基于计算机辅助药物设计方法探讨当归活血作用的物质基础和分子机制

Material basis and molecular mechanism of Angelicae Sinensis Radix in activating blood:based on computer-aided drug design

当归具有良好的活血作用,但目前对其发挥“活血”功效的现代科学原理缺乏系统研究,限制了其现代化开发。该研究采用基于结构相似性的靶点反向预测、复杂网络分析、分子对接、结合自由能计算、聚类分析、ADMET计算等计算机辅助药物设计方法结合体外酶活性测定实验系统探讨了当归发挥活血作用的成分及作用机制。靶点反向预测以及复杂网络分析结果显示当归抗凝血的潜在作用靶点有40个。GO(Gene Ontology)和KEGG(Kyoto Encyclopedia of Genes and Genomes)富集分析表明预测靶点可能通过作用于补体与凝血级联信号通路发挥抗凝血作用。其中,凝血级联反应和血栓形成中的关键酶THR(thrombin)和FXa(coagulation factor Xa)是治疗血栓栓塞性疾病的药物靶点。全成分分子对接以及聚类分析显示当归针对FXa具有更好的选择性。结合自由能打分值筛选出8个潜在活性成分进行体外酶活实验,结果显示8个化合物分别对THR和FXa具有不同程度的抑制作用,且对FXa活性的抑制作用比对THR更强。对8个活性化合物进行药效团模型构建,得到药效特征AAHH,其中A为氢键受体,H为疏水中心。ADMET计算表明8个活性化合物都具有良好的药动学性质,且安全性较高。该研究以靶点反向预测、复杂网络分析、分子对接及结合自由能计算、体外抗凝活性、分子与靶点的空间结合构象、药效团模型构建及ADMET参数计算为依据,从大数据层面初步阐明了当归活血作用的物质基础及分子机制,并对活性成分进行了药理、毒理计算,首次从全成分计算结合酶活实验揭示了当归对不同凝血蛋白具有明显的选择性和针对性,反映出不同中药的独特功效具有其生物学基础。该研究可为当归的精准用药及其活血成分的现代化开发提供线索。

Angelicae Sinensis Radix excels in activating blood,but the scientific mechanism has not been systematically analyzed,thus limiting the development of the medicinal.This study employed the computer-aided drug design methods,such as structural similarity-based target reverse prediction,complex network analysis,molecular docking,binding free energy calculation,cluster analysis,and ADMET(absorption,distribution,metabolism,excretion,toxicity)calculation,and enzyme activity assay in vitro,to explore the components and mechanism of Angelicae Sinensis Radix in activating blood.Target reverse prediction and complex network analysis yielded 40 potential anticoagulant targets of the medicinal.Gene Ontology(GO)term enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis indicated that the targets mainly acted on the complement and coagulation cascade signaling pathway to exert the anticoagulant function.Among them,the key enzymes thrombin(THR)and coagulation factor Xa(FXa)in coagulation cascade and thrombosis were the drug targets for thromboembolic diseases.At the same time,molecular docking and cluster analysis showed that the medicinal had high selectivity for FXa.According to binding free energy score,8 potential active components were selected for enzyme activity assay in vitro.The results demonstrated that 8 components inhibited THR and FXa,and the inhibition was stronger on FXa than on THR.The pharmacophore model of 8 active compounds was constructed,which suggested that the components had the common pharmacophore AAHH.The ADMET calculation result indicated that they had good pharmacokinetic properties and were safe.Based on target reverse prediction,complex network analysis,molecular docking and binding free energy calculation,anticoagulant activity in vitro,spatial binding conformation of molecules and targets,pharmacophore model construction,and ADMET calculation,this study preliminarily clarified the material basis and molecular mechanism of Angelicae Sinensis Radix in activating blood from the perspective of big data,and calculated the pharmacology and toxicology parameters of the active components.Our study,for the first time,revealed that the medicinal had obvious selectivity and pertinence for different coagulation proteins,reflecting the unique effect of different Chinese medicinals and the biological basis.Therefore,this study can provide clues for precision application of Angelicae Sinensis Radix and the development of the blood-activating components with modern technology.