Phenylalanine Residues in the Active Site of CYP2E1 Participate in Determining the Binding Orientation and Metabolism-Dependent Genotoxicity of Aromatic Compounds

Abstract

The composition of amino acids forming the active site of a CYP enzyme is impactful in its substrate selectivity. For CYP2E1, the role of PHE residues in the formation of effective binding orientations for its aromatic substrates remains unclear. In this study, molecular docking and molecular dynamics analysis were performed to reflect the interactions between PHEs in the active site of human CYP2E1 and various aromatic compounds known as its substrates. The results indicated that the orientation of 1-methylpyrene (1-MP) in the active site was highly determined by the presence of PHEs, PHE478 contributing to the binding free energy most significantly. Moreover, by building a random forest model the relationship between each of 19 molecular descriptors of polychlorinated biphenyl (PCB) compounds (from molecular docking, quantum mechanics, and physicochemical properties) and their human CYP2E1-dependent mutagenicityas established mostly in our lab, was investigated. The presence of PHEs did not appear to significantly modify the electronic or structural feature of each bound ligand (PCB), instead, the flexibility of the conformation of PHEs contributed substantially to the effective binding energy and orientation. It is supposed that PHE residues adjust their own conformation to permit a suitablly shaped cavity for holding the ligand and forming its orientation as favorable for a biochemical reaction. This study has provided some insights into the role of PHEs in guiding the interactive adaptation of the active site of human CYP2E1 for the binding and metabolism of aromatic substrates.

Keywords: CYP2E1; aromatic compounds; molecular simulation; phenylalanine; random forest.

Figure 1

Conformations of 1-MP docked into human CYP2E1 under different settings for PHE residues. (A): Docking with rigid settings for all AA residues in the active site; (B): PHE 478 being set as a flexible residue in the active site for docking; (C): all PHEs in the active site being set as flexible residues for docking. Orange dotted lines represent distances between the Cα atom of 1-MP and Fe ion (Å); the blue dotted line represents the range of the movement of PHE 478 (Å); the black dotted line represents the rotation of PHE 478.

Figure 2

RMSD (A) of wild-type and mutant human CYP2E1 protein bound with 1-MP and the variation of distance between the Cα in 1-MP and the heme in a period of 50 ns (B).

Figure 3

The energy contributions from different PHEs in the active site of 1-MP−wild−type CYP2E1 and that of each 1-MP−mutant CYP2E1 complex.

Figure 4

Relative importance of each molecular feature of PCBs in the random forest model. L_NP, the nucleophilicity of ligand; HLF, fish biotransformation half-life; DBES, binding energy score obtained from molecular docking with PHE478 set flexible; P_NP, the nucleophilicity of ligand-PHE complex; L_HLG, the HOMO-LUMO gap of ligand; DtF, the distance from SOM to Fe ion in heme; FODw, the FOD value of ligand binding to the active site of human CYP2E1; AHR, atmospheric hydroxylation rate; P_HLG, the HOMO-LUMO gap of ligand-PHE complex; L_EP, the electrophilicity of ligand; FODp, the FOD value of ligand; OP, the number of ortho-Cl-substitution; FODm, the FOD value of ligand binding to the active site of F478A mutant; P_EP, the electrophilicity of ligand-PHE complex; Kow, LogKow: octanol-water partition coefficient; MW, the molecular weight; CN, the number of Cl-substitution; MP, the number of meta-Cl-substitution; PP, the number of para-Cl-substitution.