Discovery of a Covalent FEM1B Recruiter for Targeted Protein Degradation Applications

• Published in: Journal of the American Chemical Society 2022-01, Vol.144 (2), p.701-708
• Main Authors: Henning, Nathaniel J, Manford, Andrew G, Spradlin, Jessica N, Brittain, Scott M, Zhang, Erika, McKenna, Jeffrey M, Tallarico, John A, Schirle, Markus, Rape, Michael, Nomura, Daniel K
• Format: Article
• Language: English
• Subjects: Acetamides - chemistry; Animals; Azepines - chemistry; Binding Sites; Carrier Proteins - antagonists & inhibitors; Carrier Proteins - chemistry; Carrier Proteins - metabolism; Cell Cycle Proteins - antagonists & inhibitors; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Cell Line; Cysteine - chemistry; Dasatinib - chemistry; Fusion Proteins, bcr-abl - antagonists & inhibitors; Fusion Proteins, bcr-abl - metabolism; Humans; Mice; Proteasome Endopeptidase Complex - metabolism; Protein Binding; Protein Kinase Inhibitors - chemistry; Proteolysis; Recombinant Proteins - biosynthesis; Recombinant Proteins - chemistry; Recombinant Proteins - isolation & purification; Transcription Factors - antagonists & inhibitors; Transcription Factors - metabolism; Triazoles - chemistry; Ubiquitin-Protein Ligase Complexes - antagonists & inhibitors; Ubiquitin-Protein Ligase Complexes - genetics; Ubiquitin-Protein Ligase Complexes - metabolism
• ISSN: 0002-7863; 1520-5126; 1520-5126
• DOI: 10.1021/jacs.1c03980

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.