Potential Mechanism of Action of Qiangxin Decoction （强心汤） for Chronic Heart Failure Based on Network Pharmacology and Molecular Docking / 中医杂志

ObjectiveTo reveal the targets and molecular mechanisms of the action of Qiangxin Decoction （强心汤） for the treatment of chronic heart failure based on the combination of network pharmacology and molecular docking. MethodsThe active ingredients of Qiangxin Decoction were retrieved from TCMSP database， and the targets of chronic heart failure were screened by searching GeneCards， OMIM， TTD， PharmGkb， and DrugBank databases， and the intersections were taken to obtain the intersecting targets of Qiangxin Decoction for the treatment of chronic heart failure. STRING platform was used to construct the protein-protein interaction network （PPI）， Cytoscape 3.8.0 software was used to calculate the network topology to screen the core targets， and R 4.2.3 was used to construct the “active ingredient-target” network by analyzing the GO enrichment analysis and KEGG pathway enrichment analysis. AutoDock 1.5.7 was used for molecular docking to predict the binding performance of active ingredients and core targets. ResultsSeventy-five intersecting targets were identified for the treatment of chronic heart failure with Qiangxin Decoction， among which the core targets were estrogen receptor 1 （ESR1， degree value=7）， nuclear receptor coactivator 1 （NCOA1， degree value=8）， glucocorticoid receptor （NR3C1， degree value=7）， and nuclear receptor coactivator 2 （NCOA2， degree value=7）. GO enrichment analysis showed that the top 3 items with the smallest P value in molecular function were G protein-coupled amine receptor activity， postsynaptic neurotransmitter receptor activity， and neurotransmitter receptor activity （P＜0.01）； the top 3 items with the smallest P value in biological process were adenylyl cyclase-activated adrenergic receptor signaling pathway， adrenergic receptor signaling pathway， and adenylyl cyclase-regulated G protein-coupled receptor signaling pathway （P＜0.01）； the top 3 items with the smallest P values in cellular composition were components of the postsynaptic membrane， synaptic membrane， and presynaptic membrane （P＜0.01）. KEGG enrichment analysis showed that the top 5 key signaling pathways were neuroactive ligand-receptor interactions， calcium signaling pathway， dopaminergic synapses， cocaine addiction， and cyclic guanosine monophosphate-protein kinase G （cGMP-PKG） signaling pathway. The molecular docking results showed that lignans and isoflavones had lower binding energies and more structural stability with the four core targets （ESR1， NCOA1， NR3C1， NCOA2）. ConclusionThe treatment of chronic heart failure by Qiangxin Decoction was associated with neuroactive ligand-receptor interactions， calcium signaling pathway， dopaminergic synapses， chemoattractant-receptor activation， cGMP-PKG signaling pathway， lipids and atherosclerosis， and cAMP signaling pathway， and lignans and isoflavones may be the core active compounds in its treatment of chronic heart failure.

Study on the mechanism of Dihuang Decoction in treating Alzheimer disease and diabetes mellitus with same method based on network pharmacology / 国际中医中药杂志

Objective:To study the common pharmacodynamic substance basis and potential mechanism of Dihuang Decoction in treating Alzheimer disease (AD) and diabetes mellitus (DM) with same method based on network pharmacology; To provide bioinformatics basis.Methods:The effective components of Dihuang Decoction were retrieved through Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and CNKI. The drug targets were obtained by combining and UniProt database. The targets of AD and DM related diseases were obtained by GeneCards, OMIM and TTD databases respectively. Cytoscape 3.7.1 software was used to construct the Disease - drug - component - target network. R studio software was used to construct a Circos diagram of the effective compounds and disease targets.Protein-protein interaction (PPI) network was constructed using STRING platform. GO enrichment and KEGG enrichment analysis was conducted through DAVID database, Metascape, R Studio software.Results:A total of 206 active components were obtained; PPI network construction screened 51 key targets; GO enrichment analysis revealed the functions of GABA, cholinergic synapse, estrogen response, BCL-2 family protein complex and so on; KEGG enrichment analysis revealed FoxO signaling pathway, HIF-1 signaling pathway, insulin resistance pathway and other pathways.Conclusion:Dihuang Decoction has the synergistic characteristics of multiple components, multiple targets and multiple pathways in treating AD and DM with same method, mainly through proanthocyanidin B7, proanthocyanidin B5, proanthocyanidin B1 and other active ingredients, acting on TNF, IL-6, ESR1, PPARG, AKT1 and other targets, regulating FoxO signaling pathway, HIF-1 signaling pathway, etc.

Mechanism of Dahuang Mudantang in Improving Pancreatic Injury in Rats with Acute Pancreatitis of Dampness-heat in Large Intestine Syndrome Based on Network Pharmacology and Experimental Verification / 中国实验方剂学杂志

ObjectiveTo reveal the intervention effect of Dahuang Mudantang on pancreatic injury in rats with acute pancreatitis （AP） of dampness-heat in large intestine syndrome and explore its possible mechanism based on network pharmacology. MethodNinety-six SPF-grade Wistar rats were randomly divided into the following six groups： a blank group， a model group， low-， medium-， and high-dose Dahuang Mudantang groups （3.5， 7， and 14 g·kg-1）， and a Qingyi Lidan granules group （3 g·kg-1）， with 16 rats in each group. The AP model of dampness-heat in large intestine syndrome was induced in rats except for those in the blank group by "high-temperature and high-humidity environment + high-sugar and high-fat diet + retrograde injection of 5% sodium taurocholate into the pancreaticobiliary duct". The blank and model groups received equal volumes of distilled water by gavage， while the treatment groups were administered Dahuang Mudantang or Qingyi Lidan granules 1 hour before modeling， and 12 and 24 hours after modeling. Samples were collected 1 hour after the last administration. The general conditions of the rats were observed. The AP model of dampness-heat in large intestine syndrome was evaluated. Serum amylase （AMS） and C-reactive protein （CRP） levels were determined using biochemical methods. Pancreatic tissue morphology was observed using hematoxylin-eosin （HE） staining. Network pharmacology was employed to predict potential targets of Dahuang Mudantang in the intervention in AP， and molecular biology technique was used to verify relevant targets. ResultCompared with the blank group， the model group exhibited lethargy， unkempt fur， loose and foul-smelling stools， elevated anal temperature with arching and twisting reactions， significantly increased serum levels of AMS and CRP （P<0.05）， abnormal pancreatic ductules， disordered interlobular spaces， and inflammatory cell infiltration in histopathological examination， as well as pathological changes including pancreatic acinar cell swelling， congestion， and necrosis. Compared with the model group， the treatment groups showed varying degrees of improvement in general survival conditions， reduced twisting reactions， visibly improved stool characteristics， reduced pancreatic tissue edema and necrosis， decreased serum AMS and CRP levels （P<0.05）， with the high-dose Dahuang Mudantang group showing the most pronounced effects （P<0.05）. Network pharmacology prediction indicated that hederagenin， β-sitosterol， and quercetin were the most widely connected active compounds with disease targets. Protein-protein interaction （PPI） network analysis revealed that protein kinase B （Akt）， tumor protein P53 （TP53）， tumor necrosis factor （TNF）， interleukin-6 （IL-6）， transcription factor （JUN）， vascular endothelial growth factor α （VEGFα）， interleukin-1β （IL-1β）， and vascular cell adhesion molecule-1 （VCAM1） were key targets in the "drug-disease" interaction. KEGG enrichment analysis suggested that the response of the mitogen activated protein kinase （MAPK） signaling pathway might be a core mechanism for DHMDT in the intervention in AP. Molecular biology analysis showed that compared with the blank group， the model group had significantly increased levels of TNF-α， IL-6， and VCAM-1 in pancreatic tissue （P<0.05）， as well as significantly elevated expression levels of p38 mitogen-activated protein kinase （p38 MAPK）， mitogen-activated protein kinase-activated protein kinase 2 （MK2）， and human antigen R （HUR） genes and proteins （P<0.05）. Compared with the model group， the treatment groups exhibited decreased levels of TNF-α， IL-6， and VCAM-1 in pancreatic tissue （P<0.05）， reduced expression levels of p38 MAPK， MK2， and HUR genes and proteins， with the high-dose Dahuang Mudantang group showing the most pronounced effects （P<0.05）. ConclusionDahuang Mudantang activates and regulates the p38 MAPK/MK2/HUR signaling pathway to suppress the release of inflammatory factors， thereby improving pancreatic injury.

Effective constituents of essential oil from Gleditsiae Fructus Abnormalis and anti-cerebral ischemia/reperfusion injury mechanism: based on GC-MS, network pharmacology, and experimental verification / 中国中药杂志

Based on GC-MS and network pharmacology, the active constituents, potential targets, and mechanism of essential oil from Gleditsiae Fructus Abnormalis(EOGFA) against cerebral ischemia/reperfusion(I/R) injury were explored, and the effective constituents were verified by experiment. To be specific, GC-MS was used identify the constituents of the volatile oil. Secondly, the targets of the constituents and disease were predicted by network pharmacology, and the drug-constituent-target network was constructed, followed by Gene Ontology(GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment of the core targets. Molecular docking was performed to investigate the binding affinity between the active constituents and the targets. Finally, SD rats were used for experimental verification. The I/R injury model was established, and the neurological behavior score, infarct volume, and pathological morphology of brain tissue were measured in each group. The content of interleukin-1β(IL-1β), interleukin-6(IL-6), and tumor necrosis factor-alpha(TNF-α) was determined by enzyme-linked immunosorbent assay(ELISA), and the protein expression of vascular endothelial growth factor(VEGF) by Western blot. A total of 22 active constituents and 17 core targets were screened out. The core targets were involved in 56 GO terms and the major KEGG pathways of TNF signaling pathway, VEGF signaling pathway, and sphingolipid signaling pathway. Molecular docking showed that the active constituents had high affinity to the targets. The results of animal experiment suggested that EOGFA can alleviate the neurological impairment, decrease the cerebral infarct volume and the content of IL-1β, IL-6 and TNF-α, and down-regulate the expression of VEGF. The experiment verified the part results of network pharmacology. This study reflects the multi-component, multi-target, and multi-pathway characteristics of EOGFA. The mechanism of its active constituents is related to TNF and VEGF pathways, which provides a new direction for in-depth research on and secondary development of Gleditsiae Fructus Abnormalis.

Research of the mechanism of Huganning tablet in the treatment of nonalcoholic fatty liver disease based on network pharmacology and computer-aided drug design / 药学学报

In this study, we explored the mechanism of Huganning tablet (HGNP) in the treatment of nonalcoholic fatty liver disease (NAFLD) based on network pharmacology and computer-aided drug design. Firstly, the potential ingredients and targets of HGNP were identified from TCMSP database, Swiss Target Prediction database, Chinese pharmacopoeia (2015) and literatures, and then the targets of HGNP intersected with NAFLD disease targets that obtained in GeneCards database to acquired potential targets. The bioconductor bioinformatics package of R software was used for gene ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis. The network of “potential ingredient-key target-pathway” was formed in Cytoscape software to study the interactions between potential ingredients of HGNP, key targets, pathways and NAFLD. Based on the results of network pharmacology, the molecular docking analysis of the key targets and potential active ingredients in HGNP tablets with top degree in the network was conducted using Discovery Studio 2020 software, followed by molecular dynamics simulations, binding free energy calculation, drug-likeness properties analysis and ADMET (absorption, distribution, metabolism, excretion and toxicity) properties prediction. In vitro, HepG2 cells were used to establish steatosis model, and the effects of five key compounds on hepatocyte steatosis were analyzed by oil red O staining and triglyceride (TG) content determination. The results showed that 141 ingredients and 151 potential targets were obtained. A total of 2 526 items and 151 pathways were identified by GO and KEGG enrichment analysis. The molecular docking suggested that five components, isorhamnetin, salvianolic acid B, emodin, resveratrol and rhein, exhibited strong binding ability with key targets [retinoic acid receptor RXR-alpha (RXRA), tumor necrosis factor (TNF), glycogen synthase kinase-3 beta (GSK3B), serine/threonine-protein kinase 1 (AKT1)]. It was further verified that isorhamnetin and salvianolic acid B bind to key targets with good structural stability and binding affinity based on molecular dynamics simulations and binding free energy calculations. The drug-likeness properties, pharmacokinetic properties and toxicity of five key compounds were more comprehensively analyzed through drug-likeness properties analysis and ADMET properties prediction. In vitro, all five compounds, isorhamnetin, salvianolic acid B, emodin, resveratrol, and rhein, improved hepatocyte steatosis of HepG2 cells, confirming the reliability of the present study. In conclusion, based on network pharmacology, computer-aided drug design and in vitro validation, this study investigated the mechanism of HGNP for the treatment of NAFLD at multiple levels and provided a basis for its clinical application.

Effect and mechanism of Bovis Calculus on ulcerative colitis by inhibiting IL-17/IL-17RA/Act1 signaling pathway / 中国中药杂志

This study aimed to elucidate the effect and underlying mechanism of Bovis Calculus in the treatment of ulcerative colitis(UC) through network pharmacological prediction and animal experimental verification. Databases such as BATMAN-TCM were used to mine the potential targets of Bovis Calculus against UC, and the pathway enrichment analysis was conducted. Seventy healthy C57BL/6J mice were randomly divided into a blank group, a model group, a solvent model(2% polysorbate 80) group, a salazosulfapyridine(SASP, 0.40 g·kg~(-1)) group, and high-, medium-, and low-dose Bovis Calculus Sativus(BCS, 0.20, 0.10, and 0.05 g·kg~(-1)) groups according to the body weight. The UC model was established in mice by drinking 3% dextran sulfate sodium(DSS) solution for 7 days. The mice in the groups with drug intervention received corresponding drugs for 3 days before modeling by gavage, and continued to take drugs for 7 days while modeling(continuous administration for 10 days). During the experiment, the body weight of mice was observed, and the disease activity index(DAI) score was recorded. After 7 days of modeling, the colon length was mea-sured, and the pathological changes in colon tissues were observed by hematoxylin-eosin(HE) staining. The levels of tumor necrosis factor-α(TNF-α), interleukin-1β(IL-1β), interleukin-6(IL-6), and interleukin-17(IL-17) in colon tissues of mice were detected by enzyme-linked immunosorbent assay(ELISA). The mRNA expression of IL-17, IL-17RA, Act1, TRAF2, TRAF5, TNF-α, IL-6, IL-1β, CXCL1, CXCL2, and CXCL10 was evaluated by real-time polymerase chain reaction(RT-PCR). The protein expression of IL-17, IL-17RA, Act1, p-p38 MAPK, and p-ERK1/2 was investigated by Western blot. The results of network pharmacological prediction showed that Bovis Calculus might play a therapeutic role through the IL-17 signaling pathway and the TNF signaling pathway. As revealed by the results of animal experiments, on the 10th day of drug administration, compared with the solvent model group, all the BCS groups showed significantly increased body weight, decreased DAI score, increased colon length, improved pathological damage of colon mucosa, and significantly inhibited expression of TNF-α,IL-6,IL-1β, and IL-17 in colon tissues. The high-dose BCS(0.20 g·kg~(-1)) could significantly reduce the mRNA expression levels of IL-17, Act1, TRAF2, TRAF5, TNF-α, IL-6, IL-1β, CXCL1, and CXCL2 in colon tissues of UC model mice, tend to down-regulate mRNA expression levels of IL-17RA and CXCL10, significantly inhibit the protein expression of IL-17RA,Act1,and p-ERK1/2, and tend to decrease the protein expression of IL-17 and p-p38 MAPK. This study, for the first time from the whole-organ-tissue-molecular level, reveals that BCS may reduce the expression of pro-inflammatory cytokines and chemokines by inhibiting the IL-17/IL-17RA/Act1 signaling pathway, thereby improving the inflammatory injury of colon tissues in DSS-induced UC mice and exerting the effect of clearing heat and removing toxins.

Mechanism of Yanghe Decoction against subcutaneous tumor in pulmonary metastasis from breast cancer through HIF-1α signaling pathway regulating glycolysis:based on network pharmacology and animal experiment / 中国中药杂志

This study aims to explore the mechanism of Yanghe Decoction(YHD) against subcutaneous tumor in pulmonary metastasis from breast cancer, which is expected to lay a basis for the treatment of breast carcinoma with YHD. The chemical components of medicinals in YHD, and the targets of the components were retrieved from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP) and SwissTargetPrediction. The disease-related targets were searched from GeneCards and Online Mendelian Inheritance in Man(OMIM). Excel was employed to screen the common targets and plot the Venn diagram. The protein-protein interaction network was constructed. R language was used for Gene Ontology(GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment. A total of 53 female SPF Bablc/6 mice were randomized into normal group(same volume of normal saline, ig), model group(same volume of normal saline, ig), and low-dose and high-dose YHD groups(YHD, ig, 30 days), with 8 mice in normal group and 15 mice in each of the other groups. Body weight and tumor size was measured every day. Curves for body weight variation and growth of tumor in situ were plotted. In the end, the subcutaneous tumor sample was collected and observed based on hematoxylin and eosin(HE) staining. The mRNA and protein levels of hypoxia inducible factor-1α(HIF-1α), pyruvate kinase M2(PKM2), lactate dehydrogenase A(LDHA), and glucose transporter type 1(GLUT1) were detected by PCR and Western blot. A total of 213 active components of YHD and 185 targets against the disease were screened out. The hypothesis that YHD may regulate glycolysis through HIF-1α signaling pathway to intervene in breast cancer was proposed. Animal experiment confirmed that the mRNA and protein levels of HIF-1α, PKM2, LDHA, and GLUT1 in the high-and low-dose YHD groups were lower than those in the model group. YHD has certain inhibitory effect on subcutaneous tumor in pulmonary metastasis from breast cancer in the early stage, which may intervene pulmonary metastasis from breast cancer by regulating glycolysis through HIF-1α signaling pathway.

Mechanism of Qilongtian Capsules in treatment of acute lung injury based on network pharmacology prediction and experimental validation / 中国中药杂志

This study aimed to explore the mechanism of Qilongtian Capsules in treating acute lung injury(ALI) based on network pharmacology prediction and in vitro experimental validation. Firstly, UPLC-Q-TOF-MS/MS was used to analyze the main chemical components of Qilongtian Capsules, and related databases were used to obtain its action targets and ALI disease targets. STRING database was used to build a protein-protein interaction(PPI) network. Metascape database was used to conduct enrichment analysis of Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG). AutoDock software was used to perform molecular docking verification on the main active components and key targets. Then, the RAW264.7 cells were stimulated with lipopolysaccharide(LPS) for in vitro experiments. Cell viability was measured by MTT and ROS level was measured by DCFH-DA. NO content was measured by Griess assay, and IL-1β, IL-6, and TNF-α mRNA expression was detected by RT-PCR. The predicted targets were preliminarily verified by investigating the effect of Qilongtian Capsules on downstream cytokines. Eighty-four compounds were identified by UPLC-Q-TOF-MS/MS. Through database retrieval, 44 active components with 589 target genes were screened out. There were 560 ALI disease targets, and 65 intersection targets. PPI network topology analysis revealed 10 core targets related to ALI, including STAT3, JUN, VEGFA, CASP3, and MMP9. KEGG enrichment analysis showed that Qilongtian Capsules mainly exerted an anti-ALI effect by regulating cancer pathway, AGE-RAGE, MAPK, and JAK-STAT signaling pathways. The results of molecular docking showed that the main active components in Qilongtian Capsules, including crenulatin, ginsenoside F_1, ginsenoside Rb_1, ginsenoside Rd, ginsenoside Rg_1, ginsenoside Rg_3, notoginsenoside Fe, notoginsenoside G, notoginsenoside R_1, notoginsenoside R_2, and notoginsenoside R_3, had good binding affinities with the corresponding protein targets STAT3, JUN, VEGFA, CASP3, and MMP9. Cellular experiments showed that Qilongtian Capsules at 0.1, 0.25, and 0.5 mg·mL~(-1) reduced the release of NO, while Qilongtian Capsules at 0.25 and 0.5 mg·mL~(-1) reduced ROS production, down-regulated mRNA expression of IL-1β, IL-6, TNF-α, and inhibited the inflammatory cascade. In summary, Qilongtian Capsules may exert therapeutic effects on ALI through multiple components and targets.

Exploration of potential molecular mechanism of Chuanxiong in treatment of tension-type headache based on network pharmacology and molecular docking / 中国药理学通报

Aim To analyze the active ingredients of Chuanxiong, predict its target and signaling pathways in the treatment of tension-type headache, and clarify its therapeutic mechanism based on the principle of network pharmacology.Methods The effective active ingredients in Chuanxiong were retrieved from the Chinese herbal system pharmacology platform(TCMSP), and were performed by the ADME screen to collect the potential targets; the existing tension-type headache-related disease targets were collected through the GeneCards database.The targets corresponding to the active ingredients were intersected to obtain the common target as the key target.Cytoscape was used to construct and analyze the visual "drug-active ingredient-target-disease" network, and the String database was used to construct the PPI protein interaction network; through R language the GO function and KEGG pathway enrichment of common targets in the form of bubble graphs were analyzed.Lastly, molecular docking was used for preliminary verification.Results Finally 7 active ingredients, 105 compound targets and 2 139 tension-type headache-related target genes were obtained.There were 54 nodes in the protein interaction network.GO functional enrichment analysis yielded 215 entries, and KEGG pathway enrichment analysis yielded 68 signaling pathways.Molecular docking showed that FA, Chuanxiong quinone, sitosterol, ligustalin had strong affinity with CASP3, MAPK1, MAPK14.Conclusions It is suggested that Chuanxiong may treat tension-type headaches through anti-inflammatory, antioxidant and cytoprotective effects.

The mechanism of Belamcanda chinensis in the treatment of glioma based on network pharmacology and molecular simulation / 西安交通大学学报(医学版)

【Objective】 To explore the potential molecular biological mechanism of Belamcanda chinensis in the treatment of glioma based on network pharmacology, molecular docking technology and in vitro cell experiments. 【Methods】 ① The active components, targets of Belamcanda chinensis and targets of glioma were obtained by database search. String database was used to analyze protein-protein interaction relationship, R project was used to analyze gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Cytoscape software was used to build "compound-target-disease" network and PPI network, and AutoDock software was used to verify molecular docking. ② Western blotting, qRT-PCT and apoptosis assay were used to verify the enrichment results of network pharmacology targets and protein pathway. 【Results】 ① We screened out 32 types of active components, 484 types of targets and 464 types of glioma targets, and obtained 62 kinds of therapeutic targets after mapping. We obtained 12 kinds of key pharmacodynamic molecules such as Isoiridogermanal, Iridobelamal A and Rhamnazinand and other key pharmacodynamic molecules, as well as AKT1, STAT3, HRAS and other core targets by network topology analysis. Enrichment analysis results demonstrated that they were mainly involved in biological processes such as peptide serine phosphorylation, protein kinase B signal transduction, peptide serine modification, and pathways including PI3K/AKT signal pathway and Rap1 signal pathway. The results of molecular docking verified the good binding activity of the key pharmacodynamic molecules with the core targets. ② The results of Western blotting showed that the protein expressions of VEGF and MMP9 of Belamcanda chinensis extracts in 8 mg/mL and 16 mg/mL groups were significantly lower than those in the blank control group (P<0.01 or P<0.001). Compared with the blank control group, the early apoptosis rate of Belamcanda chinensis extracts at 8 mg/mL and 16 mg/mL were significantly decreased (P<0.001 or P<0.000 1). qRT-PCR results showed that the mRNA expression levels of VEGF and MMP9 in Belamcanda chinensis extracts at 8 mg/mL and 16 mg/mL were significantly decreased (P<0.001 or P<0.0001). 【Conclusion】 The treatment of glioma with Belamcanda chinensis is the result of multi-component, multi-target and multi-channel interactions. The results of cell experiments confirmed that Belamcanda chinensis extracts can affect the expressions of related target proteins of PI3K/AKT signal pathway and VEGF and MMP9, which verified the results of network pharmacology. The results provide a theoretical basis for the clinical application of Belamcanda chinensis and studies on glioma.

Mechanism of Xiaoyong Sanjie Formula treating non-puerperal mastitis based on network pharmacology / 国际中医中药杂志

Objective:Based on network pharmacology and molecular docking to explore the targets and mechanism of Xiaoyong Sanjie Formula treating Non-Puerperal Mastitis (NPM).Methods:By retrieving the active components and the corresponding target information of each component in Xiaoyong Sanjie Formula with Pharmacology Database and Analysis Platform of Chinese Medicine System (TCMSP), and NPM-related genes in database like GeneCard, OMIM, PharmGkb, TTD, and DrugBank, the data of the core targets of Xiaoyong Sanjie Formula and disease-related genes was compared to obtain intersecting genes, and the STRING database was used to analyze the protein interaction network and find the core genes. With the help of Cytoscape 3.8.0, the active ingredient-target-pathway regulation network diagram of Xiaoyong Sanjie Formula for the treatment of NPM was established. The R language pack was used to enrich the targets with GO function and KEGG pathway enrichment, and the potential targets and mechanism of Xiaoyong Sanjie Formula in the treatment of NPM were explored. Finally, molecular docking verification was carried out to analyze the effecacy of key components and potential core targets of Xiaoyong Sanjie Formula.Results:Network pharmacological analysis showed that there were 47 active component and 1 692 NPM-related potential targets in Xiaoyong Sanjie Formula, and 235 core targets of NPM in the treatment of Xiaoyong Sanjie Formula. The key components of Xiaoyong Sanjie Formula in the treatment of NPM include Quercetin, Naringenin, Kaempferol, Diosgenin, Luteolin, etc., with the core targets of intercellular adhesion molecule-1 (ICAM-1), vascular endothelial growth factor (VEGFA), tumor necrosis factor (TNF), interleukin-6 (IL-6), Epidermal growth factor receptor (EGFR), interleukin-1β (IL-1B), chemokine-8 (CXCL8), chemokine-2 (CCL2), etc. GO enrichment obtained 1 492 biological process entries. The KEGG pathway is enriched to obtain 105 pathways, including the TNF signaling pathway, the PI3K-Akt signaling pathway, the NF-kappa B signaling pathway, and the JAK-STAT signaling pathway, IL-17 signaling pathway, C-type lectin receptor signaling pathway, etc. The final molecular docking verified that the key active ingredients of Xiaoyong Sanjie Formula could bind with the potential core targets closely.Conclusion:Xiaoyong Sanjie Formula can treat NPM with multi-component, multi-target characteristics,which plays a role of treating NPM through signaling pathways such as immuno-inflammatory response, the metabolism of the medicine, cellular adaptive stress response, and vascular function regulation.

Study on the molecular mechanism of Qifang Weitong granules in treating gastric cancer based on network pharmacology / 国际中医中药杂志

Objective:To analyze the potential mechanism of Qifang Weitong granules in the treatment of gastric cancer based on network pharmacology and molecular docking method.Methods:TCMSP, TCMID, and Swiss Target Prediction databases were used to screen out the chemical components and related targets of Qifang Weitong Granules. GeneCards and OMIM databases were used to screen out the gastric cancer targets to obtain common targets of this disease and Qifang Weitong Granules and upload them to STRING database to form a PPI network, and obtain the key targets and analyze the correlation between the key targets and gastric cancer in Oncomine tumor database. In addition, the regulatory network of gastric cancer and Qifang Weitong Granules was constructed by using Cytoscape software, and the CluoGO plug-in and R language of Cytoscape software were used to perform GO and KEGG enrichment analysis on the key targets. The possibility of the binding between the molecules of this medicine and targeted molecules is verified by molecular docking.Results:There were 168 medicinal chemical components obtained in Qifang Weitong Granules, 2 803 gastric cancer targets, and 49 common targets. In the regulatory network of gastric cancer and Qifang Weitong Granules, β-sitosterol, formononet, stigmasterol have higher values of chemical composition. The key targets in the PPI network are MAPK8, FOS, AR, etc. The GO enrichment analysis focused on the positive regulation of mitochondrial outer membrane permeability in the apoptosis signaling pathway, while the KEGG enrichment analysis is significantly enriched in apoptosis access. The result of molecular docking showed good binding and stable conformation.Conclusion:Qifang Weitong Granules can induce the expression of genes and proteins related to gastric cancer, show its effect by affecting the level of hormones, cell apoptosis and other biological processes, and activating the apoptosis signal pathway.

Study on molecular mechanism of Zuojin Pills for gastroesophageal reflux disease based on network pharmacology / 国际中医中药杂志

Objective:To analyze the possible mechanism of Zuojin Pills on gastroesophageal reflux disease based on network pharmacology. Methods:By searching for the active constituent and protein targets of Zuojin Pills in TCMSP database,the protein names were converted into gene names in Uniprot database. Cytoscape 3.7.1 was used to draw the active constituent-target-medicine network diagram of Zuojin Pills and analyze the topological parameters. Then find the target of gastroesophageal reflux disease through OMIM,GeneCards,DRUGBANK database, find the intersection target of medicine and disease, perform PPI network analysis on the intersection target in STRING 11.0, and use the Metascape database to enrich the intersection target for further analysis. Cytoscape 3.7.1 was used to draw a network diagram of the active constituent- target-pathway of the medicine and to conduct a topology parameter analysis. Results:The main active constituent of Zuojin Pills in the treatment of gastroesophageal reflux disease are quercetin, Evodiamine, R-tetrahydroberberine, 1-methyl-2-nonyl-4-quinolone, berberine, etc. Targets include PTGS2, NOS3, MAPK1, EGFR, TNF, IL6, ERBB2, VEGFA, EGF, IL1B, etc., and these processes are mainly completed through inflammatory response, cancer, cell proliferation and apoptosis, cell connection, etc. Conclusions:The treatment of gastroesophageal reflux disease with Zuojin Pills is a complex process with multiple constituent, multiple targets, and multiple pathways. It is hoped that it which could provide reference for the future research on its mechanism of action.

Explore Potential Molecular Mechanism of Gegen Qinliantang in Intervention of Atherosclerosis Based on Network Pharmacology and Molecular Docking / 中国实验方剂学杂志

ObjectiveThis study aims to explore the potential molecular mechanism of Gegen Qinliantang （GQL） in the intervention of atherosclerosis （AS） based on network pharmacology and molecular docking. MethodThe active components and targets of each medicinal in GQL were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform （TCMSP）， and AS-related genes from 7 databases. Thereby， the anti-AS targets of GQL were screened out. Cytoscape 3.8.0 was employed to construct the "component-target" network， and STRING the protein-protein interaction （PPI） network. Core targets were screened out with CytoNCA. R clusterProfiler was used for Gene Ontology （GO） term enrichment and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment of target genes， which were then visualized. Finally， molecular docking of the top ten active components with the core targets of AS was performed and the binding affinity was compared with that between atorvastatin and the core targets. ResultIn the end， 150 active components of GQL， 20 289 AS targets， and 213 common targets were retrieved， and 48 core common targets were screened out. They were mainly involved in the GO terms of nuclear receptor activity， ligand activation， and transcription factor activity and the pathways of fluid shear force and AS， advanced glycation end products-receptor for advanced glycation end products （AGE/RAGE）， interleukin-17 （IL-17）， tumor necrosis factor （TNF）， Toll-like receptor pathways and other signaling pathways closely related to AS. The molecular docking results showed that the effective components of GQL had high binding affinity to core targets of AS， and the binding affinity was even higher than that between the atorvastatin and core targets. The five groups with high binding affinity were puerarin-TNF， baicalein-inducible nitric oxide synthase 2 （NOS2）， puerarin-NOS2， and formononetin-NOS2， wogonin-NOS2. ConclusionThe above result provides new ideas for further exploration of this classical decoction.

Mechanism of Sinitang against Myocardial Ischemia-reperfusion Injury： Prediction Based on Network Pharmacology and Verification by Cellular Experiments / 中国实验方剂学杂志

ObjectiveTo predict the mechanism of Sinitang in treating myocardial ischemia-reperfusion injury （MI/RI） based on network pharmacology and verify the prediction results by cellular experiments. MethodThe traditional Chinese medicine system pharmacology database and analysis platform （TCMSP） was employed for retrieval of the main components and potential targets of Sinitang. Online Mendelian Inheritance in Man （OMIM） and GeneCards were employed to obtain the targets of Sinitang in treating MI/RI. STRING was employed to construct the protein-protein interaction （PPI） network， and DAVID to perform gene ontology （GO） annotation and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment. Finally， cellular experiments were carried out to verify the predicted anti-MI/RI mechanism of Sinitang. ResultA total of 105 active ingredients and 234 targets of Sinitang were screened out， among which 116 targets were predicted to be involved in the treatment of MI/RI. The GO annotation gave 587 entries， including 417 biological process entries， 101 cell component entries， and 69 molecular function entries. The KEGG analysis enriched 125 signaling pathways， involving vascular endothelial growth factor （VEGF）， phosphoinositide 3-kinase/protein kinase B （PI3K/Akt）， forkhead box transcription factor O （FoxO）， hypoxia-inducible factor-1 （HIF-1） apoptosis and other signaling pathways. The results of cell viability assay showed that Sinitang increased the survival rate of H9C2 cells damaged by hypoxia/reoxygenation （H/R）. Sinitang decreased the levels of tumor necrosis factor-α （TNF-α）， interleukin-6 （IL-6）， and creatine kinase-MB （CK-MB） in H9C2 cells damaged by H/R. The results of flow cytometry demonstrated that Sinitang decreased the apoptosis rate of H9C2 cells damaged by H/R. Western blot showed that Sinitang down-regulated the expression of Bcl-2 related X protein （Bax） and up-regulated that of B-cell lymphoma-2 （Bcl-2） in H/R-injured H9C2 cells. ConclusionSinitang treats MI/RI in a multi-target and multi-pathway manner， which involves the signaling pathways associated with apoptosis.

Molecular mechanism of Spatholobi Caulis in treatment of ovarian cancer based on network pharmacology and experimental verification / 中国中药杂志

The present study explored the main active ingredients and the underlying mechanism of Spatholobi Caulisin the treatment of ovarian cancer(OC) by network pharmacology, molecular docking, and in vitro cell experiments. The active ingredients and their predicted targets(AITs) were first acquired online with the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP). Theoretical disease targets(DTs) were obtained through professional databases including GeneCards, OMIM, PharmGkb, TTD, and DrugBank. The common targets in the intersection of AITs and DTs were used for the construction of a "drug-ingredient-disease-target" network by Cytoscape 3.7.1. STRING database was used to construct a protein-protein interaction(PPI) network. R 4.0.5 was used for GO and KEGG functional enrichment analyses. Schr9 dinger Maestro was used to perform and optimize the molecular docking and virtual screening.Twenty-three active ingredients of Spatholobi Caulis were screened out, involving 75 OC targets and 178 signaling pathways.Network analysis revealed that Spatholobi Caulis presumedly exerted an anti-OC effect by acting on key protein targets such as GSK-3β, Bcl-2, and Bax. Molecular docking showed that GSK-3β possessed goodbinding activity to prunetin. In vitro cell experiments preliminarily verified the core targets and pathways of prunetin, the active ingredient of Spatholobi Caulis against human OC SKOV3 cells.CCK-8 assay was used to detect the cell proliferation, and flow cytometry was used to detect the effect of prunetin on apoptosis of human OC SKOV3 cells.The expression of prunetin targets and related regulatory proteins was detected by Western blot.In vitro cell experiments demonstrated that prunetindisplayed significant inhibitory effects on the proliferation of OC cells and could induce apoptosis of SKOV3 cells. Western blot showed that prunetin could induce SKOV3 cell apoptosis by inhibiting GSK-3β phosphorylation and regulating the expression of downstream Bcl-2 and Bax proteins. This study reveals the scientific nature of network pharmacology in the prediction and guidance of experimental design, confirming that prunetin can treat OC by blocking the GSK-3β/Bcl-2/Bax cell signal transduction pathway. The findings are expected to provide a basis for the investigation of the mechanism of Spatholobi Caulis in the treatment of OC.

Molecular mechanism of Ganoderma against gastric cancer based on network pharmacology and experimental test / 中国中药杂志

This study aims to explore the molecular mechanism of Ganoderma against gastric cancer based on network pharmacology, molecular docking, and cell experiment. The active components and targets of Ganoderma were retrieved from Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform(TCMSP), and gastric cancer-related targets from GeneCards and Online Mendelian Inheritance in Man(OMIM). The protein-protein interaction(PPI) network of the common targets was constructed with STRING, followed by Gene Ontology(GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis of the common genes based on Bioconductor and R language. The medicinal-disease-component-target network and medicinal-disease-component-target-pathway network were established by Cytoscape. Molecular docking was performed between β-sitosterol(the key component in Ganoderma) and the top 15 targets in the PPI network. Cell experiment was performed to verify the findings. A total of 14 active components and 28 targets of Ganoderma were retrieved, and the medicinal and the disease shared 25 targets, including caspase-3(CASP3), caspase-8(CASP8), caspase-9(CASP9), and B-cell lymphoma-2(BCL2). The common targets involved 72 signaling pathways and apoptosis and p53 signaling pathway may play a crucial role in the effect of Ganoderma against gastric cancer. β-sitosterol had strong binding activity to the top 15 targets in the PPI network. The in vitro cell experiment demonstrated that β-sitosterol inhibited gastric cancer AGS cell proliferation by inducing cell apoptosis and cell cycle arrest in the S phase, which might be related to the regulation of the p53 pathway. This study shows the multi-component, multi-target, and multi-pathway characteristics of Ganoderma against gastric cancer, which lays a scientific basis for further research on the molecular mechanism.

Study on protective mechanism of kaempferol against cerebral ischemia/reperfusion injury in vitro and in vivo / 中国药房

OBJECTIVE To explore the protective mechanism of kaempferol （KAE）on cerebral ischemia/reperfusion （CI/R） injury in vitro and in vivo . METHODS Firstly，the potential targets of KAE in the treatment of CI/R injury were preliminarily screened by network pharmacology. AutoDock Vina software was used to conduct molecular docking between KAE and the top 10 core targets ，and the binding affinity was used as the evaluation standard to further clarify the possible mechanism of KAE in treating CI/R injury. Finally ，the above results were verified by in vivo and in vitro experiments. The oxygen glucose deprivation/ reperfusion（OGD/R）HT22 cell injury model and the middle cerebral artery occlusion （MCAO）rat model were constructed. The cell activity was detected by CCK- 8 method. The neural function score and TTC staining were performed on the rats and their brain tissues. The phosphorylation levels of protein kinase B （Akt）and Src in HT 22 cells and brain tissue of rats were detected by Western blot. RESULTS The results of network pharmacology screening showed that KAE in the treatment of CI/R injury was closely related to 10 core targets including prostaglandin-endoperoxide synthase 2，matrix metalloproteinase 9，JUN，Akt1，tumor necrosis factor ，caspase-3，mitogen activated protein kinase 8，intercellular cell adhesion molecule 1，vascular cell adhesion molecule 1 and Src. The results of molecular docking showed that KAE was stably bound with Akt 1 and Src . The results of in vitro and in vivo experiments showed that KAE could significantly improve the survival rate of OGD/R-injuried HT 22 cells （P＜0.05）， significantly reduced the neurological function score of MCAO model rats （P＜0.05），significantly reduces the volume of cerebral infarction in rats （P＜0.05），and significantly increased the phosphorylation levels of Akt and Src in HT 22 cells and brain tissue of rats（P＜0.05），which showed a dose dependent trend. CONCLUSIONS KAE may play a neuroprotective role by regulating the phosphorylation expression of Akt and Src ，thus treating CI/R injury.

Xueshuantong improves cerebral microcirculation disorder: action mechanism based on network pharmacology and experimental validation / 药学学报

This study is to explore the mechanism of Xueshuantong improving cerebral microcirculation disorder through the combination of network pharmacology and experimental validation in vivo. Structural formulas of main Panax notoginseng saponins, including notoginsenoside R1, and ginsenoside Rg1, Re, Rb1 and Rd were obtained from Pubchem website and their potential targets were predicted by Swiss Target Prediction database. Potential molecular targets of brain microcirculation disorder were acquired from OMIM and GeneCards database. The overlapped molecular targets between the drug and disease were analyzed. Protein interaction analysis and topology maps were constructed through the STRING online analysis platform and Cytoscape software. Core action targets were selected. GO function and KEGG pathway were analyzed by DAVID database. Immunohistochemical method was used to examine the expression of platelet endothelial cell adhesion molecule-1 (CD31) in the ischemic cortex of middle cerebral artery occlusion and reperfusion (MCAO/R) rats. The levels of mRNA and protein expressions of core action targets in MCAO/R model rats′ brain microvessels were verified by RT-qPCR and Western blot. Based on network pharmacology, 242 targets of Xueshuantong, 425 targets of brain microcirculation disorder, and 35 overlapped targets were obtained. The potential key targets of Xueshuantong, protein kinase B (AKT1), vascular endothelial growth factor A (VEGFA), caspase 3 (CASP3), matrix metallopeptidase 9 (MMP-9), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), signal transducer and activator of transcription 3 (STAT3) involved in the alleviation of cerebral microcirculation disorder were obtained by setting degree and betweenness centrality as screening parameters. Xueshuantong at the dose of 48 mg·kg-1 was shown to significantly improve the injury of neurological behaviors, as well as the density and morphology of microvessels of MCAO/R model rats. Xueshuantong could down-regulate the mRNA levels of AKT1, MMP-9, and STAT3, increase the protein expression levels of CD31, phosphorylated AKT and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K), and the ratio of B-cell lymphoma 2/Bcl-2-associated X (Bcl-2/Bax), but decrease the protein expression levels of MMP-9, cleaved caspase-3 and phosphorylated STAT3. In summary, Xueshuantong could improve ischemic cerebral microcirculation disorder and thereby reduce nerve damage in ischemia-reperfusion rats by regulating signaling pathways related with PI3K, AKT, MMP-9, STAT3 and caspase-3 in microvessels. The study strictly adhered to all ethical protocols that experimental animals should follow in the course of medical research.

Exploring the therapeutic mechanism of Longqi Fang for diabetic kidney disease based on network pharmacology and verification in rats / 南方医科大学学报

OBJECTIVE@#To study the therapeutic mechanism of Longqi Fang (LQF) for diabetic kidney disease (DKD) based on GEO database and network pharmacology.@*METHODS@#LQF and DKD targets were obtained using the databases including GEO, TCMSP, CNKI, ChemDraw, and SwissTarget Prediction, and LQF-DKD intersection targets were obtained with VENNY. String was used for protein-protein interaction (PPI) analysis, and R package for KEGG and GO enrichment analysis. Cytoscape 3.7.2 software Network graphs were constructed. The results of network pharmacology analysis were verified in SD rat models of DKD by daily treatment of the rats with LQF at low (1 g/kg), medium (2 g/kg), and high (2 g/kg) doses, and kidney pathology was observed with HE staining and the changes in renal function were assessed. Western blotting was used to detect the expression levels of NF-κB and p-NF-κB proteins.@*RESULTS@#We identified 760 main targets of LQF, and obtained 1026 differential genes using GEO database and 61 LQF-DKD intersection targets using Venny database. The core targets obtained through PPI network analysis included Myc, EGF, CASP3, VEGFA, CCL2, SPP1, VCAM1 and ICAM1. Go analysis showed that LQF affects mainly nuclear receptor activity and ligand activated transcription factor activity. KEGG analysis showed that LQF affects inflammatory signaling pathways by interfering with NF-κB, TNF, and PI3K-AKT. In rat models of DKD, treatment with LQF resulted in significant improvements of the renal functions (P < 0.05) and glomerular and tubular structure and arrangement in a dose-dependent manner. Western blotting results showed that LQF dose-dependently downregulated NF-κB and p-NF-κB expressions in the rat models.@*CONCLUSION@#The therapeutic mechanism of LQF for DKD involves multiple components, targets and signal pathways that mediate an inhibitory effect on NF-κB signaling pathway to protect the renal function.