Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-Å resolution

Molecular Pharmacology

Volumn 77, Issue 4, 2010, Pages 529-538

  Gay, Sean C ^a   Shah, Manish B ^a   Talakad, Jyothi C ^a   Maekawa, Keiko ^c   Roberts, Arthur G ^a   Wilderman, P Ross ^a   Sun, Ling ^d   Yang, Jane Y ^b   Huelga, Stephanie C ^b   Hong, Wen Xu ^e   Zhang, Qinghai ^e   Stout, C David ^e   Halpert, James R ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL INSTITUTE OF HEALTH SCIENCES   (Japan)

^d MEDICAL UNIVERSITY OF SOUTH CAROLINA   (United States)

^e SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4 (4 CHLOROPHENYL)IMIDAZOLE; CYTOCHROME P450 2B1; CYTOCHROME P450 2B4; CYTOCHROME P450 2B6; IMIDAZOLE DERIVATIVE; TICLOPIDINE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME BINDING; GENETIC VARIABILITY; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; SITE DIRECTED MUTAGENESIS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANIMALS; ARYL HYDROCARBON HYDROXYLASES; BINDING SITES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; ENZYME INHIBITORS; HUMANS; IMIDAZOLES; MOLECULAR SEQUENCE DATA; OXIDOREDUCTASES, N-DEMETHYLATING; PROTEIN STRUCTURE, SECONDARY; RABBITS;

EID: 77950284730     PISSN: 0026895X     EISSN: 15210111     Source Type: Journal    
DOI: 10.1124/mol.109.062570     Document Type: Article

References (39)

1. Bumpus NN and Hollenberg PF (2008) Investigation of the mechanisms underlying the differential effects of the K262R mutation of P450 2B6 on catalytic activity. Mol Pharmacol 74:990-999.
2. Bumpus NN, Sridar C, Kent UM, and Hollenberg PF (2005) The naturally occurring cytochrome P450 (P450) 2B6 K262R mutant of P450 2B6 exhibits alterations in substrate metabolism and inactivation. Drug Metab Dispos 33:795-802.
3. Chen CS, Lin JT, Goss KA, He YA, Halpert JR, and Waxman DJ (2004) Activation of the anticancer prodrugs cyclophosphamide and ifosfamide: identification of cytochrome P450 2B enzymes and site-specific mutants with improved enzyme kinetics. Mol Pharmacol 65:1278-1285.
4. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760-763.
5. Cosme J and Johnson EF (2000) Engineering microsomal cytochrome P450 2C5 to be a soluble, monomeric enzyme: mutations that alter aggregation, phospholipid dependence of catalysis, and membrane binding. J Biol Chem 275:2545-2553.
6. Domanski TL and Halpert JR (2001) Analysis of mammalian cytochrome P450 structure and function by site-directed mutagenesis. Curr Drug Metab 2:117-137.
7. Domanski TL, Schultz KM, Roussel F, Stevens JC, and Halpert JR (1999) Structure-function analysis of human cytochrome P-450 2B6 using a novel substrate, site-directed mutagenesis, and molecular modeling. J Pharmacol Exp Ther 290:1141-1147.
8. Ekins S, Iyer M, Krasowski MD, and Kharasch ED (2008) Molecular characterization of CYP2B6 substrates. Curr Drug Metab 9:363-373.
9. Emsley P and Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126-2132.
10. Gay SC, Sun L, Maekawa K, Halpert JR, and Stout CD (2009) Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand-induced structural response through α-helical repositioning. Biochemistry 48:4762-4771.
11. Hanna IH, Reed JR, Guengerich FP, and Hollenberg PF (2000) Expression of human cytochrome P450 2B6 in Escherichia coli: characterization of catalytic activity and expression levels in human liver. Arch Biochem Biophys 376:206-216.
12. Helms V and Wade RC (1995) Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study. Biophys J 69:810-824.
13. Johnson EF and Stout CD (2005) Structural diversity of human xenobiotic-metabolizing cytochrome P450 monooxygenases. Biochem Biophys Res Commun 338:331-336.
14. Kumar S, Zhao Y, Sun L, Negi SS, Halpert JR, and Muralidhara BK (2007) Rational engineering of human cytochrome P450 2B6 for enhanced expression and stability: importance of a Leu264->Phe substitution. Mol Pharmacol 72:1191-1199.
15. Leslie AG (1999) Integration of macromolecular diffraction data. Acta Crystallogr D Biol Crystallogr 55:1696-1702.
16. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, and Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40:658-674.
17. Mitsuda M and Iwasaki M (2006) Improvement in the expression of CYP2B6 by co-expression with molecular chaperones GroES/EL in Escherichia coli. Protein Expr Purif 46:401-405.
18. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, and Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J Comput Chem 19:1639-1662.
19. Nishiya Y, Hagihara K, Ito T, Tajima M, Miura S, Kurihara A, Farid NA, and Ikeda T (2009) Mechanism-based inhibition of human cytochrome P450 2B6 by ticlopidine, clopidogrel, and the thiolactone metabolite of prasugrel. Drug Metab Dispos 37:589-593.
20. Porubsky PR, Meneely KM, and Scott EE (2008) Structures of human cytochrome P450 2E1. Insights into the binding of inhibitors and both small molecular weight and fatty acid substrates. J Biol Chem 283:33698-33707.
21. Sansen S, Yano JK, Reynald RL, Schoch GA, Griffin KJ, Stout CD, and Johnson EF (2007) Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2. J Biol Chem 282:14348-14355.
22. Schoch GA, Yano JK, Wester MR, Griffin KJ, Stout CD, and Johnson EF (2004) Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site. J Biol Chem 279:9497-9503.
23. Scott EE, He YA, Wester MR, White MA, Chin CC, Halpert JR, Johnson EF, and Stout CD (2003) An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution. Proc Natl Acad Sci U S A 100:13196-13201.
24. Scott EE, Spatzenegger M, and Halpert JR (2001) A truncation of 2B subfamily cytochromes P450 yields increased expression levels, increased solubility, and decreased aggregation while retaining function. Arch Biochem Biophys 395:57-68.
25. Scott EE, White MA, He YA, Johnson EF, Stout CD, and Halpert JR (2004) Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl) imidazole at 1.9-Å resolution: insight into the range of P450 conformations and coordination of redox partner binding. J Biol Chem 279:27294-27301.
26. Shebley M and Hollenberg PF (2007) Mutation of a single residue (K262R) in P450 2B6 leads to loss of mechanism-based inactivation by phencyclidine. Drug Metab Dispos 35:1365-1371.
27. Spatzenegger M, Liu H, Wang Q, Debarber A, Koop DR, and Halpert JR (2003) Analysis of differential substrate selectivities of CYP2B6 and CYP2E1 by site-directed mutagenesis and molecular modeling. J Pharmacol Exp Ther 304:477-487.
28. Talakad JC, Kumar S, and Halpert JR (2009) Decreased susceptibility of the cytochrome P450 2B6 variant K262R to inhibition by several clinically important drugs. Drug Metab Dispos 37:644-650.
29. von Wachenfeldt C, Richardson TH, Cosme J, and Johnson EF (1997) Microsomal P450 2C3 is expressed as a soluble dimer in Escherichia coli following modification of its N-terminus. Arch Biochem Biophys 339:107-114.
30. Walsky RL, Astuccio AV, and Obach RS (2006) Evaluation of 227 drugs for in vitro inhibition of cytochrome P450 2B6. J Clin Pharmacol 46:1426-1438.
31. Wang H and Tompkins LM (2008) CYP2B6: new insights into a historically overlooked cytochrome P450 isozyme. Curr Drug Metab 9:598-610.
32. Wang Q and Halpert JR (2002) Combined three-dimensional quantitative structure-activity relationship analysis of cytochrome P450 2B6 substrates and protein homology modeling. Drug Metab Dispos 30:86-95.
33. Williams PA, Cosme J, Sridhar V, Johnson EF, and McRee DE (2000) Microsomal cytochrome P450 2C5: comparison to microbial P450s and unique features. J Inorg Biochem 81:183-190.
34. Williams PA, Cosme J, Ward A, Angove HC, Matak Vinković D, and Jhoti H (2003) Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature 424:464-468.
35. Zanger UM, Klein K, Saussele T, Blievernicht J, Hofmann MH, and Schwab M (2007) Polymorphic CYP2B6: molecular mechanisms and emerging clinical significance. Pharmacogenomics 8:743-759.
36. Zhang Q, Ma X, Ward A, Hong WX, Jaakola VP, Stevens RC, Finn MG, and Chang G (2007) Designing facial amphiphiles for the stabilization of integral membrane proteins. Angew Chem Int Ed Engl 46:7023-7025.
37. Zhao Y and Halpert JR (2006) Structure-function analysis of cytochromes P450 2B. Biochim Biophys Acta 1770:402-412.
38. Zhao Y, Sun L, Muralidhara BK, Kumar S, White MA, Stout CD, and Halpert JR (2007) Structural and thermodynamic consequences of 1-(4-chlorophenyl) imidazole binding to cytochrome P450 2B4. Biochemistry 46:11559-11567.
39. Zhao Y, White MA, Muralidhara BK, Sun L, Halpert JR, and Stout CD (2006) Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction. J Biol Chem 281:5973-5981.