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Int. J. Mol. Sci. 2018, 19(7), 1974; https://doi.org/10.3390/ijms19071974

Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes

1
Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain
2
Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
3
State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China
*
Authors to whom correspondence should be addressed.
Received: 1 June 2018 / Revised: 28 June 2018 / Accepted: 2 July 2018 / Published: 6 July 2018
(This article belongs to the Section Bioinorganic Chemistry)
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Abstract

The cytochromes P450 are drug metabolizing enzymes in the body that typically react with substrates through a monoxygenation reaction. During the catalytic cycle two reduction and protonation steps generate a high-valent iron (IV)-oxo heme cation radical species called Compound I. However, with sufficient reduction equivalents present, the catalytic cycle should be able to continue to the reduced species of Compound I, called Compound II, rather than a reaction of Compound I with substrate. In particular, since electron transfer is usually on faster timescales than atom transfer, we considered this process feasible and decided to investigate the reaction computationally. In this work we present a computational study using density functional theory methods on active site model complexes alongside quantum mechanics/molecular mechanics calculations on full enzyme structures of cytochrome P450 enzymes. Specifically, we focus on the relative reactivity of Compound I and II with a model substrate for O–H bond activation. We show that generally the barrier heights for hydrogen atom abstraction are higher in energy for Compound II than Compound I for O–H bond activation. Nevertheless, for the activation of such bonds, Compound II should still be an active oxidant under enzymatic conditions. As such, our computational modelling predicts that under high-reduction environments the cytochromes P450 can react with substrates via Compound II but the rates will be much slower. View Full-Text
Keywords: enzyme mechanism; enzyme catalysis; heme; iron; hydrogen atom abstraction; density functional theory; QM/MM; inorganic reaction mechanism enzyme mechanism; enzyme catalysis; heme; iron; hydrogen atom abstraction; density functional theory; QM/MM; inorganic reaction mechanism
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Postils, V.; Saint-André, M.; Timmins, A.; Li, X.-X.; Wang, Y.; Luis, J.M.; Solà, M.; de Visser, S.P. Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes. Int. J. Mol. Sci. 2018, 19, 1974.

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