Simeprevir suppresses SARS-CoV-2 replication and synergizes with remdesivir (preprint)

The outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global threat to human health. Using a multidisciplinary approach, we identified and validated the hepatitis C virus (HCV) protease inhibitor simeprevir as an especially promising repurposable drug for treating COVID-19. Simeprevir potently reduces SARS-CoV-2 viral load by multiple orders of magnitude and synergizes with remdesivir in vitro. Mechanistically, we showed that simeprevir inhibits the main protease (Mpro) and unexpectedly the RNA-dependent RNA polymerase (RdRp). Our results thus reveal the viral protein targets of simeprevir, and provide preclinical rationale for the combination of simeprevir and remdesivir for the pharmacological management of COVID-19 patients. One Sentence SummaryDiscovery of simeprevir as a potent suppressor of SARS-CoV-2 viral replication that synergizes with remdesivir.

Inhibition of papain-like protease PLpro blocks SARS-CoV-2 spread and promotes anti-viral immunity (preprint)

Main protease and papain-like protease (PLpro) are essential coronaviral enzymes required for polypeptide processing during viral maturation. PLpro additionally cleaves proteinous post-translational modifications from host proteins to evade anti-viral immune responses. Here, we provide biochemical, structural and functional characterizations of PLpro from SARS-CoV-2 (PLproCoV2) and reveal differences to that of SARS (PLproSARS) in controlling interferon (IFN) and NF-kB pathways. PLproCoV2 and PLproSARS share 83% sequence identity, yet they differ in their host substrate preferences: PLproCoV2 predominantly cleaves the ubiquitin-like protein ISG15 off from host proteins, while PLproSARS preferentially targets ubiquitin chains. The crystal structure of PLproCoV2 in complex with ISG15 explains the affinity and higher specificity through distinctive binding to ISG15’s unique amino-terminal ubiquitin-like domain, and enabled the identification of GRL-0617 as a non-covalent candidate inhibitor for PLproCoV2. In human cells, PLproCoV2 cleaves ISG15 from interferon responsive factor 3 (IRF3), blocks its nuclear translocation, and reduces type I interferon responses, whereas PLproSARS preferentially mediates deubiquitination of critical components of the NF-kB pathway. Pharmacological inhibition of PLproCoV2 blocks the virus-induced cytopathogenic effect upon infection with SARS-CoV-2, fosters the anti- viral interferon pathway and reduces viral release from infected cells. We propose that therapeutic targeting of PLproCoV2 can suppress SARS-CoV-2 infection and promote anti-viral immunity.