Subpocket complementarity and polar interactions dictate dual binding modes of EED inhibitors: insights from molecular dynamics, steered MD, and free energy calculations

Abstract

The EED subunit of the polycomb repressive complex 2 (PRC2) drives oncogenesis through histone methylation, and pharmacological EED inhibition effectively suppresses tumorigenic pathways. By combining molecular dynamics (MD), steered MD (SMD), and MM/GBSA calculations, we characterized five triazolopyrimidine-based inhibitors that target EED's substrate-binding cavity of EED. Geometric complementarity within the inner subpocket critically dictates binding modes, where the Glu195–Arg414 salt bridge governs the orientation of the core scaffold, inducing conformation-dependent changes in binding affinity. SMD-derived maximum pulling forces and potential of mean force (PMF) analyses revealed two distinct binding patterns: inhibitor 11e/EED226/10a/10c adopted tail-insertion conformations, whereas 11b favored head insertion. Binding free energy rankings (11e > EED226 > 10a > 11b > 10c) strongly correlated with the experimental IC50 values, validating the computational framework. This study elucidates how subpocket complementarity and polar interactions govern EED inhibitor-binding modes, providing a structural blueprint for designing next-generation PRC2-targeted epigenetic therapies.