Construction and assessment of models of CYP2E1: Predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations
Construction and assessment of models of CYP2E1: Predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations
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DOI：
10.1021/jm020538a
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发表时间：
2003-04-24
影响因子：
7.3
通讯作者：
Harris, D
中科院分区：
文献类型：
--
作者：
Park, JY;Harris, D
基于配基-原子-氧铁中心距构型采样和量子化学标准，构建了基于结构预测不同底物的2E1代谢的三维模型。根据2E1的序列与已知结构的模板，包括兔的CYP2C5(3LVdH)和细菌的CYP450构建模型。在几何和能量评估之后，该模型的实用性在基于结构的新陈代谢预测中进行了测试。用Autodock将氯唑沙宗、对硝基苯酚、N-亚硝基二甲胺、扑热息痛、咖啡因、茶碱和甲氧基氟烷对接到基于密度泛函理论的带电荷模型氧铁血红素的模型中。在所有情况下，最低能量结合的对接构型对应于底物与氧铁中心密切相关的构型。每个配体的最低能量对接形式之间的构型具有相对于氧铁中心的取向，与实验观察到的代谢物一致。长链二烷基亚硝胺的对接没有显示出血红素结合位点的配置，这与这些配体的代谢可以忽略不计一致。2E1的高亲和力底物氯唑沙宗、对硝基苯酚和N-亚硝基二甲胺的最低能量对接构型被用来启动300ps分子动力学(MD)轨迹。分子动力学采样得到的氧铁血红素配位体构型与密度泛函理论(DFT)优化的氧铁血红素配位构型吻合较好。对多个对接方向的MD采样配体-2E1构型的分析表明，反应中心与氧铁血红素暴露最近的构型与观察到的代谢物相关，并适当考虑了H-抽象能量学。对于甲氧基氟烷的具体情况，化合物I和对亚硝基苯氧基化合物I替代化合物I直接将相对自由基能量的密度泛函计算与差示抽氢活化能进行比较，结果表明两者吻合较好。
3D models of CYP2E1 were constructed for the purpose of structure-based prediction of 2E1 metabolism of diverse substrates based on configuration sampling of ligand-atom-oxyferryl center distances and quantum chemical criteria. Models were constructed on the basis of sequence alignments of 2E1 with templates of known structure, including rabbit CYP2C5 (3LVdH) and bacterial CYP450s. Following geometric and energetic assessments, the utility of the model was tested in structure-based predictions of metabolism. Autodock was used to dock chlorzoxazone, p-nitrophenol, N-nitrosodimethylamine, acetominophen, caffeine, theophylline, and methoxyflurane into the model CYP2E1 employing a model oxyferryl heme with charges based on density functional theoretical parametrization. In all cases, the lowest energy bound docked configurations corresponded to ones with the substrate intimately associated with the oxyferryl center. Configurations among the lowest energy docked forms of each of the ligands had orientations relative to the oxyferryl center consistent with the experimentally observed metabolites. Docking of long-chain dialkylnitrosoamines revealed no heme binding site bound configurations, in agreement with the negligible metabolism of these ligands. The lowest energy docked configurations of chlorzoxazone, p-nitrophenol, and N-nitrosodimethylamine, high-affinity substrates of 2E1, were used to initiate 300 ps molecular dynamics (MD) trajectories. The MD-sampled ligand-oxyferryl heme reactant configurations were in good accord with density functional theoretical (DFT) optimized oxyferryl-heme-ligand geometries. Analysis of the MD-sampled ligand-2E1 configurations from multiple docked orientations indicates the configurations with closest exposure of reactive centers to the oxyferryl heme to be correlated with observed metabolites with proper consideration of H-abstraction energetics. DFT assessment of relative radical energetics is directly compared with differential H-abstraction activation energetics by compound I and by a p-nitrosophenoxy radical compound I surrogate for the specific case of methoxyflurane and is shown to be in good agreement.