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基于生物信息学和分子对接技术探讨协心胶囊干预血脂异常的潜在分子机制

Potential molecular mechanism of the Xiexin capsule in the intervention of dyslipidemia based on bioinformatics and molecular docking.

机构信息

Hunan University of Chinese Medicine.

The First Affiliated Hospital. Hunan University of Chinese Medicine.

出版信息

Nutr Hosp. 2022 Jun 24;39(3):569-579. doi: 10.20960/nh.03918.

Abstract

Objective: bioinformatic methods and molecular docking technology were used to predict the active components, targets, and related biological pathways of the Xiexin capsule in the intervention for dyslipidemia, exploring its mechanism. Methods: the active components and targets of the Xiexin capsule were screened by the TCMSP (Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform )database. Genecards (The Human Gene Database), OMIM (Online Mendelian Inheritance in Man), PharmGkb (Pharmacogenomics Knowledge Base database), TTD (Therapeutic Target Database), and Drugbank platforms were used to search the disease targets of dyslipidemia. The Cytoscape 3.8.0 software was used to construct the 'component-target' network diagram, and the STRING (functional protein association networks) platform was used to analyze protein-protein interaction (PPI). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment analyses were performed by R language data packets to predict the mechanism of action. The AutoDockVina and PyMol software were used to dock the key active components in the Xiexin capsule and the core proteins in PPI. Results: a total of 66 effective components were screened, involving 114 targets; 87 key active compounds were screened from the 'drug-component-target' diagram. The PPI network mainly involved core proteins such as PTGS2 (prostaglandin-endoperoxide synthase 2), PTGS1 (prostaglandin-endoperoxide synthase 1), and HSP90AA1 (heat shock protein 90 alpha family class A member 1). GO and KEGG enrichment analysis results of common targets mainly involved hormone-mediated signaling pathway, steroid hormone response, lipid transport and metabolism, regulation of cholesterol storage, cyclooxygenase pathway, and other biological pathways, as well asMM PPAR (peroxisome proliferators-activated receptor) signaling pathway, IL-17 (interleukin 17) signaling pathway, PI3K-Akt (protein kinase b) signaling pathway, FcεRI signaling pathway, and other related pathways. Molecular docking verification showed that quercetin had the best binding with the core target protein HSP90AA1, and HSP90AA1 was the target protein with the best binding activity for the key chemical components in Xiexin capsules. Conclusion: the main chemical components in the Xiexin capsules may participate in the regulation of PPAR and other signaling pathways by regulating key genes such as ESR1 (estrogen receptor 1), MAPK14 (mitogen-activated protein kinase 14), and HSP90AA1, to exert the pharmacological effect of the intervention on dyslipidemia.

摘要

目的

运用生物信息学方法和分子对接技术,预测消心痛胶囊干预血脂异常的活性成分、作用靶点及相关生物学通路,探讨其作用机制。方法:通过 TCMSP(中药系统药理学数据库和分析平台)数据库筛选消心痛胶囊的活性成分及作用靶点,运用 Genecards(人类基因数据库)、OMIM(在线人类孟德尔遗传数据库)、PharmGkb(药物基因组学知识库数据库)、TTD(治疗靶点数据库)、Drugbank 等平台检索血脂异常相关疾病靶点,采用 Cytoscape 3.8.0 软件构建“成分-靶点”网络图,利用 STRING(蛋白质相互作用网络数据库)平台进行蛋白互作分析(protein-protein interaction,PPI)。采用 R 语言数据包对基因本体(gene ontology,GO)和京都基因与基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)富集分析,预测作用机制。采用 AutoDockVina 和 PyMol 软件对消心痛胶囊中关键活性成分与 PPI 中的核心蛋白进行分子对接。结果:共筛选出 66 个有效成分,涉及 114 个靶点;从“药物-成分-靶点”网络图中筛选出 87 个关键活性化合物。PPI 网络主要涉及 PTGS2(前列腺素内过氧化物合酶 2)、PTGS1(前列腺素内过氧化物合酶 1)、HSP90AA1(热休克蛋白 90α家族成员 1)等核心蛋白。共同靶点的 GO 和 KEGG 富集分析结果主要涉及激素介导的信号通路、甾体激素反应、脂质运输和代谢、胆固醇储存调节、环氧合酶通路等生物学通路,以及 MM PPAR(过氧化物酶体增殖物激活受体)信号通路、IL-17(白细胞介素 17)信号通路、PI3K-Akt(蛋白激酶 B)信号通路、FcεRI 信号通路等相关通路。分子对接验证显示,槲皮素与核心靶蛋白 HSP90AA1 的结合性最好,而 HSP90AA1 是消心痛胶囊中关键化学组分结合活性最好的靶蛋白。结论:消心痛胶囊的主要化学成分可能通过调节 ESR1(雌激素受体 1)、MAPK14(丝裂原活化蛋白激酶 14)、HSP90AA1 等关键基因,参与 PPAR 等信号通路的调节,发挥干预血脂异常的药理作用。

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