Continuous evolution of compact protein degradation tags regulated by selective molecular glues

  • Science. 2024 Mar 15;383(6688):eadk4422. doi: 10.1126/science.adk4422.
Jaron A M Mercer  #  1  2  3 ,  Stephan J DeCarlo  #  1  2  3 ,  Shourya S Roy Burman  #  4  5 ,  Vedagopuram Sreekanth  6  7  8 ,  Andrew T Nelson  1  2  3 ,  Moritz Hunkeler  4  5 ,  Peter J Chen  1  2  3 ,  Katherine A Donovan  4  5 ,  Praveen Kokkonda  6  7 ,  Praveen K Tiwari  6  7  8 ,  Veronika M Shoba  6  7 ,  Arghya Deb  6  7 ,  Amit Choudhary  6  7  8 ,  Eric S Fischer  4  5 ,  David R Liu  1  2  3
Affiliations
  • 1. Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
  • 2. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
  • 3. Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
  • 4. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
  • 5. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
  • 6. Chemical Biology and Therapeutics Science, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
  • 7. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
  • 8. Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA.
  • # Contributed equally.
PMID: 38484051 DOI: 10.1126/science.adk4422
Abstract

Conditional protein degradation tags (degrons) are usually >100 Amino acids long or are triggered by small molecules with substantial off-target effects, thwarting their use as specific modulators of endogenous protein levels. We developed a phage-assisted continuous evolution platform for molecular glue complexes (MG-PACE) and evolved a 36-amino acid zinc finger (ZF) degron (SD40) that binds the ubiquitin Ligase substrate receptor Cereblon in complex with PT-179, an orthogonal thalidomide derivative. Endogenous proteins tagged in-frame with SD40 using prime editing are degraded by otherwise inert PT-179. Cryo-electron microscopy structures of SD40 in complex with ligand-bound Cereblon revealed mechanistic insights into the molecular basis of SD40's activity and specificity. Our efforts establish a system for continuous evolution of molecular glue complexes and provide ZF tags that overcome shortcomings associated with existing degrons.

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