Deubiquitinase-Targeting Chimeras for Targeted Protein Stabilization

Henning, N. J.; Boike, L.; Spradlin, J. N.; Ward, C. C.; Belcher, B.; Brittain, S. M.; Hesse, M.; Dovala, D.; McGregor, L. M.; McKenna, J. M.; Tallarico, J. A.; Schirle, M.; Nomura, D. K.

doi:10.1101/2021.04.30.441959

bioRxiv · 10.1101/2021.04.30.441959

Deubiquitinase-Targeting Chimeras for Targeted Protein Stabilization

Henning, N. J.·Boike, L.·Spradlin, J. N.·Ward, C. C.·Belcher, B.·Brittain, S. M.·Hesse, M.·Dovala, D.·McGregor, L. M.·McKenna, J. M.·Tallarico, J. A.·Schirle, M.·Nomura, D. K.

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Abstract

Targeted protein degradation is a powerful therapeutic modality that uses heterobifunctional small-molecules to induce proximity between E3 ubiquitin ligases and target proteins to ubiquitinate and degrade specific proteins of interest. However, many proteins are ubiquitinated and degraded to drive disease pathology; in these cases targeted protein stabilization (TPS), rather than degradation, of the actively degraded target using a small-molecule would be therapeutically beneficial. Here, we present the Deubiquitinase-Targeting Chimera (DUBTAC) platform for TPS of specific proteins. 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 then developed a heterobifunctional DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds {Delta}F508-CFTR. We demonstrated proof-of-concept of TPS by showing that this DUBTAC robustly stabilized {Delta}F508-CFTR in human cystic fibrosis bronchial epithelial cells in an OTUB1-dependent manner. Our study underscores the utility of chemoproteomics-enabled covalent ligand discovery approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS. Editorial summaryWe have developed the Deubiquitinase Targeting Chimera (DUBTAC) platform for targeted protein stabilization. We have discovered a covalent recruiter against the deubiquitinase OTUB1 that we have linked to the mutant {Delta}F508-CFTR targeting cystic fibrosis drug Lumacaftor to stabilize mutant CFTR protein in cells.

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Henning, N. J., Boike, L., Spradlin, J. N., Ward, C. C., Belcher, B., Brittain, S. M., Hesse, M., Dovala, D., McGregor, L. M., McKenna, J. M., Tallarico, J. A., Schirle, M., Nomura, D. K.. 2021-04-30. Deubiquitinase-Targeting Chimeras for Targeted Protein Stabilization. https://doi.org/10.1101/2021.04.30.441959

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