Molecular Dynamics Simulations Reveal Structural Differences among Allelic Variants of Membrane-Anchored Cytochrome P450 2D6

Cytochrome
P450 2D6 (CYP2D6) is an enzyme that is involved in the
metabolism of roughly 25% of all marketed drugs and therefore belongs
to the most important enzymes in drug metabolism. CYP2D6 features
a high degree of genetic polymorphism that can significantly affect
the metabolic activity of an individual. In extreme cases, structural
changes at the level of single amino acids can either increase its
enzymatic activity abolishing the drug therapeutic effect or completely
disable the enzyme and elevate drug plasma level potentially leading
to adverse effects. In this study, starting from the crystal structure,
we built a full-length membrane-anchored all-atom model of the wild-type
CYP2D6 as well as five of its variants differing in the enzymatic
activity. We validated our models with available experimental data
and compared their structural properties with molecular dynamics simulations.
The main focus of this study was to identify differences that could
mechanistically explain the altered activity of the variants and improve
our understanding of their functioning. We observed differences in
the opening frequencies and minimal diameters of tunnels that connect
the buried active site to the surrounding solvent environment. The
variants CYP2D6*4 and CYP2D6*10 associated with missing or decreased
activity showed less frequent opening of the tunnels compared to the
wild-type. Both CYP2D6*10 and CYP2D6*17 showed a deprivation of an
important ligand tunnel suggesting a feasible reason for their altered
substrate specificity. Next, the altered fold at the N-terminal anchor
region and the decreased active site volume caused by the amino acid
mutations of the CYP2D6*4 variant offer an explanation for the absence
of its metabolic activity. The mutations in CYP2D6*53 contributed
to a significant enlargement of an important ligand tunnel and an
extension of the active site cavity. This could explain the altered
metabolic profile as well as the enhanced metabolic rates of this
particular variant supporting its designation as a possible cause
for the ultrarapid metabolizer phenotype. We believe these novel structural
insights could advance the fields of personalized medicine and enzyme
engineering. Furthermore, they could aid in guiding laboratory as
well as computational experiments in the future.