Abstract 7015: Intelligent molecular glue discovery by identifying glueable ligase-target pairs at scale

Abstract Targeted protein degradation can be induced by monovalent small molecules, called molecular glues. These molecules modify the substrate-binding interface of E3 ubiquitin ligases and reroute their binding to novel targets, opening the possibility of therapeutically inhibiting proteins previously considered “undruggable”. However, for a molecular glue to sufficiently stabilize a ligase-target interaction and induce degradation, the two proteins must exhibit proper shape complementarity and contain productive amino acid contacts - two proteins selected at random are unlikely to be glued by any small molecule. Identifying novel “glueable” ligase-target pairs requires the discovery and characterization of weak interactions (likely in the micromolar affinity range) between thousands or more potential pairs of human E3 ligases and therapeutically relevant target proteins. The need to evaluate vast numbers of potential protein interactions while maintaining exquisite sensitivity for weak interactions presents a major technical roadblock. To address this challenge, we apply AlphaSeq, a high-throughput and highly sensitive experimental platform for measuring protein-protein interactions, to discover and structurally characterize weak interactions between ligases and target proteins. We validate our approach by characterizing known ligase-target interactions, such as between the E3 ligase MDM2 and the tumor suppressor protein p53. We then leverage AlphaSeq for the discovery of molecular glues for novel ligase-target pairs and orthogonally validate these interactions with surface plasmon resonance (SPR). Finally, we use AlphaSeq mutational data to structurally characterize the interaction interface and inform the intelligent discovery of molecular glues. Citation Format: Phil Burke, Arpita Sen, David Noble, Abhishek Dogra, Ruchi Bansal, Dasha Krayushkina, Natasha Seelam Murakowska, Kerry McGowan, Charles Lin, Yeweon Lee, Randolph Lopez. Intelligent molecular glue discovery by identifying glueable ligase-target pairs at scale [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7015.