Investigating the mechanisms of ethanol-induced disruption of COVID-19 lipid bilayers through molecular dynamics simulations

IF 2.1 4区化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2025-03-17 DOI:10.1007/s00894-025-06332-9

Azadeh Kordzadeh, Ahmad Ramazani SA

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Abstract

Context

The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, began in December 2019 in Wuhan, China. To mitigate the spread of COVID-19, public health officials strongly recommended preventive measures such as disinfectants, alcohol-based hand sanitizers, and face masks. The effect of ethanol on virus structure and inactivation remains unclear, and its molecular mechanism needs to be elucidated. This study elucidates how ethanol solutions interact with the lipid bilayer of the COVID-19 virus utilizing molecular dynamics (MD) simulations. Its findings indicated that ethanol can deactivate the virus through two primary mechanisms. First, when ethanol penetrates the viral membrane, it disrupts the structural integrity of the lipid bilayer, leading to membrane disruption. This alteration in morphology is critical as it compromises the virus’s ability to maintain its structure and function.

Methods

For the simulation, a lipid bilayer containing the spike protein of SARS-CoV-2 was constructed. The interaction between the viral membrane and ethanol solution was then simulated using GROMACS 5.1.4 for molecular dynamics (MD) analysis. Also, visual molecular dynamics (VMD1.9.3) was used for visualization. The study calculated the Lennard–Jones (LJ) and electrostatic interactions between ethanol and the lipid bilayer, and it analyzed the conformational changes in the spike protein following ethanol adsorption. Additionally, the effects of ethanol penetration on the morphology of the lipid bilayer were evaluated.

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背景由 SARS-CoV-2 冠状病毒引起的 COVID-19 大流行于 2019 年 12 月在中国武汉开始。为减少 COVID-19 的传播，公共卫生官员强烈建议采取消毒剂、酒精洗手液和口罩等预防措施。乙醇对病毒结构和灭活的影响仍不清楚，其分子机制也有待阐明。本研究通过分子动力学（MD）模拟，阐明了乙醇溶液如何与 COVID-19 病毒的脂质双分子层相互作用。研究结果表明，乙醇可通过两种主要机制使病毒失活。首先，当乙醇渗入病毒膜时，它会破坏脂质双分子层的结构完整性，导致膜破坏。这种形态上的改变至关重要，因为它会损害病毒维持其结构和功能的能力。然后使用 GROMACS 5.1.4 进行分子动力学（MD）分析，模拟病毒膜与乙醇溶液之间的相互作用。此外，还使用了可视化分子动力学（VMD1.9.3）进行可视化。研究计算了乙醇与脂质双分子层之间的伦纳德-琼斯（LJ）相互作用和静电相互作用，并分析了乙醇吸附后尖峰蛋白的构象变化。此外，还评估了乙醇渗透对脂质双分子层形态的影响。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Modeling 化学-化学综合

CiteScore

3.50

自引率

4.50%

发文量

362

审稿时长

2.9 months

期刊介绍： The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.