Lessons in PROTAC Design from Selective Degradation with a Promiscuous Warhead.

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Selective inhibition of protein function is crucial in drug discovery.
• Proteolysis-targeting chimeras (PROTACs) leverage E3 ubiquitin ligases for targeted protein degradation.
• Understanding PROTAC selectivity is key to optimizing their therapeutic potential.

Purpose of the Study:

• To investigate the selectivity mechanisms of PROTACs in targeted protein degradation.
• To identify factors governing the degradation of E3 ligase-recruited target proteins.
• To establish design guidelines for potent PROTACs, including for previously undruggable targets.

Main Methods:

• Utilized promiscuous CRBN- and VHL-recruiting PROTACs targeting over 50 kinases.
• Analyzed protein degradation selectivity based on ternary complex formation and stability.
• Assessed the impact of protein-protein interactions between E3 ligases and target proteins on degradation efficiency.

Main Results:

• PROTACs binding multiple targets do not degrade all of them, indicating selectivity beyond mere binding.
• Protein degradation is contingent on the stability of the ternary complex formed by the target protein, PROTAC, and E3 ligase.
• Unstable ternary complexes prevent degradation, while stable ones, even with weak target affinity, promote efficient degradation.
• Identified protein-protein interactions as critical determinants of PROTAC-mediated degradation selectivity.

Conclusions:

• PROTAC selectivity is governed by the stability of the target:PROTAC:E3 ligase ternary complex.
• Weak target affinity can be overcome by high-affinity interactions within the ternary complex, leading to efficient degradation.
• This work provides design principles for developing potent PROTACs and offers strategies for targeting proteins resistant to conventional inhibitors.