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植物化合物作为针对 SARS-CoV-2 病毒中 m 蛋白酶的多功能药物先导物:来自分子动力学研究的见解。

Phytocompounds as versatile drug-leads targeting mProtease in the SARS-CoV-2 virus: insights from a molecular dynamics study.

机构信息

Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India.

Research Cell, Amity University Uttar Pradesh, Lucknow, India.

出版信息

J Biomater Sci Polym Ed. 2024 Nov;35(16):2528-2548. doi: 10.1080/09205063.2024.2385138. Epub 2024 Jul 30.


DOI:10.1080/09205063.2024.2385138
PMID:39264734
Abstract

SARS-CoV-2 is one of the deadly outbreaks in the present era and still showing its presence around the globe. Researchers have produced various vaccines that offer protection against infection, but we have not yet found a cure for COVID-19. Currently, efforts are focused on identifying effective therapeutic approaches to treat this infectious disease. In the present work, we investigated the main protease (Mpro) protein, a crucial component in SARS-CoV-2 viral particle formation, as a drug target and proposed phytocompounds with therapeutic potential against SARS-CoV-2. Initially, several plant-based resources were exploited to screen around one thousand phytocompounds and further their physiochemical characterization and assessment of drug likeliness were performed using SwissADME. Eventually, we screened 95 compounds based on docking analysis using AutoDock Vina. Five compounds were selected having the highest affinity for Mpro for the analysis of ligand-receptor interaction using molecular dynamic (MD) simulation. Docking and MD simulation studies elucidated the promising stable interaction of selected 5 ligands with Mpro. During MD simulation of 100 ns, Abacopterin F showed the lowest binding energy (-37.13 kcal/mol) with the highest affinity towards Mpro and this compound may be proposed as a lead molecule for further investigation. This interaction may result in modulation of the Mpro activity, consequently leading to hindrance in viral particle formation. However, and experimental validation would be needed to process the selected phytomolecules as a therapeutic lead against SARS-CoV-2.

摘要

SARS-CoV-2 是当今时代致命爆发之一,仍然在全球范围内存在。研究人员已经生产了各种疫苗,可以提供针对感染的保护,但我们尚未找到针对 COVID-19 的治愈方法。目前,研究工作集中在确定有效的治疗方法来治疗这种传染病。在目前的工作中,我们研究了主要蛋白酶(Mpro)蛋白,它是 SARS-CoV-2 病毒粒子形成的关键组成部分,作为药物靶点,并提出了具有治疗 SARS-CoV-2 潜力的植物化合物。最初,利用了几种植物资源来筛选大约一千种植物化合物,并进一步对其进行了物理化学特性表征,并使用 SwissADME 对其进行了药物相似性评估。最终,我们使用 AutoDock Vina 进行对接分析筛选了 95 种化合物。选择了 5 种具有与 Mpro 最高亲和力的化合物,用于使用分子动力学(MD)模拟分析配体-受体相互作用。对接和 MD 模拟研究阐明了所选 5 种配体与 Mpro 的有前途的稳定相互作用。在 100ns 的 MD 模拟过程中,Abacopterin F 表现出与 Mpro 最低的结合能(-37.13kcal/mol)和最高的亲和力,该化合物可能被提议作为进一步研究的先导分子。这种相互作用可能导致 Mpro 活性的调节,从而阻碍病毒粒子的形成。然而,需要进行 和 实验验证,以将选定的植物分子作为治疗 SARS-CoV-2 的先导药物。

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Phytocompounds as versatile drug-leads targeting mProtease in the SARS-CoV-2 virus: insights from a molecular dynamics study.

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