Identification of Novel Fragments Binding to the PDZ1-2 Domain of PSD-95

ChemMedChem. 2021 Mar 18;16(6):949-954. doi: 10.1002/cmdc.202000865. Epub 2020 Dec 30.

Abstract

Inhibition of PSD-95 has emerged as a promising strategy for the treatment of ischemic stroke, as shown with peptide-based compounds that target the PDZ domains of PSD-95. In contrast, developing potent and drug-like small molecules against the PSD-95 PDZ domains has so far been unsuccessful. Here, we explore the druggability of the PSD-95 PDZ1-2 domain and use fragment screening to investigate if this protein is prone to binding small molecules. We screened 2500 fragments by fluorescence polarization (FP) and validated the hits by surface plasmon resonance (SPR), including an inhibition counter-test, and found four promising fragments. Three ligand efficient fragments were shown by 1 H,15 N HSQC NMR to bind in the small hydrophobic P0 pockets of PDZ1-2, and one of them underwent structure-activity relationship (SAR) studies. Overall, we demonstrate that fragment screening can successfully be applied to PDZ1-2 of PSD-95 and disclose novel fragments that can serve as starting points for optimization towards small-molecule PDZ domain inhibitors.

Keywords: PDZ domains; PSD-95; drug discovery; fragment screening; protein-protein interactions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Disks Large Homolog 4 Protein / antagonists & inhibitors*
  • Drug Evaluation, Preclinical
  • Fluorescence Polarization
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Structure
  • PDZ Domains / drug effects
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*
  • Structure-Activity Relationship
  • Surface Plasmon Resonance

Substances

  • Disks Large Homolog 4 Protein
  • Ligands
  • Small Molecule Libraries