Traditional Chinese Medicine Systems Pharmacology Research Articles

Causal associations of tea consumption on risk of pancreatic adenocarcinoma and the mediating role of vascular endothelial growth factor D levels.

Tea is one of the most widely consumed beverages in the world. However, the association between tea and risk of pancreatic adenocarcinoma remains controversial. This study aimed to investigate the causal relationship between tea consumption and risk of pancreatic adenocarcinoma and to explore their mediating effects. The two-sample Mendelian randomisation (MR) analysis showed an inverse causal relationship between tea intake and pancreatic adenocarcinoma (OR: 0·111 (0·02, 0·85), P < 0·04). To examine the mediating effects, we explored the potential mechanisms by which tea intake reduces the risk of pancreatic adenocarcinoma. Based on the oral bioavailability and drug-like properties in Traditional Chinese Medicine Systems Pharmacology database, we selected the main active ingredients of tea. We screened out the fifteen representative targeted genes by Pharmmapper database, and the gene ontology enrichment analysis showed that these targeted genes were related to vascular endothelial growth factor (VEGF) pathway. The two-step MR analysis of results showed that only VEGF-D played a mediating role, with a mediation ratio of 0·230 (0·066, 0·394). In conclusion, the findings suggest that VEGF-D mediates the effect of tea intake on the risk of pancreatic adenocarcinoma.

Systematic review of Buzhong Yiqi method in alleviating cancer-related fatigue: a meta-analysis and exploratory network pharmacology approach

ObjectivesCancer-related fatigue (CRF) is a prevalent and distressing symptom experienced by many cancer patients, necessitating effective treatments. This study utilizes meta-analysis and network pharmacology to comprehensively assess the efficacy of the Buzhong Yiqi prescription in alleviating cancer-related fatigue and to preliminarily explore the mechanism of its core drugs.MethodsWe included randomized controlled trials (RCTs) in cancer patients. The inclusion criteria encompassed a diagnosis of cancer-related fatigue, without limitation on cancer type, the experimental group receiving Buzhong Yiqi prescription, the control group receiving conventional treatment, patients awaiting treatment, and articles published in either English or Chinese. We conducted a search through 29 February 2024, across PubMed, Cochrane Database of Systematic Reviews, Cochrane Controlled Clinical Trials (CENTRAL), China Biomedical Literature Service (CBM), China National Knowledge Infrastructure (CNKI), WANFANG Database, and Weipu Database (VIP). Journal articles that met the inclusion criteria were selected for inclusion. Two independent investigators evaluated the quality of the included studies. A meta-analysis was performed utilizing the Stata 12.0 software package, where estimates of cancer-related fatigue were aggregated through the application of a random-effects model. We employed the Cochrane Risk of Bias Tool to evaluate potential biases in RCTs. The primary outcome measures utilized to assess the efficacy and safety of CRF treatment comprised the Revised Piper Fatigue Scale (PFS-R) and the Quality of Life Questionnaire Core 30 (EORTC QLQ-C30). The secondary outcomes encompassed the KPS score, the effective rate, the TCM syndrome score, and an evaluation of adverse reactions. The Traditional Chinese Medicine Systems Pharmacology (TCMSP) was utilized to identify the active ingredients and targets of BZD. Additionally, the Drug bank, Therapeutic Target Database (TTD), DiaGeNET, and GeneCards databases were utilized to retrieve relevant targets for CRC. The Venn diagram was employed to identify overlapping targets. Cytoscape software was utilized to construct a network of “herb-ingredient-target” and identify core targets. GO and KEGG pathway enrichment analyses were performed using R language software.ResultsIn comparison to the control group, patients with CRF who received BZYQ prescription exhibited marked improvements in KPS score, QLQ-C30 quality of life score, and effective rate. Conversely, PFS, TCM syndrome score, and adverse reaction assessments significantly decreased. The primary active ingredients in its core drugs may exert a positive therapeutic effect on CRF by targeting molecules such as AKT1, IL6, IL1B, PTGS2, CASP3, ESR1, and BCL2, as well as through signaling pathways including TNF, IL17, TLR, NF-κB, and C-type lectin receptor.ConclusionBZYQ demonstrates significant efficacy in treating CRF with minimal adverse reactions. It can serve as a fundamental treatment for CRF in clinical practice, and the medication can be tailored to individual patients for personalized therapy. The potential pharmacological mechanism of BZYQ in treating CRF, as predicted by network pharmacology, offers a molecular foundation for clinical CRF treatment.Systematic Review Registration:https://inplasy.com, identifier INPLASY202430025

Network pharmacology and experimental verification unraveled the mechanism of Bailing Capsule against asthma.

Asthma is a serious public health challenge around the world. Recent studies into traditional Chinese medicine preparations for asthma have yielded promising findings regarding Bailing Capsule's potential in bronchial asthma prevention and treatment. This study aims to initially clarify the potential mechanism of Bailing Capsule in the treatment of asthma using network pharmacology and in vitro experimental approaches. Network pharmacology was adopted to detect the active ingredients of Bailing Capsule via Traditional Chinese Medicine Systems Pharmacology Database, and the key targets and signaling pathways in the treatment of asthma were predicted. Docking and molecular dynamics simulations were conducted to verify the most important interactions formed by these probes within different regions of the binding site. The predicted targets were validated in lipopolysaccharide-induced 16HBE cell experiment. Seven active ingredients were screened from Bailing Capsule, 294 overlapping targets matched with asthma were considered potential therapeutic targets, such as SRC, TP53, STAT3, and E1A binding protein P300. The main functional pathways involving these key targets include phosphatidylinositol 3-kinase/protein kinase B, mitogen-activated protein kinase, renin-angiotensin system and other signaling pathways, which were mainly involved in the inflammatory response, apoptosis, and xenobiotic stimulus. Moreover, molecular docking showed that Cerevisterol have higher affinity for SRC, TP53, STAT3, and E1A binding protein P300 than other main active components, which is close to the docking results of the co-crystallized ligands to proteins. Consequently, Cerevisterol was selected for molecular dynamics simulation and the results show that Cerevisterol can bind most tightly to SRC, TP53, and STAT3. Bailing Capsule can promote the growth of 16HBE cell, reduce the production of IL-4, TNF-α and IL-6, and down-regulate the levels of SRC and STAT3 mRNA. This study preliminarily reveals the potential mechanism of Bailing Capsule against asthma with the aid of network pharmacology and in vitro cell experiment, which provided reference and guidance for in-depth research and clinical application.

Elucidating the Mechanisms of Astragalus Membranaceus in Colorectal Cancer Patients through Bioinformatics Analysis.

Astragalus membranaceus has shown positive clinical efficacy in treating colorectal cancer (CRC). This study aimed to identify the key active components of Astragalus and determine effective targets of these components in CRC patients. We identified active components of Astragalus membranaceus and differentially expressed genes in traditional Chinese medicine systems pharmacology database and The Cancer Genome Atlas. Additionally, the enrichment analysis of differential target genes (DTGs) was performed using the R-package clusterProfiler. Immunocyte correlation analysis and non-coding regulatory network construction were performed for biomarkers using Spearman's method and NetworkAnalyst. Finally, molecular docking of biomarkers and their corresponding molecule drugs was done with Autodock Vina software. We identified 20 active components of Astragalus membranaceus and 1 403 target genes through screening. A total of 2 300 differentially expressed genes, and 3 035 hub genes in CRC were screened. The integration of the target genes with the significantly differentially expressed genes and Hub genes identified resulted in a total of 86 DTGs. Subsequently, the results showed 828 enriched GO biological processes, 184 enriched GO molecular functions, 59 enriched GO cellular components, and 46 enriched KEGG pathways. We also obtained a total of 143 PPI pairs involving 67 nodes. Additionally, we constructed 45 mRNA-TF pairs, 101 miRNA-mRNA pairs, and 200 miRNA- mRNA-TF triplets. Finally, molecular docking was performed for the active component quercetin with F2 and UGT1A1 and formic acid with FGA, AHSG, and KNG1. This study identified the active components of Astragalus membranaceus and their corresponding targets in CRC. These findings provide robust evidence for precision drug therapy in patients with CRC.

Banxia xiexin decoction prevents the development of gastric cancer.

In China banxia xiexin decoction (BXD) has been used in treating gastric cancer (GC) for thousands of years and BXD has a good role in reversing GC histopathology, but its chemical composition and action mechanism are still unknown. To investigate the mechanism of action of BXD against GC based on transcriptomics, network pharmacology, in vivo and in vitro experiments. The transplanted tumor model was prepared, and the nude mouse were pathologically examined after administration, and hematoxylin-eosin staining was performed. The active ingredients of BXD were quality controlled and identified using ultra-performance liquid chromatography tandem quadrupole electrostatic field orbitrap mass spectrometry (UPLC-Q-Orbitrap MS/MS), and traditional Chinese medicines systems pharmacology platform, drug bank and the Swiss target prediction platform to predict the relevant targets, the differentially expressed genes (DEGs) of GC were screened by RNA-seq sequencing, and the overlapping targets were analyzed to obtain the key targets and pathways. Cell Counting Kit-8, apoptosis assay, cell migration and Realtime fluorescence quantitative polymerase chain reaction were used for in vitro experiments. All dosing groups inhibited the growth of transplanted tumors in laboratory-bred strain nude, with the capecitabine group and the BXD medium-dose group being the best. A total of 29 compounds and 859 potential targets in BXD were identified by UPLC-Q-Orbitrap MS/MS and network pharmacology, RNA-seq sequencing found 4767 GC DEGs, which were combined with network pharmacology and analyzed 246 potential therapeutic targets were obtained and pathway results showed that BXD may against GC through the Phosphoinositide 3-kinase (PI3K)/protein kinase B (AKt) signaling pathway. In vitro cellular experiments confirmed that BXD-containing serum and LY294002 could inhibit the proliferation of GC cells, promote apoptosis, and inhibit the migration of GC cells by decreasing the expression of EGFR, PIK3CA, IL6, BCL2 and AKT1 in the PI3K-Akt pathway in MGC-803 expression. BXD has the effect of inhibiting tumor growth rate and delaying the development of GC. Its mechanism of action may be related to the regulation of PI3K-Akt signaling pathway.

Therapeutic Effects of Zanthoxyli Pericarpium on Intestinal Inflammation and Network Pharmacological Mechanism Analysis in a Dextran Sodium Sulfate-Induced Colitis Mouse Model.

(1) Background: IBD (inflammatory bowel disease) is characterized by chronic intestinal inflammation leading to persistent symptoms and a lack of effective treatments. ZP (Zanthoxyli Pericarpium) has been used in traditional Chinese medicine for its anti-inflammatory and antioxidant properties for the management of intestinal disorders. (2) Methods: This study aimed to investigate the components of ZP, their specific targets, and associated diseases using the TCMSP (Traditional Chinese Medicine Systems Pharmacology) analysis platform, TCMBank database, and ETCM2.0 (Encyclopedia of Traditional Chinese Medicine 2.0) database. Additionally, we explored the protective effects of ZP on the colon and the underlying molecular mechanisms in the treatment of IBD. (3) Results: We identified 59 compounds in ZP that target 38 genes related to IBD, including PTGS2, PPARG, and GPBAR1. In a mice model of DSS (dextran sodium sulfate)-induced colitis, ZP significantly reduced colonic epithelial damage and oxidative stress markers, such as iNOS and nitrotyrosine, demonstrating its antioxidant properties. (4) Conclusions: These findings suggest that ZP has protective effects against DSS-induced colonic damage owing to its anti-inflammatory and antioxidant properties, making it a potential candidate for IBD treatment. However, further research and clinical trials are required to confirm its therapeutic potential and safety in humans.

Based on Spectrum-Effect Relationship, Network Pharmacology, and Molecular Docking, the Material Basis and Mechanism of Antioxidant Effect of Miao Medicine Indigofera stachyoides Lindl Were Studied.

Indigofera stachyoides Lindl (IS.Lindl, Xuerensen in Chinese) is a traditional medicine frequently utilized by ethnic minorities; nevertheless, the chemicals responsible for these effects have not been identified. Ultraperformance liquid chromatography (UPLC) was utilized to establish the fingerprints of various origins. Free radical scavenging in 1,1-diphenyl-2-trinitrophenylhydrazine (DPPH) and 2,2-biazobis(3-ethyl-phenylpropylthiazole-6-sulfonate) diammonium salt (ABTS) assays was used to evaluate the antioxidant activity. Partial least-squares regression analysis (PLSR) and gray correlation analysis (GRA) were utilized to determine the spectral-effect relationship in order to screen the antioxidant pharmacodynamic components. The corresponding targets were obtained from Traditional Chinese Medicine Systems Pharmacology (TCMSP) and Integrated Traditional Chinese Medicine (ITCM). Disease-related targets for antioxidants were collected from GeneCards and Online Mendelian Inheritance in Man (OMIM) databases. The PPI interaction network analysis, GO enrichment analysis, and KEGG pathway analysis were established using the online analysis platform, and Autodock software assisted in aligning the components with important targets. The fingerprint profile revealed 32 common peaks, and eight standards were identified using standard comparison, with similarity ranging from 0.920 to 0.995. The primary antioxidant components include proanthocyanidin B1, epicatechin, and proanthocyanidin B3. Important targets include EGFR, CASP3, IL6, PTGS2, and TNF. Important signaling pathways include the AGE-RAGE signaling pathways in diabetic complications, the MAPK signaling pathway, the IL-17 signaling pathway, and the pathways in cancer. The results of molecular docking technology showed that the main active ingredients of the drug could bind well to the core target. In this study, we successfully established the spectral-effect relationship of IS.Lindl and clarified the effective substances of IS.Lindl. Through network pharmacology and molecular docking methods, it was clear that IS.Lindl plays an antioxidant role through multicomponent, multitarget, and multipathway synergy.

Genetic and therapeutic for oral lichen planus and diabetes mellitus: a comprehensive study

BackgroundThis study employed a bidirectional Mendelian Randomization (MR) approach to explore the causal relationships between Oral Lichen Planus (OLP), diabetes mellitus (DM), and glycemic control. It also aims to identify potential pharmacological and herbal treatments that effectively address both OLP and the metabolic dysfunctions associated with DM.MethodsThis study employs a two-way MR approach to investigate the potential causal relationships between diabetes type and glycated hemoglobin (HbA1c) levels, and the risk of OLP. We analyzed differentially expressed genes from the OLP dataset in the Genomics Expression Omnibus (GEO) database, cross-referencing these with HbA1c-related genes for enrichment analysis. Additionally, the Drug-Gene Interaction Database (DGIdb) and Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) were utilized to assess the effectiveness of specific drugs, herbs, and ingredients in treating OLP while managing blood glucose levels.ResultsThe MR analysis revealed a significant association between Type 1 Diabetes mellitus (T1DM) and an increased risk of OLP, unlike Type 2 Diabetes mellitus (T2DM). This finding indicates a unique immunological interaction in T1DM that may predispose individuals to OLP. The drug prediction analysis focused on core targets linked to OLP and HbA1c, evaluating the therapeutic potential of retinoic acid, prednisone, and thalidomide for treating OLP and regulating blood glucose levels. Additionally, herbal medicines such as Ecliptae herbaand Amygdalus communis vas, along with herbal ingredients like quercetin, luteolin, and 17-beta-estradiol, were identified for their anti-inflammatory properties and potential to mitigate metabolic dysfunction in diabetes.ConclusionThe study highlighted a complex interplay between diabetes and OLP, underscoring the efficacy of integrated therapeutic strategies that target both conditions. The findings suggest that both pharmaceutical and herbal treatments can effectively manage the clinical manifestations of OLP and associated metabolic challenges. This holistic approach to treatment could significantly enhance patient outcomes by addressing the interconnected aspects of these chronic conditions.

Multi-Target Mechanisms of Si-Ni-San on Anxious Insomnia: An Example of Network-pharmacology and Molecular Docking Analysis.

Based on comprehensive network-pharmacology and molecular docking analysis, this study was intended to unveil the multiple mechanisms of Si-Ni-San (SNS) in treating anxious insomnia. The compounds of SNS were meticulously analyzed, selected and standardized with references to their pharmacological attributes. The components included chaihu (Bupleurum chinense DC.), baishao (Paeonia lactiflora Pall.), zhishi (Citrus aurantium L.) and gancao (Glycyrrhiza uralensis Fisch. ex DC.). We used the Traditional Chinese Medicine System Pharmacology (TCMSP) Database, Traditional Chinese Medicines Integrated Database (TCMID), GeneCards database, therapeutic target database (TTD) and comparative toxicogenomic database (CTD) to construct the components-compounds-targets networks and used Cytoscape 3.9.1 software to visualize the outcome. Afterwards, the STRING database and Cytoscape 3.9.1 software were utilized to construct and visualize the protein-protein interaction (PPI) network analysis. In addition, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were also conducted through the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The molecular docking program was carried out using AutoDock 4.2 software to understand interactions between target receptors and compound ligands selected for study. We thoroughly sorted and filtered 31 pharmacologically active compounds from SNS. Subsequently, several potential target genes were predicted, of which there were 59 target genes distinctly associated with anxious insomnia. The PPI analysis indicated that the core target proteins included AKT1, IL6, TNF, SLC6A4, MAOA and GABRA2. The results of our study indicated that SNS potentially remediates anxious insomnia by reducing inflammation, neurodegeneration, and cell apoptosis of neurons. In addition, GO and KEGG enrichment analysis results indicated that SNS could modulate multiple aspects of anxious insomnia through mechanisms related to pathways of neuroactive ligand-receptor interaction. These pathways include various kinds of synaptic transmission pathways, and anti-inflammatory activity associated with response pathways. When we compared the components-compounds-targets networks and the compounds-targets-synaptic pathways networks, the five active compounds, including beta-Sitosterol, Kaempferol, Tetramethoxyluteolin, Isorhamnetin and Shinpterocarpin, were selected to conduct molecular docking experiments. Eleven target proteins, (AKT1, SLC6A4, ADRB2, MAOA, ACHE, ESR1, CYP3A4, CHRNA7, GABRA2, HTR2A and NOS3), which also play significant roles in regulating serotonergic, cholinergic, dopaminergic and GABAergic systems in the PPI network, were selected to act as receptors in molecular docking trials. The results showed that docking pairs isorhamnetin-AKT1, isorhamnetin-SLC6A4, β-sitosterol-MAOA, β- sitosterol-ACHE, isorhamnetin-CHRNA7 and shinpterocarpin-GABRA2 provided the most stable conformations of ligand-receptor binding between key compounds and core target proteins in the SNS. In the study, we offer a computational result, revealing that SNS may alleviate sleep disorders associated with anxiety through a "multi-compounds, multi-targets, and multi-pathways" mechanism. The network-pharmacology and molecular docking outcomes could theoretically confirm the anti-anxiety and anti-insomnia effects of SNS. Although this research is purely statistical and systematic without empirical validation, it serves as a stepping stone and cornerstone for subsequent experimental investigations.

Exploring the mechanisms of Cornus officinalis in the treatment of non-alcoholic steatohepatitis using network pharmacology, molecular docking and molecular dynamics simulations

Non-alcoholic steatohepatitis (NASH) is a predominant metabolic liver disease, typically characterized by hepatic steatosis, oxidative stress, and inflammation. The traditional Chinese medicine Cornus officinalis possesses anti-inflammatory and hepatoprotective pharmacological properties and has shown ameliorative effects on NASH. however, its mechanism of action remains unclear. This study aims to elucidate the mechanisms by which C. officinalis ameliorates NASH. The active components of C. officinalis were analyzed using the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP), and the corresponding targets were predicted. Subsequently, the DisGeNET, GeneCards, and GEO databases were employed to identify NASH-related targets. Venn diagrams were used to intersect the C. officinalis targets with the NASH targets. Protein–protein interaction (PPI) networks were constructed using the STRING database, and PPI network analysis was performed using Cytoscape. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using the Database for Annotation, Visualization, and Integrated Discovery (DAVID), followed by molecular docking validation. Cornus officinalis was found to contain 20 major active ingredients corresponding to 672 potential targets, 61 of which overlapped with NASH targets. PPI network, GO, and KEGG pathway analyses identified four targets with the highest correlation, and molecular docking results indicated that the active ingredients of C. officinalis exhibited strong binding affinities to NASH targets. The treatment of NASH with C. officinalis is characterized by multiple active ingredients and multiple targets, underscoring the major advantage of traditional Chinese medicine in treating NASH.

Network pharmacology analysis revealed the mechanism and active compounds of jiao tai wan in the treatment of type 2 diabetes mellitus via SRC/PI3K/AKT signaling

Ethnopharmacological relevanceJiao-tai-wan (JTW) is a traditional Chinese herbal prescription, exerts its therapeutic effects on type 2 diabetes mellitus (T2DM). However, its mechanisms and active components remain unclear. Aim of the studyTo investigate the therapeutic mechanisms of JTW in treating type 2 diabetes mellitus (T2DM), focusing on identifying active components, their targets, and validating efficacy through SRC/PI3K/AKT signaling pathway modulation in vitro and in vivo. Materials and methodsActive ingredients were retrieved from the Traditional Chinese Medicine System Pharmacology (TCMSP) and Comprehensive Traditional Chinese Medicine Database (TCMID). Targets for these components were identified using the ChemMapper database based on 3D structural similarity. T2DM-related genes were sourced from the DisGeNET and Gene Expression Omnibus (GEO) databases. Protein-protein interaction (PPI) analysis and functional enrichment analysis were conducted to construct a pathway network of “herbs-active ingredients-candidate targets”, identifying core molecular mechanisms and key active ingredients. SwissDock was used for molecular docking to predict ligands for candidate targets. The diabetic models were established using C57BL/6 mice and human liver HepG2 cell lines. Their Effectiveness and key molecules were verified through biochemical detection and immunoblotting. ResultsTotal 30 active compounds, 597 active ingredient targets, 9631 T2DM-related genes, and 521 overlapping candidate targets were found for JTW on T2DM. Go enrichment indicated the core pathways enriched on insulin and glucose metabolism. The auto-docking demonstrated SRC has potential binds to ingredients of JTW. In vivo, JTW can reduce blood glucose, and blood lipid levels, and HOMA-IR, and increase HOMA-ISI levels in T2DM mice with reduced ALT, AST, MDA levels and increased SOD levels. Meanwhile, decreased phosphorylation of SRC, along with increased levels of phosphorylated PI3K, PI3K, and phosphorylated AKT, were observed. HE staining of liver tissues further confirmed that JTW administration improved liver morphology, reducing inflammation and necrosis. In vitro, JTW significantly ameliorates upstream dysregulation by reducing SRC phosphorylation while enhancing phosphorylated PI3K, PI3K, and AKT phosphorylation levels. ConclusionJTW may alleviate glucose, insulin resistance, and lipid metabolism disorders by the SRC/PI3K/AKT signaling pathway, that provide a novel view of potential active compounds and essential targets in treating T2DM.

Exploring medication rules and mechanism of Chinese medicine for children with cough variant asthma based on data mining, network pharmacology, and molecular docking.

Cough variant asthma (CVA) is a common disease with high incidence among children. Cough is the main clinical symptom and Chinese medicine (CM) has an exact effect on CVA. However, the rules of herb formulation, the pharmacodynamic substances, and the mechanism remained unclear. Therefore, we conducted this article to explore medication rules and molecular mechanism of CM against CVA in children using data mining, network pharmacology, molecular docking, and molecular dynamics simulation. Relevant literatures were collected from China National Knowledge Infrastructure, Chinese Scientific and Technical Journals database, Wanfang database, Pubmed, and Web of science. Excel 2016 was used to extract related data and establish the database for Chinese medical frequency, properties, tastes, and meridian analysis. Association rules were analyzed based on Apriori algorithm using IBM SPSS Modeler 18.0 software and core herb combination was identified. The active ingredients and targets of the core herb combination were acquired form the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. The main targets of CVA were obtained from the GeneCards and Online Mendelian Inheritance in Man database. Core targets were selected by using STRING platform and Cytoscape 3.7.2 software. Metascape platform was utilized to perform gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. The results were verified by molecular docking. SwissADME and pkCSM website were used to analyze the pharmacokinetic profiles and toxicity of key components of the core herb combination. Molecular dynamics simulation was utilized to evaluate the stable of protein-ligand complex. Two hundred seventy-five literatures containing 202 herbs were finally collected. Statistics indicated that these herbs possessed bitter, pungent taste, and warm properties, and belonged to lung meridian. Glycyrrhizae radix et rhizome, Ephedrae herba, and Armeniacae semen amarum were the most frequently used herbs. "Glycyrrhizae radix et rhizoma-ephedrae herba-Armeniacae semen amarum" was the core herb combination with highest support and confidence. Network pharmacology predicted that the main active ingredients, like quercetin, kaempferol, luteolin, etc, might target on RAC-alpha serine/threonine-protein kinase, tumor necrosis factor, interleukin-6, vascular endothelial growth factor A, transcription factor AP-1, interleukin-1 beta, matrix metalloproteinase-9, etc. They played a pivotal role in regulating multiple signaling pathways, such as tumor necrosis factor signaling pathway, IL-17 signaling pathway, and PI3K-Akt signaling pathway. Molecular docking revealed that the key active ingredients were well docked with core targets. The absorption, distribution, metabolism, excretion, and toxicity analysis showed that formononetin, luteolin, naringenin, and quercetin have high gastrointestinal absorption, no AMES toxicity, hepatotoxicity, and skin sensitization. Molecular dynamics simulation revealed that the formononetin-matrix metalloproteinase-9 complex was relatively stable. This article revealed that CM against CVA in children focused on dispelling wind and reducing phlegm, warming lung, and relieving cough. The mechanism of the core herb combination of CM for CVA through muti-components, muti-targets, and muti-pathways.

Exploring the Mechanisms of Self-made Kuiyu Pingchang Recipe for the Treatment of Ulcerative Colitis and Irritable Bowel Syndrome using a Network Pharmacology-based Approach and Molecular Docking.

Ulcerative colitis (UC) and irritable bowel syndrome (IBS) are common intestinal diseases. According to the clinical experience and curative effect, the authors formulated Kuiyu Pingchang Decoction (KYPCD) comprised of Paeoniae radix alba, Aurantii Fructus, Herba euphorbiae humifusae, Lasiosphaera seu Calvatia, Angelicae sinensis radix, Panax ginseng C.A. Mey., Platycodon grandiforus and Allium azureum Ledeb. The aim of the present study was to explore the mechanisms of KYPCD in the treatment of UC and IBS following the Traditional Chinese Medicine (TCM) theory of "Treating different diseases with the same treatment". The chemical ingredients and targets of KYPCD were obtained using the Traditional Chinese Medicine Systems Pharmacology database and analysis platform (TCMSP). The targets of UC and IBS were extracted using the DisGeNET, GeneCards, DrugBANK, OMIM and TTD databases. The "TCM-component-target" network and the "TCM-shared target-disease" network were imaged using Cytoscape software. The protein-protein interaction (PPI) network was built using the STRING database. The DAVID platform was used to analyze the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Using Autodock Tools software, the main active components of KYPCD were molecularly docked with their targets and visualized using PyMOL. A total of 46 active ingredients of KYPCD corresponding to 243 potential targets, 1,565 targets of UC and 1,062 targets of IBS, and 70 targets among active ingredients and two diseases were screened. Core targets in the PPI network included IL6, TNF, AKT1, IL1B, TP53, EGFR and VEGFA. GO and KEGG enrichment analysis demonstrated 563 biological processes, 48 cellular components, 82 molecular functions and 144 signaling pathways. KEGG enrichment results revealed that the regulated pathways were mainly related to the PI3K-AKT, MAPK, HIF-1 and IL-17 pathways. The results of molecular docking analysis indicated that the core active ingredients of KYPCD had optimal binding activity to their corresponding targets. KYPCD may use IL6, TNF, AKT1, IL1B, TP53, EGFR and VEGFA as the key targets to achieve the treatment of UC and IBS through the PI3K-AKT, MAPK, HIF-1 and IL-17 pathways.

Apigenin inhibits epithelial mesenchymal transition in renal tubular epithelial cells through PI3K/AKT and NF-κB pathways for treating renal fibrosis

Renal fibrosis is a crucial factor in the progression of chronic kidney diseases. Previous studies have suggested that apigenin (API) has potential in ameliorating renal fibrosis, but its therapeutic mechanism remains unclear. This study aims to elucidate the mechanisms by which API treats renal fibrosis using network pharmacology and experimental validation. Initially, we used the Traditional Chinese Medicine Systems Pharmacology (TCMSP) Database and GeneCards database to identify molecular targets of API and associated genes. Next, we constructed a network of API-renal fibrosis targets, followed by protein–protein interaction (PPI) analysis. Subsequent analyses, such as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). We also performed molecular docking studies to explore API’s interactions with key proteins. To validate API’s mechanism in treating renal fibrosis, we used a Human Kidney-2 (HK-2) cell model of epithelial-mesenchymal transition (EMT) induced by transforming growth factor-β1 (TGF-β1). We identified 77 API target genes, 8434 renal fibrosis target genes, and 64 intersection genes, which were primarily enriched in nuclear factor kappa-B (NF-κB) and Phosphatidylinositide 3-kinases/protein kinase B (PI3K-AKT) pathways. API significantly inhibited EMT in TGF-β1-induced HK-2 cells by regulating the expression of α-Smooth muscle actin (α-SMA) and E-cadherin and suppressing the protein expression of p-PI3K, p-AKT, and p-P65, which are related to the PI3K-AKT and NF-κB pathways. However, co-administration of the PI3K agonist 740Y-P counteracted API’s inhibitory effects on these protein expressions. In summary, these findings highlight API’s therapeutic potential in treating renal fibrosis by modulating EMT in renal tubular epithelial cells via the PI3K-AKT and NF-κB pathways.

Research on the Regulatory Mechanism of Ginseng on the Tumor Microenvironment of Colorectal Cancer based on Network Pharmacology and Bioinformatics Validation.

A network pharmacology study on the biological action of ginseng in the treatment of colorectal cancer (CRC) by regulating the tumor microenvironment (TME). To investigate the potential mechanism of action of ginseng in the treatment of CRC by regulating TME. This research employed network pharmacology, molecular docking techniques, and bioinformatics validation. Firstly, the active ingredients and the corresponding targets of ginseng were retrieved using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), the Traditional Chinese Medicine Integrated Database (TCMID), and the Traditional Chinese Medicine Database@Taiwan (TCM Database@Taiwan). Secondly, the targets related to CRC were retrieved using Genecards, Therapeutic Target Database (TTD), and Online Mendelian Inheritance in Man (OMIM). Tertiary, the targets related to TME were derived from screening the GeneCards and National Center for Biotechnology Information (NCBI)-Gene. Then the common targets of ginseng, CRC, and TME were obtained by Venn diagram. Afterward, the Protein-protein interaction (PPI) network was constructed in the STRING 11.5 database, intersecting targets identified by PPI analysis were introduced into Cytoscape 3.8.2 software cytoHubba plugin, and the final determination of core targets was based on degree value. The OmicShare Tools platform was used to analyze the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the core targets. Autodock and PyMOL were used for molecular docking verification and visual data analysis of docking results. Finally, we verified the core targets by Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) databases in bioinformatics. A total of 22 active ingredients and 202 targets were identified to be closely related to the TME of CRC. PPI network mapping identified SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 as possible core targets. Go enrichment analysis showed that it was mainly involved in T cell co-stimulation, lymphocyte co-stimulation, growth hormone response, protein input, and other biological processes; KEGG pathway analysis found 123 related signal pathways, including EGFR tyrosine kinase inhibitor resistance, chemokine signaling pathway, VEGF signaling pathway, ErbB signaling pathway, PD-L1 expression and PD-1 checkpoint pathway in cancer, etc. The molecular docking results showed that the main chemical components of ginseng have a stable binding activity to the core targets. The results of the GEPIA database showed that the mRNA levels of PIK3R1 were significantly lowly expressed and HSP90AA1 was significantly highly expressed in CRC tissues. Analysis of the relationship between core target mRNA levels and the pathological stage of CRC showed that the levels of SRC changed significantly with the pathological stage. The HPA database results showed that the expression levels of SRC were increased in CRC tissues, while the expression of STAT3, PIK3R1, HSP90AA1, and AKT1 were decreased in CRC tissues. Ginseng may act on SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 to regulate T cell costimulation, lymphocyte costimulation, growth hormone response, protein input as a molecular mechanism regulating TME for CRC. It reflects the multi-target and multi-pathway role of ginseng in modulating TME for CRC, which provides new ideas to further reveal its pharmacological basis, mechanism of action and new drug design and development.

Integrated metabolomics and network pharmacology reveal the procoagulant mechanisms of Cirsium setosum extracts

As a medicinal plant, Cirsium setosum has excellent procoagulant effects and has long been used as a cure for hemoptysis, epistaxis, uremia and metrorrhagia caused by blood heat. However, the key medicinal part of C. setosum, as well as the biologically active substances that play a major role, are not known. In this study, the aboveground, underground and whole grass portions of C. setosum were subjected to a coagulation comparison experiment to determine the primary active procoagulant compounds. The main active procoagulant compounds of C. setosum were then screened using a comparative metabolomics analysis between aboveground and underground. Network pharmacology analysis was used to construct the “active ingredient-disease target-pathway” network. Finally, molecular docking was used to verify the binding ability and affinity between the key active ingredients obtained from the screening and the targets. The results indicated that the aboveground part of C. setosum could significantly shorten activated partial thromboplastin time (APTT) and that this part exerts substantial procoagulant effects. The total phenol, total flavonoid and total alkaloid content of the aboveground part was measured to be higher than those of the underground part and whole grass. Furthermore, comparative metabolomics analysis as well as the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database and literature search screening yielded 10 active substances, including naringenin, guanine, 2,4-di-tert-butylphenol, calycosin-7-O-beta-D-glucoside, flavone, vitexin, and tiliroside, which may be related to the coagulation-promoting properties of C. setosum and its therapeutic effects on coagulation-related disorders. Network pharmacological analysis revealed that C. setosum may exert procoagulant effects mainly through tiliroside, calycosin-7-O-beta-D-glucoside, and flavone, which act on key target proteins, such as SRC, PRKACA, EGFR, AKT1, MAPK3, and GSK3B. In summary, C. setosum exerts its procoagulant and therapeutic effects on coagulation-related diseases through multiple compounds, targets, and pathways.

Dihuangzicao Granules Regulate the AGE/RAGE/NF-κB Signaling Pathway to Inhibit Inflammation in Psoriatic Mice via Network Pharmacology and Experimental Validation.

Psoriasis is an immune-mediated skin disease that occurs worldwide and is characterized by high prevalence and chronicity. Psoriasis has a complex pathogenesis and is difficult to cure. Therefore, continuous exploration of the pathogenesis of psoriasis and the search for new drug treatment methods are crucial for improving treatment efficiency and reducing psychological damage to psoriasis patients. The active ingredients in Dihuang Zicao granules (DHZCG) can effectively treat psoriasis. Therefore, this study aimed to analyze the active ingredients of DHZCG and their potential mechanisms for treating psoriasis. The effective components of DHZCG were screened via the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Genetic information for psoriasis was retrieved from the GeneCards, OMIM and DisGENET databases. Protein-Protein Interaction (PPI) analysis was performed, and component‒target‒disease networks were constructed. Important molecular biological processes and signaling pathways were screened via GO and KEGG analyses. Molecular docking of the active ingredients and key targets was performed via AutoDock Vina (1.1.2). A mouse model of psoriasis was established and divided into a control group, model group, low-dose DHZCG group (L-DHZCG), medium-dose DHZCG group (M-DHZCG), and high-dose DHZCG group (H-DHZCG). Hematoxylin and Eosin (HE) staining was performed to determine the pathological changes in the skin of each group of mice, and the Psoriasis Area Severity Index (PASI) score was used to assess skin damage. ELISA and RT‒ PCR were used to measure the levels of the inflammatory factors TNF-a, IL-17A, and IL-23 in the serum and skin tissue of the mice, respectively. Western blotting was used to analyze the expression of proteins related to the AGE/RAGE signaling pathway. Immunofluorescence was used to examine the expression of the inflammatory factor NF-kB. Immunohistochemistry was used to measure IL-1β and TNF-a expression in skin tissues. Sixty genes associated with psoriasis treatment by DHZCG, including core genes encoding IL-6, TNF-a, AKT1, IL-1β, TP53, NFKB1, BCL2, and MAPK3, were identified. Through the construction of a psoriasis mouse model, DHZCG treatment effectively reduced skin damage and significantly decreased the levels of the validated factors TNF-a, IL-17A, IL- 23, IL-1b, and NF-kB in the serum and damaged skin. Furthermore, the reduction in the levels of these inflammatory factors by DHZCG is associated with the downregulation of the AGE/RAGE signaling pathway. DHZCG reduces inflammation and alleviates psoriasis by downregulating the AGE/RAGE/NF-kB signaling pathway. This study is beneficial for providing a theoretical basis for the development of drugs for psoriasis and for offering personalized treatment strategies for the clinical management of psoriasis.

Network Pharmacology and Experimental Verification: SanQi-DanShen Treats Coronary Heart Disease by Inhibiting the PI3K/AKT Signaling Pathway.

To employee network pharmacology to predict the components and pathways of SanQi-DanShen (SQDS) in treating coronary heart disease, followed by in vitro experiments to validate the molecular mechanism of SQDS in treating coronary heart disease. We sourced the active ingredients and targets of Panax notoginseng and Danshen from the Traditional Chinese Medicine Systems Pharmacology database. Coronary heart disease related genes were retrieved from the OMIM, Genecards, and Therapeutic Target databases. Using Cytoscape 3.7.2 software, we constructed a network diagram illustrating the components and targets of SQDS. The associated targets were then imported into the STRING database to build a protein-protein interaction network. The Metascape database and WeChat software were utilized for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Lastly, we performed molecular docking between the key components and related targets using AutoDock Vina. To validate the potential mechanism of SQDS in treating coronary heart disease, we established an acute coronary heart disease rat model via tail vein injection of pituitrin. Network pharmacology analysis revealed that 65 active ingredients and 167 targets of SQDS are implicated in the treatment of coronary heart disease. The key targets identified include AKT1, TNF, TP53, IL6, and VEGFA. Notably, the PI3K/AKT signaling pathway emerged as the primary pathway. Furthermore, animal experiments showed that, compared to the model group, SQDS significantly reduced levels of TNF-α, IL-6, Bax, and cardiac troponin I, while increasing Bcl-2 content. It also notably suppressed the expression of p-PI3K and p-AKT, thereby offering protection to myocardial tissue. Through the integrated approach of network pharmacology and molecular docking, we have established that SQDS exerts a multi-component, multi-target, and multi-pathway synergistic therapeutic effect on coronary heart disease. Its mechanism may involve the inhibition of the PI3K/AKT signaling pathway and the reduction of inflammatory factor expression.

Network pharmacology and experimental validation reveals the potential therapeutic effects of Polygonum cuspidatum against odontogenic keratocyst

This study aimed to explore active ingredients in Polygonum cuspidatum with potential effects on odontogenic keratocysts (OKCs) using network pharmacological approach and bioinformatic gene analysis. The active ingredients and targets of P. cuspidatum were selected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database, and the ingredient–target network was constructed using Cytoscape software. Differentially expressed genes (DEGs) of OKC were selected and Gene Ontology (GO) enrichment analysis were performed through bioinformatic analysis using Gene Expression Omnibus (GEO) dataset GSE38494. The STRING database platform was used to draw protein–protein interaction network diagram, then the hub gene analysis was performed by Cytoscape software. AutoDock Vina software was used to perform molecular docking verification of the effects of the active ingredients on potential core targets. Finally, we use OKC nude animal model to testify the potential effects of P. cuspidatum. Ten active ingredients of P. cuspidatum were obtained. A total of 205 drug targets and 38 potential core targets of P. cuspidatum were confirmed in OKCs. The hub genes included PPARG, SPP1, COL3A1, MMP2, HMOX1, CCL2, CXCL10, VCAM1, RUNX2 and IRF1. Molecular docking showed that the key active ingredients including luteolin and quercetin which exhibited good docking activity with key target proteins (VCAM1, HMOX1 and MMP2). GO enrichment revealed that the pathways of P. cuspidatum acting on OKCs included the response to toxic substance, response to nutrient levels and response to xenobiotic stimulus. P. cuspidatum treatment in OKC could significantly down-regulate COL3A1 and MMP2 expressions in vivo and vitro. Our study indicated that P. cuspidatum is a potential therapeutic candidate for OKCs.

Improvement effect and mechanism of XuanFuDaiZhe tang on rats with diarrheal irritable bowel syndrome induced by colorectal dilation

Ethnopharmacological relevanceXuanFuDaiZhe Tang (XFDZT) is used in traditional Chinese medicine (TCM) to treat diarrhoea-predominant irritable bowel syndrome (IBS-D). Our laboratory has demonstrated that XFDZT remarkably improves various gastrointestinal motility disorders in animal models. However, previous studies have only focused on one or several protein targets without systematically investigating dynamic changes and protein interrelations. Aim of the studyTo explore the mechanisms underlying the therapeutic action of XFDZT in IBS-D using a network pharmacology approach and in vivo experiments. Materials and methodsThe active compounds of XFDZT were selected from TCM Systems Pharmacology and TCM Integrated databases, and potential targets were identified using the Swiss Target Prediction databases. Targets related to IBS-D were mined from the DisGeNet, Drug Bank, and Therapeutic Target databases. The intersecting protein–protein interactions (PPIs) of the drug–disease crossover genes were analysed, and a central PPI network was constructed using the STRING database and Cytoscape 3.7.2. Following Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, a gene pathway network was constructed to identify key target genes and pathways. Using haematoxylin and eosin staining and western blotting, we validated how XFDZT controls water expression in the body to treat IBS-D infection. ResultsFirst, the results showed that XFDZT contained 1037 active ingredients and 1458 corresponding targets. After intersecting the 252 IBS targets, 108 targets were identified. The main targets of XFDZT were albumin, aquaporins such as AQP1 and AQP3, calmodulin, and the cellular enzyme CYP2C9. GO and KEGG enrichment predicted that the action pathways were the neuroactive ligand–receptor interaction, calcium signalling pathway, serotonergic synapse signalling pathway, cGMP–PKG signalling pathway, cAMP signalling pathway, and MLCK–MLC signalling pathway. Second, an IBS-D rat model was constructed using colorectal dilation (CRD). CRD can significantly induce IBS-D symptoms such as diarrhoea, abdominal pain, and anxiety and depression-like behaviour in rats. XFDZT (10, 20, and 40 g/kg) administered for 14, 21, and 28 days significantly reversed these changes in IBS-D rats in a time- and dose-dependent manner, suggesting that XFDZT significantly improved IBS-D. Finally, the mechanism by which XFDZT improves IBS-D was explored from the perspective of AQPs, tight junction proteins, and motility-related proteins in colon tissue. Compared with the control group, the protein expression of AQP1, AQP3, and AQP8 in the colon tissue of IBS-D rats was significantly downregulated, whereas the protein expression of AQP7 was significantly upregulated. The expression of tight junction-related proteins claudin-1, occludin, and ZO-1 in colon tissue was significantly downregulated, whereas the expression of motility-related proteins p-MLC, MLC, MLCK, and CaM in colon tissue was significantly upregulated, suggesting that IBS-D rats had AQP disorders, epithelial intercellular connections, and motility in colon tissue. The above changes were significantly reversed by XFDZT administration (5, 10, and 20 g/kg) for 14 days. ConclusionXFDZT significantly improved diarrhoea, abdominal pain, anxiety, and depression in IBS-D rats, and its mechanism of action may be related to the regulation of AQPs, tight junction proteins, and the MLCK–MLC pathway. This study provided a pharmacological experimental basis for the development of XFDZT as a novel drug for the treatment of IBS-D.