Binding affinity and mechanisms of SARS-CoV-2 variants

https://doi.org/10.1016/j.csbj.2021.07.026Get rights and content
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Highlights

  • Theoretical investigation of the binding affinity of the SARS-CoV-2 variants.

  • The 501Y.V1 variant yielded the highest enhancements in binding affinity.

  • The binding affinity mainly enhanced by forming hydrogen bonds and salt bridges.

Abstract

During the rapid worldwide spread of SARS-CoV-2, the viral genome has been undergoing numerous mutations, especially in the spike (S) glycoprotein gene that encode a type-I fusion protein, which plays an important role in the infectivity and transmissibility of the virus into the host cell. In this work, we studied the effect of S glycoprotein residue mutations on the binding affinity and mechanisms of SARS-CoV-2 using molecular dynamics simulations and sequence analysis. We quantitatively determined the degrees of binding affinity caused by different S glycoprotein mutations, and the result indicated that the 501Y.V1 variant yielded the highest enhancements in binding affinity (increased by 36.8%), followed by the N439K variant (increased by 29.5%) and the 501Y.V2 variant (increased by 19.6%). We further studied the structures, chemical bonds, binding free energies (enthalpy and entropy), and residue contribution decompositions of these variants to provide physical explanations for the changes in SARS-CoV-2 binding affinity caused by these residue mutations. This research identified the binding affinity differences of the SARS-CoV-2 variants and provides a basis for further surveillance, diagnosis, and evaluation of mutated viruses.

Keywords

SARS‐CoV‐2
Spike glycoprotein
Coronavirus variant
Residue mutation
Binding affinity

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