Structural Determinants of Coronavirus Nsp5 Function and Inhibition

Abstract

Coronavirus (CoV) infections cause a number of human diseases ranging in severity from the common cold to severe acute respiratory syndrome (SARS). Middle East respiratory syndrome CoV (MERS-CoV) and severe acute respiratory syndrome CoV (SARS-CoV) demonstrate the continued capacity of zoonotic CoVs to cause severe human respiratory disease. The likelihood of future zoonotic CoV emergence coupled with a lack of effective therapeutics or vaccines emphasizes the need to understand mechanisms of CoV replication. CoVs have a positive-sense RNA genome that is translated into polyproteins that are processed by up to three encoded proteases. The chymotrypsin-like cysteine protease (nsp5, 3CLpro) is responsible for 11 distinct cleavages within the polyprotein. Nsp5 is required for coronavirus replication; thus, it is a key target for structure function studies and for viral inhibition. We propose a series of experiments designed to elucidate the mechanism of nsp5 activity in order to inform de novo inhibitor design. Data obtained from this study will (i) define the role of the novel third domain and interdomain loop of nsp5, which connects the catalytic fold to the third domain, during substrate selection and catalytic activity, and (ii) develop novel inhibitors of nsp5 that exploit the mechanism and functional targets of nsp5.