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Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography

Published ineLife, vol. 11, e81167
Publication date2022-11-22
First online date2022-11-22
Abstract

Non-structural protein 1 (Nsp1) is a main pathogenicity factor of α - and β - coronaviruses. Nsp1 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S host ribosomal subunits and promoting host mRNA degradation. This mechanism leads to the downregulation of the translation-mediated innate immune response in host cells, ultimately mediating the observed immune evasion capabilities of SARS-CoV-2. Here, by combining extensive molecular dynamics simulations, fragment screening and crystallography, we reveal druggable pockets in Nsp1. Structural and computational solvent mapping analyses indicate the partial crypticity of these newly discovered and druggable binding sites. The results of fragment-based screening via X-ray crystallography confirm the druggability of the major pocket of Nsp1. Finally, we show how the targeting of this pocket could disrupt the Nsp1-mRNA complex and open a novel avenue to design new inhibitors for other Nsp1s present in homologous β - coronaviruses.

Keywords
  • SARS-CoV-2
  • X-ray crystallography
  • Cryptic pockets
  • Drug discovery
  • Molecular biophysics
  • Molecular dynamics
  • None
  • Structural biology
Citation (ISO format)
BORSATTO, Alberto et al. Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography. In: eLife, 2022, vol. 11, p. e81167. doi: 10.7554/eLife.81167
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Article (Published version)
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Additional URL for this publicationhttps://elifesciences.org/articles/81167
Journal ISSN2050-084X
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67downloads

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