Microsecond MD simulations of human CYP2D6 wild-type and five allelic variants reveal mechanistic insights on the function.

Charleen G Don,Martin Smieško

doi:10.1371/journal.pone.0202534

Abstract

Characterization of cytochrome P450 2D6 (CYP2D6) and the impact of the major identified allelic variants on the activity of one of the most dominating drug-metabolising enzymes is essential to increase drug safety and avoid adverse reactions. Microsecond molecular dynamics simulations have been performed to capture the dynamic signatures of this complex enzyme and five allelic variants with diverse enzymatic activity. In addition to the apo simulations, three substrates (bufuralol, veliparib and tamoxifen) and two inhibitors (prinomastat and quinidine) were included to explore their influence on the structure and dynamical features of the enzyme. Our results indicate that the altered enzyme activity can be attributed to changes in the hydrogen bonding network within the active site, and local structural differences in flexibility, position and shape of the binding pocket. In particular, the increased (CYP2D6*53) or the decreased (CYP2D6*17) activity seems to be related to a change in dynamics of mainly the BC loop due to a modified hydrogen bonding network around this region. In addition, the smallest active site volume was found for CYP2D6*4 (no activity). CYP2D6*2 (normal activity) showed no major differences in dynamic behaviour compared to the wild-type.

Highlights

Genetic polymorphism in cytochrome P450 2D6 (CYP2D6), a monooxygenase enzyme metabolizing around 25% of the therapeutic drugs [1], frequently leads to altered enzyme activity which in turn has an impact on the drug efficacy and the occurrence of adverse reactions [2]
The folding of primarily the FG loop and secondary the AB- and BC loop around the active site is reshaped upon the ligand binding, which contributed to the larger identified volumes and a more closed state
Differences in flexibility and arrangement of the key residues lining the active site, together with the intra- and intermolecular forces among the variants with changed enzymatic activity, suggest the need for a precise positioning of these factors to control optimal proceeding of the catalytic reaction, which is tightly coupled to the kinetics of the enzyme

Summary

Introduction

Genetic polymorphism in CYP2D6, a monooxygenase enzyme metabolizing around 25% of the therapeutic drugs [1], frequently leads to altered enzyme activity (increased, decreased or none) which in turn has an impact on the drug efficacy and the occurrence of adverse reactions [2]. During the last decade, increased awareness concerning the risks that CYP2D6 polymorphism can bear on treatment outcome has lead to relabeling of several CYP2D6 metabolized drugs with additional guidelines on drug dosage in case of polymorphism by the FDA [4]. The clinical pharmacogenetics implementation consortium (CPIC) has been procuring therapeutic guidelines for several drugs that have a high risk of adverse reactions when administered to patients with a phenotype deviating from the normal CYP2D6 activity (wild-type) [5].

Methods

Results

Conclusion