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Meyers M, Cismoski S, Panidapu A, Chie-Leon B, Nomura DK. Targeted Protein Degradation through Recruitment of the CUL4 Complex Adaptor Protein DDB1. ACS Chem Biol 2024; 19:58-68. [PMID: 38192078 PMCID: PMC11003717 DOI: 10.1021/acschembio.3c00487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for eliminating proteins. Thus far, most heterobifunctional proteolysis targeting chimeras (PROTACs) have utilized recruiters against substrate receptors of Cullin RING E3 ubiquitin ligases, such as cereblon and VHL. However, previous studies have surprisingly uncovered molecular glue degraders that exploit a CUL4 adaptor protein DDB1 to degrade neosubstrate proteins. Here, we sought to investigate whether DDB1 recruiters can be discovered that can be exploited for PROTAC applications. We utilized activity-based protein profiling and cysteine chemoproteomic screening to identify a covalent recruiter that targets C173 on DDB1 and exploited this recruiter to develop PROTACs against BRD4 and androgen receptor (AR). We demonstrated that the BRD4 PROTAC results in selective degradation of the short BRD4 isoform over the long isoform in a proteasome, NEDDylation, and DDB1-dependent manner. We also demonstrated degradation of AR with the AR PROTAC in prostate cancer cells. Our study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.
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Affiliation(s)
- Margot Meyers
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Sabine Cismoski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Barbara Chie-Leon
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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Meyers M, Cismoski S, Panidapu A, Chie-Leon B, Nomura DK. Targeted Protein Degradation through Recruitment of the CUL4A Complex Adaptor Protein DDB1. bioRxiv 2023:2023.08.11.553046. [PMID: 37614621 PMCID: PMC10443223 DOI: 10.1101/2023.08.11.553046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for eliminating proteins. Thus far, most heterobifunctional Proteolysis Targeting Chimeras (PROTACs) have utilized recruiters against substrate receptors of Cullin RING E3 ubiquitin ligases, such as cereblon and VHL. However, previous studies have surprisingly uncovered molecular glue degraders that exploit a CUL4A adaptor protein DDB1 to degrade neosubstrate proteins. Here, we sought to investigate whether DDB1 recruiters can be discovered that can be exploited for PROTAC applications. We utilized activity-based protein profiling and cysteine chemoproteomic screening to identify a covalent recruiter that targets C173 on DDB1 and exploited this recruiter to develop PROTACs against BRD4 and androgen receptor (AR). We demonstrated that the BRD4 PROTAC results in selective degradation of the short BRD4 isoform over the long isoform in a proteasome, NEDDylation, and DDB1-dependent manner. We also demonstrated degradation of AR with the AR PROTAC in prostate cancer cells. Our study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.
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Affiliation(s)
- Margot Meyers
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Sabine Cismoski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Barbara Chie-Leon
- Novartis-Berkeley Translational Chemical Biology Institute
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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Henning NJ, Boike L, Spradlin JN, Ward CC, Liu G, Zhang E, Belcher BP, Brittain SM, Hesse MJ, Dovala D, McGregor LM, Valdez Misiolek R, Plasschaert LW, Rowlands DJ, Wang F, Frank AO, Fuller D, Estes AR, Randal KL, Panidapu A, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Deubiquitinase-targeting chimeras for targeted protein stabilization. Nat Chem Biol 2022; 18:412-421. [PMID: 35210618 PMCID: PMC10125259 DOI: 10.1038/s41589-022-00971-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 01/09/2022] [Indexed: 12/12/2022]
Abstract
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.
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Affiliation(s)
- Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Bridget P Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthew J Hesse
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dustin Dovala
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Lynn M McGregor
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Feng Wang
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Andreas O Frank
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Daniel Fuller
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Abigail R Estes
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Katelyn L Randal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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