Fan Jing-Rong, Li Heng, Zhang Hong-Xing, Zheng Qing-Chuan
Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, People's Republic of China.
Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Science, Jilin University, Changchun, 130012, People's Republic of China.
Biopolymers. 2018 Apr;109(4):e23108. doi: 10.1002/bip.23108. Epub 2018 Feb 27.
The majority of cytochromes P450 play a critical role in metabolism of endogenous and exogenous substrates, some of its products are carcinogens. Therefore, inhibition of P450 enzymes activity can promote the detoxification and elimination of chemical carcinogens. In this study, molecular dynamics (MD) simulations and adaptive steered molecular dynamics (ASMD) simulations were performed to explore the structure features and channel dynamics of three P450 isoforms 2A6, 2A13, and 2E1 bound with the common inhibitor pilocarpine. The binding free energy results combined with the PMF calculations give a reasonable ranking of binding affinity, which are consistent with the experimental data. Our results uncover how a sequence divergence of different CYP2 enzymes causes individual variations in major channel selections. On the basis of channel bottleneck and energy decomposition analysis, we propose a gating mechanism of their respective major channels in three enzymes, which may be attributed to a reversal of Phe209 in CYP2A6/2A13, as well as the rotation of Phe116 and Phe298 in CYP2E1. The hydrophobic residues not only make strong hydrophobic interactions with inhibitor, but also act as gatekeeper to regulate the opening of channel. The present study provides important insights into the structure-function relationships of three cytochrome P450s and the molecular basis for development of potent inhibitors.
大多数细胞色素P450在内源性和外源性底物的代谢中起关键作用，其一些产物是致癌物。因此，抑制P450酶的活性可以促进化学致癌物的解毒和消除。在本研究中，进行了分子动力学（MD）模拟和自适应引导分子动力学（ASMD）模拟，以探索与常见抑制剂毛果芸香碱结合的三种P450同工型2A6、2A13和2E1的结构特征和通道动力学。结合自由能结果与PMF计算给出了合理的结合亲和力排名，这与实验数据一致。我们的结果揭示了不同CYP2酶的序列差异如何导致主要通道选择的个体差异。基于通道瓶颈和能量分解分析，我们提出了三种酶中各自主要通道的门控机制，这可能归因于CYP2A6/2A13中Phe209的反转，以及CYP2E1中Phe116和Phe298的旋转。疏水残基不仅与抑制剂形成强烈的疏水相互作用，还作为守门人调节通道的开放。本研究为三种细胞色素P450的结构 - 功能关系以及开发有效抑制剂的分子基础提供了重要见解。
