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西红花为名贵药材,来源于鸢尾科植物番红花Crocus sativus L.的干燥柱头。原产于地中海地区、希腊、小亚细亚和伊朗,后经西藏传入国内,故又名藏红花[1]。《本草纲目》中记载番红花“主治心忧郁积、气闷不散,活血,亦治惊悸”[2]。2020版《中国药典》描述西红花具有活血化瘀、凉血解毒、解郁安神的功效[3]。越来越多的现代药理研究表明,西红花具有抗肿瘤、抗血小板聚集与凋亡、抗心血管细胞凋亡、降血脂和降血糖等活性[4–6],在健康和医疗领域具有重要作用。
世界卫生组织国际癌症研究机构(IARC)发布的最新数据,2020年全球癌症新发患者病例数超过1 930万例,癌症死亡患者接近1 000万例[7]。天然活性成分是抗肿瘤药物研发的重要来源[8]。有研究表明,西红花中特有的西红花酸、西红花苷等具有抗肿瘤活性[9],已有学者在西红花治疗结直肠癌、乳腺癌等的抗肿瘤作用方面进行了相关研究[10-11],但其主要活性成分及抗肿瘤作用机制仍需进一步探索。
网络药理学[12]将系统生物学、生物信息学、计算生物学、网络科学和靶向药理学相结合,从系统层次和生物网络的整体角度探讨成分—靶标—通路的相互作用关系,为中药多靶点、多成分、系统性、整体性的作用机制研究提供了有力的技术支撑,从而指导新药研发和临床诊疗。因此,本研究应用网络药理学结合反向分子对接的方法,对西红花的抗肿瘤作用成分及靶点机制进行研究,为深入探索西红花抗肿瘤药效物质基础及作用机制提供参考。
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通过TCMSP获得70个西红花化学成分,设置OB≥30%且DL≥0.18进行筛选,再添加文献检索相关成分,共获得9个西红花活性成分,见表1。
表 1 西红花活性成分
序号 化合物编号 化合物英文名 中文名 OB (%) DL 1 MOL001389 n-heptanal 庚醛 79.74 0.59 2 MOL001406 crocetin 西红花酸 35.3 0.26 3 MOL000354 isorhamnetin 异鼠李素 49.6 0.31 4 MOL000422 kaempferol 山柰酚 41.88 0.24 5 MOL000098 quercetin 槲皮素 46.43 0.28 6 MOL001405 crocin Ⅰ 西红花苷Ⅰ 2.54 0.12 7 MOL001407 crocin Ⅱ 西红花苷Ⅱ 1.65 0.21 8 MOL000720 safranal 藏红花醛 39.56 0.04 9 MOL001409 picrocrocin 苦番红花素 33.71 0.04 -
将TCMSP平台和PharmMapper获取结果进行整理,并借助UniProt数据库进行靶基因匹配,获得201个潜在靶点。以“tumor”和“cancer”为关键词,在GeneCards、OMIM和TTD数据库进行预测整理,剔除重复,筛选得到5896个潜在疾病靶点。将得到的疾病靶点和药物靶点取交集,共得到可作为药物作用于疾病的179个预测靶点。
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将西红花的9个活性成分与预测到的179个潜在靶点导入Cytoscape 3.9.1软件,构建“药物-活性成分-靶点”网络(图1),网络中绿色代表药物作用于疾病的靶点,蓝色代表西红花活性成分,全图包括189个节点、299条边,其中degree值排名靠前的活性成分为槲皮素、山柰酚、异鼠李素、苦番红花素和西红花苷Ⅰ,这些可能是西红花发挥抗肿瘤作用的潜在活性成分。
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将疾病与活性成分的潜在靶点导入String数据库,采用Cytoscape 3.9.1软件绘制PPI网络图,依据degree值进行排序,以大于半数degree值为标准进行两次筛选,获取核心靶点37个(图2)。度值排名前5的靶点分别为EGF、MMP9、NFKBIA、IL-1B和IL-10,提示这些靶点可能是西红花发挥抗肿瘤作用的关键潜在靶点。
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GO分析常用于注释基因和基因产物生物功能,分析包括生物过程(biological process,BP)、分子功能(molecular function,MF)和细胞组成(cellular component,CC)三部分。此次GO富集分析共得到BP富集结果193个、CC富集结果83个和MF富集结果123个,选取排名前10的条目绘制GO功能分析图(图3)。如图3所示,BP主要涉及对激素的反应、对脂质的反应、对异源刺激的反应等;CC主要涉及膜筏、膜微区、囊腔、细胞质囊泡腔等;MF主要涉及转录因子结合、DNA结合转录因子结合、RNA聚合酶Ⅱ特异性DNA结合转录因子结合等。通过比较发现,细胞生物过程富集的基因数较多,说明西红花可能主要通过调节生物过程发挥抗肿瘤作用。
KEGG分析共富集到194条信号通路,其中34条癌症相关通路,并对前20条通路绘制气泡图(图4)。依据KEGG分析,西红花可能通过p53信号通路、TNF通路发挥抗肿瘤作用,可能对膀胱癌、胰腺癌、前列腺癌、非小细胞肺癌等肿瘤具有治疗作用,西红花靶点-通路相互作用网络见图5,红色三角形代表与肿瘤相关的信号通路,蓝色矩形代表关键靶点。其中,西红花通过膀胱癌信号通路调控EGF、MMPs、Raf、VEGF、ERK等基因发挥抗肿瘤作用(图6),红色矩形代表西红花可能干预的关键靶点。
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将前15个潜在核心靶点与西红花活性成分进行分子对接。结合能(affinity)<0表明配体分子能够与受体蛋白自发结合,结合能≤−17.78 kJ/mol表明配体与受体有一定的结合活性,结合能≤−20.92 kJ/mol 表明配体与受体有较好的结合活性,结合能≤−29.29 kJ/mol 表明配体与受体有强的结合活性[17],且结合能越低,表明对接的效果越好,结合的构象越稳定[18]。经AutoDock Vina对接,将得到的结合能数据使用热图展示(图7)。本研究结合自由能小于−20.92kJ/mol 的活性成分有102个,占75.6%;小于−29.29kJ/mol 的活性成分有73个,占54.1%,可见这些核心化合物与受体结合活性较高,结构相对稳定。选取结合能力最好的4个组合用Pymol软件进行可视化处理(图8)。
Anti-tumor mechanism study on saffron by network pharmacology and reverse molecular docking
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摘要:
目的 运用网络药理学和反向分子对接技术探讨西红花抗肿瘤的作用机制。 方法 通过检索文献和从中药系统药理学数据库(TCMSP)获取西红花的主要化学成分,利用PharmMapper服务器预测西红花活性成分的潜在靶点,通过UniProt数据库将西红花潜在靶点转换为对应的靶标基因,与GeneCards、OMIM和TTD数据库获得的肿瘤相关靶点进行映射分析,得到西红花抗肿瘤的潜在作用靶点。采用Cytoscape软件构建西红花“活性成分-靶点-疾病”相互作用网络,通过String数据库进行蛋白-蛋白相互作用分析,并利用Metascape平台进行GO功能和KEGG通路富集分析。使用AutoDock、Pymol软件对活性成分与关键靶点进行分子对接验证。 结果 共筛选出西红花中槲皮素、山柰酚、异鼠李素、苦番红花素和西红花苷Ⅰ等9个活性成分,可能作用于AKT1、CCND1、MMP9、EGFR、TP53等37个关键靶点,涉及P53信号通路及TNF信号通路等。分子对接显示可通过氢键、疏水作用等产生稳定结合。 结论 初步探讨了西红花抗肿瘤的主要活性成分、关键靶点及通路,提示可通过诱导细胞凋亡等方式发挥抗肿瘤作用,为后续实验验证提供参考依据。 Abstract:Objective To explore the anti-tumor mechanism of saffron (Crocus sativus L.) by network pharmacology and reverse molecular docking techniques. Methods The main chemical components of saffron were obtained by searching published literature and TCMSP database. The potential targets of these components were predicted using PharmMapper server. The corresponding target genes were identified from UniProt database. The underlying anti-tumor targets of saffron were obtained by mapping the disease genes of cancer or tumor with GeneCards, OMIM and TTD databases. Cytoscape software was used to construct the action target network of saffron active components. The protein-protein interaction analysis was performed by String database, and the GO function and KEGG pathway enrichment analysis were performed by Metascape platform. Finally, molecular docking was performed to evaluate the binding of main components with their potential targets. Results A total of 9 active ingredients in saffron including quercetin, kaempferol, isorhamnetin, picrocrocin and crocin I, were identified, which might act on 37 key targets including AKT1, CCND1, MMP9, EGFR, TP53, involved in P53, TNF and other signaling pathways. Molecular docking indicated modest binding potency through hydrogen bonding, and hydrophobic interactions. Conclusion The anti-tumor effect of saffron was evaluated via the network of components-targets-pathways, which might provide a foundation for further research. -
Key words:
- saffron /
- network pharmacology /
- molecular docking /
- anti-tumor mechanism
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表 1 西红花活性成分
序号 化合物编号 化合物英文名 中文名 OB (%) DL 1 MOL001389 n-heptanal 庚醛 79.74 0.59 2 MOL001406 crocetin 西红花酸 35.3 0.26 3 MOL000354 isorhamnetin 异鼠李素 49.6 0.31 4 MOL000422 kaempferol 山柰酚 41.88 0.24 5 MOL000098 quercetin 槲皮素 46.43 0.28 6 MOL001405 crocin Ⅰ 西红花苷Ⅰ 2.54 0.12 7 MOL001407 crocin Ⅱ 西红花苷Ⅱ 1.65 0.21 8 MOL000720 safranal 藏红花醛 39.56 0.04 9 MOL001409 picrocrocin 苦番红花素 33.71 0.04 -
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