ArticleJournal of medical virology2023
In silico study of SARS-CoV-2 spike protein RBD and human ACE-2 affinity dynamics across variants and Omicron subvariants.
Article in Journal of medical virology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- Machine learning-guided rational engineering of ACE2-derived peptides for broad-spectrum neutralization of SARS-CoV-2 variants.Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2026Article
- Establishment of a Chikungunya virus pseudotype system strictly dependent on viral protein expression.The Journal of general virology · 2025Article
- First-Time Identification of the PPAT Protein as a Novel Antibacterial Target: Antimicrobial and Antioxidant Insights from E. purpurea.ACS omega · 2025Article
- Structural and Energetic Insights into SARS-CoV-2 Evolution: Analysis of hACE2-RBD Binding in Wild-Type, Delta, and Omicron Subvariants.International journal of molecular sciences · 2025Article
- Antiangiogenic Potential of Beneficial Sterols from Parotoid Gland Secretion of Indian Common Toads (ACS omega · 2025Article
- Battling COVID-19 leveraging nanobiotechnology: Gold and silver nanoparticle-B-escin conjugates as SARS-CoV-2 inhibitors.Open life sciences · 2025Article
- Unveiling the Interplay-Vitamin D and ACE-2 Molecular Interactions in Mitigating Complications and Deaths from SARS-CoV-2.Biology · 2024Review
- The Recognition Pathway of the SARS-CoV-2 Spike Receptor-Binding Domain to Human Angiotensin-Converting Enzyme 2.Molecules (Basel, Switzerland) · 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
- Host-Directed Virus-Mimicking Particles Interacting with the ACE2 Receptor Competitively Block Coronavirus SARS-CoV-2 Entry.Nano letters · 2024Article
- Cross-protection induced by highly conserved human B, CD4Frontiers in immunology · 2024Article
- Low-Entropy Hydration Shells at the Spike RBD's Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants.Biomolecules · 2023Article
- In silico study of SARS-CoV-2 spike protein RBD and human ACE-2 affinity dynamics across variants and Omicron subvariants.Journal of medical virology · 2023Article
- The effects of amino acid substitution of spike protein and genomic recombination on the evolution of SARS-CoV-2.Frontiers in microbiology · 2023Review
- Development and validation of a prognostic model based on immune variables to early predict severe cases of SARS-CoV-2 Omicron variant infection.Frontiers in immunology · 2023Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The coronavirus disease 2019 virus outbreak continues worldwide, with many variants emerging, some of which are considered variants of concern (VOCs). The WHO designated Omicron as a VOC and assigned it under variant B.1.1.529. Here, we used computational studies to examine the VOCs, including Omicron subvariants, and one variant of interest. Here we found that the binding affinity of human receptor angiotensin-converting enzyme 2 (hACE2) and receptor-binding domain (RBDs) increased in the order of wild type (Wuhan-strain) < Beta < Alpha < OmicronBA.5 < Gamma < Delta < Omicron BA.2.75 < BA.1 < BA.3 < BA.2. Interactions between docked complexes revealed that the RBD residue positions like 452, 478, 493, 498, 501, and 505 are crucial in creating strong interactions with hACE2. Omicron BA.2 shows the highest binding capacity to the hACE2 receptor among all the mutant complexes. The BA.5's L452R, F486V, and T478K mutation significantly impact the interaction network in the BA.5 RBD-hACE2 interface. Here for the first time, we report the His505, an active residue on the RBD forming a salt bridge in the BA.2, leading to increased mutation stability. When the active RBD residues are mutated, binding affinity and intermolecular interactions increase across all mutant complexes. By examining the differences in different variants, this study may provide a solid foundation for structure-based drug design for newly emerging variants.
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