A Kinetic Scout Approach Accelerates Targeted Protein Degrader Development

Area of Science:

• Biochemistry
• Chemical Biology
• Drug Discovery

Background:

• Bifunctional molecules, like targeted protein degraders, are crucial for gain-of-function pharmacology.
• Accelerating the identification and optimization of these molecules is a key focus in academia and industry.
• Previous work utilized chemical proteomics to map degradable targets and predict degradability.

Purpose of the Study:

• To develop generalizable chemistry strategies for accelerating the development of new bifunctional degraders.
• To investigate the impact of ligand residence time on targeted protein degradation.
• To establish a workflow for mechanistic characterization and optimization of degrader activity.

Main Methods:

• Implementation of lysine-targeted reversible-covalent chemistry to tune binding kinetics across 25 targets.
• Global proteomics analysis to assess target engagement and degradation.
• Immunoprecipitation followed by mass spectrometry (IP/MS) of ternary complexes to study molecular interactions.
• E-STUB assay to mechanistically characterize the degradation process.

Main Results:

• Target residence time was identified as a major determinant of degrader activity.
• Reversible-covalent chemistry enabled rational tuning of binding kinetics.
• A minimal number of analogues were synthesized to rapidly optimize degrader performance.
• The developed workflow provided mechanistic insights into target degradation.

Conclusions:

• Ligand residence time is a critical, tunable parameter for targeted protein degrader efficacy.
• The presented chemistry strategies and workflow accelerate early-stage degrader discovery and optimization.
• This approach facilitates the rational design of more effective bifunctional degraders.