P2-substituted N-acylprolylpyrrolidine inhibitors of prolyl oligopeptidase: biochemical evaluation, binding mode determination, and assessment in a cellular model of synucleinopathy

J Med Chem. 2012 Nov 26;55(22):9856-67. doi: 10.1021/jm301060g. Epub 2012 Nov 13.


We have investigated the effect of regiospecifically introducing substituents in the P2 part of the typical dipeptide derived basic structure of PREP inhibitors. This hitherto unexplored modification type can be used to improve target affinity, selectivity, and physicochemical parameters in drug discovery programs focusing on PREP inhibitors. Biochemical evaluation of the produced inhibitors identified several substituent types that significantly increase target affinity, thereby reducing the need for an electrophilic "warhead" functionality. Pronounced PREP specificity within the group of Clan SC proteases was generally observed. Omission of the P1 electrophilic function did not affect the overall binding mode of three representative compounds, as studied by X-ray crystallography, while the P2 substituents were demonstrated to be accommodated in a cavity of PREP that, to date, has not been probed by inhibitors. Finally, we report on results of selected inhibitors in a SH-SY5Y cellular model of synucleinopathy and demonstrate a significant antiaggregation effect on α-synuclein.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoptosis / drug effects*
  • Cell Membrane Permeability / drug effects
  • Crystallography, X-Ray
  • Enzyme Inhibitors / chemical synthesis
  • Enzyme Inhibitors / pharmacology*
  • Humans
  • Kinetics
  • Mitochondrial Proteins / antagonists & inhibitors*
  • Mitochondrial Proteins / metabolism
  • Models, Molecular
  • Molecular Structure
  • Neuroblastoma / drug therapy*
  • Neuroblastoma / metabolism
  • Protein Multimerization / drug effects
  • Pyrrolidines / chemistry*
  • Serine Endopeptidases / metabolism
  • Structure-Activity Relationship
  • Substrate Specificity
  • Tumor Cells, Cultured
  • alpha-Synuclein / metabolism*


  • Enzyme Inhibitors
  • Mitochondrial Proteins
  • Pyrrolidines
  • alpha-Synuclein
  • PREP protein, human
  • Serine Endopeptidases
  • pyrrolidine