Electronic Structure of Compound I in Human Isoforms of Cytochrome P450 from QM/MM Modeling

Abstract

Human cytochromes P450 play a vital role in drug metabolism. The key step in substrate oxidation involves hydrogen atom abstraction or C=C bond addition by the oxygen atom of the Compound I intermediate. The latter has three unpaired electrons, two on the Fe-O center and one shared between the porphyrin ring and the proximal cysteinyl sulfur atom. Changes in its electronic structure have been suggested to affect reactivity. The electronic and geometric structure of Compound I in three important human subfamilies of cytochrome P450 (P450, 2C, 2B, and 3A) that are major contributors to drug metabolism is characterized here using combined quantum mechanical/molecular mechanical (QM/MM) calculations at the B3LYP:CHARMM27 level. Compound I is remarkably similar in all isoforms, with the third unpaired electron located mainly on the porphyrin ring, and this prediction is not very sensitive to details of the QM/MM methodology, such as the DFT functional, the basis set, or the size of the QM region. The presence of substrate also has no effect. The main source of variability in spin density on the cysteinyl sulfur (from 26 to 50%) is the details of the system setup, such as the starting protein geometry used for QM/MM minimization. This conformational effect is larger than the differences between human isoforms, which are therefore not distinguishable on electronic grounds, so it is unlikely that observed large differences in substrate selectivity can be explained to a large extent in these terms.

X-ray absorption spectroscopy of chloroperoxidase compound I: Insight into the reactive intermediate of P450 chemistry

“…Density functional calculations predict that the donating thiolate ligand is oxidized during compound I formation (12)(13)(14). This result (which deviates from the standard porphyrin-radical cation model) provides a satisfactory explanation for the unique electronic coupling observed in CPO-I (12).…”

Understanding the determinants of selectivity in drug metabolism through modeling of dextromethorphan oxidation by cytochrome P450

“…The initial structure used in the simulations was constructed on the basis of the crystallographic structure of P450 2D6 (42) obtained from the Protein Data Bank (PDB code 2F9Q). The CHARMM27 force field (43) and the CHARMM package version c27b2 (44) were used in all MM minimizations and MD simulations, with Compound I parameters for the heme group (45). For dextromethorphan, standard CHARMM27 parameters were used, extended with parameters for the ether group (SI Appendix) (46).…”

“…Then, hydrogen atoms were added to the initial enzyme/substrate complexes, and their positions were optimized. Histidine protonation states were assigned according to the local environment, as in our previous work (45). The protein was truncated to a 25-Å sphere centered on the heme iron.…”

Biomolecular simulation and modelling: status, progress and prospects

“…by including electronic polarization), and avoiding the need for time-consuming development of MM parameters for the ligand. Also, MM methods may be inadequate for some types of pharmaceutically important target proteins, particularly metalloproteins (such as cytochrome P450 enzymes involved in drug metabolism; Bathelt et al 2005). For such biomolecular systems, the use of QM/MM approaches for the predictions of relative binding affinity or binding mode may be significantly better.…”