ArticleJournal of chemical information and modeling2021
SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: A Computational Model of Epitope Loss in Variants of Concern.
Article in Journal of chemical information and modeling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Reinfection in patients with COVID-19: a systematic review.Global health research and policy · 2022Pooled it
- Mass spectrometry-based mapping of conformational epitopes on SARS-CoV-2 antigens targeted by monoclonal antibodies.International journal of biological macromolecules · 2026Article
- Flexible Multimodal Wearable Biosensors for Continuous Health Monitoring: Recent Advances and Challenges.Biosensors · 2026Review
- Adaptive Disorder as the Hallmark of Nanobodies Antigen-Binding Loops.Journal of chemical information and modeling · 2026Article
- Generative prediction of real-world prevalent SARS-CoV-2 mutation with in silico virus evolution.Briefings in bioinformatics · 2025Article
- A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.The journal of physical chemistry letters · 2025Review
- Structural and Conformational Impact of Deleterious Spike Protein Mutations in SARS-CoV-2 Omicron Lineages.bioRxiv : the preprint server for biology · 2025Article
- In-silico evaluation of the T-cell based immune response against SARS-CoV-2 omicron variants.Scientific reports · 2024Article
- Simulation-driven design of stabilized SARS-CoV-2 spike S2 immunogens.Nature communications · 2024Article
- Review
- Analysis of SARS-CoV-2 genome evolutionary patterns.Microbiology spectrum · 2024Article
- SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid.Journal of molecular cell biology · 2023Article
- Deep-learning-enabled protein-protein interaction analysis for prediction of SARS-CoV-2 infectivity and variant evolution.Nature medicine · 2023Article
- Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces.Journal of chemical information and modeling · 2023Article
- Article
- Emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis, therapeutics and vaccines.Annals of medicine · 2022Review
- A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs.GeroScience · 2022Article
- Computation of the Binding Energies between Human ACE2 and Spike RBDs of the Original Strain, Delta and Omicron Variants of the SARS-CoV-2: A DFT Simulation Approach.Advanced theory and simulations · 2022Article
- SARS-CoV-2 variants and spike mutations involved in second wave of COVID-19 pandemic in India.Transboundary and emerging diseases · 2022Article
- Singular Interface Dynamics of the SARS-CoV-2 Delta Variant Explained with Contact Perturbation Analysis.Journal of chemical information and modeling · 2022Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy. To develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.
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