Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• CREB-binding protein (CBP) and EP300 are homologous enzymes vital for transcription.
• Targeting these enzymes offers therapeutic potential.
• Novel PROTAC development is crucial for targeted protein degradation.

Purpose of the Study:

• To develop and characterize dCE-2, a novel Proteolysis-Targeting Chimera (PROTAC).
• To investigate the mechanism of action for dCE-2 in degrading CBP and EP300.
• To evaluate the role of cooperativity in PROTAC-mediated protein degradation.

Main Methods:

• Structure-based design of dCE-2 utilizing fragment docking and crystal structure data.
• In vitro and in cellulo characterization of ternary complex formation.
• Molecular dynamics simulations to assess conformational dynamics.

Main Results:

• dCE-2, a novel PROTAC, effectively degrades CBP and EP300.
• Degradation activity is driven by cooperativity rather than solely binding affinity.
• Ternary complex formation was confirmed both in vitro and in cellulo.
• Molecular dynamics simulations revealed conformations promoting cell permeability and complex formation.

Conclusions:

• dCE-2 demonstrates significant protein degradation activity against CBP/EP300.
• Cooperativity is a key factor in the efficacy of dCE-2.
• The conformational flexibility of dCE-2 may enhance its therapeutic potential.