Inhibitor Recognition Specificity of MERS-CoV Papain-like Protease May Differ from That of SARS-CoV

The Middle East, Respiratory Syndrome coronavirus (MERS-CoV) papain-like protease (PLpro) blocking loop 2 (BL2) structure differs significantly from that of SARS-CoV PLpro, where it has been proven to play a crucial role in SARS-CoV PLpro inhibitor binding. Four SARS-CoV PLpro lead inhibitors were tested against MERS-COV PLpro, none of which were effective against MERS-CoV PLprO. Structure and, sequence alignments revealed that two residues, Y269 and Q270, responsible for inhibitor binding to SARS-CoV PLpro, were replaced by T274 and A275 in MERS-CoV PLpro, making critical binding interactions difficult to form for similar types of inhibitors. High throughput screening (HTS) of 25 000 compounds against both PLpro enzyme identified a small fragment-like non-covalent dual inhibitor. Mode of inhibition studies by enzyme kinetics and competition surface plasmon resonance, (SPR) analyses suggested that this compound. acts as a competitive inhibitor, with an IC50 of 6 mu M against MERS-CoV PLpro, indicating that it-binds to the active site, whereas it acts as an allosteric inhibitor against SARS-CoV PLpro With an IC50 of 11 mu M. These results raised the possibility that inhibitor recognition specificity of MERS-CoV PLpto may differ from that of SARS-CoV PLpro. In addition, inhibitory activity of this compound was selective for SARS-CoV and MERS-CoV PLpro enzymes over two human homologues, the ubiquitin C-terminal hydrolases 1 and 3 (hUCH-L1 and hUCH-L3).