ArticleJournal of molecular graphics & modelling2022
Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern.
Article in Journal of molecular graphics & modelling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- Integrated Genomic and Epidemiological Surveillance to Monitor SARS-CoV-2 Variants in Italy: Insights From the JN.1 Case Study (2023-2024).Journal of medical virology · 2026Article
- Nanopore sequencing reveals the genomic diversity of the variants of concern of SARS-CoV-2 during 2021 disease outbreak in Pakistan.Scientific reports · 2025Article
- Subtle Changes at the RBD/hACE2 Interface During SARS-CoV-2 Variant Evolution: A Molecular Dynamics Study.Biomolecules · 2025Article
- Many Roles of Carbohydrates: A Computational Spotlight on the Coronavirus S Protein Binding.ACS applied bio materials · 2024Review
- Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2).International journal of molecular sciences · 2024Article
- Low-Entropy Hydration Shells at the Spike RBD's Binding Site May Reveal the Contagiousness of SARS-CoV-2 Variants.Biomolecules · 2023Article
- Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein.The journal of physical chemistry. B · 2023Article
- Article
- Identification of inhibitors against SARS-CoV-2 variants of concern using virtual screening and metadynamics-based enhanced sampling.Chemical physics · 2023Article
- Bionics design of affinity peptide inhibitors for SARS-CoV-2 RBD to block SARS-CoV-2 RBD-ACE2 interactions.Heliyon · 2023Article
- Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2.Protein science : a publication of the Protein Society · 2022Article
- Genomic diversity of SARS-CoV-2 in Pakistan during the fourth wave of pandemic.Journal of medical virology · 2022Article
- Molecular dynamics simulations highlight the altered binding landscape at the spike-ACE2 interface between the Delta and Omicron variants compared to the SARS-CoV-2 original strain.Computers in biology and medicine · 2022Article
- Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Review
- Scanning the RBD-ACE2 molecular interactions in Omicron variant.Biochemical and biophysical research communications · 2022Article
- SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility.Frontiers in medical technology · 2022Article
- Comparative Structural Analysis of Human ACE2 Receptor with Spike Protein of SARS-CoV-2 Variants: Implications to Understand Infectivity of the Virus.Advances and applications in bioinformatics and chemistry : AABC · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected the lives and livelihood of millions of individuals around the world. It has mutated several times after its first inception, with an estimated two mutations occurring every month. Although we have been successful in developing vaccines against the virus, the emergence of variants has enabled it to escape therapy. Few of the generated variants are also reported to be more infectious than the wild-type (WT). In this study, we analyze the attributes of all RBD/ACE2 complexes for the reported VOCs, namely, Alpha, Beta, Gamma, and Delta through computer simulations. Results indicate differences in orientation and binding energies of the VOCs from the WT. Overall, it was observed that electrostatic interactions play a major role in the binding of the complexes. Detailed residue level energetics revealed that the most prominent changes in interaction energies were seen particularly at the mutated residues which were present at RBD/ACE2 interface. We found that the Delta variant is one of the most tightly bound variants of SARS-CoV-2 with dynamics similar to WT. The high binding affinity of RBD towards ACE2 is indicative of an increase in viral transmission and infectivity. The details presented in our study provide additional information for the design and development of effective therapeutic strategies for the emerging variants of the virus in the future.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.