Exploring The Molecular Mechanism Of Wumei Pill In The Treatment Of Diarrheal Irritable Bowel Based On GEO Database And Network Pharmacology

Purposes:(1)Using a bioinformatics approach,we analyzed key differential genes and related signaling pathways in IBS-D to explore the underlying pathological mechanisms.(2)Within this investigation,the exploration of the essential active constituents,pivotal targets,and intricate signaling pathways concerning the therapeutic potential of Wumei Pill for the management of diarrheapredominant irritable bowel syndrome(IBS-D)was conducted employing the dynamic methodologies of network pharmacology and molecular docking.By unraveling the intricacies of this therapeutic modality,a deeper comprehension of the underlying mechanisms behind Wumei Pill’s efficacy in addressing IBS-D was achieved,thereby providing valuable insights into its clinical application.This comprehensive approach not only enhances our understanding of the intricate interplay between Wumei Pill and IBS-D but also establishes a solid foundation for further research and the optimization of clinical treatment strategies.Methods:(1)The cutting-edge field of bioinformatics involves analyzing complex biological data using computational tools and techniques.In one such study,the GSE36701 data set was meticulously downloaded from the GEO database using R 4.1.2 software,before being normalized using the Normalize function to obtain a normalized sample diagram.The differential genes and expression matrix were then scrupulously screened out using the Limma package,with the resulting differential genes plotted into both volcanic and thermal maps using sophisticated packages like Ggplot2 and Pheatmap.In order to gain a deeper understanding of the biological network at play,the differential genes were then imported into the state-of-the-art software Cytoscape 3.8.0,where the plug-in Cyto NCA was used to perform a rigorous gene analysis,screening out only the key genes before masterfully drawing the PPI network diagram.The analysis didn’t stop there,however.The Clusterprofiler package in R language was then meticulously utilized to conduct both GO functional enrichment analysis of gene ontology and KEGG pathway analysis of Kyoto Encyclopedia of Genes and Genome for DEGs,with the related results painstakingly visualized for ease of analysis.Opens up new avenues for potential therapeutic interventions.(2)To explore the potential therapeutic effects of Wumei Pill on IBS-D,we employed the Chinese Medicine System Pharmacology Database and Analysis Platform(TCMSP database)to retrieve and predict the active components and corresponding targets of each drug in Wumei Pill.We screened IBS-D targets from five databases including "GENECARDS","OMIM","TTD","DRUGBANK" and "PHARMGKB".We then combined these targets with the differential genes obtained by bioinformatics analysis.To visualize the relationship between the active ingredients,targets and their actions,we constructed a Venn diagram,a "Chinese medicine-active ingredient-target" action network diagram,and a PPI protein interaction network diagram.To gain further insight into the potential therapeutic effects of Wumei Pill on IBS-D,we performed GO and KEGG analysis,molecular docking analysis,and visualized the related results.Results:(1)The dataset GSE36701 was subjected to a comprehensive bioinformatics analysis,and the findings revealed that a total of 17,137 genes exhibited differential expression between 77 normal and 53 diseased samples.Out of these,25 genes were up-regulated,whereas 17,112 genes were down-regulated.Through a detailed protein interaction analysis,we were able to identify 17 key genes,namely "RUVBL1,MCRS1,BMS1,IMP4,NAT10,SNRNP200,DDX49,SART1,DDX55,PRPF8,RRP9,SNRPD2,PRPF19,PSMC3,SNRNP40,MAP3K14 and PSMC5",whose expression levels were significantly down-regulated in IBS-D patients.Further,gene ontology(GO)enrichment analysis showed that the differentially expressed genes(DEGs)were primarily associated with ribonucleoprotein complex biogenesis,mitochondrial gene expression,mitochondrial proteincontaining complex,mitochondrial inner membrane,mitochondrial matrix,helicase activity,ATP hydrolysis activity,and RNA helicase activity.Additionally,the Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment results revealed that the TNF signaling pathway,apoptosis,and PI3K-Akt signaling pathway were strongly implicated in the pathogenesis of IBS-D.(2)Through the use of network pharmacology and molecular docking,the active components,core targets,and signaling pathways of Wumei Pill for treating diarrhea-predominant irritable bowel syndrome(IBS-D)were analyzed with a high degree of complexity.A total of 129 active components and 147 therapeutic targets were identified,with the top ten active components including quercetin,β-sitosterol,kaempferol,stigmasterol,corydalis alkaloid,tetrahydro-africanine,palmatine,tetrahydro-berberine,berberine,and R-hydrogenated berberine.PPI network analysis revealed 30 core targets,such as HSP90AA1,MAPK1,JUN,RELA,AKT1,IL6,ESR1,FOS,and MAPK8,among others.GO functional enrichment analysis showed that Wumei Pill primarily affected DNA-binding transcription factor binding,RNA polymerase II-specific DNA-binding transcription factor binding,cytokine receptor binding,ubiquitin-like protein ligase binding,and cytokine activity in membrane rafts,membrane microareas,and plasma membrane rafts.The results of the KEGG pathway analysis indicated that the IL-17 signaling pathway,TNF signaling pathway,and Toll-like receptor signaling pathway played a crucial role in the treatment of IBS-D by Wumei Pill.Molecular docking analysis showed that HSP90AA1,MAPK1,JUN,RELA,IL6,IL2,ESR1,and FOS could dock with berberine,palmatine,tetrahydroberberine,β-sitosterol,quercetin,and corydalis alkaloid,with good docking results.Conclusions:(1)Through bioinformatics analysis,we found that the expression levels of 17 key genes were significantly down-regulated in IBS-D patients,and these genes might be closely related to the pathogenesis of IBS-D.(2)Through network pharmacology analysis,it was found that the treatment of IBS-D with Wumei Pill exerted its therapeutic effects by affecting numerous genes including HSP90AA1 、MAPK1、JUN and RELA,and pathways such as IL-17 signaling,TNF signaling and Toll-like receptor.It could be inferred that the treatment of IBS-D with Wumei Pill was mediated by various active components,targets and pathways,ultimately resulting in reduced inflammatory reactions,modulation of gut microbiota and enhanced immunity to achieving the purpose of treating IBS-D.