目的:基于网络药理学手段探究栀子对疾病的作用机制和治疗潜能。方法:采用TCMSP数据库对栀子的活性成分和治疗靶点进行预测和筛选,随后去重。Cytoscape 3.9.0绘制了活性组分和靶标网络,并筛选出核心靶点,String数据库分析了蛋白–蛋白相互作用(PPI),去重后的靶点输入到DAVID数据库中查询其涉及的信号通路,进行GO和KEGG通路富集分析。最后将查询的信号通路输入CTD数据库,筛选出相应疾病,栀子的“成分–靶点–通路–疾病”网络图利用Cytoscape 3.9.0软件进行构建,并对其作用机制分析。结果:筛选出98个化学成分,去重后靶点保留了248个,这些靶点涉及了188条通路,参与了多种疾病,本文主要对6种疾病进行分析。结论:通过网络药理学发现,栀子对多种疾病具有治疗潜能,其中用KEGG前10条通路进行疾病分析,发现对癌瘤、前列腺肿瘤、腺癌、乳腺肿瘤、肝硬化、胃癌的频次较多,此外,对阿尔茨海默病、神经变性等也有一定的作用,这都为后续深入探究栀子作为新药的研究提供了基础。 Aims: To investigate the mechanism of action and therapeutic potential of Gardenia jasminoides for disease based on network pharmacological tools. Methods: The TCMSP database was used to predict and screen the active components and therapeutic targets of gardenia, followed by de-duplication. Cytoscape 3.9.0 mapped the active components and target networks and screened the core targets, String database was analyzed for Protein-Protein Interactions (PPI), and the deduplicated targets were entered into the DAVID database to query the signaling pathways they were involved in the GO and KEGG pathways were enriched for analysis. Finally, the queried signalling pathways were entered into the CTD database to screen out the corresponding diseases. The network map was constructed using Cytoscape 3.9.0 software, and the mechanism of action was analysed. Results: 98 chemical components were screened and 248 targets were retained after de-duplication. These targets involved 188 pathways and were involved in a variety of diseases. In this paper, 6 kinds of diseases were mainly analysed. Conclusion: Gardenia jasminoides was found to have therapeutic potential for a variety of diseases through network pharmacology, where disease analysis using the first 10 pathways of KEGG revealed a higher frequency for carcinoma, prostate tumour, adenocarcinoma, breast tumour, liver cirrhosis and gastric cancer. In addition, it also has a certain effect on Alzheimer’s disease, neurodegeneration, etc. All these provide a basis for subsequent indepth exploration of gardenia as a new drug.
目的:基于网络药理学手段探究栀子对疾病的作用机制和治疗潜能。方法:采用TCMSP数据库对栀子的活性成分和治疗靶点进行预测和筛选,随后去重。Cytoscape 3.9.0绘制了活性组分和靶标网络,并筛选出核心靶点,String数据库分析了蛋白–蛋白相互作用(PPI),去重后的靶点输入到DAVID数据库中查询其涉及的信号通路,进行GO和KEGG通路富集分析。最后将查询的信号通路输入CTD数据库,筛选出相应疾病,栀子的“成分–靶点–通路–疾病”网络图利用Cytoscape 3.9.0软件进行构建,并对其作用机制分析。结果:筛选出98个化学成分,去重后靶点保留了248个,这些靶点涉及了188条通路,参与了多种疾病,本文主要对6种疾病进行分析。结论:通过网络药理学发现,栀子对多种疾病具有治疗潜能,其中用KEGG前10条通路进行疾病分析,发现对癌瘤、前列腺肿瘤、腺癌、乳腺肿瘤、肝硬化、胃癌的频次较多,此外,对阿尔茨海默病、神经变性等也有一定的作用,这都为后续深入探究栀子作为新药的研究提供了基础。
栀子,网络药理学,有效成分,靶点,通路,疾病
Lingli Yang, Rongying Gong, Changyan Wu, Weiyi Tian, Haijun Jin, Jiandong Liang*
Guizhou University of Traditional Chinese Medicine, Guiyang Guizhou
Received: Dec. 6th, 2022; accepted: Jan. 2nd, 2023; published: Jan. 10th, 2023
Aims: To investigate the mechanism of action and therapeutic potential of Gardenia jasminoides for disease based on network pharmacological tools. Methods: The TCMSP database was used to predict and screen the active components and therapeutic targets of gardenia, followed by de-duplication. Cytoscape 3.9.0 mapped the active components and target networks and screened the core targets, String database was analyzed for Protein-Protein Interactions (PPI), and the de-duplicated targets were entered into the DAVID database to query the signaling pathways they were involved in the GO and KEGG pathways were enriched for analysis. Finally, the queried signalling pathways were entered into the CTD database to screen out the corresponding diseases. The network map was constructed using Cytoscape 3.9.0 software, and the mechanism of action was analysed. Results: 98 chemical components were screened and 248 targets were retained after de-duplication. These targets involved 188 pathways and were involved in a variety of diseases. In this paper, 6 kinds of diseases were mainly analysed. Conclusion: Gardenia jasminoides was found to have therapeutic potential for a variety of diseases through network pharmacology, where disease analysis using the first 10 pathways of KEGG revealed a higher frequency for carcinoma, prostate tumour, adenocarcinoma, breast tumour, liver cirrhosis and gastric cancer. In addition, it also has a certain effect on Alzheimer’s disease, neurodegeneration, etc. All these provide a basis for subsequent in-depth exploration of gardenia as a new drug.
Keywords:Gardenia, Network Pharmacology, Active Ingredient, Target, Pathway, Disease
Copyright © 2023 by author(s) and Hans Publishers Inc.
This work is licensed under the Creative Commons Attribution International License (CC BY 4.0).
http://creativecommons.org/licenses/by/4.0/
栀子(Gardenia jasminoides Ellis)又叫山栀子,在中医药领域中的应用已延续了几千年,最早记载于《神农本草经》,药性苦寒,归心、肺和三焦经,能泻肺火、去肌表之热,质地轻清上行,在外感热病、表里有热之际能起到表里双解的作用,临床上主要使用方法是炮制用和生用。其含有的黄色素、有机酸、环烯醚萜类等能很好地起到降温镇痛、降血糖、降血脂、抗炎消肿、保护神经、保肝利胆、心血管防护等作用。除环烯醚萜苷和黄色素外,还有熊果酸、β-谷甾醇和栀子花乙酸等三萜类、5,7,3',3'-二羟基-7,4',5'-三甲氧基等黄酮类、多糖,现代研究表明都具有一定的药理活性 [
网络药理学是一门借助网络方法能将药物与疾病、靶点、通路之间的协同作用关系进行可视化的一门学科,具有整体性、系统性等优点 [
以栀子为关键词,对栀子相关靶点和已知化学成分在TCMSP数据库(https://tcmsp-e.com/)中检索并下载,将靶点的重复项删除之后即为栀子治疗疾病的潜在靶点。再通过UniProt数据库将所有靶点转化为基因简称。
将筛选出的靶点导入String (https://string-db.org/)中,设置种类为“Homo sapiens (人类)”构建靶点互作网络图(PPI),置信度设置过低不利于可视化分析,所以设置置信度为> 0.9,隐藏网络中离散点,将结果以TSV文件进行保存,导入Cytoscape 3.9.0中,采用其“Network Analyzer”选项进行分析,根据Degree值确定的核心靶点。
将药物共有靶点导入DAVID数据库(https://david.ncifcrf.gov/)中,下载细胞组分(Cellular Component, CC)、生物过程(Biological Process, BP)和分子功能(Molecular Function, MF)文件进行GO富集分析,按照FDR值大小降序排列选前10条,结果以柱形图的形式进行展示。下载KEGG信号通路文件,按照FDR值大小降序排列选前10条,结果以气泡图的形式进行展示。
在CTD数据库(http://ctdbase.org/)中导入筛选的KEGG信号通路,通过“Batch Query”进行批量查询并下载每条通路相关联的疾病。将所有通路获得的疾病通过EXCEL进行同类合并统计,筛选出频次出现最多的前6个疾病。
为明确栀子对治疗疾病的作用机制,直观地呈现栀子各成分治疗筛选出的疾病的作用途径,将栀子的成分、各成分对应的靶点、通路及通路对应的疾病导入Cytoscape 3.9.0做网络图
通过TCMSP共获得栀子化学成分包括藏花酸(crocetin)、京尼平(genipin)、京尼平苷(geniposide)、芦丁(rutin)、乌苏酸(ursolic acid)、槲皮素(quercetin)等98个,能查到靶点的化学成分共有61个,对应靶点654个,删除重复靶点后,栀子共获得的潜在靶点有CHRM3、CHRM1、ADRA1A、CHRM2等248个。
将248个靶点导入String数据库,构建栀子的蛋白互作网络,如图1,该网络中共有number of nodes:248个,number of edges:976个,average node degree:7.87,avg. local clustering coefficient:0.391,expected number of edges:344个。用Cytoscape 3.9.0软件筛选出Degree值靠前的前10个节点作为栀子的核心靶点,进行可视化处理,如图2。包括TNF、TP53、AKT1、MAPK1、RELA、STAT3、JUN、MAPK8、FOS、MAPK14。
图1. 蛋白互作网络图
图2. 栀子核心靶点网络图
将栀子的靶点248个导入DAVID数据库进行GO富集分析,共得到CC (Cellular Component)共101个、MF (Molecular Function)共178个、BP (Biological Process)共874个,以FDR值进行筛选,分别对排名前10的GO注释条目进行可视化处理,结果如图3。结果显示,生物过程包括response to hydrogen peroxide、circadian rhythm、adenylate cyclase-activating adrenergic receptor signaling pathway、negative regulation of apoptotic signaling pathway、positive regulation of endothelial cell proliferation等;细胞组分主要有RNA polymerase II transcription factor complex、receptor complex、glutamatergic synapse、nucleoplasm、chromatin等;分子功能包括peptidase activity、cytokine activity、binding, bridging、protein domain specific binding等,这表明栀子发挥治疗作用可能主要是通过调节这些生物过程,作用机制涉及多个途径。
图3. 栀子作用靶点GO富集分析图
栀子的248个靶点经过KEGG通路富集分析,将物种定义为“人类”,共得到信号通路188条,以FDR值从大到小顺序排名后,通过筛选栀子KEGG富集结果显著性较强的前10条信号通路进行展示,结果如图4。其中,排名较前的有Chagas disease、Chagas disease、Growth hormone synthesis, secretion and action、cAMP signaling pathway、Salivary secretion和Pancreatic cancer、Diabetic cardiomyopathy、Natural killer cell mediated cytotoxicity、Hepatitis C、Prolactin signaling pathway等。这表明栀子治疗疾病可能是通过调控这些通路。
以FDR进行降序排序,选取KEGG前10条通路用CTD数据库进行疾病分析,得到出现频次前6的疾病,分别为癌瘤、前列腺肿瘤、腺癌、乳腺肿瘤、肝硬化、胃癌,见表1。
图4. KEGG富集结果气泡图
疾病 | 频次 | 交集靶点 |
---|---|---|
癌瘤 | 362 | ADRA1A、RELA、TNF、CXCL8、ESR1、ESR2、STAT3、VEGFA、CCND1、BCL2L1、FOS、CDKN1A、JUN、TP53、NFKBIA、CSF2、FASLG、EGFR、AKT1、MAPK1、EGF、RB1、RAF1、STAT1、ERBB2、PPARA、RASSF1、E2F1、E2F2、RAC1、PPP3CA、SLC2A2 |
前列腺肿瘤 | 156 | CXCL8、ESR1、ESR2、GSK3B、STAT3、VEGFA、CCND1、CDKN1A、CASP9、TP53、ICAM1、CCND2、FASLG、ADRB2、RXRA、EGFR、AKT1、EGF、RB1、RAF1、ERBB2、PPARA、PPP3CA |
腺癌 | 130 | RELA、TNF、CXCL8、ESR1、ESR2、STAT3、VEGFA、CCND1、TP53、EGFR、AKT1、EGF、ERBB2、RASSF1、PPP3CA |
乳腺肿瘤 | 112 | RELA、TNF、CXCL8、ESR1、ESR2、STAT3、CCND1、FOS、JUN、TP53、NFKBIA、CSF2、EGFR、AKT1、EGF、RB1、RAF1、ERBB2、IFNG、CLDN4、E2F1、SLC2A2 |
肝硬化 | 102 | CHRM3、ADRA1A、ADRA1B、RELA、TNF、PRKCB、ITGB2、MAPK14、VEGFA、FOS、CDKN1A、NFKBIA、EGF、STAT1、IFNG |
胃癌 | 88 | RELA、TNF、CXCL8、PRKCB、STAT3、CCND1、BCL2L1、CDKN1A、JUN、TP53、MAPK8、ADRB2、EGFR、MAPK1、ERBB2、IRF1、ADRB1、BDNF |
表1. 栀子治疗疾病的潜在靶点
注:交集靶点是指栀子成分作用靶点与疾病靶点的共有靶点。
用Cytoscape 3.9.0软件建立栀子“成分–靶点–通路–疾病”交互网络,见图5,清楚地展现栀子的活性成分、通路、靶点与不同疾病的作用关系,也揭示栀子的药效作用机制。
图5. 栀子的“成分–靶点–通路–疾病”交互网络
中药的一个成分对应多个靶点与多个通路,一个靶点又对应多个成分与多个通路,通过网络药理学更能直观地展示中药“多途径、多层次、多靶点”的特点 [
祖国医学对于癌瘤,远在两千年前已有记载,《中国医学百科全书》中指出,恶性肿瘤又称癌瘤 [
肝硬化指由一种或多种病因长期、反复刺激肝脏而造成的肝弥漫性损伤,属于中医学“臌胀”、“积证”的范畴,隶属中医古代四大疑难症(风、痨、鼓、膈)之一 [
综上所述,本文通过网络药理学分析,初步对栀子的作用机制与治疗潜能进行了探索,发现栀子对多种疾病具有一定的治疗意义。其中,栀子可以通过cAMP信号传导途径、催乳素信号通路等信号通路对癌瘤、前列腺肿瘤、腺癌、乳腺肿瘤、肝硬化、胃癌等疾病发挥治疗潜能。且通过网络药理学的预测结果与栀子的现有药效研究的吻合度较高,对栀子的现有研究与临床应用进行了佐证,为后续开发栀子治疗前列腺癌、肝硬化等疾病提供了研究基础。
贵州省科技基金项目(黔科合基础[
杨灵丽,龚荣英,吴昌燕,田维毅,晋海军,梁建东. 基于网络药理学探究栀子的治疗潜能及作用机制Exploring the Therapeutic Potential and Mechanism of Action of Gardenia jasminoides Based on Network Pharmacology[J]. 药物资讯, 2023, 12(01): 5-13. https://doi.org/10.12677/PI.2023.121002