Abstract：
Diabetic nephropathy (DN) is one of the most serious complications of diabetes and the main cause of end-stage renal failure. Rhubarb is a widely used traditional Chinese herb, and it has exhibited efficacy in reducing proteinuria, lowering blood sugar levels and improving kidney function in patients with DN. However, the exact pharmacological mechanism by rhubarb improves DN remain unclear due to the complexity of its ingredients. Hence, we systematically explored the underlying mechanisms of rhubarb in the treatment of DN. We adopted a network pharmacology approach, focusing on the identification of active ingredients, drug target prediction, gene collection, Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes enrichment. Molecular docking technology was used to verify the binding ability between the main active compounds and central therapeutic targets, and screen out the core active ingredients in rhubarb for the treatment of DN. Finally, molecular dynamics simulation was performed for the optimal core protein-ligand obtained by molecular docking using GROMACS software. The network analysis identified 16 active compounds in rhubarb that were linked to 37 possible therapeutic targets related to DN. Through protein-protein interaction analysis, TP53, CASP8, CASP3, MYC, JUN and PTGS2 were identified as the key therapeutic targets. By validation of molecular docking, finding that the central therapeutic targets have good affinities with the main active compounds of rhubarb, and rhein, beta-sitosterol and aloe-emodin were identified as the core active ingredients in rhubarb for the treatment of DN. Results from molecular dynamics simulations showed that TP53 and aloe-emodin bound very stably with a binding free energy of - 26.98 kcal/mol between the two. The results of the gene enrichment analysis revealed that the PI3K-Akt signalling pathway, p53 signalling pathway, AGE-RAGE signalling pathway and MAPK signalling pathway might be the key pathways for the treatment of DN, and these pathways were involved in podocyte apoptosis, glomerular mesangial cell proliferation, inflammation and renal fibrosis. Based on the network pharmacology approach and molecular docking technology, we successfully predicted the active compounds and their respective targets. In addition, we illustrated the molecular mechanisms that mediate the therapeutic effects of rhubarb against DN. These findings provided an important scientific basis for further research of the mechanism of rhubarb in the treatment of DN.
摘要：
糖尿病肾病(DN)是糖尿病最严重的并发症之一,也是导致终末期肾功能衰竭的主要原因。大黄是一种广泛使用的传统中药，它显示出减少蛋白尿的功效，降低糖尿病肾病患者的血糖水平和改善肾功能。然而,由于大黄成分的复杂性，大黄改善DN的确切药理机制尚不清楚。因此，系统探讨大黄治疗DN的作用机制。我们采用了网络药理学方法，专注于活性成分的识别，药物靶标预测，基因收集,基因本体论富集和京都百科全书的基因和基因组富集。分子对接技术用于验证主要活性化合物与中心治疗靶点的结合能力,筛选出大黄中治疗DN的核心活性成分。最后,使用GROMACS软件对分子对接获得的最佳核心蛋白-配体进行分子动力学模拟。网络分析确定了大黄中的16种活性化合物，它们与与DN相关的37种可能的治疗靶标有关。通过蛋白质-蛋白质相互作用分析，TP53,CASP8,CASP3,MYC,JUN和PTGS2被确定为关键治疗靶标。通过分子对接的验证,发现中心治疗靶点与大黄的主要活性化合物具有良好的亲和力，还有大黄,β-谷甾醇和芦荟大黄素被确定为大黄治疗DN的核心活性成分。分子动力学模拟的结果表明，TP53和芦荟大黄素结合非常稳定，两者之间的结合自由能为〜26.98kcal/mol。基因富集分析结果表明,PI3K-Akt信号通路,p53信号通路,AGE-RAGE信号通路和MAPK信号通路可能是治疗DN的关键通路,这些途径与足细胞凋亡有关，肾小球系膜细胞增殖，炎症和肾纤维化。基于网络药理学方法和分子对接技术,我们成功地预测了活性化合物和它们各自的目标。此外,我们阐明了介导大黄对DN治疗作用的分子机制。这些发现为进一步研究大黄治疗DN的作用机制提供了重要的科学依据。
