A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling

被引:0
作者
Hien T. T. Lai
Ly H. Nguyen
Anh D. Phan
Agata Kranjc
Toan T. Nguyen
Duc Nguyen-Manh
机构
[1] Vietnam National University,Key Laboratory for Multiscale Simulation of Complex Systems, VNU University of Science
[2] Phenikaa University,Faculty of Materials Science and Engineering, Phenikaa Institute for Advanced Study
[3] Forschungszentrum Jülich,Institute of Neuroscience and Medicine (INM
[4] Université de Paris,9)/ Institute for Advanced Simulation (IAS
[5] SL Research University,5)
[6] United Kingdom Atomic Energy Authority,Laboratoire de Biochimie Théorique, UPR 9080 CNRS
来源
Journal of Molecular Modeling | 2022年 / 28卷
关键词
SARS-CoV; SARS-CoV-2; RBD-ACE2; Molecular modeling;
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摘要
The pandemic of COVID-19 severe acute respiratory syndrome, which was fatal for millions of people worldwide, triggered the race to understand in detail the molecular mechanisms of this disease. In this work, the differences of interactions between the SARS-CoV/SARS-CoV-2 Receptor binding domain (RBD) and the human Angiotensin Converting Enzyme 2 (ACE2) receptor were studied using in silico tools. Our results show that SARS-CoV-2 RBD is more stable and forms more interactions with ACE2 than SARS-CoV. At its interface, three stable binding patterns are observed and named red-K31, green-K353 and blue-M82 according to the central ACE2 binding residue. In SARS-CoV instead, only the first two binding patches are persistently formed during the MD simulation. Our MM/GBSA calculations indicate the binding free energy difference of about 2.5 kcal/mol between SARS-CoV-2 and SARS-CoV which is compatible with the experiments. The binding free energy decomposition points out that SARS-CoV-2 RBD–ACE2 interactions of the red-K31 (-23.5±0.2kcal/mol\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-23.5~\pm ~0.2~kcal/mol$$\end{document}) and blue-M82 (-9.1±0.1kcal/mol\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-9.1~\pm ~0.1~kcal/mol$$\end{document}) patterns contribute more to the binding affinity than in SARS-CoV (-1.8±0.02kcal/mol\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-1.8~\pm ~0.02~kcal/mol$$\end{document} for red-K31), while the contribution of the green-K353 pattern is very similar in the two strains (-17.8±0.2kcal/mol\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-17.8~\pm ~0.2~kcal/mol$$\end{document} and -22.7±0.1kcal/mol\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-22.7~\pm ~0.1~kcal/mol$$\end{document} for SARS-CoV-2 and SARS-CoV, respectively). Five groups of mutations draw our attention at the RBD–ACE2 binding interface, among them, the mutation –PPA469-471/GVEG482-485 has the most important and favorable impact on SARS-CoV-2 binding to the ACE2 receptor. These results, highlighting the molecular differences in the binding between the two viruses, contribute to the common knowledge about the new corona virus and to the development of appropriate antiviral treatments, addressing the necessity of ongoing pandemics.
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