ArticleComputers in biology and medicine2021
Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach.
Article in Computers in biology and medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 45 citations in OpenAlex.
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- Back to the wildtype: SARS-CoV-2 evolution in critically ill patients with severe lung failure.Infection · 2026Article
- An Italian Single-Center Genomic Surveillance Study: Two-Year Analysis of SARS-CoV-2 Spike Protein Mutations.International journal of molecular sciences · 2025Article
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- Genomic epidemiology reveals early transmission of SARS-CoV-2 and mutational dynamics in Nanning, China.Heliyon · 2023Article
- Structural and pKa Estimation of the Amphipathic HR1 in SARS-CoV-2: Insights from Constant pH MD, Linear vs. Nonlinear Normal Mode Analysis.International journal of molecular sciences · 2023Article
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- Design of novel pyrimidine based remdesivir analogues with dual target specificity for SARS CoV-2: A computational approach.International journal of biological macromolecules · 2023Article
- Repurposing and computational design of PARP inhibitors as SARS-CoV-2 inhibitors.Scientific reports · 2023Article
- Molecular insights into the inhibition mechanism of harringtonine against essential proteins associated with SARS-CoV-2 entry.International journal of biological macromolecules · 2023Article
- Role of Natural Products in the Management of COVID-19: A Saudi Arabian Perspective.Healthcare (Basel, Switzerland) · 2023Article
- Deciphering molecular mechanisms of SARS-CoV-2 pathogenesis and drug repurposing through GRN motifs: a comprehensive systems biology study.3 Biotech · 2023Article
- Insights on the interaction of SARS-CoV-2 variant B.1.617.2 with antibody CR3022 and analysis of antibody resistance.Journal, genetic engineering & biotechnology · 2023Article
- Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach.Molecules (Basel, Switzerland) · 2023Article
- Global landscape of SARS-CoV-2 mutations and conserved regions.Journal of translational medicine · 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
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- VOC-alarm: mutation-based prediction of SARS-CoV-2 variants of concern.Bioinformatics (Oxford, England) · 2022Article
- Passive Immunotherapy Against SARS-CoV-2: From Plasma-Based Therapy to Single Potent Antibodies in the Race to Stay Ahead of the Variants.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2022Review
- Spike Mutation Profiles Associated With SARS-CoV-2 Breakthrough Infections in Delta Emerging and Predominant Time Periods in British Columbia, Canada.Frontiers in public health · 2022Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
COVID-19 is an infectious and pathogenic viral disease caused by SARS-CoV-2 that leads to septic shock, coagulation dysfunction, and acute respiratory distress syndrome. The spreading rate of SARS-CoV-2 is higher than MERS-CoV and SARS-CoV. The receptor-binding domain (RBD) of the Spike-protein (S-protein) interacts with the human cells through the host angiotensin-converting enzyme 2 (ACE2) receptor. However, the molecular mechanism of pathological mutations of S-protein is still unclear. In this perspective, we investigated the impact of mutations in the S-protein and their interaction with the ACE2 receptor for SAR-CoV-2 viral infection. We examined the stability of pathological nonsynonymous mutations in the S-protein, and the binding behavior of the ACE2 receptor with the S-protein upon nonsynonymous mutations using the molecular docking and MM_GBSA approaches. Using the extensive bioinformatics pipeline, we screened the destabilizing (L8V, L8W, L18F, Y145H, M153T, F157S, G476S, L611F, A879S, C1247F, and C1254F) and stabilizing (H49Y, S50L, N501Y, D614G, A845V, and P1143L) nonsynonymous mutations in the S-protein. The docking and binding free energy (ddG) scores revealed that the stabilizing nonsynonymous mutations show increased interaction between the S-protein and the ACE2 receptor compared to native and destabilizing S-proteins and that they may have been responsible for the virulent high level. Further, the molecular dynamics simulation (MDS) approach reveals the structural transition of mutants (N501Y and D614G) S-protein. These insights might help researchers to understand the pathological mechanisms of the S-protein and provide clues regarding mutations in viral infection and disease propagation. Further, it helps researchers to develop an efficient treatment approach against this SARS-CoV-2 pandemic.
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