Quantifying Cooperativity through Binding Free Energies in Molecular Glue Degraders

Molecular glues represent a novel therapeutic modality facilitating the stabilization of protein-protein interactions (PPIs), thus enabling the targeting of previously "undruggable" proteins. We develop a computational procedure to screen for molecular glues using a pathway-independent free energy calculation method for accurately assessing the cooperativity. We employ a combined ligand and protein free energy perturbation (FEP) method to calculate the cooperative effect of a ligand for ternary binding. We study the cooperative binding mechanisms of molecular glue degraders, specifically cereblon (CRBN) modulators targeting Ikaros family zinc finger 2 (IKZF2), a transcription factor implicated in cancer immunotherapy. We present a comprehensive computational protocol for screening large molecular libraries to identify potent molecular glues. By leveraging cooperative binding principles in ternary complex formation, our approach effectively predicts ligand-induced PPIs and their degradation potential. Benchmarking against experimental data for CRBN-Ikaros complexes, our protocol demonstrates high accuracy in identifying superior molecular glues, highlighting L4 and L5 as top performers. Furthermore, our high-throughput screening identified novel candidates from extensive chemical libraries, validated through advanced FEP+ simulations. This study not only underscores the transformative potential of molecular glues in targeted protein degradation but also sets the stage for their broader application across diverse protein targets, paving the way for innovative therapeutic strategies in drug discovery.