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 a 3-methyl-cinnoline acetyl-lysine mimic acetyl-lysine
mimic discovered by high-throughput fragment docking. Our study shows
that, despite its modest binding affinity to CBP/EP300-BRD, dCE-2’s remarkable protein degradation activity stems
from its good cooperativity, which we demonstrate by the characterization
of its ternary complex formation both in vitro and in cellulo. Molecular dynamics simulations indicate that
in aqueous solvents, this active degrader populates both folded and
extended conformations, which are likely to promote cell permeability
and ternary complex formation, respectively.