E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones

SLAS Discov. 2021 Apr;26(4):484-502. doi: 10.1177/2472555220965528. Epub 2020 Nov 3.


Bifunctional degrader molecules, also called proteolysis-targeting chimeras (PROTACs), are a new modality of chemical tools and potential therapeutics to understand and treat human disease. A required PROTAC component is a ligand binding to an E3 ubiquitin ligase, which is then joined to another ligand binding to a protein to be degraded via the ubiquitin-proteasome system. The advent of nonpeptidic small-molecule E3 ligase ligands, notably for von Hippel-Lindau (VHL) and cereblon (CRBN), revolutionized the field and ushered in the design of drug-like PROTACs with potent and selective degradation activity. A first wave of PROTAC drugs are now undergoing clinical development in cancer, and the field is seeking to extend the repertoire of chemistries that allow hijacking new E3 ligases to improve the scope of targeted protein degradation.Here, we briefly review how traditional E3 ligase ligands were discovered, and then outline approaches and ligands that have been recently used to discover new E3 ligases for PROTACs. We will then take an outlook at current and future strategies undertaken that invoke either target-based screening or phenotypic-based approaches, including the use of DNA-encoded libraries (DELs), display technologies and cyclic peptides, smaller molecular glue degraders, and covalent warhead ligands. These approaches are ripe for expanding the chemical space of PROTACs and usher in the advent of other emerging bifunctional modalities of proximity-based pharmacology.

Keywords: E3 ubiquitin ligase; PROTACs; binding ligands; molecular glues; targeted protein degradation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism
  • Biological Assay*
  • Drug Design / methods*
  • Eukaryotic Cells / cytology
  • Eukaryotic Cells / metabolism
  • Gene Library
  • Humans
  • Ligands
  • Molecular Targeted Therapy / methods*
  • Peptides, Cyclic / chemical synthesis
  • Peptides, Cyclic / metabolism
  • Proteasome Endopeptidase Complex / metabolism*
  • Protein Binding
  • Protein Processing, Post-Translational*
  • Proteolysis
  • Structure-Activity Relationship
  • Ubiquitin-Protein Ligases / genetics
  • Ubiquitin-Protein Ligases / metabolism*
  • Ubiquitination / drug effects
  • Von Hippel-Lindau Tumor Suppressor Protein / genetics
  • Von Hippel-Lindau Tumor Suppressor Protein / metabolism


  • Adaptor Proteins, Signal Transducing
  • CRBN protein, human
  • Ligands
  • Peptides, Cyclic
  • Ubiquitin-Protein Ligases
  • Von Hippel-Lindau Tumor Suppressor Protein
  • Proteasome Endopeptidase Complex
  • VHL protein, human