SARS-CoV-2的爆发,也称为COVID-19大流行,仍然是人类生活和全球经济的关键风险因素。虽然,文献中已经介绍了几种有希望的疗法来抑制SARS-CoV-2,其中大多数是合成药物,可能对人体产生一些不利影响。因此,这项研究的主要目的是对麻黄病的药用特性进行计算机研究(P.alliaceaL.)介导的植物化合物用于治疗SARS-CoV-2感染,因为与合成药物相比,植物化学物质的不良反应较少。目的:探索百里香潜在的植物化合物作为候选药物分子,我们选择SARS-CoV-2的引起感染的主要蛋白酶(Mpro)作为受体蛋白。使用AutoDockVina进行这些受体蛋白与不同植物化合物的分子对接分析。然后,我们选择了三种排名最高的植物化合物(杨梅素,Engeletin,和astilbin)作为候选药物分子,其最高结合亲和力评分为-8.9,-8.7和-8.3(Kcal/mol),分别。然后,使用YASARA软件对它们与Mpro的复合物进行了100ns分子动力学(MD)模拟研究,计算的RMSD,RMSF,PCA,DCCM,MM/PBSA,和自由能源景观(FEL),并发现它们几乎稳定的结合性能。此外,生物活性,ADME/T,DFT,和药物相似度分析显示了所选植物化合物的合适药代动力学特性。因此,在湿实验室和临床试验中进行实验验证后,这项研究的结果可能是制定SARS-CoV-2感染安全治疗计划的有用资源.
The outbreak of SARS-CoV-2, also known as the COVID-19 pandemic, is still a critical risk factor for both human life and the global economy. Although, several promising therapies have been introduced in the literature to inhibit SARS-CoV-2, most of them are synthetic drugs that may have some adverse effects on the human body. Therefore, the main objective of this study was to carry out an in-silico investigation into the medicinal properties of Petiveria alliacea L. (P. alliacea L.)-mediated phytocompounds for the treatment of SARS-CoV-2 infections since phytochemicals have fewer adverse effects compared to synthetic drugs. To explore potential phytocompounds from P. alliacea L. as candidate drug molecules, we selected the infection-causing main protease (Mpro) of SARS-CoV-2 as the receptor protein. The molecular docking analysis of these receptor proteins with the different phytocompounds of P. alliacea L. was performed using AutoDock Vina. Then, we selected the three top-ranked phytocompounds (myricitrin, engeletin, and astilbin) as the candidate drug molecules based on their highest binding affinity scores of -8.9, -8.7 and -8.3 (Kcal/mol), respectively. Then, a 100 ns molecular dynamics (MD) simulation study was performed for their complexes with Mpro using YASARA software, computed RMSD, RMSF, PCA, DCCM, MM/PBSA, and free energy landscape (FEL), and found their almost stable binding performance. In addition, biological activity, ADME/T, DFT, and drug-likeness analyses exhibited the suitable pharmacokinetics properties of the selected phytocompounds. Therefore, the results of this study might be a useful resource for formulating a safe treatment plan for SARS-CoV-2 infections after experimental validation in wet-lab and clinical trials.