Metastable Protein-Protein Interactions as a Design Principle for PROTACs: Insights from the RIPK1-VHL System

Area of Science:

• Biochemistry
• Molecular Biology
• Drug Discovery

Background:

• Proteolysis-Targeting Chimeras (PROTACs) leverage transient protein-protein interactions (PPIs) to eliminate disease-causing proteins.
• Predicting and modeling these short-lived, metastable PPIs is challenging for current structure-based or AI-only methods.

Purpose of the Study:

• To establish metastable PPIs as a key design principle for rational PROTAC development.
• To explore the dynamics of RIPK1-VHL interactions for optimized PROTAC design.

Main Methods:

• Utilized large-scale molecular dynamics (MD) simulations and integrative generalized master equation (IGME) modeling.
• Mapped metastable PPIs between RIPK1 and VHL E3 ligase to identify suitable interaction sites.
• Developed a virtual screening workflow for linker design based on identified PPIs.

Main Results:

• Identified four distinct metastable RIPK1-VHL PPIs amenable to PROTAC engagement.
• Demonstrated that different PPIs accommodate varying linker lengths, explaining experimental observations.
• Discovered a novel linkage site on the VHL ligand, leading to potent PROTACs with subnanomolar to low-nanomolar degradation efficacy.

Conclusions:

• Explicitly modeling metastable PPIs is crucial for effective PROTAC design.
• Protein dynamics significantly expand the design space for developing novel PROTAC therapeutics.
• Rationally designed PROTACs incorporating dynamic interactions achieve high potency and efficacy.