Download MendeleyIdentification of beta-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation.
Hegedus, Z., Hobor, F., Shoemark, D.K., Celis, S., Lian, L.Y., Trinh, C.H., Sessions, R.B., Edwards, T.A., Wilson, A.J.(2021) Chem Sci 12: 2286-2293
- PubMed: 34163995
- DOI: https://doi.org/10.1039/d0sc05694d
- Primary Citation of Related Structures:
6YWZ, 6YX0, 6YX1, 6YX2 - PubMed 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.
Organizational Affiliation:
School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK a.j.wilson@leeds.ac.uk.
