Catalytic Proximal Protein Oligomerization as an Anti-Tumor Strategy Targeting WDR5

Abstract Inducing protein oligomerization holds therapeutic promise, yet identifying or rationally designing effective inducers remains challenging. In this study, we leverage nanopore technology to screen small molecules capable of modulating WD repeat domain 5 (WDR5) protein oligomerization and uncover a oligomerization mechanism which we term Catalytic Proximal Protein Oligomerization (CaPPO). Nanopore sensing enabled rapid identification of WZ-1, a selective WDR5 oligomerization inducer, from our in-house compound library. Biochemical and cryo-EM analyses reveal that WZ-1 binds the WBM site of WDR5 through its 2-aminothiazole moiety, reacts with Cys248 to form an intramolecular disulfide, and, through N-terminal tail-induced proximity of WDR5 molecules, triggers oligomerization via thio–disulfide exchange. Structure–activity relationship studies indicate that the disulfide motif within WZ-1 acts as a molecular scout initiating oligomerization. In cellular assays, WZ-1 exhibits potent anti-tumor activity by disrupting WDR5 interactions at both WIN and WBM sites, leading to transcriptional downregulation of target genes. Collectively, this work not only establishes a nanopore-based screening platform for identifying protein oligomerization inducers, but also validates CaPPO as a promising small-molecule design strategy for therapeutic development.