Chinese Journal of Tissue Engineering Research ›› 2025, Vol. 29 ›› Issue (35): 7669-7678.doi: 10.12307/2025.953
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Wang Tong1, Zheng Yu2, Jia Chengming2, Yang Hu1, Zhang Guangfei1, Ji Yaoyao1
Received:
2024-10-16
Accepted:
2024-12-14
Online:
2025-12-18
Published:
2025-05-07
Contact:
Zheng Yu, MD, Associate chief physician, Master’s supervisor, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 710000, Shaanxi Province, China
About author:
Wang Tong, Master candidate, Shaanxi University of Chinese Medicine, Xianyang 712000, Shaanxi Province, China
Supported by:
CLC Number:
Wang Tong, Zheng Yu, Jia Chengming, Yang Hu, Zhang Guangfei, Ji Yaoyao. Action mechanism of Gegenmaqi prescription in treatment of periarthritis of shoulder combined with type 2 diabetes based on TCMSP database[J]. Chinese Journal of Tissue Engineering Research, 2025, 29(35): 7669-7678.
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蛋白靶点63个;穿山龙有效成分1种,对应蛋白靶点15个;白芍有效成分8种,对应蛋白靶点92个;生姜有效成分4种,对应蛋白靶点54个;大枣有效成分17种,对应蛋白靶点117个;炙甘草有效成分 88种,对应蛋白靶点144个。将所有蛋白质靶点导入Uniprot数据库进行标准化处理,去除重复项,最终获得葛根麻芪方相关的蛋白靶点基因共217个,将数据以图片的形式可视化(图1)以表明各单味药之间的相互作用关系。 2.2 肩周炎和2型糖尿病蛋白靶点的收集 通过GenCards、OMIM、drugbank数据库分别获得肩周炎蛋白靶点1 236个、634个、64个,分别获得2型糖尿病蛋白靶点1 093个、522个、126个。利用 Uniprot 数据库进行确认并转换,剔除重复的蛋白靶点,整理得到肩周炎蛋白靶点1 843个,2型糖尿病蛋白靶点1 662个,共计肩周炎并2型糖尿病蛋白靶点2 830个。 2.3 葛根麻芪方蛋白靶点- 肩周炎并2型糖尿病蛋白靶点网络构建 通过数据库获得葛根麻芪方蛋白靶点217个,肩周炎并2型糖尿病疾病蛋白靶点2 830个。将两者靶点取交集,得到交集靶点基因65个,并制作韦恩图(图2)。 2.4 蛋白质-蛋白质相互作用网络的构建和核心靶点的筛选 通过导入数据,设置筛选条件后,将得到的剩余节点及其相互作用关系输入 Cytoscape 3.9.1 软件,以生成蛋白质-蛋白质相互作用网络图(图3)。此图共计56节点,251条边,颜色越深,圆圈越大,度值越高,在网络图中越重要。根据度值筛选核心靶点(表3),确定了AKT1、肿瘤坏死因子、JUN、TP53、白细胞介素10等5个核心靶点。因此作者猜想这些核心靶点在葛根麻芪方治疗肩周炎并2型糖尿病过程中发挥着关键作用。 2.5 靶点基因GO生物信息富集分析 David数据库是一个生物信息学资源系统,包括一个Web服务器和一个用于基因列表功能注释和富集分析的Web服务[15]。借助David数据库对65个交集靶点开展GO和KEGG富集分析。GO富集分析得到生物过程、"
分子功能和细胞组分共计508条GO条目。其中生物过程相关条目390条,主要包括基因表达的调控、miRNA转录的正调控、DNA模板转录的正调控、细胞缺氧、细胞凋亡过程的正向调节、磷脂酰肌醇3-激酶/蛋白激酶B信号转导的正调控、异种生物刺激的反应、对脂多糖的调控作用等。分子功能相关条目77条,主要涵盖蛋白质、酶、血红素的结合部位,以及类固醇结合蛋白、丝氨酸型内肽酶、蛋白同型二聚化、辅酶Ⅱ、核受体等细胞因子的活性。细胞组分相关条目41条,包括细胞核、细胞质基质、细胞外间隙、胞外区、内质网膜、线粒体等细胞结构。选择生物过程、分子功能、细胞组分前20条通路,利用微生信在线工具制作GO富集分析图(图4)。 2.6 靶点基因KEGG生物信息富集分析 KEGG富集分析得到146条KEGG功能条目(P < 0.05),取前20条通路进行富集分析,以网格图形式可视化。结果显示基因主要富集在高级糖基化终末产物-受体信号通路、脂质和动脉粥样硬化信号通路、肿瘤坏死因子信号通路、白细胞介素17信号通路(图5)。此外通过分析数据发现以上筛选的核心靶点AKT1、JUN、肿瘤坏死因子、TP53、白细胞介素10在此20条通路上显著出现。 2.7 中药有效成分-疾病通路-交集蛋白靶点网络图构建 将葛根麻芪方有效成分、KEGG前20条通路,通路对应靶点基因和交集靶点基因导入Cytoscape 3.9.1 软件构建网络图(图6)。 2.8 分子对接与分子动力学结果 分子对接结果显示,核心成分与核心靶点均有较好的结合活性(表4),一般认为,当结合能< -17.808 kJ/mol时,表示配体和受体之间存在一定的结合活性;结合能< -20.92 kJ/mol时,表示有较好的结合活性;而结合能< -29.288 kJ/mol时,则表示有强烈的结合活性[16]。研究所得结果均 < -20.92 kJ/mol,说明核心成分与核心靶点具有较好的结合活性。在葛根麻芪方治疗肩周炎并2型糖尿病的过程中,β-谷甾醇与核心靶点之间显示出较强的结合活性,这表明β-谷甾醇可能在其中扮演着关键角色。为了直观展示这一发现,使用Pymol软"
件对β-谷甾醇效果最佳的对接结果进行了可视化展示(图7)。 均方根偏差是评价蛋白质结构变化的指标,此次对配体-受体复合物进行常规30 ns的分子动力学模拟,图8展示了主链Cα的均方根偏差波动情况。在5 ns之后AKT1-β-谷甾醇体系的均方根偏差趋于稳定;白细胞介素10-β-谷甾醇体系在15 ns 后波动趋势稳定;肿瘤坏死因子-β-谷甾醇体系在10 ns后波动趋势稳定。3个体系在模拟过程中均达到了平衡,说明β-谷甾醇与3种关键核心蛋白的结合比较稳定。 均方根波动值能够体现每个氨基酸残基在模拟过程中的稳定性,如图9所示,AKT1-β-谷甾醇体系中残基4-45,245-273,286-293,315-343位点波动极小,很有可能通过氢键、疏水作用等作用力将配体包裹在活性口袋中,形成稳定复合物体系。白细胞介素10-β-谷甾醇体系在31-45氨基酸位点波动极大,不易形成氢键和疏水作用区域。肿瘤坏死因子-β-谷甾醇体系在30-58,71-95,98-115,118-133,137-146,160-175,180-195位点波动< 0.3,相对稳定,有理由猜测这些位点易形成活性空腔,配体可在其中稳定存在。 AKT1-β-谷甾醇、白细胞介素10-β-谷甾醇、肿瘤坏死因子-β-谷甾醇体系平均结合自由能分别是-126.44,-191.12,-130.73 kJ/mol(表5)。结合自由能越小,配体与受体之间的亲和力越高,配体越能稳定嵌入蛋白的活性口袋,利用ORIGIN 2022软件绘制在28-30 ns的能量变化曲线图(图10),其中EVDW代表范德华力,Elect代表静电势能。综合以上分析,白细胞介素10-β-谷甾醇的亲和力最高,与分子对接结果一致,白细胞介素10的Pro141,Phe139和Arg138与β-谷甾醇之间形成3个氢键(图7)。"
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