ArticleInternational journal of molecular sciences2022
Mutations of Omicron Variant at the Interface of the Receptor Domain Motif and Human Angiotensin-Converting Enzyme-2.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Analysis of the Relationship Between the Charge Increment of the SARS-CoV-2 Spike Protein and Evolution.Viruses · 2025Article
- Electronic Interactions Between the Receptor-Binding Domain of Omicron Variants and Angiotensin-Converting Enzyme 2: A Novel Amino Acid-Amino Acid Bond Pair Concept.Molecules (Basel, Switzerland) · 2025Article
- Increased preference for lysine over arginine in spike proteins of SARS-CoV-2 BA.2.86 variant and its daughter lineages.PloS one · 2025Article
- Article
- Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study.International journal of molecular sciences · 2024Article
- Predicting potential SARS-CoV-2 mutations of concern via full quantum mechanical modelling.Journal of the Royal Society, Interface · 2024Article
- Changes in total charge on spike protein of SARS-CoV-2 in emerging lineages.Bioinformatics advances · 2024Article
- Dynamics of water-mediated interaction effects on the stability and transmission of Omicron.Scientific reports · 2023Article
- The anti-SARS-CoV-2 effect and mechanism of Chiehyuan herbal oral protection solution.Heliyon · 2023Article
- Towards Quantum-Chemical Level Calculations of SARS-CoV-2 Spike Protein Variants of Concern by First Principles Density Functional Theory.Biomedicines · 2023Review
- Evolutionary changes in the number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants.Virus evolution · 2023Article
- Elucidation of novel compounds and epitope-based peptide vaccine design against C30 endopeptidase regions of SARS-CoV-2 using immunoinformatics approaches.Frontiers in cellular and infection microbiology · 2023Article
- 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
- Molecular Mechanisms of Pathogenesis, Prevention, and Therapy of COVID-19: Summarizing the Results of 2021.International journal of molecular sciences · 2022Article
- Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein.Microorganisms · 2022Article
- Effect of Delta and Omicron Mutations on the RBD-SD1 Domain of the Spike Protein in SARS-CoV-2 and the Omicron Mutations on RBD-ACE2 Interface Complex.International journal of molecular sciences · 2022Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The most recent Omicron variant of SARS-CoV-2 has caused global concern and anxiety. The only thing certain about this strain, with a large number of mutations in the spike protein, is that it spreads quickly, seems to evade immune defense, and mitigates the benefits of existing vaccines. Based on the ultra-large-scale ab initio computational modeling of the receptor binding motif (RBM) and the human angiotensin-converting enzyme-2 (ACE2) interface, we provide the details of the effect of Omicron mutations at the fundamental atomic scale level. In-depth analysis anchored in the novel concept of amino acid-amino acid bond pair units (AABPU) indicates that mutations in the Omicron variant are connected with (i) significant changes in the shape and structure of AABPU components, together with (ii) significant increase in the positive partial charge, which facilitates the interaction with ACE2. We have identified changes in bonding due to mutations in the RBM. The calculated bond order, based on AABPU, reveals that the Omicron mutations increase the binding strength of RBM to ACE2. Our findings correlate with and are instrumental to explain the current observations and can contribute to the prediction of next potential new variant of concern.
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