Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling

Journal of Molecular Modeling

Volumn 13, Issue 6-7, 2007, Pages 851-860

  Shaikh, Abdul Rajjak ^a   Broclawik, Ewa ^b   Tsuboi, Hideyuki ^a   Koyama, Michihisa ^a   Endou, Akira ^a   Takaba, Hiromitsu ^a   Kubo, Momoji ^c   Carpio, Carlos A ^a   Miyamoto, Akira ^a  

^a TOHOKU UNIVERSITY   (Japan)

^b INSTITUTE OF CATALYSIS AND SURFACE CHEMISTRY   (Poland)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Aromatic oxidation by Cpd I; Cytochrome CYP3A4; DFT modeling; Metabolism mechanism

Indexed keywords

ALCOHOL; CYTOCHROME P450 3A4; KETONE; N [1 (3 MORPHOLIN 4 YLPHENYL)ETHYL] 3 PHENYLACRYLAMIDE; POTASSIUM CHANNEL STIMULATING AGENT; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DENSITY FUNCTIONAL THEORY; DRUG METABOLISM; DRUG OXIDATION; DRUG PROTEIN BINDING; DRUG STRUCTURE; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME SUBSTRATE; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULAR MODEL; OXIDATION KINETICS; PRIORITY JOURNAL;

ALCOHOLS; ALGORITHMS; BINDING SITES; CINNAMATES; COMPUTER SIMULATION; CYTOCHROME P-450 ENZYME SYSTEM; ELECTROSTATICS; HYDROGEN; HYDROGEN BONDING; HYDROPHOBICITY; KETONES; METABOLIC NETWORKS AND PATHWAYS; MODELS, CHEMICAL; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; MORPHOLINES; NITROGEN; OXIDATION-REDUCTION; OXYGEN; PROTONS; QUANTUM THEORY; REPRODUCIBILITY OF RESULTS; SUBSTRATE SPECIFICITY;

EID: 34347376517     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-007-0196-5     Document Type: Article

References (42)

1. Rendic S, Di Carlo FJ (1997) Drug Metab Rev 29:413-580
2. Kumar GN, Surapaneni S (2001) Med Res Rev 21:397-411
3. Guengerich FP (2001) Chem Res Toxicol 14:611-650
4. Anzenbacher P, Anzenbacherova E (2001) Cell Mol Life Sci 58:737-747
5. Ekins S, Bravi G, Binkley S, Gillespie JS, Ring BJ, Wikel JH, Wrighton SA (1999) J Pharmacol Exp Ther 290:429-438
6. Lewis DF, Lake BG (1998) Toxicology 125:31-44
7. Wu YJ, Boissard CG, Greco C, Gribkoff VK, Harden DG, He H, L'Heureux A, Kang SH, Kinney GG, Knox RJ, Natale J, Newton AE, Lehtinen-Oboma S, Sinz MW, Sivarao DV, Starrett JE Jr, Sun L, Tertyshnikova S, Thompson MW, Weaver D, Wong HS, Zhang L, Dworetzky SI (2003) J Med Chem 46:3197-3200
8. Wu YJ, Davis CD, Dworetzky S, Fitzpatrick WC, Harden D, He H, Knox RJ, Newton AE, Philip T, Polson C, Sivarao DV, Sun L, Tertyshnikova S, Weaver D, Yeola S, Zoeckler M, Sinz MW (2003) J Med Chem 46:3778-3781
9. Williams PA, Cosme J, Vinkovic DM, Ward A, Angove HC, Day PJ, Vonrhein C, Tickle IJ, Jhoti H (2004) Science 305:683-686
10. Yano JK, Wester MR, Schoch GA, Griffin KJ, Stout CD, Johnson EF (2004) J Biol Chem 279:38091-38094
11. Ekroos M, Sjogren T (2006) Proc Natl Acad Sci USA 103:13682-13687
12. Sono M, Roach MP, Coulter ED, Dawson JH (1996) Chem Rev 96:2841-2888
13. Denisov IG, Makris TM, Sligar SG, Schlichting I (2005) Chem Rev 105:2253-2278
14. Shaik S, Kumar D, de Visser SP, Altun A, Thiel W (2005) Chem Rev 105:2279-2328
15. Ortiz de Montellano PR, De Voss JJ (2002) Nat Prod Rep 19:477-493
16. Klamt A, Schüürmann G (1993) J Chem Soc Perkin Trans 2:799-805
17. Klamt A, Jonas V, Burger T, Lohrenz J (1998) J Phys Chem A 102:5074-5085
18. Shaikh AR, Broclawik E, Ismael M, Tsuboi H, Koyama M, Kubo M, Del Carpio CA, Miyamoto A (2006) Chem Phys Lett 419:523-527
19. Visser SP, Shaik S (2003) J Am Chem Soc 125:7413-7424
20. Bathelt CM, Ridder L, Mulholland AJ, Harvey JN (2003) J Am Chem Soc 125:15004-15005
21. Bathelt CM, Lars Ridder L, Mulholland AJ, Harvey JN (2004) Org Biomol Chem 2:2998-3005
22. Luty BA, Wasserman ZR, Stouten PFW, Hodge CN, Zacharias M, McCammon JA (1995) J Comput Chem 16:454-464
23. Pattabiraman N, Levitt M, Ferrin TE, Langridge R (1985) J Comput Chem 6:432-436
24. Meng EC, Shoichet BK, Kuntz ID (1992) J Comput Chem 13:505-524
25. Paulsen MD, Ornstein RL (1991) Proteins 11:184-204
26. Endou A, Teraishi K, Yajima K, Yoshizawa K, Ohashi N, Takami S, Kubo M, Miyamoto A, Broclawik E (2000) Jpn J Appl Phys 39:4255-4260
27. Onozu T, Miura R, Takami S, Kubo M, Miyamoto A, Iyechika Y, Maeda T (2000) Jpn J Appl Phys 39:4400-4403
28. Onozu T, Gunji I, Miura R, Ammal SSC, Kubo M, Teraishi K, Miyamoto A, Iyechika Y, Maeda T (1999) Jpn J Appl Phys 38:2544-2548
29. Koyama M, Hayakawa J, Onodera T, Ito K, Tsuboi H, Endou A, Kubo M, Del Carpio CA, Miyamoto A (2006) J Phys Chem B 110:17507-17511
30. Delley B (1990) J Chem Phys 92:508-517
31. Delley B (2000) J Chem Phys 113:7756-7769
32. Lundberg M, Siegbahn PEM (2005) J Comput Chem DOI 1002/jcc.2026
33. Pierloot K, private communication
34. Radon M, Broclawik E, J Chem Theory Comput (in press)
35. Dowers TS, Rock DA, Jones JP (2004) J Am Chem Soc 126:8868-8869
36. Schlichting I, Berendzen J, Chu K, Stock AM, Maves SA, Benson DE, Sweet RM, Ringe D, Petsko GA, Sligar SG (2000) Science 287:1615-1622
37. Kaizer J, Klinker EJ, Oh NY, Rohde JU, Song WJ, Stubna A, Kim J, Munck E, Nam W, Que L Jr (2004) J Am Chem Soc 126:472-473
38. Davydov R, Makris TM, Kofman V, Werst DE, Sligar SG, Hoffman BM (2001) J Am Chem Soc 123:1403-1453
39. Schoneboom JC, Niese F, Thiel W (2005) J Am Chem Soc 127:5840-5853
40. Yoshizawa K (2002) Coord Chem Rev 226:251-259
41. Kamachi T, Yoshizawa K (2003) J Am Chem Soc 125:4652-4661
42. Kamachi T, Shestakov AF, Yoshizawa K (2004) J Am Chem Soc 126:3672-3673