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中华肾病研究电子杂志 ›› 2021, Vol. 10 ›› Issue (04) : 189 -197. doi: 10.3877/cma.j.issn.2095-3216.2021.04.002

论著

基于网络药理学和分子对接研究益肾健脾利水方治疗肾小球肾炎的作用机制
金美玲1, 李典耕2, 张伟光3, 尹智炜4,(), 杨洪娟5,()   
  1. 1. 100020 北京,首都医科大学附属北京朝阳医院肾内科
    2. 100020 北京,首都医科大学附属北京朝阳医院科研处
    3. 100853 北京,解放军总医院第一医学中心肾脏病医学部、解放军肾脏病研究所、肾脏疾病国家重点实验室、国家慢性肾病临床医学研究中心、肾脏疾病研究北京市重点实验室
    4. 100853 北京,解放军总医院第一医学中心肾脏病医学部、解放军肾脏病研究所、肾脏疾病国家重点实验室、国家慢性肾病临床医学研究中心、肾脏疾病研究北京市重点实验室;050017 石家庄,河北医科大学中西医结合学院
    5. 050031 石家庄,河北医科大学第一医院中西医结合肾内科
  • 收稿日期:2021-06-21 出版日期:2021-08-26
  • 通信作者: 尹智炜, 杨洪娟
  • 基金资助:
    国家自然科学基金(81900605, 81901404); 北京市自然科学基金(7204308); 河北省重点研发计划项目(18277746D)

Mechanisms of Yishen-Jianpi-Lishui recipe in the treatment of glomerulonephritis: a study based on network pharmacology and molecular docking

Meiling Jin1, Diangeng Li2, Weiguang Zhang3, Zhiwei Yin4,(), Hongjuan Yang5,()   

  1. 1. Department of Nephrology, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing 100020
    2. Department of Scientific Research, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing 100020
    3. Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing 100853
    4. Department of Nephrology, First Medical Center of Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases, Beijing 100853; College of Integrated Chinese and Western Medicine, Hebei Medical University, Shijiazhuang 050017, Hebei Province
    5. Department of Nephrology of Integrated Chinese and Western Medicine, First Hospital of Hebei Medical University, Shijiazhuang 050031, Hebei Province; China
  • Received:2021-06-21 Published:2021-08-26
  • Corresponding author: Zhiwei Yin, Hongjuan Yang
引用本文:

金美玲, 李典耕, 张伟光, 尹智炜, 杨洪娟. 基于网络药理学和分子对接研究益肾健脾利水方治疗肾小球肾炎的作用机制[J]. 中华肾病研究电子杂志, 2021, 10(04): 189-197.

Meiling Jin, Diangeng Li, Weiguang Zhang, Zhiwei Yin, Hongjuan Yang. Mechanisms of Yishen-Jianpi-Lishui recipe in the treatment of glomerulonephritis: a study based on network pharmacology and molecular docking[J]. Chinese Journal of Kidney Disease Investigation(Electronic Edition), 2021, 10(04): 189-197.

目的

应用网络药理学及分子对接技术探究益肾健脾利水方(肾炎舒片)治疗肾小球肾炎的活性成分及分子机制。

方法

通过中药系统药理数据库和分析平台(TCMSP)查询方中主要的7味中药(苍术、茯苓、白茅根、人参、枸杞子、金银花、蒲公英)的主要活性成分,并对其靶点进行预测。检索GeneCards、OMIM、PharmGKB、TTD、DrugBank数据库。利用UniProt数据库注释所有靶标蛋白。将活性成分作用靶点和疾病靶点交集部分作为肾炎舒片治疗肾小球肾炎的潜在作用靶点,并利用GO数据库和KEGG数据库进行通路富集分析,将得到的核心有效成分与核心靶标进行分子对接。

结果

筛选出81个活性成分、219个基因靶点、肾小球肾炎相关靶点1 952个、116个肾炎舒片治疗肾小球肾炎的潜在靶点蛋白。GO富集分析结果提示:肾炎舒片治疗肾小球肾炎的潜在靶点蛋白,主要参与脂多糖反应、细菌源分子反应、氧化反应以及细胞化学压力反应等生物学过程。KEGG富集分析结果提示:可能的作用通路包括脂质和动脉粥样硬化通路、糖尿病并发症的AGE-RAGE信号通路、乙型肝炎相关通路以及卡波西肉瘤相关疱疹病毒感染通路等。蛋白互作(PPI)网络分析结果显示:肾炎舒片可通过MYC、JUN、MAPK8、FOS、NR3C1、TP53、MAPK14、IL-2、MAPK1、AKT1、TNF、RELA这12个关键靶点治疗肾小球肾炎。分子对接结果提示肾炎舒片主要活性成分与多种治疗肾小球肾炎靶点蛋白均有较好结合(S>4.5)。

结论

本研究结果提示益肾健脾利水方(肾炎舒片)治疗肾小球肾炎具有多成分、多靶点、多通路的特点,为进一步阐释其药理作用机制及开发新药奠定了研究基础。

Objective

To explore the active ingredients and molecular mechanisms of Yishen-Jianpi-Lishui recipe (Shenyanshu tablet, SYST) in the treatment of glomerulonephritis by the network pharmacology and molecular docking methods.

Methods

Through the analysis platform of Traditional Chinese Medicine Systems Pharmacology (TCMSP), the main active ingredients of the 7 main Chinese medicines (Atractylodes, Poria, Imperata, ginseng, wolfberry, honeysuckle, and dandelion) in the recipe were queried, and their targets were also predicted. The databases were searched including the human gene database (GeneCards), the database of Online Mendelian Inheritance in Man (OMIM), the Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB), the Therapeutic Target Database (TTD), and the drug action target database (DrugBank). The UniProt database was used to annotate all targets proteins. The intersection of the active ingredients′ targets and diseases′ targets were taken as the potential targets for the treatment of glomerulonephritis by SYST, for which the gene ontology (GO) database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were applied for the pathway enrichment analysis, and the core active ingredients and core targets obtained were analyzed with the molecular docking method.

Results

A total of 81 active ingredients, 219 gene targets, 1, 952 glomerulonephritis-related targets, and 116 potential targets proteins for the treatment of glomerulonephritis with SYST were screened out. The GO enrichment analysis results suggested that the potential targets proteins for the treatment of glomerulonephritis with SYST were mainly involved in the biological processes such as lipopolysaccharide reaction, bacterial-derived molecular reaction, oxidation reaction, and cytochemical pressure reaction. The KEGG enrichment analysis results suggested that possible pathways included the lipid and atherosclerosis pathways, the advanced glycation end products (AGEs) and the receptor for AGE (RAGE) signaling pathways for diabetic complications, hepatitis B-related pathways, and Kaposi′s sarcoma-related herpes virus infection pathways, etc. The Protein-Protein Interaction (PPI) network analysis showed that SYST could act in the treatment of glomerulonephritis through 12 key targets including MYC, JUN, MAPK8, FOS, NR3C1, TP53, MAPK14, IL-2, MAPK1, AKT1, TNF, and RELA. The molecular docking results indicated that the main active components of SYST combined well with a variety of targets proteins for the treatment of glomerulonephritis (S>4.5).

Conclusion

The results of this study suggested that SYST has the characteristics of multiple components, multiple targets, and multiple pathways in the treatment of glomerulonephritis, which laid a research foundation for further elucidating its pharmacological mechanism and developing new drugs.

图1 肾小球肾炎相关靶蛋白筛选韦恩分析图
图2 肾炎舒片-肾小球肾炎靶标的韦恩分析图
表1 肾炎舒片治疗肾小球肾炎潜在靶蛋白的GO分析
GO分类 GO ID 描述 基因比例 P
生物过程 GO:0032496 对脂多糖的反应 33/116 8.31E-31
生物过程 GO:0002237 对细菌来源分子的反应 33/116 6.88E-30
生物过程 GO:0006979 抗氧化反应 34/116 1.44E-27
生物过程 GO:0062197 细胞对化学应激的反应 31/116 4.65E-27
生物过程 GO:0072593 活性氧代谢过程 28/116 6.73E-26
生物过程 GO:0000302 对活性氧的反应 26/116 1.57E-25
生物过程 GO:0034599 细胞对氧化应激的反应 28/116 5.28E-25
生物过程 GO:0071222 细胞对脂多糖的反应 24/116 4.90E-24
生物过程 GO:0071216 细胞对生物刺激的反应 25/116 1.26E-23
生物过程 GO:0071219 细胞对细菌来源分子的反应 24/116 2.40E-23
细胞组分 GO:0045121 膜筏 18/116 9.25E-13
细胞组分 GO:0098857 膜微结构域 18/116 9.74E-13
细胞组分 GO:0098589 膜区 18/116 1.87E-12
细胞组分 GO:0044853 质膜筏 9/116 2.36E-08
细胞组分 GO:0005901 小窝 8/116 2.97E-08
细胞组分 GO:0090575 RNA聚合酶II转录调节复合物 9/116 4.98E-07
细胞组分 GO:0005667 转录调节复合物 13/116 1.06E-06
细胞组分 GO:0031983 囊腔 11/116 4.10E-06
细胞组分 GO:0000307 周期蛋白依赖性蛋白激酶全酶复合物 5/116 5.41E-06
细胞组分 GO:0034774 分泌颗粒内腔 10/116 2.22E-05
分子功能 GO:0140297 DNA结合转录因子结合 20/116 5.35E-14
分子功能 GO:0061629 RNA聚合酶Ⅱ特异性DNA结合转录因子 18/116 7.56E-14
分子功能 GO:0004879 核受体活性 10/116 8.68E-13
分子功能 GO:0098531 配体激活的转录因子活性 10/116 8.68E-13
分子功能 GO:0005126 细胞因子受体结合 16/116 1.52E-11
分子功能 GO:1901338 儿茶酚胺结合 6/116 1.61E-10
分子功能 GO:0003707 类固醇激素受体活性 7/116 2.00E-10
分子功能 GO:0005125 细胞因子活性 14/116 2.76E-10
分子功能 GO:0001223 转录辅激活结合 7/116 4.67E-10
分子功能 GO:0004252 丝氨酸蛋白酶肽链内切酶活性 11/116 9.94E-09
表2 肾炎舒片治疗肾小球肾炎潜在靶蛋白的KEGG分析
表3 肾炎舒片治疗肾小球肾炎的核心靶蛋白的KEGG分析
图3 肾炎舒片治疗肾小球肾炎的蛋白-蛋白互作网络图
图4 肾炎舒片治疗肾小球肾炎的核心蛋白的筛选
图5 草药-活性成分-核心靶标网络构建
图6 肾炎舒片治疗肾小球肾炎核心靶标在MAPK信号通路富集图
表4 肾炎舒片活性分子与肾小球肾炎核心靶标分子对接结果
图7 活性分子与靶标蛋白分子对接示意图
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