Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease

Proteins. 2019 Jul;87(7):579-587. doi: 10.1002/prot.25682. Epub 2019 Apr 1.


Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb RNA genome which encodes a polyprotein precursor that is processed by a virus-encoded 3C-like cysteine protease (NV 3CLpro) to generate at least six mature nonstructural proteins. Processing of the polyprotein is essential for virus replication, consequently, NV 3CLpro has emerged as an attractive target for the discovery of norovirus therapeutics and prophylactics. We have recently described the structure-based design of macrocyclic transition state inhibitors of NV 3CLpro. In order to gain insight and understanding into the interaction of macrocyclic inhibitors with the enzyme, as well as probe the effect of ring size on pharmacological activity and cellular permeability, additional macrocyclic inhibitors were synthesized and high resolution cocrystal structures determined. The results of our studies tentatively suggest that the macrocyclic scaffold may hamper optimal binding to the active site by impeding concerted cross-talk between the S2 and S4 subsites.

Keywords: active site; macrocyclic inhibitors; norovirus 3CL protease; structural rearrangement.

Publication types

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

MeSH terms

  • Animals
  • Caliciviridae Infections / drug therapy
  • Caliciviridae Infections / virology
  • Catalytic Domain / drug effects
  • Cell Line
  • Crystallography, X-Ray
  • Cysteine Proteases / chemistry
  • Cysteine Proteases / metabolism*
  • Cysteine Proteinase Inhibitors / chemistry
  • Cysteine Proteinase Inhibitors / pharmacology*
  • Gastroenteritis / drug therapy
  • Gastroenteritis / virology
  • Humans
  • Macrocyclic Compounds / chemistry
  • Macrocyclic Compounds / pharmacology*
  • Mice
  • Models, Molecular
  • Norovirus / chemistry
  • Norovirus / drug effects
  • Norovirus / enzymology*
  • Protein Conformation / drug effects
  • RAW 264.7 Cells


  • Cysteine Proteinase Inhibitors
  • Macrocyclic Compounds
  • Cysteine Proteases