PhenoDEL as a Novel Screening Strategy Based on Intracellular Protein Degradation Activity

Abstract Targeted protein degradation (TPD), including proteolysis targeting chimeras (PROTACs) and molecular glue degraders (MGDs), is a promising therapeutic approach. However, systematic discovery of such small molecules remains a major challenge. Here, we present PhenoDEL, a novel phenotypic DNA-encoded library (DEL) screening platform that integrates one-bead one-compound DEL (OBOC-DEL) with the Beacon® optofluidic system for high-throughput, single-cell analysis. By co-culturing individual OBOC-DEL beads and engineered reporter cells in nanoliter-scale chambers, PhenoDEL enables direct observation of compound-induced protein degradation at single-cell resolution. We demonstrate this approach by identifying compounds that induce degradation of FKBP12 F36V -EGFP fusion proteins in PC-3 cells. The workflow allows precise linkage between compound identity and cellular phenotype via DNA barcoding and next-generation sequencing. PhenoDEL overcomes limitations of conventional screening methods, offering high sensitivity, spatial control, and scalability. This platform holds significant potential for mechanism-driven drug discovery, including identification of novel PROTACs and MGDs. Graphical abstract