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Henning NJ, Manford AG, Spradlin JN, Brittain SM, Zhang E, McKenna JM, Tallarico JA, Schirle M, Rape M, Nomura DK. Discovery of a Covalent FEM1B Recruiter for Targeted Protein Degradation Applications. J Am Chem Soc 2022; 144:701-708. [PMID: 34994556 PMCID: PMC8928484 DOI: 10.1021/jacs.1c03980] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [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] [Indexed: 12/12/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs), heterobifunctional compounds that consist of protein-targeting ligands linked to an E3 ligase recruiter, have arisen as a powerful therapeutic modality for targeted protein degradation (TPD). Despite the popularity of TPD approaches in drug discovery, only a small number of E3 ligase recruiters are available for the >600 E3 ligases that exist in human cells. Here, we have discovered a cysteine-reactive covalent ligand, EN106, that targets FEM1B, an E3 ligase recently discovered as the critical component of the cellular response to reductive stress. By targeting C186 in FEM1B, EN106 disrupts recognition of the key reductive stress substrate of FEM1B, FNIP1. We further establish that EN106 can be used as a covalent recruiter for FEM1B in TPD applications by demonstrating that a PROTAC linking EN106 to the BET bromodomain inhibitor JQ1 or the kinase inhibitor dasatinib leads to the degradation of BRD4 and BCR-ABL, respectively. Our study showcases a covalent ligand that targets a natural E3 ligase-substrate binding site and highlights the utility of covalent ligand screening in expanding the arsenal of E3 ligase recruiters suitable for TPD applications.
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Affiliation(s)
- Nathaniel J. Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Andrew G. Manford
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Jessica N. Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Scott M. Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Jeffrey M. McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - John A. Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
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