Importance of H-Abstraction in the Final Step of Nitrosoalkane Formation in the Mechanism-Based Inactivation of Cytochrome P450 by Amine-Containing Drugs

Hajime Hirao,Nandun Thellamurege,Pratanphorn Chuanprasit,Kai Xu

doi:10.3390/ijms141224692

Abstract

The metabolism of amine-containing drugs by cytochrome P450 enzymes (P450s) is prone to form a nitrosoalkane metabolic intermediate (MI), which subsequently coordinates to the heme iron of a P450, to produce a metabolic-intermediate complex (MIC). This type of P450 inhibition, referred to as mechanism-based inactivation (MBI), presents a serious concern in drug discovery processes. We applied density functional theory (DFT) to the reaction between N-methylhydroxylamine (NMH) and the compound I reactive species of P450, in an effort to elucidate the mechanism of the putative final step of the MI formation in the alkylamine metabolism. Our DFT calculations show that H-abstraction from the hydroxyl group of NMH is the most favorable pathway via which the nitrosoalkane intermediate is produced spontaneously. H-abstraction from the N–H bond was slightly less favorable. In contrast, N-oxidation and H-abstraction from the C–H bond of the methyl group had much higher energy barriers. Hence, if the conversion of NMH to nitrosoalkane is catalyzed by a P450, the reaction should proceed preferentially via H-abstraction, either from the O–H bond or from the N–H bond. Our theoretical analysis of the interaction between the MI and pentacoordinate heme moieties provided further insights into the coordination bond in the MIC.

Highlights

Human cytochrome P450 enzymes (P450s) are known as versatile biological catalysts with remarkably broad substrate specificity [1,2,3,4,5,6,7,8,9,10,11,12,13,14]
A density functional theory (DFT) study was undertaken to elucidate the mechanism of the P450-catalyzed conversion of NMH into a nitrosomethane intermediate that eventually causes P450 inhibition
Based on the energy data, we conclude that the pathways involving H-abstraction from the O–H or the N–hydrogen bond (H bond) are more plausible than the N-oxidation and C–H activation pathways

Summary

Introduction

Human cytochrome P450 enzymes (P450s) are known as versatile biological catalysts with remarkably broad substrate specificity [1,2,3,4,5,6,7,8,9,10,11,12,13,14]. We examine the mechanism in which an oxoiron(IV) porphyrin π-cation radical intermediate, compound I (Cpd I), of a P450, is responsible for this oxidative process, it should be mentioned that 4 may not always require a P450 for the oxidation because it readily undergoes autoxidation [39,42]. As this step is not well explored, we here attempt to find a plausible reaction mechanism using density functional theory (DFT) calculations. We investigate the nature of the coordination bonds in ferrous and ferric MICs

Models

Reaction Mechanism

Coordination Bond in MIC

Energy Decomposition Analysis of MIC

Experimental Section

Conclusions