基于氧化应激相关基因的三七与黄精对近视作用的生物信息学分析

doi:10.5246/jcps.2024.05.033

摘要/Abstract

摘要：

本研究采用网络药理学的研究方法挖掘三七与黄精治疗近视的物质基础及其作用机制。通过中药系统药理学数据库与分析平台(TCMSP)数据库检索中药三七和黄精的主要活性成分, 并进行靶点预测, 靶点应用uniprot数据库查询出相对应的基因名。通过GeneCards数据库检索近视、氧化应激的相关靶点, 将中药靶点与近视、氧化应激的靶点取交集, 得到交集靶点。同时使用String数据库构建蛋白互作网络和Cytoscape软件, 筛选出关键基因和网络药理图; DAVID数据库, 对交集靶点进行GO和KEGG富集分析。三七活性成分7个; 黄精活性成分5个。删除重复项后得到187个靶点和近视、氧化应激共同靶点92个。通过PPI蛋白互作关系, 得到5个hub基因; 功能注释结果显示: 富集于细胞核、细胞膜等。KEGG通路富集分析表明交集靶点的KEGG信号通路主要为癌症通路、脂质与动脉粥样硬化等。通过调节JUN、TP53、ESR1、IL6、TNF等靶点基因, 特别是在细胞核和细胞膜等细胞组分中的靶点基因, 有可能实现抗近视作用。

关键词: 药理学, 近视, 氧化应激, 三七, 黄精

Abstract:

To investigate the material basis and mechanism of Panax notoginseng and Polygonati Rhizoma in the treatment of myopia using network pharmacology, we retrieved the primary active components of Panax notoginseng and Polygonati Rhizoma from the Chinese Medicine Systematic Pharmacology Database and Analysis Platform (TCMSP). The target sites for these components were predicted, and the corresponding gene names were obtained from the UniProt database. Targets associated with myopia and oxidative stress were extracted from the GeneCards database, and the intersection of targets from traditional Chinese medicine (TCM) with those related to myopia and oxidative stress was identified. Subsequently, the String database was utilized to construct a protein interaction network, and Cytoscape software was employed to identify key genes and generate network pharmacological maps. GO and KEGG enrichment analyses were performed on the intersection targets using the DAVID database. The results revealed seven active components of Panax notoginseng and five active ingredients of Polygonati Rhizoma. After removing duplicates, 187 targets were obtained, with 92 targets common to the drugs, myopia, and oxidative stress. Five hub genes were identified through protein-protein interaction analysis. GO analysis indicated enrichment in cellular components such as the nucleus and plasma membrane. KEGG pathway analysis revealed that the signaling pathways of the intersection targets were primarily associated with “Pathways in cancer” and “Lipid and atherosclerosis”. In conclusion, the regulation of target genes such as JUN, TP53, ESR1, IL6, and TNF, particularly in cellular components like the nucleus and plasma membrane, may contribute to the anti-myopic effects of Panax notoginseng and Polygonati Rhizoma.

Key words: Network pharmacology, Myopia, Oxidative stress, Panax notoginseng, Polygonati Rhizoma

Supporting:

王丹. 基于氧化应激相关基因的三七与黄精对近视作用的生物信息学分析[J]. 中国药学(英文版), 2024, 33(5): 438-447.

Dan Wang. Bioinformatic analysis of the impact of Panax notoginseng and Polygonati Rhizoma on myopia: insights from oxidative stress-related genes[J]. Journal of Chinese Pharmaceutical Sciences, 2024, 33(5): 438-447.

图/表 10

Figure 1. Intersection targets.

Figure 2. PPI networks constructed by intersection targets.

Figure 3. Degree (A), MCC (B), MNC (C) algorithm hub gene and algorithm intersection gene (D).

Figure 4. Network diagram of effective components and 92 targets of Panax notoginseng and Fructus flavescens. Note: Purple represents genes; Green represents Chinese medicine and active ingredients. SQ: Panax notoginseng, HJ: Polygonati Rhizoma.

Table 1. Effective chemical components of drugs.

Figure 5. Target-pathway network of notoginseng, flavin, myopia, and oxidative stress. Note: Red represents genes, and green represents pathways.

Table 2. GO function annotation of intersection targets.

Figure 6. Functional enrichment of intersecting genes (GO ontology).

Table 3. KEGG pathway enrichment at intersection targets.

Figure 7. KEGG pathway enrichment of intersection genes.

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