基于网络药理学和分子对接法的益智清心方治疗阿尔茨海默病作用机制探索

目的:运用网络药理学及分子对接方法探讨益智清心方(YZQXF)对阿尔茨海默病(Alzheimer′s disease,AD)的作用靶点,构建活性成分-靶点-通路网络并分析其作用信号通路,探讨其对AD的防治作用及可能的分子机制。方法:根据YZQXF药味组成,在中药系统药理学数据库与分析平台(TCMSP)检索各药材的有效化学成分及各成分相应的作用靶点;利用GeneCard、OMIM、PharmGKB、TTD、DrugBank数据库搜索AD相关靶点,同时将药物靶点及疾病靶点数据进行比对,获得交集靶点,上传STRING 11.5数据库对其进行蛋白质-蛋白质相互作用(PPI)网络分析并找到核心靶点;通过Cytoscape 3.7.1构建YZQXF治疗AD的活性成分-作用靶点-通路网络;借助BioConductor软件的R语言包对作用靶点进行基因本体(GO)注释和京都基因与基因组百科全书(KEGG)通路富集分析;最后将核心基因分别与关键靶标进行分子对接,验证YZQXF关键成分与核心靶点的作用特征。结果:YZQXF中共有43个化学成分作用于2871个AD相关靶点,共存在129个化学成分-靶点相互作用关系。YZQXF治疗AD的关键成分包括槲皮素、山柰酚、β-谷甾醇、四氢小檗碱、豆甾醇、原阿片碱、杨梅酮、氧代小檗碱、巴马汀、马卡因、小檗碱,核心靶点为丝裂原活化蛋白激酶1(MAPK1)、Myc、Fos、MAPK14、Jun、核转录因子-κB p65(RELA)、蛋白激酶B1(Akt1)、MAPK8、白细胞介素-1β(IL-1B)、肿瘤蛋白p53(TP53)。GO富集得到2359个生物过程条目,主要涉及对脂多糖的反应、对细菌来源的分子反应等生物过程,膜筏、膜微域等细胞组分及G蛋白偶联受体活性、神经递质受体活性等分子功能。KEGG通路富集得到168个通路,主要包括流体剪切应力与动脉粥样硬化(fluid shear stress and atherosclerosis)、糖尿病并发症晚期糖基化终末产物及其受体(AGE-RAGE)信号通路(AGE-RAGE signaling pathway in diabetic complications)等。分子对接结果显示,YZQXF中的关键活性成分与治疗AD的核心靶点有较好的结合性。结论:YZQXF可通过多种活性成分、多个关键靶点及多种作用途径治疗AD。

Mechanism of Yizhi Qingxin Formula Against Alzheimer's Disease Based on Network Pharmacology and Molecular Docking Technologies

Objective:To investigate the targets of Yizhi Qingxin Formula(YZQXF)against Alzheimer′s disease(AD)by network pharmacology and molecular docking,construct an active ingredient-target-pathway network,analyze the corresponding signaling pathways,and explore its prevention and treatment effects on AD and underlying molecular mechanisms.Methods:The effective chemical ingredients and relevant targets of drugs in YZQXF were retrieved in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP),and the targets related to AD were obtained from GeneCard,OMIM,PharmGKB,TTD,and DrugBank.The common targets were obtained by intersection analysis.The protein-protein interaction(PPI)network of therapeutic targets was constructed by STRING 11.5,and the core targets were identified.The active ingredient-target-pathway network for YZQXF in the treatment of AD was constructed by Cytoscape 3.7.1.Gene Ontology(GO)function analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis of targets were performed with the help of the R programming language in Bioconductor.Finally,the interaction characteristics of key ingredients and core therapeutic targets were verified based on molecular docking of core genes to key targets.Results:Forty-three chemical ingredients of YZQXF acted on 2871 AD-related targets,resulting in 129 chemical ingredient-target interactions.The key ingredients of YZQXF in the treatment of AD included quercetin,kaempferol,β-sitosterol,(r)-canadine,stigmasterol,fumarine,myricanone,berlambine,palmatine,maackiain,and berberine,and the core targets of YZQXF in the treatment of AD were mitogen-activated protein kinase 1(MAPK1),proto-oncogene proteins(Myc,Fos,and Jun),MAPK14,nuclear factor-kappa B/p65(RELA),protein kinase B1(Akt1),MAPK8,interleukin-1β(IL-1β),and tumor protein p53(TP53).A total of 2359 entries were obtained by GO enrichment analysis,mainly involving biological processes such as response to lipopolysaccharide and molecular response to the bacterial origin,cellular components such as membrane raft and membrane microdomain,and molecular functions such as G-protein-coupled amine receptor activity and neurotransmitter receptor activity.KEGG pathway analysis revealed 168 pathways,mainly involving fluid shear stress and atherosclerosis and the advanced glycation end products-receptor for advanced glycation end products(AGE-RAGE)signaling pathway in diabetic complications.The results of molecular docking showed that the active ingredients of YZQXF had a good affinity with the core targets against AD.Conclusion:YZQXF can treat AD in a multi-component,multi-target,and multi-pathway way.