Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity

Nature. 2020 Nov;587(7835):657-662. doi: 10.1038/s41586-020-2601-5. Epub 2020 Jul 29.

Abstract

The papain-like protease PLpro is an essential coronavirus enzyme that is required for processing viral polyproteins to generate a functional replicase complex and enable viral spread1,2. PLpro is also implicated in cleaving proteinaceous post-translational modifications on host proteins as an evasion mechanism against host antiviral immune responses3-5. Here we perform biochemical, structural and functional characterization of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) PLpro (SCoV2-PLpro) and outline differences with SARS-CoV PLpro (SCoV-PLpro) in regulation of host interferon and NF-κB pathways. SCoV2-PLpro and SCoV-PLpro share 83% sequence identity but exhibit different host substrate preferences; SCoV2-PLpro preferentially cleaves the ubiquitin-like interferon-stimulated gene 15 protein (ISG15), whereas SCoV-PLpro predominantly targets ubiquitin chains. The crystal structure of SCoV2-PLpro in complex with ISG15 reveals distinctive interactions with the amino-terminal ubiquitin-like domain of ISG15, highlighting the high affinity and specificity of these interactions. Furthermore, upon infection, SCoV2-PLpro contributes to the cleavage of ISG15 from interferon responsive factor 3 (IRF3) and attenuates type I interferon responses. Notably, inhibition of SCoV2-PLpro with GRL-0617 impairs the virus-induced cytopathogenic effect, maintains the antiviral interferon pathway and reduces viral replication in infected cells. These results highlight a potential dual therapeutic strategy in which targeting of SCoV2-PLpro can suppress SARS-CoV-2 infection and promote antiviral immunity.

MeSH terms

  • Animals
  • COVID-19 / drug therapy
  • COVID-19 / immunology*
  • COVID-19 / virology*
  • Coronavirus Papain-Like Proteases / antagonists & inhibitors
  • Coronavirus Papain-Like Proteases / chemistry*
  • Coronavirus Papain-Like Proteases / metabolism*
  • Cytokines / chemistry
  • Cytokines / metabolism
  • Deubiquitinating Enzymes / antagonists & inhibitors
  • Deubiquitinating Enzymes / chemistry
  • Deubiquitinating Enzymes / metabolism
  • Humans
  • Immunity, Innate*
  • Interferon Regulatory Factor-3 / metabolism
  • Interferons / immunology
  • Interferons / metabolism
  • Mice
  • Models, Molecular
  • Molecular Dynamics Simulation
  • NF-kappa B / immunology
  • NF-kappa B / metabolism
  • Protein Binding
  • SARS-CoV-2 / drug effects
  • SARS-CoV-2 / enzymology*
  • SARS-CoV-2 / immunology*
  • SARS-CoV-2 / physiology
  • Ubiquitination
  • Ubiquitins / chemistry
  • Ubiquitins / metabolism

Substances

  • Cytokines
  • G1p2 protein, mouse
  • IRF3 protein, human
  • Interferon Regulatory Factor-3
  • NF-kappa B
  • Ubiquitins
  • ISG15 protein, human
  • Interferons
  • Deubiquitinating Enzymes
  • Coronavirus Papain-Like Proteases