scholarly journals Network Pharmacology Identifies the Mechanisms of Action of Tongxie Anchang Decoction in the Treatment of Irritable Bowel Syndrome with Diarrhea Predominant

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Xiang Tan ◽  
Wenjing Pei ◽  
Chune Xie ◽  
Zhibin Wang ◽  
Tangyou Mao ◽  
...  
Keyword(s):  
Irritable Bowel Syndrome ◽  
Target Genes ◽  
Alternative Therapy ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Complementary And Alternative Therapy ◽  
Pharmacological Mechanism ◽  
Target Network ◽  
Irritable Bowel

Aim. This study aims to uncover the pharmacological mechanism of Tongxie Anchang Decoction (TXACD), a new and effective traditional Chinese medicine (TCM) prescription, for treating irritable bowel syndrome with diarrhea predominant (IBS-D) using network pharmacology. Methods. The active compounds and putative targets of TXACD were retrieved from TCMSP database and published literature; related target genes of IBS-D were retrieved from GeneCards; PPI network of the common target hub gene was constructed by STRING. Furthermore, these hub genes were analyzed using gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Results. A total of 54 active compounds and 639 targets were identified through a database search. The compound-target network was constructed, and the key compounds were screened out according to the degree. By using the PPI and GO and KEGG enrichment analyses, the pharmacological mechanism network of TXACD in the treatment of IBS-D was constructed. Conclusions. This study revealed the possible mechanisms by which TXACD treatment alleviated IBS-D involvement in the modulation of multiple targets and multiple pathways, including the immune regulation, inflammatory response, and oxidative stress. These findings provide novel insights into the regulatory role of TXACD in the prevention and treatment of IBS-D and hold promise for herb-based complementary and alternative therapy.

scholarly journals Exploring the Pharmacological Mechanism of Cassiae Semen a Cting on Cataracts Based on a Network Pharmacology Approach

2020 ◽  
Author(s):  
Ying Zhong ◽  
Youfa Fang
Keyword(s):  
Signaling Pathway ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Pharmacological Mechanism ◽  
Ppi Networks ◽  
Target Network ◽  
Central Network

Abstract BackgroundCassiae Semen (CS) is one of the most well-known herbs used in the treatment of cataracts in China. However, the potential mechanisms of its anti-cataracts effects have not been fully explored.MethodThe active compounds of CS were obtained from TCMSP database, and their targets were retrieved from the TCMSP, STITCH and DrugBank databases. Cataracts related target genes were identified from the GeneCard, Malacard, and OMIM databases. GO and KEGG analysis were performed using DAVID online tools, and Cytoscape were used to construct compound-targets network and protein-protein interaction (PPI) networks, cluster analysis were carried out using MCODE plugin for Cytoscape.ResultsWe obtained 13 active compounds from CS and 105 targets in total to construct a compound-target network, which indicated that emodin, stigmastero, and rhein served as the main ingredients in CS. A total of 238 cataracts related targets were identified from public databases. PPI networks of compound targets and cataract-related targets were constructed and merged to obtained the central network, enrichment analysis showed 50 key targets in the central network enriched in several important signaling pathways, such as thyroid hormone signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway. The top 4 genes with higher degree in the central network were TP53, HSP90, ESR1, EGFR, indicating their important roles in the treatment of cataracts.ConclusionsThe present study systematically revealed the multi-target mechanisms of CS on cataracts using network pharmacology approach, and provided indications for further mechanistic studies and also for the development of CS as a potential treatment for cataracts patients.

scholarly journals Revealing the Pharmacological Mechanism of Acorus tatarinowii in the Treatment of Ischemic Stroke Based on Network Pharmacology

2020 ◽  
Vol 2020 ◽  
pp. 1-16
Author(s):  
FengZhi Liu ◽  
Qian Zhao ◽  
Suxian Liu ◽  
Yingzhi Xu ◽  
Dongrui Zhou ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Target Genes ◽  
Enrichment Analysis ◽  
Basic Mechanism ◽  
Signal Pathway ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Pharmacological Mechanism ◽  
Interactive Network ◽  
Acorus Tatarinowii

Aim. Stroke is the second significant cause for death, with ischemic stroke (IS) being the main type threatening human being’s health. Acorus tatarinowii (AT) is widely used in the treatment of Alzheimer disease, epilepsy, depression, and stroke, which leads to disorders of consciousness disease. However, the systemic mechanism of AT treating IS is unexplicit. This article is supposed to explain why AT has an effect on the treatment of IS in a comprehensive and systematic way by network pharmacology. Methods and Materials. ADME (absorbed, distributed, metabolized, and excreted) is an important property for screening-related compounds in AT, which were screening out of TCMSP, TCMID, Chemistry Database, and literature from CNKI. Then, these targets related to screened compounds were predicted via Swiss Targets, when AT-related targets database was established. The gene targets related to IS were collected from DisGeNET and GeneCards. IS-AT is a common protein interactive network established by STRING Database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were analysed by IS-AT common target genes. Cytoscape software was used to establish a visualized network for active compounds-core targets and core target proteins-proteins interactive network. Furthermore, we drew a signal pathway picture about its effect to reveal the basic mechanism of AT against IS systematically. Results. There were 53 active compounds screened from AT, inferring the main therapeutic substances as follows: bisasaricin, 3-cyclohexene-1-methanol-α,α,4-trimethyl,acetate, cis,cis,cis-7,10,13-hexadecatrienal, hydroxyacoronene, nerolidol, galgravin, veraguensin, 2′-o-methyl isoliquiritigenin, gamma-asarone, and alpha-asarone. We obtained 398 related targets, 63 of which were the same as the IS-related genes from targets prediction. Except for GRM2, remaining 62 target genes have an interactive relation, respectively. The top 10 degree core target genes were IL6, TNF, IL1B, TLR4, NOS3, MAPK1, PTGS2, VEGFA, JUN, and MMP9. There were more than 20 terms of biological process, 7 terms of cellular components, and 14 terms of molecular function through GO enrichment analysis and 13 terms of signal pathway from KEGG enrichment analysis based on P < 0.05 . Conclusion. AT had a therapeutic effect for ischemic via multicomponent, multitarget, and multisignal pathway, which provided a novel research aspect for AT against IS.

scholarly journals A Network Pharmacology Approach to Explore the Pharmacological Mechanism of Xiaoyao Powder on Anovulatory Infertility

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Huiping Liu ◽  
Liuting Zeng ◽  
Kailin Yang ◽  
Guomin Zhang
Keyword(s):  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Active Compounds ◽  
Pharmacological Mechanism ◽  
Go Enrichment ◽  
Human Proteins ◽  
Network Pictures ◽  
Go Enrichment Analysis ◽  
Anovulatory Infertility

Aim.To explore the pharmacological mechanism of Xiaoyao powder (XYP) on anovulatory infertility by a network pharmacology approach.Method.Collect XYP’s active compounds by traditional Chinese medicine (TCM) databases, and input them into PharmMapper to get their targets. Then note these targets by Kyoto Encyclopedia of Genes and Genomes (KEGG) and filter out targets that can be noted by human signal pathway. Get the information of modern pharmacology of active compounds and recipe’s traditional effects through databases. Acquire infertility targets by Therapeutic Target Database (TTD). Collect the interactions of all the targets and other human proteins via String and INACT. Put all the targets into the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to do GO enrichment analysis. Finally, draw the network by Cytoscape by the information above.Result.Six network pictures and two GO enrichment analysis pictures are visualized.Conclusion.According to this network pharmacology approach some signal pathways of XYP acting on infertility are found for the first time. Some biological processes can also be identified as XYP’s effects on anovulatory infertility. We believe that evaluating the efficacy of TCM recipes and uncovering the pharmacological mechanism on a systematic level will be a significant method for future studies.

scholarly journals Deciphering the Key Pharmacological Pathways and Targets of Yisui Qinghuang Powder That Acts on Myelodysplastic Syndromes Using a Network Pharmacology-Based Strategy

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Zijian Han ◽  
Luping Song ◽  
Kele Qi ◽  
Yang Ding ◽  
Mingjun Wei ◽  
...  
Keyword(s):  
Myelodysplastic Syndromes ◽  
Target Genes ◽  
Network Pharmacology ◽  
Analysis Tool ◽  
Antitumor Effects ◽  
Active Compounds ◽  
Pharmacological Mechanism ◽  
Putative Target ◽  
Target Disease ◽  
Qinghuang Powder

Background. Yisui Qinghuang powder (YSQHP) is an effective traditional Chinese medicinal formulation used for the treatment of myelodysplastic syndromes (MDS). However, its pharmacological mechanism of action is unclear. Materials and Methods. In this study, the active compounds of YSQHP were screened using the traditional Chinese medicine systems pharmacology (TCMSP) and HerDing databases, and the putative target genes of YSQHP were predicted using the STITCH and DrugBank databases. Then, we further screened the correlative biotargets of YSQHP and MDS. Finally, the compound-target-disease (C-T-D) network was conducted using Cytoscape, while GO and KEGG analyses were conducted using R software. Furthermore, DDI-CPI, a web molecular docking analysis tool, was used to verify potential targets and pathways. Finally, binding site analysis was performed to identify core targets using MOE software. Results. Our results identified 19 active compounds and 273 putative target genes of YSQHP. The findings of the C-T-D network revealed that Rb1, CASP3, BCL2, and MAPK3 showed the most number of interactions, whereas indirubin, tryptanthrin, G-Rg1, G-Rb1, and G-Rh2 showed the most number of potential targets. The GO analysis showed that 17 proteins were related with STPK activity, PUP ligase binding, and kinase regulator activity. The KEGG analysis showed that PI3K/AKT, apoptosis, and the p53 pathways were the main pathways involved. DDI-CPI identified the top 25 proteins related with PI3K/AKT, apoptosis, and the p53 pathways. CASP8, GSK3B, PRKCA, and VEGFR2 were identified as the correlative biotargets of DDI-CPI and PPI, and their binding sites were found to be indirubin, G-Rh2, and G-Rf. Conclusion. Taken together, our results revealed that YSQHP likely exerts its antitumor effects by binding to CASP8, GSK3B, PRKCA, and VEGFR2 and by regulating the apoptosis, p53, and PI3K/AKT pathways.

scholarly journals Network Pharmacology Strategy to Investigate the Pharmacological Mechanism of Siwu Decoction on Primary Dysmenorrhea and Molecular Docking Verification

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Dandan Jiang ◽  
Xiaoyan Wang ◽  
Lijun Tian ◽  
Yufeng Zhang
Keyword(s):  
Molecular Docking ◽  
Target Genes ◽  
Network Pharmacology ◽  
Primary Dysmenorrhea ◽  
Ppi Network ◽  
Active Compounds ◽  
Docking Simulations ◽  
Active Target ◽  
Target Network ◽  
Compound Target

Objective. To study the pharmacological mechanisms of Siwu decoction (SWD) on primary dysmenorrhea (PDM) and verify with molecular docking. Methods. The  Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was utilized to acquire the active compounds and their corresponding target genes. The GeneCards database was utilized in the search for target genes that were associated with PDM. The intersection genes from the active target genes of SWD and those associated with PDM represented the active target genes of SWD that act on PDM. The Gene Ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were both carried out by RGUI 3.6.1 and Cytoscape 3.6.0 software. Cytoscape was also utilized for creating a compound-target network, and a protein-protein interaction (PPI) network was created through the STRING database. Molecular docking simulations of the macromolecular protein target receptors and their corresponding compounds were performed using AutoDockTool 1.5.6 and AutoDock Vina software. Results. We identified 14 active compounds as well as 97 active target genes of SWD by using the TCMSP. We compared the 97 active target genes of SWD to the 299 target genes related to PDM, and 23 active target genes for SWD that act on PDM which correlated with 11 active compounds were detected. The compound-target network as well as the PPI network were created, in addition to selecting the most essential compounds and their targets in order to create a key compound-target network. The most essential compounds were kaempferol, beta-sitosterol, stigmasterol, and myricanone. The key targets were AKT1, PTGS2, ESR1, AHR, CASP3, and PGR. Lastly, molecular docking was used to confirm binding of the target with its corresponding compound. Conclusion. The pharmacological mechanisms of SWD that act on PDM were investigated, and the active compounds in the SWD for treating PDM were further verified.

scholarly journals Effects and Components of Herb Pair Huanglian-Banxia on Diabetic Gastroparesis by Network Pharmacology

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Guoqiang Liang ◽  
Lurong Zhang ◽  
Guorong Jiang ◽  
Xuanyi Chen ◽  
Yang Zong ◽  
...  
Keyword(s):  
Alternative Therapy ◽  
Diabetic Gastroparesis ◽  
Network Pharmacology ◽  
Active Components ◽  
Complementary And Alternative Therapy ◽  
Pharmacological Approach ◽  
Target Network ◽  
Heavy Burden ◽  
Bioactive Ingredients ◽  
Coptidis Rhizoma

Diabetic gastroparesis (DGP) is a serious and chronic complication of long-standing diabetes mellitus, which brings a heavy burden to individuals and society. Traditional Chinese medicine (TCM) is considered a complementary and alternative therapy for DGP patients. Huanglian (Coptidis Rhizoma, HL) and Banxia (Pinelliae Rhizoma, BX) combined as herb pair have been frequently used in TCM prescriptions, which can effectively treat DGP in China. In this article, a practical application of TCM network pharmacological approach was used for the research on herb pair HL-BX in the treatment of DGP. Firstly, twenty-seven potential active components of HL-BX were screened from the TCMSP database, and their potential targets were also retrieved. Then, the compound-target network and PPI network were constructed from predicted common targets, and several key targets were found based on the degree of the network. Next, GO and KEGG enrichment analyses were conducted to obtain several significantly enriched terms. Finally, the experimental verification was made. The results demonstrated that network pharmacological approach was a powerful means for identifying bioactive ingredients and mechanisms of action for TCM. Network pharmacology provided an effective strategy for TCM modern research.

scholarly journals Network Pharmacology Analysis of the active components and anticancer targets of Rhubarb

2021 ◽  
Author(s):  
Hu Junrui ◽  
Duan Yongqiang ◽  
Cui Gongning ◽  
Luo Qiang ◽  
Xi Shanshan ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Drug Targets ◽  
Target Genes ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Active Components ◽  
Active Compounds ◽  
Cellular Targets ◽  
Kegg Pathway Analysis

AbstractTo investigate the mechanisms and active components governing the anticancer activity of rhubarb.The TCMSP database was screened to identify the active components of rhubarb and Swiss target predictions were generated to predict their cellular targets. TTD and OMIM databases were used to predict tumor-related target genes. "Cytoscape" was used to construct drug targets. PPI network analysis, GO enrichment analysis and KEGG pathway analysis of the key targets were investigated using String and David databases. A total of 33 components and 116 corresponding targets were screened. Amongst them, the key active compounds in rhubarb included emodin, aloe emodin, β-sitosterol, emodin methyl ether and rhein, which were predicted to target TP53, AKT1, STAT3, PIK3CA, HRAS, and VEGFA. GO analysis revealed that the cellular targets clustered into 159 biological processes, including those involved in cellular composition (n=24) and molecular functions (n=42, P<0.01). KEGG pathway analysis revealed 85 (P < 0.01) pathways related to cancer. The active compounds in rhubarb target TP53, AKT1 and PIK3CA. Rhubarb therefore regulates cancer development through an array of biological pathways.

scholarly journals Exploring Molecular Mechanism of Traditional Chinese Medicine Euphorbiae Semen on Reversing of Multidrug Resistance in Leukemia Based on Network Pharmacology Strategy and Molecular Docking Technology

2020 ◽  
Author(s):  
Xiao Song ◽  
Fei Guo ◽  
Xiao-Chen Sun ◽  
Shu-Yue Wang ◽  
Yao-Hui Yuan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Biological Functions ◽  
Active Compounds ◽  
The Core ◽  
The World ◽  
Target Network ◽  
Compound Target

Abstract Background: Leukemia was listed by the World Health Organization as one of the five most intractable diseases in the world. The multi-drug resistance (MDR) of leukemia cells limits the efficacy of anti-tumor drugs and is the major reason for the chemotherapy failure and recurrence of leukemia chemotherapy. Some studies have shown that Euphorbiae semen (ES) possesses the characteristics of new therapeutic drugs for MDR. However, the molecular mechanisms and active compounds have not yet been fully clarified. Therefore, there is a need for explore its active compounds and demonstrate its mechanisms through network pharmacology and molecular docking technology.Method: First, the TCMSP database was searched and screened the active compounds of the ES, supplemented with compounds verified by literature, so as to further identify the core compounds in the active ingredient. Simultaneously, the TCMSP and Swiss database were searched to the targets of active compounds, and the targets of reverses leukemia multidrug resistance (RL-MDR) were screened in the relevant databases, such as GeneCards and DrugBank. Then, the targets of active compounds were intersected with RL-MDR targets to obtain potential targets of ES acting on MDR. The compound–target network was constructed by Cytoscape. The target protein–protein interaction network was built using STRING and Cytoscape database. Second, the R language and DAVID database were used to analyse Gene Ontology (GO) biological functions analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) signal pathways enrichment. Finally, molecular docking method was utilized to investigate the binding activity between the core targets and the active compounds of ES.Results: Compound–target network mainly contained 22 compounds and 81 corresponding targets. Finally, seven components in ES were selected and 10 core targets were identified; Key targets contained JUN, CASP3, MAOA, AR, PPARG, DRD2, ADRA2A, CHRM2, PTGS2 and MAPK14. GO enrichment analysis indicated the main biological functions of potential genes of ES in the treatment of MDR. KEGG pathway enrichment analysis showed the main pathways, mainly including apoptosis, pathways in cancer, p53 signaling pathway, VEGF signaling pathway, TNF signaling pathway and PI3K–Akt signaling pathway. Finally, we chose the top 10 common targets for molecular docking with the 7 active compounds of ES. The results of molecular docking indicated that the compounds of ES, which had good affinity with targets. Conclusion: The molecular mechanism of ES in the treatment of MDR showed the synergistic reaction of multi-compound, multi-target, and multi-pathway of traditional Chinese medicine, which provided ideas for further clinical research.

Study on the Anti-Tumor Mechanism and Target of Triptolide based on Network Pharmacology and Molecular Docking

2021 ◽  
Vol 16 ◽  
Author(s):  
Tao Zou ◽  
Yuanqiong Huang ◽  
Yifan Hu ◽  
Mingyu Wu ◽  
Yueshui Zhao ◽  
...  
Keyword(s):  
Target Genes ◽  
Inflammatory Responses ◽  
Tumor Development ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Therapeutic Effects ◽  
Specific Target ◽  
Pharmacological Mechanism ◽  
The Core ◽  
Core Genes

Background: According to the special physiological and pharmacological activities of natural compounds, many drugs with special therapeutic effects have been developed. The triptolide (TP) is a kind of natural anti-tumor drug with a world patent, but its target and mechanism are yet not known. Objective: The study aims to explore and predict the target and mechanism of TP on non-small cell lung cancer (NSCLC), pancreatic cancer (PC) and colorectal cancer (CC) through network pharmacology technology. Methods: We screened the core targets of TP with NSCLC, PC and CC, respectively, and carried out network analysis, enrichment analysis and ligand-receptor docking to clarify its potential pharmacological mechanism. Results: By screening the core genes between TP with NSCLC, PC and CC, respectively, it was found that PTGS2 was the common target gene in the three cancers. NSCLC, CCL2, IL6, HMOX1 and COL1A1 are the specific target genes, while MMP2, JUN, and CXCL8 are the specific target genes in PC. In CC, the specific target genes includeERBB2, VEGFA, STAT1 andMAPK8. In enrichment analysis, it was found that the NF- κB, toll-like receptors and IL-17 signaling pathway were mainly involved in TP for these cancers. The binding energy of TP to the core target is less than that of cyclophosphamide. Conclusions: This study preliminarily revealed that TP may prevent and treat cancers\ through multiple targets and pathways. The possible mechanisms of TP include regulating immune and inflammatory responses, promoting apoptosis and inhibiting tumor development. It shows that TP may have a potential in treating kinds of tumors.

scholarly journals Deciphering the Molecular Targets and Mechanisms of HGWD in the Treatment of Rheumatoid Arthritis via Network Pharmacology and Molecular Docking

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Wei Liu ◽  
Yihua Fan ◽  
Chunying Tian ◽  
Yue Jin ◽  
Shaopeng Du ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Molecular Docking ◽  
Signaling Pathway ◽  
Differentially Expressed Genes ◽  
Target Genes ◽  
Differentially Expressed ◽  
Network Pharmacology ◽  
Active Compounds ◽  
Target Proteins ◽  
Target Network

Background. Huangqi Guizhi Wuwu Decoction (HGWD) has been applied in the treatment of joint pain for more than 1000 years in China. Currently, most physicians use HGWD to treat rheumatoid arthritis (RA), and it has proved to have high efficacy. Therefore, it is necessary to explore the potential mechanism of action of HGWD in RA treatment based on network pharmacology and molecular docking methods. Methods. The active compounds of HGWD were collected, and their targets were identified from the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and DrugBank database, respectively. The RA-related targets were retrieved by analyzing the differentially expressed genes between RA patients and healthy individuals. Subsequently, the compound-target network of HGWD was constructed and visualized through Cytoscape 3.8.0 software. Protein-protein interaction (PPI) network was constructed to explore the potential mechanisms of HGWD on RA using the plugin BisoGenet of Cytoscape 3.8.0 software. Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed in R software (Bioconductor, clusterProfiler). Afterward, molecular docking was used to analyze the binding force of the top 10 active compounds with target proteins of VCAM1, CTNNB1, and JUN. Results. Cumulatively, 790 active compounds and 1006 targets of HGWD were identified. A total of 4570 differentially expressed genes of RA with a p value <0.05 and log 2fold change > 0.5 were collected. Moreover, 739 GO entries of HGWD on RA were identified, and 79 pathways were screened based on GO and KEGG analysis. The core target gene of HGWD in RA treatment was JUN. Other key target genes included FOS, CCND1, IL6, E2F2, and ICAM1. It was confirmed that the TNF signaling pathway and IL-17 signaling pathway are important pathways of HGWD in the treatment of RA. The molecular docking results revealed that the top 10 active compounds of HGWD had a strong binding to the target proteins of VCAM1, CTNNB1, and JUN. Conclusion. HGWD has important active compounds such as quercetin, kaempferol, and beta-sitosterol, which exert its therapeutic effect on multiple targets and multiple pathways.

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