIC ALGORITHM; IC 50; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REGRESSION ANALYSIS;

ALGORITHMS; COUMARINS; CYTOCHROME P-450 ENZYME SYSTEM; ENZYME INHIBITORS; MODELS, BIOLOGICAL; PHARMACEUTICAL PREPARATIONS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0141789965     PISSN: 07248741     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1025702009611     Document Type: Article

References (36)

1. F. P. Guengerich. Role of cytochrome P450 enzymes in drug-drug interactions. Adv. Pharmacol. 43:7-35 (1997).
2. M. F. Paine, M. Khalighi, J. M. Fisher, D. D. Shen, K. L. Kunze, C. L. Marsh, J. D. Perkins, and K. E. Thummel. Characterization of interintestinal and intraintestinal variations in human CYP 3A-dependent metabolism. J. Pharmacol. Exp. Ther. 283:1552-1562 (1997).
3. P. K. Honig, D. C. Wortham, K. Zamani, D. Conner, J. C. Mullin, and L. R. Cantilena. Terfenadine-ketonazole interaction. JAMA 269:1513-1518 (1993).
4. D. M. Stresser, A. P. Blanchard, S. D. Turner, J. C. L. Erve, A. A. Dandeneau, V. P. Miller, and C. L. Crespi. Substrate-dependent modulation of CYP 3A4 catalytic activity: analysis of 27 test compounds with four fluorometric substrates. Drug Metab. Dispos. 28:1440-1448 (2000).
5. C. M. Masimirembwa, R. Thompson, and T. B. Andersson. In vitro high throughput screening of compounds for favorable metabolic properties in drug discovery. Comb: Chem. High Throughput Screen. 4:245-263 (2001).
6. J. Langowski and A. Long. Computer systems for the prediction of xenobiotic metabolism. Adv. Drug Deliv. Rev. 54:407-415 (2002).
7. S. Ekins, M. J. de Groot, and J. P. Jones. Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome p450 active sites. Drug Metab. Dispos. 29:936-944 (2001).
8. D. F. V. Lewis and B. G Lake. Molecular modelling of CYP 1A subfamily members based on an alignment with CYP 102: Rationalization of CYP 1A substrate specificity in terms of active site amino acid residues. Xenobiotica 26:723-753 (1996).
9. G. D. Szklarz and J. R. Halpert. Molecular modeling of cytochrome P450 3A4. J. Comp. Aided. Mol. Des. 11:265-272 (1997).
10. S. Ekins, G. Bravi, J. H. Wikel, and S. A. Wrighton. Three-dimensional quantitative structure activity relationship analysis of cytochrome P-450 3A4 substrates. J. Pharmacol. Exp. Ther. 291:424-433 (1999).
11. S. Ekins, G. Bravi, S. Binkley, J. S. Gillespie, B. J. Ring, J. H. Wikel, and S. A. Wrighton. Three- and four-dimensional quantitative structure activity relationship analyses of cytochrome P-450 3A4 inhibitors. J. Pharmacol. Exp. Ther. 290:429-438 (1999).
12. D. F. Lewis, S. Modi, and M. Dickins. Structure-activity relationship for human cytochrome P450 substrates and inhibitors. Drug Metab. Rev. 34:69-82 (2002).
13. K. R. Korzekwa, N. Krishnamachary, M. Shou, A. Ogai, R. A. Parise, A. E. Rettie, F. J. Gonzalez, and T. S. Tracy. Evaluation of atypical cytochrome P450 kinetics with two-substrate models: evidence that multiple substrates can simultaneously bind to cytochrome P450 active sites. Biochemistry 37:4137-4147 (1998).
14. J. J. Huuskonen, A. E. P. Villa, and I. V. Tetko. Prediction of partition coefficient based on atom-type electrotopological state indices. J. Pharm. Sci. 88:229-233 (1999).
15. L. H. Hall and C. T. Story. Boiling point and critical temperature of a heterogeneous data set: QSAR with atom type electrotopological state indices using artificial neural networks. J. Chem. Inf. Comp. Sci. 36:1004-1014 (1996).
16. S. Wanchana, F. Yamashita, and M. Hashida. Quantitative structure/property relationship analysis on aqueous solubility using genetic algorithm-combined partial least squares method. Pharmazie 57:127-129 (2002).
17. F. Yamashita, S. Wanchana, and M. Hashida. Quantitative structure/property relationship analysis of Caco-2 permeability using a genetic algorithm-based partial least squares method. J. Pharm. Sci. 90:2230-2239 (2002).
18. L. B. Kier and L. H. Hall. Topological information. In L. B. Kier and L. H. Hall (eds.), Molecular Connectivity in Structure-Activity Analysis. Research Studies, Hertfordshire, 1986, pp. 43-68.
19. W. Bridge, A. J. Crocker, T. Cubin, and A. Robertson. Experiments on the synthesis of rotenone and its derivatives. Part XIII. J Chem. Soc. 1530-1535 (1937).
20. A. P. Li, D. L. Kaminski, and A. Rasmussen. Substrates of human hepatic cytochrome P450 3A4. Toxicology 104:1-8 (1995).
21. L. B. Kier and L. H. Hall. Intermolecular accessibility: the meaning of molecular connectivity. J. Chem. Inf. Comput. Sci. 40:792-795 (2000).
22. L. H. Hall and L. B. Kier. The E-state as the basis for molecular structure space definition and structure similarity. J. Chem. Inf. Comput. Sci. 40:784-791 (2000).
23. A. Varhe, K. T. Olkkola, and P. J. Neuvonen. Oral triazolam is potentially hazardous to patients receiving systemic antimycotics ketoconazole or itraconazole. Clin. Pharmacol. Ther. 56:601-607 (1994).
24. P. Geladi and B. R. Kowalski. Partial least-squares regression: a tutorial. Anal. Chim. Acta 185:1-17 (1986).
25. K. Hasegawa, Y. Miyashita, and K. Funatsu. GA strategy for variable selection in QSAR studies: GA-based PLS analysis of calcium channel antagonists. J. Chem. Inf. Comput. Sci. 37:306-310 (1997).
26. B. Hoffman, S. J. Cho, W. Zheng, S. Wyrick, D. E. Nichols, R. B. Mailman, and A. Tropsha. Quantitative structure activity relationship modeling of dopamine D1 antagonists using comparative molecular field analysis, genetic algorithms-partial least squares, and K nearest neighbor methods. J. Med. Chem. 42:3217-3226 (1999).
27. D. E. Goldberg. Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley, New York, 1989.
28. C. Hansch. Quantitative relationships between lipophilic character and drug metabolism. Drug Metab. Rev. 1:1-14 (1972).
29. R. P. Austin, P. Barton, S. L. Cockroft, and M. C. Wenlock. The influence of nonspecific microsomal binding on apparent intrinsic clearance, and its prediction from physicochemical properties. Drug Metab. Dispos. 30:1497-1503 (2002).
30. A. Leo, C. Hansch, and P. Y. C. Jow. Dependence of hydrophobicity of apolar molecules on their molecular volume. J. Med. Chem. 19:611-615 (1976).
31. R. J. Riley, A. J. Parker, S. Trigg, and C. N. Manners. Development of a generalized, quantitative physicochemical model of CYP 3A4 inhibition for use in early drug discovery. Pharm. Res. 18:652-655 (2001).
32. F. Yoshida and J. G. Topliss. QSAR model for drug human oral bioavailability. J. Med. Chem. 43:2575-2585 (2000).
33. oct: a toot for lipophilicity determination in drug discovery. 2. Basic and neutral compounds. J. Med. Chem. 44:2490-2497 (2001).
34. C. Zhu, L. Jiang, T. M. Chen, and K. K. Hwang. A comparative study of artificial membrane permeability assay for high throughput profiling of drug absorption potential. Eur. J. Med. Chem. 37:399-407 (2002).
35. J. H. Van Drie, D. Weininger, and Y. C. Martin. ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures. J. Comput. Aided Mol. Des. 3:225-251 (1989).
36. R. D. Cramer, D. E. Patterson, and J. D. Bunce. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 110:5959-5967 (1988).