Objective:To study the mechanism of action of Xiayuxue Tang in treating hepatic fibrosis by combining GEO data mining,network pharmacology,and molecular docking technology,and provide new research directions for the t...Objective:To study the mechanism of action of Xiayuxue Tang in treating hepatic fibrosis by combining GEO data mining,network pharmacology,and molecular docking technology,and provide new research directions for the treatment of hepatic fibrosis.Method:Utilizing multiple databases,we aim to identify the relevant targets of various components in Xiayuxue Tang and their associations with hepatic fibrosis.After pinpointing the key targets through interaction analysis,we will construct both the compound-target network and the protein interaction network for Xiayuxue Tang.Conclusively,we will conduct GO and KEGG enrichment analyses on these key targets,followed by molecular docking verification.Result:Through mining the GEO database,171 related targets were identified.When combined with other databases,a total of 2,343 hepatic fibrosis-related targets were obtained.Xiayuxue Tang comprises 82 related components,which include 26 active components from rhubarb,1 from ground beetle worm,46 from peach kernels,with a total of 314 predicted targets.The GO enrichment analysis revealed 748 biological processes,32 cellular components,and 73 molecular functions,while the KEGG enrichment analysis identified 222 pathways.Molecular docking verification confirmed that effective compounds can bind stably to key proteins,exhibiting strong binding activity.This underscores the potential efficacy of Xiayuxue Tang in addressing hepatic fibrosis.Conclusion:Xiayuxue Tang exerts regulatory effects on hepatic fibrosis through different targets and pathways,suggesting that the herbal compound has the characteristics of multiple pathways and targets.展开更多
Objective:Based on network pharmacology and molecular docking technology to explore the mechanism of Professor Cao Enze's application of Panax notoginseng in the treatment of membranous nephropathy.Methods:TCMSP d...Objective:Based on network pharmacology and molecular docking technology to explore the mechanism of Professor Cao Enze's application of Panax notoginseng in the treatment of membranous nephropathy.Methods:TCMSP database was used to obtain the effective components and corresponding target information of Panax notoginseng,and Gene Cards database was used to obtain the disease target genes of membranous nephropathy.The intersection targets of the two were taken and the Venn diagram was drawn.The STRING database was used to obtain the protein interaction relationship,and the PPI network diagram was constructed by Cytoscape 3.9.1 software to screen out the core targets of Panax notoginseng in the treatment of membranous nephropathy.GO function and KEGG pathway enrichment analysis were performed using the David database to obtain the potential pathway of Panax notoginseng in the treatment of membranous nephropathy.Finally,Autodock software was used to verify the molecular docking of the main active components of the drug with the core targets.Results:A total of 7 effective components such as quercetin,ginsenoside rh2,Mandenol and Stigmasterol were retrieved,and 127 potential targets of Panax notoginseng in the treatment of membranous nephropathy were screened out.By PPI network topology analysis,23 core targets such as JUN,TP53,RELA,AKT1 and MAPK1 were screened out.GO functional enrichment analysis contained 703 biological processes,55 cell components and 121 molecular functions,and KEGG signal pathway enrichment analysis enriched 171 signal pathways.The results of molecular docking showed that there was a strong binding ability between the main core targets and the main components of Panax notoginseng.Conclusion:Through network pharmacology,it is concluded that Panax notoginseng treats membranous nephropathy through multiple targets and multiple pathways,which provides a theoretical basis for subsequent basic research.展开更多
Background:Siwu decoction(SWD)is a traditional Chinese herbal decoction commonly used for treating various symptoms of blood deficiency and blood stasis,including cancer-related anemia(CRA).However,due to its complex ...Background:Siwu decoction(SWD)is a traditional Chinese herbal decoction commonly used for treating various symptoms of blood deficiency and blood stasis,including cancer-related anemia(CRA).However,due to its complex composition,the key active ingredients and underlying mechanisms of its therapeutic effects often remain unknown.This research aims to use network pharmacology and molecular docking technology to systematically elucidate the potential mechanisms underlying the efficacy of SWD in treating cancer-related anemia.Methods:The key constituents of SWD were procured from the TCMSP database.Leveraging the Swiss ADME and Swiss Target Prediction databases,potential targets were recognized.Disease-related targets were assembled via the GeneCards and DrugBank databases.Constructing the PPI network involved the utilization of the STRING database,followed by visualization through Cytoscape 3.9.1 software.Subsequently,GO and KEGG enrichment analysis was conducted utilizing the DAVID database,with visual analysis performed on the macrobiotic platform.For molecular docking,the Autodock software was employed,and the molecular docking outcomes were visualized using the PyMOL software.Results:In this investigation,a comprehensive revelation of 18 primary active compounds and 511 associated targets linked to CRA was accomplished.The outcomes of protein-protein interaction(PPI)analysis unequivocally identified AKT1,EGFR,SRC,VEGFA,HRAS,MAPK3,and STAT3 as pivotal proteins within the SWD’s framework for effective CRA intervention.Notably,signaling pathways such as the HIF-1,JAK-STAT,TNF-α,and PI3K-Akt pathways,intricately involved in hematopoietic stem cell proliferation,differentiation,and inflammatory response,emerged as closely intertwined with the therapeutic application of SWD for CRA treatment.The congruence between these potential targets and SWD’s primary therapeutic constituents for CRA treatment was substantiated by the outcomes of molecular docking analysis.Conclusion:This work provided a reference for further fundamental research by outlining the primary active ingredients and putative molecular mechanisms of SWD in the treatment of CRA.展开更多
Objective:Based on the analysis of a biochemical information database,the“target-pathway”network of anlotinib in the treatment of non-small cell lung cancer was constructed by using network pharmacological methods t...Objective:Based on the analysis of a biochemical information database,the“target-pathway”network of anlotinib in the treatment of non-small cell lung cancer was constructed by using network pharmacological methods to explore the mechanism of multi-target and multi-pathway treatment of non-small cell lung cancer.Methods:The 3D molecular structure formula of anlotinib was obtained by searching the PubChem database,and the target of anlotinib was predicted by using the PharmMapper database;obtain non-small cell lung cancer related targets through the GeneCards database,screen common genes related to drug targets and diseases by Venny 2.1.0,and build the relationship between drugs and diseases.Through the STRING11.5 database,the interaction relationship between action targets was built,the protein-protein interaction network was constructed,and the target degree was analyzed by Cytocsape 3.7.2 software to screen molecular docking objects.The DAVID database was used for Gene Ontology gene enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis to predict its mechanism,and the AutoDock software was used for molecular docking of the main targets.Results:The analysis results showed that there were 76 possible targets involved in the treatment of non-small cell lung cancer with anlotinib,mainly acting on epidermal growth factor receptor,mitogen-activated protein kinase 14,tyrosine-protein phosphatase non-receptor type 11,heat shock protein HSP 90-alpha,tyrosine-protein kinase Lck,cAMP-dependent protein kinase catalytic subunit alpha and other target protein genes,Kyoto Encyclopedia of Genes and Genomes pathway analysis obtained 60 possible pathways related to its treatment of non-small cell lung cancer,mainly involving progesterone-mediated oocyte maturation,prostate cancer,proteoglycans in cancer,FoxO signaling pathway,pathways in cancer,Ras signaling pathway,PI3K-Akt signaling pathway,etc.Conclusion:Anlotinib has the characteristics of multi-targets and multi-pathways in the treatment of non-small cell lung cancer,which provides a scientific basis for the follow-up study on the optimization of its efficacy in the treatment of non-small cell lung cancer and the revelation of the pharmacological effects of anlotinib.展开更多
Background:Rehmanniae Radix Praeparata(RRP,Shu Dihuang in Cinese)is a traditional Chinese herb with multiple pharmacological effects and is commonly used to treat blood deficiency syndrome,such as cancer-related anemi...Background:Rehmanniae Radix Praeparata(RRP,Shu Dihuang in Cinese)is a traditional Chinese herb with multiple pharmacological effects and is commonly used to treat blood deficiency syndrome,such as cancer-related anemia(CRA),alone or in combination with other herbs.However,its main active ingredients and mechanisms of action in treating CRA remain unknown.This study aims to elucidate RRP’s potential mechanism and main active components in treating CRA by using network pharmacology and molecular docking technology system.Methods:The main components of RRP were obtained by the TCMSP database and literature search,and active components and potential targets were obtained by the SwissADME and SwissTargetPridiction databases.CRA targets were collected through GeneCards,DisGeNET,and DrugBank databases.Protein-protein interaction networks of potential targets were constructed via STRING 11.5 and analyzed visually with Cytoscape 3.9.1.The Metascape platform was used for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis,which were subsequently visualized with Cytoscape 3.9.1 or SangerBox platform.Moreover,Autodock Vina was used for the molecular docking of potential targets and main active ingredients that were visualized with PyMOL software.Results:In this study,31 main active ingredients of PPR were screened,and 155 related targets related to CRA were unearthed.Protein-protein interaction results showed that PPR’s core proteins for CRA intervention correlate to STAT3,SRC,MAPK3,MAPK1,PIK3R1,PIK3CA,and AKT.Multiple signaling pathways were closely related to the treatment of CRA intervened by PPR,including the PI3K-Akt signaling pathway,HIF-1 signaling pathway,JAK-STAT3 signaling pathway,TNF-αsignaling,cytokine signaling pathway and NF-kappB signaling pathway,which are closely involved in the proliferation and differentiation of hematopoietic stem cell and inflammatory response.Molecular docking results showed that these potential targets had good conformation with the core active components of RRP for treating CRA.Conclusion:This study revealed RRP’s main active components and potential molecular mechanisms in treating CRA,providing a reference for subsequent basic research.展开更多
Objective:Use network pharmacology to explore the anti-COVID-19 mechanism of Huashi Baidu Recipe,supplemented by molecular docking verification.Methods:Thorugh databases such as TCMSP,GeneCard,String,and software such...Objective:Use network pharmacology to explore the anti-COVID-19 mechanism of Huashi Baidu Recipe,supplemented by molecular docking verification.Methods:Thorugh databases such as TCMSP,GeneCard,String,and software such as Cytoscape,AutoDockVina,network relationships was established,and the binding ability of active ingredients and targets is calculated through molecular docking,and biological function enrichment analysis was conducted.Result:The ingredients in Huashi Baidu Recipe that had strong affinity with SARS-CoV-23CL hydrolase(3CLpro)and angiotensin converting enzyme 2(ACE2)receptors include Quercetin,Baicalein,Astragaloside IV,Wogonin and other ingredients;25 active ingredients which obtained by screening had strong affinity with targets such as IL6,IL1B,NOS2 and CCL2.The biological function enrichment analysis mainly focused on Th17,Th1 and Th2 cell differentiation,NF-κB,MAPK,TNF,IL-17signaling pathway,etc.Conclusion:The active ingredients of Huashi Baidu Recipe may inhibit the infection and replication of SARS-CoV-2 virus,regulate RAS system’balance,inhibit excessive immune inflammatory response,and prevent inflammatory storm from appearing to fight COVID-19.展开更多
[Objectives]The action mechanism of Tingli Dazao Xiefei Decoction in the treatment of COPD was explored by the network pharmacology and molecular docking technology.[Methods]The TCMSP database was used to perform acti...[Objectives]The action mechanism of Tingli Dazao Xiefei Decoction in the treatment of COPD was explored by the network pharmacology and molecular docking technology.[Methods]The TCMSP database was used to perform active ingredient screening and target prediction on Chinese medicines contained in Tingli Dazao Xiefei Decoction,and COPD-related targets were searched through disease databases.Common targets of Tingli Dazao Xiefei Decoction and COPD were imported into Metascape database for GO analysis and KEGG pathway enrichment analysis.The STRING database was used to perform PPI analysis on common targets,and core targets were screened through the Cytoscape software.The Pymol,AutoDockTools,Vina and other software were used for molecular docking of some core targets and ingredients.[Results]From Tingli Dazao Xiefei Decoction,26 active ingredients which shared 211 common targets and 22 core targets with COPD,were screened out.Enrichment analysis revealed a total of 1892 biological processes,78 cell components,152 molecular functions,and 164 signal paths.The molecular docking of part of the core targets and corresponding ingredients obtained better results.[Conclusions]Tingli Dazao Xiefei Decoction treats COPD through multiple targets and multiple pathways,revealing its mechanism for treating COPD.展开更多
[Objectives]To explore the potential mechanism of Danggui Buxue Decoction in treating the iron deficiency anemia(IDA)based on network pharmacology and molecular docking technology.[Methods]The active components and ta...[Objectives]To explore the potential mechanism of Danggui Buxue Decoction in treating the iron deficiency anemia(IDA)based on network pharmacology and molecular docking technology.[Methods]The active components and target proteins of Danggui Buxue Decoction were searched in databases such as TCMSP,OMIM,GeneCards,Drugbank,String,Metascape,etc.,and the target proteins shared with IDA were screened out,and the information about the signal pathways and biological functions of these target proteins was obtained.[Results]17 active components of Danggui Buxue Decoction and 24 potential targets for the treatment of IDA were obtained.With the aid of String database and Cytoscape software,the protein interaction network was obtained and the network topology analysis was performed.Four potential core targets with higher scores were obtained,namely F2,NOS2,NOS3,and PPARG.Using the Metascape database,GO function enrichment analysis and KEGG pathway enrichment analysis were performed on the potential targets of Danggui Buxue Decoction in the treatment of IDA,and the important biological processes,cell composition,molecular functions and signal pathways related to the target were screened through the R language.The results show that biological processes are related to positive regulation of growth,cell composition is related to membrane microdomain,and molecular functions are related to oxidoreductase activity.The signal pathways involved are mainly AGE-RAGE signal pathway,TNF signal pathway and IL-17 signal pathway.Finally,the molecular docking results confirmed that the active components of Danggui Buxue Decoction have a good binding ability with the target.[Conclusions]Danggui Buxue Decoction treats the IDA through multiple components,multiple targets,multiple signal pathways,and multiple biological functions.展开更多
Computer-aid molecular docking is a simulative process that receptors and ligands recognize each other through energy matching and geometric matching. It is widely used in bioactive compounds simulative screening and ...Computer-aid molecular docking is a simulative process that receptors and ligands recognize each other through energy matching and geometric matching. It is widely used in bioactive compounds simulative screening and preliminary exploring the bioactivity and toxicity of molecular, which plays an important guiding role in toxicity and bioactivity study of molecular entities. In our study, we used the computer-aid molecular docking software-discovery studio 3.1 client to test the mechanism of aflatoxins such as aflatoxin B1, B2, M1, M2, G1, G2 and the results of our experiment help to illustrate the pathway of aflatoxin’s toxication. We also used this technology to test the preliminary toxicity of zearalenone (ZEN) and its two degradation products:α-zearalenol (α-ZOL) and β-zearalenol (β-ZOL), which indicates that these three products possessed significant estrogenic activity. The order of the estrogenic activity is:α-zearalenol > zearalenone >β-zearalenol.展开更多
[Objectives]To explore the active components and mechanism of Bupleurum and Asarum in the treatment of traumatic brain injury(TBI).[Methods]All the active components and potential action targets of Bupleurum and Asaru...[Objectives]To explore the active components and mechanism of Bupleurum and Asarum in the treatment of traumatic brain injury(TBI).[Methods]All the active components and potential action targets of Bupleurum and Asarum pairs were collected by online platform Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)database and literature search.Target genes related to traumatic brain injury were obtained by Online Mendelian Inheritance in Man(OMMI),Therapeutic Target Database(TTD),PharmGKB,Genecards and Drugbank.The"drug-ingredient-target"network diagram was constructed by using Cytoscape software.Venny 2.1.0 was used to integrate the intersection targets of drug targets and disease targets,and the String platform was used to construct a target protein-protein interaction network(PPI).Topological analysis and core target screening of the constructed PPI network were performed using the"CytoNCA"plug-in in Cytoscape software.Gene Ontology(GO)annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were performed on the intersection targets using the DAVID database.Finally,Autodock and Pymol software were used to simulate the binding activity of key candidate active components and core genes.[Results]25 active components were screened from Bupleurum-Asarum and 111 potential targets involved in the disease process.GO analysis and KEGG results showed that potential therapeutic targets were mainly enriched in biological processes such as inflammatory response,oxidative stress,cell membrane repair,and cytokine regulation.Network analysis and molecular docking showed that the key compounds of Bupleurum and Asarum were kaempferol and quercetin,which were well docked with the active pockets of four core genes of traumatic brain injury.[Conclusions]Bupleurum and Asarum may be involved in the regulation of inflammatory response,oxidative stress,cell membrane repair through multiple targets and multiple pathways in the treatment of traumatic brain injury.展开更多
To predict the potential mechanism of prevention and treatment of colorectal adenoma canceration by berberine and the docking of main key targets by computer virtual method.Methods:The related targets of berberine,col...To predict the potential mechanism of prevention and treatment of colorectal adenoma canceration by berberine and the docking of main key targets by computer virtual method.Methods:The related targets of berberine,colorectal adenoma and colorectal cancer were collected in various databases;the key targets were obtained by intersection;the protein protein interaction network and 6 kinds of enrichment analysis of key potential targets were completed by corresponding databases;the main key targets and berberine molecules were obtained for molecular docking.Results:There were 319 unique targets for berberine,3,279 for intestinal adenoma and 4,119 for colorectal cancer.The protein protein interaction network of key target involved 66 proteins.In the results of Gene Ontology enrichment,28 items related to biological process,28 items related to cell composition,30 items related to molecular function,26 items related to Kyoto Encyclopedia of Genes and Genomes pathway enrichment,35 items related to TargetScan microRNA,15 items related to Human Phenotype Ontology.TP53 and CYCS are the 2 key targets involved in the system enrichment.After docking,berberine was closely bound to theα-helix and β-fold of TP53 protein,and to theα-helix of CYCS protein.Conclusion:The potential mechanism of berberine in the prevention and treatment of colorectal adenoma canceration may be related to the regulation of cell apoptosis,metabolic pathways and biological activities of various enzymes.berberine,as a small molecular ligand,has the characteristics of multi-target,multi-channel and multi-system mechanism.In the prediction results,berberine,as a small molecular ligand,can closely bind with the main key targets related to colorectal adenoma canceration.展开更多
Objective:In this study,we used network pharmacology and molecular docking technology to analyze the mechanism of Bushen Tongluo granule in the treatment of osteoarthritis.Methods:The main active components and corres...Objective:In this study,we used network pharmacology and molecular docking technology to analyze the mechanism of Bushen Tongluo granule in the treatment of osteoarthritis.Methods:The main active components and corresponding targets of Bushen Tongluo granule were screened from thetraditional Chinese medicine systems pharmacology database.The targets related to osteoarthritis were collected from the Online Mendelian Inheritance in Man,Therapeutic Target database,GeneCards,Pharmacogenomics Knowledgebases and Drugbank databases.Cytoscape3.9.0 software was used to construct the action network diagram of“Bushen Tongluo Granule-Active Component-Target”.Builded a protein-protein interaction network from the STRING database.The Bioconductor platform and R language 4.0.3 were used for Gene Ontologyfunction andKyoto Encyclopedia of Genes and Genomespathway enrichment analysis.Then,selected the pathway most associated with osteoarthritis for specific analysis.Finally,the core genes were screened and verified by molecular docking using AutoDockTools software.Results:71 principal components of Bushen Tongluo granule and 183 potential therapeu-tic targets for osteoarthritis were obtained.Twenty-eight key targets of Bushen Tongluo granulein the treatment of osteoarthritis are enriched in 158 pathways.Among them,the tumor necrosis factor signaling pathway,interleukin-17 signaling pathway,Toll-like receptor signaling pathway,T helper cell 17 cell differentiation and hypoxia-inducible factor-1signaling pathway involved in key targets are closely related to osteoarthritis.The relevant vital targets were involved in the regulation of DNA transcription factor activity,the response to chemical stress,the response to reactive oxygen species,the response to oxidative stress,the proliferation of muscle cells,the proliferation of epithelial cells and the biological processes such as responses to lipopolysaccharides,responses to molecules of bacterial origin.Molecular docking showed that protein kinase B 1-β-sitosterol,the tumor necrosis factor-naringenin,interleukin-6-luteolin,mitogen-activated protein kinase-quercetin,vascular endothelial growth factor A-quercetin and prostaglandin-endoperoxide synthase 2-luteolin have strong docking activities.Conclusions:Bushen Tongluo granule can reduce the inflammatory response and inhibit articular cartilage angiogenesis in the treatment of osteoarthritis,which may be achieved by regulating the inflammatory signaling pathway and hypoxia-inducible factor-1 signaling pathway.展开更多
Objective:Based on the network pharmacology approach and molecular docking technology,the core targets of dihydrotanshinone I(DHT)for the treatment of helicobacter pylori(Hp)infection were searched and the potential m...Objective:Based on the network pharmacology approach and molecular docking technology,the core targets of dihydrotanshinone I(DHT)for the treatment of helicobacter pylori(Hp)infection were searched and the potential mechanisms of drug therapy were explored.Methods:The TCMSPdatabase and Swiss Target Prediction database were employed to identify drug targets.To mine disease targets based on GeneCards,OMIM,DrugBank,DisGeNET,and TTDdatabases.Then the two were intersected to obtain common targets.The proteinproteininteraction(PPI)networkmap of common targets was constructed on the basis of the String network platform and Cytoscape software,and the targets with degree values over 1/2 maximum degree value were selected as core targets.Molecular docking verification of DHTand core targets were performed using AutoDock and PyMOL software.Finally,gene ontology(GO)functional enrichment analysis andKyoto Encyclopediaof Genes and Genomes(KEGG)pathway enrichment analysis of the common targets were carried out using the Metascape database and R-4.0.2-win software.Results:A total of 13 targets of DHTwas extracted for the treatment of Hp,and five core targets,includingSignal transducerand activator of transcription 1(STAT1),Signal transducerand activator of transcription 3(STAT3),Prostaglandin G synthase 2(PTGS2),Signal transducerand activator of transcription 4(STAT4)and Indoleamine 2,3-dioxygenase 1(IDO1),were screened according to their degree values.Molecular docking indicated that DHThad an excellent binding to the core target.29 pathways were yielded by KEGG enrichment analysis,and a total of 48 biological processes,7 cellular components and 13 molecular functions were derived from GO enrichment analysis.Conclusion:DHTmay decrease pro-inflammatory factor expression and immune cell infiltration to treat Hpinfection via the janus kinase(JAK)-signal transducer and activator of transcription(STAT)signaling pathway regulated by STAT1,STAT3,STAT4,etc.展开更多
Background:To explore the effective components and mechanism of Classic ancient prescription Wuji pill on lung cancer(LC)with the help of network pharmacology and molecular docking technology.Methods:TCMSP database,Ch...Background:To explore the effective components and mechanism of Classic ancient prescription Wuji pill on lung cancer(LC)with the help of network pharmacology and molecular docking technology.Methods:TCMSP database,Chinese Pharmacopoeia(2020 Edition)and related literature were searched to identify the main chemical composition and targets of constituent drugs in Wuji pill,including Houpo(Magnoliae Officinalis Cortex),Huangqin(Scutellariae Radix),Badou(Crotonis Fructus),Huanglian(Coptidis Rhizoma)and Renshen(Ginseng Radix et Rhizoma).Meanwhile,Genecards,OMIM,TTD,Drugbank and PharmGkb databases were used to obtain the main targets of LC.The"chemical compound-target"network was constructed by using Cytoscape 3.8.2 software with the disease drug intersection gene as the research target.The PPI network was constructed by using the string database for protein interaction analysis,and the core target genes were sorted out.The Gene ontology go function enrichment analysis and KEGG signal pathway enrichment analysis were carried out based on the ClusterProfiler of R software.Finally,the Autodock Vina software was used to conduct molecular docking between the core target with high value and the key components.Results:A total of 60 active components,190 corresponding targets and 2516 GO and 163 KEGG pathways of Wuji pill were screened out,including 179 potential targets of LC.The core targets were ESR1,CDKN1A,TP53,NR3C1,MAPK1,AKT1,MAPK8,JUN,RELA,the core components were quercetin,kaempferol,β-sitosterol,stigmasterol,tetrahedron,protoopioid,etc,and the core pathways were PI3K-Akt,MAPK,IL-17,etc.Conclusion:This study preliminarily revealed the mechanism of action of Wuji pill on multi component-multi target-multi pathway of LC,which provided reference for the further clinical development and research of Wuji pill.展开更多
Wild edible Termitomyces mushrooms are popular in Southwest China and umami is important flavor qualities of edible mushrooms.This study aimed to understand the umami taste of Termitomyces intermedius and Termitomyces...Wild edible Termitomyces mushrooms are popular in Southwest China and umami is important flavor qualities of edible mushrooms.This study aimed to understand the umami taste of Termitomyces intermedius and Termitomyces aff.bulborhizus.Ten umami peptides from aqueous extracts were separated using a Sephadex G-15 gel filtration chromatography.The intense umami fraction was evaluated by both sensory evaluation and electronic tongue.They were identified as KLNDAQAPK,DSTDEKFLR,VGKGAHLSGEH,MLKKKKLA,SLGFGGPPGY,TVATFSSSTKPDD,AMDDDEADLLLLAM,VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK.Seven peptides,except VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK were selectively synthesized to verify their taste characteristics.All these 10 peptides had umami or salt taste.The 10 peptides were conducted by molecular docking to study their interaction with identified peptides and the umami taste receptor T1R1/T1R3.All these 10 peptides perfectly docked the active residues in the T1R3 subunit.Our results provide theoretical basis for the umami taste and address the umami mechanism of two wild edible Termitomyces mushrooms.展开更多
Background:In this study,we used network pharmacology and molecular docking combined with vitro experiments to explore the potential mechanism of action of Gualou Qumai pill(GLQMP)against DKD.Methods:We screened effec...Background:In this study,we used network pharmacology and molecular docking combined with vitro experiments to explore the potential mechanism of action of Gualou Qumai pill(GLQMP)against DKD.Methods:We screened effective compounds and drug targets using Chinese medicine systemic pharmacology database and analysis platform and Chinese medicine molecular mechanism bioinformatics analysis tools;and searched for DKD targets using human online Mendelian genetics and gene cards.The potential targets of GLQMP for DKD were obtained through the intersection of drug targets and disease targets.Cytoscape software was applied to build herbal medicine-active compound-target-disease networks and analyze them;protein-protein interaction networks were analyzed using the STRING database platform;gene ontology and Kyoto Encyclopedia of Genes and Genomes were used for gene ontology and gene and genome encyclopedia to enrich potential targets using the DAVID database;and the AutoDock Vina 1.1.2 software for molecular docking of key targets with corresponding key components.In vitro experiments were validated by CCK8,oil red O staining,TC,TG,RT-qPCR,and Western blot.Results:Through network pharmacology analysis,a total of 99 potential therapeutic targets of GLQMP for DKD and the corresponding 38 active compounds were obtained,and 5 core compounds were identified.By constructing the protein-protein interaction network and performing network topology analysis,we found that PPARA and PPARG were the key targets,and then we molecularly docked these two key targets with the 38 active compounds,especially the 5 core compounds,and found that PPARA and PPARG had good binding ability with a variety of compounds.In vitro experiments showed that GLQMP was able to ameliorate HK-2 cell injury under high glucose stress,improve cell viability,reduce TC and TG levels as well as decrease the accumulation of lipid droplets,and RT-qPCR and Western blot confirmed that GLQMP was able to promote the expression levels of PPARA and PPARG.Conclusion:Overall,this study revealed the active compounds,important targets and possible mechanisms of GLQMP treatment for DKD,and conducted preliminary verification experiments on its correctness,provided novel insights into the treatment of DKD by GLQMP.展开更多
Background:In order to investigate the possible pharmacological mechanism of digallate in Galla Chinensis for treating enteritis,providing reference for the search and exploration of effective drugs for treating enter...Background:In order to investigate the possible pharmacological mechanism of digallate in Galla Chinensis for treating enteritis,providing reference for the search and exploration of effective drugs for treating enteritis.Method:Traditional Chinese Medicines Systems Pharmacology Database and Analysis Platform,PharmMapper,DisGeNET,DrugBank,and GeneCards databases were used to obtain drug and disease-related target information.Gene ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment were performed,and the main therapeutic pathways and targets were identified by combining protein-protein interaction networks and cytoHubba plug-in.Molecular docking was used to validate the results.Result:297 drug related targets,2436 disease related targets,and 66 target points related to digallate were predicted to be associated with enteritis.10 related signal pathways and 10 key genes were identified.Conclusion:Digallate may be utilized to treat enteritis by acting on similar pathways,such those related to pathways in cancer,lipid and atherosclerosis,proteoglycans in cancer,Rap1 signaling pathway,PI3K-Akt signaling pathway and other targets such as IGF1,EGFR,SRC,IGF1R,PPARG.展开更多
Objective:To explore the potential mechanism of action of quercetin in the treatment of diarrhea irritable bowel syndrome(IBS-D).Methods:The potential targets of quercetin were obtained from the TCMSP,SwissTar-getPred...Objective:To explore the potential mechanism of action of quercetin in the treatment of diarrhea irritable bowel syndrome(IBS-D).Methods:The potential targets of quercetin were obtained from the TCMSP,SwissTar-getPrediction,and BATMAN-TCM databases.The targets of IBS-D were obtained by searching the GeneCards database with"diarrhea irritable bowel syndrome"as the keyword,and the targets of quercetin and IBS-D were intersected.The PPI network was constructed by Cytoscape 3.7.1 software.The intersected targets were imported into the DAVID database for GO functional analysis and KEGG pathway enrichment analysis.The binding ability of quercetin to the core targets was observed using molecular docking.Based on this,we established an IBS-D rat model,administered quercetin for intervention,and experimentally validated the network pharmacology prediction results by HE staining and ELISA assay.Results:Network pharmacology analysis showed that TP53,TNF-α,AKT1,VEGF-A,IL-6 factors and MAPK,PI3K-Akt signaling pathway as the core targets and pathways of quercetin for the treatment of IBS-D.The results of animal experiments revealed that quercetin could inhibit the secretion of TP53,TNF-α,AKT1,VEGF-A,IL-1βand IL-6,reduce the inflammatory response and improve IBS-D.Conclusion:Quercetin could protect colon tissue by regulating the expression of TP53,TNF-α,AKT1,VEGF-A,IL-1βand IL-6,thereby treating IBS-D.展开更多
Background:Lotus seedpod(Receptaculum Nelumbinis)is the abundant by-products produced during lotus seed processing,and the sources are usually considered to be wastes and are abandoned outdoors or incinerated.This stu...Background:Lotus seedpod(Receptaculum Nelumbinis)is the abundant by-products produced during lotus seed processing,and the sources are usually considered to be wastes and are abandoned outdoors or incinerated.This study aims at predicting its bioactive compounds and cancer-related molecular targets against six cancers,including lung cancer,gastric cancer,liver cancer,breast cancer,ovarian cancer and cervical cancer.Methods:Network pharmacology and molecular docking methods were performed.Results:Network pharmacology results indicated that 14 core compounds(liensinine,tetrandrine,lysicamine,tricin,sanleng acid,cireneol G,ricinoleic acid,linolenic acid,5,7-dihydroxycoumarin,apigenin,luteolin,morin,quercetin and isorhamnetin)and 10 core targets(AKT1,ESR1,HSP90AA1,JUN,MAPK1,MAPK3,PIK3CA,PIK3R1,SRC and STAT3)were screened for lotus seedpod against the six cancers.Molecular docking analysis suggested that the binding abilities between the core compounds and the core targets were mostly strong.GO analysis revealed that the intersected targets between the bioactive compounds of lotus seedpod and the six cancers were significantly related to biological processes,cell compositions and molecular functions.KEGG analysis showed that PI3K-Akt,TNF,Ras,MAPK,HIF-1 and C-type lectin receptor signaling pathways were notably involved in the anti-cancer activities of lotus seedpod against the six cancers.Conclusions:14 core compounds and 10 core targets were screened for lotus seedpod against lung cancer,gastric cancer,liver cancer,breast cancer,ovarian cancer and cervical cancer.This study supports the application of lotus seedpod in treating cancers,and promotes the recycling and the high-value utilization.展开更多
The purpose of this project is used for exploring the mechanism of Callistephus chinensis in the treatment of diabetes by network pharmacology and molecular docking methods.The target of Callistephus chinensis was obt...The purpose of this project is used for exploring the mechanism of Callistephus chinensis in the treatment of diabetes by network pharmacology and molecular docking methods.The target of Callistephus chinensis was obtained from SwissTargetPrediction database,while the target related to diabetes was obtained from GeneCards and OMIM databases.The target was added in String database to build the protein interaction network.GO biological process enrichment analysis and KEGG pathway enrichment analysis were carried out by Metascape software,then the target-pathway network was constructed.Molecular docking was carried out in Discovery Studio 2016 Client software to verify the binding force of Callistephus chinensis flavonoid compounds with key targets.In this study,10 potential active components were selected from the flavonoid monomer compounds of Callistephus chinensis.1847 biological processes(BP),126 cell compositions(CC)and 256 molecular functions(MF)were obtained by GO enrichment analysis;a total of 194 pathways were involved in KEGG enrichment analysis of 192 cross targets.Network analysis showed that quercetin was the main active component of flavonoids in the treatment of diabetes,AKT1,TNF,VEGFA,EGFR,SRC and other related signals were in relation to the treatment of diabetes.This study showed that Callistephus chinensis flavonoid compounds play a role in the treatment of diabetes by regulating multi-target and multi-pathway.展开更多
基金funded by the National Natural Science Foundation of China(Grant Nos.82204755,81960751,and 81660705)the Guangxi Young and Middle-aged Teachers’Research Ability Improvement Project(Grant No.2022KY1667)+4 种基金the Guangxi Zhuangyao Pharmaceutical Key Laboratory(Grant Nos.GXZYZZ2019-1,GXZYZZ2020-07)the Guangxi Natural Science Foundation Youth Project(Grant No.2020GXNSFBA297094)the Guangxi University of Traditional Chinese Medicine School-level Project Youth Fund(Grant No.2022QN008)Faculty of Chinese Medicine Science Guangxi University of Chinese Medicine Research Project(2022MS008,2022QJ001)Faculty of Chinese Medicine Science Guangxi University of Chinese Medicine,Autonomous Region-level Innovation and Entrepreneurship Training Program for College Students(S202213643016).
文摘Objective:To study the mechanism of action of Xiayuxue Tang in treating hepatic fibrosis by combining GEO data mining,network pharmacology,and molecular docking technology,and provide new research directions for the treatment of hepatic fibrosis.Method:Utilizing multiple databases,we aim to identify the relevant targets of various components in Xiayuxue Tang and their associations with hepatic fibrosis.After pinpointing the key targets through interaction analysis,we will construct both the compound-target network and the protein interaction network for Xiayuxue Tang.Conclusively,we will conduct GO and KEGG enrichment analyses on these key targets,followed by molecular docking verification.Result:Through mining the GEO database,171 related targets were identified.When combined with other databases,a total of 2,343 hepatic fibrosis-related targets were obtained.Xiayuxue Tang comprises 82 related components,which include 26 active components from rhubarb,1 from ground beetle worm,46 from peach kernels,with a total of 314 predicted targets.The GO enrichment analysis revealed 748 biological processes,32 cellular components,and 73 molecular functions,while the KEGG enrichment analysis identified 222 pathways.Molecular docking verification confirmed that effective compounds can bind stably to key proteins,exhibiting strong binding activity.This underscores the potential efficacy of Xiayuxue Tang in addressing hepatic fibrosis.Conclusion:Xiayuxue Tang exerts regulatory effects on hepatic fibrosis through different targets and pathways,suggesting that the herbal compound has the characteristics of multiple pathways and targets.
基金2022 Anhui Provincial Health Research Project (No.AHWJ2022b041)2021 Anhui Provincial Key Medical and Health Specialty Construction Project (No.Anhui Health Letter 2021-273)。
文摘Objective:Based on network pharmacology and molecular docking technology to explore the mechanism of Professor Cao Enze's application of Panax notoginseng in the treatment of membranous nephropathy.Methods:TCMSP database was used to obtain the effective components and corresponding target information of Panax notoginseng,and Gene Cards database was used to obtain the disease target genes of membranous nephropathy.The intersection targets of the two were taken and the Venn diagram was drawn.The STRING database was used to obtain the protein interaction relationship,and the PPI network diagram was constructed by Cytoscape 3.9.1 software to screen out the core targets of Panax notoginseng in the treatment of membranous nephropathy.GO function and KEGG pathway enrichment analysis were performed using the David database to obtain the potential pathway of Panax notoginseng in the treatment of membranous nephropathy.Finally,Autodock software was used to verify the molecular docking of the main active components of the drug with the core targets.Results:A total of 7 effective components such as quercetin,ginsenoside rh2,Mandenol and Stigmasterol were retrieved,and 127 potential targets of Panax notoginseng in the treatment of membranous nephropathy were screened out.By PPI network topology analysis,23 core targets such as JUN,TP53,RELA,AKT1 and MAPK1 were screened out.GO functional enrichment analysis contained 703 biological processes,55 cell components and 121 molecular functions,and KEGG signal pathway enrichment analysis enriched 171 signal pathways.The results of molecular docking showed that there was a strong binding ability between the main core targets and the main components of Panax notoginseng.Conclusion:Through network pharmacology,it is concluded that Panax notoginseng treats membranous nephropathy through multiple targets and multiple pathways,which provides a theoretical basis for subsequent basic research.
基金supported by the Natural Science Foundation of Shandong Province(ZR2023QH427)the program for Academic promotion program of Shandong First Medical University(N02019LJ003)the Innovation Team of Shandong Higher School Youth Innovation Technology Program(2022KJ197).
文摘Background:Siwu decoction(SWD)is a traditional Chinese herbal decoction commonly used for treating various symptoms of blood deficiency and blood stasis,including cancer-related anemia(CRA).However,due to its complex composition,the key active ingredients and underlying mechanisms of its therapeutic effects often remain unknown.This research aims to use network pharmacology and molecular docking technology to systematically elucidate the potential mechanisms underlying the efficacy of SWD in treating cancer-related anemia.Methods:The key constituents of SWD were procured from the TCMSP database.Leveraging the Swiss ADME and Swiss Target Prediction databases,potential targets were recognized.Disease-related targets were assembled via the GeneCards and DrugBank databases.Constructing the PPI network involved the utilization of the STRING database,followed by visualization through Cytoscape 3.9.1 software.Subsequently,GO and KEGG enrichment analysis was conducted utilizing the DAVID database,with visual analysis performed on the macrobiotic platform.For molecular docking,the Autodock software was employed,and the molecular docking outcomes were visualized using the PyMOL software.Results:In this investigation,a comprehensive revelation of 18 primary active compounds and 511 associated targets linked to CRA was accomplished.The outcomes of protein-protein interaction(PPI)analysis unequivocally identified AKT1,EGFR,SRC,VEGFA,HRAS,MAPK3,and STAT3 as pivotal proteins within the SWD’s framework for effective CRA intervention.Notably,signaling pathways such as the HIF-1,JAK-STAT,TNF-α,and PI3K-Akt pathways,intricately involved in hematopoietic stem cell proliferation,differentiation,and inflammatory response,emerged as closely intertwined with the therapeutic application of SWD for CRA treatment.The congruence between these potential targets and SWD’s primary therapeutic constituents for CRA treatment was substantiated by the outcomes of molecular docking analysis.Conclusion:This work provided a reference for further fundamental research by outlining the primary active ingredients and putative molecular mechanisms of SWD in the treatment of CRA.
基金This research was supported by Innovation and Entrepreneurship Training Plan for College Students in Jiangsu Province(202112688022Y)Suzhou Science and Technology Bureau Minsheng Science and Technology Medical and Health Application Basic Research Project(SYSD2019082).
文摘Objective:Based on the analysis of a biochemical information database,the“target-pathway”network of anlotinib in the treatment of non-small cell lung cancer was constructed by using network pharmacological methods to explore the mechanism of multi-target and multi-pathway treatment of non-small cell lung cancer.Methods:The 3D molecular structure formula of anlotinib was obtained by searching the PubChem database,and the target of anlotinib was predicted by using the PharmMapper database;obtain non-small cell lung cancer related targets through the GeneCards database,screen common genes related to drug targets and diseases by Venny 2.1.0,and build the relationship between drugs and diseases.Through the STRING11.5 database,the interaction relationship between action targets was built,the protein-protein interaction network was constructed,and the target degree was analyzed by Cytocsape 3.7.2 software to screen molecular docking objects.The DAVID database was used for Gene Ontology gene enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis to predict its mechanism,and the AutoDock software was used for molecular docking of the main targets.Results:The analysis results showed that there were 76 possible targets involved in the treatment of non-small cell lung cancer with anlotinib,mainly acting on epidermal growth factor receptor,mitogen-activated protein kinase 14,tyrosine-protein phosphatase non-receptor type 11,heat shock protein HSP 90-alpha,tyrosine-protein kinase Lck,cAMP-dependent protein kinase catalytic subunit alpha and other target protein genes,Kyoto Encyclopedia of Genes and Genomes pathway analysis obtained 60 possible pathways related to its treatment of non-small cell lung cancer,mainly involving progesterone-mediated oocyte maturation,prostate cancer,proteoglycans in cancer,FoxO signaling pathway,pathways in cancer,Ras signaling pathway,PI3K-Akt signaling pathway,etc.Conclusion:Anlotinib has the characteristics of multi-targets and multi-pathways in the treatment of non-small cell lung cancer,which provides a scientific basis for the follow-up study on the optimization of its efficacy in the treatment of non-small cell lung cancer and the revelation of the pharmacological effects of anlotinib.
基金supported by the program for academic promotion program of Shandong First Medical University(No.2019LJ003)the Innovation Team of Shandong Higher School Youth Innovation Technology Program(2022KJ197).
文摘Background:Rehmanniae Radix Praeparata(RRP,Shu Dihuang in Cinese)is a traditional Chinese herb with multiple pharmacological effects and is commonly used to treat blood deficiency syndrome,such as cancer-related anemia(CRA),alone or in combination with other herbs.However,its main active ingredients and mechanisms of action in treating CRA remain unknown.This study aims to elucidate RRP’s potential mechanism and main active components in treating CRA by using network pharmacology and molecular docking technology system.Methods:The main components of RRP were obtained by the TCMSP database and literature search,and active components and potential targets were obtained by the SwissADME and SwissTargetPridiction databases.CRA targets were collected through GeneCards,DisGeNET,and DrugBank databases.Protein-protein interaction networks of potential targets were constructed via STRING 11.5 and analyzed visually with Cytoscape 3.9.1.The Metascape platform was used for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis,which were subsequently visualized with Cytoscape 3.9.1 or SangerBox platform.Moreover,Autodock Vina was used for the molecular docking of potential targets and main active ingredients that were visualized with PyMOL software.Results:In this study,31 main active ingredients of PPR were screened,and 155 related targets related to CRA were unearthed.Protein-protein interaction results showed that PPR’s core proteins for CRA intervention correlate to STAT3,SRC,MAPK3,MAPK1,PIK3R1,PIK3CA,and AKT.Multiple signaling pathways were closely related to the treatment of CRA intervened by PPR,including the PI3K-Akt signaling pathway,HIF-1 signaling pathway,JAK-STAT3 signaling pathway,TNF-αsignaling,cytokine signaling pathway and NF-kappB signaling pathway,which are closely involved in the proliferation and differentiation of hematopoietic stem cell and inflammatory response.Molecular docking results showed that these potential targets had good conformation with the core active components of RRP for treating CRA.Conclusion:This study revealed RRP’s main active components and potential molecular mechanisms in treating CRA,providing a reference for subsequent basic research.
基金National Natural Science Foundation of China(No.81273662,81473592)。
文摘Objective:Use network pharmacology to explore the anti-COVID-19 mechanism of Huashi Baidu Recipe,supplemented by molecular docking verification.Methods:Thorugh databases such as TCMSP,GeneCard,String,and software such as Cytoscape,AutoDockVina,network relationships was established,and the binding ability of active ingredients and targets is calculated through molecular docking,and biological function enrichment analysis was conducted.Result:The ingredients in Huashi Baidu Recipe that had strong affinity with SARS-CoV-23CL hydrolase(3CLpro)and angiotensin converting enzyme 2(ACE2)receptors include Quercetin,Baicalein,Astragaloside IV,Wogonin and other ingredients;25 active ingredients which obtained by screening had strong affinity with targets such as IL6,IL1B,NOS2 and CCL2.The biological function enrichment analysis mainly focused on Th17,Th1 and Th2 cell differentiation,NF-κB,MAPK,TNF,IL-17signaling pathway,etc.Conclusion:The active ingredients of Huashi Baidu Recipe may inhibit the infection and replication of SARS-CoV-2 virus,regulate RAS system’balance,inhibit excessive immune inflammatory response,and prevent inflammatory storm from appearing to fight COVID-19.
文摘[Objectives]The action mechanism of Tingli Dazao Xiefei Decoction in the treatment of COPD was explored by the network pharmacology and molecular docking technology.[Methods]The TCMSP database was used to perform active ingredient screening and target prediction on Chinese medicines contained in Tingli Dazao Xiefei Decoction,and COPD-related targets were searched through disease databases.Common targets of Tingli Dazao Xiefei Decoction and COPD were imported into Metascape database for GO analysis and KEGG pathway enrichment analysis.The STRING database was used to perform PPI analysis on common targets,and core targets were screened through the Cytoscape software.The Pymol,AutoDockTools,Vina and other software were used for molecular docking of some core targets and ingredients.[Results]From Tingli Dazao Xiefei Decoction,26 active ingredients which shared 211 common targets and 22 core targets with COPD,were screened out.Enrichment analysis revealed a total of 1892 biological processes,78 cell components,152 molecular functions,and 164 signal paths.The molecular docking of part of the core targets and corresponding ingredients obtained better results.[Conclusions]Tingli Dazao Xiefei Decoction treats COPD through multiple targets and multiple pathways,revealing its mechanism for treating COPD.
文摘[Objectives]To explore the potential mechanism of Danggui Buxue Decoction in treating the iron deficiency anemia(IDA)based on network pharmacology and molecular docking technology.[Methods]The active components and target proteins of Danggui Buxue Decoction were searched in databases such as TCMSP,OMIM,GeneCards,Drugbank,String,Metascape,etc.,and the target proteins shared with IDA were screened out,and the information about the signal pathways and biological functions of these target proteins was obtained.[Results]17 active components of Danggui Buxue Decoction and 24 potential targets for the treatment of IDA were obtained.With the aid of String database and Cytoscape software,the protein interaction network was obtained and the network topology analysis was performed.Four potential core targets with higher scores were obtained,namely F2,NOS2,NOS3,and PPARG.Using the Metascape database,GO function enrichment analysis and KEGG pathway enrichment analysis were performed on the potential targets of Danggui Buxue Decoction in the treatment of IDA,and the important biological processes,cell composition,molecular functions and signal pathways related to the target were screened through the R language.The results show that biological processes are related to positive regulation of growth,cell composition is related to membrane microdomain,and molecular functions are related to oxidoreductase activity.The signal pathways involved are mainly AGE-RAGE signal pathway,TNF signal pathway and IL-17 signal pathway.Finally,the molecular docking results confirmed that the active components of Danggui Buxue Decoction have a good binding ability with the target.[Conclusions]Danggui Buxue Decoction treats the IDA through multiple components,multiple targets,multiple signal pathways,and multiple biological functions.
文摘Computer-aid molecular docking is a simulative process that receptors and ligands recognize each other through energy matching and geometric matching. It is widely used in bioactive compounds simulative screening and preliminary exploring the bioactivity and toxicity of molecular, which plays an important guiding role in toxicity and bioactivity study of molecular entities. In our study, we used the computer-aid molecular docking software-discovery studio 3.1 client to test the mechanism of aflatoxins such as aflatoxin B1, B2, M1, M2, G1, G2 and the results of our experiment help to illustrate the pathway of aflatoxin’s toxication. We also used this technology to test the preliminary toxicity of zearalenone (ZEN) and its two degradation products:α-zearalenol (α-ZOL) and β-zearalenol (β-ZOL), which indicates that these three products possessed significant estrogenic activity. The order of the estrogenic activity is:α-zearalenol > zearalenone >β-zearalenol.
基金Supported by Program of Guangxi Natural Science Foundation (2018GXNSFBA050069&2022GXNSFAA035459)the R&D Project of Guangxi Zhuang Autonomous Region Key Trauma Surgery
文摘[Objectives]To explore the active components and mechanism of Bupleurum and Asarum in the treatment of traumatic brain injury(TBI).[Methods]All the active components and potential action targets of Bupleurum and Asarum pairs were collected by online platform Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)database and literature search.Target genes related to traumatic brain injury were obtained by Online Mendelian Inheritance in Man(OMMI),Therapeutic Target Database(TTD),PharmGKB,Genecards and Drugbank.The"drug-ingredient-target"network diagram was constructed by using Cytoscape software.Venny 2.1.0 was used to integrate the intersection targets of drug targets and disease targets,and the String platform was used to construct a target protein-protein interaction network(PPI).Topological analysis and core target screening of the constructed PPI network were performed using the"CytoNCA"plug-in in Cytoscape software.Gene Ontology(GO)annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were performed on the intersection targets using the DAVID database.Finally,Autodock and Pymol software were used to simulate the binding activity of key candidate active components and core genes.[Results]25 active components were screened from Bupleurum-Asarum and 111 potential targets involved in the disease process.GO analysis and KEGG results showed that potential therapeutic targets were mainly enriched in biological processes such as inflammatory response,oxidative stress,cell membrane repair,and cytokine regulation.Network analysis and molecular docking showed that the key compounds of Bupleurum and Asarum were kaempferol and quercetin,which were well docked with the active pockets of four core genes of traumatic brain injury.[Conclusions]Bupleurum and Asarum may be involved in the regulation of inflammatory response,oxidative stress,cell membrane repair through multiple targets and multiple pathways in the treatment of traumatic brain injury.
文摘To predict the potential mechanism of prevention and treatment of colorectal adenoma canceration by berberine and the docking of main key targets by computer virtual method.Methods:The related targets of berberine,colorectal adenoma and colorectal cancer were collected in various databases;the key targets were obtained by intersection;the protein protein interaction network and 6 kinds of enrichment analysis of key potential targets were completed by corresponding databases;the main key targets and berberine molecules were obtained for molecular docking.Results:There were 319 unique targets for berberine,3,279 for intestinal adenoma and 4,119 for colorectal cancer.The protein protein interaction network of key target involved 66 proteins.In the results of Gene Ontology enrichment,28 items related to biological process,28 items related to cell composition,30 items related to molecular function,26 items related to Kyoto Encyclopedia of Genes and Genomes pathway enrichment,35 items related to TargetScan microRNA,15 items related to Human Phenotype Ontology.TP53 and CYCS are the 2 key targets involved in the system enrichment.After docking,berberine was closely bound to theα-helix and β-fold of TP53 protein,and to theα-helix of CYCS protein.Conclusion:The potential mechanism of berberine in the prevention and treatment of colorectal adenoma canceration may be related to the regulation of cell apoptosis,metabolic pathways and biological activities of various enzymes.berberine,as a small molecular ligand,has the characteristics of multi-target,multi-channel and multi-system mechanism.In the prediction results,berberine,as a small molecular ligand,can closely bind with the main key targets related to colorectal adenoma canceration.
基金supported by G20 Support and Guarantee Project of Beijing Municipal Science and Technology Commission(Z151100003815013).
文摘Objective:In this study,we used network pharmacology and molecular docking technology to analyze the mechanism of Bushen Tongluo granule in the treatment of osteoarthritis.Methods:The main active components and corresponding targets of Bushen Tongluo granule were screened from thetraditional Chinese medicine systems pharmacology database.The targets related to osteoarthritis were collected from the Online Mendelian Inheritance in Man,Therapeutic Target database,GeneCards,Pharmacogenomics Knowledgebases and Drugbank databases.Cytoscape3.9.0 software was used to construct the action network diagram of“Bushen Tongluo Granule-Active Component-Target”.Builded a protein-protein interaction network from the STRING database.The Bioconductor platform and R language 4.0.3 were used for Gene Ontologyfunction andKyoto Encyclopedia of Genes and Genomespathway enrichment analysis.Then,selected the pathway most associated with osteoarthritis for specific analysis.Finally,the core genes were screened and verified by molecular docking using AutoDockTools software.Results:71 principal components of Bushen Tongluo granule and 183 potential therapeu-tic targets for osteoarthritis were obtained.Twenty-eight key targets of Bushen Tongluo granulein the treatment of osteoarthritis are enriched in 158 pathways.Among them,the tumor necrosis factor signaling pathway,interleukin-17 signaling pathway,Toll-like receptor signaling pathway,T helper cell 17 cell differentiation and hypoxia-inducible factor-1signaling pathway involved in key targets are closely related to osteoarthritis.The relevant vital targets were involved in the regulation of DNA transcription factor activity,the response to chemical stress,the response to reactive oxygen species,the response to oxidative stress,the proliferation of muscle cells,the proliferation of epithelial cells and the biological processes such as responses to lipopolysaccharides,responses to molecules of bacterial origin.Molecular docking showed that protein kinase B 1-β-sitosterol,the tumor necrosis factor-naringenin,interleukin-6-luteolin,mitogen-activated protein kinase-quercetin,vascular endothelial growth factor A-quercetin and prostaglandin-endoperoxide synthase 2-luteolin have strong docking activities.Conclusions:Bushen Tongluo granule can reduce the inflammatory response and inhibit articular cartilage angiogenesis in the treatment of osteoarthritis,which may be achieved by regulating the inflammatory signaling pathway and hypoxia-inducible factor-1 signaling pathway.
基金supported by Graduate quality engineering project(2021CX79)and“Yifang”graduate innovation project(2022YF03).
文摘Objective:Based on the network pharmacology approach and molecular docking technology,the core targets of dihydrotanshinone I(DHT)for the treatment of helicobacter pylori(Hp)infection were searched and the potential mechanisms of drug therapy were explored.Methods:The TCMSPdatabase and Swiss Target Prediction database were employed to identify drug targets.To mine disease targets based on GeneCards,OMIM,DrugBank,DisGeNET,and TTDdatabases.Then the two were intersected to obtain common targets.The proteinproteininteraction(PPI)networkmap of common targets was constructed on the basis of the String network platform and Cytoscape software,and the targets with degree values over 1/2 maximum degree value were selected as core targets.Molecular docking verification of DHTand core targets were performed using AutoDock and PyMOL software.Finally,gene ontology(GO)functional enrichment analysis andKyoto Encyclopediaof Genes and Genomes(KEGG)pathway enrichment analysis of the common targets were carried out using the Metascape database and R-4.0.2-win software.Results:A total of 13 targets of DHTwas extracted for the treatment of Hp,and five core targets,includingSignal transducerand activator of transcription 1(STAT1),Signal transducerand activator of transcription 3(STAT3),Prostaglandin G synthase 2(PTGS2),Signal transducerand activator of transcription 4(STAT4)and Indoleamine 2,3-dioxygenase 1(IDO1),were screened according to their degree values.Molecular docking indicated that DHThad an excellent binding to the core target.29 pathways were yielded by KEGG enrichment analysis,and a total of 48 biological processes,7 cellular components and 13 molecular functions were derived from GO enrichment analysis.Conclusion:DHTmay decrease pro-inflammatory factor expression and immune cell infiltration to treat Hpinfection via the janus kinase(JAK)-signal transducer and activator of transcription(STAT)signaling pathway regulated by STAT1,STAT3,STAT4,etc.
基金the General Program of National Natural Science Foundation of China(No.81873399)Major research project of oncology of scientific and technological innovation project of China Academy of Chinese Medical Sciences(No.CI2021A01805).
文摘Background:To explore the effective components and mechanism of Classic ancient prescription Wuji pill on lung cancer(LC)with the help of network pharmacology and molecular docking technology.Methods:TCMSP database,Chinese Pharmacopoeia(2020 Edition)and related literature were searched to identify the main chemical composition and targets of constituent drugs in Wuji pill,including Houpo(Magnoliae Officinalis Cortex),Huangqin(Scutellariae Radix),Badou(Crotonis Fructus),Huanglian(Coptidis Rhizoma)and Renshen(Ginseng Radix et Rhizoma).Meanwhile,Genecards,OMIM,TTD,Drugbank and PharmGkb databases were used to obtain the main targets of LC.The"chemical compound-target"network was constructed by using Cytoscape 3.8.2 software with the disease drug intersection gene as the research target.The PPI network was constructed by using the string database for protein interaction analysis,and the core target genes were sorted out.The Gene ontology go function enrichment analysis and KEGG signal pathway enrichment analysis were carried out based on the ClusterProfiler of R software.Finally,the Autodock Vina software was used to conduct molecular docking between the core target with high value and the key components.Results:A total of 60 active components,190 corresponding targets and 2516 GO and 163 KEGG pathways of Wuji pill were screened out,including 179 potential targets of LC.The core targets were ESR1,CDKN1A,TP53,NR3C1,MAPK1,AKT1,MAPK8,JUN,RELA,the core components were quercetin,kaempferol,β-sitosterol,stigmasterol,tetrahedron,protoopioid,etc,and the core pathways were PI3K-Akt,MAPK,IL-17,etc.Conclusion:This study preliminarily revealed the mechanism of action of Wuji pill on multi component-multi target-multi pathway of LC,which provided reference for the further clinical development and research of Wuji pill.
基金supported by the Yunnan Key Project of Science and Technology(202202AE090001)Postdoctoral Directional Training Foundation of Yunnan Province(E23174K2)Postdoctoral Research Funding Projects of Yunnan Province,China(E2313442)。
文摘Wild edible Termitomyces mushrooms are popular in Southwest China and umami is important flavor qualities of edible mushrooms.This study aimed to understand the umami taste of Termitomyces intermedius and Termitomyces aff.bulborhizus.Ten umami peptides from aqueous extracts were separated using a Sephadex G-15 gel filtration chromatography.The intense umami fraction was evaluated by both sensory evaluation and electronic tongue.They were identified as KLNDAQAPK,DSTDEKFLR,VGKGAHLSGEH,MLKKKKLA,SLGFGGPPGY,TVATFSSSTKPDD,AMDDDEADLLLLAM,VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK.Seven peptides,except VEDEDEKPKEK,SPEEKKEEET and PEGADKPNK were selectively synthesized to verify their taste characteristics.All these 10 peptides had umami or salt taste.The 10 peptides were conducted by molecular docking to study their interaction with identified peptides and the umami taste receptor T1R1/T1R3.All these 10 peptides perfectly docked the active residues in the T1R3 subunit.Our results provide theoretical basis for the umami taste and address the umami mechanism of two wild edible Termitomyces mushrooms.
基金supported by the grants from National Natural Science Foundation of China(No.82174334)Hainan Provincial Key Laboratory of Tropical Brain Science Research and Transformation Research Project(JCKF2021001)Innovative Research Projects for Graduate Students(HYYS2021B01).
文摘Background:In this study,we used network pharmacology and molecular docking combined with vitro experiments to explore the potential mechanism of action of Gualou Qumai pill(GLQMP)against DKD.Methods:We screened effective compounds and drug targets using Chinese medicine systemic pharmacology database and analysis platform and Chinese medicine molecular mechanism bioinformatics analysis tools;and searched for DKD targets using human online Mendelian genetics and gene cards.The potential targets of GLQMP for DKD were obtained through the intersection of drug targets and disease targets.Cytoscape software was applied to build herbal medicine-active compound-target-disease networks and analyze them;protein-protein interaction networks were analyzed using the STRING database platform;gene ontology and Kyoto Encyclopedia of Genes and Genomes were used for gene ontology and gene and genome encyclopedia to enrich potential targets using the DAVID database;and the AutoDock Vina 1.1.2 software for molecular docking of key targets with corresponding key components.In vitro experiments were validated by CCK8,oil red O staining,TC,TG,RT-qPCR,and Western blot.Results:Through network pharmacology analysis,a total of 99 potential therapeutic targets of GLQMP for DKD and the corresponding 38 active compounds were obtained,and 5 core compounds were identified.By constructing the protein-protein interaction network and performing network topology analysis,we found that PPARA and PPARG were the key targets,and then we molecularly docked these two key targets with the 38 active compounds,especially the 5 core compounds,and found that PPARA and PPARG had good binding ability with a variety of compounds.In vitro experiments showed that GLQMP was able to ameliorate HK-2 cell injury under high glucose stress,improve cell viability,reduce TC and TG levels as well as decrease the accumulation of lipid droplets,and RT-qPCR and Western blot confirmed that GLQMP was able to promote the expression levels of PPARA and PPARG.Conclusion:Overall,this study revealed the active compounds,important targets and possible mechanisms of GLQMP treatment for DKD,and conducted preliminary verification experiments on its correctness,provided novel insights into the treatment of DKD by GLQMP.
基金supported by National Science Fund for Young Scholars of China (Grant No.82204594).
文摘Background:In order to investigate the possible pharmacological mechanism of digallate in Galla Chinensis for treating enteritis,providing reference for the search and exploration of effective drugs for treating enteritis.Method:Traditional Chinese Medicines Systems Pharmacology Database and Analysis Platform,PharmMapper,DisGeNET,DrugBank,and GeneCards databases were used to obtain drug and disease-related target information.Gene ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment were performed,and the main therapeutic pathways and targets were identified by combining protein-protein interaction networks and cytoHubba plug-in.Molecular docking was used to validate the results.Result:297 drug related targets,2436 disease related targets,and 66 target points related to digallate were predicted to be associated with enteritis.10 related signal pathways and 10 key genes were identified.Conclusion:Digallate may be utilized to treat enteritis by acting on similar pathways,such those related to pathways in cancer,lipid and atherosclerosis,proteoglycans in cancer,Rap1 signaling pathway,PI3K-Akt signaling pathway and other targets such as IGF1,EGFR,SRC,IGF1R,PPARG.
基金National Natural Science Foundation of China(No.82160890)Guangxi Health Appropriate Technology Development and Application Project(No.GZSY23-21)+1 种基金Graduate Education Innovation Project,Guangxi University of Traditional Chinese Medicine(No.YCSW2023383)Research Program of Guangxi University of Traditional Chinese Medicine(No.2019MS016)。
文摘Objective:To explore the potential mechanism of action of quercetin in the treatment of diarrhea irritable bowel syndrome(IBS-D).Methods:The potential targets of quercetin were obtained from the TCMSP,SwissTar-getPrediction,and BATMAN-TCM databases.The targets of IBS-D were obtained by searching the GeneCards database with"diarrhea irritable bowel syndrome"as the keyword,and the targets of quercetin and IBS-D were intersected.The PPI network was constructed by Cytoscape 3.7.1 software.The intersected targets were imported into the DAVID database for GO functional analysis and KEGG pathway enrichment analysis.The binding ability of quercetin to the core targets was observed using molecular docking.Based on this,we established an IBS-D rat model,administered quercetin for intervention,and experimentally validated the network pharmacology prediction results by HE staining and ELISA assay.Results:Network pharmacology analysis showed that TP53,TNF-α,AKT1,VEGF-A,IL-6 factors and MAPK,PI3K-Akt signaling pathway as the core targets and pathways of quercetin for the treatment of IBS-D.The results of animal experiments revealed that quercetin could inhibit the secretion of TP53,TNF-α,AKT1,VEGF-A,IL-1βand IL-6,reduce the inflammatory response and improve IBS-D.Conclusion:Quercetin could protect colon tissue by regulating the expression of TP53,TNF-α,AKT1,VEGF-A,IL-1βand IL-6,thereby treating IBS-D.
基金This work was funded by the Science and Technology Research Project of Jiangxi Provincial Education Department[GJJ190805&GJJ211507]Jiangxi Provincial Natural Science Foundation[20232BAB215062&20202BABL216081]+1 种基金University-Level Scientific Research Projects of Gannan Medical University[QD201913&QD202128]and the Jiangxi Provincial College Students Innovation and Entrepreneurship Training Programs[S202210413028&S202310413031].
文摘Background:Lotus seedpod(Receptaculum Nelumbinis)is the abundant by-products produced during lotus seed processing,and the sources are usually considered to be wastes and are abandoned outdoors or incinerated.This study aims at predicting its bioactive compounds and cancer-related molecular targets against six cancers,including lung cancer,gastric cancer,liver cancer,breast cancer,ovarian cancer and cervical cancer.Methods:Network pharmacology and molecular docking methods were performed.Results:Network pharmacology results indicated that 14 core compounds(liensinine,tetrandrine,lysicamine,tricin,sanleng acid,cireneol G,ricinoleic acid,linolenic acid,5,7-dihydroxycoumarin,apigenin,luteolin,morin,quercetin and isorhamnetin)and 10 core targets(AKT1,ESR1,HSP90AA1,JUN,MAPK1,MAPK3,PIK3CA,PIK3R1,SRC and STAT3)were screened for lotus seedpod against the six cancers.Molecular docking analysis suggested that the binding abilities between the core compounds and the core targets were mostly strong.GO analysis revealed that the intersected targets between the bioactive compounds of lotus seedpod and the six cancers were significantly related to biological processes,cell compositions and molecular functions.KEGG analysis showed that PI3K-Akt,TNF,Ras,MAPK,HIF-1 and C-type lectin receptor signaling pathways were notably involved in the anti-cancer activities of lotus seedpod against the six cancers.Conclusions:14 core compounds and 10 core targets were screened for lotus seedpod against lung cancer,gastric cancer,liver cancer,breast cancer,ovarian cancer and cervical cancer.This study supports the application of lotus seedpod in treating cancers,and promotes the recycling and the high-value utilization.
文摘The purpose of this project is used for exploring the mechanism of Callistephus chinensis in the treatment of diabetes by network pharmacology and molecular docking methods.The target of Callistephus chinensis was obtained from SwissTargetPrediction database,while the target related to diabetes was obtained from GeneCards and OMIM databases.The target was added in String database to build the protein interaction network.GO biological process enrichment analysis and KEGG pathway enrichment analysis were carried out by Metascape software,then the target-pathway network was constructed.Molecular docking was carried out in Discovery Studio 2016 Client software to verify the binding force of Callistephus chinensis flavonoid compounds with key targets.In this study,10 potential active components were selected from the flavonoid monomer compounds of Callistephus chinensis.1847 biological processes(BP),126 cell compositions(CC)and 256 molecular functions(MF)were obtained by GO enrichment analysis;a total of 194 pathways were involved in KEGG enrichment analysis of 192 cross targets.Network analysis showed that quercetin was the main active component of flavonoids in the treatment of diabetes,AKT1,TNF,VEGFA,EGFR,SRC and other related signals were in relation to the treatment of diabetes.This study showed that Callistephus chinensis flavonoid compounds play a role in the treatment of diabetes by regulating multi-target and multi-pathway.
