A scalable, high-throughput glue perturbation screening platform for molecular glue discovery

Summary: The discovery of molecular glue degraders (MGDs) is undergoing a paradigm shift from serendipitous discovery toward empirical design. However, efficiently prioritizing active leads from synthetic libraries while simultaneously confirming their E3 dependency remains a formidable challenge. In this study, we introduce the glue perturbation screening (GPS) platform, a conceptual and technical advance that integrates high-throughput, low-cost Digital RNA with pertUrbation of Genes 2 (DRUG-seq2) with isogenic cereblon (CRBN) wild-type/knockout (WT/KO) models. The significance of our work lies in the development of a multi-dimensional readout that digitizes compound activity and mechanism in a single step. By mapping transcriptomic perturbations onto a coordinate system of differential expression and gene set enrichment, we establish a tiered prioritization strategy: distinguishing high-potency glues from non-specific toxic molecules and recognizing latent biological activities in sub-threshold compounds that guide further structural optimization. This platform provides a scalable, mechanism-aware roadmap for the rational discovery of next-generation degraders, offering a powerful tool to accelerate the targeting of “undruggable” proteins.