Use of density functional calculations to predict the regioselectivity of drugs and molecules metabolized by aldehyde oxidase

Journal of Medicinal Chemistry

Volumn 50, Issue 19, 2007, Pages 4642-4647

  Torres, Rhonda A ^a,b   Korzekwa, Kenneth R ^a   McMasters, Daniel R ^a   Fandozzi, Christine M ^a   Jones, Jeffrey P ^b  

^a MERCK RESEARCH LABORATORIES   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE DERIVATIVE; ALDEHYDE OXIDASE; HETEROCYCLIC COMPOUND; NITROGEN DERIVATIVE; XANTHINE OXIDASE; XENOBIOTIC AGENT;

ARTICLE; BIOTRANSFORMATION; DENSITY FUNCTIONAL THEORY; DRUG METABOLISM; ENZYME SUBSTRATE; OXIDATION; PREDICTION; STEREOCHEMISTRY;

EID: 34648830277     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm0703690     Document Type: Article

References (32)

1. Beedham, C. The Role of Non-P450 Enzymes in Drug Oxidation. Pharm. World Sci. 1997, 19, 255-263.
2. Obach, R. S.; Huynh, P.; Allen, M. C.; Beedham, C. Human Liver Aldehyde Oxidase: Inhibition by 239 Drugs. J. Clin. Pharmacol. 2004, 44, 7-19.
3. Obach, R. S.; Walsky, R. L. Drugs That Inhibit Oxidation Reactions Catalyzed by Aldehyde Oxidase Do Not Inhibit the Reductive Metabolism of Ziprasidone to Its Major Metabolite, S-Methyldihydroziprasidone: An in Vitro Study. J. Clin. Psychopharmacol. 2005, 25, 605-608.
4. Obach, R. S. Potent Inhibition of Human Liver Aldehyde Oxidase by Raloxifene. Drug Metab. Dispos. 2004, 32, 89-97.
5. Terao, M.; Kurosaki, M.; Barzago, M. M.; Varasano, E.; Boldetti, A.; Bastone, A.; Fratelli, M.; Garattini, A. Avian and Canine Aldehyde Oxidases: Novel Insights into the Biology and Evolution of Molybdo-flavoenzymes. J. Biol. Chem. 2006, 281, 19748-19761.
6. Huang, D.-Y.; Furukawa, A.; Ichikawa, Y. Molecular Cloning of Retinal Oxidase/Aldehyde Oxidase cDNAs from Rabbit and Mouse Livers and Functional Expression of Recombinant Mouse Retinal Oxidase cDNA in Escherichia coli. Arch. Biochem. Biophys. 1999, 364, 264-272.
7. Berger, R.; Mezey, E.; Clancy, K. P.; Harta, G.; Wright, R. M.; Repine, J. E.; Brown, R. H.; Brownstein, M.; Patterson, D. Analysis of Aldehyde Oxidase and Xanthine Dehydrogenase/Oxidase as Possible Candidate Genes for Autosomal Recessive Familial Amyotrophic Lateral Sclerosis. Somatic Cell Mol. Genet. 1995, 21, 121-131.
8. Panoutsopoulos, G. I.; Beedham, C. Kinetics and Specificity of Guinea Pig Liver Aldehyde Oxidase and Bovine Milk Xanthine Oxidase Towards Substituted Benzaldehydes. Acta Biochim. Pol. 2004, 51, 649-663.
9. Kawashima, K.; Hosoi, K.; Naruke, T.; Shiba, T.; Kitamura, M.; Watabe, T. Aldehyde Oxidase-Dependent Marked Species Difference in Hepatic Metabolism of the Sedative-Hypnotic, Zaleplon, between Monkeys and Rats. Drug Metab. Dispos. 1999, 27, 422-428.
10. Rashidi, M. R.; Smith, J. A.; Clarke, S. E.; Beedham, C. In Vitro Oxidation of Famciclovir and 6-Deoxypenciclovir by Aldehyde Oxidase from Human, Guinea Pig, Rabbit, and Rat Liver. Drug Metab. Dispos. 1997, 25, 805-813.
11. Hille, R. Molybdenum-Containing Hydroxylases. Arch. Biochem. Biophys. 2005, 433, 107-116.
12. Enemark, J. H.; Cooney, J. J. A.; Wang, J.-J.; Holm, R. H. Synthetic Analogues and Reaction Systems Relevant to the Molybdenum and Tungsten Oxotransferases. Chem. Rev. 2003, 104, 1175-1200.
13. Massey, V.; Harris, C. M. Milk Xanthine Oxidoreductase: The First One Hundred Years. Biochem. Soc. Trans. 1997, 25, 750-755.
14. 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.
15. 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, 1330-1336.
16. Cruciani, G.; Carosati, E.; De Boeck, B.; Ethirajulu, K.; Mackie, C.; Howe, T.; Vianello, R. MetaSite: Understanding Metabolism in Human Cytochromes from the Perspective of the Chemist. J. Med. Chem. 2005, 48, 6970-6979.
17. Beedham, C. Molybdenum Hydroxylases: Biological Distribution and Substrate-Inhibitor Specificity. Progress in Medicinal Chemistry; Elsevier Science Publishers, B.V.: London, 1987.
18. Okamoto, K.; Matsumoto, K.; Hille, R.; Eger, B. T.; Pai, E. F.; Nishino, T. The Crystal Structure of Xanthine Oxidoreductase during Catalysis: Implications for Reaction Mechanism and Enzyme Inhibition. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7931-7936.
19. Hammond, G. S. A Correlation of Reaction Rates. J. Am. Chem. Soc. 1955, 77, 334-338.
20. Krenitsky, T. A.; Neil, S. M.; Elion, G. B.; Hitchings, G. H. A Comparison of the Specificities of Xanthine Oxidase and Aldehyde Oxidase. Arch. Biochem. Biophys. 1972, 150, 585-599.
21. Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior. Phys. Rev. 1988, A38, 3908-3100.
22. Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648-5652.
23. Becke, A. D. Density-Functional Thermochemistry. I. The Effect of the Exchange-Only Gradient Correction. J. Chem. Phys. 1992, 96, 2155-2160.
24. Becke, A. D. Density-Functional Thermochemistry. II. The Effect of the Perdew-Wang Generalized-Gradient Correlation Correction. J. Chem. Phys. 1992, 97, 9173-9177.
25. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.; Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 03, revision C.01; Gaussian, Inc.: Wallingford, CT, 2004.
26. Bauschlicher, C. W. J. A Comparison of the Accuracy of Different Functionals. Chem. Phys. Lett. 1995, 246, 40-44.
27. Guner, V.; Khuong, K. S.; Leach, A. G.; Lee, P. S.; Bartberger, M. D.; Houk, K. N. A Standard Set of Pericyclic Reactions of Hydrocarbons for the Benchmarking of Computational Methods: The Performance of ab Initio, Density Functional, CASSCF, CASPT2, and CBS-QB3 Methods for the Prediction of Activation Barriers, Reaction Energetics and Transition State Geometries. J. Phys. Chem. A 2003, 107, 11445-11459.
28. Grimme, S. Improved Second-Order Møller-Plesset Perturbation Theory by Separate Scaling of Parallel- and Antiparallel-Spin Pair Correlation Energies. J. Chem. Phys. 2003, 118, 9095-9102.
29. Lynch, B. J.; Truhlar, D. G. How Well Can Hybrid Density Functional Methods Predict Transition State Geometries and Barrier Heights? J. Phys. Chem. A 2001, 105, 2936-2941.
30. Koch, W.; Holthausen, M. C. A Chemist's Guide to Density Functional Theory, 2nd ed.; Wiley-VCH: Weinheim, Germany, 2001.
31. Besler, B. H.; Merz, K. M. J.; Kollman, P. A. Atomic Charges Derived from Semiempirical Methods. J. Comput. Chem. 1990, 11, 431-439.
32. DeLano, W. L. The PyMOL Molecular Graphics System, version 0.98; DeLano Scientific: San Carlos, CA.