Traditional System Of Medicine Research Articles

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.

Advancing Cardiovascular Health: Unveiling the Role of Traditional and Natural Medicine

In the quest for optimizing cardiovascular health, contemporary research increasingly explores the potential benefits of traditional and natural medicinal modalities. This paper provides insights into the therapeutic avenues offered by traditional medicine systems and natural remedies in cardiovascular care. Incorporating knowledge from ancient healing traditions like Ayurveda and Traditional Chinese Medicine (TCM) alongside contemporary research on the efficacy of natural compounds, the paper aims to elucidate their cardiovascular effects. Specifically, it examines the impact of lifestyle modifications, dietary supplements, and botanical extracts on cardiovascular health. Synthesizing evidence from clinical trials, preclinical studies, and traditional knowledge systems, the paper underscores the importance of integrating traditional and natural medicine practices with conventional medical interventions. This integration is vital for enhancing our understanding and management of cardiovascular diseases, contributing to more effective preventive strategies and optimized therapeutic outcomes in cardiovascular medicine.

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.

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.

Integrative analysis of the efficacy and pharmacological mechanism of Xuefu Zhuyu decoction in idiopathic pulmonary fibrosis via evidence-based medicine, bioinformatics, and experimental verification

ObjectiveWe used evidence-based medicine, bioinformatics and experimental verification to comprehensively analyze the efficacy and pharmacological mechanism of Xuefu Zhuyu decoction (XFZYD) in the treatment of idiopathic pulmonary fibrosis (IPF). MethodsMajor databases were retrieved for randomized controlled trials (RCTs) of XFZYD treating IPF to perform meta-analysis. Active ingredients and target genes of XFZYD were identified from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). IPF-related differentially expressed genes (DEGs) were identified from the Gene Expression Omnibus (GEO) database. The RGUI software was utilized for Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The ingredient-target and protein-protein interaction (PPI) networks were achieved through Cytoscape software and the STRING database to identify the key compounds and target proteins. Molecular docking was performed using AutoDockTool and AutoDock Vina software. The effect between key compounds and target proteins was verified in animal experiments. ResultsSix RCTs were included for meta-analysis, which uncovered that the total effective rate of clinical efficacy was higher in the experimental group than control group. Then, 156 active ingredients and 254 target genes of XFZYD, and 1,566 IPF-related DEGs were identified. The intersection analysis identified 48 target genes correlating with 130 active ingredients of XFZYD treating IPF. GO functional enrichment, KEGG pathway enrichment, ingredient-target network and PPI network were achieved. Following the identification of key compounds and target proteins, we performed molecular docking. Ultimately, our research focused on the key compound quercetin for experimental validation to assess its interactions with two key target proteins, JUN and PTGS2. ConclusionThe effectiveness of XFZYD on IPF has been substantiated through evidence-based medicine. The pharmacological mechanism of XFZYD for IPF treatment involves a complex interplay of various compounds and targets, with quercetin exerting pronounced impacts on JUN and PTGS2 proteins.

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.

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.

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 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.

Role and molecular mechanisms of HuangQiSiJunZi decoction for treating triple-negative breast cancer as explored via network pharmacology and bioinformatics analyses

ObjectiveIn this study, we evaluated the molecular mechanisms of HuangQiSiJunZi Decoction (HQSJZD) for treating triple-negative breast cancer (TNBC) using network pharmacology and bioinformatics analyses.MethodsEffective chemical components together with action targets of HQSJZD were selected based on the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Meanwhile, differentially expressed genes (DEGs) were extracted from TNBC sample data in The Cancer Genome Atlas (TCGA) database. Additionally, we built a protein-protein interaction (PPI) network and acquired hub genes. Gene Expression Omnibus(GEO) datasets were utilized to verify the accuracy of hub gene expression. Additionally, enrichment analyses were conducted on key genes. Furthermore, TNBC severity-related high-risk factors were screened through univariate together with multivariate Cox regressions; next, the logistic regression prediction model was built. Moreover, differential levels of 22 immune cell types in TNBC tissues compared with normal tissues were analyzed. The hub gene levels within pan-cancer and the human body were subsequently visualized and analyzed. Finally, quantitative PCR (RT-qPCR) was used to validate the correlation of the hub genes in TNBC cells.ResultsThe study predicted 256 targets of active ingredients and 1791 DEGs in TNBC, and obtained 16 hub genes against TNBC. The prognostic signature based on FOS, MMP9, and PGR was independent in predicting survival. A total of seven types of immune cells, such as CD4 + memory T cells, showed a significant difference in infiltration (p < 0.05), and immune cells were related to the hub genes. The HPA database was adopted for hub gene analyses, and as determined, FOS was highly expressed in most human organs. The results of RT-qPCR validation for the FOS hub gene were consistent with those of bioinformatic analyses.ConclusionHQSJZD might regulate the interleukin-17 and aging pathways via FOS genes to increase immune cell infiltration in TNBC tissues, and thus, may treat TNBC and improve the prognosis. The FOS genes are likely to be a new marker for TNBC.

Exploring the therapeutic potential of Xiangsha Liujunzi Wan in Crohn's disease: from network pharmacology approach to experimental validation

Ethnopharmacological relevanceXiangsha Liujunzi Wan (LJZW) is a traditional Chinese medicine (TCM) formula containing a variety of traditional Chinese herb components. Its principal components are often used in the treatment of gastrointestinal diseases and contribute to the treatment of Crohn's disease (CD). Aim of the studyTo explore the therapeutic potential of LJZW in CD through network pharmacology, bioinformatics, molecular docking, and experimental verification. MethodsThe principal bioactive components and corresponding targets of LJZW were ascertained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Potential targets for CD were identified in GeneCards, OMIM, DrugBank, DisGeNET, CTD, and Gene Expression Omnibus (GEO) databases. Intersection targets of LJZW and CD were identified using a Venn diagram and visualized using Cytoscape 3.8.0 to construct a protein-protein interaction (PPI) network. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were employed to assess the function of intersection targets. AutoDockTools and PyMOL were used for molecular docking to recognize the association between the core ingredients of LJZW and the core targets of CD. Subsequently, a series of experiments were conducted for validation. ResultsThe network pharmacology results indicated that there were 156 bioactive components and 268 corresponding targets for LJZW, 3023 primary relevant targets for CD, and 169 intersection targets for LJZW and CD. The PPI network was employed to identify five hub genes and six clusters. The GO functional analysis indicated that intersection targets are primarily correlated with oxidative stress and inflammatory responses. KEGG pathway analysis revealed that these targets were primarily associated with the phosphotylinosital 3 kinase (PI3K)-protein kinase B (AKT) and mitogen-activated protein kinase (MAPK) signaling pathways. The molecular docking results showed that the core ingredients of LJZW had good binding ability with the core targets of CD. A series of experiments demonstrated that LJZW could effectively attenuate TNBS-induced colitis symptoms, inhibit the inflammatory response, and protect intestinal barrier function by inhibiting the PI3K-AKT and MAPK signaling pathways, thus preventing and treating CD. ConclusionLJZW has the characteristics of multi-component, multi-target, and multi-pathway treatment, which helps to improve the treatment of CD, protect the intestinal barrier, and exert the effect of anti-inflammatory therapy by inhibiting PI3K-AKT and MAPK signaling pathways.

Potential mechanisms of ZiGongDing in treating HPV-induced cervical intraepithelial neoplasia: a network pharmacology and experimental verification study.

The onset of cervical intraepithelial neoplasia (CIN) is strongly associated with persistent infection caused by high-risk human papillomavirus (HPV). ZiGongDing (ZGD), a traditional Chinese medicine, has progressed to clinical application in HPV-induced CIN treatment, yet the underlying mechanism remains unclear. The objective of this paper is to explore the mechanism of ZGD in treating HPV-induced CIN by integrating a combination of network pharmacology and experimental validation. The active ingredients and targets of ZGD were obtained from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) database. CIN-related targets were sourced from GeneCards and the Online Mendelian Inheritance in Man (OMIM) database. Protein-protein interaction (PPI) and functional enrichment analyses were conducted to determine the potential molecular mechanism. The herb-active ingredient-target network was constructed by Cytoscape software. To further validate the therapeutic mechanism, molecular docking and in vitro experiments were performed. In this study, we identified 60 active ingredients in ZGD and 46 common targets in of CIN treatment. The PPI network analysis revealed estrogen receptor 1 (ESR1) as a pivotal target in ZGD against CIN. Functional enrichment analysis showed that the estrogen signaling pathway was mostly enriched, and ESR1 was involved. The herb-active ingredient-target network and relative literature identified cnidimol B as the primary active ingredient. Molecular docking demonstrated a strong binding affinity between ESR1 and cnidimol B. Cellular experiments revealed that cnidimol B could significantly decrease the viability of HeLa and CaSki cells. Moreover, the expression of ESR1 was notably upregulated in HeLa and CaSki cells after treatment with cnidimol B. Our study proposes a novel mechanism underlying ZGD against CIN, which involves the modulation of ESR1. This insight lays a solid foundation for further exploring and optimizing ZGD's therapeutic potential.

Exploring the Mechanism of Action of the "Scutellaria Barbata D.Don-Prunella Vulgaris L." Herb Pair in the Treatment of Lung Cancer Using Network Pharmacology and Molecular Docking Techniques

Objective: To explore the mechanism of action of the herbal pair "Scutellaria barbata D.Don-Prunella vulgaris L." in the treatment of lung cancer through network pharmacology and molecular docking techniques. Methods: Active ingredients and their targets of Scutellaria barbata D.Don and Prunella vulgaris L. were collected and screened from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Disease-related targets were obtained and screened from the Genecards and OMIM databases. The intersection Venn diagram of the targets of "Scutellaria barbata D.Don-Prunella vulgaris L." and lung cancer disease targets was obtained using R 4.4.1 software and packages such as "ggvenn". A drug-active ingredient-target-disease association network was constructed in Cytoscape 3.10.0, and core active ingredients were screened using the Analyze Network function. A PPI network for drug-disease common targets was constructed using the String database website, and the TSV format of protein interaction relationship files was imported into Cytoscape 3.10.0 software,install and run CytoHubba to calculate and obtain the core targets in the network. GO function and KEGG pathway enrichment analyses were performed on drug-disease common targets using R 4.4.1 software. Finally, molecular docking validation was performed on core ingredients and core targets using AutoDock, and the three best binding molecular docking patterns were displayed using PyMol software. Results: A total of 33 active drug components and 108 drug-disease common targets were obtained. Among them, there are 5 core active components: quercetin, luteolin, wogonin, kaempferol, and baicalein; core targets include TP53, AKT1, JUN, HSP90AA1, etc. GO analysis yielded 2, 010 related entries. KEGG analysis identified 147 signaling pathways. Molecular docking showed that the core active components have strong affinity with the core targets. Conclusion: The drug pair of Scutellaria barbata D.Don and Prunella vulgaris L. may exert anti-tumor effects by acting on targets such as TP53, AKT1, JUN, HSP90AA1, and through signaling pathways like PI3K-AKT, inhibiting tumor cell proliferation, promoting tumor cell apoptosis, suppressing its proliferation, differentiation, and metastasis, thereby achieving therapeutic effects on lung cancer.

Integrating network pharmacology and bioinformatics to explore the mechanism of Xiaojian Zhongtang in treating major depressive disorder: An observational study.

Major depressive disorder (MDD) is a common mental illness. The traditional Chinese medicine compound Xiaojian Zhongtang (XJZT) has a good therapeutic effect on MDD, but the specific mechanism is not clear. The aim of this study is to explore the molecular mechanism of XJZT in the treatment of MDD through network pharmacology and bioinformatics. The traditional Chinese medicine system pharmacology database was used to screen the chemical components and targets of XJZT, while the online Mendelian inheritance in man, DisGeNET, Genecards, and therapeutic target database databases were used to collect MDD targets and identify the intersection targets of XJZT and MDD. A "drugs-components-targets" network was constructed using the Cytoscape platform, and the STRING was used for protein-protein interaction analysis of intersecting targets. Gene Ontology and Kyoto encyclopedia of genes and genomes analysis of intersecting targets was performed using the DAVID database. Obtain serum and brain transcriptome datasets of MDD from the gene expression omnibus database, and perform differentially expressed genes, weighted gene co-expression network analysis, gene set enrichment analysis, and receiver operating characteristic analysis. A total of 127 chemical components and 767 targets were obtained from XJZT, among which quercetin, kaempferol, and maltose are the core chemical components, and 1728 MDD targets were screened out, with 77 intersecting targets between XJZT and MDD. These targets mainly involve AGE-RAGE signaling pathway in diabetic complexes, epidermal growth factor receptor tyrosine kinase inhibitor resistance, and HIF-1 signaling pathway, and these core targets have strong binding activity with core components. In addition, 1166 differentially expressed genes were identified in the MDD serum transcriptome dataset, and weighted gene co-expression network analysis identified the most relevant gene modules (1269 genes), among which RAC-alpha serine/threonine-protein kinase (AKT1), D(4) dopamine receptor (DRD4), and kynurenine 3-monooxygenase (KMO) were target genes for the treatment of MDD with XJZT, these 3 genes are mainly related to the ubiquitin-mediated proteolysis, arachidonic acid (AA) metabolism, and Huntington disease pathways, and the expression of AKT1, DRD4, and KMO was also found in the MDD brain transcriptome dataset, which is significantly correlated with the occurrence of MDD. We have identified 3 key targets for XJZT treatment of MDD, including AKT1, KMO, and DRD4, and they can be regulated by the key components of XJZT, including quercetin, maltose, and kaempferol. This provides valuable insights for the early clinical diagnosis and development of therapeutic drugs for MDD.

Efficacy and mechanism of Schisandra chinensis active component Gomisin A on diabetic skin wound healing: network pharmacology and in vivo experimental validation

Ethnopharmacological relevanceSchisandra chinensis (Turcz.) Baill., a common traditional Chinese herbal medicine, has been used for the treatment of diabetes mellitus and its complications. However, the major active component for treating diabetic foot ulcers, a serious complication of diabetes mellitus, was unclear. This study aimed to predict the treatment effect of the active components in Schisandra chinensis against diabetic skin wound using network pharmacology and to confirm the underlying mechanism using a diabetic skin wound model in vivo. Aim of the studyTo study the effects and underlying mechanisms of Schisandra chinensis and its main component Gomisin A on diabetic skin wound healing by network pharmacology and high-fat diet (HFD)-induced obese mice model in vivo. Materials and methodsTo determine the effectiveness of Schisandra chinensis on diabetic skin wound, network pharmacology was first used. Components of Schisandra chinensis were obtained from the Traditional Chinese Medicine Systems Pharmacology database. The active components were further verified through absorption, distribution, metabolism and excretion. The potential targets of the active components were identified from the Traditional Chinese Medicine Systems Pharmacology, SwissTargetPrediction, TargetNet, and the Comparative Toxicogenomics Database. Targets related to diabetic skin wound were collected from the GeneCards, OMIM, DisGeNET, and PharmGKB databases. The interaction network formed by the intersection of the two datasets was analyzed using Gephi. Network-based proximity was used to predict the network distance between the active components of Schisandra chinensis and diabetic skin wound. Gomisin A was found to have the lowest Z-score and was administered either orally or via topical injection to HFD-induced obese mice daily until the wounds healed, and its effects on skin wound healing were evaluated. ResultsOnly five active ingredients of Schisandra chinensis were screened in our system: Gomisin A, Longikaurin A, Deoxyharringtonine, Wuweizisu C, and Interiotherin B, which can regulate biological processes related to diabetic skin wound, including positive regulation of phosphorous metabolic process, positive regulation of cell migration, and response to wounding. Network proximity analysis found that Gomisin A has the closest distance-based Z-score among the diabetic skin wound modules and drug targets in the human protein-protein interaction network. The HFD-induced obese mice model further revealed that Gomisin A accelerated skin wound healing by increasing insulin sensitivity and decreasing the advanced glycation end-products mediated toll-like receptor 4 (TLR4)-p38 MAPK-IL6 inflammation signaling pathway. ConclusionsThe network pharmacology and in vivo studies indicated that Gomisin A from Schisandra chinensis played a crucial role in improving diabetic skin wound healing.

Exploring the antifungal properties of neem (Azadirachta indica) during: A comprehensive review (2010-2020)

Neem (Azadirachta indica) is a versatile medicinal plant with a long history of use in traditional medicine systems. Among its various therapeutic properties, neem has gained attention for its potent antifungal activity. This paper provides a comprehensive review of the antifungal properties of neem, highlighting its mechanisms of action, efficacy against fungal pathogens, and potential applications in clinical and agricultural settings. By synthesizing findings from a wide range of research studies, this review aims to deepen our understanding of neem's antifungal properties and explore its potential as a natural alternative for combating fungal infections.

Predicting prospective therapeutic targets of Bombyx batryticatus for managing diabetic kidney disease through network pharmacology analysis.

We conducted network pharmacology and molecular docking analyses, and executed in vitro experiments to assess the mechanisms and prospective targets associated with the bioactive components of Bombyx batryticatus in the treatment of diabetic kidney disease (DKD). The bioactive components and potential targets of B batryticatus were sourced from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform. Using 5 disease databases, we conducted a comprehensive screening of potential disease targets specifically associated with DKD. Common targets shared between the bioactive components and disease targets were identified through the use of the R package, and subsequently, a protein-protein interaction network was established using data from the STRING database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses pertaining to the identified common targets were conducted using the Database for Annotation, Visualization, and Integrated Discovery. Molecular docking simulations involving the bioactive components and their corresponding targets were modeled through AutoDock Vina and Pymol. Finally, to corroborate and validate these findings, experimental assays at the cellular level were conducted. Six bioactive compounds and 142 associated targets were identified for B batryticatus. Among the 796 disease targets associated with DKD, 56 targets were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed the involvement of these shared targets in diverse biological processes and signaling pathways, notably the PI3K-Akt signaling pathway. Molecular docking analyses indicated a favorable binding interaction between quercetin, the principal bioactive compound in B batryticatus, and RAC-alpha serine/threonine-protein kinase. Subsequently, in vitro experiments substantiated the inhibitory effect of quercetin on the phosphorylation level of PI3K and Akt. The present study provides theoretical evidence for a comprehensive exploration of the mechanisms and molecular targets by which B batryticatus imparts protective effects against DKD.

Predicting and Validating the Mechanism of Action of the Enema Formula in Treating Colorectal Cancer by Using Network Pharmacology, GEO, and TCGA Databases

Background: The GCF, created by Professor Liu Shenlin, an esteemed expert in traditional Chinese medicine, is rooted in principles to improve blood flow, relieve blood congestion, clear heat, and detoxify the body. Developed as an empirical formula, it holds significance in CRC treatment. Objective: This study aimed to predict and confirm the active elements, possible targets, and molecular mechanisms against colorectal cancer (CRC) in the GCF enema formula. Methods: Using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), we screened active elements and drug targets. Colorectal cancer (CRC)-related targets were collected from the Online Mendelian Inheritance in Man (OMIM) database, Disease Gene Network (DisGeNET) database, and Therapeutic Target Database (TTD). The overlap between action targets of all active elements and CRC-related targets was determined to find common targets. A Protein-Protein Interaction (PPI) network of common targets was built using the String database, and Cytoscape software was used for visual analysis to identify core targets. Simultaneously, the common targets were analyzed using the Metascape database for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment. Additionally, core targets and active elements were tested using Discovery Studio 2019 for molecular docking. Furthermore, the expression differences and prognostic impacts of core targets were examined across various cancer databases. Results: Screening revealed 90 active elements and 251 drug targets in the GCF. There were 6113 disease targets, with 113 common targets between CRC and the GCF. Core targets identified through PPI analysis included AKT1, STAT3, MYC, SRC, EGFR, and IL6. KEGG enrichment analysis uncovered 101 relevant pathways related to these targets. Molecular docking experiments confirmed favorable interactions between core targets and multiple active elements in the GCF. Additionally, examination of the Human Protein Atlas (HPA) database highlighted differential expression of core targets MYC and EGFR in normal colorectal tissue compared to CRC tissue. Conclusion: The GCF, comprising a combination of three drugs, appears to counteract CRC by influencing core targets, such as AKT1, STAT3, MYC, SRC, EGFR, and IL6. This process involves regulating multiple cancer-related signaling pathways, notably the PI3K-AKT pathway.

Exploration of the potential mechanism of Yiyi Tongfeng Formula in the treatment of acute gouty arthritis based on network pharmacology and molecular docking: A review.

The global prevalence of gout is on the rise. Yiyi Tongfeng Formula (YTF), a traditional herbal compound, has gained recognition for its efficacy in managing acute gouty arthritis (AGA). Despite its widespread use, the underlying mechanisms of YTF in AGA treatment remain largely undefined. This study employed network pharmacology and molecular docking to elucidate these mechanisms. We utilized the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, SymMap database, and various literature sources to identify active components and corresponding targets of YTF. Relevant AGA-associated targets were identified through the Genecards, Drugbank, Therapeutic Target Database, and Online Mendelian Inheritance in Man databases. A protein-protein interaction network was constructed to delineate interactions between YTF targets and AGA. Key ingredients and central targets were further analyzed using Cytoscape. Functional enrichment analyses, including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, were conducted via Metascape. Additionally, molecular docking studies were performed using PyMOL and AutoDock4. It was found that quercetin, kaempferol, and luteolin may be the main active components of YTF for AGA treatment. Gene Ontology enrichment analysis shows that the main biological processes involved are cellular responses to lipids, and inflammatory responses. Kyoto Encyclopedia of Genes and Genomes enrichment analysis suggests the involvement of the IL-17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, and so on. The findings suggest a multi-faceted therapeutic approach of YTF in treating AGA, involving multiple components, targets, biological processes, and signaling pathways. This comprehensive mechanism offers a foundation for further experimental validation.