School of Chemistry and Centre for Computational Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom.
Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6050-5. doi: 10.1073/pnas.1010194108. Epub 2011 Mar 28.
Cytochrome P450 enzymes play key roles in the metabolism of the majority of drugs. Improved models for prediction of likely metabolites will contribute to drug development. In this work, two possible metabolic routes (aromatic carbon oxidation and O-demethylation) of dextromethorphan are compared using molecular dynamics (MD) simulations and density functional theory (DFT). The DFT results on a small active site model suggest that both reactions might occur competitively. Docking and MD studies of dextromethorphan in the active site of P450 2D6 show that the dextromethorphan is located close to heme oxygen in a geometry apparently consistent with competitive metabolism. In contrast, calculations of the reaction path in a large protein model [using a hybrid quantum mechanical-molecular mechanics (QM/MM) method] show a very strong preference for O-demethylation, in accordance with experimental results. The aromatic carbon oxidation reaction is predicted to have a high activation energy, due to the active site preventing formation of a favorable transition-state structure. Hence, the QM/MM calculations demonstrate a crucial role of many active site residues in determining reactivity of dextromethorphan in P450 2D6. Beyond substrate binding orientation and reactivity of Compound I, successful metabolite predictions must take into account the detailed mechanism of oxidation in the protein. These results demonstrate the potential of QM/MM methods to investigate specificity in drug metabolism.
细胞色素 P450 酶在大多数药物的代谢中起着关键作用。改进的可能代谢产物预测模型将有助于药物开发。在这项工作中，使用分子动力学（MD）模拟和密度泛函理论（DFT）比较了右美沙芬的两种可能的代谢途径（芳环碳氧化和 O-去甲基化）。在一个小的活性位点模型上的 DFT 结果表明，这两种反应可能会发生竞争。右美沙芬在 P450 2D6 的活性位点的对接和 MD 研究表明，右美沙芬位于与血红素氧接近的位置，其几何形状显然与竞争性代谢一致。相比之下，在一个大的蛋白质模型中[使用混合量子力学-分子力学（QM/MM）方法]计算反应路径表明，O-去甲基化具有很强的偏好，这与实验结果一致。由于活性位点阻止了有利的过渡态结构的形成，芳环碳氧化反应的活化能很高。因此，QM/MM 计算表明，许多活性位点残基在决定右美沙芬在 P450 2D6 中的反应性方面起着至关重要的作用。除了底物结合取向和化合物 I 的反应性之外，成功的代谢产物预测还必须考虑蛋白质中氧化的详细机制。这些结果表明 QM/MM 方法在研究药物代谢特异性方面具有潜力。
