Network Pharmacology and Molecular Docking Analysis of the Mechanism Underlying Yikunyin's Therapeutic Effect on Menopausal Syndrome

Abstract

Objective: Yikunyin is an empirical prescription that exhibits good efficacy in the clinical treatment of menopausal syndrome; however, its underlying mechanism remains unclear. This study investigates the mechanism implicated in the therapeutic effect of Yikunyin by identifying its hub genes, central pathways, and key active ingredients.

Method: The active ingredients and targets of Yikunyin were obtained from the Traditional Chinese Medicine Systems Pharmacology database, whereas the targets related to menopausal syndrome were obtained from GeneCards, PharmGKB, Therapeutic Target Database (TTD), and Comparative Toxicogenomics Database (CTD). To reveal the pharmacological mechanism, the component-target and the intersecting protein-protein interaction (PPI) networks were constructed, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Finally, molecular docking was carried out to assess the strength of binding between the key active ingredients and key targets.

Results: A total of 418 targets and 121 active ingredients were identified in Yikunyin. The intersection of Yikunyin's 418 targets with the 2822 targets related to menopausal syndrome shows that there are 247 common targets that can be considered potential targets of Yikunyin in the treatment of menopausal syndrome. The topology analysis of the constructed PPI network conducted using the Cytoscape software shows that there are 15 hub genes implicated in the therapeutic effect of Yikunyin: AKT1, PRKCA, TLR9, CXCL10, PRKCD, PARP1, ABCB1, TP53, CAV1, MAPK8, PPARA, GRB2, EGFR, IL-6, and JAK2. Moreover, the key active components acting on these genes are paeoniflorin, luteolin, quercetin, beta-sitosterol, and kaempferol. GO and KEGG analyses indicate that Yikunyin can treat menopausal syndrome by regulating cellular response to chemical stress (GO:0062197), cellular response to oxidative stress (GO:0034599), phosphatase binding (GO:0019902), cytokine receptor binding (GO:0005126), PI3K-Akt signaling (hsa04151), lipid and atherosclerosis (hsa05417), and hepatitis B (hsa05161). Finally, the results of molecular docking suggest that the key active ingredients and key targets can bind well, with binding energies of less than -5 kJ/mol.

Conclusion: The research conducted herein reveals that Yikunyin treats menopausal syndrome by targeting AKT1 and IL-6 and by regulating the PI3K-Akt signaling pathway. Moreover, it provides a new idea for understanding the therapeutic effects of traditional Chinese medicines.

Figure 1

Diagram showing the 247 common targets among the 418 targets of Yikunyin and 2822 targets of menopausal syndrome.

Figure 2

Common target-active ingredient network. The circles and triangles represent the active ingredients in Yikunyin and the common targets, respectively, and the lines indicate relationships between nodes. Different colors are used to pinpoint the active ingredients in different herbs. The molecular IDs corresponding to signs in circles are listed in Supplementary File 2. Nodes A1, A2, A3, and A4, (B), (C), and (D) represent the common components of two or more herbs.

Figure 3

“(a) PPI network of the 247 common targets. (b) Topology analysis of the 12 subnetworks generated using the 12 algorithms in CytoHubba, a Cytoscape plug-in. Deeper red colors signify higher algorithm scores and more important targets”.

Figure 4

“(a) Hub gene PPI network. (b) The two modules of the hub gene PPI network determined using the MCODE plug-in. AKT1 and IL-6 in the center are seed nodes”.

Figure 5

“Hub gene-component network. The yellow and pink nodes represent the 15 hub genes and the active ingredients acting on them, respectively”.

Figure 6

“(a) GO and (b) KEGG enrichment analyses of hub genes. The deeper the red color, the smaller the P value, the longer the bar, and the greater the enrichment of the gene”.

Figure 7

“Molecular docking 3D diagram. Small drug molecules are represented by sky blue sticks, hydrogen bonds by yellow dotted lines, and amino acid residues bound to small drug molecules by green sticks. (a) Paeoniflorin-AKT1 (binding energy = −8.35 kcal·mol-1). (b) Luteolin-AKT1 (binding energy = −8.61 kcal·mol-1). (c) Beta-sitosterol-AKT1 (binding energy = −10.09 kcal·mol-1). (d) Kaempferol-AKT1 (binding energy = −7.38 kcal·mol-1). (e) Quercetin-AKT1 (binding energy = −7.24 kcal·mol-1). (f) Beta-sitosterol-IL-6 (binding energy = −8.9 kcal·mol-1). (g) Kaempferol-IL-6 (binding energy = −8.17 kcal·mol-1). (h) Luteolin-IL-6 (binding energy = −7.34 kcal·mol-1). (i) Paeoniflorin-IL-6 (binding energy = −14.76 kcal·mol-1). (j) Quercetin-IL-6 (binding energy = −8.0 kcal·mol-1)”.