Fa Botao, Cong Shan, Wang Jingfang
Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Molecules. 2015 Apr 24;20(5):7558-73. doi: 10.3390/molecules20057558.
Human Cytochrome P450 3A4 (CYP3A4) is an important member of the cytochrome P450 superfamily with responsibility for metabolizing ~50% of clinical drugs. Experimental evidence showed that CYP3A4 can adopt multiple substrates in its active site to form a cooperative binding model, accelerating substrate metabolism efficiency. In the current study, we constructed both normal and cooperative binding models of human CYP3A4 with antifungal drug ketoconazoles (KLN). Molecular dynamics simulation and free energy calculation were then carried out to study the cooperative binding mechanism. Our simulation showed that the second KLN in the cooperative binding model had a positive impact on the first one binding in the active site by two significant pi-pi stacking interactions. The first one was formed by Phe215, functioning to position the first KLN in a favorable orientation in the active site for further metabolism reactions. The second one was contributed by Phe304. This pi-pi stacking was enhanced in the cooperative binding model by the parallel conformation between the aromatic rings in Phe304 and the dioxolan moiety of the first KLN. These findings can provide an atomic insight into the cooperative binding in CYP3A4, revealing a novel pi-pi stacking mechanism for drug-drug interactions.
人细胞色素P450 3A4（CYP3A4）是细胞色素P450超家族的重要成员，负责代谢约50%的临床药物。实验证据表明，CYP3A4可以在其活性位点采用多种底物形成协同结合模式，提高底物代谢效率。在本研究中，我们构建了人CYP3A4与抗真菌药物酮康唑（KLN）的正常结合模型和协同结合模型。然后进行分子动力学模拟和自由能计算，以研究协同结合机制。我们的模拟表明，协同结合模型中的第二个KLN通过两个显著的π-π堆积相互作用对活性位点中第一个KLN的结合产生积极影响。第一个由Phe215形成，其作用是将第一个KLN以有利的方向定位在活性位点中，以便进行进一步的代谢反应。第二个由Phe304贡献。在协同结合模型中，这种π-π堆积通过Phe304中的芳香环与第一个KLN的二氧戊环部分之间的平行构象而增强。这些发现可以为CYP3A4中的协同结合提供原子水平的见解，揭示一种新的药物-药物相互作用的π-π堆积机制。
