Metabolism of 4-Aminopiperidine Drugs by Cytochrome P450s: Molecular and Quantum Mechanical Insights into Drug Design

Cytochrome P450 enzymes are found in all life forms. P450s play an important role in drug metabolism, and have potential uses as biocatalysts. Human P450s are membrane-bound proteins. However, the interactions between P450s and their membrane environment are not well-understood. To date, all P450 crystal structures have been obtained from engineered proteins, from which the transmembrane helix was absent. A significant number of computational studies have been performed on P450s, but the majority of these have been performed on the solubilised forms of P450s. Here we present a multiscale approach for modelling P450s, spanning from coarse-grained and atomistic molecular dynamics simulations to reaction modelling using hybrid quantum mechanics/molecular mechanics (QM/MM) methods. To our knowledge, this is the first application of such an integrated multiscale approach to modelling of a membrane-bound enzyme. We have applied this protocol to a key human P450 involved in drug metabolism: CYP3A4. A biologically realistic model of CYP3A4, complete with its transmembrane helix and a membrane, has been constructed and characterised. The dynamics of this complex have been studied, and the oxidation of the anticoagulant R-warfarin has been modelled in the active site. Calculations have also been performed on the soluble form of the enzyme in aqueous solution. Important differences are observed between the membrane and solution systems, most notably for the gating residues and channels that control access to the active site. The protocol that we describe here is applicable to other membrane-bound enzymes.

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“…[49] However, in the current work no interactions were observed between R-warfarin and this residue.…”

Section: Resultscontrasting

confidence: 62%

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes

et al. 2014

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“…We found the hydrophobic Ϫ stacking interactions between the pyrimidine ring of CP-945,598 and the side chain of phenylalanine-108 at the B-C loop (ϳ3.7 Å), as well as the potential formation of the hydrogen bond between the amide carbonyl group of CP-945,598 and the hydroxyl group of serine-119 at the B-C loop (ϳ3.3 Å between two oxygen atoms), juxtapose the methylene carbon over the heme iron-oxo (ϳ2.8Å from the carbon to the iron-oxo). The calculated activation energy of the methylene carbon is 97.24 kcal/mol (Table 6), in a similar range as those previously reported for N-dealkylation reactions (Sun and Scott, 2011). Thus, this binding pose suggests an N-deethylation pathway, which is indeed the predominant metabolic route we observed in our in vitro studies.…”

Section: Biotransformation Of Cp-945598supporting

confidence: 87%

“…The Gasteiger atomic charges were assigned with flexible torsions defined for CP-945,598 and M1. The protein template was recalculated based on a series of the X-ray crystallography-determined three-dimensional coordinates of CYP3A4 in the Protein Data Bank (codes 1TQN, 1W0E, 1W0F, 1W0G, 2J0D, 2V0M, and 3NXU) and Pfizer's Protein Structure Database (Sun et al, 2009a,b;Sun and Scott, 2011). An oxygen atom was added on top of the heme iron at a distance of 1.7 Å to simulate P450 compound I.…”

Section: Miao Et Almentioning

confidence: 99%

Excretion, Metabolism, and Pharmacokinetics of 1-(8-(2-Chlorophenyl)-9-(4-Chlorophenyl)-9H-Purin-6-yl)-4-(Ethylamino)Piperidine-4-Carboxamide, a Selective Cannabinoid Receptor Antagonist, in Healthy Male Volunteers

Miao

Sun²,

Liras³

et al. 2011

Drug Metab Dispos

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“…This observation is supported by recent work on 4-aminopiperidines (Sun & Scott, 2011), where steric bulk on the piperidine nitrogen (e.g. indoramine, lorcainide, sabeluzole, and astemizole) resulted in unfavorable, high-energy conformations at the enzyme active site, ultimately reducing the N-dealkylation pathways.…”

Section: Discussionmentioning

confidence: 53%

Strategies toward optimization of the metabolism of a series of serotonin-4 partial agonists: investigation of azetidines as piperidine isosteres

Obach¹,

LaChapelle²,

Brodney

et al. 2016

Xenobiotica

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1.The first generation 5HT-4 partial agonist, 4-{4-[4-Tetrahydrofuran-3-yloxy)-benzo[d]isoxazol-3-yloxymethyl]-piperidin-1-ylmethyl}-tetrahydropyran-4-ol, PF-4995274 (TBPT), was metabolized to N-dealkylated (M1) and an unusual, cyclized oxazolidine (M2) metabolites. M1 and M2 demonstrated pharmacological activity at 5HT receptor subtypes warranting further investigation into their dispositional properties in humans; M2 was a minor component in vitro but was the pre-dominant metabolite identified in human plasma. 2.To shift metabolism away from the piperidine ring of TBPT, a series of heterocyclic replacements were designed, synthesized, and profiled. Groups including azetidines, pyrrolidines, as well as functionalized piperidines were evaluated with the goal of identifying an alternative group that maintained the desired potency, functional activity, and reduced turnover in human hepatocytes. 3.Activities of 4-substituted piperidines or pyrrolidine analogs at the pharmacological target were not significantly altered, but the same metabolic pathways of N-dealkylation and oxazolidine formation were still observed. Altering these to bridged ring systems lowered oxazolidine metabolite formation, but not N-dealkylation. 4.The effort concluded with identification of azetidines as second-generation 5HT partial agonists. These were neither metabolized via N-dealkylation nor converted to cyclized oxazolidine metabolites rather oxidized on the isoxazole ring. The use of azetidine as a replacement for aliphatic aza-heterocyclic rings in drug design to alter drug metabolism and pharmacology is discussed.

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Metabolism of 4-Aminopiperidine Drugs by Cytochrome P450s: Molecular and Quantum Mechanical Insights into Drug Design

Cited by 43 publications

References 16 publications

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes

Excretion, Metabolism, and Pharmacokinetics of 1-(8-(2-Chlorophenyl)-9-(4-Chlorophenyl)-9H-Purin-6-yl)-4-(Ethylamino)Piperidine-4-Carboxamide, a Selective Cannabinoid Receptor Antagonist, in Healthy Male Volunteers

Strategies toward optimization of the metabolism of a series of serotonin-4 partial agonists: investigation of azetidines as piperidine isosteres

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