基于网络药理学、分子对接、分子动力学模拟探讨茸菖胶囊治疗小儿癫痫的靶点机制

Exploration of the target mechanism of Rongchang Capsule in the treatment of epilepsy in children based on network pharmacology, molecular docking and molecular dynamics simulation

关键词:  癫痫  茸菖胶囊  网络药理学  分子对接  分子动力学模拟

Key words:  epilepsy  Rongchang Capsule  network pharmacology  molecular docking  molecular dynamics simulation

摘要:

[目的] 笔者团队前期研究已证实茸菖胶囊治疗小儿癫痫（epilepsy）与雌激素水平、自噬过程、AMPK、mTOR信号通路有关，但暂无成份与靶点间的关系，研究将通过网络药理学、分子对接、分子动力学模拟的方法探讨茸菖胶囊多分子、多靶点、多通路的作用机制，为其基础及临床研究提供参考。[方法] 通过TCMSP、TCMID、BATMAN-TCM及文献检索筛选出茸菖胶囊的生物活性成分及靶点，通过GeneCards、OMIM、DisGeNET数据库检索疾病靶点信息并取药物、疾病的交集靶点；使用String数据库获得蛋白相互作用关系，并利用Cytoscape软件构建药物-活性成分-靶点图以及药物-靶点-KEGG网络关系图；利用AutoDockTools、Vina软件进行分子对接；利用Gromacs软件对ESR1与柚皮素进行分子动力学模拟。[结果] 茸菖胶囊中共筛选出117个活性成份，115个药物疾病交集靶点，通过CytoNCA插件筛选出18个核心靶点；GO分析表明，主要涉及类固醇代谢过程、对金属离子的反应等；KEGG分析表明，主要涉及脂质和动脉粥样硬化通路、AGE-RAGE信号通路等；分子对接结果显示30对组合Affinity值均≤-5 kcal/mol；分子动力学模拟中RMSD及ROG数值波动较小，RMSF中Res 307-350，Res 525-551数值较大。[结论] 通过网络药理学预测了茸菖胶囊治疗癫痫的潜在作用机制，主要通过槲皮素、山柰酚、β-谷甾醇等分子涉及AKT1、TNF、IL-6等靶点，作用于脂质和动脉粥样硬化通路、AGE-RAGE信号通路、白介素-17信号通路等干预癫痫，这些通路与神经炎症及氧化应激关系最为密切，且预测了前期研究通路中的药物-靶点关系；分子对接结果表明，排名前5的分子与排名前6的靶点结合较紧密；分子动力学模拟结果表明ESR1与柚皮素结合稳定且紧密，提示调节雌激素水平可能是茸菖胶囊治疗癫痫的潜在作用机制之一。

Abstract:

[Objective] The team's previous research has confirmed that the treatment of epilepsy by Rongchang Capsules are associated with estrogen levels, autophagy, AMPK, and mTOR signaling pathways, but there is no relationship between components and targets at this time. This paper will use network pharmacology, the multi-molecular, multi-target and multi-pathway mechanism of action of Rongchang Capsule was discussed by docking and molecular dynamics simulation, which provided a reference reference for its basic and clinical research. [Methods] Screening of bioactive components and targets of velvet calamus capsules by TCMSP, TCMID, BATMAN-TCM and literature search, retrieve the disease target information and take the intersection target of drug and disease by GeneCards, OMIM, DisGeNET database;use String database to obtain the protein interaction relationship and use Cytoscape software to construct drug-active ingredient-target maps and drug-target-KEGG network relationship maps;use AutoDockTools, Vina software to perform molecular docking, use Gromacs software to perform molecular dynamics simulations of ESR1 and naringenin. [Results] The 117 active ingredients and 115 drug-disease intersecting targets were screened out of Rongchang Capsules, and 18 core targets were screened by the CytoNCA plug-in. GO analysis showed that it is mainly involved in steroid metabolic process, response to the metal ion, etc. KEGG analysis showed that it was primarily involved in lipid and atherosclerosis pathway, AGE-RAGE, etc. Molecular docking results showd that the Affinity values of 30 pairs of combinations are all ≤ -5(kcal/mol). In molecular dynamics simulation, the values of RMSD and ROG in molecular dynamics simulations fluctuated less, and the values of Res 307-350 and Res 525-551 in RMSF were large. [Conclusion] The potential mechanism of action of Rongchang Capsule in the treatment of epilepsy was predicted by network pharmacology, mainly involving quercetin, kaempferol, β-sitosterol molecule and AKT1, TNF, IL-6 targets, acting on lipid and atherosclerosis pathways, AGE-RAGE signaling pathway, and interleukin-17 signaling pathway to intervention for epilepsy. These pathways are most closely related to neuroinflammation and oxidative stress, and predict the early stage of epilepsy. These pathways were most closely related to neuroinflammation and oxidative stress, and predicted drug-target relationships in the previously studied pathways;molecular docking results showed that the top 5 molecules bound more tightly to the top 6 targets;molecular dynamics simulations showed that ESR1 bound stably and tightly to naringenin, suggesting that regulation of estrogen levels may be one of the potential mechanisms of action of velvet calamus capsules in the treatment of epilepsy.