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 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 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 A Network Pharmacology Perspective Investigation of the Pharmacological Mechanisms of the Herbal Drug FDY003 in Gastric Cancer

2022 ◽  
Vol 17 (1) ◽  
pp. 1934578X2110730
Author(s):  
Ho-Sung Lee ◽  
In-Hee Lee ◽  
Kyungrae Kang ◽  
Sang-In Park ◽  
Minho Jung ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cellular Proliferation ◽  
Malignant Tumors ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Herbal Drug ◽  
Cellular Processes ◽  
Go Enrichment ◽  
Phytochemical Compounds ◽  
Go Enrichment Analysis

Gastric cancer (GC) is one of the most common and deadly malignant tumors worldwide. While the application of herbal drugs for GC treatment is increasing, the multicompound–multitarget pharmacological mechanisms involved are yet to be elucidated. By adopting a network pharmacology strategy, we investigated the properties of the anticancer herbal drug FDY003 against GC. We found that FDY003 reduced the viability of human GC cells and enhanced their chemosensitivity. We also identified 8 active phytochemical compounds in FDY003 that target 70 GC-associated genes and proteins. Gene ontology (GO) enrichment analysis suggested that the targets of FDY003 are involved in various cellular processes, such as cellular proliferation, survival, and death. We further identified various major FDY003 target GC-associated pathways, including PIK3-Akt, MAPK, Ras, HIF-1, ErbB, and p53 pathways. Taken together, the overall analysis presents insight at the systems level into the pharmacological activity of FDY003 against GC.

scholarly journals The Mechanism of Aidi Injection on Breast Cancer Based on Network Pharmacologyanalysis

2020 ◽  
Author(s):  
Jing Su ◽  
Kedi Liu ◽  
Xingru Tao ◽  
Fei Li ◽  
Shi Zhao ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Bioactive Components ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
Pharmacological Mechanism ◽  
Target Network ◽  
Aidi Injection

Abstract Background: Aidi injection (ADI)is a Chinese patent medicine with anti-cancer effect, which has been used to treat breast cancer (BC) in China for many years, but its potential pharmacological mechanism is still indeterminacy. In this resaearch, network pharmacology, a systematic and comprehensive approach, was used to reveal ADI's potential pharmacological mechanism in treating BC for the first time.Methods: Databases were used to collect targets related to the bioactive components of ADI and BC. the relevant networks were established by the string database, and were screened potential bioactive components and core targets. Eventually, core targets and pathway enrichment were analyzed by DAVID database.Results: As the results showed, we collected 99 bioactive ingredients,345 ADI-related targets after deduplication and 368 BC-related targets. Of these, 108 common targets were overlapped. We then performed an enrichment analysis on the common target network and the protein-protein interaction (PPI) network.Conclusion: The results showed that ADI may inhibit breast cancer through seven important signal pathways involved in the "regulation of vascular endothelial function", "inflammatory response" and "apoptosis” biological processes. Through further clustering and enrichment analysis of the PPI network of ADI’s bioactive component targets and BC-related targets, we found that cancer, ErbB, MAPK, TLR, chemokine, p53 and cell cycle signaling pathway, mainly contributed to the effects of ADI in treating BC. In conclusion, this study reveals the possible mechanism of ADI in treating BC, and provides a new direction for drug development for ADI in treating BC.

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 The Mechanism of Prevention and Treatment of Maxing Shigan Decoction on Pulmonary Heart Injury Caused by Novel Coronavirus Pneumonia

2020 ◽  
Author(s):  
Dongling Liu ◽  
Jing Su ◽  
Wenqian Hou ◽  
Weiyu Ren ◽  
Yijun Zheng ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Myocardial Injury ◽  
Enrichment Analysis ◽  
Converting Enzyme ◽  
Active Compounds ◽  
Angiotensin Converting Enzyme 2 ◽  
Gm Csf ◽  
Go Enrichment ◽  
Heart Injury ◽  
Go Enrichment Analysis

Abstract Background To explore the mechanism of Maxing Shigan Decoction in the treatment of myocardial injury and lung injury through network pharmacology and molecular docking technology. Methods In Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (BATMAN-TCM) and the Comparative Toxicogenomics Database, National Center for Biotechnology Information database, Online Mendelian Inheritance in Man database, the compounds and targets of each drug in Maxing Shigan Decoction and the targets of “acute lung intervention” and “myocardial injury” diseases were searched. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed by the DAVID database. GOLD 5.1 was used for molecular docking. Results Maxing Shigan Decoction includes 327 compounds and 2722 targets, including 30 key targets. 2125 items were obtained by GO enrichment analysis, including 2047 items of Biological Process, 28 items of Cell Composition and 50 items of Molecular Function. The KEGG pathway was enriched to obtain 149 pathways. The results of molecular docking showed that Gancaonin H and Licorice Glycoside E were well combined with Angiotensin-Converting Enzyme 2-A (ACE2-A) and Angiotensin-Converting Enzyme 2-B (ACE2-B), respectively, and Licorice was well combined with Granulocyte-Macrophage Colony Stimulating Factor (GM-CSF) and Interleukin 6 (IL-6). Supraene is an active compound of Ephedra. It has good binding with ACE2-A, ACE2-B, GM-CSF and IL-6, respectively. (6Z, 10E, 14E, 18E)-2, 6, 10, 15, 19, 23- hexamethyletracosa-2, 6, 10, 14, 18, 22- hexaene are the active compounds of Almond, which are well combined with ACE2-A, ACE2-B, GM-CSF and IL-6. Conclusion Maxing Shigan Decoction may act on ACE2, GM-CSF and IL-6 targets through the active compounds Supraene of Ephedra, and Almond (6Z, 10E, 14E, 18E)-2, 6, 10, 15, 19, 23-hexamethyletracosa-2, 6, 10, 14, 18, 22-hexaene. Gancainin H and licorice Glycide E are the active compounds of Licorice, act on A and B sites of ACE2 respectively, and Glycyrin acts on GM-CSF and IL-6 targets, coordinating multiple signal pathways to play anti-inflammatory and antiviral roles to prevent and treat lung and heart injury caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2).

scholarly journals Network pharmacology and molecular docking analysis on molecular targets and mechanisms of Angelicae Pubescentis Radix in the treatment of rheumatoid arthritis

2021 ◽  
Author(s):  
yanni yang ◽  
yirixiati aihaiti ◽  
peng xu ◽  
haishi zheng
Keyword(s):  
Rheumatoid Arthritis ◽  
Molecular Docking ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Receptor Interaction ◽  
Active Components ◽  
Target Proteins ◽  
Go Enrichment ◽  
Go Enrichment Analysis

Abstract Purpose:To explore the potential target proteins underlying the effect of Angelicae Pubescentis Radix(APR) on rheumatoid arthritis (RA) using a network pharmacology and molecular docking approach .Methods:First, the active components and target proteins of APR and RA related disease targets were obtained from the TCMSP, Gene Card,OMIM,DisGeNET and STRING databases. Then the active ingredient target in the RA network diagram was drawn using Cytoscape 3.7.1 software. Protein-protein interaction analysis, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analyses were carried out using the STRING and David databases. The crystal structures of RA related targets were retrieved from the RCSB PDB database. Finally, the potential active compounds and their related targets were validated using molecular docking technology.Results: Five active components of Angelicae Pubescentis Radix(APR) were screened out, including ammidin, isoimperatorin, beta-sitosterol, O-acetylcolumbianetin and angelicone and 80 key targets including MAPK8,EGFR,PTGS2,CASPASE3,MTOR,SRC,KDR,MAPK1,NOS3 and MAPK14, etc were obtained. GO enrichment analysis showed that 222 biological processes, 34 cell components and 72 molecular functions were identified; KEGG analysis showed that the targets of APR in the treatment of RA were significantly enriched in pathways in cancer, the PI3K−Akt signaling pathway, Proteoglycans in cancer, osteoclast differentiation, neuroactive ligand−receptor interaction, tuberculosis,TNF signaling pathway, serotonergic synapse, Rap1 signaling pathway,cAMP signaling pathway. The results of molecular docking showed that ammidin, isoimperatorin, beta-sitosterol, O-acetylcolumbianetin and angelicone had strong affinity for PTGS2, EGFR and MAPK8.Conclusion: APR treats RA through the characteristics of multi-component, multi-target and multi-pathway regulation.

scholarly journals Exploring the Molecular Mechanism of Liuwei Dihuang Pills for Treating Diabetic Nephropathy by Combined Network Pharmacology and Molecular Docking

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Gaoxiang Wang ◽  
Lin Zeng ◽  
Qian Huang ◽  
Zhaoqi Lu ◽  
Ruiqing Sui ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Molecular Docking ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Active Components ◽  
Active Compounds ◽  
Liuwei Dihuang Pills ◽  
Web Platform

Background. Diabetic nephropathy (DN) is a common and serious complication of diabetes, but without a satisfactory treatment strategy till now. Liuwei Dihuang pills (LDP), an effective Chinese medicinal formula, has been used to treat DN for more than 1000 years. However, its underlying mechanism of action is still vague. Methods. Active compounds and corresponding targets of LDP were predicted from the TCMSP database. DN disease targets were extracted from the OMIM, GeneCards, TTD, DisGeNET, and DrugBank databases. Subsequently, the “herbal-compound-target” network and protein-protein interaction (PPI) network were constructed and analyzed via the STRING web platform and Cytoscape software. GO functional and KEGG pathway enrichment analyses were carried out on the Metascape web platform. Molecular docking utilized AutoDock Vina and PyMOL software. Results. 41 active components and 186 corresponding targets of LDP were screened out. 131 common targets of LDP and DN were acquired. Quercetin, kaempferol, beta-sitosterol, diosgenin, and stigmasterol could be defined as five crucial compounds. JUN, MAPK8, AKT1, EGF, TP53, VEGFA, MMP9, MAPK1, and TNF might be the nine key targets. The enrichment analysis showed that common targets were mainly associated with inflammation reaction, oxidative stress, immune regulation, and cell apoptosis. AGE-RAGE and IL-17 were the suggested two significant signal pathways. Molecular docking revealed that the nine key targets could closely bind to their corresponding active compounds. Conclusion. The present study fully reveals the multicompound’s and multitarget’s characteristics of LDP in DN treatment. Furthermore, this study provides valuable evidence for further scientific research of the pharmacological mechanisms and broader clinical application.

scholarly journals Network Pharmacology-Based Identification of the Mechanisms of Shen-Qi Compound Formula in Treating Diabetes Mellitus

2020 ◽  
Vol 2020 ◽  
pp. 1-15 ◽  
Author(s):  
Zhipeng Hu ◽  
Maoyi Yang ◽  
Liangjun Yang ◽  
Chunguang Xie ◽  
Hong Gao ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Active Components ◽  
Protein Protein Interaction ◽  
Go Enrichment ◽  
System Pharmacology ◽  
Target Network ◽  
Integrated Pathway ◽  
Go Enrichment Analysis

Aim. The purpose of this research is to identify the mechanisms of Shen-Qi compound formula (SQC), a traditional Chinese medicine (TCM), for treating diabetes mellitus (DM) using system pharmacology. Methods. The active components and therapeutic targets were identified, and these targets were analyzed using gene ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein-protein interaction (PPI) analysis. Finally, an integrated pathway was constructed to show the mechanisms of SQC. Results. A total of 282 active components and 195 targets were identified through a database search. The component-target network was constructed, and the key components were screened out according to their degree. Through the GO, PPI, and KEGG analyses, the mechanism network of SQC treating DM was constructed. Conclusions. This study shows that the mechanisms of SQC treating DM are related to various pathways and targets. This study provides a good foundation and basis for further in-depth verification and clinical application.

scholarly journals Exploration of underlying molecular mechanism of Lycii Cortex in Treating Type 2 Diabetes Mellitus Based on Network Pharmacology and Molecular Docking

2021 ◽  
Vol 233 ◽  
pp. 02007
Author(s):  
Dongjun Li ◽  
Denghui Wang ◽  
Shikai Yan
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Kegg Pathway Analysis ◽  
Go Enrichment ◽  
Core Components ◽  
Receptor Signaling Pathway ◽  
Go Enrichment Analysis

Objective: To explore the potential molecular mechanism of Lycii Cortex in treating type 2 diabetes mellitus (T2DM) by virtue of network pharmacology and molecular docking method. Methods: Ingredients of Lycii Cortex were collected from TCMSP and BATMAN-TCM databases, and the corresponding targets and T2DM-related targets were obtained respectively from SwissTargetPrediction and GenCards databases. Venn diagram was applied to derive the potential active components and effect targets of Lycii Cortex in the treatment of T2DM. GO enrichment analysis and KEGG pathway analysis were performed in the database of DAVID. Cytoscape 3.6.1 was used to produce the “core components-core targets” network. The molecular docking between core components and core targets was implemented through Autodock Vina. Results: Six core components and twelve core targets of Lycii Cortex in treating T2DM were identified. GO enrichment analysis and KEGG pathway analysis suggested the following signaling pathways and biological processes were involved in the treatment of T2DM by Lycii Cortex: PI3K-Akt signaling pathway, TNF signaling pathway, HIF-1 signaling pathway, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and peptidyl-threonine phosphorylation, the positive regulation of cyclase activity, the positive regulation of genetic expression, and lipoprotein translocation. The binding results demonstrated a relatively high affinity between core components of Lycii Cortex, including kulactone, hederagenin, scopolin, etc., and core targets, containing IL6, PPARγ, TNF, and mTOR, indicating the efficacy of Lycii Cortex in treating T2DM. Conclusion: Lycii Cortex plays a role in the treatment of T2DM with its ingredients such as kulactone, linarin, hederagenin, and scopolin regulating glycometabolism, affecting cell apoptosis and weakening inflammatory response through targets like IL6, PPARγ, TNF, and mTOR.

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