Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3.
Three newly discovered drug metabolizing mutants of cytochrome P450 BM3 (van Vugt-Lussenburg et al., Identification of critical residues in novel drug metabolizing mutants of Cytochrome P450 BM3 using random mutagenesis, J Med Chem 2007;50:455-461) have been studied at an atomistic level to provide structural explanations for a number of their characteristics. In this study, computational methods are combined with experimental techniques. Molecular dynamics simulations, resonance Raman and UV-VIS spectroscopy, as well as coupling efficiency and substrate-binding experiments, have been performed. The computational findings, supported by the experimental results, enable structural rationalizations of the mutants. The substrates used in this study are known to be metabolized by human cytochrome P450 2D6. Interestingly, the major metabolites formed by the P450 BM3 mutants differ from those formed by human cytochrome P450 2D6. The computational findings, supported by resonance Raman data, suggest a conformational change of one of the heme propionate groups. The modeling results furthermore suggest that this conformational change allows for an interaction between the negatively charged carboxylate of the heme substituent and the positively charged nitrogen of the substrates. This allows for an orientation of the substrates favorable for formation of the major metabolite by P450 BM3.
Stjernschantz
Eva
E
Leiden/Amsterdam Centre for Drug Research, Division of Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
van Vugt-Lussenburg
Barbara M A
BM
Bonifacio
Alois
A
de Beer
Stephanie B A
SB
van der Zwan
Gert
G
Gooijer
Cees
C
Commandeur
Jan N M
JN
Vermeulen
Nico P E
NP
Oostenbrink
Chris
C
D003198:Computer Simulation; D019389:Cytochrome P-450 CYP2D6 / Q000737:chemistry / Q000235:genetics; D003577:Cytochrome P-450 Enzyme System / Q000737:chemistry* / Q000235:genetics*; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D009154:Mutation; D004364:Pharmaceutical Preparations / Q000378:metabolism; D011487:Protein Conformation
D008024:Ligands; D004364:Pharmaceutical Preparations; D003577:Cytochrome P-450 Enzyme System; D019389:Cytochrome P-450 CYP2D6