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ObjectiveThe active ingredients， action targets， and signaling pathways of Cuscutae Semen to control premature ovarian failure were initially predicted by network pharmacology and molecular docking techniques， and an animal model of premature ovarian failure was constructed to explore the mechanism of Cuscutae Semen based on lipid and atherosclerosis signaling pathways. MethodThe effective components and corresponding targets of drugs were obtained from Traditional Chinese Medicines Systems Pharmacology Platform （TCMSP）， Swiss Target Prediction， Pharmmapper， and other databases. GeneCards database was used to collect disease-related targets. Venny2.1.0 online tool was used to screen out the intersection targets of drugs and diseases， and STRING database and Cytoscape v3.7.2 software were used to construct the network diagram of "drug-component-target" and protein-protein interaction （PPI）. The gene ontology （GO） and the Kyoto encyclopedia of genes and genomes （KEGG） enrichment analyses of the intersection targets were performed by running the R language script. The molecular docking technology was utilized to dock drug components with targets and visualize some of the docking results. The mice were randomly divided into a blank group， a model group， a Cuscutae Semen group， and an estradiol valerate group， and the ovarian premature failure model was prepared by chronic stress. The blank group and the model group were gavaged with the same amount of normal saline， and the Cuscutae Semen group was given a Cuscutae Semen decoction of 2.6 g·kg-1·d-1. The estradiol valerate group was given an estradiol valerate solution of 0.13 mg·kg-1·d-1. After four weeks， samples were collected， and hematoxylin-eosin （HE） staining was performed to observe the histopathological changes in the ovary. Serum levels of follicle-stimulating hormone （FSH）， luteinizing hormone （LH）， estradiol （E2）， Muller's tube inhibitor/anti-Muller's tube hormone （AMH）， total cholesterol （TC）， high-density lipoprotein cholesterol （HDL-C）， and low-density lipoprotein cholesterol （LDL-C） were determined by enzyme-linked immunosorbent assay （ELISA）. The expression levels of extracellular regulatory protein kinase （ERK）， nuclear transcription factor-κB p65 （NF-κB p65）， nuclear transcription factor-κB suppressor α （IκBα）， interleukin-1β （IL-1β）， IL-6， and tumor necrosis factor-α （TNF-α） were measured by Western blot. ResultA total of 171 targets of Cuscutae Semen for the prevention and treatment of premature ovarian failure were screened， mainly including tumor protein p53 （TP53）， protein kinase B1 （Akt1）， sarcoma （SRC）， tumor necrosis factor （TNF）， epidermal growth factor receptor （EGFR）， etc. KEGG pathway enrichment analysis predicts that Cuscutae Semen is mainly involved in lipid and atherosclerosis， TNF signaling pathway， and TP53 signaling pathway to control premature ovarian failure. The animal experiments show that compared with the premature ovarian failure model group， the Cuscutae Semen group can significantly upregulate AMH， E2， and HDL-C （P<0.05， P<0.01）， significantly downregulate LH， TC， and LDL-C （P<0.01）， greatly reduce IL-1β， IL-6， and TNF-α protein levels， as well as ERK， NF-κB p65， and their phosphorylation levels （P<0.01）. ConclusionCuscutae Semen can regulate hormone levels and improve ovarian function through a multi-component， multi-target， and multi-pathway approach， and the mechanism may be related to the regulation of lipid and atherosclerosis signaling pathways.
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Aim To explore the potential targets and related signaling pathways of Agaricus blazei Murill (AbM ) extract in the treatment of chronic myeloid leukemia (CML) based on liquid chromatography mass spectrometry ( LC-MS ), network pharmacology, molecular docking, and were further verified by experiments in vitro. Methods The active components of AbM extract were retrieved from LC-MS, Swiss Target Prediction database was used to predict related targets, and CML disease target genes were obtained from Gen- eCards and DisGeNET databases. After screening the common targets of drug and CML, the protein-protein interaction network of the common targets was performed by STRING, and GO and KEGG enrichment a- nalysis were done by DAVID database. Cytoscape software was used to construct the network of target protein. Molecular docking was carried out by DockThor, and the Pymol software was used to make a visual picture. The inhibitory effect of AbM extract on leukemia cells K562 was determined by CCK-8 experiment, and the effect of AbM extract on the expression and phosphorylation level of related proteins was verified by Western blot. Results The prediction results showed that 126 active components of AbM extract, and 172 common targets were collected. KEGG pathway analysis results showed that PI3K/Akt/mTOR signaling pathway might play an important role in the treatment of CML disease. The IC
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Objective:To the molecular mechanism of Yinjiushu in the treatment of non-alcoholic fatty liver disease (NAFLD) by network pharmacology based on the theory of homology of medicine and food; To conduct experimental verification.Methods:The active components and targets of the Yinjiushu were screened through the TCMSP platform. Cytoscape 3.7.2 was used to construct the "Chinese materia medica-component-target" network of Yinjiushu. The potential targets of NAFLD were obtained by using TTD, GeneCards database and DisGeNET database, and the intersection targets of Yinjiushu and NAFLD were obtained by mapping targets with Venn diagram. The high confidence interaction relationship of intersection targets was obtained in STRING database, and the core targets of Yinjiushu in treating NAFLD were screened out. GO function and KEGG pathway enrichment of common targets were analyzed by David database, and the above results were further verified by animal experiments. The rats were divided into blank group, model group, Western medicine group and Yinjiushu high-, medium- and low-dosage groups according to random number table method, with 8 rats in each group. Except the blank group, rats in other groups were fed with high-fat diet to prepare NAFLD model. Each group was given corresponding drugs for intervention. The rats were weighed regularly. The serum contents of GPT, GOT, TC, TG, IL-6, TNF-α, MPO of rats were detected by ELISA. The liver index was calculated. The degree of fatty degeneration of hepatocytes was observed by HE. The expressions of CAT, NOS3, SOD, PI3K, p-Akt, Akt protein were detected by Western blot.Results:A total of 8 418 NAFLD-related targets, 118 kinds of active components from Yinjiushu, and 137 targets acting on NAFLD were screened. The core targets included IL-6, TNF, VEGFA, TP53, JUN, CAT, NOS3, SOD, etc. 20 related signaling pathways were screened from KEGG enrichment pathway, among which PI3K/Akt pathway, calcium ion pathway, cAMP pathway and TNF pathway may play key roles in the treatment. Yinjiushu was closely related to inflammatory reaction, oxidative stress, angiogenesis, autophagy, cell proliferation, differentiation, metabolism, apoptosis, etc., or it could treat NAFLD by promoting cell apoptosis, inhibiting cell proliferation, inhibiting cell migration, etc. The animal experiment proved that Yinjiushu could reduce the body weight, wet liver weight and liver-body ratio of NAFLD rats, reduce some liver function and blood lipid indexes (GPT, GOT, TG, TC), down-regulate serum IL-6, TNF-α and MPO, up-regulate the expression of CAT, NOS3 and SOD in hepatocytes, and activate the expression of PI3K/Akt key protein.Conclusion:Yinjiushu can play a role in treating NAFLD by inhibiting the release of inflammatory mediators, improving lipid metabolism disorder of hepatocytes, repairing oxidative stress injury and promoting the recovery of liver function.
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Objective:To explore the mechanism of Shuerjing Capsule in treating primary dysmenorrhea based on molecular docking of network pharmacology and in vivo experiment.Methods:By using TCMSP to screen the active components and targets of Shuerjing Capsule; by using GeneCards and DrungBank databases to retrieve targeted proteins of primary dysmenorrhea, and the intersection targets of drugs and diseases were obtained through Weishengxin online platform; by using Cytoscape 3.9.1 software to produce component-target network of Shuerjing Capsule for the treatment of primary dysmenorrhea; by STRING databases to construct drug-disease target PPI network; by DAVID database to perform GO and KEGG pathway enrichment analysis.The key active components of the drug and the core targets of the disease were obtained with molecular docking. The rats were randomly divided into control group, model group, the low-dose group, medium-dose group and high-dose group of Shujing Capsule (0.15, 0.21, 0.42 g/kg), and ibuprofen group (20 mg/kg), with 10 rats in each group. The animal model of primary dysmenorrhea was established by subcutaneous injection of estradiol benzoate and intervented by drugs. The number of writhing reaction, uterine contractile inhibition rate and uterine index of rats were observed. The expressions of TNF-α, IL-6 and IL-1 in serum and the levels of PTGS2 and VEGFA in uterine tissue were detected by ELISA.Results:A total of 188 active ingredients of Shuerjing Capsule were screened, and 51 targets of Shuerjing Capsule and primary dysmenorrhea were identified. TNF, IL-6, AKT1 and TP53 may be the key targets of Shuerjing Capsule in the treatment of primary dysmenorrhea. A total of 519 GO biological processes and 119 related signaling pathways were obtained, among which estrogen, IL-17, HIF-1 and other signaling pathways were closely related to the treatment of primary dysmenorrhea. The results of molecular docking were good, among which stigmasterol had the strongest binding ability to TP53. The experimental results showed that compared with the model group, the uterine index and the number of torsion were decreased in the low -, medium - and high-dose Shuojing Capsule groups ( P<0.05), the uterine contraction inhibition rate increased ( P<0.05); Serum levels of TNF-α, IL-6 and IL-1 of medium and high dose group decreased ( P<0.05), the levels of PTGS2 and VEGFA in uterine tissues decreased ( P<0.05). Conclusion:Shuerjing Capsule has the effect of anti-inflammatation and improveing hypoxia, which may be related to the inhibition of TNF-α, IL-6 and IL-1 inflammatory factors in serum and the expression of PTGS2 and VEGFA proteins in uterine tissues.
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Objective:To explore the mechanism of Tripterygium wilfordii in treating renal cell carcinoma using network pharmacology and experimental validation. Methods:The traditional Chinese medicine systems pharmacology (TCMSP) database and analysis platform was utilized to screen the active ingredients of T. wilfordii and predict the targets using the Swiss database. Renal cell carcinoma related targets were collected from DisGeNET, GeneCards, and OMIM databases, and intersecting targets were obtained through Venny 2.1.0. Protein-protein interaction (PPI) networks were mapped using the STRING database and Cytoscape software, and gene ontology (GO) and kyoto encyclopedia of genes and genomics (KEGG) enrichment analyses were performed. Component-target-pathway networks were constructed using Cytoscape software. To induce the subcutaneous transplantation tumor model of renal cell carcinoma, nude mice were randomly divided into a control group and a treatment group, with 5 mice in each group. In the treatment group, mice were gastrically instilled with 615 mg/ml of T. wilfordii solution (1 845 mg T. wilfordii granules dissolved into 3 ml water) 2.46 g/kg, 10 μl/time, once daily for 21 d. In the control group, mice were gastrically instilled with an equal amount of saline. Tumor volume was measured once every 5 days, and the expression of serine/threonine protein kinase 1 (AKT1), signal transduction and transcription activator 3 (STAT3), tumor necrosis factor (TNF), tumor protein p53 (TP53), JUN, mitogen-activated protein kinase 8 (MAPK8), and MAPK14 was detected by enzyme-linked immunoassay. Results:Twenty-eight active pharmaceutical ingredients and 117 potential targets of T. wilfordii were screened; 13 425 related disease targets were identified; and finally, 113 drug-disease intersecting targets were obtained. In the PPI network, AKT1, STAT3, TNF, TP53, JUN, MAPK8, and MAPK14 were the core targets. GO analysis showed that BP mainly included nuclear receptor activity, ligand-activated transcription factor activity, RNA polymerase-specific DNA-binding transcription factor binding, nuclear steroid receptor activity, and adrenergic receptor activity, etc. CC mainly included the response to hormones, the cellular response to lipids, the positive regulation of cell migration, the response to TNF, the inflammatory response, the cellular response to hormonal stimulation, the response to hypoxia, the response to metal ions, etc. MF involves membrane rafts, membrane microregions, the outer side of the plasma membrane, the lateral side of the membrane, plasma membrane rafts, presynaptic membranes, vesicles, transcriptional regulatory complexes, post-synaptic membranes, synaptic membranes, etc. KEGG analysis showed that T. wilfordii treatment of RCC involves signaling pathways such as lipid and atherosclerosis, advanced glycosylation end product-receptor for advanced glycosylation end products (AGE-RAGE), TNF, Toll-like receptor, phosphatidylinositol 3-kinase-protein kinase B (PI3K-Akt), and MAPK. The experimental validation results showed that the tumor volume was reduced after treatment with tretinoin ( P < 0.05), the expression of TP53 protein was increased ( P < 0.001), and the expression of AKT1, STAT3, TNF, JUN, MAPK8, and MAPK14 proteins were all reduced (all P < 0.001). Conclusions:In this study, the target and signaling pathways of T. wilfordii treatment of renal cell carcinoma were initially predicted, providing a reference basis for further research on its protective mechanism and clinical application.
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Objective:To explore the mechanism of action of Coptis chinensis in the treatment of dental caries using a network pharmacology approach and animal experiments. Methods:The active ingredients of C. chinensis and their targets were screened by the traditional Chinese medicine systems pharmacology (TCMSP) database and analysis platform, and the targets were searched online through the GeneCards database. The intersecting targets of C. chinensis and dental caries were screened at Venny 2.1, and the intersection targets were analyzed online for protein-protein interaction analysis and gene ontology (GO) and kyoto encyclopedia of genes and genomics (KEGG) enrichment. Then, Cytoscape was used to create a "component-target-pathway" network diagram. Rats were randomly divided into the model group and the C. chinensis group to establish a rat model of dental caries. Rats in the model group were repeatedly rubbed with a cotton ball soaked in 150 μl of 0.9% NaCl solution for 5 min, and rats in the C. chinensis group were repeatedly rubbed with a cotton ball soaked in C. chinensis (5.8 mg of C. chinensis in 150 μl of 0.9% NaCl solution) for 5 min. The two groups of rats were treated once a week for four consecutive weeks. The number of Streptococcus mutans colonies was counted, and serum serine/threonine protein kinase 1 (AKT1), JUN, interleukin-6 (IL-6), tumor necrosis factor (TNF), and B-cell lymphoma-2 (Bcl-2) were detected by enzyme immunoassay. Results:A total of 11 active ingredients in C. chinensis were found, which regulate multiple molecular pathways by intervening in 54 targets, thereby treating dental caries. Quercetin, berberine, flavodoxin, berberine infusion, and tetrahydroberberine were the core components, and AKT1, JUN, IL-6, TNF, and Bcl-2 were the core targets. GO analysis showed that BP mainly included cytokine activity, signaling receptor activator activity, signaling receptor modulator activity, cytokine receptor binding, and receptor ligand activity, etc.; and CC mainly included the response to lipopolysaccharides, the response to bacterial molecules, cellular responses to lipids, inflammatory responses, and negative regulation of cell population proliferation; MF mainly includes membrane rafts, membrane microregions, extracellular matrix, external encapsulated structures, and plasma membrane protein complexes, etc. KEGG analysis showed that advanced glycosylation end product-receptor for advanced glycosylation end products (AGE-RAGE), TNF, IL-17, Toll-like receptor, hypoxia-inducible factor-1 (HIF-1), mitogen-activated protein kinase (MAPK), nuclear factor-κB (NF-κB), epidermal growth factor receptor (EGFR), Janus kinase-signal transducer and activator of transcription (JAK-STAT), and phosphatidylinositol 3-kinase-protein kinase B (PI3K-Akt) signaling pathways have been associated with C. chinensis treatment. The results of animal experiments showed that serum Bcl-2 protein expression increased and serum AKT1, JUN, IL-6, TNF, and other proteins decreased after the C. chinensis treatment. Conclusions:C. chinensis can be involved in regulating the targets of dental caries through multiple pathways, with good therapeutic effects and a wide range of mechanisms of action, and is expected to be an important component in the development of proprietary Chinese medicines for the treatment of dental caries.
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This study aimed to explore the mechanism of Cistanches Herba in the treatment of cancer-induced fatigue(CRF) by network pharmacology combined with in vivo and in vitro experiments to provide a theoretical basis for the clinical medication. The chemical constituents and targets of Cistanches Herba were searched from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP). The targets of CRF were screened out by GeneCards and NCBI. The common targets of traditional Chinese medicine and disease were selected to construct a protein-protein interaction(PPI) network, followed by Gene Ontology(GO) functional and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analyses. A visual signal pathway rela-ted to Chinese medicine and disease targets was constructed. The CRF model was induced by paclitaxel(PTX) in mice. Mice were divided into a control group, a PTX model group, and low-and high-dose Cistanches Herba extract groups(250 and 500 mg·kg~(-1)). The anti-CRF effect in mice was evaluated by open field test, tail suspension test, and exhaustive swimming time, and the pathological morphology of skeletal muscle was evaluated by hematoxylin-eosin(HE) staining. The cancer cachexia model in C2C12 muscle cells was induced by C26 co-culture, and the cells were divided into a control group, a conditioned medium model group, and low-, medium-, and high-dose Cistanches Herba extract groups(62.5, 125, and 250 μg·mL~(-1)). The reactive oxygen species(ROS) content in each group was detected by flow cytometry, and the intracellular mitochondrial status was evaluated by transmission electron microscopy. The protein expression levels of hypoxia-inducible factor-1α(HIF-1α), BNIP3L, and Beclin-1 were detected by Western blot. Six effective constituents were screened out from Cistanches Herba. The core genes of Cistanches Herba in treating CRF were AKT1, IL-6, VEGFA, CASP3, JUN, EGFR, MYC, EGF, MAPK1, PTGS2, MMP9, IL-1B, FOS, and IL10, and the pathways related to CRF were AGE-RAGE and HIF-1α. Through GO enrichment analysis, it was found that the main biological functions involved were lipid peroxidation, nutrient deficiency, chemical stress, oxidative stress, oxygen content, and other biological processes. The results of the in vivo experiment showed that Cistanches Herba extract could significantly improve skeletal muscle atrophy in mice to relieve CRF. The in vitro experiment showed that Cistanches Herba extract could significantly reduce the content of intracellular ROS, the percentage of mitochondrial fragmentation, and the protein expression of Beclin-1 and increase the number of autophagosomes and the protein expression of HIF-1α and BNIP3L. Cistanches Herba showed a good anti-CRF effect, and its mechanism may be related to the key target proteins in the HIF-1α signaling pathway.
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Animals , Mice , Cistanche , Network Pharmacology , Beclin-1 , Reactive Oxygen Species , Plant Extracts , Drugs, Chinese Herbal/pharmacology , Molecular Docking Simulation , Medicine, Chinese Traditional , Neoplasms/geneticsABSTRACT
The material basis and mechanism of Chaenomelis Fructus in the treatment of rheumatoid arthritis(RA) were explored by network pharmacology, and the potential anti-RA targets of Chaenomelis Fructus were verified by molecular docking and animal experiments. The active components and targets of Chaenomelis Fructus were searched against the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform. GeneCards, DisGeNET, and OMIM were used to obtain RA-related targets. The common targets shared by Chaenomelis Fructus and RA were considered as the potential targets of Chaenomelis Fructus in the treatment of RA. Cytoscape 3.9.0 was employed to establish a "traditional Chinese medicine-active component-common target-disease" network. The protein-protein interaction(PPI) network was established by STRING, and the core genes were visualized by RStudio 4.1.0. DAVID was used for Gene Ontology(GO) annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment to predict and visualize the involved signaling pathways. Molecular docking was carried out with the active components screened out as ligands and RA core genes as the targets. Finally, the prediction results were verified by animal experiments. Four main active components of Chaenomelis Fructus were obtained, which corresponded to 137 targets. Chaenomelis Fructus and RA shared 37 common targets. GO annotation yielded 239 terms(P<0.05), and KEGG pathway enrichment analysis screened out 94 signaling pathways(P<0.05), mainly involving interleukin-17(IL-17), tumor necrosis factor, Toll-like receptor, and nuclear factor-kappa B(NF-κB) signaling pathways. Molecular docking results showed that the main active components of Chaenomelis Fructus bound well with the core targets of RA. The results of animal experiments proved that Chaenomelis Fructus can alleviate joint swelling in the mice with RA. The results of ELISA showed that Chaenomelis Fructus lowered the levels of interleukin-6(IL-6) and interleukin-1β(IL-1β). Western blot showed that Chaenomelis Fructus down-regulated the protein level of vascular endothelial growth factor A(VEGFA). Chaenomelis Fructus exerts anti-inflammatory effect and reduces pannus formation by regulating the core targets such as VEGFA, IL-1β, and IL6 in the treatment of RA. The findings of this study provide new ideas for the future treatment of RA with Chaenomelis Fructus.
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Animals , Mice , Network Pharmacology , Vascular Endothelial Growth Factor A , Molecular Docking Simulation , Arthritis, Rheumatoid/genetics , Tumor Necrosis Factor-alpha , NF-kappa B , Drugs, Chinese Herbal/therapeutic use , Medicine, Chinese TraditionalABSTRACT
Aim To study the protective effect of Qingjie HuaGong decoction ( QJHGD) for severe acute pancreatitis ( SAP ) model rats induced by cerulein based on TLR4/NF-kB/MYD88 pathway.Methods The effective component groups and potential targets of QJHGD were collected by network pharmacology method , and we constructed the component-target network.The GO and KEGG of important targets were enriched and analyzed by metascape database, and we selected the targeted pathways related with SAP inflammation mechanism.The rat model of severe acute pancreatitis was established by cerulein combined with lipopolysac- charide, followed by QJHGD gavage.Pancreatic tissues were observed by hematoxylin and eosin staining.We verified the therapeutic effect of QJHGD on SAP rats and the regulatory effect on TLR4/NF-kB/MyD88 target pathway, by Enzyme linked immunosorbent and immunohistochemistry methods.Results A total of 105 active components and 148 key targets for SAP were screened; KEGG was enriched 320 different channels including toll like receptor and NF-kB classical pathways.Animal experiments showed that QJHGD harl protective changes in pancreatic pathological tissues, which was observed by HE staining; QJHGD reduced amylase, lipase, 1L-6 and TNF-a in SAP rat serum, inhibiting the positive expression of key proteins on TLR4/N F- kB/MyD88 inflammatory transduction j j pathways.Conclusion The mechanisms of QJHGD protecting pancreatic injury of SAP rat may be related to reducing the expression of key proteins on TLR4/ NF-kB/MvD88 pathway.
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ObjectiveTo predict the molecular mechanism of Erxian decoction and Wenshen prescription （modified Erxian decoction） in the treatment of depression based on network pharmacology and explore the feasibility of Wenshen prescription in the treatment of depression by comparing the efficacy and mechanism of the two decoctions based on a depression model induced by maternal separation combined with chronic restraint stress. MethodActive components and targets of Erxian decoction and Wenshen prescription were collected through Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP） and Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine （BATMAN-TCM）. Targets related to depression were screened out from databases such as GeneCards， Online Mendelian Inheritance in Man database （OMIM）， and DrugBank. Common targets of drugs and disease were obtained and imported to Cytoscape 3.8.2 to plot the drug-active component-target-disease network. STRING platform was used to construct a protein-protein interaction （PPI） network and core targets and related core components were screened out. Gene Ontology （GO） enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） functional enrichment analysis were performed on common targets through Metascape platform. The depression model was induced in mice by maternal separation combined with chronic restraint stress. From the 21st day of maternal separation （PD21） to the 111th day of restraint stress completion （PD111）， mice were fed with the diet mixed with Erxian decoction or Wenshen prescription for intervention. The depressive state of mice was evaluated according to the sucrose preference test， tail suspension test， open field test， and elevated O-maze test. The expression of ionized calcium-binding adapter molecule 1 （Iba1） in the microglia was observed by immunohistochemistry （IHC）. Western blot and Real-time fluorescence-based quantitative polymerase chain reaction （Real-time PCR） were used to detect the expression levels of protein kinase B1（Akt1）， brain-derived neurotrophic factor （BDNF）， postsynaptic density-95 （PSD95）， and synaptophysin （Syn）. ResultA total of 126 and 118 targets of Erxian decoction and Wenshen prescription in the treatment of depression were screened out， with only eight more targets of Erxian decoction than Wenshen prescription. The two decoctions shared the same core targets， mainly including Akt1， interleukin-6 （IL-6）， interleukin-1β （IL-1β）， and tumor necrosis factor-α （TNF-α）. KEGG pathway enrichment analysis predicted that Erxian decoction and Wenshen prescription mainly treated depression through the phosphatidylinositol-3 kinase （PI3K）/Akt signaling pathway， mitogen-activated protein kinase （MAPK） signaling pathway， and neuroactive ligand-receptor interaction pathway. Animal experiments showed that compared with the results in the model group， Erxian decoction and Wenshen prescription could up-regulate the sucrose preference index， prolong the time spent in the central zone， increase the number of crossings， prolong the time spent in opened arm， increase the number of crossings in the opened arm， elevate the expression levels of p-Akt1， BDNF， PSD95， and Syn （P<0.05， P<0.01）， shorten the immobility time of tail suspension， and reduce the expression level of Iba-1 in the hippocampal microglia （P<0.05， P<0.01）. No significant difference between the two decoctions was found. ConclusionUnder the pathogenesis and syndrome law of depression dominated by kidney yang deficiency， Wenshen prescription modified from Erxian decoction is feasible in the treatment of depression. The mechanism may be attributed to the fact that both decoctions can improve neuroinflammation and synaptic plasticity in the hippocampus by affecting Akt1， IL-1β， IL-6， TNF-α， and other core targets and regulating the PI3K/Akt， MAPK， and neuroactive ligand-receptor interaction signaling pathways.
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ObjectiveTo predict the potential targets and mechanism of Jingfang mixture in the treatment of H1N1 influenza and provide references for clinical application of Jingfang mixture. MethodThe active components and targets of Jingfang mixture against H1N1 influenza were screened out by Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform（TCMSP），SwissTargetPrediction， and TargetNet. The targets of H1N1 influenza were obtained from GeneCards，Online Mendelian Inheritance in Man （OMIM）， and DisGeNET and standardized by UniProt KB. The intersection targets were obtained by Venny 2.1.0. The "drug-component-target" network was constructed with Cytoscape 3.2.1 and analyzed for the topological attributes. The intersection targets were uploaded to STRING 11.5 to obtain the protein-protein interaction （PPI） network. Gene Ontology （GO） enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） analysis were carried out by Metascape. Finally，the top active components ranked by degree were docked to the core targets by Autodock vina and visually analyzed by PyMOL. Balb/c female rats were used for experimental verification. Hematoxylin-eosin（HE） staining was used to observe the pathological changes in lung tissues. Enzyme-linked immunosorbent assay（ELISA）was used to detect the levels of tumor necrosis factor-α（TNF-α），interleukin-10（IL-10）， and interleukin-17（IL-17）. Real-time fluorescence-based quantitative polymerase chain reaction（Real-time PCR） and Western blot were used to detect the mRNA and protein expression levels in lung tissues. ResultThere were 144 active components in Jingfang mixture. A total of 421 target genes of Jingfang mixture and 2 956 targets of H1N1 influenza were identified，including 199 common targets. Topological analysis showed that the core components of Jingfang mixture against H1N1 influenza included quercetin，luteolin， and kaempferol，and the core targets included prostaglandin-endoperoxide synthase 2（PTGS2），estrogen receptor alpha（ESR1），inducible nitric oxide synthase 2（iNOS2），peroxisome proliferator-activated receptorγ（PPARγ），and cyclooxygenase-1（PTGS1）. GO enrichment yielded 697 items in biological process （BP） （P<0.01）， 59 items in molecular function （MF）（P<0.01）， and 21 items in cellular component （CC） （P<0.01）. A total of 132 signaling pathways （P<0.01） were obtained by KEGG enrichment analysis， including phosphatidylinositol 3-kinases（PI3K）/protein kinase B（Akt） signaling pathway and mitogen-activated protein kinase（MAPK） signaling pathway，most of which were related to the regulation of immune inflammation. Molecular docking showed that the binding energy of the active components of Jingfang mixture to the core targets was less than -5.0 kcal·mol-1，indicating good binding activity. HE staining showed that the lung tissues were significantly improved after drug intervention，and Real-time PCR and Western blot showed that Jingfang mixture could reduce the mRNA and protein expression of PI3K and Akt in lung tissues. ConclusionJingfang mixture can play an anti-viral effect against the influenza A virus through multiple components，multiple targets， and multiple pathways. The active components quercetin，luteolin， and kaempferol may control the inflammation and regulate immunity on the PI3K/Akt，MAPK， and other signaling pathways by acting on targets such as PTGS2，ESR1，iNOS2，PPARγ， and PTGS1.
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ObjectiveTo investigate the targets and mechanism of Baofeikang granules in the treatment of pulmonary fibrosis based on network pharmacology and verify the predicted mechanism based on animal experiment. MethodThe active ingredients and targets of Baofeikang granules were screened via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform， and the targets of pulmonary fibrosis were searched in various disease databases. The common targets shared by Baofeikang granules and the disease were extracted for the establishment of the protein-protein interaction （PPI） network in STRING. Cytoscape 3.8.0 was used to analyze the network topology of the key targets and to establish the ''active ingredient-target'' network. Gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analyses were performed on the core targets to explore their possible molecular mechanisms. The rats were assigned into four groups： normal group， model group， prednisone acetate group， and Baofeikang granules group. The rat model of interstitial lung fibrosis was established by tracheal instillation of bleomycin. After 21 days of gavage， the lung tissues of rats were stained with hemotoxylin and eosin （HE） for the observation of morphological changes， and phosphatidylinositol 3-kinase （PI3K） and protein kinase B （Akt） were detected via immunohistochemical （IHC） staining. ResultBased on network pharmacology， 18 key targets of Baofeikang granules were identified for the treatment of pulmonary interstitial fibrosis， including Akt1， mitogen-activated protein kinase （MAPK） 1， myelocytomatosis oncogene （MYC）， hypoxia-inducible factor-1α （HIF-1α）， cyclin-dependent kinase inhibitor 1A （CDKN1A）， epidermal growth factor receptor （EGFR）， and Runt-related transcription factor （RUNX2）. KEGG pathway enrichment predicted that Baofeikang granules exerted anti-fibrotic effect mainly through PI3K/Akt， tumor necrosis factor （TNF）， and interleukin-17 （IL-17） signaling pathways. The IHC results in animal experiment showed that the protein levels of PI3K and Akt were lower in the Baofeikang granules group than in the model group （P<0.05， P<0.01）. ConclusionBaofeikang granules has low toxicity， multiple targets， and multiple pathways in the treatment of pulmonary fibrosis. It may alleviate pulmonary fibrosis through regulating PI3K/Akt signaling pathway， so as to improve the lung function.
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ObjectiveTo explore the effective components and mechanism of Epimedii Folium in the treatment of oligoasthenotspermia by using network pharmacology and molecular docking technique. MethodThe main active components and corresponding target genes of Epimedii Folium were screened out from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP）. Target genes of oligospermia were obtained by GeneCards and Online Mendelian Inheritance in Man （OMIM） database. Uniprot was used to correct all genes. The drug-active component-key target regulatory network was constructed by Cytoscape3.9.0， and the key active components were screened out according to the degree value. The active components and common targets of the disease were uploaded to STRING 11.5 database to construct the Epimedii Folium and oligoasthenotspermia target protein-protein interaction （PPI） network， and the key protein targets were screened out according to the degree value. The key targets of gene ontology （GO） functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analysis were performed using DAVID database. Protein Data Bank （PDB） and TCMSP were used to obtain the molecular structure of target proteins and active components. AutoDock Vina 1.1.2 was used to perform molecular docking of the active components and the core protein targets. Finally， icariin， the active component of Epimedii Folium， was used to intervene in the rat model of oligoasthenotspermia to verify the effect of icariin on the expression level of protein targets. ResultTwenty-three active components from Epimedii Folium were screened out， and 50 common targets and 6 core targets of oligoasthenotspermia and Epimedii Folium were obtained， including tumor protein p53 （TP53）， epidermal growth factor receptor （EGFR）， prostaglandin-endoperoxide synthase 2 （PTGS2）， cysteine aspartate-specific protease （Caspase）-3， erb-b2 receptor tyrosine kinase 2 （ERBB2）， and caspase-9. Through GO enrichment and KEGG pathway enrichment analysis， the active components of Epimedii Folium were mainly involved in the P53 signaling pathway， the pathways in cancer， cell proliferation， and apoptosis， etc. Molecular docking results indicated that icariin， quercetin， and 8-isopentenol had strong binding ability to target protein. The results of icariin intervention experiment showed that as compared with the control group， the expression of target proteins in testis of rats with oligoasthenotspermia was significantly down-regulated. As compared with the model group， icariin significantly up-regulated the expression of target protein in testis of rats with oligoasthenotspermia （P<0.05）. ConclusionEpimedii Folium treats oligoasthenotspermia through regulating the P53 signaling pathway， the pathways in cancer， cell proliferation， and apoptosis by icariin， quercetin， and 8-isopentenol.
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ObjectiveTo explore the effective components and mechanism of Epimedii Folium in the treatment of oligoasthenotspermia by using network pharmacology and molecular docking technique. MethodThe main active components and corresponding target genes of Epimedii Folium were screened out from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP）. Target genes of oligospermia were obtained by GeneCards and Online Mendelian Inheritance in Man （OMIM） database. Uniprot was used to correct all genes. The drug-active component-key target regulatory network was constructed by Cytoscape3.9.0， and the key active components were screened out according to the degree value. The active components and common targets of the disease were uploaded to STRING 11.5 database to construct the Epimedii Folium and oligoasthenotspermia target protein-protein interaction （PPI） network， and the key protein targets were screened out according to the degree value. The key targets of gene ontology （GO） functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analysis were performed using DAVID database. Protein Data Bank （PDB） and TCMSP were used to obtain the molecular structure of target proteins and active components. AutoDock Vina 1.1.2 was used to perform molecular docking of the active components and the core protein targets. Finally， icariin， the active component of Epimedii Folium， was used to intervene in the rat model of oligoasthenotspermia to verify the effect of icariin on the expression level of protein targets. ResultTwenty-three active components from Epimedii Folium were screened out， and 50 common targets and 6 core targets of oligoasthenotspermia and Epimedii Folium were obtained， including tumor protein p53 （TP53）， epidermal growth factor receptor （EGFR）， prostaglandin-endoperoxide synthase 2 （PTGS2）， cysteine aspartate-specific protease （Caspase）-3， erb-b2 receptor tyrosine kinase 2 （ERBB2）， and caspase-9. Through GO enrichment and KEGG pathway enrichment analysis， the active components of Epimedii Folium were mainly involved in the P53 signaling pathway， the pathways in cancer， cell proliferation， and apoptosis， etc. Molecular docking results indicated that icariin， quercetin， and 8-isopentenol had strong binding ability to target protein. The results of icariin intervention experiment showed that as compared with the control group， the expression of target proteins in testis of rats with oligoasthenotspermia was significantly down-regulated. As compared with the model group， icariin significantly up-regulated the expression of target protein in testis of rats with oligoasthenotspermia （P<0.05）. ConclusionEpimedii Folium treats oligoasthenotspermia through regulating the P53 signaling pathway， the pathways in cancer， cell proliferation， and apoptosis by icariin， quercetin， and 8-isopentenol.
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ObjectiveTo investigate the targets and mechanism of Baofeikang granules in the treatment of pulmonary fibrosis based on network pharmacology and verify the predicted mechanism based on animal experiment. MethodThe active ingredients and targets of Baofeikang granules were screened via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform， and the targets of pulmonary fibrosis were searched in various disease databases. The common targets shared by Baofeikang granules and the disease were extracted for the establishment of the protein-protein interaction （PPI） network in STRING. Cytoscape 3.8.0 was used to analyze the network topology of the key targets and to establish the ''active ingredient-target'' network. Gene ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analyses were performed on the core targets to explore their possible molecular mechanisms. The rats were assigned into four groups： normal group， model group， prednisone acetate group， and Baofeikang granules group. The rat model of interstitial lung fibrosis was established by tracheal instillation of bleomycin. After 21 days of gavage， the lung tissues of rats were stained with hemotoxylin and eosin （HE） for the observation of morphological changes， and phosphatidylinositol 3-kinase （PI3K） and protein kinase B （Akt） were detected via immunohistochemical （IHC） staining. ResultBased on network pharmacology， 18 key targets of Baofeikang granules were identified for the treatment of pulmonary interstitial fibrosis， including Akt1， mitogen-activated protein kinase （MAPK） 1， myelocytomatosis oncogene （MYC）， hypoxia-inducible factor-1α （HIF-1α）， cyclin-dependent kinase inhibitor 1A （CDKN1A）， epidermal growth factor receptor （EGFR）， and Runt-related transcription factor （RUNX2）. KEGG pathway enrichment predicted that Baofeikang granules exerted anti-fibrotic effect mainly through PI3K/Akt， tumor necrosis factor （TNF）， and interleukin-17 （IL-17） signaling pathways. The IHC results in animal experiment showed that the protein levels of PI3K and Akt were lower in the Baofeikang granules group than in the model group （P<0.05， P<0.01）. ConclusionBaofeikang granules has low toxicity， multiple targets， and multiple pathways in the treatment of pulmonary fibrosis. It may alleviate pulmonary fibrosis through regulating PI3K/Akt signaling pathway， so as to improve the lung function.
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Based on network pharmacology, the mechanism of Polygoni Cuspidati Rhizoma et Radix-Ligustri Lucidi Fructus(PL) combination against acute gouty arthritis(AGA) was explored and preliminarily verified by animal experiment. The chemical components and corresponding targets of PL were retrieved from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP). The active components with oral bioavailability(OB)≥30% and drug-likeness(DL)≥0.18 were screened based on literature, and the related protein targets were collected. Then the protein targets were standardized with the help of UniProt database. The AGA-related targets were searched from GeneCards, NCBI, and DrugBank. The common targets of the disease and the medicinals were yielded by FunRich V3, and the protein-protein interaction(PPI) network was constructed to screen the key targets, followed by Gene Ontology(GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis of the key targets. Afterwards, some of the key targets were verified by sodium urate crystal-induced AGA mouse model. A total of 25 active components and 287 targets of PL, 811 targets of AGA, and 88 common targets were screened out. PPI network analysis showed that tumor necrosis factor(TNF), interleukin-6(IL-6), and interleukin-1β(IL-1β) may be the core targets of PL in the treatment of AGA. The key targets were mainly involved in 566 GO terms(P<0.05), including multiple biological processes such as inflammatory response and immune response. Moreover, they were related to 116 KEGG pathways and these pathways were involved in inflammation and immunity, mainly including NOD-like receptor signaling pathway and TNF signaling pathway. Animal experiment confirmed that PL can alleviate ankle swelling, improve abnormal gait, and down-regulate the protein expression of TNF-α, IL-6, and IL-1β in AGA mice, indicating that PL can treat AGA through TNF-α, IL-6, and IL-1β and the feasibility of network pharmacology to predict drug targets. This study preliminarily discussed the key targets and biological signaling pathways involved in the treatment of AGA with PL combination, which reflected the multi-pathway and multi-target action characteristics of Chinese medicine. Moreover, this study laid a scientific basis for research on the treatment of AGA with PL combination, as well as the mechanism of action.
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Animals , Mice , Arthritis, Gouty/drug therapy , Drugs, Chinese Herbal/therapeutic use , Ligustrum , Network Pharmacology , RhizomeABSTRACT
UPLC-Q-TOF-MS combined with network pharmacology and experimental verification was used to explore the mechanism of acupoint sticking therapy(AST) in the intervention of bronchial asthma(BA). The chemical components of Sinapis Semen, Cory-dalis Rhizoma, Kansui Radix, Asari Radix et Rhizoma, and Zingiberis Rhizoma Recens were retrieved from TCMSP as self-built database. The active components in AST drugs were analyzed by UPLC-Q-TOF-MS, and the targets were screened out in TCMSP and Swiss-TargetPrediction. Targets of BA were collected from GeneCards, and the intersection of active components and targets was obtained by Venny 2.1.0. The potential targets were imported into STRING and DAVID for PPI, GO, and KEGG analyses. The asthma model induced by house dust mite(HDM) was established in mice. The mechanism of AST on asthmatic mice was explored by pulmonary function, Western blot, and flow cytometry. The results indicated that 54 active components were obtained by UPLC-Q-TOF-MS and 162 potential targets were obtained from the intersection. The first 53 targets were selected as key targets. PPI, GO, and KEGG analyses showed that AST presumedly acted on SRC, PIK3 CA, and other targets through active components such as sinoacutine, sinapic acid, dihydrocapsaicin, and 6-gingerol and regulated PI3 K-AKT, ErbB, chemokine, sphingolipid, and other signaling pathways to intervene in the pathological mechanism of BA. AST can improve lung function, down-regulate the expression of PI3 K and p-AKT proteins in lung tissues, enhance the expression of PETN protein, and reduce the level of type Ⅱ innate immune cells(ILC2 s) in lung tissues of asthmatic mice. In conclusion, AST may inhibit ILC2 s by down-regulating the PI3 K-AKT pathway to relieve asthmatic airway inflammation and reduce airway hyperresponsiveness.
Subject(s)
Animals , Mice , Acupuncture Points , Asthma/drug therapy , Drugs, Chinese Herbal , Immunity, Innate , Lymphocytes , Network PharmacologyABSTRACT
A fundamental challenge that arises in biomedicine is the need to characterize compounds in a relevant cellular context in order to reveal potential on-target or off-target effects. Recently, the fast accumulation of gene transcriptional profiling data provides us an unprecedented opportunity to explore the protein targets of chemical compounds from the perspective of cell transcriptomics and RNA biology. Here, we propose a novel Siamese spectral-based graph convolutional network (SSGCN) model for inferring the protein targets of chemical compounds from gene transcriptional profiles. Although the gene signature of a compound perturbation only provides indirect clues of the interacting targets, and the biological networks under different experiment conditions further complicate the situation, the SSGCN model was successfully trained to learn from known compound-target pairs by uncovering the hidden correlations between compound perturbation profiles and gene knockdown profiles. On a benchmark set and a large time-split validation dataset, the model achieved higher target inference accuracy as compared to previous methods such as Connectivity Map. Further experimental validations of prediction results highlight the practical usefulness of SSGCN in either inferring the interacting targets of compound, or reversely, in finding novel inhibitors of a given target of interest.
Subject(s)
Drug Delivery Systems , Proteins , TranscriptomeABSTRACT
Objective To screen and verify hub genes TPM1 and CALD1 that can affect the diagnosis and prognosis of bladder cancer (BLCA). Methods We obtained gene chip expression data of 414 and 188 cases of bladder cancer from TCGA and GEO, respectively. By constructing a weighted gene co-expression network analysis (WGCNA) and identifying differentially-expressed genes between tumor tissues and normal tissues, the pivotal genes that were highly associated with bladder cancer were obtained, and the STRING database was used to construct a protein interaction network to screen out prognostic-related pivotal genes. We took 29 cases of bladder cancer samples from People's Hospital of Zhengzhou as external verification results. Results A total of 915 and 464 differentially-expressed genes were screened from the TCGA database and GSE13507, respectively. Two modules with the strongest correlation were obtained through WGCNA: the blue module (Pearson cor=0.60, P=1E-44) and the cyan module (Pearson cor=0.52, P=7E-19), and 156 intersection genes were obtained. Through protein interaction network analysis, 10 pivotal genes were screened out. TPM1 and CALD1 genes had the greatest correlation with the survival of bladder cancer patients, which was verified by external experimental verification group. Conclusion TPM1 and CALD1 are closely related to the prognosis of bladder cancer patients. They are also pivotal genes to promote tumor progression.
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Objective To study the phase correlation of cutaneous multichannel impedance measurements and the contractions, peristalsis of stomach and the conduction properties in space.Methods A spiral gastric body model was rotated to simulate shrinkage and creep of the stomach.In order to verify the feasibility and validity of the multichannel impedance gastric dynamic measurement, experiments with emulation of multichannel impedance gastric motility measuring principle were conducted through three-dimensional simulation on the electrical characteristics of gastric body model in saline tank simulator.Results The emulation results showed that the change of epigastric current density and potential distribution is consistent with the course of moving from top to bottom when lateral edge of model (namely the intumescent location when the stomach is full) after detecting electrodes in sequence.Meanwhile, the measurement voltage wave forms clearly showed the contraction location of stomach after the model rotating for three cycles in a row, and the phase relationship between adjacent measurement channels was also measured.The sixty seconds data acquired by the experiment device proved that voltage wave form of three measurement channels corresponded to the phase relationship of movement status of the gastric body model.Conclusions Cutaneous multichannel wave forms prove a cyclical movement of stomach, and phase difference among the multichannel signals relating to speed of peristaltic wave, position of the measuring electrodes and channel spacing, etc.This study provides simulation and experimental basis for explanation of quantitative study of conduction properties in space and phase relationship between the results of surface multichannel impedance measurements and the contractions, peristalsis of stomach.