Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element

Eur J Med Chem. 2018 Apr 25:150:334-346. doi: 10.1016/j.ejmech.2018.03.004. Epub 2018 Mar 6.


There are currently no approved vaccines or small molecule therapeutics available for the prophylaxis or treatment of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infections. MERS-CoV 3CL protease is essential for viral replication; consequently, it is an attractive target that provides a potentially effective means of developing small molecule therapeutics for combatting MERS-CoV. We describe herein the structure-guided design and evaluation of a novel class of inhibitors of MERS-CoV 3CL protease that embody a piperidine moiety as a design element that is well-suited to exploiting favorable subsite binding interactions to attain optimal pharmacological activity and PK properties. The mechanism of action of the compounds and the structural determinants associated with binding were illuminated using X-ray crystallography.

Keywords: 3CL protease; Antiviral; MERS-CoV; Peptidomimetic inhibitors; Piperidine moiety.

MeSH terms

  • 3C Viral Proteases
  • Animals
  • Antiviral Agents / chemical synthesis
  • Antiviral Agents / chemistry
  • Antiviral Agents / pharmacology*
  • Cats
  • Cell Death / drug effects
  • Cells, Cultured
  • Chlorocebus aethiops
  • Crystallography, X-Ray
  • Cysteine Endopeptidases / metabolism
  • Cysteine Proteinase Inhibitors / chemical synthesis
  • Cysteine Proteinase Inhibitors / chemistry
  • Cysteine Proteinase Inhibitors / pharmacology*
  • Dose-Response Relationship, Drug
  • Drug Design*
  • Middle East Respiratory Syndrome Coronavirus / drug effects*
  • Middle East Respiratory Syndrome Coronavirus / enzymology
  • Models, Molecular
  • Molecular Structure
  • Piperidines / chemical synthesis
  • Piperidines / chemistry
  • Piperidines / pharmacology*
  • Structure-Activity Relationship
  • Vero Cells
  • Viral Proteins / antagonists & inhibitors*
  • Viral Proteins / metabolism


  • Antiviral Agents
  • Cysteine Proteinase Inhibitors
  • Piperidines
  • Viral Proteins
  • piperidine
  • Cysteine Endopeptidases
  • 3C Viral Proteases