Network Pharmacology and Molecular Docking Explore the Mechanism of Mubiezi-Yinyanghuo Herb Pair in the Treatment of Rheumatoid Arthritis

Abstract

Objective: Our previous studies have shown that the Mubiezi-Yinyanghuo (MBZ-YYH) herb pair inhibits rheumatoid arthritis (RA) cell proliferation and glycolysis, promising results with an obscure mechanism of action.

Methods: Therefore, it is necessary to explore the main components of MBZ-YYH and unravel the potential mechanism in RA based on network pharmacology and molecular docking methods. Components and targets of MBZ-YYH were retrieved from the TCMSP. Relevant targets of RA were searched in GeneCards, therapeutic target database (TTD), and DisGeNET databases; the common targets of the MBZ-YYH compounds and RA were obtained by comparison; and a component-target interaction network was established by Cytoscape 3.9.1. Gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis were performed through the David database. Molecular docking was performed by PyMoL2.3.0 and AutoDock Vina1.1.2 software.

Results: 7 active ingredients and 58 putatively identified target genes were screened from MBZ, and 16 effective components of YYH and 230 potential targets were identified. There were 29 mutual targets between the two herbs and RA. Through the PPI network, 9 hub targets which contain JUN, CASP3, PPARG, PTGS2, GSK3B, CASP8, HMOX1, ICAM1, and HK2 were screened out. GO term enrichment analysis indicated that positive regulation of the apoptotic process, response to drugs, and response to hypoxia were significantly enriched. Based on KEGG analysis, it was mainly associated with the IL-17 signaling pathway, the TNF signaling pathway, and the p53 signaling pathway. The docking analysis revealed that the effective components showed strong binding activity with the receptors.

Conclusion: The effects of the MBZ-YYH herb pair on RA were coordinated by the interaction of diverse components, which may be through the IL-17 signaling pathway and the TNF signaling pathway, which target GSK3B, HK2, caspase 3, and caspase 8, inhibiting the proliferation and glycolysis of rheumatoid arthritis fibroblast-like synovial cells (RA-FLS) and tending towards an increasing efficacy and decreasing toxicity effect on RA.

Figure 1

Flowchart of network pharmacology of MBZ-YYH in the treatment of RA.

Figure 2

CCK-8 detection of the effect of MBZ and YYH on RA cells. The concentration is greater than 200 μg/ml; the difference is significant. 200 μg/ml (P=0.029), 400 μg/ml (P=0.0008), and 800 μg/ml (P=0.002).

Figure 3

Effects of MBZ and YYH on glycolysis of RA cells. (a) Determination of glucose content (^∗∗P=0.0097); (b) hexokinase activity assay (^∗∗∗P=0.001); and (c) determination of lactic acid content (^∗∗P=0.002). Here, control means no drug. Treatment shows the cells treated with MBZ and YYH.

Figure 4

Network of compound targets and RA targets. (a) MBZ-RA-YYH PPI network; (b) Venn diagram showed that RA and compound targets had 28 common targets; (c) MBZ-YYH PPI network; (d) potential target network diagram; and (e) MBZ-RA/YYH-RA PPI network.

Figure 5

GO and KEGG enrichment analyses of potential targets. (a) GO enrichment analysis; (b) KEGG enrichment analysis.

Figure 6

GO and KEGG enrichment analyses of common targets in MBZ-YYH. (a) GO enrichment analysis. (b) KEGG enrichment analysis.

Figure 7

Molecular docking visualization. (a) GSK3B-Yinyanghuo C (−9.4 kcal/mol), (b) ICAM1-bessisterol (−8.0 kcal/mol), (c) CASP8-oleanolic acid (−8.9 kcal/mol), (d) CASP3-3R,4aR,6aS,6bS,8aS,11R,12aR,14bS)-4,4,6a,6b,8a,11,14b-heptamethyl-11-methylol-1,2,3,4a,7,8,9,10,12,12a,13,14-dodecahydropicen-3-ol (−8.8 kcal/mol), (e) JUN-Yinyanghuo A (−7.3 kcal/mol), (f) HMOX1-8-(3-methylbut-2-enyl)-2-phenyl-chromone (−9.3 kcal/mol), (g) PPARG-8-(3-methylbut-2-enyl)-2-phenyl-chromone (−9.7 kcal/mol), (h) PTGS2-Yinyanghuo C (−10.7 kcal/mol), and (i) HK2-Yinyanghuo C (−9.6 kcal/mol).

Figure 8

Binding energy heat map of protein and active ingredient molecule docking. The active ingredient is shown vertically; the active ingredient of MBZ is shown in red; and YYH is shown in blue. The protein is shown horizontally.