Exploring The Mechanism Of Action Of Yiqi Huayu Jiedu Prescription In The Treatment Of COPD Based On Network Pharmacology And Molecular Dockin

Objective:Based on network pharmacology,molecular docking technology and gene expression synthesis(GEO)database,a bioinformatics approach was used to predict and analyze the molecular basis and mechanism of action of YQHYJD in the treatment of COPD,and to provide new ideas for the clinical treatment of COPD.Methods:1.By searching the active active ingredients of the constituent herbs of YQHYJD in the TCM Systematic Pharmacology Database and Analysis Platform(TCMSP)and the TCM Integrated Pharmacology Research Platform v2.0(TCMIP),and using the Uniprot database to standardize the target names,we established the "Yiqi Huayu Detoxification Formula The active ingredient database and the target database of "Yiqi,Huayu,Detoxification Formula"were retrieved from the GeneCards database,TTD database,DrugBank database,OMIM database,DisGeNET database and TCMIP disease target database,and the disease target database of COPD was established after standardizing the gene names;the active ingredient and disease target of the drug were retrieved from the GeneCards database,TTD database,DrugBank database,OMIM database,DisGeNET database and TCMIP.The intersection of the active ingredient and the disease target was used as the pharmacodynamic target,and the corresponding active ingredient was screened;Cytoscape 3.9.1 software was used to construct a quadratic network diagram of drug-active ingredient-common target-disease interaction;STRING database and Cytoscape 3.9.1 software were used to conduct protein interaction analysis and network topology analysis;Finally,we used AutoDock to dock the core components with key genes and proteins to initially verify the binding ability of the core components and key proteins in the pathway,in order to predict the possible active components of Yiqi,Huayu and Detoxification Formula for the treatment of COPD.2.Download the chronic obstructive pulmonary disease(COPD)microarray expression profile dataset GSE5058 from the GEO database,and perform gene differential analysis on the dataset GSE5058 with the help of the R language "limma" package to screen the differentially expressed genes in the airway epithelial cells of COPD patients.Then,we imported the String database and Cytoscape 3.9.1 software to build the protein interaction network,and used the CytoHubba plug-in to calculate and screen the key hub genes in the PPI network,and the MCODE plug-in of Cytoscape 3.9.1 to calculate the core gene network,and imported the gene data into the Metascape platform for GO and KEGG enrichment analysis.The core targets were integrated with the pharmacology and molecular docking of the first part of the network,and the "drug-disease" targets were obtained after screening and processing,and the same differential gene targets were screened and processed to obtain"Clinical disease" targets.The information of both targets was imported into the software to analyze the key pivotal genes and explore the potential gene targets of Yiqi,Huayu,and Detoxification Formula for COPD treatment.Results:(1)176 active ingredients,corresponding to 478 targets,were retrieved through the TCMSP database and TCMIP database.(2)3534 COPD disease targets were obtained from the GeneCards database;116 COPD disease targets were obtained from the DrugBank database;668 COPD disease targets were obtained from the OMIM database;44 COPD disease targets were obtained from the TTD database;43 COPD disease targets were obtained from the DigGENET database 3025;43 COPD disease targets were obtained from the TCMIP disease database.After combined and de-duplicated,4050 COPD disease targets were obtained.(3)The screened 301 drug-effective targets were imported into STRING platform to obtain PPI network graph,including 281 nodes,2509 edges,average degree of freedom 17.9,and sub-networks were extracted with the median values of Degree,BC and CC as thresholds to obtain a set of closely related core gene groups,a PPI network graph with 52 nodes and 615 kinds of associations.MAPK14,HIF1A,EGF,FOS,TLR4,PTGS2,NFKBIA,IL4.6 key gene targets were calculated using CytoHubba plugin,as TP53,AKT1,JUN,ACTB,MAPK3,EGFR.(4)KEGG enrichment analysis of pharmacodynamic targets was performed using Metascape database,and the top 20 key signaling pathways were obtained,which contained the atherosclerotic pathway of lipids,AGE-RAGE signaling pathway,MAPK pathway,NFκB signaling pathway,FoxO signaling pathway,cAMP signaling pathway,calcium signaling pathway,and relaxin signaling pathway,which are related to These pathways are closely related to the development of COPD.The main enrichment entries of BP for pharmacological targets are on biological processes such as cellular responses to organic cyclic compounds,cellular responses to lipids,responses to foreign body stimuli,responses to nutrient levels,responses to oxygen levels,and regulation of defense responses;the main enrichment entries of CC are on membrane rafts,vesicle lumen,postsynaptic,dendrites,plasma membrane protein complexes,receptor complexes,transcriptional regulator complexes,cellular apical part,myofilaments,etc.MF is mainly enriched for entries on nuclear receptor activity,protein domain specific binding,oxidoreductase activity,kinase binding,steroid binding,protein homogenization activity,protein kinase activity,ubiquitin-like protein ligase binding,heme binding,neurotransmitter receptor activity,etc.(5)Analyzing the component-target-pathway network map constructed by Cytoscape,the key signaling pathways were obtained as hsa05200(cancer pathway),hsa05417(lipid and atherosclerosis pathway),hsa04010(MAPK signaling pathway),hsa04926(relaxin signaling pathway),hsa04068(FoxO signaling pathway)The top 5 target genes are PTGS2,HSP90AA1,ESR1,PTGS1,ESR2,and the top 5 active ingredients are Q1(quercetin),L1(luteolin),K1(kaempferol),I1(isorhamnetin),HQN10(Skullcapflavone II).(6)The molecular docking results showed that the three active ingredients,quercetin,lignocaine and kaempferol,docked well with TP53,MAPK3,EGFR,AKT1,ACTB and JUN,with lignocaine requiring the lowest energy for binding to MAPK3 protein and AKT1 having a stronger affinity for the three active ingredients.(7)Analysis of the GSE5058 gene set yielded AFR1B10,CYP1A1 and GPR1 as significantly up-regulated genes,and VIPR2 and MUC8 as significantly down-regulated genes,suggesting a key role in COPD pathogenesis;applying Cytoscap key differential hub genes,three common key genes were derived,namely EGF,NCAM1,and ALDH3A1;using MCODE plug-in calculation,the three Seed networks with the highest network scores were selected,including 16 genes,as AKR1C2,PAX5,MYLK2,RRP12,GGT5,EGFL7,SPC24,THRAP3,RDH11,HSF4,PTPN20A,RGS20,KIR2DL3,CGB5,KAT6B,SLC30A2,PRH2.(8)After integrating the core targets obtained from the two parts of the analysis,a total of 44 common targets were identified and a PPI network was constructed to obtain a set of closely related core gene clusters,a PPI network with 26 nodes and 288 associations,and a core cluster with 22 nodes and 155 associations was derived by the MCODE plug-in,and only one of the differential genes,EGF,entered the core cluster.Only one of the differential genes,EGF,entered the core cluster,suggesting that EGF gene may be a deep gene target linking Yiqi,Huayu and Detoxification Formula and COPD.Conclusions:(1)Among the core components of YQHYJD Formula,quercetin,kaempferol,βsitosterol,lignan,baicalein,isorhamnetin,dousterol,astragalus flavonoid II,naringenin,and weixin have the most targets of action,among which quercetin,kaempferol,and lignan dock well with TP53,AKT1,JUN,ACTB,MAPK3,and EGFR in the key pathways,indicating that these core components and targets may be the molecular basis for the treatment of COPD with Yi Qi,Huayu and Detoxification Formula.(2)The treatment of COPD with Yiqi Huayu Detoxification Formula may be related to the presence of quercetin,kaempferol,β-sitosterol,lignan,baicalein,isorhamnetin,dousterol,astragalus flavonoid II,naringenin,and weiflowerin,which can play a therapeutic role in antiinflammatory,antioxidant,antibacterial,and inhibition of mucus hypersecretion.The specific mechanism may be related to the regulation of MAPK pathway,NF-κB signaling pathway,FoxO signaling pathway,cAMP signaling pathway and calcium signaling pathway.(3)EGF,as a key target shared by Chinese medicine and COPD,may play an important role in the biological process of Yiqi,Huayu,and Detoxification Formula in treating COPD,and EGF and EGF receptor family may be the key targets of this formula in treating COPD.