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

Mikołaj Słabicki¹, Jiho Park², Radosław P Nowak³, Shourya S Roy Burman², Jesse Pellman⁴, Charles Zou⁴, Hlib Razumkov⁵, Jeannie Carreiro⁴, Simran Rastogi⁴, Anna Goldstein⁴, Marek M Nagiec⁴, Katherine A Donovan², Jianwei Che², Moritz Hunkeler², Qixiang Geng⁶, Chi-Lin Hsu⁷, Megha Lakshminarayan⁷, Chelsea Shu⁷, Rebecca L Zon⁴, Zuzanna Kozicka⁴, Paul M C Park⁴, Jonathan M Tsai⁴, Hojong Yoon⁴, Lyn H Jones⁸, Adam S Sperling⁹, Nathanael S Gray¹⁰, Eric S Fischer¹¹, Benjamin L Ebert¹²

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
PMCID: PMC12458990 (available on 2026-08-21)
DOI: 10.1016/j.molcel.2025.07.019

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

Mikołaj Słabicki et al. Mol Cell. 2025.

. 2025 Aug 21;85(16):3184-3201.e14.

doi: 10.1016/j.molcel.2025.07.019.

Authors

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
PMCID: PMC12458990 (available on 2026-08-21)
DOI: 10.1016/j.molcel.2025.07.019

Abstract

Glutarimide analogs, such as thalidomide, redirect the E3 ubiquitin ligase CRL4^CRBN 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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Conflict of interest statement

Declaration of interests M.S. received funding from Calico Life Sciences LLC. K.A.D. received consulting fees from Neomorph Inc and Kronos Bio. L.H.J. co-founded Anvia; advises Rapafusyn Pharmaceuticals, ONO Pharma, Matchpoint Therapeutics, Immunovalence, and Belharra Therapeutics; and holds equity in Jnana Therapeutics, Hyku Biosciences, and Rapafusyn Pharmaceuticals. N.S.G. is a founder, SAB member, and equity holder in Syros, C4, Allorion, Lighthorse, Voronoi, Inception, Shenandoah, Larkspur, and Soltego. The Gray lab received funding from Novartis, Takeda, Astellas, Taiho, Jansen, Kinogen, Arbella, Deerfield, Springworks, Interline, and Sanofi. E.S.F. is a founder, SAB member, and equity holder in Civetta, Proximity, Stelexis, and Neomorph, Inc; an equity holder and SAB member in Avilar, Photys, and Ajax; an equity holder in Lighthorse, Anvia, and CPD4; and a consultant to Novartis, EcoR1 capital, Odyssey, and Deerfield. E.S.F. receives or has received research funding from Deerfield, Novartis, Ajax, Interline, Bayer, and Astellas. B.L.E. received research funding from Novartis and Calico and consulting fees from Abbvie. He is an SAB member and shareholder for Neomorph Inc., TenSixteen Bio, Skyhawk Therapeutics, and Exo Therapeutics.

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources