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

DOI: 10.1039/D0SC05694D DOI Help

Authors: Zsofia Hegedus (University of Leeds) , Fruzsina Hobor (University of Leeds) , Deborah K. Shoemark (University of Bristol) , Sergio Celis (University of Leeds) , Lu-yun Lian (University of Liverpool) , Chi H. Trinh (University of Leeds) , Richard B. Sessions (University of Bristol) , Thomas A. Edwards (University of Leeds) , Andrew J. Wilson (University of Leeds)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Chemical Science , VOL 153

State: Published (Approved)
Published: January 2021
Diamond Proposal Number(s): 19248

Open Access Open Access

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.

Subject Areas: Chemistry, Biology and Bio-materials

Instruments: I03-Macromolecular Crystallography , I04-Macromolecular Crystallography , I24-Microfocus Macromolecular Crystallography


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