Quantum mechanics/molecular mechanics modeling of drug metabolism: Mexiletine N-hydroxylation by cytochrome P450 1A2

Richard Lonsdale, Rachel Fort, Patrik Rydberg, Jeremy Harvey, Adrian Mulholland

Research output: Contribution to journalArticle (Academic Journal)peer-review

20 Citations (Scopus)
371 Downloads (Pure)

Abstract

The mechanism of cytochrome P450(CYP)-catalyzed hydroxylation of primary amines is currently unclear, and is relevant to drug metabolism. Previous small model calculations have suggested two possible mechanisms: direct N-oxidation and H-abstraction/rebound. We have modeled the N-hydroxylation of (R)-mexiletine in CYP1A2 with hybrid quantum mechanics/molecular mechanics (QM/MM) methods, providing a more detailed and realistic model. Multiple reaction barriers have been calculated at the QM(B3LYP- D)/MM(CHARMM27) level for the direct N-oxidation and H-abstraction/rebound mechanisms. Our calculated barriers indicate that the direct N-oxidation mechanism is preferred and proceeds via the doublet spin state of Compound I. Molecular dynam- ics simulations indicate that the presence of an ordered water molecule in the active site assists in the binding of mexiletine in the active site, but is not a prerequisite for reaction via either mechanism. Several active site residues play a role in the binding of mexiletine in the active site, including Thr124 and Phe226. This work reveals key details in the N-hydroxylation of mexiletine and further demonstrates that mechanistic studies using QM/MM methods are useful for understanding drug metabolism.
Original languageEnglish
Pages (from-to)963-971
Number of pages9
JournalChemical Research in Toxicology
Volume29
Issue number6
Early online date11 Apr 2016
DOIs
Publication statusPublished - 20 Jun 2016

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