Design of inhibitors of SARS-CoV-2 papain-like protease deriving from GRL0617: Structure–activity relationships

Abstract

The unique and complex structure of papain-like protease (PL^pro) of the SARS-CoV-2 virus represents a difficult challenge for antiviral development, yet it offers a compelling validated target for effective therapy of COVID-19. The surge in scientific interest in inhibiting this cysteine protease emerged after its demonstrated connection to the cytokine storm in patients with COVID-19 disease. Furthermore, the development of new inhibitors against PL^pro may also be beneficial for the treatment of respiratory infections caused by emerging coronavirus variants of concern.

This review article provides a comprehensive overview of PL^pro inhibitors, focusing on the structural framework of the known inhibitor GRL0617 and its analogs. We categorize PL^pro inhibitors on the basis of their structures and binding site: Glu167 containing site, BL2 groove, Val70^Ub site, and Cys111 containing catalytic site. We summarize and evaluate the majority of GRL0617-like inhibitors synthesized so far, highlighting their published biochemical parameters, which reflect their efficacy. Published research has shown that strategic modifications to GRL0617, such as decorating the naphthalene ring, extending the aromatic amino group or the orthomethyl group, can substantially decrease the IC₅₀ from micromolar up to nanomolar concentration range. Some advantageous modifications significantly enhance inhibitory activity, paving the way for the development of new potent compounds. Our review places special emphasis on structures that involve direct modifications to the GRL0617 scaffold, including piperidine carboxamides and modified benzylmethylnaphthylethanamines (Jun9 scaffold). All these compounds are believed to inhibit the proteolytic, deubiquitination, and deISGylation activity of PL^pro, biochemical processes linked to the severe progression of COVID-19.

Finally, we summarize the development efforts for SARS-CoV-2 PL^pro inhibitors, in detailed structure–activity relationships diagrams. This aims to inform and inspire future research in the search for potent antiviral agents against PL^pro of current and emerging coronavirus threats.