Macrocyclic peptides that inhibit Wnt signalling via interaction with Wnt3a

Manuel E Otero-Ramirez; Kyoko Matoba; Emiko Mihara; Toby Passioura; Junichi Takagi; Hiroaki Suga

doi:10.1039/d0cb00016g

Macrocyclic peptides that inhibit Wnt signalling via interaction with Wnt3a

RSC Chem Biol. 2020 Mar 24;1(1):26-34. doi: 10.1039/d0cb00016g. eCollection 2020 Apr 16.

Authors

Manuel E Otero-Ramirez¹, Kyoko Matoba², Emiko Mihara², Toby Passioura^{1

3}, Junichi Takagi², Hiroaki Suga¹

Affiliations

¹ Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan hsuga@chem.s.u-tokyo.ac.jp.
² Laboratory of Protein Synthesis and Expression, Institute for Protein Research, Osaka University 3-2 Yamadaoka Suita-shi Osaka 565-0871 Japan takagi@protein.osaka-u.ac.jp.
³ Sydney Analytical, School of Chemistry and School of Life and Environmental Sciences, The University of Sydney Sydney 2006 Australia.

Abstract

Here we report de novo macrocyclic peptide binders to Wnt3a, a member of the Wnt protein family. By means of the Random non-standard Peptides Integrated Discovery (RaPID) system, we have performed in vitro selection against the complex of mouse Wnt3a (mWnt3a) with human afamin (hAFM) to discover macrocyclic peptides that bind mWnt3a with K _D values as tight as 110 nM. One of these peptides, WAp-D04 (Wnt-AFM-peptide-D04), was able to inhibit the receptor-mediated signaling process, which was demonstrated in a Wnt3a-dependent reporter cell-line. Based on this initial hit, we applied a block-mutagenesis scanning display to identify a mutant inhibitor, WAp-D04-W10P, with 5-fold greater potency in a reporter assay. This work represents the first instance of molecules capable of inhibiting Wnt signaling through direct interaction with a Wnt protein, a molecular class for which targeting has been challenging due its highly hydrophobic nature.