Exploring the mechanism of Erchen decoction in the treatment of atherosclerosis based on network pharmacology and molecular docking
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ABSTRACT:
SUBMITTER: Li W
PROVIDER: S-EPMC10659732 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Objective: To explore the functional mechanisms of Suanzaoren decoction (SZRD) for treating insomnia using network pharmacology and molecular docking. Methods: The active ingredients and corresponding targets of SZRD were obtained from the Traditional Chinese Medicine Systems Pharmacology database, and then, the names of the target proteins were standardized using the UniProt database. The insomnia-related targets were obtained from the GeneCards, DisGeNET, and DrugBank databases. Next, a Venn diagram comprising the drug and disease targets was created, and the intersecting targets were used to draw the active ingredient-target network diagram using Cytoscape software. Next, the STRING database was used to build a protein-protein interaction network, followed by cluster analysis using the MCODE plug-in. The Database for Annotation, Visualization, Integrated Discovery (i.e., DAVID), and the Metascape database were used for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. AutoDock Vina and Pymol software were used for molecular docking. Results: SZRD contained 138 active ingredients, corresponding to 239 targets. We also identified 2,062 insomnia-related targets, among which, 95 drug and disease targets intersected. The GO analysis identified 490, 62, and 114 genes related to biological processes, cellular components, and molecular functions, respectively. Lipid and atherosclerosis, chemical carcinogen-receptor activation, and neuroactive ligand-receptor interaction were the most common pathways in the KEGG analysis. Molecular docking demonstrated that the primary active components of SZRD for insomnia had good binding capabilities with the core proteins in PPI network. Conclusion: Insomnia treatment with SZRD involves multiple targets and signaling pathways, which may improve insomnia by reducing inflammation, regulating neurotransmitters.
| S-EPMC10475534 | biostudies-literature
Project description:ObjectiveStudies have demonstrated that the combination of antipsychotics and Pingxin Dingzhi Decoction (PXDZD) can effectively enhance treatment efficacy for schizophrenia (SCZ), while simultaneously reducing the adverse reactions associated with antipsychotic treatment. However, the exact mechanism by which PXDZD exerts its therapeutic effects is still unknown. The aim of this study is to investigate the action mechanism of PXDZD using network pharmacology and molecular docking techniques.MethodsThe primary components and their protein targets of PXDZD were extracted from TCMSP, SYMMAP, and HERB databases. The targets related to SCZ were acquired from OMIM and DisGeNET databases. The overlapping targets between composite targets and disease targets were used to construct a protein-protein interaction (PPI) network in the STRING database. The identified targets underwent GO and KEGG enrichment analysis, followed by molecular docking studies of the core target proteins and active compounds.ResultThe screening process yielded 285 PXDZD component targets and 1982 disease targets, ultimately leading to the identification of 120 shared targets. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that PXDZD treatment for SCZ engages a diverse range of biological mechanisms, including inflammatory responses and apoptotic processes, while also modulating various signaling pathways such as the PI3K-Akt, mitogen-activated protein kinase (MAPK), and tumor necrosis factor (TNF) signaling pathways. The molecular docking results revealed a strong affinity of Estrogen Receptor 1 (ER1) toward both β-sitosterol and stigmasterol, while kaempferol, β-sitosterol, and stigmasterol demonstrated significant binding potential against TNF-α.ConclusionPingxin Dingzhi Decoction can play a role in treating SCZ through its multi-component, multi-target, and multi-pathway approach.
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Project description:Gyejibokryeong-hwan (GBH) is a traditional formula comprised of five herbal medicines that is frequently used to treat blood stasis and related complex multifactorial disorders such as atherosclerosis. The present study used network pharmacology and molecular docking simulations to clarify the effect and mechanism of the components of GBH. Active compounds were selected using Oriental Medicine Advanced Searching Integrated System (OASIS) and the Traditional Chinese Medicine System Pharmacology Database and Analysis Platform (TCMSP), and target genes linked to the selected components were retrieved using Search Tool for Interacting Chemicals (STITCH) and GeneCards. Functional analysis of potential target genes was performed through the Annotation, Visualization and Integrated Discovery (DAVID) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and molecular docking confirmed the correlation between five core compounds (quercetin, kaempferol, baicalein, ellagic acid, and baicalin) and six potential target genes (AKT1, CASP3, MAPK1, MAPK3, NOS2, and PTGS2). Molecular docking studies indicated that quercetin strongly interacted with six potential target proteins. Thus, these potential target proteins were closely related to TNF, HIF-1, FoxO, and PI3K-Akt signal pathways, suggesting that these factors and pathways may mediate the beneficial effects of GBH on atherosclerosis. Our results identify target genes and pathways that may mediate the clinical effects of the compounds contained within GBH on atherosclerosis.
| S-EPMC7764045 | biostudies-literature
Project description:BackgroundVascular dementia (VaD) is a degenerative cerebrovascular disease that leads to progressive decline of patients' cognitive ability and memory. Yizhi Tongmai (YZTM) decoction is an empirical prescription first formulated by Professor Guomin Si. Our previous experiments proved the effectiveness of this prescription in the treatment of VaD. In this study, we aimed to use network pharmacology and molecular docking technology to systematically explain the potential anti-VaD mechanism of YZTM.MethodsWe identified the core compounds of YZTM and their potential targets through the TCMSP, BATMAN, and SwissTargetPrediction databases. Then, we identified the molecular targets of YZTM in VaD using the Online Mendelian Inheritance in Man and GeneCards databases. The common targets of YZTM and VaD were screened out, and then the pathways of these target genes were analyzed using the Database for Annotation, Visualization and Integrated Discovery v6.8. Molecular docking was used to verify the relationship between the core compounds and proteins.ResultsThrough network pharmacology analysis, we discovered that the 5 core compounds in YZTM exert an anti-VaD effect. The potential mechanism of YZTM anti-VaD may be through inhibiting the NLRP3 inflammasome, TNF signaling pathway, and toll-like receptor signaling pathways. Subsequently, key compounds were docked with related proteins in the NLRP3 inflammasome (NLRP3, ASC, caspase-1, interleukin-18, and interleukin-1 β) using molecular docking technology. The compounds were found to spontaneously bind to the proteins.ConclusionsYZTM may exert an anti-VaD effect through inhibition of the NLRP3 inflammasome. In addition, TNF signaling pathway and toll-like receptor signaling pathway may also be its underlying mechanism. The application of network pharmacology and molecular docking technology may provide a novel method for research of Chinese herbal medicine. YZTM may also provide a complementary treatment option for patients with VaD.
| S-EPMC7867933 | biostudies-literature
Project description:To explore the potential active compounds and molecular mechanism of Xuefu Zhuyu decoction (XFZYD) in the treatment of atherosclerosis (AS) based on network pharmacology and molecular docking. The effective components and action targets of XFZYD were screened by using TCMSP database. And then, the action targets of AS were collected by GeneCards database. The intersection targets between the effective components' targets of XFZYD and AS-related action targets were used to construct PPI networks. GO and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed on these intersection targets. Finally, molecular docking software was used to excavate the active compounds of the core targets VEGFA and AKT1. We detected 225 active components of XFZYD, and found that quercetin, kaempferol, luteolin, naringenin, β-sitosterol, isorhamnetin, stigmasterol, baicalein, nobiletin, and β-carotene are the potential active compounds of XFZYD; STAT3, IL6, JUN, VEGFA, MAPK14, and AKT1 are the core target proteins of the active compounds, among which VEGFA and AKT1 are the key target proteins. PPI network results showed that β-carotene, quercetin, kaempferol, luteolin, and naringenin had higher degree values and more corresponding targets than other 5 active compounds and had the stable binding ability to regulatory proteins VEGFA and AKT1. The core components β-carotene, quercetin, kaempferol, and luteolin exerted their therapeutic effects on AS by acting on the key target proteins VEGFA and AKT1 to regulate fluid shear stress and the AGE-RAGE signaling pathway and IL-17 signaling pathway of diabetic complications of AS. The molecular docking results showed that VEGFA and AKT1 had great docking ability with the targeted active compounds, and β-carotene is the best. The active components of XFZYD, including β -carotene, quercetin, kamanol, and luteolin, can act on VEGFA and AKT1. These active ingredients play a role in alleviating and treating AS by regulating fluid shear stress and participating in signaling pathways such AS AGE-RAGE of atherosclerosis and diabetes mellitus complicated with AS. β-carotene is a potential inhibitor of VEGFA and AKT1 and treats AS through antioxidant action.
| S-EPMC9371493 | biostudies-literature
Project description:BackgroundTraditional Chinese medicine (TCM) has been used in China for a long time and is gradually gaining more and more recognition worldwide. Gualou Guizhi Decoction (GGD) has long been used as a folk medicine for the treatment of rheumatic diseases, but its bioactive components and therapeutic mechanisms are still unclear.MethodsAn integrated approach using network pharmacology and molecular docking and using methotrexate as a positive control drug.ResultsWe obtained 157 active ingredients of GGD, 7542 RA disease targets and 49 intersecting targets. GO and KEGG enrichment analysis revealed that their functions were mainly related to cytokine active metal ion binding, enzyme binding and DNA binding, and enriched in TNF signaling pathway, T cell receptor signaling pathway, Toll-like receptor signaling pathway, RA pathway and other signaling pathways that are closely related to RA. The molecular docking results show that the effector components of GGD bind better to the core targets of RA, and some are even better than methotrexate.ConclusionThe therapeutic effect of GGD for RA is achieved by affecting the core targets such as VEGFA, IL-1β, IL6, CXCL8, CCL2, and JUN, which together interfere with the tumor necrosis factor signaling pathway and RA pathway to treat RA. The above study provides new ideas for further exploration of this classic formula in the future.
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Project description:Myocardial infarction (MI) is one of the leading causes of death worldwide because of its high morbidity and mortality. Traditional Chinese Medicine compounds play a crucial role in preventing cardiovascular diseases. Danggui Sini Decoction (DSD) is widely used clinically for cardiovascular diseases. However, the mechanism, main components, and main targets of DSD in treating MI are still unclear. In this study, we utilized network pharmacology and molecular docking for exploration. MI-related genes were examined using the Genecards database, and the active ingredients of DSD were screened based on System Pharmacology Database and Analysis Platform of Traditional Chinese Medicine by oral bioavailability ≥ 30% and drug-likeness ≥ 0.18. The protein-protein interaction network diagram was generated using the STRING database. The DAVID web platform was used to carry out gene ontology and Kyoto encyclopedia of gene and genome signaling pathway analysis. DSD's screening study revealed 120 primary active ingredients and 561 putative active target genes. The main therapeutic targets were TP53, EGFR, AKT1, IL6, TNF, STAT3, IL1B, CTNNB1, SRC, MYC, JUN, and INS. Gene ontology and Kyoto encyclopedia of gene and genome analyses revealed that DSD treatment of MI mainly involves the positive regulation of the ERK1 and ERK2 cascades, positive regulation of cell proliferation, inflammatory responses, aging, and the MAPK cascade, along with other biological processes. The molecular docking results indicate that DSD drugs may interact with AKT1, EGFR, TP53, and TNF through formononetin, isorhamnetin, β-Sitosterol, and kaempferol, potentially contributing to the treatment of MI. By utilizing a multi-component, multi-pathway, and multi-target mode of action, DSD may have the potential to prevent MI.
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Project description:Buyang Huanwu Decoction, a traditional Chinese medicine decoction, is widely used to treat spinal cord injury in China. However, the underlying mechanism of this decoction in treating spinal cord injury is unclear. This study used network pharmacology and molecular docking to examine the pharmacological mechanism of Buyang Huanwu Decoction in prevention and treatment of spinal cord injury. The active compounds and target genes of Buyang Huanwu Decoction were collected from the Traditional Chinese Medicine Systems Pharmacology and the SwissTargetPrediction Database. The network diagram of "traditional Chinese medicine compound target" was constructed by Cytoscape software. Genetic data of spinal cord injury were obtained by GeneCards database. According to the intersection of Buyang Huanwu Decoction's targets and disease targets, the core targets were searched. The protein-protein interaction network were constructed using the STRING and BisoGenet platforms. Meanwhile, gene ontology enrichment and Kyoto encyclopedia of genes, and genome pathway were performed on the intersection targets by Metascape. Molecular docking technology was adopted to verify the combination of main components and core targets. A total of 109 active compounds and 5440 prediction targets were screened from 7 Chinese herbal medicines of Buyang Huanwu Decoction, with 98 active components and 49 related prediction targets being strongly linked to Spinal Cord Injury. By studying protein-protein interaction network, a total of 8 core proteins were identified, primarily interleukin-6, tumor protein P53, epidermal growth factor receptor, and others. Positive regulation of kinase activity regulation of reaction to inorganic chemicals are the basic biological processes. Buyang Huanwu Decoction cures Spinal Cord Injury primarily by moderating immunological inflammation, apoptosis, and oxidative stress, which involves the cancer pathway, the HIF-1 signaling pathway, the p53 signaling pathway, the MAPK signaling pathway, and so on. The results of molecular docking demonstrated that the primary components could attach to the target protein effectively. Finally, the mechanism of Buyang Huanwu Decoction in the treatment of spinal cord injury through multicomponent, multitarget, and multichannel was deeply explored. And it offers new ideas and directions for future research on the mechanism of the treatment of spinal cord injury.
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Project description:Atherosclerosis (AS) is a disease characterized by the buildup of fat and fibrous elements within the walls of arteries and is a primary factor in the occurrence of heart failure and mortality. The potential targets and mechanisms underlying the anti-atherosclerotic effects of avenanthramide (Avn) were investigated using network pharmacology, molecular docking, and molecular dynamics simulations. Target information for Avn A, B, and C was collected from the PubChem and Swiss Target Prediction databases. Potential therapeutic targets for AS were identified by mining the OMIM, DrugBank, DisGeNET, and GeneCards databases. A protein-protein interaction (PPI) network of shared targets was constructed and visualized using the STRING database and Cytoscape 3.9.1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were conducted to explore the functions of core targets within the PPI network. Molecular docking was performed using the AutoDockTool to verify the correlation between the 3 types of Avns and the core targets. Furthermore, molecular dynamics simulations were performed using the 3 highest molecular docking binding energies to validate and confirm the binding of potent compounds to the target. The results revealed 109 respective targets for Avn, with 55 common targets identified by intersection with AS-related targets. Five pivotal genes, matrix metalloproteinase-9 (MMP9), epidermal growth factor receptor (EGFR), ICAM1, CASP3, and MMP2, were selected from the PPI network. Molecular docking results showed a strong binding affinity between Avn and MMP9 as well as EGFR. Molecular dynamics simulations showed good binding capacity of Avn A, B, and C with EGFR, validating the reliability of the molecular docking results. Avn potentially exerts its effects through multiple targets and displays anti-inflammatory and anti-oxidative stress properties.
| S-EPMC11666176 | biostudies-literature
Project description:IntroductionNetwork pharmacology is in line with the holistic characteristics of TCM and can be used to elucidate the complex network of interactions between disease-specific genes and compounds in TCM herbal medicines. Here, we investigate the pharmacological mechanism of Xiaokui Jiedu decoction (XJD) for the treatment of ulcerative colitis (UC).MethodsThe Computational Systems Biology Laboratory Platform (TCMSP) database was searched and screened for the active ingredients of all drugs in XJD. The Uniport database was used to retrieve possible gene targets for the therapeutic effects of XJD. GeneCards, PharmGKB, TTD, and OMIM databases were used to retrieve XJD-related gene targets. A herb-compound-protein network and a protein-protein interaction (PPI) network were constructed, and hub genes were screened for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, molecular docking was performed to validate the interrelationship between disease target proteins and active drug components.ResultsA total of 135 XJD potential action targets, 5097 UC-related gene targets, and 103 XJD-UC intersection gene targets were screened. The hub gene targets of XJD that exert therapeutic effects on UC are RB1, MAPK1, TP53, JUN, NR3C1, MAPK3, and ESR1. GO enrichment analysis showed 741 biofunctional enrichments, and KEGG enrichment analysis showed 124 related pathway enrichments. Molecular docking showed that the active components of XJD (β-sitosterol, kaempferol, formononetin, quercetin, and luteolin) showed good binding activities to five of the six hub gene targets. Discussion. The active ingredients of XJD (β-sitosterol, kaempferol, formononetin, quercetin, and luteolin) may regulate the inflammatory and oxidative stress-related pathways of colon cells during the course of UC by binding to the hub gene targets. This may be a potential mechanism of XJD in the treatment of UC.
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