Loading publication...

Noodle always counts identifier-free feature events for service operation. With your permission, Google Analytics can also estimate audience and engagement. Search text, publication identifiers, cookies, IP addresses and browser fingerprints are never included in Noodle's first-party event counters.

Privacy details

Topics Community

Article

Beyond the Mutation Abyss: Revisiting SARS-CoV-2 Receptor-Binding Domain Evolution from ACE2 Binding Optimization to Immune Epitope Remodeling.

Pathogens (Basel, Switzerland) - 3 Mar 2026

Soliman Omar A, Shahine Yasmine, Baecker Daniel, Amer Ahmed Noby

Abstract excerpt

The SARS-CoV-2 Omicron variant and its descendants accumulated unprecedented numbers of spike substitutions yet remained transmissible, implying compensatory mechanisms that preserve entry while eroding humoral immunity. We analyzed 32 variants for sequence-level mutation, physicochemical profiling, and epitope disruption; 25 had growth-advantage estimates, and 18 underwent molecular dynamics/MM-PBSA simulations....

Topics

Join the communities discussing this publication.

Angiotensin-Converting Enzyme 2
COVID-19
Epitopes, B-Lymphocyte
Epitopes, T-Lymphocyte
Molecular Dynamics Simulation

Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

Protein Domains

Spike Glycoprotein, Coronavirus

Source

Open in PubMed Open full text

Identifiers

PMID: 41901725
DOI: 10.3390/pathogens15030272
PMCID: PMC13029211

Genes

ACE2

Variants

Provenance

PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 31 Aug 2026.

Community interpretation

Discuss the evidence

Ask a question, add context or challenge an interpretation. Community activity is separate from scientific evidence strength.

0

discussions

0

replies

Citations encouraged

Claims remain attributable.

No discussion yet

Be the first to add a careful, cited interpretation.

Related research

Semantic proximity does not establish scientific evidence.

Research trail→

Click a neighbor to travelStep 1 · 12 closest

Beyond the Mutation Abyss: Revisiting SARS-CoV-2 Receptor-Binding Domain Evolution from ACE2 Binding Optimization to Immune Epitope Remodeling.PMID 41901725Read ↗

Deep mutational scanning of recent SARS-CoV-2 variants highlights changing amino acid preferences within epistatic hotspot residues.Semantic proximity Read ↗

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.Semantic proximity Read ↗

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 EscapeSemantic proximity Read ↗

Deep mutational scanning of recent SARS-CoV-2 variants highlights changing amino acid preferences within epistatic hotspot residuesSemantic proximity Read ↗

AlphaFold2-Enabled Atomistic Modeling of Structure, Conformational Ensembles, and Binding Energetics of the SARS-CoV-2 Omicron BA.2.86 Spike Protein with ACE2 Host Receptor and Antibodies: Compensatory Functional Effects of Binding Hotspots in Modulating Mechanisms of Receptor Binding and Immune Escape.Semantic proximity Read ↗

Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains.Semantic proximity Read ↗

Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variantSemantic proximity Read ↗

Deep mutational scanning of SARS-CoV-2 Omicron BA.2.86 and epistatic emergence of the KP.3 variantSemantic proximity Read ↗

Quantitative Characterization and Prediction of the Binding Determinants and Immune Escape Hotspots for Groups of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling of the SARS-CoV-2 Spike Complexes with Antibodies.Semantic proximity Read ↗

Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic AntibodiesSemantic proximity Read ↗

Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes.Semantic proximity Read ↗

Dissecting binding and immune evasion mechanisms for ultrapotent Class I and Class 4/1 neutralizing antibodies of SARS-CoV-2 spike protein using a multi-pronged computational approach: neutral frustration architecture of binding interfaces and immune escape hotspots drives adaptive evolution.Semantic proximity Read ↗

⌁Select a neighboring publication to make it the new centre.