Zheng Mei Lin, Li Chao Rui, Bai Qun Hua, Xiao Hong, Hu Wei, Xue Ying, Gao Jie Ying
School of Public Health and Management, Chongqing Medical University, Chongqing 400016, PR China.
Chengdu FenDi Technology Co., Ltd., Chengdu 610000, PR China.
J Mol Graph Model. 2018 Mar;80:173-181. doi: 10.1016/j.jmgm.2018.01.005. Epub 2018 Jan 12.
The metabolic mechanisms for imidazolidine oxidation of imidacloprid (IMI) by cytochrome P450 3A4 (CYP3A4) have been investigated using quantum mechanical/molecular mechanical (QM/MM) calculations. The binding mode of CYP3A4 with IMI is examined by molecular docking in collaboration with molecular dynamics (MD) simulations. The results show that there are six amino acid residues, involving Arg192, Phe195, Ile349, Ala285, Phe284 and Phe88, closely distributed around the IMI. The binding free energy analysis exhibits that the CYP3A4-IMI binding structure is stabilized by electrostatic interaction and van der Waals interaction. Arg192 plays a major role in the binding of CYP3A4 with IMI based on its polarity and the hydrogen bond between the H atom in Arg192 side chain and the nitryl O atom of IMI. Two possible pathways, pathway 1 and pathway 2, are evaluated. Two spin states of the Fe (III) center, quartet and doublet, are considered. The free energy calculations are done using QM/MM steered molecular dynamics (SMD) simulation at the B3LYP/6-31 + G(d):ff14SB level for two pathways. The ONIOM QM/MM single-point calculations at the B3LYP/6-311 + G(2d,2p):ff99SB//B3LYP/6-31 + G(d): ff14SB and M06-2X/6-311 + G(2d,2p):ff99SB//B3LYP/6-31 + G(d):ff14SB levels are carried out to obtain more credible energy information. The results indicate that for both pathways, the free energy barriers on the low-spin doublet state are lower than those on the high-spin quartet state. Both pathways are the stepwise processes. Pathway 1 has higher possibility to occur with the free energy barriers being lower by 10-15 kcal·mol compared with pathway 2, which gives rise to trans-5'-hydroxyl-IMI as the final product. The first proton-transfer is the rate-limiting step and the calculated activation free energy is consistent with the experimental conclusion.
利用量子力学/分子力学（QM/MM）计算研究了细胞色素P450 3A4（CYP3A4）对吡虫啉（IMI）进行咪唑烷氧化的代谢机制。通过分子对接结合分子动力学（MD）模拟研究了CYP3A4与IMI的结合模式。结果表明，有6个氨基酸残基，包括Arg192、Phe195、Ile349、Ala285、Phe284和Phe88，紧密分布在IMI周围。结合自由能分析表明，CYP3A4-IMI结合结构通过静电相互作用和范德华相互作用得以稳定。基于其极性以及Arg192侧链中的H原子与IMI的硝基O原子之间的氢键，Arg192在CYP3A4与IMI的结合中起主要作用。评估了两条可能的途径，途径1和途径2。考虑了Fe（III）中心的两种自旋态，四重态和二重态。使用QM/MM引导分子动力学（SMD）模拟在B3LYP/6-31 +G（d）:ff14SB水平上对两条途径进行自由能计算。在B3LYP/6-311 +G（2d,2p）:ff99SB//B3LYP/6-31 +G（d）:ff14SB和M06-2X/6-311 +G（2d,2p）:ff99SB//B3LYP/6-31 +G（d）:ff14SB水平上进行ONIOM QM/MM单点计算以获得更可靠的能量信息。结果表明，对于两条途径，低自旋二重态的自由能垒均低于高自旋四重态。两条途径均为逐步过程。与途径2相比，途径1发生的可能性更高，其自由能垒低10-15 kcal·mol，最终产物为反式5'-羟基-IMI。第一次质子转移是限速步骤，计算得到的活化自由能与实验结论一致。
