A Computational Understanding of Inter-Individual Variability in CYP2D6 Activity to Investigate the Impact of Missense Mutations on Ochratoxin A Metabolism

Abstract

Cytochrome P-450 (CYP) enzymes have a key role in the metabolism of xenobiotics of food origin, and their highly polymorphic nature concurs with the diverse inter-individual variability in the toxicokinetics (TK) and toxicodynamics (TD) of food chemicals. Ochratoxin A is a well-known mycotoxin which contaminates a large variety of food and is associated with food safety concerns. It is a minor substrate of CYP2D6, although the effects of CYP2D6 polymorphisms on its metabolism may be overlooked. Insights on this aspect would provide a useful mechanistic basis for a more science-based hazard assessment, particularly to integrate inter-individual differences in CYP2D6 metabolism. This work presents a molecular modelling approach for the analysis of mechanistic features with regard to the metabolic capacity of CYP2D6 variants to oxidise a number of substrates. The outcomes highlighted that a low-frequency CYP2D6 variant (CYP2D6*110) is likely to enhance ochratoxin A oxidation with possible consequences on TK and TD. It is therefore recommended to further analyse such TK and TD consequences. Generally speaking, we propose the identification of mechanistic features and parameters that could provide a semi-quantitative means to discriminate ligands based on the likelihood to undergo transformation by CYP2D6 variants. This would support the development of a fit-for-purpose pipeline which can be extended to a tool allowing for the bulk analysis of a large number of compounds. Such a tool would ultimately include inter-phenotypic differences of polymorphic xenobiotic-metabolising enzymes in the hazard assessment and risk characterisation of food chemicals.

Keywords: CYP2D6; food safety; hazard assessment; ochratoxin A; polymorphism metabolism; toxicokinetics.

Figure 1

Chemical structure of molecules under analysis (drawn with ChemDraw version 20.1.1; PerkinElmer Informatics). The asterisk indicates the atom undergoing the reaction considered in this study. (A) OTA. (B) Dextromethorphan. (C) Bufuralol.

Figure 2

Docking poses of dextromethorphan, bufuralol and OTA within CYP2D6*1. Protein is represented in cartoon, while ligands and heme group are represented in sticks. Fe ion is represented in sphere. Yellow dashed lines indicate the distance between Fe and the atom undergoing the reaction.

Figure 3

Molecular dynamics results on CYP2D6*1, CYP2D6*14A and CYP2D6*51. (A) Interatomic distances between dextromethorphan’s atom undergoing reaction and Fe-heme within CYP2D6*1, CYP2D6*14A or CYP2D6*51. (B) Interatomic distances between bufuralol’s atom undergoing reaction and Fe-heme within CYP2D6*1, CYP2D6*14A or CYP2D6*51. (C) Time-step representations of the trajectories of atom undergoing reaction (shown in sphere) of dextromethorphan or bufuralol within CYP2D6*1, CYP2D6*14A or CYP2D6*51. Proteins are represented in cartoon, while heme is represented in sticks. The from-red-to-blue colour switch indicates the stepwise changes of coordinates along the simulation. The white arrows retrace the direction of trajectories. (D) Interatomic distances between Fe-heme and the atom undergoing reaction of dextromethorphan, bufuralol or OTA within CYP2D6*1. (E) Inter-atomic distances between OTA’s atom undergoing reaction and Fe-heme within CYP2D6*1, CYP2D6*14A or CYP2D6*51.

Figure 4

Molecular dynamics results of CYP2D6*1, CYP2D6*110 and CYP2D6*122. (A) Interatomic distances between OTA’s atom undergoing reaction and Fe-heme within CYP2D6*1, CYP2D6*110 or CYP2D6*122. (B) Time-step representations of the trajectories of atom undergoing reaction (shown in sphere) of OTA within CYP2D6*1, CYP2D6*110 or CYP2D6*122. Proteins are represented in cartoon, while heme is represented in sticks. The from-red-to-blue colour switch indicates the stepwise changes of coordinates along the simulation. The white arrows retrace the direction of trajectories.

Figure 5

Flowchart of key methodological steps for the ligand-CYP2D6 analysis.