基于网络药理学、机器学习和分子对接分析健脾益肾方联合雷公藤多苷片治疗免疫球蛋白A 肾病的作用机制
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R285

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深圳市“医疗三名工程”项目(SZZYSM202311004)


Analysis of Mechanism of Jianpi Yishen Prescription Combined with Tripterygium Glycosides Tablets in Treating Immunoglobulin A Nephropathy Based on Network Pharmacology , Machine Learning , and Molecular Docking
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    目的:采用网络药理学和分子对接技术结合GEO数据集机器学习方法分析健脾益肾方联合雷公藤多苷片治疗免疫球蛋白A肾病(IgAN) 的作用机制。方法:通过TCMSP和UniProt筛选健脾益肾方和雷公藤多苷片活性成分和对应靶点。检索GeneCards、OMIM、TTD、DrugBank、DisGeNET、Ensembl数据库获得IgAN相关靶点。使用Venn在线工具获取药物与疾病交集靶点。基于STRING蛋白互作(PPI) 信息,借助Cytoscape可视化工具建立PPI网络筛选核心靶点。使用Metascape进行基因本体(GO) 功能和京都基因与基因组百科全书(KEGG) 通路富集分析。在R软件中通过最小绝对收缩和选择算子(LASSO)、随机森林(RF) 及支持向量机递归特征消除(SVM-RFE) 算法评估核心靶点对GSE93798数据集中病例组和对照组的识别能力以确定关键基因。运用Cytoscape构建网络筛选主要活性成分。并进行分子对接验证。结果:健脾益肾方联合雷公藤多苷片治疗IgAN的主要活性成分有槲皮素、山奈酚、木犀草素、β谷甾醇和刺芒柄花素等,核心靶点有白细胞介素(IL) -6、B细胞淋巴瘤2(BCL2)、肿瘤蛋白p53(TP53) 等12个。机器学习筛选出2个关键基因:小鼠骨肉瘤病毒癌基因同源物(FOS)、禽类肉瘤病毒17癌基因同源物(JUN)。GO富集分析显示生物过程(BP)主要涉及细胞迁移的正向调节、细胞对脂质的反应等;细胞组分(CC) 主要涉及质膜的外侧面、膜筏、囊腔等;分子功能(MF) 主要涉及转录因子结合、蛋白激酶结合等。KEGG通路主要涉及癌症、糖尿病并发症中的晚期糖基化终末产物-受体(AGE-RAGE) 等信号通路。分子对接结果显示核心靶点与主要活性成分之间存在稳定的结合力。结论:健脾益肾方联合雷公藤多苷片可能作用于FOS、JUN等核心靶点,调控细胞增殖与炎症反应,发挥抗氧化、抗纤维化作用治疗IgAN。

    Abstract:

    Abstract: Objective: To analyze the mechanism of Jianpi Yishen Prescription combined with Tripterygium Glycosides Tablets in treating immunoglobulin A nephropathy (IgAN) using network pharmacology and molecular docking technology combined with GEO dataset machine learning methods. Methods: The active ingredients and corresponding targets of Jianpi Yishen Prescription and Tripterygium Glycosides Tablets were screened through TCMSP and UniProt. IgAN-related targets were retrieved from GeneCards, OMIM, TTD, DrugBank, DisGeNET, and Ensembl databases. The Venn online tool was used to obtain intersecting targets between drugs and disease. Based on protein-protein interaction (PPI) information from the STRING database, a PPI network was constructed using Cytoscape visualization tools to screen core targets. Gene Ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using Metascape. In R software,the Least Absolute Shrinkage and Selection Operator (LASSO),Random Forest (RF),and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) algorithms were used to evaluate the identification ability of core targets for case and control groups in the GSE93798 dataset to determine key genes. Cytoscape was employed to construct a network and screen main active ingredients. Molecular docking validation was then performed. Results: The main active ingredients of Jianpi Yishen Prescription combined with Tripterygium Glycosides Tablets in treating IgAN included quercetin, kaempferol, luteolin, β-sitosterol, and formononetin. There were 12 core targets, including interleukin-6 (IL-6),B-cell lymphoma 2 (BCL2),and tumor protein p53 (TP53). Two key genes were screened out by machine learning: FBJ murine osteosarcoma viral oncogene homolog (FOS) and avian sarcoma virus 17 oncogene homolog (JUN). GO enrichment analysis showed that biological processes (BP) mainly involved positive regulation of cell migration and cellular response to lipids;cellular components (CC) mainly involved the external side of the plasma membrane, membrane rafts, and vesicle lumen; molecular functions (MF) mainly involved transcription factor binding and protein kinase binding. KEGG pathways primarily involved pathways in cancer and the advanced glycation end products-receptor for AGE (AGE-RAGE) signaling pathway in diabetic complications. Molecular docking results demonstrated stable binding forces between core targets and main active ingredients. Conclusion: Jianpi Yishen Prescription combined with Tripterygium Glycosides Tablets may act on core targets such as FOS and JUN to regulate cell proliferation and inflammatory responses,exerting antioxidant and anti-fibrotic effects in treating IgAN.

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钟林裕,吴异浙,叶小丹,祁爱蓉.基于网络药理学、机器学习和分子对接分析健脾益肾方联合雷公藤多苷片治疗免疫球蛋白A 肾病的作用机制[J].新中医,2026,58(9):168-177

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