Transition-state docking of flunitrazepam and progesterone in cytochrome P450

Journal of Chemical Theory and Computation

Volumn 4, Issue 4, 2008, Pages 673-681

  Rydberg, Patrik ^a,b   Hansen, Sine Myrup ^a   Kongsted, Jacob ^b   Norrby, Per Ola ^c   Olsen, Lars ^a   Ryde, Ulf ^b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b LUND UNIVERSITY   (Sweden)

^c UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 58149107172     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct700313j     Document Type: Article

References (41)

1. Hodgson, J. ADMET - turning chemicals into drugs. Nat. Biotechnol. 2001, 19, 722-726.
2. Harris, D.; Loew, G. Prediction of regiospecific hydroxylation of camphor analogs by cytochrome P450. J. Am. Chem. Soc. 1995, 117, 2738-2746.
3. Rydberg, P. Theoretical Studies of Cytochrome P450; Lund University: Lund, 2007.
4. Shaik, S.; Kumar, D.; de Visser, S. P.; Altun, A.; Thiel, W. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. Chem. Rev. 2005, 105, 2279-2328.
5. Olsen, L.; Rydberg, P.; Rod, T. H.; Ryde, U. Prediction of activation energies for hydrogen abstraction by cytochrome P450. J. Med. Chem. 2006, 49, 6489-6499.
6. Jones, J. P.; Korzekwa, K. R. Predicting the rates and regioselectivity of reactions mediated by the P450 superfamily. Cytochrome P450, B 1996, 272, 326-335.
7. 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.
8. 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.
9. Zamora, I.; Afzelius, L.; Cruciani, G. Predicting drug metabolism: A site of metabolism prediction tool applied to the cytochrome P4502C9. J. Med. Chem. 2003, 46, 2313-2324.
10. Park, J. Y.; 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, 1645-1660.
11. Afzelius, L.; Arnby, C. H.; Broo, A.; Carlsson, L.; Isaksson, C.; Jurva, U.; Kjellander, B.; Kolmodin, K.; Nilsson, K.; Raubacher, F.; Weidolf, L. State-of-the-art tools for computational site of metabolism predictions: Comparative analysis, mechanistical insights, and future applications. Drug Metab. Rev. 2007, 39, 61-86.
12. Rydberg, P.; Olsen, L.; Norrby, P. O.; Ryde, U. General Transition-State Force Field for Cytochrome P450 Hydroxylation. J. Chem. Theory Comput 2007, 3, 1765-1773.
13. Hermann, J. C.; Ghanem, E.; Li, Y.; Raushel, F. M.; Irwin, J. J.; Shoichet, B. K. Predicting substrates by docking high-energy intermediates to enzyme structures. J. Am. Chem. Soc. 2006, 128, 15882-15891.
14. Hermann, J. C.; Marti-Arbona, R.; Dedorov, A. A.; Fedorov, E.; Almo, C. A.; Shoichet, B. K.; Raushel, F. M. Structure-based activity prediction for an enzyme of unknown function. Nature 2007, 448, 775-779.
15. Jensen, F.; Norrby, P. O. Transition states from empirical force fields. Theor. Chem. Acc. 2003, 109, 1-7.
16. van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. ReaxFF: A reactive force field for hydrocarbons. J. Phys. Chem. A 2001, 105, 9396-9409.
17. Norrby, P. O. Molecular mechanics as a predictive tool in asymmetric catalysis. In Transition State Modeling for Catalysis; Truhlar, D. G., Morokuma, K., Eds.; American Chemical Society: Washington, DC., 1999; pp 163-172.
18. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33, 889-897.
19. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
20. Wester, M. R.; Yano, J. K.; Schoch, G. A.; Yang, C.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. The structure of human cytochrome P4502C9 complexed with flurbiprofen at 2.0-angstrom resolution. J. Biol. Chem. 2004, 279, 35630-35637.
21. Yano, J. K.; Wester, M. R.; Schoch, G. A.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-angstrom resolution. J. Biol. Chem. 2004, 279, 38091-38094.
22. Rydberg, P.; Rod, T. H.; Olsen, L.; Ryde, U. Dynamics of water molecules in the active-site cavity of human cytochromes P450. J. Phys. Chem. B 2007, 111, 5445-5457.
23. Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general AMBER force field. J. Comput Chem. 2004, 25, 1157-1174.
24. Case, D. A.; Darden, T. A.; Cheatham, I. T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Pearlman, D. A.; Crowley, M.; Walker, R. C.; Zhang, W.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S.; Tsui, V.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Homak, V.; Cui, G.; Beroza, P.; Mathews, D. H.; Schafmeister, C.; Ross, W. S.; Kollman, P. A. AMBER, version 9; University of California: San Fransisco, 2006.
25. Berendsen, H. J. C.; Postma, J. P. M.; van gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684-3690.
26. Bashford, D.; Case, D. A. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 2000, 51, 129-152.
27. Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized Born model. Proteins 2004, 55, 383-394.
28. Hermann, R. B. Theory of hydrophobic bonding. 2. Correlation of hydrocarbon solubility in water with solvent cavity surfacearea. J. Phys. Chem. 1972, 76, 2754-2759.
29. Swanson, J. M. J.; Henchman, R. H.; McCammon, J. A. Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys. J. 2004, 86, 67-74.
30. Weis, A.; Katebzadeh, K.; Soderhjelm, P.; Nilsson, I.; Ryde, U. Ligand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field. J. Med. Chem. 2006, 49, 6596-6606.
31. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical-integration of Cartesian equations of motion of a system with constraints - molecular-dynamics of N-alkanes. J. Comput Phys. 1977, 23, 327-341.
32. Rocchia, W.; Alexov, E.; Honig, B. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions. J. Phys. Chem. B 2001, 105, 6507-6514.
33. Kongsted, J.; Ryde, U. Improved method for entropy term in the MM/PBSA approach. Chem. Phys. Lett., submitted.
34. de Graaf, C.; Oostenbrink, C.; Keizers, P. H. J.; van der Wijst, T.; Jongejan, A.; Vemleulen, N. P. E. Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J. Med. Chem. 2006, 49, 2417-2430.
35. Coller, J. K.; Somogyi, A. A.; Bochner, F. Quantification of flunitrazepam's oxidative metabolites, 3-hydroxyflunitrazepam and desmethylflunitrazepam, in hepatic microsomal incubations by high-performance liquid chromatography. J. Chromatogr. B Biomed. Sci. Appl. 1998, 719, 87-92.
36. Hesse, L. M.; Venkatakrishnan, K.; von Moltke, L. L.; Shader, R. I.; Greenblatt, D. J. CYP3A4 is the major CYP isoform mediating the in vitro hydroxylation and demethylation of flunitrazepam. Drug Metab. Dispos. 2001, 29, 133-140.
37. Waxman, D. J.; Lapenson, D. P.; Aoyama, T.; Gelboin, H. V.; Gonzalez, F. J.; Korzekwa, K. Steroid-hormone hydroxylase specificities of 11 cDNA-expressed human cytochrome-P450S. Arch. Biochem. Biophys. 1991, 290, 160-166.
38. Richardson, T. H.; Jung, F.; Griffin, K. J.; Wester, M.; Raucy, J. L.; Kemper, B.; Bornheim, L. M.; Hassett, C.; Omiecinski, C. J.; Johnson, E. F. Universal approach to the expression of human and rabbit cytochrome P450S of the 2C subfamily in Escherichia-coli. Arch. Biochem. Biophys. 1995, 323, 87-96.
39. Yamazaki, H.; Shimada, T. Progesterone and testosterone hydroxylation by cytochromes P450 2C19, 2C9, and 3A4 in human liver microsomes. Arch. Biochem. Biophys. 1997, 346, 161-169.
40. Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem., Int. Ed. Engl. 2002, 41, 2645-2676.
41. Kirton, S. B.; Kemp, C. A.; Tomkinson, N. P.; St.-Gallay, S.; Sutcliffe, M. J. Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6. Proteins 2002, 49, 216-231.