Rationalizing PROTAC-Mediated Ternary Complex Formation Using Rosetta.

Area of Science:

• Biochemistry
• Computational Chemistry
• Drug Discovery

Background:

• Proteolysis-targeting chimaeras (PROTACs) induce targeted protein degradation by forming a ternary complex between a target protein and an E3 ligase.
• PROTAC development often involves extensive empirical optimization of the chemical linker connecting the target-binding warhead and E3 ligase ligand.
• Predicting linker suitability for productive ternary complex formation remains a challenge.

Purpose of the Study:

• To develop and validate a structure-based computational method for evaluating PROTAC linker suitability.
• To assess the role of ternary complex formation in PROTAC activity and selectivity.
• To provide computational tools and models for broader PROTAC research.

Main Methods:

• Utilized Rosetta software for docking protein components and modeling PROTAC assembly within the ternary complex.
• Refined complete models of the ternary complex structures.
• Retrospectively applied the method to analyze existing PROTACs from literature across diverse target proteins.

Main Results:

• The computational method sufficiently explains reported PROTAC activity and selectivity, suggesting ternary complex formation is a key determinant.
• PROTAC activity interpretation benefits from considering an ensemble of ternary complex structures, not just a single conformation.
• Identified that PROTACs can recruit proteins within a conserved family via distinct binding modes.

Conclusions:

• A structure-based computational approach can effectively guide PROTAC design by predicting ternary complex formation.
• This method aids in understanding and optimizing PROTAC efficacy and selectivity.
• Dissemination of methods and models aims to accelerate the development of PROTAC therapeutics and chemical probes.