Deubiquitinating Enzymes in Coronaviruses and Possible Therapeutic Opportunities for COVID-19

Abstract

Following the outbreak of novel severe acute respiratory syndrome (SARS)-coronavirus (CoV)2, the majority of nations are struggling with countermeasures to fight infection, prevent spread and improve patient survival. Considering that the pandemic is a recent event, no large clinical trials have been possible and since coronavirus specific drug are not yet available, there is no strong consensus on how to treat the coronavirus disease 2019 (COVID-19) associated viral pneumonia. Coronaviruses code for an important multifunctional enzyme named papain-like protease (PLP), that has many roles in pathogenesis. First, PLP is one of the two viral cysteine proteases, along with 3-chymotripsin-like protease, that is responsible for the production of the replicase proteins required for viral replication. Second, its intrinsic deubiquitinating and deISGylating activities serve to antagonize the host's immune response that would otherwise hinder infection. Both deubiquitinating and deISGylating functions involve the removal of the small regulatory polypeptides, ubiquitin and ISG15, respectively, from target proteins. Ubiquitin modifications can regulate the innate immune response by affecting regulatory proteins, either by altering their stability via the ubiquitin proteasome pathway or by directly regulating their activity. ISG15 is a ubiquitin-like modifier with pleiotropic effects, typically expressed during the host cell immune response. PLP inhibitors have been evaluated during past coronavirus epidemics, and have showed promising results as an antiviral therapy in vitro. In this review, we recapitulate the roles of PLPs in coronavirus infections, report a list of PLP inhibitors and suggest possible therapeutic strategies for COVID-19 treatment, using both clinical and preclinical drugs.

Keywords: COVID-19; COVID-19 therapy; DUBs; PLP inhibitors; SARS; SARS-CoV2; coronavirus; papain-like protease.

Figure 1

Schematic representation of the role of severe acute respiratory syndrome (SARS)-coronavirus (CoV) papain-like protease (PLP) role during infection. The figure represents the early roles of SARS-CoV PLP during the replication phase. The replicase/transcription complex (RTC), is coded by two open reading frames, ORF1a and ORF1b, that, with a ribosomal frame-shift mechanism, allow for the translation of two polyproteins (pps): pp1a and pp1ab. Pps are in turn constituted by 16 non-structural proteins (nsp), 1-11 for pp1a and 1-16 for pp1ab. SARS-Cov PLP is encoded within nsp3 and is responsible for the cleavage of the N-terminal portion of pps, cutting the bonds between nsp1/2, nsp2/3 and nsp3/4.

Figure 2

Schematic representation of the effect of SARS-CoV PLP on host cells’ immune system. The two proposed immune pathways affected by the SARS-CoV PLP are schematically represented here. Once the virus is detected by pathogen recognition receptors as RIG-I, the signal is transduced via MAVS to the activating kinases of the transcription factors: IRF3 and NF-kB. TBK1 and IKKi phosphorylate IRF3 and thus trigger its dimerization and nuclear translocation. IKKα-γ free NF-kB, that moves to the nucleus, by phosphorylating its inhibitor, IkBα. Activated STING and TRAF3 form complexes with IRF3 upstream regulators and thus increase the activation state. Finally, IRF3 and NF-kB promote the activation of the type I INF antiviral response. The PLP DUB activity antagonizes these pathways at multiple steps, resulting in a global antagonism of the signaling and lower activation of INF-β. For a detailed description of the interplays between the PLP and the proteins, the reader should refer to the text.