Discovery of 1-Benzoyl 4-Phenoxypiperidines as Small-Molecule Inhibitors of the β-Catenin/B-Cell Lymphoma 9 Protein–Protein Interaction

Abstract

Structure-based design and optimization were performed to develop small-molecule β-catenin/B-cell lymphoma 9 (BCL9) inhibitors and improve their inhibitory activities. Compound ZL3138 with a novel 1-benzoyl 4-phenoxypiperidine scaffold was discovered to disrupt the β-catenin/BCL9 protein–protein interaction (PPI) with a K i of 0.96 μM in AlphaScreen competitive inhibition assays and displayed good selectivity for β-catenin/BCL9 over β-catenin/E-cadherin PPIs. The binding mode of new inhibitors was characterized by structure–activity relationship and site-directed mutagenesis studies. Protein pull-down assays indicate that this series of compounds directly binds with β-catenin. Cellular target engagement and co-immunoprecipitation experiments demonstrate that ZL3138 binds with β-catenin and disrupts the β-catenin/BCL9 interaction without affecting the β-catenin/E-cadherin interaction in living cells. Further cell-based studies show that ZL3138 selectively suppresses transactivation of Wnt/β-catenin signaling, regulates transcription and expression of Wnt target genes, and inhibits the growth of Wnt/β-catenin-dependent cancer cells.

Helical sulfono-γ-AApeptides with predictable functions in protein recognition

“…Although there have been reports of using small molecule and peptide inhibitors to block the b-catenin-BCL9 interaction, there are few examples of unnatural peptidomimetic inhibitors. [48][49][50][51][52][53][54][55][56][57] It is still a big challenge to design effective peptidomimetic inhibitors to enter cells and block the b-catenin-BCL9 interaction.…”

Medicinal Chemistry Strategies for the Development of Inhibitors Disrupting β-Catenin’s Interactions with Its Nuclear Partners

“…Co-immunoprecipitation (co-IP) can investigate endogenous interactions between two proteins in intact cells and uses a bait-specific antibody to precipitate the bait protein as well as binding partners, which are then detected by MS or Western blotting . Li et al used a co-IP assay to evaluate the effect and selectivity of inhibitors on the β-catenin and BCL9 association in HCT116 cells with hyperactive β-catenin signaling . However, co-IP may not detect low-affinity interactions and transient PPIs.…”

Protein-protein interactions between RUNX3 and ZEB1 in chronic lung injury induced by methamphetamine abuse

“…With recent development in pharmaceuticals, various novel drugs targeting PPIs are currently in the pre-clinical and clinical stages. For example, 1-benzoyl 4-phenoxypiperidines, a small molecular inhibitor, blocks the PPIs between β-catenin and B-cell lymphoma 9 ( Li et al, 2021 ). A previous study has shown that the PPIs between B-cell lymphoma-2 and Parkin mediate mitophagy via the PTEN-induced putative kinase 1/Parkin pathway in the lipopolysaccharide-induced lung injury ( Zhang Z et al, 2020 ).…”