ArticleThe journal of physical chemistry. B2022
SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation.
Article in The journal of physical chemistry. B, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 43 citations in OpenAlex.
- Cardiac Effects in Post-COVID-19 Heart Failure: A Systematic Review of Longitudinal Imaging- and Biomarker-Based Structural and Functional Remodeling.Annals of cardiac anaesthesia · 2026Pooled it
- Exploring the diverse binding ability of SARS-CoV-2 variant RBDs to different antibody classes: a computational study.RSC advances · 2026Article
- Molecular mechanisms of SARS-CoV-2 entry: implications for biomedical strategies.Microbiology and molecular biology reviews : MMBR · 2025Review
- Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights.Biophysical reviews · 2025Review
- Integration of Experimental and Computational Methods to Characterize Glycoproteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Development of a Recombinant Omicron BA.1 Subunit Vaccine Candidate in Pichia pastoris.Microbial biotechnology · 2025Article
- Characterization of biotinylated human ACE2 and SARS-CoV-2 Omicron BA.4/5 spike protein reference materials.Analytical and bioanalytical chemistry · 2024Article
- SARS-CoV-2 Omicron Subvariants Do Not Differ Much in Binding Affinity to Human ACE2: A Molecular Dynamics Study.The journal of physical chemistry. B · 2024Article
- Unraveling the binding mechanisms of SARS-CoV-2 variants through molecular simulations.Heliyon · 2024Article
- Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2.The Journal of chemical physics · 2024Article
- Comparative Computational Analysis of Spike Protein Structural Stability in SARS-CoV-2 Omicron Subvariants.International journal of molecular sciences · 2023Article
- A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo.Communications biology · 2023Article
- The impact of mutation sets in receptor-binding domain of SARS-CoV-2 variants on the stability of RBD-ACE2 complex.Future virology · 2023Article
- Atomistic insights into the binding of SARS-CoV-2 spike receptor binding domain with the human ACE2 receptor: The importance of residue 493.Journal of molecular graphics & modelling · 2023Article
- Article
- SARS-CoV-2 and its impact on the cardiovascular and digestive systems - The interplay between new virus variants and human cells.Computational and structural biotechnology journal · 2023Review
- Conformational Dynamics of the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein.Biomedicines · 2022Article
- Electrostatic Interactions Are the Primary Determinant of the Binding Affinity of SARS-CoV-2 Spike RBD to ACE2: A Computational Case Study of Omicron Variants.International journal of molecular sciences · 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
- Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India.Indian journal of medical microbiologyArticle
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The emergence of the variant of concern Omicron (B.1.1.529) of the severe acute respiratory syndrome coronavirus 2 has aggravated the Covid-19 pandemic due to its very contagious ability. The high infection rate may be due to the high binding affinity of Omicron to human cells, but both experimental and computational studies have yielded conflicting results on this issue. Some studies have shown that the Omicron variant binds to human angiotensin-converting enzyme 2 (hACE2) more strongly than the wild type (WT), but other studies have reported comparable binding affinities. To shed light on this open problem, in this work, we calculated the binding free energy of the receptor binding domain (RBD) of the WT and Omicron spike protein to hACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson-Boltzmann surface area method. We showed that Omicron binds to human cells more strongly than the WT due to increased RBD charge, which enhances electrostatic interaction with negatively charged hACE2. N440K, T478K, E484A, Q493R, and Q498R mutations in the RBD have been found to play a critical role in the stability of the RBD-hACE2 complex. The effect of homogeneous and heterogeneous models of glycans coating the viral RBD and the peptidyl domain of hACE2 was examined. Although the total binding free energy is not sensitive to the glycan model, the distribution of per-residue interaction energies depends on it. In addition, glycans have a little effect on the binding affinity of the WT RBD to hACE2.
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