天然产物研究与开发 ›› 2022, Vol. 34 ›› Issue (1): 121-132.doi: 10.16333/j.1001-6880.2022.1.016

• 数据研究 • 上一篇    下一篇

基于网络药理学和分子对接探索桑白皮治疗糖尿病周围神经病变的潜在机制

张欢1,丁纪茹2,张效科1*   

  1. 1陕西中医药大学,咸阳 712046;2成都中医药大学附属医院,成都 610075
  • 出版日期:2022-01-28 发布日期:2022-01-28
  • 基金资助:
    国家自然科学基金面上项目(81774304)

Exploration of the potential mechanism of Mori Cortex on treating diabetic peripheral neuropathy based on network pharmacology and molecular docking

ZHANG Huan1,DING Ji-ru2,ZHANG Xiao-ke1*   

  1. 1Shaanxi University of Traditional Chinese Medicine,Xianyang 712046,China;2Affiliated Hospital of Chengdu University of Traditional Chinese Medicine,Chengdu 610075,China
  • Online:2022-01-28 Published:2022-01-28

摘要:

本研究运用网络药理学和分子对接方法对中药桑白皮治疗糖尿病周围神经病变(DPN)的活性成分、潜在作用靶点和信号通路进行研究,探索桑白皮治疗DPN的可能作用机制。首先从中药系统药理学数据库(TCMSP)筛选出桑白皮的活性成分及靶点基因。通过GeneCards数据库及OMIM数据库筛选出DPN的疾病靶点基因,并用Cytoscape软件构建“药物-有效成分-靶基因-疾病”中药调控网络图。将有效成分靶标与疾病靶标上传到STRING数据库,构建蛋白互作网络图(PPI),并使用R语言对得到的PPI进行核心基因的筛选。运用R语言对关键靶点进行GO富集分析和KEGG通路富集分析。其次从活性成分及靶点基因中根据degree值筛选出前3个关键成分,并将该网络中的基因靶点以degree值高低进行排序,选择前3个核心靶点,然后从RCSB数据库下载相关蛋白的结构,使用Pymol软件去除溶剂分子与配体,使用AutoDock软件进行分子对接。最后通过酶联免疫吸附实验和荧光光谱实验验证网络药理学富集分析的结果。最终预测到31个桑白皮活性成分,312个活性成分相关靶点,120个桑白皮-糖尿病周围神经病变共同有效靶点。活性成分中度值最高的为槲皮素,其次为山柰酚。PPI网络核心基因为转录因子AP-1(JUN)、丝裂原活化蛋白激酶1(MAPK1)、转录因子p65(RELA)、丝氨酸-苏氨酸蛋白激酶1(AKT1)、白介素6(IL-6)等;GO富集分析显示会影响基因的转录、细胞因子表达和蛋白激酶活性等;KEGG通路富集分析显示AGE-RAGE信号通路、流体剪切力和动脉粥样硬化为显著性最高的通路,其次为卡波西肉瘤相关疱疹病毒感染、MAPK信号通路、人巨细胞病毒感染、TNF信号通路。分子对接结果显示关键成分中槲皮素与对应靶点具有较好的结合活性。酶联免疫吸附实验提示桑白皮能够降低IL-6和TNF-α的表达,荧光光谱实验证实桑白皮能够减少AGEs。可见中药桑白皮治疗糖尿病周围神经病变具有多成分、多靶点、多功能、多通路的作用特点,其潜在的作用机制可能与AGE-RAGE信号通路、肿瘤坏死因子信号通路等有关。

关键词: 桑白皮, 糖尿病周围神经病变, 网络药理学, 分子对接

Abstract:

To investigate the main active components,the potential targets and molecular pathways of Mori Cortex in the treatment of diabetic peripheral neuropathy (DPN) by using network pharmacology-molecular docking,and to explore the mechanism of Mori Cortex treating on DPN.The main active components and the gene targets of Mori Cortex were screened from the Chinese Medicine System Pharmacology Database (TCMSP).DPN targets genes were screened by searching the following databases of GeneCards database and OMIM database.Using the Cytoscape software to construct the Chinese herbs regulatory network diagram of “Chinese herb-active ingredient- target gene-disease”.The active component targets and disease targets were uploaded into the STRING database to construct PPI.We used R language for screening core genes in PPI.GO enrichment and KEGG pathway analysis were performed using R language.The three-dimensional structure and chemical structure of targets and components were obtained from RCSB database.Pymol software was used to remove water and phosphate from protein molecules.AutoDock software was used to convert compound and core protein gene pdb format into pdbqt format and search for active pockets,and finally run AutoDockTools for molecular docking.Enzyme-linked immunosorbent assay (ELISA) and fluorescence spectra were used to verify the results of network pharmacology enrichment analysis.Finally,31 active ingredients and 312 targets were extracted from Mori Cortex,and the highest target counts were quercetin and kaempferol.The core gene in PPI were JUN,MAPK1,RELA,AKT1,IL-6 and so on.GO analysis revealed that it was possibly influenced by the transcriptional activity of corresponding genes,cytokine expression and protein secretion.KEGG pathway analysis also showed enrichment of AGE-RAGE signaling pathway in diabetic complications,Fluid shear stress and atherosclerosis,Kaposi sarcoma-associated herpesvirus infection,MAPK signaling pathway,human cytomegalovirus infection,and TNF signaling pathway.The results of molecular docking showed that the key components have good binding activity with corresponding targets,for example,quercetin.The expression of IL-6 and TNF-α were decreased by ELISA,and the AGEs were decreased by fluorescence spectroscopy.Therefore,Mori Cortex has the characteristics of multi-components,multi-targets,multi-channels and multi-pathways in the treatment of DPN.Its potential mechanism may be related to AGE-RAGE signaling pathway,MAPK signaling pathway,and TNF signaling pathway.

Key words: Mori Cortex, diabetic peripheral neuropathy, network pharmacology, molecular docking

中图分类号:  R285