基于转录组学、网络药理学和分子对接技术探究石斛防治冠状动脉粥样硬化性心脏病的作用机制

The mechanism of Shihu in prevention and treatment of coronary heart disease based on transcriptomics,network pharmacology and molecular docking techniques

目的:利用转录组学、网络药理学和分子对接技术探究石斛防治冠状动脉粥样硬化性心脏病(Coronary Artery Disease,CAD)的作用机制。方法:通过基因表达综合数据库寻找CAD的芯片数据,并利用R语言、Perl语言等计算机软件筛选出疾病的差异表达基因;利用中国知网、PubMed等数据库检索石斛活性成分,并通过Swiss Target Predictoin数据库进行药物靶点预测;通过R语言计算出药物与疾病的交集基因;使用DAVID和KOBAS数据库进行基因本体论(GO)基因功能注释和京都基因与基因组学百科全书(KEGG)信号通路富集分析并用RStudio 1.2软件可视化数据结果;使用STRING数据库和Cytoscape 3.9.1软件筛选核心靶点并绘制“活性成分-靶点-疾病-信号通路”网络;通过Chem 3D软件最小化配体石斛活性成分的能量构象,蛋白质结构数据库网站检索受体交集基因表达蛋白的最佳构象,利用Autodock Vina 1.2软件进行分子对接验证,并通过PyMol 2.5软件可视化分子对接结果。结果:一共检索到石斛活性成分靶点815个,其中包含芹菜素、铁皮石斛素T等成分靶点,CAD的差异表达基因497个,两者之间的交集基因共21个,其中涉及信号转导和转录激活因子3(Signal Transducers and Activators of Transcription 3,STAT3)、磷酸肌醇3激酶调控亚基1(Phosphoinositide-3-Kinase Regulatory Subunit 1,PIK3R1)等核心基因。交集基因主要富集于81个基因功能及118条信号通路。配体与受体之间的分子对接实验提示两者均有较好的结合活性。结论:石斛中芹菜素、铁皮石斛素T等化合物主要通过磷脂酰肌醇3激酶(Phosphatidylinositol 3-kinase,PI3K)-蛋白激酶B(Akt)、酪氨酸蛋白激酶(Janus-Activated Kinase,Jak)-信号转导和转录激活因子(Signal Transducer and Activator of Transcription,STAT)等信号通路调控PIK3R1、STAT3等基因的表达,改变Akt及胰岛素受体底物结合活性等作用,从而揭示了石斛防治CAD的相关机制,为药物开发奠定了理论基础。

Objective:To explore the mechanism of Dendrobium in the prevention and treatment of coronary heart disease by utilizing transcriptomics,network pharmacology and molecular docking techniques.Methods:The chip data of coronary heart disease were searched through GEO database,and the differentially expressed genes of disease were screened by R language,Perl language and other computer saftware.Active constituents of Dendrobium were retrieved from CNKI and PubMed databases,and drug targets were predicted by Swiss Target Predictoin database.The intersection genes of drugs and diseases were calculated by R language.DAVID and KOBAS databases were used for the GO gene functional annotation and KEGG signaling pathway enrichment analysis,and RStudio 1.2 software was used to visualize the data results.The STRING database and Cytoscape 3.9.1 software were used to screen core targets and map the active ingredient-target-disease-signaling pathway network.Chem 3D software was used to minimize the energy conforms of the active components of the ligand Dendrobium.PDB website was used to search for the optimal conforms of the receptor intersection gene expression proteins.Autodock Vina 1.2 software was used for molecular docking verification,and PyMol 2.5 software was used to visualize the molecular docking results.Results:A total of 815 targets of active components of Dendrobium were retrieved,including apigenin,Dendrobium T,etc.There were 497 differentially expressed genes of coronary heart disease.There were 21 overlapping genes between the two,including STAT3,PIK3R1 and other core genes.Intersection genes were mainly concentrated in 81 gene functions and 118 signaling pathways.The molecular docking experiment between ligand and receptor indicated that both ligand and receptor had good binding activity.Conclusion:In Dendrobium,apigenin,Dendrobium officinale T and other compounds regulate the expression of PIK3R1,STAT3 and other genes through PI3K-Akt,Jak-STAT and other signaling pathways,and change the activities of Akt and insulin receptor substrate binding,thus revealing the mechanism of Dendrobium in the prevention and treatment of coronary heart disease,which lays a theoretical foundation for drug development.