QM/MM modeling of benzene hydroxylation in human cytochrome P450 2C9

J Phys Chem A. 2008 Dec 18;112(50):13149-56. doi: 10.1021/jp8016908.

Abstract

The mechanism of benzene hydroxylation was investigated in the realistic enzyme environment of the human CYP 2C9 by using quantum mechanical/molecular mechanical (QM/MM) calculations of the whole reaction profile using the B3LYP method to describe the QM region. The calculated QM/MM barriers for addition of the active species Compound I to benzene are consistent with experimental rate constants for benzene metabolism in CYP 2E1. In contrast to gas-phase model calculations, our results suggest that competing side-on and face-on geometries of arene addition may both occur in the case of aromatic ring oxidation in cytochrome P450s. QM/MM profiles for three different rearrangement pathways of the initially formed sigma-adduct, leading to formation of epoxide, ketone, and an N-protonated porphyrin species, were calculated. Our results suggest that epoxide and ketone products form with comparable ease in the face-on pathway, whereas epoxide formation is preferred in the side-on pathway. Additionally, rearrangement to the N-protonated porphyrin species was found to be competitive with side-on epoxide formation. This suggests that overall, the competition between formation of epoxide and phenol final products in P450 oxidation of aromatic substrates is quite finely balanced.

MeSH terms

  • Aryl Hydrocarbon Hydroxylases / chemistry*
  • Aryl Hydrocarbon Hydroxylases / metabolism*
  • Benzene / metabolism*
  • Calorimetry
  • Computer Simulation
  • Crystallography, X-Ray
  • Cytochrome P-450 CYP2C9
  • Epoxy Compounds / chemistry
  • Epoxy Compounds / metabolism
  • Heme / chemistry
  • Heme / metabolism
  • Humans
  • Hydroxylation
  • Ketones / chemistry
  • Ketones / metabolism
  • Porphyrins / chemistry
  • Porphyrins / metabolism
  • Quantum Theory
  • Thermodynamics

Substances

  • Epoxy Compounds
  • Ketones
  • Porphyrins
  • Heme
  • CYP2C9 protein, human
  • Cytochrome P-450 CYP2C9
  • Aryl Hydrocarbon Hydroxylases
  • Benzene