ArticleBiochemical and biophysical research communications2021
Evolutionary and structural analysis elucidates mutations on SARS-CoV2 spike protein with altered human ACE2 binding affinity.
Article in Biochemical and biophysical research communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 62 citations in OpenAlex.
- Emergence and transmission dynamics of the FY.4 Omicron variant in Kenya.Virus evolution · 2025Article
- Real-time identification of epistatic interactions in SARS-CoV-2 from large genome collections.Genome biology · 2024Article
- Unraveling the binding mechanisms of SARS-CoV-2 variants through molecular simulations.Heliyon · 2024Article
- Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolutionary trajectory of SARS-CoV-2 genome shifts during widespread vaccination and emergence of Omicron variant.Npj viruses · 2023Article
- Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective.ACS omega · 2023Review
- HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2.Communications biology · 2023Article
- Identifying promising druggable binding sites and their flexibility to target the receptor-binding domain of SARS-CoV-2 spike protein.Computational and structural biotechnology journal · 2023Article
- Pseudotyped Viruses.Advances in experimental medicine and biology · 2023Article
- Monitoring and tracking the spread of SARS-CoV-2 in Asturias, Spain.Access microbiology · 2023Article
- Decoding molecular factors shaping human angiotensin converting enzyme 2 receptor usage by spike glycoprotein in lineage B beta-coronaviruses.Biochimica et biophysica acta. Molecular basis of disease · 2022Article
- Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Vaccine Effectiveness.Vaccines · 2022Review
- Mutation informatics: SARS-CoV-2 receptor-binding domain of the spike protein.Drug discovery today · 2022Review
- SARS-CoV-2 intra-host evolution during prolonged infection in an immunocompromised patient.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Article
- The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects.Biophysical chemistry · 2022Review
- SARS-CoV-2 Infections in Vaccinated and Unvaccinated Populations in Camp Lemonnier, Djibouti, from April 2020 to January 2022.Viruses · 2022Article
- Predicting the mutational drivers of future SARS-CoV-2 variants of concern.Science translational medicine · 2022Article
- Pre-Existing Oxidative Stress Creates a Docking-Ready Conformation of the SARS-CoV-2 Receptor-Binding Domain.ACS bio & med chem Au · 2022Article
- Impact of mutations in SARS-COV-2 spike on viral infectivity and antigenicity.Briefings in bioinformatics · 2022Article
- SARS-CoV-2: Molecular Structure, Pathogenesis, Potential Therapeutic Targets, and Immune Response of the Infected Subject.Interdisciplinary perspectives on infectious diseases · 2022Review
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Abstract
The recognition of ACE2 by the receptor-binding domain (RBD) of spike protein mediates host cell entry. The objective of the work is to identify SARS-CoV2 spike variants that emerged during the pandemic and evaluate their binding affinity with ACE2. Evolutionary analysis of 2178 SARS-CoV2 genomes identifies RBD variants that are under selection bias. The binding efficacy of these RBD variants to the ACE2 has been analyzed by using protein-protein docking and binding free energy calculations. Pan-proteomic analysis reveals 113 mutations among them 33 are parsimonious. Evolutionary analysis reveals five RBD variants A348T, V367F, G476S, V483A, and S494P are under strong positive selection bias. Variations at these sites alter the ACE2 binding affinity. A348T, G476S, and V483A variants display reduced affinity to ACE2 in comparison to the Wuhan SARS-CoV2 spike protein. While the V367F and S494P population variants display a higher binding affinity towards human ACE2. Reorientation of several crucial residues at the RBD-ACE2 interface facilitates additional hydrogen bond formation for the V367F variant which enhances the binding energy during ACE2 recognition. On the other hand, the enhanced binding affinity of S494P is attributed to strong interfacial complementarity between the RBD and ACE2.
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