A network pharmacology approach to explore the molecular mechanism of active peptide ingredients of Carapax Trionycis on liver fibrosis

IF 1.5 4区生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY

Peptide Science Pub Date : 2023-10-19 DOI:10.1002/pep2.24335

Zhibin Yan, Guangyu Zhao, Qihao Lin, Guiping Zhuang, Jiayi Zhu, Juan Jin

{"title":"A network pharmacology approach to explore the molecular mechanism of active peptide ingredients of <i>Carapax Trionycis</i> on liver fibrosis","authors":"Zhibin Yan, Guangyu Zhao, Qihao Lin, Guiping Zhuang, Jiayi Zhu, Juan Jin","doi":"10.1002/pep2.24335","DOIUrl":null,"url":null,"abstract":"Abstract Carapax Trionycis is a traditional Chinese medicine and it has been clear that oligo‐peptides from Carapax Trionycis extract (CTP) are the main active substances for the treatment of liver diseases. However, little is known about the mechanism of CTP against liver fibrosis. Here, network pharmacology combined with molecular docking were performed to identify the in‐silico molecular mechanism and the potential targets for CTP to ameliorate liver fibrosis. We collected eight active peptides ingredients that published in public databases and predicted the targets. Liver fibrosis related genes were acquired from the GeneCards and DisGeNET platform. Then, we identified a total of 52 peptides‐liver fibrosis‐related genes. KEGG and GO enrichment analyses indicated that these targets are significantly enriched in relaxin signaling pathway, IL‐17 signaling pathway, TNF signaling pathway. We identified the top 10 genes with high centrality measures from the network by CytoHubba, including CASP3, AKT1, IL1B, MMP9, and PTGS2. The molecular docking between these hub genes and the corresponding CTP was performed in GRAMM and visualized by PyMOL. Our results provide an important reference and scientific basis for treating liver fibrosis with CTP.","PeriodicalId":19825,"journal":{"name":"Peptide Science","volume":"64 1","pages":"0"},"PeriodicalIF":1.5000,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Peptide Science","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1002/pep2.24335","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Abstract Carapax Trionycis is a traditional Chinese medicine and it has been clear that oligo‐peptides from Carapax Trionycis extract (CTP) are the main active substances for the treatment of liver diseases. However, little is known about the mechanism of CTP against liver fibrosis. Here, network pharmacology combined with molecular docking were performed to identify the in‐silico molecular mechanism and the potential targets for CTP to ameliorate liver fibrosis. We collected eight active peptides ingredients that published in public databases and predicted the targets. Liver fibrosis related genes were acquired from the GeneCards and DisGeNET platform. Then, we identified a total of 52 peptides‐liver fibrosis‐related genes. KEGG and GO enrichment analyses indicated that these targets are significantly enriched in relaxin signaling pathway, IL‐17 signaling pathway, TNF signaling pathway. We identified the top 10 genes with high centrality measures from the network by CytoHubba, including CASP3, AKT1, IL1B, MMP9, and PTGS2. The molecular docking between these hub genes and the corresponding CTP was performed in GRAMM and visualized by PyMOL. Our results provide an important reference and scientific basis for treating liver fibrosis with CTP.

Abstract Image

查看原文本刊更多论文

采用网络药理学方法探讨龙爪草活性肽成分抗肝纤维化的分子机制

摘要甲鱼是一种中药，甲鱼提取物(CTP)的低聚肽是治疗肝脏疾病的主要活性物质。然而，CTP抗肝纤维化的机制尚不清楚。本研究通过网络药理学结合分子对接，确定CTP改善肝纤维化的硅分子机制和潜在靶点。我们收集了公开数据库中发表的8种活性肽成分，并对其靶点进行了预测。从GeneCards和DisGeNET平台获得肝纤维化相关基因。然后，我们鉴定了总共52个肽-肝纤维化相关基因。KEGG和GO富集分析表明，这些靶点在松弛素信号通路、IL - 17信号通路、TNF信号通路中显著富集。我们通过CytoHubba从网络中确定了10个具有高中心性的基因，包括CASP3、AKT1、IL1B、MMP9和PTGS2。这些枢纽基因与相应的CTP之间的分子对接在GRAMM中进行，并通过PyMOL可视化。本研究结果为CTP治疗肝纤维化提供了重要参考和科学依据。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Peptide Science Biochemistry, Genetics and Molecular Biology-Biophysics

CiteScore

5.20

自引率

4.20%

发文量

期刊介绍： The aim of Peptide Science is to publish significant original research papers and up-to-date reviews covering the entire field of peptide research. Peptide Science provides a forum for papers exploring all aspects of peptide synthesis, materials, structure and bioactivity, including the use of peptides in exploring protein functions and protein-protein interactions. By incorporating both experimental and theoretical studies across the whole spectrum of peptide science, the journal serves the interdisciplinary biochemical, biomaterials, biophysical and biomedical research communities. Peptide Science is the official journal of the American Peptide Society.