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Mutational Scanning and Binding Free Energy Computations of the SARS-CoV-2 Spike Complexes with Distinct Groups of Neutralizing Antibodies: Energetic Drivers of Convergent Evolution of Binding Affinity and Immune Escape Hotspots.

作者信息

Alshahrani Mohammed, Parikh Vedant, Foley Brandon, Raisinghani Nishank, Verkhivker Gennady

机构信息

Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.

Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.

出版信息

Int J Mol Sci. 2025 Feb 11;26(4):1507. doi: 10.3390/ijms26041507.


DOI:10.3390/ijms26041507
PMID:40003970
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11855367/
Abstract

The rapid evolution of SARS-CoV-2 has led to the emergence of variants with increased immune evasion capabilities, posing significant challenges to antibody-based therapeutics and vaccines. In this study, we conducted a comprehensive structural and energetic analysis of SARS-CoV-2 spike receptor-binding domain (RBD) complexes with neutralizing antibodies from four distinct groups (A-D), including group A LY-CoV016, group B AZD8895 and REGN10933, group C LY-CoV555, and group D antibodies AZD1061, REGN10987, and LY-CoV1404. Using coarse-grained simplified simulation models, rapid energy-based mutational scanning, and rigorous MM-GBSA binding free energy calculations, we elucidated the molecular mechanisms of antibody binding and escape mechanisms, identified key binding hotspots, and explored the evolutionary strategies employed by the virus to evade neutralization. The residue-based decomposition analysis revealed energetic mechanisms and thermodynamic factors underlying the effect of mutations on antibody binding. The results demonstrate excellent qualitative agreement between the predicted binding hotspots and the latest experiments on antibody escape. These findings provide valuable insights into the molecular determinants of antibody binding and viral escape, highlighting the importance of targeting conserved epitopes and leveraging combination therapies to mitigate the risk of immune evasion.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/273205403ea3/ijms-26-01507-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/d87e2593aa62/ijms-26-01507-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/cbef6c4faef2/ijms-26-01507-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/691c786dbce4/ijms-26-01507-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/a4e0225b6bde/ijms-26-01507-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/83578c3098e0/ijms-26-01507-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/df37fddf1b7d/ijms-26-01507-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/273205403ea3/ijms-26-01507-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/d87e2593aa62/ijms-26-01507-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/cbef6c4faef2/ijms-26-01507-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/691c786dbce4/ijms-26-01507-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/a4e0225b6bde/ijms-26-01507-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/83578c3098e0/ijms-26-01507-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/df37fddf1b7d/ijms-26-01507-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fa50/11855367/273205403ea3/ijms-26-01507-g007.jpg

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引用本文的文献

[1]
Evolving SARS-CoV-2 Vaccines: From Current Solutions to Broad-Spectrum Protection.

Vaccines (Basel). 2025-6-12

[2]
Integrative Computational Modeling of Distinct Binding Mechanisms for Broadly Neutralizing Antibodies Targeting SARS-CoV-2 Spike Omicron Variants: Balance of Evolutionary and Dynamic Adaptability in Shaping Molecular Determinants of Immune Escape.

Viruses. 2025-5-22

本文引用的文献

[1]
Enhanced immune evasion of SARS-CoV-2 variants KP.3.1.1 and XEC through N-terminal domain mutations.

Lancet Infect Dis. 2025-1

[2]
Neutralization of SARS-CoV-2 KP.1, KP.1.1, KP.2 and KP.3 by human and murine sera.

NPJ Vaccines. 2024-11-11

[3]
Virological characteristics of the SARS-CoV-2 XEC variant.

Lancet Infect Dis. 2024-12

[4]
Evolving antibody response to SARS-CoV-2 antigenic shift from XBB to JN.1.

Nature. 2025-1

[5]
A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.

Cell. 2024-12-12

[6]
AlphaFold2 Modeling and Molecular Dynamics Simulations of the Conformational Ensembles for the SARS-CoV-2 Spike Omicron JN.1, KP.2 and KP.3 Variants: Mutational Profiling of Binding Energetics Reveals Epistatic Drivers of the ACE2 Affinity and Escape Hotspots of Antibody Resistance.

Viruses. 2024-9-13

[7]
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Recurrent SARS-CoV-2 spike mutations confer growth advantages to select JN.1 sublineages.

Emerg Microbes Infect. 2024-12

[9]
Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants.

Nat Commun. 2024-9-4

[10]
Virological characteristics of the SARS-CoV-2 KP.3.1.1 variant.

Lancet Infect Dis. 2024-10

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