Structure-Based Design of Bicyclic Helical Peptides That Target the Oncogene β-Catenin

The inhibition of intracellular protein-protein interactions is challenging, in particular, when involved interfaces lack pronounced cavities. The transcriptional co-activator protein and oncogene beta-catenin is a prime example of such a challenging target. Despite extensive targeting efforts, available high-affinity binders comprise only large molecular weight inhibitors. This hampers the further development of therapeutically useful compounds. Herein, we report the design of a considerably smaller peptidomimetic scaffold derived from the alpha-helical beta-catenin-binding motif of Axin. Sequence maturation and bicyclization provided a stitched peptide with an unprecedented crosslink architecture. The binding mode and site were confirmed by a crystal structure. Further derivatization yielded a beta-catenin inhibitor with single-digit micromolar activity in a cell-based assay. This study sheds light on how to design helix mimetics with reduced molecular weight thereby improving their biological activity. A bicyclic peptide is reported that combines two hydrocarbon staples with i,i+4 and i,i+3 spacing, respectively. In the resulting i,i+4,i+7 crosslink topology, a central spiro center connects two macrocycles that are formed during ring-closing metathesis. After affinity maturation, we obtain a high-affinity binder of the oncogenic protein beta-catenin which inhibits the Wnt signaling pathway in a cell-based assay. image