Mechanistic insights into PROTAC-mediated degradation through an integrated framework of molecular dynamics, free energy landscapes, and quantum mechanics: A case study on kinase degraders.

Targeted protein degradation by proteolysis-targeting chimeras (PROTAC) is dependent on formation and plasticity of ternary complexes enabling ubiquitination. In this study, we employed long-timescale molecular dynamics (MD) simulations, free energy landscape analysis, and quantum mechanical (QM) calculations to investigate the molecular determinants of PROTAC efficacy. Using three model systems (FAK-VHL, BTK-CRBN, and TTK-CRBN), each with three PROTACs of varying potencies, we analyzed a total of nine ternary complexes over 500 ns MD simulations each. Simulation events analysis revealed that potent PROTACs maintain stable and important interactions between the protein of interest (POI) and the E3 ligase, while weaker PROTACs exhibit diminished or no interactions. Conformational dynamics and changes in the interaction patterns between the POI-E3-ligase complexes highlighted the importance of ternary complex plasticity in degradation efficiency. These findings were also supported by the distribution of free energy landscape during simulations. Distributions of the free energy landscape offer insights into the stability of population states and open new avenues for understanding their degradation potential. Additionally, to overcome the limitation of conventional docking models, we highlight the importance of QM and DFT based methods to predict the impact of binding at the E3-ligase site which corelates with the degradation potentials of PROTACs. These insights provide a new computational framework for rational PROTAC design.