Study on Mechanism of Ginseng Regulating Pyroptosis in Atherosclerosis

ZHAO Peizhang; YANG Zhen; HE Zhanzhan; TAO Xuguang; CHEN Xiangyun; DING Wei; CHU Ce; YUAN Yulu; XU Yongqi; ZHANG Yuxin; ZHAO Hongxia; WANG Wenlai

Abstract：Objective To explore the key compounds,targets and signaling pathways associated with ginseng in the regulation of pyroptosis in atherosclerosis(AS)and explain the mechanism of ginseng in regulating pyroptosis in AS.Method The TCMSP database,HERB database and Swiss Target Prediction database were deployed to detect active compounds and their standardized targets in ginseng.Targets related to AS were obtained from OMIM,GeneCards and TTD database,and integration with differentially expressed genes(DEGs)analyzed from RNA sequencing data of AS tissues and normal tissues from the Gene Expression Omnibus(GEO)database.Pyroptosis-related targets were identified using GeneCards,and bioinformatics platforms were utilized to determine intersecting genes.Protein-protein interaction networks were constructed to analyze key targets.Gene Ontology(GO)and Kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis of the targets was conducted using the"clusterProfiler"package in R language.Cytoscape 3.9.1 software was employed to construct the Network diagram of"active compound-target-pathway-disease"illustrating the relationships among active compounds,targets,pathways,and disease.AutoDock Vina was deployed to validate the molecular docking between the core target and key compounds.Gromacs was employed to perform 50 ns molecular dynamics simulation of the results of molecular docking between TNF and key compounds,the free binding energies of the last 10 ns between proteins and ligands were analyzed through the molecular dynamics/Poisson Boltzmann surface area method(MM/PBSA).Results 22 active compounds,588 targets of ginseng and 36 ginseng-pyroptosis associated atherosclerosis targets were obtained from the analysis.4 key targets were predicted:tumor necrosis factor(TNF),serine/threonine kinase(AKT)1,interleukin(IL)-1β and peroxisome proliferator-activated receptor gamma(PPARG).The results of GO and KEGG enrichment indicated that ginseng-pyroptosis associated atherosclerosis targets were mainly associated with response to lipopolysaccharide,DNA-binding transcription factor binding,nuclear receptor activity,TNF signaling pathway and nuclear factor(NF)-κB signaling pathway.After analyzing the network diagram of"active compound-target-pathway-disease",the key compounds of ginseng were analyzed as Kaempferol,Girinimbin,Deoxyharringtonine,and Gomisin B.Molecular docking using AutoDock Vina affirmed superior binding capabilities between key targets and compounds.Molecular dynamics simulations demonstrated low fluctuations and high stabilities in the solution environment of NaCl for key complexes.Analysis of free binding energies over the last 10 ns indicated a superior binding capacity of key targets and key compounds.Conclusion This study revealed that ginseng may inhibit pyroptosis in AS by regulating the TNF signaling pathway,NF-κB and other signaling pathways through core targets such as TNF,AKT1,IL-1β,and PPARG.