scholarly journals To explore the material basis and mechanism of Lianhua Qingwen Prescription against COVID-19 based on network pharmacology

2020 ◽  
Vol 1 ◽  
pp. 3
Author(s):  
Wenpan Peng ◽  
Di Han ◽  
Yong Xu ◽  
Fanchao Feng ◽  
Zhichao Wang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
T Cell Activation ◽  
Mechanism Of Action ◽  
Cell Activation ◽  
Chemical Constituents ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Network Pharmacology ◽  
Material Basis

Objective: In the treatment of COVID-19, the application of Lianhua Qingwen Prescription has become growingly widespread, however, the mechanism of action is still unclear. To explore the material basis and mechanism of Lianhua Qingwen Prescription against SARS-CoV-2, to provide a reference for the treatment of COVID-19. Methods: Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), SwissTargetPrediction, and Similarity Ensemble Approach (SEA) database were used to search the chemical constituents and targets of Lianhua Qingwen Prescription. The targets of COVID-19 were screened by GeneCards, Therapeutic Target Database (TTD), and Comparative Toxicogenomics Database (CTD). Cytoscape software was used to construct a “drug-component-target” network diagram and the mechanism of action was predicted by enrichment analysis. Results: Two hundred and twenty four active components, 246 drug therapeutic targets, and 16,611 potential targets of Lianhua Qingwen Prescription were mined out. Moreover, 163 common targets were obtained, including PTGS2, IL6, CASP3, mapk1, EGFR, ACE2, etc. Thirty seven items were obtained by Gene Ontology (GO) enrichment analysis, mainly involving T-cell activation, virus receptor, and inflammatory reaction, etc. One hundred and forty items were obtained by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enriched analysis, including TNF signaling pathway, MAPK signaling pathway, and IL-17 signaling pathway. Conclusion: Compounds such as quercetin and kaempferol play an important role in anti-COVID-19 through the TNF signaling pathway and MAPK signaling pathway.

scholarly journals Exploring the Mechanism of Quercetin for the Treatment of Atrial Fibrillation by Geo Gene Chip Combined With Network Pharmacology and Molecular Docking

2021 ◽  
Author(s):  
tan xin ◽  
Wei Xian ◽  
Xiaorong Li ◽  
Yongfeng Chen ◽  
Jiayi Geng ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Mechanism Of Action ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Binding Activity ◽  
Network Pharmacology ◽  
Chemical Structures ◽  
Drug Mechanism

Abstract PurposeAtrial fibrillation (AF) is a common atrial arrhythmia. Quercetin (Que) has some advantages in the treatment of cardiovascular disease arrhythmias, but its specific drug mechanism of action needs further investigation. To explore the mechanism of action of Que in AF, core target speculation and analysis were performed using network pharmacology and molecular docking methods.MethodsQue chemical structures were obtained from Pubchem. TCMSP, Swiss Target Prediction, Drugbank , STITCH, Binding DB, Pharmmapper, CTD, GeneCards, DISGENET and TTD were used to obtain drug component targets and AF-related genes, and extract AF from normal tissues by GEO database differentially expressed genes. Then, the intersecting genes were obtained by online Wayne mapping tool. The intersection genes were introduced into the top five targets selected for molecular docking via protein-protein interaction (PPI) network to verify the binding activity between Que and the target proteins. GO and KEGG enrichment analysis of the intersected genes using program R was performed to further screen for key genes and key pathways.ResultsThere were 65 effective targets for Que and AF. Through further screening, the top 5 targets were IL6, VEGFA, JUN, MMP9 and EGFR. Que treatment of AF may involve signaling pathways such as lipid and atherosclerosis pathway, AGE-RAGE signaling pathway in diabetic complications, MAPK signaling pathway and IL-17 signaling pathway. Molecular docking suggests that Que has strong binding to key targets.ConclusionThis study systematically elucidates the key targets of Que treatment for AF and the specific mechanisms through network pharmacology as well as molecular docking, providing a new direction for further basic experimental exploration and clinical treatment.

scholarly journals Based on Network Pharmacology to Explore the Potential Bioactive Compounds and Mechanisms of Zuojin Pill for the Treatment of Ulcerative Colitis

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Ying Wei ◽  
Sichen Ren ◽  
Ruilin Wang ◽  
Manyi Jing ◽  
Honghong Liu ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Signaling Pathway ◽  
Bioactive Compounds ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Akt Signaling ◽  
Mapk Signaling Pathway ◽  
Network Pharmacology ◽  
Akt Signaling Pathway ◽  
Active Components

Background. Zuojin Pill (ZJP), a classic prescription, has the potential to prevent ulcerative colitis (UC). However, the active components and mechanisms of ZJP are still arcane. This study aimed to use a network pharmacology approach to find the bioactive compounds and potential action mechanisms of ZJP in the treatment of UC. Methods. Firstly, the components and putative targets of ZJP were collected based on herbal medicine target databases, and a network containing the interaction between the targets of ZJP and the potential therapeutic targets of UC was established. Then, topological parameters were calculated to identify the key targets in the network and, in turn, to import them into the David database to perform path enrichment analysis. Results. 14 potential therapeutic components of ZJP and 26 key targets were obtained. These targets were related to signal transduction, MAPK cascade, inflammatory response, immune response, and the apoptotic process of UC. Moreover, the PI3K-Akt signaling pathway, MAPK signaling pathway, toll-like receptor signaling pathway, and Prolactin signaling pathway were predicted to participate in ZJP treating UC. Among them, 14 active components of ZJP directly regulate these pathways. Conclusion. ZJP could alleviate UC through the predicted components and mechanisms. The 14 predicted active components of ZJP may mainly play a therapeutic role for UC through synergistic regulation of the PI3K-Akt signaling pathway and MAPK signaling pathway.

scholarly journals Network Pharmacology-Based Strategy to Investigate Pharmacological Mechanisms of the Drug Pair Astragalus-Angelica for Treatment of Male Infertility

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Feng Zhao ◽  
Yingjun Deng ◽  
Guanchao Du ◽  
Shengjing Liu ◽  
Jun Guo ◽  
...  
Keyword(s):  
Male Infertility ◽  
Signaling Pathway ◽  
Mechanism Of Action ◽  
Protein Interactions ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Protein Protein Interactions ◽  
Drug Pair ◽  
Effective Components ◽  
New Ideas

Background. The traditional Chinese medicines Astragalus and Angelica are often combined to treat male infertility, but the specific therapeutic mechanism is not clear. Therefore, this study applies a network pharmacology approach to investigate the possible mechanism of action of the drug pair Astragalus-Angelica (PAA) in the treatment of male infertility. Methods. Relevant targets for PAA treatment of male infertility are obtained through databases. Protein-protein interactions (PPIs) are constructed through STRING database and screen core targets, and an enrichment analysis is conducted through the Metascape platform. Finally, molecular docking experiments were carried out to evaluate the affinity between the target protein and the ligand of PAA. Results. The active ingredients of 112 PAA, 980 corresponding targets, and 374 effective targets of PAA for the treatment of male infertility were obtained, which are related to PI3K-Akt signaling pathway, HIF-1 signaling pathway, AGE-RAGE signaling pathway, IL-17 signaling pathway, and thyroid hormone signaling pathway. Conclusion. In this study, using a network pharmacology method, we preliminarily analyzed the effective components and action targets of the PAA. We also explored the possible mechanism of action of PAA in treating male infertility. They also lay a foundation for expanding the clinical application of PAA and provide new ideas and directions for further research on the mechanisms of action of the PAA and its components for male infertility treatment.

scholarly journals Uncovering the Mechanisms and Molecular Targets of Weibing Formula 1 against Gastritis: Coupling Network Pharmacology with GEO Database

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Ke Chen ◽  
Luojian Zhang ◽  
Zhen Qu ◽  
Feng Wan ◽  
Jia Li ◽  
...  
Keyword(s):  
Real Time ◽  
Signaling Pathway ◽  
Quantitative Pcr ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Gene Expression Omnibus ◽  
Network Pharmacology ◽  
Receptor Interaction ◽  
Pathway Enrichment Analysis ◽  
Real Time Quantitative Pcr

Weibing Formula 1, a classic traditional formula, has been widely used clinically to treat gastritis in recent years. However, the potential pharmacological mechanism of Weibing Formula 1 is still unclear to date. A network pharmacology-based strategy was performed to uncover the underlying mechanisms of Weibing Formula 1 against gastritis. Furthermore, we structured the drug-active ingredients-genes–disease network and PPI network of shared targets, and function enrichment analysis of these targets was carried out. Ultimately, Gene Expression Omnibus (GEO) datasets and real-time quantitative PCR were used to verify the related genes. We found 251 potential targets corresponding to 135 bioactive components of Weibing Formula 1. Then, 327 gastritis-related targets were known gastritis-related targets. Among which, 60 common targets were shared between potential targets of Weibing Formula 1 and known gastritis-related targets. The results of pathway enrichment analysis displayed that 60 common targets mostly participated in various pathways related to Toll-like receptor signaling pathway, MAPK signaling pathway, cytokine-cytokine receptor interaction pathway, chemokine signaling pathway, and apoptosis. Based on the GSE60427 dataset, 15 common genes were shared between differentially expressed genes and 60 candidate targets. The verification results of the GSE5081 dataset showed that except for DUOX2 and VCAM1, the other 13 genes were significantly upregulated in gastritis, which was consistent with the results in the GSE60427 dataset. More importantly, real-time quantitative PCR results showed that the expressions of PTGS2, MMP9, CXCL2, and CXCL8 were significantly upregulated and NOS2, EGFR, and IL-10 were downregulated in gastritis patients, while the expressions of PTGS2, MMP9, CXCL2, and CXCL8 were significantly downregulated and NOS2, EGFR, and IL-10 were upregulated after the treatment of Weibing Formula 1. PTGS2, NOS2, EGFR, MMP9, CXCL2, CXCL8, and IL-10 may be the important direct targets of Weibing Formula 1 in gastritis treatment. Our study revealed the mechanism of Weibing Formula 1 in gastritis from an overall and systematic perspective, providing a theoretical basis for further knowing and application of this formula in the future.

scholarly journals Identification of the Crucial Gene in Overflow Arteriovenous Fistula by Bioinformatics Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhengde Zhao ◽  
Qining Fu ◽  
Liangzhu Hu ◽  
Yangdong Liu
Keyword(s):  
Signaling Pathways ◽  
Signaling Pathway ◽  
Intimal Hyperplasia ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Biological Processes ◽  
Hub Genes ◽  
Av Fistula ◽  
Core Genes

Objective: The aim was to study the preliminary screening of the crucial genes in intimal hyperplasia in the venous segment of arteriovenous (AV) fistula and the underlying potential molecular mechanisms of intimal hyperplasia with bioinformatics analysis.Methods: The gene expression profile data (GSE39488) was analyzed to identify differentially expressed genes (DEGs). We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of DEGs. Gene set enrichment analysis (GSEA) was used to understand the potential activated signaling pathway. The protein–protein interaction (PPI) network was constructed with the STRING database and Cytoscape software. The Venn diagram between 10 hub genes and gene sets of 4 crucial signaling pathways was used to obtain core genes and relevant potential pathways. Furthermore, GSEAs were performed to understand their biological functions.Results: A total of 185 DEGs were screened in this study. The main biological function of the 111 upregulated genes in AV fistula primarily concentrated on cell proliferation and vascular remodeling, and the 74 downregulated genes in AV fistula were enriched in the biological function mainly relevant to inflammation. GSEA found four signaling pathways crucial for intimal hyperplasia, namely, MAPK, NOD-like, Cell Cycle, and TGF-beta signaling pathway. A total of 10 hub genes were identified, namely, EGR1, EGR2, EGR3, NR4A1, NR4A2, DUSP1, CXCR4, ATF3, CCL4, and CYR61. Particularly, DUSP1 and NR4A1 were identified as core genes that potentially participate in the MAPK signaling pathway. In AV fistula, the biological processes and pathways were primarily involved with MAPK signaling pathway and MAPK-mediated pathway with the high expression of DUSP1 and were highly relevant to cell proliferation and inflammation with the low expression of DUSP1. Besides, the biological processes and pathways in AV fistula with the high expression of NR4A1 similarly included the MAPK signaling pathway and the pathway mediated by MAPK signaling, and it was mainly involved with inflammation in AV fistula with the low expression of NR4A1.Conclusion: We screened four potential signaling pathways relevant to intimal hyperplasia and identified 10 hub genes, including two core genes (i.e., DUSP1 and NR4A1). Two core genes potentially participate in the MAPK signaling pathway and might serve as the therapeutic targets of intimal hyperplasia to prevent stenosis after AV fistula creation.

scholarly journals Integrated Bioinformatics Analysis Identifies ELAVL1 and APP as Candidate Crucial Genes for Crohn’s Disease

2020 ◽  
Vol 2020 ◽  
pp. 1-20
Author(s):  
Heli Li ◽  
Qianru Li ◽  
Shiran Sun ◽  
Ping Lei ◽  
Xiong Cai ◽  
...  
Keyword(s):  
Crohn’S Disease ◽  
T Cell ◽  
Crohn's Disease ◽  
Signaling Pathway ◽  
T Cell Activation ◽  
Peripheral Blood ◽  
Cell Activation ◽  
Mapk Signaling ◽  
Gene Set Enrichment Analysis ◽  
Infliximab Treatment

Immune imbalance and barrier destruction of intestinal mucosa are the central pathogenic factors of Crohn’s disease (CD). In this study, three independent microarray studies of CD were integrated and 9912 differentially expressed genes (DEGs) were analysed by NetworkAnalyst to screen candidate crucial genes. NetworkAnalyst identified ELAV-like RNA binding protein 1 (ELAVL1) as the most crucial upregulated gene and amyloid-β precursor protein (APP) as the most crucial downregulated gene in peripheral blood of CD patients. By computing significance with hypergeometric test based on the KEGG pathway database, upregulated DEGs highlight the pathways of T cell receptor signaling and the differentiation of T helpers. Downregulated DEGs were found enriched in pathways in multiple cancers, MAPK signaling, Rap1 signaling, and PI3K-AKT signaling. Further taking all DEGs together, Gene Set Enrichment Analysis (GSEA) brought out the NOD-like receptor (NLR) signaling pathway which could be regulated by ELAVL1. xCell found decreased naïve and differentiated T cell proportions in the peripheral blood of CD patients suggesting T cell migration to the intestinal tissue and/or exhaustion. Further, ELAVL1 expression correlating with multiple T cell proportions suggests that ELAVL1 may regulate T cell activation. These findings illustrated that ELAVL1 and APP were candidate crucial genes in the peripheral blood of CD patients. ELAVL1 possibly acts as a key regulator of T cell activation via the NLR signaling pathway. APP might be a downstream effector of infliximab treatment connecting with MAPK signaling.

scholarly journals A Network Pharmacology-based Analysis of the Molecular Mechanism of Tanreqing in the Treatment of the Coronavirus Disease 2019 (COVID-19)

2020 ◽  
Author(s):  
Liuliu Yang ◽  
Minyong Wen ◽  
Wenjiang Zheng ◽  
Xiaohong Liu ◽  
yong wang
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Chemical Constituents ◽  
Hypoxia Inducible Factor ◽  
Enrichment Analysis ◽  
Clinical Treatment ◽  
Laboratory Research ◽  
Network Pharmacology ◽  
Receptor Interaction ◽  
Protein Protein Interaction

Abstract Background: This paper discusses the molecular mechanism of Tanreqing (TRQ) in the treatment of the coronavirus disease 2019 (COVID-19) using the network pharmacology approach. Our study provides new ideas on the laboratory research and clinical treatment of the disease. Method: Information on the chemical constituents of TRQ and the genes targeted by the disease was collected. The common gene targets of the drug and the disease were input into the Search Tool for the Retrieval of Interacting Genes/Proteins（STRING）database to understand the interaction among target proteins. The protein–protein interaction (PPI) network and a network of the chemical constituents of TRQ and their targets were constructed using Cytoscape. Gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the R program and other relevant software packages. Results: Twenty-eight active chemical constituents and 365 gene targets were identified for TRQ. Out of these genes, 113 were also found to be involved in the pathogenesis of the disease. Enrichment analysis revealed the therapeutic role that TRQ could have played in the treatment of COVID-19, via the regulation of important pathways such as the renin–angiotension system, neuroactive ligand–receptor interaction, phospholipase D (PLD) signaling pathway, calcium signaling pathway, and the hypoxia-inducible factor 1 (HIF-1) signaling pathway. Conclusions: This study attempts to predict the molecular mechanism of TRQ in the treatment of COVID-19, and suggests TRQ intervention through multiple targets and pathways in processes including inflammatory response, immune regulation, and apoptosis during the treatment of the disease. This study indicates the potential rational application of TRQ in the clinical treatment of COVID-19.

scholarly journals Exploring the Pharmacological Mechanism of Duhuo Jisheng Decoction in Treating Osteoporosis Based on Network Pharmacology

2021 ◽  
Vol 2021 ◽  
pp. 1-21
Author(s):  
Zhencheng Xiong ◽  
Can Zheng ◽  
Yanan Chang ◽  
Kuankuan Liu ◽  
Li Shu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Signaling Pathway ◽  
Enrichment Analysis ◽  
Mapk Signaling ◽  
Network Pharmacology ◽  
Pathway Enrichment Analysis ◽  
Hub Genes ◽  
Active Compounds ◽  
Treatment Of Osteoporosis ◽  
Target Proteins

Objective. The purpose of this work is to study the mechanism of action of Duhuo Jisheng Decoction (DHJSD) in the treatment of osteoporosis based on the methods of bioinformatics and network pharmacology. Methods. In this study, the active compounds of each medicinal ingredient of DHJSD and their corresponding targets were obtained from TCMSP database. Osteoporosis was treated as search query in GeneCards, MalaCards, DisGeNET, Therapeutic Target Database (TTD), Comparative Toxicogenomics Database (CTD), and OMIM databases to obtain disease-related genes. The overlapping targets of DHJSD and osteoporosis were identified, and then GO and KEGG enrichment analysis were performed. Cytoscape was employed to construct DHJSD-compounds-target genes-osteoporosis network and protein-protein interaction (PPI) network. CytoHubba was utilized to select the hub genes. The activities of binding of hub genes and key components were confirmed by molecular docking. Results. 174 active compounds and their 205 related potential targets were identified in DHJSD for the treatment of osteoporosis, including 10 hub genes (AKT1, ALB, IL6, MAPK3, VEGFA, JUN, CASP3, EGFR, MYC, and EGF). Pathway enrichment analysis of target proteins indicated that osteoclast differentiation, AGE-RAGE signaling pathway in diabetic complications, Wnt signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, JAK-STAT signaling pathway, calcium signaling pathway, and TNF signaling pathway were the specifically major pathways regulated by DHJSD against osteoporosis. Further verification based on molecular docking results showed that the small molecule compounds (Quercetin, Kaempferol, Beta-sitosterol, Beta-carotene, and Formononetin) contained in DHJSD generally have excellent binding affinity to the macromolecular target proteins encoded by the top 10 genes. Conclusion. This study reveals the characteristics of multi-component, multi-target, and multi-pathway of DHJSD against osteoporosis and provides novel insights for verifying the mechanism of DHJSD in the treatment of osteoporosis.

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