Development of MERS and SARS Protease Inhibitors as Potential Therapeutics

The Middle East Respiratory Syndrome (MERS) coronavirus has caused major public health concerns. Johnson has used high-throughput screening and structure-based design principles to discover and develop lead inhibitors against the papain-like (PLpro) and the chymotrypsin-like (3CLpro or Mpro) proteases of both MERS and Severe Acute Respiratory Syndrom (SARS) coronaviruses. Most recently, he has solved the structure of the MERS coronavirus (MERS-CoV) papain-like protease (PLpro) to 1.8 Å resolution. The MERS-CoV PLpro blocking loop 2 (BL2) structure differs significantly from that of SARS-CoV PLpro, where it plays a crucial role in inhibitor binding. Four previously designed SARS-CoV PLpro lead inhibitors with SARS-PLpro IC₅₀ values ranging from 0.2 to 2.0 µM showed no efficacy against MERS-CoV PLpro. Structure and sequence alignments demonstrated that two residues, Y269 and Q270, strongly responsible for inhibitor binding to SARS-CoV PLpro are replaced by T274 and A275 in MERS-CoV PLpro, eliminating critical binding interactions for similar types of inhibitors. Subsequent high-throughput screening (HTS) of a 25,000 a compound library against both PLpro enzymes identified a small fragment-like non-covalent dual inhibitor. This newly identified compound acts as a competitive inhibitor of MERS-CoV PLpro with an IC50 of 6 µM, indicating that it binds to the active site, and also exhibits an IC₅₀ of 11 µM against SARS-CoV PLpro. Significantly, 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). These combined results demonstrate that while inhibitor recognition specificity of MERS-CoV PLpro differs from that of SARS-CoV PLpro, promising inhibitor specificity can be obtained. This work has potential to lead to future therapeutics.