Molecular Editing in Protein Degradation: From a Dual NSD2/GSPT1 Degrader to an NSD2-Selective PROTAC and a GSPT1-Selective Molecular Glue

Abstract

Molecular editing, rooted in synthetic chemistry, has emerged as a powerful tool for structure optimization in medicinal chemistry but remains underutilized in targeted protein degradation. Here, we demonstrate the utility of molecular editing by repurposing the NSD2 degrader LLC0424 with GSPT1 neosubstrate engagement to generate two structurally analogous molecules with divergent modes of action: 424-ND, a PROTAC selective for NSD2, and 424-GD, a selective GSPT1 molecular glue. 424-ND drove NSD2 degradation selectively in a CRBN- and proteasome-dependent manner and functionally suppressed androgen receptor (AR) signaling in prostate cancer cells. 424-GD induced selective degradation of GSPT1 and robustly upregulated the integrated stress response markers ATF4 and ATF3. Biolayer interferometry revealed distinct ternary complex cooperativity profiles in the presence of NSD2 or GSPT1, which directly correlate with the observed biased degradation activity. Further molecular dynamics and metadynamics simulations showed that the compounds adopt distinct low-energy conformational ensembles with different spatial orientations, likely underlying their divergent cooperativity and selectivity. These findings not only deliver highly selective chemical probes for NSD2 and GSPT1 but also demonstrate that molecular editing enables precision control over target selectivity, providing a generalizable strategy to tune selectivity in targeted protein degradation. Table of Contents Graphic