Discovery and Identification of a Novel PORCN Inhibitor via Structure-Based Virtual Screening

Dysregulated activation of the Wnt pathway is closely associated with oncogenesis and the progression of various cancers. Palmitoylation catalyzed by porcupine (PORCN) is essential for the secretion of Wnts and the activation of the Wnt pathway. Given its critical role in regulating Wnt signaling, PORCN has been recognized as a promising therapeutic target for cancers driven by aberrant Wnt pathway activation. Herein, we explored the binding modes of reported inhibitors with different scaffolds using molecular docking and molecular dynamics simulations, establishing an optimized structure-based virtual screening model, which discovered a novel PORCN inhibitor, Y-99. Y-99 demonstrated promising inhibitory activity against the Wnt/β-catenin signaling pathway (IC₅₀ = 155.4 nM) and exhibited high binding affinity to PORCN (K_D = 33.1 nM). Notably, Y-99 exerted a significant antiproliferation effect in Wnt-addicted tumor cell lines, accompanied by reduced LRP6 phosphorylation and downregulation of Wnt-related gene expression, including AXIN2 and CCND1. Taken together, these findings highlight that Y-99, which was identified through in silico screening and validated in vitro, is a promising PORCN inhibitor, which has the potential for further research and development.