Chinese Journal of Tissue Engineering Research ›› 2021, Vol. 25 ›› Issue (35): 5662-5669.doi: 10.12307/2021.297
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An Yang1, 2, 3, Liao Yinan4, Xie Chengxin2, Li Qinglong2, Huang Ge2, Jin Xin2, Yin Dong1, 2
Received:
2020-10-15
Revised:
2020-10-17
Accepted:
2020-11-13
Online:
2021-12-18
Published:
2021-08-05
Contact:
Yin Dong, MD, Chief physician, Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China; The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, Guangxi Zhuang Autonomous Region, China
About author:
An Yang, Master candidate, Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning 530001, Guangxi Zhuang Autonomous Region, China; The People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, Guangxi Zhuang Autonomous Region, China; Guangxi Key Laboratory of Regenerative Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
CLC Number:
An Yang, Liao Yinan, Xie Chengxin, Li Qinglong, Huang Ge, Jin Xin, Yin Dong. Mechanism of Inulae flos in the treatment of osteoporosis: an analysis based on network pharmacology[J]. Chinese Journal of Tissue Engineering Research, 2021, 25(35): 5662-5669.
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2.3 药物-成分-靶点-疾病网络的构建及关键有效药物成分的筛选 作者通过4个数据库的数据,确认了180个旋覆花治疗骨质疏松症的潜在作用靶点。然后使用Cytoscape 3.7.2软件,将药物-成分、成分-靶点、疾病-靶点的信息导入后,进行可视化调整,得到旋覆花治疗骨质疏松症的药物-成分-靶点-疾病网络图,见图2。作者把有效药物成分节点设置为连接的潜在靶点越多,节点越大,可以观察到quercetin (MOL000098,槲皮素)、luteolin (MOL0000006,木犀草素)、kaempferol (MOL000422,山奈酚)3个成分显著大于其他节点,说明此3个节点为药物成分的关键节点,所对应的单体可视为旋覆花治疗骨质疏松症的关键有效药物成分,见图3。"
2.4 旋覆花对骨质疏松症作用靶点的蛋白互作网络及关键靶点分子对接结果 得到了180个旋覆花治疗骨质疏松症的潜在作用靶点,使用String数据库对这些靶点进行分析,得到蛋白质相互作用网络,共涉及到178个靶点,3 409对蛋白互作关系。使用Cytoscape 3.7.2软件对所得到的结果进行可视化调整,得到潜在作用靶点的PPI网络图,见图4,其中靶点颜色越深,代表其Degree值越高,而Degree高低代表了蛋白相互作用的可信度。随后作者使用“Cytohubba”插件,筛选出PPI网络图中Degree值前30的靶点,见图5。在图5可以观察到,AKT1,TP53,VEGFA等靶点在网络中的Degree值都排名靠前,可以认为是旋覆花对骨质疏松症作用靶点中的关键靶点。"
作者使用autodock vina软件对Degree前10的靶点与3个关键活性节点进行了分子对接结果预测,见表2,图6,一般认为结合能越低,配体与受体结合的构象越稳定,≤?20.9 kJ/mol (?5.0 kcal/mol )说明两者可以结合,≤ ?29.3 kJ/mol (?7.0 kcal/mol) 说明有较好的结合能力,结果显示关键靶点和关键成分均可以结合,其中PTGS2,CASP3和EGFR与3个活性成分有较好的结合能力。 2.5 GO分析和KEGG通路富集分析结果 David数据库一直被广泛用于对基因和靶点进行功能和通路富集分析。作者在David 6.8数据库在线平台对旋覆花对骨质疏松症的潜在作用靶点进行GO分析和KEGG通路富集分析,P < 0.01为筛选参数。使用 ImageGP在线作图工具将GO和KEGG分析的结果进行可视化调整,制成对应的气泡图。"
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