目的:基于网络药理学方法分析雷公藤治疗银屑病的作用机制。方法:使用中药系统药理学平台(TCMSP)数据库搜集雷公藤的主要活性成分和作用靶点,通过Uniprot进行标准化;随后通过Genecard、OMIM、DrugBank数据库筛选出银屑病的作用靶点。将银屑病与雷公藤作用靶点取交集,得到交互靶点。随后通过Draw Venn Diagram构建韦恩图,将雷公藤与银屑病的共同作用靶点运用STRING网站进行蛋白质–蛋白互作分析PPI),并使用Cytoscape进行可视化以及构建疾病–药物–靶点网络图,使用R语言进行GO富集分析与KEGG通路富集分析。结果:雷公藤与银屑病的共同靶点70个,GO富集1647条生物过程,100项分子功能相关,19项细胞组成相关。KEGG通路富集获得136条信号通路,主要涉及的通路有Th17细胞分化、IL-17信号通路等。结论:雷公藤治疗银屑病可能存在多通路、多靶点的可能,为雷公藤的进一步研发用药提供了参考,也为银屑病的治疗提供了生物信息学基础。 Objective: To explore the mechanism of treatment of psoriasis based on internet pharmacology Tripterygium wilfordii. Methods: The main active components and targets of Tripterygium wilfordii were collected using the Traditional Chinese Medicine System Pharmacology Platform (TCMSP) database, and standardized by Uniprot; then the targets of psoriasis were screened through Genecard, OMIM, and DrugBank databases. The intersection of psoriasis and Tripterygium wilfordii action targets was obtained to obtain interactive targets. Then, a Venn diagram was constructed by Draw Venn Diagram, and the common targets of Tripterygium wilfordii and psoriasis were used for protein-protein interaction analysis (PPI) using the STRING website, and Cytoscape was used for visualization and construction of disease-drug-target network diagrams , using R language for GO enrichment analysis and KEGG pathway enrichment analysis. Results: There are 70 common targets of Tripterygium wilfordii and psoriasis, 1647 biological processes are enriched by GO, 100 molecular functions are related, and 19 are related to cellular composition. KEGG pathway enrichment obtained 136 signaling pathways, mainly involving Th17 cell differentiation and IL-17 signaling pathway. Conclusion: Tripterygium wilfordii may have multiple pathways and multiple targets in the treatment of psoriasis, which provides a reference for the further research and development of Tripterygium wilfordii and also provides the basis of bioinformatics for the treatment of psoriasis.
目的:基于网络药理学方法分析雷公藤治疗银屑病的作用机制。方法:使用中药系统药理学平台(TCMSP)数据库搜集雷公藤的主要活性成分和作用靶点,通过Uniprot进行标准化;随后通过Genecard、OMIM、DrugBank数据库筛选出银屑病的作用靶点。将银屑病与雷公藤作用靶点取交集,得到交互靶点。随后通过Draw Venn Diagram构建韦恩图,将雷公藤与银屑病的共同作用靶点运用STRING网站进行蛋白质–蛋白互作分析PPI),并使用Cytoscape进行可视化以及构建疾病–药物–靶点网络图,使用R语言进行GO富集分析与KEGG通路富集分析。结果:雷公藤与银屑病的共同靶点70个,GO富集1647条生物过程,100项分子功能相关,19项细胞组成相关。KEGG通路富集获得136条信号通路,主要涉及的通路有Th17细胞分化、IL-17信号通路等。结论:雷公藤治疗银屑病可能存在多通路、多靶点的可能,为雷公藤的进一步研发用药提供了参考,也为银屑病的治疗提供了生物信息学基础。
雷公藤,银屑病,网络药理学
Jie Yan1, Min Yao2, Yang Liu3*
1Affiliated Hospital of Qingdao University, Qingdao Shandong
2Rongchang District People’s Hospital, Chongqing
3Chongqing Traditional Chinese Medicine Hospital, Chongqing
Received: Mar. 20th, 2022; accepted: Apr. 14th, 2022; published: Apr. 24th, 2022
Objective: To explore the mechanism of treatment of psoriasis based on internet pharmacology Tripterygium wilfordii. Methods: The main active components and targets of Tripterygium wilfordii were collected using the Traditional Chinese Medicine System Pharmacology Platform (TCMSP) database, and standardized by Uniprot; then the targets of psoriasis were screened through Genecard, OMIM, and DrugBank databases. The intersection of psoriasis and Tripterygium wilfordii action targets was obtained to obtain interactive targets. Then, a Venn diagram was constructed by Draw Venn Diagram, and the common targets of Tripterygium wilfordii and psoriasis were used for protein-protein interaction analysis (PPI) using the STRING website, and Cytoscape was used for visualization and construction of disease-drug-target network diagrams , using R language for GO enrichment analysis and KEGG pathway enrichment analysis. Results: There are 70 common targets of Tripterygium wilfordii and psoriasis, 1647 biological processes are enriched by GO, 100 molecular functions are related, and 19 are related to cellular composition. KEGG pathway enrichment obtained 136 signaling pathways, mainly involving Th17 cell differentiation and IL-17 signaling pathway. Conclusion: Tripterygium wilfordii may have multiple pathways and multiple targets in the treatment of psoriasis, which provides a reference for the further research and development of Tripterygium wilfordii and also provides the basis of bioinformatics for the treatment of psoriasis.
Keywords:Tripterygium wilfordii, Psoriasis, Network Pharmacology
Copyright © 2022 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/
雷公藤是我国一种历史悠久、广泛应用的传统中药,其使用有数百年历史。来源于卫矛科植物雷公藤的木质部,具有祛风、解毒、除湿、止痒、消炎、杀虫等功效 [
通过中药系统药理学平台(TCMSP) (https://tcmspw.com/tcmsp.php)对雷公藤进行检索,以口服生物利用度(OB) ≥ 30%,类药性(DL) ≥ 0.18作为条件进行筛选 [
利用Genecard、OMIM、DrugBank数据库分别以“psoriasis”作为关键词进行检索,得到与银屑病相关的疾病靶点。在Genecard数据库中,以score值(相关度值)为限制条件舍去在中位数以下的靶点。在DrugBank中,将基因名通过Uniprot进行基因名的标准化,并删除无效靶点。
将雷公藤的主要活性成分潜在靶点与银屑病的作用靶点取交集得到药物疾病共有靶点,并于Draw Venn Diagra在线绘制网站,绘制韦恩图。
利用雷公藤的有效成分相对应的靶点基因与疾病的相关靶点基因,使用Cytoscape3.7.1构建网络图并做可视化,得到药物–有效成分–疾病–作用靶点的网路图。
将药物与疾病的共同靶点输入String数据库(https://string-db.org/cgi/input.pl)进行PPI网络的构建 [
为进一步阐明雷公藤作用机制,利用String平台,选取P值≤0.05的项目进行筛选,使用R 3.6.3,进行柱状图与气泡图的绘制。
通过TCMSP数据库检索关键词“雷公藤”得到活性成分144个,调整药代动力学参数(ADME),以OB ≥ 30%,DL ≥ 0.18作为筛选条件,获得雷公藤有效成分51个,详见表1。根据获得的雷公藤有效成分于TCMSP数据库中找出对应的作用靶点,利用Uniprot对进行基因标准化并删掉无效靶点及其对应有效成分重复值,得雷公藤靶点基因共142个。详见表1。
序号 | MOLID | 化合物 | OB/% | DL |
---|---|---|---|---|
1 | MOL000296 | hederagenin | 36.91 | 0.8 |
2 | MOL003182 | (+)-Medioresinol di-O-beta-D-glucopyranoside_qt | 60.69 | 0.6 |
3 | MOL003184 | 81827-74-9 | 45.42 | 0.5 |
4 | MOL003185 | (1R,4aR,10aS)-5-hydroxy-1-(hydroxymethyl)-7-isopropyl- 8-methoxy-1,4a-dimethyl-4,9,10,10a-tetrahydro-3H- phenanthren-2-one | 48.84 | 0.4 |
5 | MOL003187 | triptolide | 51.29 | 0.7 |
6 | MOL003188 | Tripchlorolide | 78.72 | 0.7 |
7 | MOL003189 | WILFORLIDE A | 35.66 | 0.7 |
8 | MOL003192 | Triptonide | 67.66 | 0.7 |
9 | MOL003196 | Tryptophenolide | 48.5 | 0.4 |
10 | MOL003198 | 5 alpha-Benzoyl-4 alpha-hydroxy-1 beta,8 alpha-dinicotinoyl- dihydro-agarofuran | 35.26 | 0.7 |
11 | MOL003199 | 5,8-Dihydroxy-7-(4-hydroxy-5-methyl-coumarin-3)-coumarin | 61.85 | 0.5 |
12 | MOL003206 | Canin | 77.41 | 0.3 |
13 | MOL003208 | Celafurine | 72.94 | 0.4 |
14 | MOL003209 | Celallocinnine | 83.47 | 0.6 |
15 | MOL003210 | Celapanine | 30.18 | 0.8 |
16 | MOL003211 | Celaxanthin | 47.37 | 0.6 |
17 | MOL003217 | Isoxanthohumol | 56.81 | 0.4 |
18 | MOL003222 | Salazinic acid | 36.34 | 0.8 |
19 | MOL003224 | Tripdiotolnide | 56.4 | 0.7 |
20 | MOL003225 | Hypodiolide A | 76.13 | 0.5 |
21 | MOL003229 | Triptinin B | 34.73 | 0.3 |
22 | MOL003231 | Triptoditerpenic acid B | 40.02 | 0.4 |
23 | MOL003232 | Triptofordin B1 | 39.55 | 0.8 |
24 | MOL003233 | Triptofordin B2 | 107.7 | 0.8 |
25 | MOL003234 | Triptofordin C2 | 30.16 | 0.8 |
26 | MOL003235 | Triptofordin D1 | 32 | 0.8 |
27 | MOL003236 | Triptofordin D2 | 30.38 | 0.7 |
28 | MOL003238 | Triptofordin F1 | 33.91 | 0.6 |
29 | MOL003239 | Triptofordin F2 | 33.62 | 0.7 |
30 | MOL003241 | Triptofordin F4 | 31.37 | 0.7 |
31 | MOL003242 | Triptofordinine A2 | 30.78 | 0.5 |
32 | MOL003244 | Triptonide | 68.45 | 0.7 |
33 | MOL003245 | Triptonoditerpenic acid | 42.56 | 0.4 |
34 | MOL003248 | Triptonoterpene | 48.57 | 0.3 |
35 | MOL003266 | 21-Hydroxy-30-norhopan-22-one | 34.11 | 0.8 |
36 | MOL003267 | Wilformine | 46.32 | 0.2 |
37 | MOL003278 | salaspermic acid | 32.19 | 0.6 |
38 | MOL003279 | 99694-86-7 | 75.23 | 0.7 |
39 | MOL003280 | TRIPTONOLIDE | 49.51 | 0.5 |
40 | MOL000358 | beta-sitosterol | 36.91 | 0.8 |
41 | MOL000211 | Mairin | 55.38 | 0.8 |
42 | MOL000422 | kaempferol | 41.88 | 0.2 |
43 | MOL000449 | Stigmasterol | 43.83 | 0.8 |
44 | MOL002058 | 40957-99-1 | 57.2 | 0.6 |
45 | MOL003283 | (2R,3R,4S)-4-(4-hydroxy-3-methoxy-phenyl)-7- methoxy-2,3-dimethylol-tetralin-6-ol | 66.51 | 0.4 |
46 | MOL004443 | Zhebeiresinol | 58.72 | 0.2 |
47 | MOL005828 | nobiletin | 61.67 | 0.5 |
48 | MOL007415 | [(2S)-2-[[(2S)-2-(benzoylamino)-3-phenylpropanoyl]amino]- 3-phenylpropyl] acetate | 58.02 | 0.5 |
49 | MOL007535 | (5S,8S,9S,10R,13R,14S,17R)-17-[(1R,4R)-4-ethyl-1,5- dimethylhexyl]-10,13-dimethyl-2,4,5,7,8,9,11,12,14,15,16,17- dodecahydro-1H-cyclopenta[a]phenanthrene-3,6-dione | 33.12 | 0.8 |
50 | MOL009386 | 3,3’-bis-(3,4-dihydro-4-hydroxy-6-methoxy)-2H-1-benzopyran | 52.11 | 0.5 |
51 | MOL011169 | Peroxyergosterol | 44.39 | 0.8 |
表1. 雷公藤有效成分
在Genecard、OMIM、DrugBank数据库以关键词为“psoriasis”进行检索,使用Uniprot进行基因名标准化、删除无靶点及去除重复值后得到银屑病相关基因有1348个。
将获得的1348个药物作用靶点与142个疾病作用靶点取交集,共获得交集靶点70个,于Venn绘制韦恩图(见图1)。
图1. 雷公藤与银屑病交集靶点韦恩图
利用Cytoscape筛选出22个药物有效成分,构建雷公藤–银屑病的作用靶点的Network与Type文件,导入Cytoscape,得到雷公藤–成分–银屑病–靶点网络图。该图共94个节点,其中橙红色代表疾病,紫色代表药物,蓝色代表共同作用靶点,绿色代表药物活性成分。雷公藤治疗银屑病主要通过22个有效成分作用于有可能对银屑病有影响的该70个基因(见图2)。
图2. 雷公藤–成分–银屑病–靶点网络图
将70个药物–疾病交集靶点输入String数据库,得到蛋白质相互作用关系的PPI网络图,再将其导入Cytoscape进行PPI网络绘制,节点颜色和大小根据Degree值进行调整,越大、颜色越深,度值越大,靶点越重要(见图3)。其中Degree值较高的是TNF、CXCL8、TP53、PTGS2、VEGFA、IL4、STAT3、MMP9、MAPK8、ICAM1,其对应的Degree值分别为51,45,45,43,43,42,40,40,39,39。使用NetworkAnalyzer工具,以degree, betweenness centrality, average shortest path length和closeness centrality这四个参数为参考标准,通过度值排序,选取分值大于平均分的基因作为关键靶点,总共筛选出33个关键靶点,将这33个靶点使用R软件进行图片绘制(见图4)。
图3. 雷公藤–银屑病相关基因蛋白质互作网络图
图4. 雷公藤–银屑病核心靶点柱状图
使用String数据库,将校正P值≤0.05的项目进行筛选,总共富集到1647条生物过程,100项分子功能相关,19项细胞组成相关。使用R软件进行气泡图绘制(见图5)。
将药物疾病共有靶点进行KEGG通路富集分析,引用String数据库,将校正P值≤0.05的项目进行筛选,总共富集到136条信号通路,使用R软件对主要的20个信号通路进行柱状图和气泡图绘制(见图6)。
为了更好的揭示中药、成分与其相应靶点之间的复杂相互作用关系,以雷公藤对应的主要有效成分、疾病,富集KEGG信号通路以及作用靶点为基础,进行了中药复方–有效成分–疾病–信号通路–作用靶点网络图的绘制(见图7)。
图5. 雷公藤治疗银屑病GO富集分析气泡图
图6. 雷公藤治疗银屑病的KEGG通路富集分析气泡图
图7. 雷公藤–成分–银屑病–通路靶点网络图(网络图中黄色为靶点,蓝色菱形为中药成分,绿色为通路)
中医网络药理学是从中医的经验医学到循证医学转化的新型研究模式,通过预测中药的药理学成分及其靶基因寻找疾病相关基因,然后构建中药–基因–疾病的网络关系图,揭示药物–基因–疾病的关联模型 [
本研究结果显示雷公藤的有效化合物有51个,作用于银屑病的靶点基因有142个。雷公藤活性成分中主要有雷公藤甲素、川陈皮素、山奈酚。雷公藤甲素是具有多种生物活性的二萜内酯,其治疗银屑病基础为通过干扰早期活化信号转导通路进而抑制T细胞的活化与增值 [
综上所述,本研究基于网络药理学的技术与方法分析了雷公藤治疗银屑病的作用机制,我们可得出雷公藤对银屑病的治疗可通过多成分–多靶点的特点发挥药理学作用,并找出了发挥治疗作用的主要药物成分。通过雷公藤–银屑病共同作用靶点做GO生物功能与KEGG信号通路分析,我们可以推测到雷公藤通过复杂的整体调节、多功能、多通路的方式以达到治疗银屑病的目的。根据银屑病的发病机制,推测出雷公藤治疗银屑病的机制与过Th17细胞分化、IL-17信号通路密切相关,并通过多种炎性介质发挥抗炎、调节免疫及细胞凋亡等发挥治疗作用。为后续深入研究雷公藤治疗银屑病的机制提供了靶点和方向。
鄢 洁,姚 闵,刘 洋. 基于网络药理学探讨雷公藤治疗银屑病作用机制的研究Study on the Mechanism of Tripterygium wilfordii in the Treatment of Psorisis Based on Network Pharmacology[J]. 临床医学进展, 2022, 12(04): 3141-3152. https://doi.org/10.12677/ACM.2022.124454