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

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.

An attempt to evaluate the effect of proton-coupled electron transfer on the H-abstraction step of the reaction between 1,1-dimethylhydrazine and cytochrome P450 compound I

“…Again, this state will be significantly destabilized, as the N H distance becomes longer. State II may be less stable than I at the reactant state, because even though having an N H covalent bond will stabilize II, a single ET from the substrate to the a 2u orbital is not a facile process in our experience [43], although exceptional cases have been shown to exist [14,15,44].…”

“…This seems to suggest that the ET and PT occur in a stepwise manner. However, as mentioned above, the ET process is usually not energetically favorable in P450 reactions and does not yield a stable intermediate for a stepwise mechanism [43]. Therefore, the ET and PT processes are regarded as effectively concerted.…”

Suicide Inhibition of Cytochrome P450 Enzymes by Cyclopropylamines via a Ring-Opening Mechanism: Proton-Coupled Electron Transfer Makes a Difference

“…Owing to the newly-formed hydrogen-bonding between O-H and N, dichotomous behaviors are encountered at the following step. The amino radical IM species could undergo either a traditional O-rebound process to yield hydroxylamine which has been deemed to be the precursor to oxime (Cerny and Hanzlik, 2005 ; Hirao et al, 2013b ), or a rapid ring-opening of the cyclopropyl group forming a C -centered radical species, which is essential for the enzyme inactivation and could be converted to 3HP via a further oxidation.…”

Applications of density functional theory to iron-containing molecules of bioinorganic interest

“…Rather, one must use quantum mechanical methods such as DFT. In recent years, several research groups have reported DFT studies of P450 MBI (de Visser et al, 2004 ; Rydberg and Olsen, 2011 ; Hirao et al, 2012 , 2013a , b ; Taxak et al, 2012 , 2013a , b ).…”

“…More recently, Hirao et al investigated part of the MBI process caused by amine-containing drugs (Hirao et al, 2013b ). Amines are prone to form nitrosoalkane metabolic intermediates in P450-mediated metabolism, and the nitrosoalkanes form a quasi-irreversible metabolic-intermediate complex (MIC) to inhibit P450s (Scheme 6 ) (Hanson et al, 2010 ).…”