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SARS-CoV-2 receptor-binding mutations and antibody contact sites.

ABSTRACT: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations can impact infectivity, viral load, and overall morbidity/mortality during infection. In this analysis, we look at the mutational landscape of the SARS-CoV-2 receptor-binding domain, a structure that is antigenic and allows for viral binding to the host. We develop a bioinformatics platform and analyze 104 193 Global Initiative on Sharing All Influenza Data sequences acquired on 15 October 2020, with a majority of sequences (96%) containing point mutations. We report high frequency mutations with improved binding affinity to ACE2 including S477N, N439K, V367F, and N501Y and address the potential impact of RBD mutations on antibody binding. The high frequency S477N mutation is present in 6.7% of all SARS-CoV-2 sequences, co-occurs with D614G, and is currently present in 14 countries. To address RBD-antibody interactions, we take a subset of human-derived antibodies and define their interacting residues using PDBsum. Our analysis shows that RBD mutations were found in approximately 9% of our dataset, with some mutations improving RBD-ACE2 interactions. We also show that antibody-mediated immunity against SARS-CoV-2 enlists broad coverage of the RBD, with multiple antibodies targeting a variety of RBD regions. These data suggest that it is unlikely for neutralization/RBD antibody binding to be significantly impacted, as a whole, in the presence of RBD point mutations that conserve the RBD structure.

SUBMITTER: Mejdani M

PROVIDER: S-EPMC8353666 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Since 2020, the receptor-binding domain (RBD) of the spike protein of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been constantly mutating, producing most of the notable missense mutations in the context of "variants of concern", probably in response to the vaccine-driven alteration of immune profiles of the human population. The Delta variant, in particular, has become the most prevalent variant of the epidemic, and it is spreading in countries with the highest vaccination rates, causing the world to face the risk of a new wave of the contagion. Understanding the physical mechanism responsible for the mutation-induced changes in the RBD's binding affinity, its transmissibility, and its capacity to escape vaccine-induced immunity is the "urgent challenge" in the development of preventive measures, vaccines, and therapeutic antibodies against the coronavirus disease 2019 (COVID-19) pandemic. In this study, entropy-enthalpy compensation and the Gibbs free energy change were used to analyze the impact of the RBD mutations on the binding affinity of SARS-CoV-2 variants with the receptor angiotensin converting enzyme 2 (ACE2) and existing antibodies. Through the analysis, we found that the existing mutations have already covered almost all possible detrimental mutations that could result in an increase of transmissibility, and that a possible mutation in amino-acid position 498 of the RBD can potentially enhance its binding affinity. A new calculation method for the binding energies of protein-protein complexes is proposed based on the entropy-enthalpy compensation rule. All known structures of RBD-antibody complexes and the RBD-ACE2 complex comply with the entropy-enthalpy compensation rule in providing the driving force behind the spontaneous protein-protein docking. The variant-induced risk of breakthrough infections in vaccinated people is attributed to the L452R mutation's reduction of the binding affinity of many antibodies. Mutations reversing the hydrophobic or hydrophilic performance of residues in the spike RBD potentially cause breakthrough infections of coronaviruses due to the changes in geometric complementarity in the entropy-enthalpy compensations between antibodies and the virus at the binding sites.

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SARS-CoV-2 receptor-binding mutations and antibody contact sites.

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