探讨 L. 植物化学物质的治疗潜力:抑制 SARS-CoV-2 主要蛋白酶(Mpro)的计算研究。
Exploring the Therapeutic Potential of L. Phytochemicals: A Computational Study on Inhibiting SARS-CoV-2's Main Protease (Mpro).
机构信息
Bioinformatics Laboratory, Department of Statistics, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh.
Department of Chemistry, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh.
出版信息
Molecules. 2024 May 27;29(11):2524. doi: 10.3390/molecules29112524.
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 L. ( 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 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 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.
新型冠状病毒(SARS-CoV-2)的爆发,也就是我们熟知的 COVID-19 大流行,仍然是人类生命和全球经济的重大风险因素。尽管文献中已经介绍了几种有前途的抑制 SARS-CoV-2 的疗法,但它们大多数是合成药物,可能对人体有一些不良反应。因此,本研究的主要目的是对 L.(李属)介导的植物化合物治疗 SARS-CoV-2 感染的药用特性进行计算机研究,因为与合成药物相比,植物化学物质的不良反应较少。为了从 L. 中探索潜在的植物化合物作为候选药物分子,我们选择 SARS-CoV-2 的感染主要蛋白酶(Mpro)作为受体蛋白。使用 AutoDock Vina 对这些受体蛋白与 L. 的不同植物化合物进行分子对接分析。然后,我们根据它们的最高结合亲和力评分(-8.9、-8.7 和-8.3(Kcal/mol)),选择了三种排名最高的植物化合物(杨梅素、茵陈素和槲皮素)作为候选药物分子。然后,使用 YASARA 软件对它们与 Mpro 的复合物进行了 100ns 的分子动力学(MD)模拟研究,计算了 RMSD、RMSF、PCA、DCCM、MM/PBSA 和自由能景观(FEL),发现它们具有几乎稳定的结合性能。此外,生物活性、ADME/T、DFT 和药物相似性分析表明所选植物化合物具有合适的药代动力学特性。因此,在进行湿实验室和临床试验的实验验证后,本研究的结果可能为制定 SARS-CoV-2 感染的安全治疗方案提供有用的资源。