Yuichi Onda, Yurika Ochi, Toshihiro Araki, Miho Kageoka-Takahashi, Shuzo Takeda, Kazunori Yamada, Takehiko Ueda, Ken Ohno, Minoru Tanaka, Daiki Sakai, Miki Hasegawa, Yoshihito Tanaka

ACS Chemical Biology

DOI: 10.1021/acschembio.6c00234

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 single-cell analysis. By coculturing individual OBOC-DEL beads and engineered reporter cells in nanoliter-scale chambers, PhenoDEL enables time-resolved, single-cell phenotypic evaluation and direct linkage between compound identity and intracellular response. As a proof-of-concept, we demonstrate discrimination of active and inactive on-bead compounds using an FKBP12F36V-EGFP degradation reporter in PC-3 cells, followed by DNA barcode decoding.