基于HERB数据库草药成分的新型冠状病毒多靶点新型抑制剂虚拟筛选

Virtual screening of novel multi-target inhibitors against SARS-CoV-2 based on herbal ingredients of HERB database

目的通过计算机虚拟筛选从HERB数据库草药成分中筛选出靶向新型冠状病毒主蛋白酶(main protease,Mpro)、木瓜样蛋白酶(papain-like protease,PLpro)和受体结合域(receptor binding domain,RBD)的新型潜在抑制剂并阐述其相互作用机制。方法以从HERB数据库中获得的天然化合物为筛选对象,综合运用药效团模型、分子对接、ADME-T预测、分子动力学模拟和分子力学泊松-玻尔兹曼表面积(molecular mechanics Poisson-Boltzmann surface area,MM-PBSA)等计算方法,获取靶向新型冠状病毒中Mpro、PLpro和RBD等多个靶点的潜在抑制剂,并采用酶活性抑制实验评价其植物提取物对Mpro的抑制效果。结果化合物HBIN006454、HBIN032286和HBIN031053对SARS-CoV-2的Mpro、PLpro和RBD靶点均具有较高的结合亲和力。其中,巴戟天中的HBIN031053具有更好的类药性和药动学特性,且与各靶点所形成的复合物在分子动力学模拟中均表现出良好的稳定性。MM-PBSA分析结果进一步揭示了在HBIN031053-Mpro、HBIN031053-PLpro以及HBIN031053-RBD的结合中发挥关键作用的氨基酸残基,并深入阐述了其抑制病毒蛋白酶活性的机制。酶活性抑制实验表明,巴戟天提取物对Mpro有抑制效果。结论天然化合物HBIN031053可作为靶向SARS-CoV-2中Mpro、PLpro和RBD等靶点的潜在新型抑制剂。

Objective To screennovel potential inhibitors against SARS-CoV-2 main protease(Mpro),papain-like protease(PLpro),and receptor binding domain(RBD),and elucidate their interaction mechanisms through computervirtual screening from herbal ingredients of the HERB database.Methods Natural compounds obtained from the HERB database were prepared for screeningobjects.Computational methods involving pharmacophore modeling,molecular docking,ADME-T prediction,molecular dynamics(MD)simulation and molecular mechanics Poisson-Boltzmann surface area(MM-PBSA)were comprehensively used to obtain potent inhibitors against SARS-CoV-2 Mpro,PLpro,and RBD.The enzyme activity inhibition assay was used to evaluate the inhibitory effect of the plant extracts on Mpro.Results Compounds HBIN006454,HBIN032286,and HBIN031053 all showed high binding affinities against SARS-CoV-2 Mpro,PLpro,and RBD.Among them,HBIN031053 from Morindae Officilis Radixhad better drug-likeness and pharmacokinetic properties,and the complexes formed with each target demonstrated favorable stability in MD simulations.The results of MM-PBSA analysis revealed the amino acid residues that playeda key role in the binding of HBIN031053-Mpro,HBIN031053-PLpro and HBIN031053-RBD,and further elaborated on their mechanism of inhibiting viral protease activity.Enzyme activity inhibition assay showed that the plant extract of Morindae Officilis Radixhad an inhibitory effect on Mpro.Conclusion The natural compound HBIN031053 can be used as a novel potential inhibitor targeting SARS-CoV-2 Mpro,PLpro,and RBD.