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

Onda, Y.; Ochi, Y.; Araki, T.; Kageoka, M.; Takeda, S.; Yamada, K.; Ueda, T.; Ohno, K.; Tanaka, M.; Sakai, D.; Hasegawa, M.; Tanaka, Y.

doi:10.1101/2025.11.26.690606

bioRxiv · 10.1101/2025.11.26.690606

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

Onda, Y.·Ochi, Y.·Araki, T.·Kageoka, M.·Takeda, S.·Yamada, K.·Ueda, T.·Ohno, K.·Tanaka, M.·Sakai, D.·Hasegawa, M.·Tanaka, Y.

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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(R) 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 FKBP12F36V-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 O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/690606v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@fe27bforg.highwire.dtl.DTLVardef@1e38ef5org.highwire.dtl.DTLVardef@be958aorg.highwire.dtl.DTLVardef@4bc48a_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Onda, Y., Ochi, Y., Araki, T., Kageoka, M., Takeda, S., Yamada, K., Ueda, T., Ohno, K., Tanaka, M., Sakai, D., Hasegawa, M., Tanaka, Y.. 2025-11-27. PhenoDEL as a Novel Screening Strategy Based on Intracellular Protein Degradation Activity. https://doi.org/10.1101/2025.11.26.690606

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