Inhibition of β-catenin/B cell lymphoma 9 protein−protein interaction using α-helix–mimicking sulfono-γ-AApeptide inhibitors

Abstract

The rational design of α-helix-mimicking peptidomimetics provides a streamlined approach to discover potent inhibitors for protein−protein interactions (PPIs). However, designing cell-penetrating long peptidomimetic scaffolds equipped with various functional groups necessary for interacting with large protein-binding interfaces remains challenging. This is particularly true for targeting β-catenin/ BCL9 PPIs. Here we designed a series of unprecedented helical sulfono-γ-AApeptides that mimic the binding mode of the α-helical HD2 domain of B Cell Lymphoma 9 (BCL9). Our studies show that sulfono-γ-AApeptides can structurally and functionally mimic the α-helical domain of BCL9 and selectively disrupt β-catenin/BCL9 PPIs with even higher potency. More intriguingly, these sulfonoγ-AApeptides can enter cancer cells, bind with β-catenin and disrupt β-catenin/BCL9 PPIs, and exhibit excellent cellular activity, which is much more potent than the BCL9 peptide. Furthermore, our enzymatic stability studies demonstrate the remarkable stability of the helical sulfono-γ-AApeptides, with no degradation in the presence of pronase for 24 h, augmenting their biological potential. This work represents not only an example of helical sulfono-γ-AApeptides that mimic α-helix and disrupt protein-protein interactions, but also an excellent example of potent, selective, and cell-permeable unnatural foldameric peptidomimetics that disrupt the β-catenin/BCL9 PPI. The design of helical sulfono-γ-AApeptides may lead to a new strategy to modulate a myriad of protein-protein interactions.α-helix mimetics | β-catenin | B-cell lymphoma 9 | protein-protein interactions | inhibitors Author contributions: H.J. and J.C. designed research; P.S., M.Z., Y.S., and C.L. performed research; P.S., S.A., Q.L., H.J., and J.C. analyzed data; and P.S., H.J., and J.C. wrote the paper.The authors declare no conflict of interest. This article is a PNAS Direct Submission.Published under the PNAS license. 1 P.S., M.Z., and Y.S. contributed equally to this work.

Systematic Analysis of Lysine Lactylation in the Plant Fungal Pathogen Botrytis cinerea

“…Histone PTMs have been shown to be important for many biological processes, including gene regulation, DNA repair, accurate genome organization, and DNA replication (Leach and Brown, 2012). Through mass spectrometry analyses, 26 and 16 histone Kla sites were identified from human and mouse, respectively (Zhang et al, 2019). In our study, the 273 Kla sites include 6 sites on histones, four of them conserved in human and two of them have not been reported thus far ( Supplementary Figure 3).…”

“…Alpha-helix structure is the most abundant secondary structure in proteins and often located at surface of core, with hydrophobic residues on inner-facing side, hydrophilic on other side. It is reported that alpha-helix structure is involved in a variety of functions including DNA binding, protein interaction, and stability of membrane proteins (Mckay et al, 2018;Manav et al, 2019;Sang et al, 2019). Thus, the preference of Kla on alpha-helix suggested a potential role of Kla in the above mentioned biological pathways.…”

“…Kla is a previously unknown histone modification which was newly discovered in 2019 (Zhang et al, 2019). Kla dynamics in M1 macrophages are associated with gene expression and homeostatic response; however, nothing is known about the effects of Kla on non-histone proteins.…”

“…In M1 macrophages, lactate is derived from incompletely oxidized glucose and then generate lactyl-CoA, which is transferred to lysine tails of histone proteins via the acetyl transferase p300. This modification was high in gene promoter regions that lack acetylation and associated with activation of genes expression (Zhang et al, 2019). As a large number of studies have demonstrated that lysine acylation possessed a diverse range of substrate proteins, however, no systematic analysis has been reported for lysine lactylation.…”

Stapled Peptides as HIF‐1α/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency

“…[4] In particular, a-helix mediatedP PIs [8] have received attention, in part due to the defined structural component of binding conferred by docking of an a-helix from one protein into ac left on another, but also as ac onsequence of the regularp attern of hot-spot residues that are characteristic of such PPIs. [9][10][11] This has facilitated the development of constrained peptide [12][13][14][15] and foldamer based [16][17][18] topological mimics of the helix (i.e.,m imicking the local conformation of the helix), alongside topographical mimics [19][20][21][22][23] of the helix (i.e.,m imicking the surfacef eatures of the helix).…”