De Novo-Designed APC/C Inhibitors Provide a Rationale for Targeting RING-Type E3 Ubiquitin Ligases

J Med Chem. 2025 Jun 12;68(11):11468-11483. doi: 10.1021/acs.jmedchem.5c00416. Epub 2025 May 21.

Abstract

The ubiquitin system represents an attractive pharmacological target for numerous pathological processes, including cancer and neurodegeneration. RING domain-containing E3 ubiquitin ligases constitute the largest class of ubiquitin enzymes, providing a scaffold for substrate recognition and catalysis. Their shallow groove recognition interfaces involving discontinuous epitopes and a lack of defined binding pockets have largely rendered them undruggable. Inspired by natural RING inhibitors, we have developed a pharmacophore-based strategy for the rational design of peptidomimetics targeting RING domains, and we demonstrate its feasibility by using the macromolecular APC/C complex (anaphase-promoting complex/cyclosome). We designed scaffolds binding to the APC/C RING domain and efficiently inhibiting its activity in vitro. Iterative structure-based design and experimental studies to optimize their chemical stability, permeability, and specificity lead to new hydrocarbon-stapled-based molecules inhibiting APC/C in vitro and in cancer cells. Our results provide a robust rationale for targeting RING-containing enzymes of therapeutic value and promising leads for clinical APC/C inhibition.

MeSH terms

  • Anaphase-Promoting Complex-Cyclosome* / antagonists & inhibitors
  • Anaphase-Promoting Complex-Cyclosome* / metabolism
  • Cell Line, Tumor
  • Drug Design*
  • Enzyme Inhibitors* / chemical synthesis
  • Enzyme Inhibitors* / chemistry
  • Enzyme Inhibitors* / pharmacology
  • Humans
  • Peptidomimetics* / chemical synthesis
  • Peptidomimetics* / chemistry
  • Peptidomimetics* / pharmacology
  • Structure-Activity Relationship
  • Ubiquitin-Protein Ligases* / antagonists & inhibitors
  • Ubiquitin-Protein Ligases* / metabolism

Substances

  • Anaphase-Promoting Complex-Cyclosome
  • Ubiquitin-Protein Ligases
  • Enzyme Inhibitors
  • Peptidomimetics