Chinese Journal of Tissue Engineering Research ›› 2022, Vol. 26 ›› Issue (15): 2419-2425.doi: 10.12307/2022.601
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Wang Xinyuan1, Huang Xiabing2, Li Juan2, Deng Xin1
Received:2021-09-01
Revised:2021-10-30
Accepted:2021-11-20
Online:2022-05-28
Published:2022-01-06
Contact:
Huang Xiabing, Master, Associate chief physician, First Affiliated Hospital of Guangxi University of Traditional Chinese Medicine, Nanning 530012, Guangxi Zhuang Autonomous Region, China
About author:Wang Xinyuan, Master, Lecturer, Guangxi University of Traditional Chinese Medicine, Nanning 530012, Guangxi Zhuang Autonomous Region, China
Supported by:CLC Number:
Wang Xinyuan, Huang Xiabing, Li Juan, Deng Xin. Network pharmacology and molecular docking analysis on Taohong Siwu Decoction for rheumatoid arthritis and osteoarthritis based on the concept of “Treating Different Diseases with the Same Therapeutic Principle”[J]. Chinese Journal of Tissue Engineering Research, 2022, 26(15): 2419-2425.
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2.5 GO功能富集分析和KEGG信号通路富集分析结果 为了探究药物与疾病的共同靶点的功能,通过R在线工具进行了富集分析。结果显示在GO功能富集中,生物过程(BP)中,主要参与对氧化应激的反应、细胞对化学应激的反应、对活性氧的反应、对金属离子的反应对脂多糖的反应。在细胞成分(CC)中主要富集于转录调节复合体、质膜筏、小窝、膜区、膜微区、膜筏。在分子功能(MF)中主要与泛素样蛋白连接酶结合、DNA结合转录因子结合、RNA聚合酶Ⅱ-特异性DNA-结合转录因子结合、类固醇激素受体活性、配体激活的转录因子活性的活动有关。此外,在KEGG通路富集结果中,骨关节炎与类风湿性关节炎与IL17信号通路、TNF信号通路、MAPK信号通路、PT53信号通路等密切相关,见图5。"
2.6 分子对接结果 将2.5筛选到的核心靶点与主要的化学成分采用分子操作平台软件MOE (molecule operating environment)进行对接验证,更能直观展示关键成分的最佳构型和核心靶点之间的相互作用,分子与标靶蛋白的最低结合能均小于0,说明配体与受体均可以自发结合。Hsin KY就分子对接的研究而言,结合能(kJ/mol)越小,表明活性物质与蛋白质之间对接的结果就会越牢固。当结合能的数值小于-4.25 kJ/mol时,则表示活性物质与蛋白质之间有一定结合活性,小于-5.0 kJ/mol时有较好的结合活性,小于-7.0 kJ/mol时有强烈的结合活性[18]。用MOE中的Dock模块进行分子对接,选择基于蛋白和配体间相互作用能的打分函数ASE,分别得到每个化合物与受体的对接打分,打分越低,配体与受体结合越稳定,结果见表2。"
总体来说,AKT1、EGF、JUN、TNF、MAPK1、MAPK8、TP53与化合物结合相对稳定,其中AKT1、EGF、TNF、MAPK8与beta-carotene的结合能分别是-8.88,-8.66,-9.33,-7.70 kJ/mol,JUN与Myricanone结合能是-8.14 kJ/mol,MAPK1与paeoniflorin的结合能是-7.84 kJ/mol。主要活性成分和核心靶点之间的结合情况与预测关系相符。将结合将为稳定的化学成分与靶点进行对接可视化,见图6。如图6A,AKT1与beta-carotene对接打分为-8.88,化合物完全被包裹在活性口袋之中,OH原子分别与lys163形成氢键,距离分别为2.81 nm,键能分别为-7.4 kJ/mol;如图6C,EGFR与beta-carotene对接打分为-8.66 kJ/mol,化合物完全被包裹在活性口袋之中,2个碳原子分别与ASP 855,PHE 856形成氢键,距离分别为3.54和3.62 nm,键能分别为-0.7 kJ/mol和-0.6 kJ/mol,氨基的氮原子与残基MET 793形成氢键受体,距离为2.90 nm,键能为-5.4 kJ/mol,化合物的相对分子质量为444.52,logP为3.03。桃红四物汤中的主要活性成分与核心靶点的高结合亲和力表明,桃红四物汤可能是通过调节以上相关靶标发挥治疗类风湿关节炎和骨关节炎的作用。"
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