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

Bo-Tao Xin; Eva M Huber; Gerjan de Bruin; Wolfgang Heinemeyer; Elmer Maurits; Christofer Espinal; Yimeng Du; Marissa Janssens; Emily S Weyburne; Alexei F Kisselev; Bogdan I Florea; Christoph Driessen; Gijsbert A van der Marel; Michael Groll; Herman S Overkleeft

doi:10.1021/acs.jmedchem.8b01884

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.

Authors

Affiliations

¹ Gorlaeus Laboratories , Leiden Institute of Chemistry and Netherlands Proteomics Centre , Einsteinweg 55 , 2333 CC Leiden , Netherlands.
² Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie , Technische Universität München , 85748 Garching , Germany.
³ Department of Molecular and Systems Biology and Norris Cotton Cancer Center , Geisel School of Medicine at Dartmouth , 1 Medical Centre Drive HB7936 , Lebanon , New Hampshire 03756 , United States.
⁴ Department of Hematology and Oncology , Kantonsspital St. Gallen , 9007 St. Gallen , Switzerland.

Abstract

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

Substances

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

Grants and funding

R01 CA213223/CA/NCI NIH HHS/United States