基于计算机辅助药物设计及网络药理学方法探究活络丸治疗骨关节炎的分子机制

Explore the Molecular Mechanism of Treating Osteoarthritis with Huoluo Pill Based on Computer Aided Drug Design and Network Pharmacology

关键词:  骨关节炎  活络丸  COX-2  5-LOX  F2  多靶点分子对接  药效团模型  网络药理学

Key words:  osteoarthritis  Huoluo pill  COX-2  5-LOX  F2  multi-target molecular docking  pharmacophore model  network pharmacology

摘要:

目的 基于骨关节炎的发病机制以及临床药物需求,运用计算机辅助药物设计以及网络药理方法探究活络丸治疗骨关节炎的潜在药效成分及分子机制。方法 采用TCMSP、TCMID和化学专业数据库检索活络丸中药化合物。多靶点分子对接、结合自由能计算逐级对化合物与骨关节炎治疗靶点COX-2、5-LOX以及凝血因子F2的亲和力进行评估,对潜在活性化合物进行层次聚类及药效团模型的构建。利用Swiss Target Prediction预测化合物潜在靶点,Cytoscape构建"药味-成分-潜在靶点"网络。GeneCards、DrugBank、TTD和CTD检索骨关节炎疾病靶点。DAVID进行GO和KEGG分析,STRING分析蛋白相互作用。结果 分子对接及结合自由能计算获得了具有靶向COX-2、5-LOX、F2潜在亲和力的成分,经层次聚类分析后构建药效团模型,得到针对COX-2、5-LOX及F2的药效团模型AAH、AAA、AAR。裂叶苣荚莱内酯、芦荟大黄素、光甘草定等化合物具有的骨架结构可能对治疗骨关节炎有潜在作用。活络丸与骨关节炎共有靶点180个,PPI分析得到STAT3、SRC、CXCR4、EP300等潜在靶点179个,GO和KEGG分析得到GO条目686个、KEGG通路108条。结论 本研究选择花生四烯酸代谢靶点COX-2、5-LOX以及凝血靶点F2,通过多靶点分子对接和结合自由能计算逐级筛选、聚类分析、药效团模型及网络药理学等方法,初步揭示活络丸"多点显效,协同增效"的分子机制,为具有潜在较低不良反应的骨关节炎活性中药组分或组分配伍的开发提供靶点组合和研究基础。

Abstract:

OBJECTIVE To explore the potential pharmacodynamic components and molecular mechanism of Huoluo pill in the treatment of osteoarthritis by using computer aided drug design and network pharmacology based on the pathogenesis of osteoarthritis and the need for clinical drugs. METHODS TCMSP, TCMID and Chemistry database were used to search the traditional Chinese medicine compounds of Huoluo pill. The affinity of compounds for therapeutic targets of osteoarthritis such as COX-2, 5-LOX and coagulation factor F2 was evaluated by molecular docking and binding free energy calculations. The hierarchical clustering and pharmacophore model of potential active compounds were constructed. Swiss Target Prediction was used to predict the potential targets of compounds. Cytoscape constructed a network of "drug flavor-component-potential target". Genecards, DrugBank, TTD and CTD databases were used to search for osteoarthritis targets. DAVID performed GO and KEGG analyses, and STRING analyzed the target protein interactions.RESULTS The components with potential affinity for therapeutic targets of osteoarthritis such as COX-2, 5-LOX and coagulation factor F2 were obtained. The pharmacop was constructed after hierarchical cluster analysis, and the pharmacophore models AAH, AAA and AAR for COX-2, 5-LOX and F2 were obtained by molecular docking and binding free energy calculation. The skeleton structure represented by santamarine, aloe emodin and glabridin might had potential effect on the treatment of osteoarthritis. There were 180 targets in Huoluo pill and osteoarthritis. Through PPI analysis, 179 potential targets such as STAT3, SRC, CXCR4 and EP300 were obtained. Six hundred and eighty six GO items and one hundred and eight KEGG pathways were obtained through GO and KEGG analyses. CONCLUSION In this study, arachidonic acid metabolic targets COX-2, 5-LOX and coagulation target F2 are selected. Through multi-target molecular docking and binding free energy calculation step by step screening, cluster analysis, pharmacophore model and network pharmacology, the molecular mechanism of "multi-point effect and synergistic effect" of Huoluo pill is preliminarily revealed. It provides target combination and research basis for the development of active Chinese medicine components or component compatibility with osteoarthritis with low potential adverse reactions.