Cytochrome P450 reactivity and specificity from QM/MM modelling
Lonsdale, Richard #
The cytochromes P450 (CYPs) are an important family of enzymes involved in the metabolism of drugs. The prediction of the selectivity of CYP-mediated metabolism will assist in the avoidance of adverse drug reactions. A detailed understanding of the factors that govern the selectivity is of fundamental importance to the development of predictive models.
Selectivity of CYP enzymes is partially attributed to the relative reactivity of different functional groups of a substrate with respect to the active oxidizing species, Compound I. A combined quantum mechanical/molecular mechanical (QM/MM) approach has been employed to model the chemoselectivity of alkene oxidation in P450cam. Two model compounds were used, yielding relative energy barriers that are consistent with experiment.
The regioselectivity of oxidation is governed by the orientation of substrate relative to Compound I, determined by the residues surrounding the active site of the enzyme. The anticoagulant drug S-warfarin has been modelled in the active site of the human CYP2C9 isoform using molecular dynamics (MD), to probe the mobility of the substrate in the enzyme pocket. The hydroxylation of S-warfarin was modelled in CYP2C9 using QM/MM. The reaction energies predict the major metabolite formed in experimental studies and suggest the formation of reactive intermediates such as epoxides. A two- substrate model has been considered, showing that it may be possible for CYP2C9 to oxidize a substrate molecule whilst simultaneously accommodating an additional substrate molecule.
Experimental characterization of Compound I is prevented by its high reactivity. The electronic structure of Compound I was shown previously to be sensitive to its environment, and postulated to vary between different CYP isoforms. The electronic structure of Compound I has been compared in different CYP isoforms using QM/MM. Although the electronic structure was found not to vary significantly between isoforms, the presence of substrate has been found to have an effect.