Issue 6, 2021

Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation

Abstract

β-Strand mediated protein–protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.

Graphical abstract: Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation

Supplementary files

Article information

Article type
Edge Article
Submitted
15 Oct 2020
Accepted
01 Dec 2020
First published
06 Jan 2021
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2021,12, 2286-2293

Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation

Z. Hegedüs, F. Hóbor, D. K. Shoemark, S. Celis, L. Lian, C. H. Trinh, R. B. Sessions, T. A. Edwards and A. J. Wilson, Chem. Sci., 2021, 12, 2286 DOI: 10.1039/D0SC05694D

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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