Identification and design of novel small molecule inhibitors against MERS-CoV papain-like protease via high-throughput screening and molecular modeling

Bioorg Med Chem. 2019 May 15;27(10):1981-1989. doi: 10.1016/j.bmc.2019.03.050. Epub 2019 Mar 26.


The development of new therapeutic agents against the coronavirus causing Middle East Respiratory Syndrome (MERS) is a continuing imperative. The initial MERS-CoV epidemic was contained entirely through public health measures, but episodic cases continue, as there are currently no therapeutic agents effective in the treatment of MERS-CoV, although multiple strategies have been proposed. In this study, we screened 30,000 compounds from three different compound libraries against one of the essential proteases, the papain-like protease (PLpro), using a fluorescence-based enzymatic assay followed by surface plasmon resonance (SPR) direct binding analysis for hit confirmation. Mode of inhibition assays and competition SPR studies revealed two compounds to be competitive inhibitors. To improve upon the inhibitory activity of the best hit compounds, a small fragment library consisting of 352 fragments was screened in the presence of each hit compound, resulting in one fragment that enhanced the IC50 value of the best hit compound by 3-fold. Molecular docking and MM/PBSA binding energy calculations were used to predict potential binding sites, providing insight for design and synthesis of next-generation compounds.

Keywords: Fragment screening; High-throughput screening; Middle East Respiratory Syndrome Coronavirus (MERS-CoV); Molecular modeling; Papain-like protease; Small molecule inhibitor.

Publication types

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

MeSH terms

  • Binding Sites
  • Drug Design*
  • Electron Spin Resonance Spectroscopy
  • High-Throughput Screening Assays
  • Humans
  • Middle East Respiratory Syndrome Coronavirus / enzymology*
  • Molecular Docking Simulation
  • Peptide Hydrolases / chemistry*
  • Peptide Hydrolases / metabolism
  • Protease Inhibitors / chemistry*
  • Protease Inhibitors / metabolism
  • Protein Structure, Tertiary
  • Small Molecule Libraries / chemistry*
  • Small Molecule Libraries / metabolism
  • Structure-Activity Relationship
  • Viral Proteins / antagonists & inhibitors*
  • Viral Proteins / metabolism


  • Protease Inhibitors
  • Small Molecule Libraries
  • Viral Proteins
  • Peptide Hydrolases