Inhibitor recognition specificity of MERS-CoV papain-like protease may differ from that of SARS-CoV

ACS Chem Biol. 2015 Jun 19;10(6):1456-65. doi: 10.1021/cb500917m. Epub 2015 Mar 16.


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 enzymes identified a small fragment-like noncovalent 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 μM 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 μM. These results raised the possibility that inhibitor recognition specificity of MERS-CoV PLpro 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).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Allosteric Regulation
  • Amino Acid Sequence
  • Antiviral Agents / chemistry*
  • Catalytic Domain
  • Coronavirus 3C Proteases
  • Cysteine Endopeptidases / chemistry
  • Endopeptidases / chemistry
  • High-Throughput Screening Assays
  • Humans
  • Kinetics
  • Middle East Respiratory Syndrome Coronavirus / chemistry*
  • Middle East Respiratory Syndrome Coronavirus / enzymology
  • Models, Molecular
  • Molecular Sequence Data
  • Protease Inhibitors / chemistry*
  • Protein Binding
  • Protein Structure, Secondary
  • Recombinant Proteins / chemistry
  • Severe acute respiratory syndrome-related coronavirus / chemistry*
  • Severe acute respiratory syndrome-related coronavirus / enzymology
  • Species Specificity
  • Surface Plasmon Resonance
  • Ubiquitin Thiolesterase / antagonists & inhibitors
  • Ubiquitin Thiolesterase / chemistry
  • Viral Proteins / antagonists & inhibitors*
  • Viral Proteins / chemistry


  • Antiviral Agents
  • Protease Inhibitors
  • Recombinant Proteins
  • UCHL1 protein, human
  • Viral Proteins
  • Endopeptidases
  • UCHL3 protein, human
  • Ubiquitin Thiolesterase
  • Cysteine Endopeptidases
  • Coronavirus 3C Proteases