Mechanism of the N-Hydroxylation of Primary and Secondary Amines by Cytochrome P450

Abstract

Cytochrome P450 enzymes (CYPs) metabolize alkyl- and arylamines, generating several different products. For the primary and secondary amines, some of these reactions result in hydroxylated amines, which may be toxic. Thus, when designing new drugs containing amine groups, it is important to be able to predict if a given compound will be a substrate for CYPs, in order to avoid toxic metabolites, and hence to understand the mechanism that is utilized by CYPs. Two possible mechanisms, for the N-hydroxylation of primary and secondary amines mediated by CYPs, are studied by density functional theory (DFT) for four different amines (aniline, N-methylaniline, propan-2-amine, and dimethylamine). The hydrogen abstraction and rebound mechanism is found to be preferred over a direct oxygen transfer mechanism for all four amines. However, in contrast to the same mechanism for the hydroxylation of aliphatic carbon atoms, the rebound step is shown to be rate-limiting in most cases.

Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2

“…The highest H-abstraction barriers are observed for the models where the H-bond between one of the amine protons and Thr124 via a bridging water molecule is not present (A-1, A-3 and C-1). The doublet and quartet barriers tend to be similar for the hydrogen abstraction step, which is consistent with the small model DFT studies of propan-2-amine hydroxylation, 33,34 and also with QM and QM/MM studies of C-H abstraction from alkanes. 59 The Boltzmann-weighted average barrier for the H-abstraction step is 8.1 kcal/mol and is accessible to both the doublet and quartet spin states of Cpd I.…”

Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s.

“…They have investigated mainly two different mechanism: i) hydrogen abstraction followed by rebound of a nitrogen centered radical and ii) direct oxygen transfer to nitrogen, then displacement of oxidation product by water, followed by proton transfer to give the hydroxylamine metabolite. Mechanism where oxygen insertion into N−H bond takes place was not considered due to higher barriers reported in earlier QM only studies . Protein‐ligand complex geometries generated from docking which corresponded to reported metabolic products (i.e.…”

“…Mechanism where oxygen insertion into NÀH bond takes place was not considered due to higher barriers reported in earlier QM only studies. [169,170] Protein-ligand complex geometries generated from docking which corresponded to reported metabolic products (i.e. where implicated SOM was close to heme FeO group) were selected for MD simulations.…”

Enzymatic Late‐Stage Oxidation of Lead Compounds with Solubilizing Biomimetic Docking/Protecting groups

“…[4] Chemists utilizing biotransformations for LSO of drug candidates may come across various obstacles such as limited substrate scope, poor substrate aqueous solubility,o ru nwanted metabolism of reactive functionality (e.g.,a mines,t hiols, or CÀ Hb onds alpha to heteroatoms). [5] As many biologically active molecules contain amine functionalities, the reactivity of amines can be particularly problematic when considering these structuresf or bio-LSO modification as not only unstable metabolites are formed, but aminesa nd their metabolites can inhibit P450 enzymes (see Figure 1). [6] Whilst protein engineering can be used to addresst he issues of substrate scope, [8] solubility [9] and regioselectivity, [8d, 10] this strategy is not often conveniently availablei nm ost organic chemistry laboratories.…”

“…Composition of P450 BM3-F87V oxidation reactions with protected Vabicaserin analogues(2)(3)(4)(5)(6). The regiono fo xidation (%AUCa sd etermined by LC-MS/MS)isd ependent on the positioning of the protecting groupc arboxylate moiety.The numbersi nbrackets refer to the number of metabolites found within each regional classification (stereoisomers could not be separated).…”