Deubiquitinase-targeting chimeras for targeted protein stabilization

• Published in: Nature chemical biology Vol. 18; no. 4; pp. 412 - 421
• Main Authors: Henning, Nathaniel J., Boike, Lydia, Spradlin, Jessica N., Ward, Carl C., Liu, Gang, Zhang, Erika, Belcher, Bridget P., Brittain, Scott M., Hesse, Matthew J., Dovala, Dustin, McGregor, Lynn M., Valdez Misiolek, Rachel, Plasschaert, Lindsey W., Rowlands, David J., Wang, Feng, Frank, Andreas O., Fuller, Daniel, Estes, Abigail R., Randal, Katelyn L., Panidapu, Anoohya, McKenna, Jeffrey M., Tallarico, John A., Schirle, Markus, Nomura, Daniel K.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.04.2022; Nature Publishing Group
• Subjects: 631/92/475; 631/92/613; Allosteric properties; Biochemical Engineering; Biochemistry; Bioorganic Chemistry; Cell Biology; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Chimera - metabolism; Chimeras; Chloride conductance; Chloride ions; Cystic fibrosis; Cystic Fibrosis - drug therapy; Cystic Fibrosis - metabolism; Cystic fibrosis transmembrane conductance regulator; Cystic Fibrosis Transmembrane Conductance Regulator - genetics; Cystic Fibrosis Transmembrane Conductance Regulator - metabolism; Deubiquitinating Enzymes - metabolism; Deubiquitinating Enzymes - therapeutic use; Epithelial cells; Epithelium; Hepatoma; Humans; Ion channels; Kinases; Ligands; Proteins; Stabilization; Tumor suppressor genes; Tumors; Ubiquitin; Ubiquitin - metabolism
• ISSN: 1552-4450; 1552-4469
• DOI: 10.1038/s41589-022-00971-2

Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS. A targeted protein stabilization platform termed deubiquitinase-targeting chimera (DUBTAC) was developed based on heterobifunctional small molecules consisting of a deubiquitinase OTUB1 recruiter linked to a protein-targeting ligand.