Structure-Based Design of Inhibitors Selective for Human Proteasome β2c or β2i Subunits

J Med Chem. 2019 Feb 14;62(3):1626-1642. doi: 10.1021/acs.jmedchem.8b01884. Epub 2019 Feb 5.


Subunit-selective proteasome inhibitors are valuable tools to assess the biological and medicinal relevance of individual proteasome active sites. Whereas the inhibitors for the β1c, β1i, β5c, and β5i subunits exploit the differences in the substrate-binding channels identified by X-ray crystallography, compounds selectively targeting β2c or β2i could not yet be rationally designed because of the high structural similarity of these two subunits. Here, we report the development, chemical synthesis, and biological screening of a compound library that led to the identification of the β2c- and β2i-selective compounds LU-002c (4; IC50 β2c: 8 nM, IC50 β2i/β2c: 40-fold) and LU-002i (5; IC50 β2i: 220 nM, IC50 β2c/β2i: 45-fold), respectively. Co-crystal structures with β2 humanized yeast proteasomes visualize protein-ligand interactions crucial for subunit specificity. Altogether, organic syntheses, activity-based protein profiling, yeast mutagenesis, and structural biology allowed us to decipher significant differences of β2 substrate-binding channels and to complete the set of subunit-selective proteasome inhibitors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Catalytic Domain
  • Cell Line, Tumor
  • Crystallography, X-Ray
  • Drug Design
  • Humans
  • Mice
  • Mutation
  • Oligopeptides / chemical synthesis
  • Oligopeptides / metabolism
  • Oligopeptides / pharmacology*
  • Peptide Library
  • Proteasome Endopeptidase Complex / genetics
  • Proteasome Endopeptidase Complex / metabolism
  • Proteasome Inhibitors / chemical synthesis
  • Proteasome Inhibitors / metabolism
  • Proteasome Inhibitors / pharmacology*
  • Protein Binding
  • Protein Engineering
  • Protein Subunits / antagonists & inhibitors*
  • Protein Subunits / genetics
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Small Molecule Libraries / chemical synthesis
  • Small Molecule Libraries / metabolism
  • Small Molecule Libraries / pharmacology*
  • Stereoisomerism


  • Oligopeptides
  • Peptide Library
  • Proteasome Inhibitors
  • Protein Subunits
  • Recombinant Fusion Proteins
  • Saccharomyces cerevisiae Proteins
  • Small Molecule Libraries
  • PSMB2 protein, human
  • Proteasome Endopeptidase Complex