Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Ave, Portland, Maine 04103, United States.
J Phys Chem B. 2024 Jul 25;128(29):7188-7198. doi: 10.1021/acs.jpcb.4c03097. Epub 2024 Jul 17.
Human cytochrome P450 (CYP) proteins metabolize 75% of small-molecule pharmaceuticals, which makes structure-based modeling of CYP metabolism and inhibition, bolstered by the current availability of X-ray crystal structures of CYP globular catalytic domains, an attractive prospect. Accounting for this broad metabolic capacity is a combination of the existence of multiple different CYP proteins and the capacity of a single CYP protein to metabolize multiple different small molecules. It is thought that structural plasticity and flexibility contribute to this latter property; therefore, incorporating diverse conformational states of a particular CYP is likely an important consideration in structure-based CYP metabolism and inhibition modeling. While all-atom explicit-solvent molecular dynamics simulations can be used to generate conformational ensembles under biologically relevant conditions, existing CYP crystal structures are of the globular domain only, whereas human CYPs contain N-terminal transmembrane and linker peptides that anchor the globular catalytic domain to the endoplasmic reticulum. To determine whether this can cause significant differences in the sampled binding site conformations, microsecond scale all-atom explicit-solvent molecular dynamics simulations of the CYP2D6 globular domain in an aqueous environment were compared with those of the full-length protein anchored in a POPC lipid bilayer. While bilayer-anchoring damped some structural fluctuations in the globular domain relative to the aqueous simulations, none of the affected residues included binding site pocket residues. Furthermore, clustering of molecular dynamics snapshots based on either pairwise binding site pocket RMSD or volume differences demonstrated a lack of separation of snapshots from the two simulation conditions into different clusters. These results suggest the substantially simpler and computationally cheaper aqueous simulation approach can be used to generate a relevant conformational ensemble of the CYP2D6 binding site for structure-based metabolism and inhibition modeling.
人类细胞色素 P450（CYP）蛋白代谢了 75%的小分子药物，这使得基于结构的 CYP 代谢和抑制建模成为可能，因为目前已经获得了 CYP 球状催化结构域的 X 射线晶体结构。这种广泛的代谢能力归因于多种不同 CYP 蛋白的存在以及单个 CYP 蛋白代谢多种不同小分子的能力。人们认为结构的可塑性和灵活性促成了这一特性；因此，纳入特定 CYP 的多种构象状态可能是基于结构的 CYP 代谢和抑制建模中的一个重要考虑因素。虽然全原子显式溶剂分子动力学模拟可用于在生物学相关条件下生成构象系综，但现有的 CYP 晶体结构仅为球状结构域，而人类 CYP 包含 N 端跨膜和连接肽，将球状催化结构域锚定在内质网上。为了确定这是否会导致结合位点构象的显著差异，在水相环境中对 CYP2D6 球状结构域进行了微秒级全原子显式溶剂分子动力学模拟，并与锚定在 POPC 脂质双层中的全长蛋白进行了比较。虽然双层锚定相对于水相模拟降低了球状结构域的一些结构波动，但受影响的残基中没有包含结合口袋残基。此外，基于结合口袋 RMSD 或体积差异的分子动力学快照聚类表明，两种模拟条件下的快照无法分离到不同的簇中。这些结果表明，大大简化和计算成本更低的水相模拟方法可用于生成基于结构的 CYP2D6 结合位点代谢和抑制建模的相关构象系综。
