A rapid computational filter for cytochrome P450 1A2 inhibition potential of compound libraries

Journal of Medicinal Chemistry

Volumn 48, Issue 16, 2005, Pages 5154-5161

  Chohan, Kamaldeep K ^a   Paine, Stuart W ^a   Mistry, Jaina ^a   Barton, Patrick ^a   Davis, Andrew M ^a  

^a ASTRAZENECA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUND; CYTOCHROME P450 1A2;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CALCULATION; CLASSIFICATION AND REGRESSION TREE; ENERGY; ENZYME INHIBITION; HUMAN; LINEAR REGRESSION ANALYSIS; LIPOPHILICITY; MOLECULAR LIBRARY; NONHUMAN; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REGRESSION ANALYSIS; STATISTICAL ANALYSIS; STATISTICAL MODEL; SURFACE CHARGE;

BAYES THEOREM; CYTOCHROME P-450 CYP1A2; DATABASES, FACTUAL; ENZYME INHIBITORS; MODELS, MOLECULAR; NEURAL NETWORKS (COMPUTER); QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REGRESSION ANALYSIS;

EID: 23444437988     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm048959a     Document Type: Article

References (56)

1. Brosen, K. Drug interactions and the cytochrome P450 system. The role of cytochrome P450 1A2. Clin. Pharmacokinet. 1995, 29, 20-25.
2. Guengerich, F. P.; Shimada, T. Oxidation of toxic and carcinogenic chemicals by human cytochrome P-450 enzymes. Chem. Res. Toxicol. 1991, 4, 391-407.
3. Jeppesen, U.; Loft, S.; Poulsen, H. E.; Broesen, K. A fluvoxamine-caffeine interaction study. Pharmacogenetics 1996, 6, 213-222.
4. Shimada, T.; Iwasaki, M.; Martin, M. V.; Guengerich, F. P. Human liver microsomal cytochrome P-450 enzymes involved in the bioactivation of procarcinogens detected by umu gene response in Salmonella typhimurium TA 1535/pSK1002. Cancer Res. 1989, 49, 3218-3228.
5. Yamashita, K.; Umemoto, A.; Grivas, S.; Kato, S.; Sato, S.; Sugimura, T. Heterocyclic amine-DNA adducts analyzed by 32P-postlabeling method. Nucleic Acids Symp. Ser. 1988, 19, 111-114.
6. Zhai, S.; Dai, R.; Wei, X.; Friedman, F. K.; Vestal, R. E. Inhibition of methoxyresorufin demethylase activity by flavonoids in human liver microsomes. Life Sci. 1998, 63, 119-123.
7. So, F. V.; Guthrie, N.; Chambers, A. F.; Moussa, M.; Carroll, K. K. Inhibition of human breast cancer cell proliferation and delay of mammary tumorigenesis by flavonoids and citrus juices. Nutr. Cancer 1996, 26, 167-181.
8. Wattenberg, L. W. Inhibition of carcinogenesis by minor dietary constituents. Cancer Res. 1992, 52, 2085-2091.
9. Steinmetz, K. A.; Potter, J. D. Vegetables, fruit, and cancer. II. Mechanisms. Cancer, Causes Control 1991, 2, 427-442.
10. Moon, T.; Chi, M. H.; Kim, D.-H.; Yoon, C. N.; Choi, Y.-S. Quantitative Structure-Activity Relationships (QSAR) Study of Flavonoid Derivatives for Inhibition of Cytochrome P450 1A2. Quant. Struct.-Act. Relat. 2000, 19, 257-263.
11. Höskuldsson, A. Prediction Methods in Science and Technology; Thor Publishing: Copenhagen, Denmark, 1996.
12. Wold, S.; Albano, C.; Dunn, W. J.; Edlund, U.; Esbensen, K.; Geladi, P.; Hellberg, S.; Johansson, E.; Lindberg, W.; Sjöström, M. Multivariate Data Analysis in Chemistry. In Chemometrics: Mathematics and statistics in Chemistry; Kowalski, B. R., Ed.; D. Reidel Publishing Company: Dordrecht, Holland, 1984.
13. Wold, S.; Eriksson, L.; Sjöström, M. PLS in Chemistry, Encyclopedia of Computational Chemistry; Wiley: 2000.
14. Breiman, L.; Friedman, J.; Olshen, R.; Stone, C. Classification and Regression Trees; Chapman and Hall/CRC and Place: Pacific Grove, CA, 1984.
15. Steinberg, D.; Colla, P. CART: Tree-Structured Non-Parametric Data Analysis; Salford Systems: San Diego, CA, 1995.
16. Neal, R. M. Bayesian Learning for Neural Networks; Lecture Notes in Statistics No. 118; Springer-Verlag: New York, 1996.
17. Asikainen, A. H.; Ruuskanen, J.; Tuppurainen, K. A. Performance of (consensus) kNN QSAR for predicting estrogenic activity in a large diverse set of organic compounds. SAR QSAR Environ. Res. 2004, 15, 19-32.
18. Baurin, N.; Mozziconacci, J.-C.; Arnoult, E.; Chavatte, P.; Marot, C.; Morin-Allory, L. Two-Dimensional QSAR Consensus Prediction for High-Throughput Virtual Screening. An Application to COX-2 Inhibition Modeling and Screening of the NCI Database. J. Chem. Inf. Comput. Sci. 2004, 44, 276-285.
19. Stouch, T. R.; Kenyon, J. R.; Johnson, S. R.; Chen, X.-Q.; Doweyko, A.; Li, Y. J. In silico ADME/Tox: why models fail. J. Comput.-Aided Mol. Des. 2003, 17, 83-92.
20. Bruneau, P. Search for Predictive Generic Model of Aqueous Solublity using Bayesian Neural Networks. J. Chem. Inf. Comput. Sci, 2001, 41, 1605-1616.
21. Lewis, D. F. V. On the recognition of mammalian microsomal cytochrome P450 substrates and their characteristics. Biochem. Pharmacol. 2000, 60, 293-306.
22. Xu, Y.; Gao, H. Dimension related distance and its application in QSAR/QSPR model error estimation. QSAR Comb. Sci. 2003, 22, 422-429
23. McGinnity, D. F.; Griffin, S. J.; Moody, G. C.; Voice, M.; Hanlon, S.; Friedburg, T.; Riley, R. J. Rapid characterisation of the major drug-metabolising human hepatic cytochrome P-450 enzymes expressed in Escherichia coli. Drug Metab. Dispos. 1999, 27, 1017-1023.
24. McGinnity, D. F.; Parker, A. J.; Soars, M.; Riley, R. J. Automated definition of the enzymology of drug oxidation by the major human drug metabolising cytochrome P450s. Drug Metab. Dispos. 2000, 28, 1327-1334.
25. Obermeier, M. T.; White, R. E.; Yang, C. S. Effects of bioflavonoids on hepatic P450 activities. Xenobiotica 1995, 25, 575-584.
26. Shimada, T.; Yamazaki, H.; Foroozesh, M.; Hopkins, N. E.; Alworth, W. L.; Guengerich, F. P. Selectivity of polycyclic inhibitors for human cytochrome P450s 1A1, 1A2, and 1B1. Chem. Res. Toxicol. 1998, 11, 1048-1056.
27. Obach, R. S. Inhibition of human cytochrome P450 enzymes by constituents of St. John's Wort, an herbal preparation used in the treatment of depression. J. Pharmacol. Exp. Ther. 2000, 294, 88-95.
28. Fuhr, U.; Wolff, S.; Harder, S.; Schymanski, P.; Staib, A. H. Quinoline inhibition of cytochrome P-450-dependent caffeine metabolism in human liver microsomes. Drug Metab. Dispos. 1990, 18, 1005-1010.
29. Brosen, K.; Naranjo, C. A. Review of pharmacokinetic and pharmacodynamic interaction studies with citalopram. Eur. Neuropsychopharmacol. 2001, 11, 275-283.
30. Von Moltke, L. L.; Greenblatt, D. J.; Duan, S. X.; Schmider, J.; Kudchadker, L.; Fogelmann, S. M.; Harmatz, J. S.; Shader, R. I. Phenacetin O-deethylation by human liver microsomes in vitro. Inhibition by chemical probes, SSRI antidepressants, nefazodone and venlafaxine. Psychopharmacology 1996, 128, 398-407.
31. Kunze, K. L.; Wienkers, L. C.; Thummel, K. E.; Trager, W. F. Warfarin-Fluconazole. I. Inhibition of the human cytochrome P450-dependent metabolism of warfarin by fluconazole: in vitro studies. Drug Metab. Dispos. 1996, 24, 414-21.
32. Langoue, S.; Purge, L. L.; Kerriguy, N.; Nakamura, K.; Guillouzo, A.; Guengerich, F. P. Mechanism-based inactivation of human cytochrome P-450 1A2 by oltipraz. Abstracts of Papers, 219th National Meeting of the American Chemical Society, San Francisco, CA, March 26-30, 2000; American Chemical Society: Washington, DC, 2000; TOXI-086.
33. Kinzig-Schippers, M.; Fuhr, U.; Zaigler, M.; Dammeyer, J.; Rusing, G.; Labedzki, A.; Bulitta, J.; Sorgel, F. Interaction of pefloxacin and enoxacin with the human cytochrome P450 enzyme CYP1A2. Clin. Pharmacol. Ther. 1999, 65, 262-274.
34. Shader, R. I.; Granda, B. W.; Von Moltke, L. L.; Giancarlo, G. M.; Greenblatt, D. J. Inhibition of human cytochrome P450 isoforms in vitro by zafirlukast. Biopharm. Drug Dispos. 1999, 20, 385-388.
35. Katritzky, A.; Wang, Y.; Sild, S.; Tamm, T.; Kalrelson, M. QSPR Studies on Vapor Pressure, Aqueous Solubility, and the Prediction of Water-Air Partition Coefficient. J. Chem. Inf. Comput. Sci. 1998, 38, 720-725.
36. Selma is an AstraZeneca in-house software package. For further information contact: Olsson, T.; Sherbukhin, V. Synthesis and Structure Administration (SaSA), AstraZeneca R&D Mölndal.
37. Physicians' Desk Reference, 53rd ed.; Medical Economics Company: Montvale, 1999.
38. Wenlock, M. C.; Austin, R. P.; Barton, P.; Davis, A. M.; Leeson, P. D. A Comparison of Physiochemical Property Profiles of Development and Marketed Oral Drugs. J. Med. Chem. 2003, 46, 1250-1256.
39. Jackson, J. E. A User's Guide to Principal Components; ISBN 0-471-62267-2; John Wiley: New York, 1991.
40. Wold, S.; Geladi, P.; Esbensen, K.; Öhman, J. Multiway Principal Components and PLS-Analysis. J. Chemom. 1987, 1, 41-56.
41. Baroni, M.; Costatino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Generating Optimal Linear PLS Estimations (GOLPE): An Advanced Chemometric Tool for Handling 3D-QSAR Problems. Quant. Struct.-Act. Relat. 1993, 12, 9-20.
42. http://www.JMPdiscovery.com (June 2002).
43. Sarle, W. ftp://ftp.sas.com/pub/neural/FAQ3.html (February 2003).
44. Ajay, W.; Murcko, M. Can We Learn To Distinguish Between "Drug-like" and "Nondrug-like" Molecule? J. Med. Chem. 1998, 41, 3314-3324.
45. Burden, F.; Winkler, D. Robust QSAR Models Using Bayesian Regularized Neural Networks. J. Med. Chem. 1999, 42, 3183-3187.
46. Burden, F.; Winkler, D. New QSAR Methods Applied to Structure-Activity Mapping and Combinatorial Chemistry. J. Chem. Inf. Comput. Sci. 1999, 39, 236-242.
47. Sorich, M. J.; McKinnon, R. A.; Miners, J. O.; Winkler, D. A.; Smith, P. A. Rapid Prediction of Chemical Metabolism by Human UDP-Glucuronosyltransferase Isoforms Using Quantum Chemical Descriptors Derived with the Electronegativity Equalization Method. J. Med. Chem. 2004, 47, 5311-5317.
48. Neal, R. M. Software for Flexible Bayesian Modeling, http:// www.cs.utoronto.ca/~radford (February 2003).
49. Burden, F.; Ford, M.; Whitley, D.; Winkler, D. Use of Automatic Relevance Determination in QSAR Studies Using Bayesian Neural Networks. J. Chem. Inf. Comput. Sci. 2000, 40, 1423-1430.
50. Fielding, A. H.; Bell, J. F. A review of methods for the assessment of prediction errors in conservation presence/absence models. Environ. Consent. 1997, 24, 38-49.
51. Cohen, J. A coefficient of agreement for nominal scales. Educ. Psychol. Meas. 1960, 20, 37-46.
52. Cohen, J. Weighted Kappa: Nominal scale agreement with provision for scaled disagreement or partial credit. Psychol. Bull. 1968, 70, 426-443.
53. Fleiss, J. L.; Cohen, J.; Everitt, B. S. Large sample standard errors of Kappa and weighted Kappa. Psychol. Bull. 1969, 72, 323-327.
54. Landis, J. R.; Koch, G. C. The measurement of observer agreement for categorical data. Biometrics 1977, 33, 159-174.
55. O'Brien, S. E.; de Groot, M. J. Greater Than the Sum of Its Parts: Combining Models for Useful ADMET Prediction J. Med. Chem. 2005, 48, 1287-1291.
56. Refsgaard, H. H. F.; Jensen, B. F.; Brockhoff, P. B.; Padkjær, S. B.; Guldbrandt, M.; Christensen, M. C. In Silico Prediction of Membrane Permeability from Calculated Molecular Parameters J. Med. Chem. 2005, 48, 805-811.