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
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
Coronary atherosclerotic heart disease(CHD)is the main type of cardiovascular disease.The efficacy of Uyghur drug compound Saffron formula in CHD has been clinically proven.However,the underlying mechanism remains unc...Coronary atherosclerotic heart disease(CHD)is the main type of cardiovascular disease.The efficacy of Uyghur drug compound Saffron formula in CHD has been clinically proven.However,the underlying mechanism remains unclear.In this study,researchers investigated the active ingredients and mechanism of action of Crocus sativus and Rosa rugosa in the treatment of CHD by network pharmacology and molecular docking techniques,collected target information with the help of TCMSP,GEO,GeneCards,and other databases,constructed protein-protein interaction(PPI)network diagrams by STRING database,performed GO and KEGG pathway enrichment analysis on common targets,and finally molecularly docked the active ingredients with core targets.C.sativus-R.rugosa have a variety of polyphenol compounds,a total of 12 active ingredients,including quercetin and kaempferol,were screened.The first three targets intersected with the core targets of CHD as AKT1,TNF,and IL-1B.Enrichment results of KEGG pathway showed that C.sativus-R.rugosa against CHD involved atherosclerosis pathways.The molecular docking results showed that quercetin and kaempferol were well bound to the core targets,and it was speculated that these components might be the main active ingredients for the treatment of CHD.The potential mechanism of action of C.sativus-R.rugosa for the treatment of coronary heart disease was initially revealed.展开更多
Background:Explore the anti-tumor mechanism of herb pair Pinellia ternate-Magnolia officinalis(BX-HP)in liver cancer through network pharmacology using molecular docking methods.Method:The active ingredients and corre...Background:Explore the anti-tumor mechanism of herb pair Pinellia ternate-Magnolia officinalis(BX-HP)in liver cancer through network pharmacology using molecular docking methods.Method:The active ingredients and corresponding targets of the herb pair Pinellia ternate-Magnolia officinalis were obtained from the HERB database.The relevant targets for liver cancer were obtained from GeneCards,DisGeNET,TTD,and Drugbank databases.Obtain common targets between herb pair Pinellia ternate-Magnolia officinalis and liver cancer through the Bioinformatics platform,establish a PPI network diagram using STRING software,and perform GO functional enrichment and KEGG pathway enrichment analysis on the DAVID platform.AutoDockTools 1.5.7 software and molecular dynamics simulation analysis are used to evaluate the binding of components to target proteins.HERB database,SwissTargetPrediction database,SwissADME database,UniProt database,GeneCards database,TTD database,DRUGBANK database,DisGeNET database,String,DAVID.Bioinformatics platform,PDB database,PubChem and TCMSP database.Result:A total of 22 active ingredients with a Probability>0.1 targets in Magnolia officinalis were screened,26 active ingredients with a Probability>0.1 targets in Pinellia ternata,ten vital active ingredients,corresponding to 979 and 803 targets with a Probability>0.1 targets,2536 liver cancer-related targets,and 279 targets in the herb pair Pinellia ternata-Magnolia officinalis.The GO functional enrichment analysis resulted in 1297 entries,namely 971 biological process entries,118 cell localization entries,and 208 molecular function entries.Three signaling pathways were annotated through the KEGG pathway.Based on molecular docking,ten vital active ingredients and five target proteins were validated to exhibit an excellent binding affinity.The above data indicates that combining the herb pair Pinellia ternata-Magnolia officinalis may treat liver cancer through specific targets and signaling pathways.Conclusion:Herb pair Pinellia ternata-Magnolia officinalis has a synergistic effect on treating liver cancer through multicomponent,multitarget,and multi-pathway approaches.This study provides a sufficient theoretical basis for subsequent research.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
Background:To explore the effective chemical constituents of Feiduqing formula for prevention and treatment of coronavirus disease 2019(COVID-19).Methods:The compounds and action targets of twelve herbal medicines in ...Background:To explore the effective chemical constituents of Feiduqing formula for prevention and treatment of coronavirus disease 2019(COVID-19).Methods:The compounds and action targets of twelve herbal medicines in Feiduqing formula were collected via Traditional Chinese Medicine Systems Pharmacology Database and Analytic Platform.The genes corresponding to the targets were queried through the UniProt database.The“herbal medicine-ingredient-target”network was established by Cytoscape software.The Gene Ontology function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed by Database for Annotation,Visualization and Integrated Discovery.Molecular docking was used to analyze the binding force of core active compounds of Feiduqing formula with PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and angiotensin converting enzyme II(ACE2).Results:The“herbal medicine-ingredient-target”network included 434 nodes and 1948 edges,including 222 components such as quercetin,kaempferol,luteolin,etc.The key targets are PTGS2,HSP90AA1,PTGS1,ESR1,AR,NOS2,etc.Gene Ontology function enrichment analysis revealed 2530 items,including RNA polymerase II-specific,response to oxidative stress,transcription factor activity,etc.Kyoto Encyclopedia of Genes and Genomes pathway enrichment screened 169 signal pathways,including Human cytomegalovirus infection,Kaposi sarcoma-associated herpesvirus infection,Hepatitis B,Hepatitis C,IL-17,TNF,etc.The results of molecular docking showed that quercetin,luteolin,β-sitosterol,stigmasterol and other core active compounds have a certain degree of affinity with PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and ACE2.Conclusion:The active compounds of Feiduqing formula may have a therapeutic effect on COVID-19 pneumonia through the action on PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and ACE2,and regulating many signaling pathways.展开更多
Glabridin is the main ingredient of hydrophobic fraction in licorice extract and has been shown to have anti-melanogenesis activity in skins.However,the underlying mechanism(s)remain not completely understood.The aim ...Glabridin is the main ingredient of hydrophobic fraction in licorice extract and has been shown to have anti-melanogenesis activity in skins.However,the underlying mechanism(s)remain not completely understood.The aim of this study is thus to elucidate the possible mechanisms related to the melanogenesis suppression by glabridin in cultured B16 murine melanoma cells and in UVA radiation induced hyperpigmentation model of BALB/c mice as well.Molecular docking simulations revealed that between catalytic core residues and the compound.The treatment by glabridin significantly downregulated both transcriptional and/or protein expression of melanogenesis-related factors including melanocyte stimulating hormone receptor(MC1R),microphthalmia-associated transcription factor(MITF),tyrosinase(TYR),TYR-related protein-1(TRP-1)and TRP-2 in B16 cells.Both PKA/MITF and MAPK/MITF signaling pathways were found to be involved in the suppression of melanogenesis by glabridin in B16 cells.Also in vivo glabridin therapy significantly reduced hyperpigmentation,epidermal thickening,roughness and inflammation induced by frequent UVA exposure in mice skins,thus beneficial for skin healthcare.These data further look insights into the molecular mechanisms of melanogenesis suppression by glabridin,rationalizing the application of the natural compound for skin healthcare.展开更多
Oncorhynchus mykiss is delicious and contains abundant flavor substances.However,few studies focused on umami peptides of O.mykiss.In the current work,umami peptides derived from O.mykiss were identified using virtual...Oncorhynchus mykiss is delicious and contains abundant flavor substances.However,few studies focused on umami peptides of O.mykiss.In the current work,umami peptides derived from O.mykiss were identified using virtual screening,molecular docking,and electronic tongue analysis.First,the O.mykiss protein was hydrolyzed using the PeptideCutter online enzymolysis program.Subsequently,water-soluble and toxicity screening were performed by Innovagen and ToxinPred software,respectively.The potential peptides were docked with umami receptor T1R1/T1R3.Furthermore,taste properties of potential peptides were validated by electronic tongue.Docking results suggested that the three tetrapeptide EANK,EEAK,and EMQK could enter the binding pocket in the T1R1 cavity,wherein Arg151,Asp147,Gln52,and Arg277 may play key roles in the production of umami taste.Electronic tongue results showed that the umami value of EANK,EEAK,and EMQK were stronger than monosodium glutamate.This work provides a new insight for the screening of umami peptides in O.mykiss.展开更多
BACKGROUND Diabetic nephropathy(DN)stands as the most prevalent chronic microvascular complication of diabetes mellitus.Approximately 50%of DN patients progress to end-stage renal disease,posing a substantial health b...BACKGROUND Diabetic nephropathy(DN)stands as the most prevalent chronic microvascular complication of diabetes mellitus.Approximately 50%of DN patients progress to end-stage renal disease,posing a substantial health burden.AIM To employ network pharmacology and molecular docking methods to predict the mechanism by which glycyrrhetinic acid(GA)treats DN,subsequently validating these predictions through experimental means.METHODS The study initially identified GA targets using Pharm Mapper and the TCMSP database.Targets relevant to DN were obtained from the Genecards,OMIM,and TTD databases.The Venny database facilitated the acquisition of intersecting targets between GA and DN.The String database was used to construct a protein interaction network,while DAVID database was used to conducted Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis and Gene Ontology(GO)analysis.Molecular docking experiments were performed using Autodock software with selected proteins.Experimental validation was conducted using renal proximal tubular cells(HK-2)as the study subjects.A hyperglycemic environment was simulated using glucose solution,and the effect of GA on cell viability was assessed through the cell counting kit-8 method.Flow cytometry was employed to detect cell cycle and apoptosis,and protein immunoblot(western blot)was used to measure the expression of proteins of the phosphatidylinositol 3-kinase(PI3K)/protein kinase B(AKT)signaling pathway and insulin resistance pathway,including insulin receptor(INSR),PI3K,p-PI3K,AKT,p-AKT,and glycogen synthase kinase-3(GSK3).RESULTS A total of 186 intersecting targets between GA and DN were identified,which were associated with 144 KEGGrelated enrichment pathways,375 GO biological process entries,45 GO cellular component entries,and 112 GO cellular function entries.Molecular docking demonstrated strong binding of GA to mitogen-activated protein kinase(MAPK)-1,SRC,PIK3R1,HSP90AA1,CASPASE9,HARS,KRAS,and MAPK14.In vitro experiments revealed that GA inhibited HK-2 cell viability,induced cell cycle arrest at the G2/M phase,and reduced apoptosis with increasing drug concentration.Western blot analysis showed that GA differentially up-regulated GSK3 protein expression,up-regulated AKT/p-AKT expression,down-regulated INSR,AKT,p-AKT,PI3K,and p-PI3K protein expression,and reduced p-PI3K/PI3K levels under high glucose conditions.CONCLUSION GA may protect renal intrinsic cells by modulating the PI3K/AKT signaling pathway,thereby inhibiting HK-2 cell viability,reducing HK-2 cell apoptosis,and inducing cell cycle arrest at the G0/G1 phase.展开更多
BACKGROUND Although Liu-Wei-Bu-Qi capsule(LBC)inhibits tumor progression by improving the physical condition and immunity of patients with lung cancer(LC),its exact mechanism of action is unknown.AIM To through compou...BACKGROUND Although Liu-Wei-Bu-Qi capsule(LBC)inhibits tumor progression by improving the physical condition and immunity of patients with lung cancer(LC),its exact mechanism of action is unknown.AIM To through compound multi-dimensional network of chemical ingredient-targetdisease-target-protein-protein interaction(PPI)network,the principle of action of Chinese medicine prescription was explained from molecular level.METHODS Network pharmacology and molecular docking simulations were used to analyze the relationship among the main components,targets,and signaling pathways of LBC in treatment of LC.RESULTS From the analysis,360 LBC active ingredient-related targets and 908 LC-related targets were identified.PPI network analysis of the LBC and LC overlapping targets identified 16 hub genes.Kyoto Encyclopedia of Genes and Genomes analysis suggested that LBC can target the vascular endothelial growth factor signaling pathway,Toll-like receptor signaling pathway,prolactin signaling pathway,FoxO signaling pathway,PI3K-Akt signaling pathway and HIF-1 signaling pathway in the treatment of LC.Molecular docking simulations showed that quercetin had the best affinity for MAPK3,suggesting that quercetin in LBC may play an important role in the treatment of LC.CONCLUSION The results showed that the active ingredients in LBC can play a crucial role in the treatment of LC by regulating multiple signaling pathways.These results provide insights into further studies on the mechanism of action of LBC in the treatment of LC.展开更多
Background:1,2,3,4,6-penta-O-galloyl-beta-D-glucose(PGG)is a natural polyphenolic compound derived from multiple medicinal plants with favorable anticancer activity.Methods:In this study,the mechanisms of PGG against ...Background:1,2,3,4,6-penta-O-galloyl-beta-D-glucose(PGG)is a natural polyphenolic compound derived from multiple medicinal plants with favorable anticancer activity.Methods:In this study,the mechanisms of PGG against gastric cancer were explored through network pharmacology and molecular docking.First,the targets of PGG were searched in the Herbal Ingredients’Targets(HIT),Similarity Ensemble Approach(SEA),and Super-PRED databases.The potential targets related to gastric cancer were predicted from the Human Gene Database(GeneCards)and DisGeNET databases.The intersecting targets of PGG and gastric cancer were obtained by Venn diagram and then subjected to protein-protein interaction analysis to screen hub targets.Functional and pathway enrichment of hub targets were analyzed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases.The differential expression and survival analysis of hub targets in gastric cancer were performed based on The Cancer Genome Atlas database.Finally,the affinity of PGG with hub targets was visualized by molecular docking.Results:Three hub targets were screened,including mitogen-activated protein kinase 14(MAPK14),BCL2 like 1(BCL2L1),and vascular endothelial growth factor A(VEGFA).MAPK14 had a higher expression,while BCL2L1 and VEGFA had lower expression in gastric cancer than in normal conditions.Enrichment analysis indicated enrichment of these hub targets in MAPK,neurotrophin,programmed death-ligand 1(PD-L1)checkpoint,phosphatidylinositol 3-kinases/protein kinase B(PI3K-Akt),Ras,and hypoxia-inducible factor-1(HIF-1)signaling pathways.Conclusion:Therefore,network pharmacology and molecular docking analyses revealed that PGG exerts a therapeutic efficacy on gastric cancer by multiple targets(MAPK14,BCL2L1,and VEGFA)and pathways(MAPK,PD-L1 checkpoint,PI3K-Akt,Ras,and HIF-1 pathways).展开更多
OBJECTIVE To investigate the regulatory effects of icariin(ICA)on cardiac micro⁃vascular endothelial cells(CMEC)after oxygenglucose deprivation reperfusion(OGD/R)injury.METHODS CMEC were subjected to OGD/R treatment t...OBJECTIVE To investigate the regulatory effects of icariin(ICA)on cardiac micro⁃vascular endothelial cells(CMEC)after oxygenglucose deprivation reperfusion(OGD/R)injury.METHODS CMEC were subjected to OGD/R treatment to construct a myocardial ischemiareperfusion model,and were divided into normal,model,low(10μmol·L^(-1)),medium(20μmol·L^(-1))and high(40μmol·L^(-1))ICA group,and high ICA+inhibitor group(40μmol·L^(-1)+20 nmol·L^(-1)).CCK-8 assay was used to assess the protective ability of ICA against CMEC,and cell migration assay and tube-formation assay were used to detect the migration and generation ability of CMEC.The TCMSP database,Swiss-Target database and literature mining methods were used to col⁃lect ICA-related targets,the GeneCards data⁃base was used to collect target genes related to myocardial ischemia/reperfusion,and Cytoscape 3.8.0 software was used to construct a"drug-tar⁃get-disease"network.The potential targets were imported into STRING 11.5 database to obtain the PPI network.GO and KEGG enrichment analyses were performed on the potential targets using the DAVID database.Molecular docking was performed using AutoDock-vina 1.1.2 soft⁃ware.Western blot detected the expression of related proteins.RESULTS After CMEC was subjected to OGD/R treatment,ICA had a protec⁃tive effect at 10^(-1)60μmol·L^(-1);the results of the cell migration assay showed that each group of ICA could promote the migratory effect of CMEC(P<0.01,P<0.01);and the results of tube-for⁃mation assay showed that each group of ICA could significantly promote the generation of branches(P<0.01)and the capillary length exten⁃sion(P<0.05).Network pharmacology collected a total of 23 ICA action targets,1500 disease tar⁃gets and 12 key targets.GO function enrichment analysis found 85 results.KEGG pathway enrich⁃ment analysis found 53 results,involving AGERAGE signaling pathway,sphingolipid signaling pathway and VEGF signaling pathway.Molecu⁃lar docking results showed that ICA had better binding with core targets PRKCB,PRKCA and PTGS2.Western blot results showed that ICA could regulate the expression of PRKCB,PRKCA and PTGS2 proteins.The results of cell migra⁃tion assay,tube-formation assay and protein expression were reversed after addition of PKC inhibitor.CONCLUSION The potential mecha⁃nism of action of ICA against myocardial isch⁃emia-reperfusion injury may be related to the reg⁃ulation of processes such as CMEC migration and angiogenesis,and it functions through the key target gene PKC.展开更多
Background:Diabetic nephropathy(DN)is a serious complication of diabetes with rising prevalence worldwide.We aimed to explore the anti-DN mechanisms of the compound celastrol derived from the medicinal plant Tripteryg...Background:Diabetic nephropathy(DN)is a serious complication of diabetes with rising prevalence worldwide.We aimed to explore the anti-DN mechanisms of the compound celastrol derived from the medicinal plant Tripterygium wilfordii.Methods:Celastrol-related targets were obtained from Herbal Ingredients’Targets(HIT)and GeneCards databases.DN-related targets were retrieved from GeneCards,DisGeNET,and Therapeutic Targets Database(TTD).A Protein-protein interaction(PPI)network was established using the Search Tool for the Retrieval of Interacting Genes(STRING)database.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses were performed using ClusterProfiler.The cytoHubba plugin was used to select the top 10 hub targets.Molecular docking was performed employing PyMOL and AutoDock software.Cell counting kit-8(CCK-8)and flow cytometry assays were used to detect the viability and apoptosis of NRK-52E cells,respectively.The mRNA expression levels of mitogen-activated protein kinase 3(MAPK3),tumor necrosis factor(TNF),and AKT serine/threonine kinase 1(AKT1)in NRK-52E cells were assessed using quantitative real-time polymerase chain reaction(qRT-PCR).Results:We obtained sixty-six overlapping targets of celastrol and DN.GO and KEGG analyses demonstrated that the core targets of celastrol and DN were mainly involved in the inflammatory and immune response,oxidative stress,advanced glycation end products(AGEs)and their receptors(RAGEs)(AGE-RAGE),TNF,interleukin 17(IL-17),and MAPK signaling pathways.Finally,based on the good binding activity with celastrol,MAPK3,TNF,and AKT1 were identified as the foremost targets of celastrol.We observed that celastrol enhanced the viability of high glucose(HG)-treated NRK-52E cells and inhibited apoptosis in the in vitro assays.Moreover,celastrol decreased the mRNA expression levels of MAPK3,TNF,and AKT1 in high glucose(HG)-treated NRK-52E cells.Conclusion:Celastrol may treat DN by targeting APK3,TNF,and AKT1 and regulating inflammatory responses and oxidative stress through the AGE-RAGE,TNF,IL-17,and MAPK signaling pathways.展开更多
Background:Magnolol,a bioactive extract of the Chinese herb Magnolia officinalis has a protective effect against periodontitis.This study is aimed to explore the mechanisms involved in the functioning of magnolol agai...Background:Magnolol,a bioactive extract of the Chinese herb Magnolia officinalis has a protective effect against periodontitis.This study is aimed to explore the mechanisms involved in the functioning of magnolol against periodontitis and provide a basis for further research.Methods:Network pharmacology analysis was performed based on the identification of related targets from public databases.The Protein-protein interaction(PPI)network was constructed to visualize the significance between the targets of magnolol and periodontitis.Subsequently,Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis were performed to predict the functions and the signal regulatory pathways involved in the action of magnolol against periodontitis.The“functiontarget-pathway”networks were constructed to analyze the core targets and pathways of magnolol against periodontitis.Molecular docking was used to verify the interaction of magnolol and core targets.Results:A total of 58 active targets of magnolol and 644 periodontitis-related targets were collected from public databases.A total of 25 targets of magnolol against periodontitis were identified based on the Venn diagram.GO analysis showed that magnolol has a role in the response to oxidative stress,nicotine,and lipopolysaccharide.KEGG enrichment analysis indicated that the mechanism of magnolol against periodontitis was mainly related to the tumor necrosis factor(TNF),phosphoinositide 3-kinase(PI3K/Akt),and mitogen-activated protein kinase(MAPK)signaling pathways.Combined with PPI network and molecular docking results,the core targets of magnolol against periodontitis included AKT1,MAPK8,MAPK14,TNF,and TP53.Conclusion:To summarize,the anti-periodontitis mechanisms of magnolol are potentially through regulating the TNF,PI3K/Akt,and MAPK signaling pathways.展开更多
Background:Despite its widespread therapeutic use and effectiveness,the underlying pharmacologic mechanisms of Wendan decoction(WDD)and how it works to treat sudden deafness(SD)remain unclear.In this study,the pharmac...Background:Despite its widespread therapeutic use and effectiveness,the underlying pharmacologic mechanisms of Wendan decoction(WDD)and how it works to treat sudden deafness(SD)remain unclear.In this study,the pharmacological mechanisms of WDD underlying SD were analyzed using network pharmacology and molecular docking.Methods:The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)was employed to identify the active compounds and target genes of WDD,and genes associated with SD were screened on five databases.RGUI conducted Gene Ontology(GO)functional and the Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses.A compound-target network was established using Cytoscape,and the STRING database created a protein-protein interaction(PPI)network to identify the key compounds and targets.Subsequently,a network of crucial compound-target was generated for further molecular docking analysis.For molecular docking simulations of the macromolecular target proteins and their matching ligand molecules,AutoDock Vina and AutoDockTool were utilized.Results:TCMSP identified 162 active target genes and 36 active compounds for WDD.The active target genes were compared with the 2271 genes associated with SD to identify 70 intersecting active target genes linked to 34 active compounds.The GO functional enrichment and KEGG pathway enrichment analyses were undertaken,and compound–target,and PPI networks were built.The key compounds and protein targets were identified and integrated to form a key compound–target network.Eventually,molecular docking was performed to investigate the interactions of the protein targets with their respective compounds.Conclusion:This study highlights the mechanisms of multi-compounds,targets,and pathways of WDD acting on SD and provides further evidence of crucial compounds and their matching target proteins of WDD acting on SD.展开更多
Objective:To explore the therapeutic potential of Cordyceps sinensis(Berk.)Sacc.(C.sinensis,Dong Chong Xia Cao)in an ischemic stroke(IS)model and predict its possible mechanism through network pharmacology.Methods:Thi...Objective:To explore the therapeutic potential of Cordyceps sinensis(Berk.)Sacc.(C.sinensis,Dong Chong Xia Cao)in an ischemic stroke(IS)model and predict its possible mechanism through network pharmacology.Methods:Thirty-three SpragueeDawley rats were randomly divided into the Sham,model,and C.sinensis groups.After 5 days of pre-treatment,the model group and the C.sinensis group were sub-jected to middle cerebral artery occlusion(MCAO)modeling.Effect of C.sinensis on MCAO rats was evaluated by comparing cerebral infarct size,neurological function,cerebral water content,pathological changes,and certain biochemical indicators.Intersection targets between C.sinensis and IS was screened using network pharmacology analysis.Relationship among core components,targets and pathways of C.sinensis in treating IS was constructed through network pharmacology analysis and further verified by molecular docking.Finally,the DAVID v8.8 database was used for performing GO analysis and KEGG pathway enrichment analysis by importing the intersection targets.Results:Compared with the model group,C.sinensis significantly reduced the volume of cerebral infarction(P=0.026),the cerebral water content(P¼.0013),the mNSS score(P<0.001),and the levels of IL-17(P=0.031),TNF-α(P=0.016),MDA(P=0.014),and glutamate(P=0.014)in serum,while upregulating the level of SOD in serum and improving the pathological morphology in MCAO rat ischemic brains.The results of network pharmacology analysis showed that core targets(such as CASP3,PTGS2,and PPARG)and the main enrichment pathways(IL-17,AGE-RAGE,and TNF signaling pathways)were regulated by 30 chemical components of C.sinensis,which effectively treated IS in MCAO rats.Conclusion:The results of this study showed that C.sinensis effectively interfered with MCAO rats,and the mechanism may be related to the regulation of blood lipids and to anti-apoptosis and anti-inflammatory effects.展开更多
Cancer is considered one of the most lethal diseases responsible for causing deaths worldwide.Although there have been many breakthroughs in anticancer development,cancer remains the major cause of death globally.In t...Cancer is considered one of the most lethal diseases responsible for causing deaths worldwide.Although there have been many breakthroughs in anticancer development,cancer remains the major cause of death globally.In this regard,targeting cancer-causing enzymes is one of the efficient therapeutic strategies.Biological functions like cell cycle,transcription,metabolism,apoptosis,and other depend primarily on cyclin-dependent kinases(CDKs).These enzymes help in the replication of DNA in the normal cell cycle process,and deregulation in the functioning of any CDK can cause abnormal cell growth,which leads to cancer.This review is focused on anticancer drug discovery against cell cycle CDK enzyme using an in silico technique,i.e.,molecular docking studies.Molecular docking helps in deciphering the key interactions formed within the inhibitor and the respective enzyme.This concise study provides an overview of the most current in silico research advancements made in the field of anticancer drug discovery.The findings presented in the current review article can help in understanding the nature of inhibitor-target interactions and provide information on the structural and molecular prerequisites for the inhibition of cell cycle CDKs.展开更多
BACKGROUND Polygoni Cuspidati Rhizoma et Radix(PCRR),a well-known traditional Chinese medicine(TCM),inhibits inflammation associated with various human diseases.However,the anti-inflammatory effects of PCRR in acute l...BACKGROUND Polygoni Cuspidati Rhizoma et Radix(PCRR),a well-known traditional Chinese medicine(TCM),inhibits inflammation associated with various human diseases.However,the anti-inflammatory effects of PCRR in acute lung injury(ALI)and the underlying mechanisms of action remain unclear.AIM To determine the ingredients related to PCRR for treatment of ALI using multiple databases to obtain potential targets for fishing.METHODS Recognized and candidate active compounds for PCRR were obtained from Traditional Chinese Medicine Systems Pharmacology,STITCH,and PubMed databases.Target ALI databases were built using the Therapeutic Target,DrugBank,DisGeNET,Online Mendelian Inheritance in Man,and Genetic Association databases.Network pharmacology includes network construction,target prediction,topological feature analysis,and enrichment analysis.Bioinformatics resources from the Database for Annotation,Visualization and Integrated Discovery were utilized for gene ontology biological process and Kyoto Encyclopedia of Genes and Genomes network pathway enrichment analysis,and molecular docking techniques were adopted to verify the combination of major active ingredients and core targets.RESULTS Thirteen bioactive compounds corresponding to the 433 PCRR targets were identified.In addition,128 genes were closely associated with ALI,60 of which overlapped with PCRR targets and were considered therapeutically relevant.Functional enrichment analysis suggested that PCRR exerted its pharmacological effects in ALI by modulating multiple pathways,including the cell cycle,cell apoptosis,drug metabolism,inflammation,and immune modulation.Molecular docking results revealed a strong associative relationship between the active ingredient and core target.CONCLUSION PCRR alleviates ALI symptoms via molecular mechanisms predicted by network pharmacology.This study proposes a strategy to elucidate the mechanisms of TCM at the network pharmacology level.展开更多
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.
基金supported by Young and Middle Aged Teachers’Career Development Support Project of Shenyang Pharmaceutical University(ZQN2019005).
文摘Coronary atherosclerotic heart disease(CHD)is the main type of cardiovascular disease.The efficacy of Uyghur drug compound Saffron formula in CHD has been clinically proven.However,the underlying mechanism remains unclear.In this study,researchers investigated the active ingredients and mechanism of action of Crocus sativus and Rosa rugosa in the treatment of CHD by network pharmacology and molecular docking techniques,collected target information with the help of TCMSP,GEO,GeneCards,and other databases,constructed protein-protein interaction(PPI)network diagrams by STRING database,performed GO and KEGG pathway enrichment analysis on common targets,and finally molecularly docked the active ingredients with core targets.C.sativus-R.rugosa have a variety of polyphenol compounds,a total of 12 active ingredients,including quercetin and kaempferol,were screened.The first three targets intersected with the core targets of CHD as AKT1,TNF,and IL-1B.Enrichment results of KEGG pathway showed that C.sativus-R.rugosa against CHD involved atherosclerosis pathways.The molecular docking results showed that quercetin and kaempferol were well bound to the core targets,and it was speculated that these components might be the main active ingredients for the treatment of CHD.The potential mechanism of action of C.sativus-R.rugosa for the treatment of coronary heart disease was initially revealed.
基金the National Natural Science Foundation of China(No.82204250)China Postdoctoral Science Foundation(No.2021M693961)+2 种基金Young and Middle-Aged Talent Project of Hubei Provincial Department of Education(No.Q20222808)Hubei University of Science and Technology Doctoral Startup Fund Project(No.BK202029)Outstanding Young and Middle-Aged Scientific and Technological Innovation Team in Colleges and Universities in Hubei Province(No.T2021022).
文摘Background:Explore the anti-tumor mechanism of herb pair Pinellia ternate-Magnolia officinalis(BX-HP)in liver cancer through network pharmacology using molecular docking methods.Method:The active ingredients and corresponding targets of the herb pair Pinellia ternate-Magnolia officinalis were obtained from the HERB database.The relevant targets for liver cancer were obtained from GeneCards,DisGeNET,TTD,and Drugbank databases.Obtain common targets between herb pair Pinellia ternate-Magnolia officinalis and liver cancer through the Bioinformatics platform,establish a PPI network diagram using STRING software,and perform GO functional enrichment and KEGG pathway enrichment analysis on the DAVID platform.AutoDockTools 1.5.7 software and molecular dynamics simulation analysis are used to evaluate the binding of components to target proteins.HERB database,SwissTargetPrediction database,SwissADME database,UniProt database,GeneCards database,TTD database,DRUGBANK database,DisGeNET database,String,DAVID.Bioinformatics platform,PDB database,PubChem and TCMSP database.Result:A total of 22 active ingredients with a Probability>0.1 targets in Magnolia officinalis were screened,26 active ingredients with a Probability>0.1 targets in Pinellia ternata,ten vital active ingredients,corresponding to 979 and 803 targets with a Probability>0.1 targets,2536 liver cancer-related targets,and 279 targets in the herb pair Pinellia ternata-Magnolia officinalis.The GO functional enrichment analysis resulted in 1297 entries,namely 971 biological process entries,118 cell localization entries,and 208 molecular function entries.Three signaling pathways were annotated through the KEGG pathway.Based on molecular docking,ten vital active ingredients and five target proteins were validated to exhibit an excellent binding affinity.The above data indicates that combining the herb pair Pinellia ternata-Magnolia officinalis may treat liver cancer through specific targets and signaling pathways.Conclusion:Herb pair Pinellia ternata-Magnolia officinalis has a synergistic effect on treating liver cancer through multicomponent,multitarget,and multi-pathway approaches.This study provides a sufficient theoretical basis for subsequent research.
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.
基金Key Projects in Xianning science and technology project (No.2020SFYF01)Youth Talent Project of Health Commission of Hubei Province (No.ZY2021Q026).
文摘Background:To explore the effective chemical constituents of Feiduqing formula for prevention and treatment of coronavirus disease 2019(COVID-19).Methods:The compounds and action targets of twelve herbal medicines in Feiduqing formula were collected via Traditional Chinese Medicine Systems Pharmacology Database and Analytic Platform.The genes corresponding to the targets were queried through the UniProt database.The“herbal medicine-ingredient-target”network was established by Cytoscape software.The Gene Ontology function enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed by Database for Annotation,Visualization and Integrated Discovery.Molecular docking was used to analyze the binding force of core active compounds of Feiduqing formula with PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and angiotensin converting enzyme II(ACE2).Results:The“herbal medicine-ingredient-target”network included 434 nodes and 1948 edges,including 222 components such as quercetin,kaempferol,luteolin,etc.The key targets are PTGS2,HSP90AA1,PTGS1,ESR1,AR,NOS2,etc.Gene Ontology function enrichment analysis revealed 2530 items,including RNA polymerase II-specific,response to oxidative stress,transcription factor activity,etc.Kyoto Encyclopedia of Genes and Genomes pathway enrichment screened 169 signal pathways,including Human cytomegalovirus infection,Kaposi sarcoma-associated herpesvirus infection,Hepatitis B,Hepatitis C,IL-17,TNF,etc.The results of molecular docking showed that quercetin,luteolin,β-sitosterol,stigmasterol and other core active compounds have a certain degree of affinity with PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and ACE2.Conclusion:The active compounds of Feiduqing formula may have a therapeutic effect on COVID-19 pneumonia through the action on PTGS2,HSP90AA1,SARS-CoV-23CL hydrolase and ACE2,and regulating many signaling pathways.
基金supported by the Inner Mongolia Autonomous Region Science and Technology Revitalization Foundation (2021CG0029)the National Natural Science Foundation of China (22178070)
文摘Glabridin is the main ingredient of hydrophobic fraction in licorice extract and has been shown to have anti-melanogenesis activity in skins.However,the underlying mechanism(s)remain not completely understood.The aim of this study is thus to elucidate the possible mechanisms related to the melanogenesis suppression by glabridin in cultured B16 murine melanoma cells and in UVA radiation induced hyperpigmentation model of BALB/c mice as well.Molecular docking simulations revealed that between catalytic core residues and the compound.The treatment by glabridin significantly downregulated both transcriptional and/or protein expression of melanogenesis-related factors including melanocyte stimulating hormone receptor(MC1R),microphthalmia-associated transcription factor(MITF),tyrosinase(TYR),TYR-related protein-1(TRP-1)and TRP-2 in B16 cells.Both PKA/MITF and MAPK/MITF signaling pathways were found to be involved in the suppression of melanogenesis by glabridin in B16 cells.Also in vivo glabridin therapy significantly reduced hyperpigmentation,epidermal thickening,roughness and inflammation induced by frequent UVA exposure in mice skins,thus beneficial for skin healthcare.These data further look insights into the molecular mechanisms of melanogenesis suppression by glabridin,rationalizing the application of the natural compound for skin healthcare.
基金supported by The National Key R&D Program of China (2019YFD0901702)
文摘Oncorhynchus mykiss is delicious and contains abundant flavor substances.However,few studies focused on umami peptides of O.mykiss.In the current work,umami peptides derived from O.mykiss were identified using virtual screening,molecular docking,and electronic tongue analysis.First,the O.mykiss protein was hydrolyzed using the PeptideCutter online enzymolysis program.Subsequently,water-soluble and toxicity screening were performed by Innovagen and ToxinPred software,respectively.The potential peptides were docked with umami receptor T1R1/T1R3.Furthermore,taste properties of potential peptides were validated by electronic tongue.Docking results suggested that the three tetrapeptide EANK,EEAK,and EMQK could enter the binding pocket in the T1R1 cavity,wherein Arg151,Asp147,Gln52,and Arg277 may play key roles in the production of umami taste.Electronic tongue results showed that the umami value of EANK,EEAK,and EMQK were stronger than monosodium glutamate.This work provides a new insight for the screening of umami peptides in O.mykiss.
基金Supported by Ningxia Natural Science Foundation,No.2022AAC02039National Natural Science Foundation of China,No.81860894,82260879,81674096Ningxia Innovation Team of the Foundation and Clinical Researches of Diabetes and its Complications,No.NXKJT2019010.
文摘BACKGROUND Diabetic nephropathy(DN)stands as the most prevalent chronic microvascular complication of diabetes mellitus.Approximately 50%of DN patients progress to end-stage renal disease,posing a substantial health burden.AIM To employ network pharmacology and molecular docking methods to predict the mechanism by which glycyrrhetinic acid(GA)treats DN,subsequently validating these predictions through experimental means.METHODS The study initially identified GA targets using Pharm Mapper and the TCMSP database.Targets relevant to DN were obtained from the Genecards,OMIM,and TTD databases.The Venny database facilitated the acquisition of intersecting targets between GA and DN.The String database was used to construct a protein interaction network,while DAVID database was used to conducted Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analysis and Gene Ontology(GO)analysis.Molecular docking experiments were performed using Autodock software with selected proteins.Experimental validation was conducted using renal proximal tubular cells(HK-2)as the study subjects.A hyperglycemic environment was simulated using glucose solution,and the effect of GA on cell viability was assessed through the cell counting kit-8 method.Flow cytometry was employed to detect cell cycle and apoptosis,and protein immunoblot(western blot)was used to measure the expression of proteins of the phosphatidylinositol 3-kinase(PI3K)/protein kinase B(AKT)signaling pathway and insulin resistance pathway,including insulin receptor(INSR),PI3K,p-PI3K,AKT,p-AKT,and glycogen synthase kinase-3(GSK3).RESULTS A total of 186 intersecting targets between GA and DN were identified,which were associated with 144 KEGGrelated enrichment pathways,375 GO biological process entries,45 GO cellular component entries,and 112 GO cellular function entries.Molecular docking demonstrated strong binding of GA to mitogen-activated protein kinase(MAPK)-1,SRC,PIK3R1,HSP90AA1,CASPASE9,HARS,KRAS,and MAPK14.In vitro experiments revealed that GA inhibited HK-2 cell viability,induced cell cycle arrest at the G2/M phase,and reduced apoptosis with increasing drug concentration.Western blot analysis showed that GA differentially up-regulated GSK3 protein expression,up-regulated AKT/p-AKT expression,down-regulated INSR,AKT,p-AKT,PI3K,and p-PI3K protein expression,and reduced p-PI3K/PI3K levels under high glucose conditions.CONCLUSION GA may protect renal intrinsic cells by modulating the PI3K/AKT signaling pathway,thereby inhibiting HK-2 cell viability,reducing HK-2 cell apoptosis,and inducing cell cycle arrest at the G0/G1 phase.
文摘BACKGROUND Although Liu-Wei-Bu-Qi capsule(LBC)inhibits tumor progression by improving the physical condition and immunity of patients with lung cancer(LC),its exact mechanism of action is unknown.AIM To through compound multi-dimensional network of chemical ingredient-targetdisease-target-protein-protein interaction(PPI)network,the principle of action of Chinese medicine prescription was explained from molecular level.METHODS Network pharmacology and molecular docking simulations were used to analyze the relationship among the main components,targets,and signaling pathways of LBC in treatment of LC.RESULTS From the analysis,360 LBC active ingredient-related targets and 908 LC-related targets were identified.PPI network analysis of the LBC and LC overlapping targets identified 16 hub genes.Kyoto Encyclopedia of Genes and Genomes analysis suggested that LBC can target the vascular endothelial growth factor signaling pathway,Toll-like receptor signaling pathway,prolactin signaling pathway,FoxO signaling pathway,PI3K-Akt signaling pathway and HIF-1 signaling pathway in the treatment of LC.Molecular docking simulations showed that quercetin had the best affinity for MAPK3,suggesting that quercetin in LBC may play an important role in the treatment of LC.CONCLUSION The results showed that the active ingredients in LBC can play a crucial role in the treatment of LC by regulating multiple signaling pathways.These results provide insights into further studies on the mechanism of action of LBC in the treatment of LC.
基金supported by the Natural Science Foundation of Gansu Province[Grant Numbers 22JR5RA930,22JR5RA894]the Talent Project of Lanzhou Science and Technology Bureau[Grant Number 2022-3-44]+1 种基金the projects managed by the Administration of Traditional Chinese Medicine[Grant Number GZKG-2022-54]Intra Hospital Fund of the First Hospital of Lanzhou University[Grant Number ldyyyn2021101].
文摘Background:1,2,3,4,6-penta-O-galloyl-beta-D-glucose(PGG)is a natural polyphenolic compound derived from multiple medicinal plants with favorable anticancer activity.Methods:In this study,the mechanisms of PGG against gastric cancer were explored through network pharmacology and molecular docking.First,the targets of PGG were searched in the Herbal Ingredients’Targets(HIT),Similarity Ensemble Approach(SEA),and Super-PRED databases.The potential targets related to gastric cancer were predicted from the Human Gene Database(GeneCards)and DisGeNET databases.The intersecting targets of PGG and gastric cancer were obtained by Venn diagram and then subjected to protein-protein interaction analysis to screen hub targets.Functional and pathway enrichment of hub targets were analyzed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway databases.The differential expression and survival analysis of hub targets in gastric cancer were performed based on The Cancer Genome Atlas database.Finally,the affinity of PGG with hub targets was visualized by molecular docking.Results:Three hub targets were screened,including mitogen-activated protein kinase 14(MAPK14),BCL2 like 1(BCL2L1),and vascular endothelial growth factor A(VEGFA).MAPK14 had a higher expression,while BCL2L1 and VEGFA had lower expression in gastric cancer than in normal conditions.Enrichment analysis indicated enrichment of these hub targets in MAPK,neurotrophin,programmed death-ligand 1(PD-L1)checkpoint,phosphatidylinositol 3-kinases/protein kinase B(PI3K-Akt),Ras,and hypoxia-inducible factor-1(HIF-1)signaling pathways.Conclusion:Therefore,network pharmacology and molecular docking analyses revealed that PGG exerts a therapeutic efficacy on gastric cancer by multiple targets(MAPK14,BCL2L1,and VEGFA)and pathways(MAPK,PD-L1 checkpoint,PI3K-Akt,Ras,and HIF-1 pathways).
基金National Natural Science Foundation of China(82030124)National Natural Science Foundation of China(82174015)Science and Technology Innovation Project of China Academy of Traditional Chinese Medicine(CI2021A04609)。
文摘OBJECTIVE To investigate the regulatory effects of icariin(ICA)on cardiac micro⁃vascular endothelial cells(CMEC)after oxygenglucose deprivation reperfusion(OGD/R)injury.METHODS CMEC were subjected to OGD/R treatment to construct a myocardial ischemiareperfusion model,and were divided into normal,model,low(10μmol·L^(-1)),medium(20μmol·L^(-1))and high(40μmol·L^(-1))ICA group,and high ICA+inhibitor group(40μmol·L^(-1)+20 nmol·L^(-1)).CCK-8 assay was used to assess the protective ability of ICA against CMEC,and cell migration assay and tube-formation assay were used to detect the migration and generation ability of CMEC.The TCMSP database,Swiss-Target database and literature mining methods were used to col⁃lect ICA-related targets,the GeneCards data⁃base was used to collect target genes related to myocardial ischemia/reperfusion,and Cytoscape 3.8.0 software was used to construct a"drug-tar⁃get-disease"network.The potential targets were imported into STRING 11.5 database to obtain the PPI network.GO and KEGG enrichment analyses were performed on the potential targets using the DAVID database.Molecular docking was performed using AutoDock-vina 1.1.2 soft⁃ware.Western blot detected the expression of related proteins.RESULTS After CMEC was subjected to OGD/R treatment,ICA had a protec⁃tive effect at 10^(-1)60μmol·L^(-1);the results of the cell migration assay showed that each group of ICA could promote the migratory effect of CMEC(P<0.01,P<0.01);and the results of tube-for⁃mation assay showed that each group of ICA could significantly promote the generation of branches(P<0.01)and the capillary length exten⁃sion(P<0.05).Network pharmacology collected a total of 23 ICA action targets,1500 disease tar⁃gets and 12 key targets.GO function enrichment analysis found 85 results.KEGG pathway enrich⁃ment analysis found 53 results,involving AGERAGE signaling pathway,sphingolipid signaling pathway and VEGF signaling pathway.Molecu⁃lar docking results showed that ICA had better binding with core targets PRKCB,PRKCA and PTGS2.Western blot results showed that ICA could regulate the expression of PRKCB,PRKCA and PTGS2 proteins.The results of cell migra⁃tion assay,tube-formation assay and protein expression were reversed after addition of PKC inhibitor.CONCLUSION The potential mecha⁃nism of action of ICA against myocardial isch⁃emia-reperfusion injury may be related to the reg⁃ulation of processes such as CMEC migration and angiogenesis,and it functions through the key target gene PKC.
基金supported by the Zhejiang Province Chinese Medicine Modernization Program Grant[Number 2020ZX001]the“Pioneer”and“Leading Goose”R&D Program of Zhejiang Grant[Number 2023C03075].
文摘Background:Diabetic nephropathy(DN)is a serious complication of diabetes with rising prevalence worldwide.We aimed to explore the anti-DN mechanisms of the compound celastrol derived from the medicinal plant Tripterygium wilfordii.Methods:Celastrol-related targets were obtained from Herbal Ingredients’Targets(HIT)and GeneCards databases.DN-related targets were retrieved from GeneCards,DisGeNET,and Therapeutic Targets Database(TTD).A Protein-protein interaction(PPI)network was established using the Search Tool for the Retrieval of Interacting Genes(STRING)database.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses were performed using ClusterProfiler.The cytoHubba plugin was used to select the top 10 hub targets.Molecular docking was performed employing PyMOL and AutoDock software.Cell counting kit-8(CCK-8)and flow cytometry assays were used to detect the viability and apoptosis of NRK-52E cells,respectively.The mRNA expression levels of mitogen-activated protein kinase 3(MAPK3),tumor necrosis factor(TNF),and AKT serine/threonine kinase 1(AKT1)in NRK-52E cells were assessed using quantitative real-time polymerase chain reaction(qRT-PCR).Results:We obtained sixty-six overlapping targets of celastrol and DN.GO and KEGG analyses demonstrated that the core targets of celastrol and DN were mainly involved in the inflammatory and immune response,oxidative stress,advanced glycation end products(AGEs)and their receptors(RAGEs)(AGE-RAGE),TNF,interleukin 17(IL-17),and MAPK signaling pathways.Finally,based on the good binding activity with celastrol,MAPK3,TNF,and AKT1 were identified as the foremost targets of celastrol.We observed that celastrol enhanced the viability of high glucose(HG)-treated NRK-52E cells and inhibited apoptosis in the in vitro assays.Moreover,celastrol decreased the mRNA expression levels of MAPK3,TNF,and AKT1 in high glucose(HG)-treated NRK-52E cells.Conclusion:Celastrol may treat DN by targeting APK3,TNF,and AKT1 and regulating inflammatory responses and oxidative stress through the AGE-RAGE,TNF,IL-17,and MAPK signaling pathways.
文摘Background:Magnolol,a bioactive extract of the Chinese herb Magnolia officinalis has a protective effect against periodontitis.This study is aimed to explore the mechanisms involved in the functioning of magnolol against periodontitis and provide a basis for further research.Methods:Network pharmacology analysis was performed based on the identification of related targets from public databases.The Protein-protein interaction(PPI)network was constructed to visualize the significance between the targets of magnolol and periodontitis.Subsequently,Gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis were performed to predict the functions and the signal regulatory pathways involved in the action of magnolol against periodontitis.The“functiontarget-pathway”networks were constructed to analyze the core targets and pathways of magnolol against periodontitis.Molecular docking was used to verify the interaction of magnolol and core targets.Results:A total of 58 active targets of magnolol and 644 periodontitis-related targets were collected from public databases.A total of 25 targets of magnolol against periodontitis were identified based on the Venn diagram.GO analysis showed that magnolol has a role in the response to oxidative stress,nicotine,and lipopolysaccharide.KEGG enrichment analysis indicated that the mechanism of magnolol against periodontitis was mainly related to the tumor necrosis factor(TNF),phosphoinositide 3-kinase(PI3K/Akt),and mitogen-activated protein kinase(MAPK)signaling pathways.Combined with PPI network and molecular docking results,the core targets of magnolol against periodontitis included AKT1,MAPK8,MAPK14,TNF,and TP53.Conclusion:To summarize,the anti-periodontitis mechanisms of magnolol are potentially through regulating the TNF,PI3K/Akt,and MAPK signaling pathways.
基金funded by the Traditional Chinese Medicine Science and Technology Development Plan Project of Jiangsu Province(ZT202113 to Haibing Hua)the 510 Talent Training Project of Yizheng City(2022 to Shiming Ye)+1 种基金the Scientific Research Project of Jiangyin Association of Chinese Medicine(Y202205 to Yufeng Zhang)the ChengXing Talent Training Plan of Jiangyin Hospital of Traditional Chinese Medicine(2022 to Yufeng Zhang).
文摘Background:Despite its widespread therapeutic use and effectiveness,the underlying pharmacologic mechanisms of Wendan decoction(WDD)and how it works to treat sudden deafness(SD)remain unclear.In this study,the pharmacological mechanisms of WDD underlying SD were analyzed using network pharmacology and molecular docking.Methods:The Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP)was employed to identify the active compounds and target genes of WDD,and genes associated with SD were screened on five databases.RGUI conducted Gene Ontology(GO)functional and the Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analyses.A compound-target network was established using Cytoscape,and the STRING database created a protein-protein interaction(PPI)network to identify the key compounds and targets.Subsequently,a network of crucial compound-target was generated for further molecular docking analysis.For molecular docking simulations of the macromolecular target proteins and their matching ligand molecules,AutoDock Vina and AutoDockTool were utilized.Results:TCMSP identified 162 active target genes and 36 active compounds for WDD.The active target genes were compared with the 2271 genes associated with SD to identify 70 intersecting active target genes linked to 34 active compounds.The GO functional enrichment and KEGG pathway enrichment analyses were undertaken,and compound–target,and PPI networks were built.The key compounds and protein targets were identified and integrated to form a key compound–target network.Eventually,molecular docking was performed to investigate the interactions of the protein targets with their respective compounds.Conclusion:This study highlights the mechanisms of multi-compounds,targets,and pathways of WDD acting on SD and provides further evidence of crucial compounds and their matching target proteins of WDD acting on SD.
基金This study was supported by Key Project at Central Government Level:The Ability Establishment of Sustainable Use for Valuable Chinese Medicine Resources(2060302).
文摘Objective:To explore the therapeutic potential of Cordyceps sinensis(Berk.)Sacc.(C.sinensis,Dong Chong Xia Cao)in an ischemic stroke(IS)model and predict its possible mechanism through network pharmacology.Methods:Thirty-three SpragueeDawley rats were randomly divided into the Sham,model,and C.sinensis groups.After 5 days of pre-treatment,the model group and the C.sinensis group were sub-jected to middle cerebral artery occlusion(MCAO)modeling.Effect of C.sinensis on MCAO rats was evaluated by comparing cerebral infarct size,neurological function,cerebral water content,pathological changes,and certain biochemical indicators.Intersection targets between C.sinensis and IS was screened using network pharmacology analysis.Relationship among core components,targets and pathways of C.sinensis in treating IS was constructed through network pharmacology analysis and further verified by molecular docking.Finally,the DAVID v8.8 database was used for performing GO analysis and KEGG pathway enrichment analysis by importing the intersection targets.Results:Compared with the model group,C.sinensis significantly reduced the volume of cerebral infarction(P=0.026),the cerebral water content(P¼.0013),the mNSS score(P<0.001),and the levels of IL-17(P=0.031),TNF-α(P=0.016),MDA(P=0.014),and glutamate(P=0.014)in serum,while upregulating the level of SOD in serum and improving the pathological morphology in MCAO rat ischemic brains.The results of network pharmacology analysis showed that core targets(such as CASP3,PTGS2,and PPARG)and the main enrichment pathways(IL-17,AGE-RAGE,and TNF signaling pathways)were regulated by 30 chemical components of C.sinensis,which effectively treated IS in MCAO rats.Conclusion:The results of this study showed that C.sinensis effectively interfered with MCAO rats,and the mechanism may be related to the regulation of blood lipids and to anti-apoptosis and anti-inflammatory effects.
文摘Cancer is considered one of the most lethal diseases responsible for causing deaths worldwide.Although there have been many breakthroughs in anticancer development,cancer remains the major cause of death globally.In this regard,targeting cancer-causing enzymes is one of the efficient therapeutic strategies.Biological functions like cell cycle,transcription,metabolism,apoptosis,and other depend primarily on cyclin-dependent kinases(CDKs).These enzymes help in the replication of DNA in the normal cell cycle process,and deregulation in the functioning of any CDK can cause abnormal cell growth,which leads to cancer.This review is focused on anticancer drug discovery against cell cycle CDK enzyme using an in silico technique,i.e.,molecular docking studies.Molecular docking helps in deciphering the key interactions formed within the inhibitor and the respective enzyme.This concise study provides an overview of the most current in silico research advancements made in the field of anticancer drug discovery.The findings presented in the current review article can help in understanding the nature of inhibitor-target interactions and provide information on the structural and molecular prerequisites for the inhibition of cell cycle CDKs.
基金Supported by Shandong Province Integrated Traditional Chinese and Western Medicine Professional Disease Prevention and Control Project,No.YXH2019ZXY010.
文摘BACKGROUND Polygoni Cuspidati Rhizoma et Radix(PCRR),a well-known traditional Chinese medicine(TCM),inhibits inflammation associated with various human diseases.However,the anti-inflammatory effects of PCRR in acute lung injury(ALI)and the underlying mechanisms of action remain unclear.AIM To determine the ingredients related to PCRR for treatment of ALI using multiple databases to obtain potential targets for fishing.METHODS Recognized and candidate active compounds for PCRR were obtained from Traditional Chinese Medicine Systems Pharmacology,STITCH,and PubMed databases.Target ALI databases were built using the Therapeutic Target,DrugBank,DisGeNET,Online Mendelian Inheritance in Man,and Genetic Association databases.Network pharmacology includes network construction,target prediction,topological feature analysis,and enrichment analysis.Bioinformatics resources from the Database for Annotation,Visualization and Integrated Discovery were utilized for gene ontology biological process and Kyoto Encyclopedia of Genes and Genomes network pathway enrichment analysis,and molecular docking techniques were adopted to verify the combination of major active ingredients and core targets.RESULTS Thirteen bioactive compounds corresponding to the 433 PCRR targets were identified.In addition,128 genes were closely associated with ALI,60 of which overlapped with PCRR targets and were considered therapeutically relevant.Functional enrichment analysis suggested that PCRR exerted its pharmacological effects in ALI by modulating multiple pathways,including the cell cycle,cell apoptosis,drug metabolism,inflammation,and immune modulation.Molecular docking results revealed a strong associative relationship between the active ingredient and core target.CONCLUSION PCRR alleviates ALI symptoms via molecular mechanisms predicted by network pharmacology.This study proposes a strategy to elucidate the mechanisms of TCM at the network pharmacology level.
