2. Academic Validation
  3. Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation

Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation

  • Mol Cell. 2025 Aug 21;85(16):3184-3201.e14. doi: 10.1016/j.molcel.2025.07.019.
Mikołaj Słabicki 1,  Jiho Park 2,  Radosław P Nowak 3,  Shourya S Roy Burman 2,  Jesse Pellman 4,  Charles Zou 4,  Hlib Razumkov 5,  Jeannie Carreiro 4,  Simran Rastogi 4,  Anna Goldstein 4,  Marek M Nagiec 4,  Katherine A Donovan 2,  Jianwei Che 2,  Moritz Hunkeler 2,  Qixiang Geng 6,  Chi-Lin Hsu 7,  Megha Lakshminarayan 7,  Chelsea Shu 7,  Rebecca L Zon 4,  Zuzanna Kozicka 4,  Paul M C Park 4,  Jonathan M Tsai 4,  Hojong Yoon 4,  Lyn H Jones 8,  Adam S Sperling 9,  Nathanael S Gray 10,  Eric S Fischer 11,  Benjamin L Ebert 12
Affiliations

Affiliations

  • 1 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA. Electronic address: mslabicki@mgh.harvard.edu.
  • 2 Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
  • 3 Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Institute of Structural Biology, Medical Faculty, University of Bonn, Bonn, Germany.
  • 4 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • 5 Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA; Department of Chemistry, Stanford School of Humanities and Sciences, Stanford University, Stanford, CA 94305, USA.
  • 6 Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
  • 7 Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
  • 8 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
  • 9 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
  • 10 Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
  • 11 Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: eric_fischer@dfci.harvard.edu.
  • 12 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: benjamin_ebert@dfci.harvard.edu.
PMID: 40845806 DOI: 10.1016/j.molcel.2025.07.019
Abstract

Glutarimide analogs, such as thalidomide, redirect the E3 ubiquitin Ligase CRL4CRBN to induce degradation of certain zinc finger (ZF) proteins. Although the core structural motif recognized by CRBN has been characterized, it does not fully explain substrate specificity. To explore the role of residues adjacent to this core motif, we constructed a comprehensive ZF reporter library of 9,097 reporters derived from 1,655 human ZF proteins and conducted a library-on-library screen with 29 glutarimide analogs to identify compounds that collectively degrade 38 ZF reporters. Cryo-electron microscopy and crystal structures of ZFs in complex with CRBN revealed the importance of interactions beyond the core ZF degron. We used systematic mutagenesis of ZFs and CRBN to identify modes of neosubstrate recruitment requiring distinct Amino acids. Finally, we found subtle chemical variations in glutarimide analogs that alter target scope and selectivity, thus providing a roadmap for their rational design.

Keywords

CRBN; CRL4(CRBN) E3 ligase; ZF; cereblon; degron specificity; flow-based sorting screens; functional genomics; glutarimide analogs; molecular glue; targeted protein degradation; zinc finger proteins.

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