Structure-based Design of CBP/EP300 Degraders: When Coopera-tivity Overcomes Affinity

Here we present the development of dCE-2, a structurally novel PROTAC targeting the CREB-binding protein (CBP) and E1A-associated protein (EP300) – two homologous multidomain enzymes crucial for enhancer-mediated transcription. The design of dCE-2 was based on the crystal structure of an in-house bromodomain (BRD) inhibitor featuring as acetyl-lysine mimic a 3-methyl cinnoline discovered by high-throughput fragment docking. Our study shows that, despite its modest binding affinity to CBP/EP300-BRD, dCE-2 remarkable protein degradation activity stems from its excellent cooperativity, which we demonstrate by the characterisation of its ternary complex formation both in vitro and in cellulo. Molecular dynamics simulations indicate that in aqueous solvent this active degrader populates both folded and extended conformations which are likely to promote cell permeabil-ity and ternary complex formation, respectively.