Exploring the Molecular Mechanism of Liuwei Dihuang Pills for Treating Diabetic Nephropathy by Combined Network Pharmacology and Molecular Docking

Abstract

Background: Diabetic nephropathy (DN) is a common and serious complication of diabetes, but without a satisfactory treatment strategy till now. Liuwei Dihuang pills (LDP), an effective Chinese medicinal formula, has been used to treat DN for more than 1000 years. However, its underlying mechanism of action is still vague.

Methods: Active compounds and corresponding targets of LDP were predicted from the TCMSP database. DN disease targets were extracted from the OMIM, GeneCards, TTD, DisGeNET, and DrugBank databases. Subsequently, the "herbal-compound-target" network and protein-protein interaction (PPI) network were constructed and analyzed via the STRING web platform and Cytoscape software. GO functional and KEGG pathway enrichment analyses were carried out on the Metascape web platform. Molecular docking utilized AutoDock Vina and PyMOL software.

Results: 41 active components and 186 corresponding targets of LDP were screened out. 131 common targets of LDP and DN were acquired. Quercetin, kaempferol, beta-sitosterol, diosgenin, and stigmasterol could be defined as five crucial compounds. JUN, MAPK8, AKT1, EGF, TP53, VEGFA, MMP9, MAPK1, and TNF might be the nine key targets. The enrichment analysis showed that common targets were mainly associated with inflammation reaction, oxidative stress, immune regulation, and cell apoptosis. AGE-RAGE and IL-17 were the suggested two significant signal pathways. Molecular docking revealed that the nine key targets could closely bind to their corresponding active compounds.

Conclusion: The present study fully reveals the multicompound's and multitarget's characteristics of LDP in DN treatment. Furthermore, this study provides valuable evidence for further scientific research of the pharmacological mechanisms and broader clinical application.

Figure 1

The flowchart of LDP in treating DN.

Figure 2

Venn diagram. (a) DN disease targets. (b) The intersection of LDP and DN disease targets.

Figure 3

The “herbs-active compounds-disease targets” network. The circular nodes indicate active compounds, and the square nodes indicate the possible therapeutic targets in LDP. Different colors in the circular nodes represent that active compounds are included in different herbs. The yellow is Shanzhuyu, the green is Shanyao, the blue is Mudanpi, the red is Fuling, the pink is Zexie, and the purple is Shudihuang.

Figure 4

PPI network of LDP and DN common targets.

Figure 5

Screening of the key targets in the PPI network. (a) 122 nodes and 914 edges. The yellow genes are core genes, and they have a higher betweenness, closeness, and degree. (b) 43 nodes and 440 edges. (c) 20 nodes and 155 edges. (d) 9 nodes and 77 edges. The 9 targets in this network are considered the key targets in the whole PPI network, including JUN, MAPK8, AKT1, EGF, TP53, VEGFA, MMP9, MAPK1, and TNF.

Figure 6

GO functional and KEGG pathway enrichment analyses. (a) The top 10 terms of BP, CC, and MF in GO functional enrichment analysis are shown. The height of the column in each part is closely related to the counts of potential targets. (b) The top 10 KEGG terms were closely associated with LDP in the treatment of DN. The redder the color, the larger the −log10 (P value). The bigger the size, the more potential targets are involved in the pathways.

Figure 7

AGE-RAGE signaling pathway in diabetic complications. The pink nodes are the common targets of DN and LDP, and the blue nodes are others in the pathway.

Figure 8

Four best molecular docking results. Molecular docking results between quercetin and JUN, quercetin and MAKP1, kaempferol and JUN, quercetin and AKT1, respectively.