Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography
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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.
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- Authors
- Borsatto, A., Akkad, O., Galdadas, I., Ma, S., Damfo, S., Haider, S., Kozielski, F., Estarellas, C., & Gervasio, F. L.
- Affiliations
- University of Geneva (CH)
- UCL School of Pharmacy (GB)
- Universitat de Barcelona (ES)
- Corresponding author
- Gervasio, Francesco Luigi
- ORCID
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2022-11-22
- Volume
- 11
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC9681203
- OpenAlex
- W4309657977
- Cited by
- 32
- References
- 56
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- FWCI
- 2.93
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
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- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- Swiss National Science Foundation (200021_204795, 40B2-0_203628)
- Swiss National Supercomputing Centre (pr126, s1107)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- Nsp1, SARS-CoV-2, betacoronaviruses, cryptic binding sites, druggable pockets, host shutoff, immune evasion, 40S ribosomal subunit, fragment screening, solvent accessibility, antiviral agents, molecular dynamics simulation
- MeSH terms
- COVID-19, SARS-CoV-2, Crystallography, Humans, Viral Nonstructural Proteins, RNA Stability
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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