南方医科大学学报

南方医科大学学报 ›› 2022, Vol. 42 ›› Issue (1): 71-77.doi: 10.12122/j.issn.1673-4254.2022.01.08

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隐孔菌倍半萜类成分抗肿瘤的作用机制：基于分子对接方法

周凌云，赵梓童，熊 枫，陈云艳，孙 玉   

  1. 皖南医学院药学院，安徽 芜湖 241002；安徽省皖南地区植物药活性物质筛选与再评价工程实验室，安徽 芜湖 241002；中国科学院昆明植物研究所，云南 昆明 650201
  • 出版日期:2022-01-20 发布日期:2022-03-02

Anti-tumor mechanism of sesquiterpenoids from Cryptoporus volvatus based on molecular docking

ZHOU Lingyun, ZHAO Zitong, XIONG Feng, CHEN Yunyan, SUN Yu   

  1. School of Pharmacy, Wannan Medical College, Wuhu 241002, China; Provincial Engineering Laboratory for Screening and Reevaluation of Active Compounds of Herbal Medicines in Southern Anhui, Wuhu 241002, China; Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China
  • Online:2022-01-20 Published:2022-03-02

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摘要： 目的 应用分子对接技术及分子动力学模拟，探讨隐孔菌中倍半萜类成分抗肿瘤作用对应靶基因及可能的作用机制。方 法 基于该类成分化学结构，利用在线反向找靶网站Pharm Mapper、SEA、Target Hunter及相关文献研究对可能的抗肿瘤靶标进行初步预测。运用Discovery Studio 4.0（Libdock功能）和Maestro12.3将隐孔菌中倍半萜分子与潜在可能靶标进行分子对接，根据打分情况，推测可能结合靶标；通过2D相互作用图对倍半萜分子与靶标相互作用情况进行分析；结合实验测得活性数据，推测不同倍半萜骨架对于活性的影响因素；选取体外细胞毒活性最好的化合物4结合的最佳构象与靶标形成复合物，与纯靶标蛋白序列一起进行分子动力学模拟，分析均方根偏差（RMSD）值和均方根浮动（RMSF）值，探讨化合物与靶标结合的稳定性。结果 隐孔菌类倍半萜类化合物与Akt（蛋白激酶B）前端蛋白序列（1UNQ）结合最优。2D相互作用图显示氢键和静电力是两者产生相互作用的最主要方式。通过分析不同倍半萜骨架分子的结合最优3D构象，认为分子骨架的微小改变产生了位阻效应，引起各分子活性差异。通过对化合物4的最佳构象与1UNQ形成复合物进行10 ns 的动力学模拟，其RMSD 值小于靶标纯蛋白序列的RMSD值，表明化合物4与1UNQ结合稳定。结合文献报道的1UNQ活性位点，推测隐孔菌中倍半萜类分子抗肿瘤的作用机制是该类分子能够引起Lys-14位乙酰化，导致Akt无法与下游PIP3结合，从而影响肿瘤细胞的增殖。结论 隐孔菌中倍半萜类化合物潜在作用靶点为蛋白激酶B前端蛋白序列1UNQ，通过对靶标Lys-14位乙酰化的方式影响肿瘤细胞的增殖，该研究为隐孔菌中倍半萜类成分作用机制的研究和进一步开发利用提供了科学依据。

关键词: 分子对接；隐孔菌；倍半萜类化合物；抗肿瘤作用机制

Abstract: Objective To identify the target genes mediating anti-tumor effect of sesquiterpenoids from Cryptoporus volvatus and explore the possible mechanism using molecular docking and molecular dynamics simulation. Methods Based on the chemical structure of sesquiterpenes from C. volvatus, we explored the online reverse target finding websites PharmMapper, SEA, Target Hunter and related literature for preliminary prediction of possible anti-tumor targets. Discovery Studio 4.0 (Libdock function) and Maestro 12.3 were used to connect sesquiterpenes with the possible targets, and the potential targets were selected according to the scores. The interaction between the sesquiterpenes and the targets were analyzed using 2D interaction diagram, and the influence of different sesquiterpene skeletons on their activity was inferred based on their activity measurements in experiment. Kinetic simulation was performed for front-end protein sequence (1UNQ) of the Akt (protein kinase B) and for the complex formed by 1UNQ and compound 4 (which had the best cytotoxic activity in vitro) in its optimal conformation, and the root mean square deviation (RMSD) value and root mean square float (RMSF) value of the complex and 1UNQ were measured to evaluate the stability of the binding of compound 4 to the target. Results The sesquiterpenes showed optimal binding with 1UNQ. Analysis of 2D interaction diagram suggested that the hydrogen bonding and electrostatic force were the most important forces mediating the interaction between the sesquiterpenes and 1UNQ. Analysis of the optimal 3D conformation showed that for different sesquiterpenes, a slight change of the molecular framework produced a steric hindrance effect and caused changes in their bioactivity. Kinetic simulation showed that the complex formed by compound 4 and1UNQ had a lower RMSD than the target pure protein sequence, indicating that compound 4 could stably bind to 1UNQ. The anti-tumor effect of the sesquiterpenoids from C. volvatus was associated with their ability to cause Lys-14 acetylation, which blocks Akt binding to the downstream PIP3 and thus affects the proliferation of tumor cells. Conclusion 1UNQ is the target of sesquiterpenoids from C. volvatus, which affects the proliferation of tumor cells by acetylating Lys-14.

Key words: molecular docking; Cryptoporus volvatus; sesquiterpenoids; anti-tumor mechanism