Discovery of small molecules targeting the tandem tudor domain of the epigenetic factor UHRF1 using fragment-based ligand discovery

Sci Rep. 2021 Jan 13;11(1):1121. doi: 10.1038/s41598-020-80588-4.

Abstract

Despite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, we use fragment-based ligand discovery to identify novel scaffolds for targeting the isolated UHRF1 tandem Tudor domain (TTD), which recognizes the heterochromatin-associated histone mark H3K9me3 and supports intramolecular contacts with other regions of UHRF1. Using both binding-based and function-based screens of a ~ 2300-fragment library in parallel, we identified 2,4-lutidine as a hit for follow-up NMR and X-ray crystallography studies. Unlike previous reported ligands, 2,4-lutidine binds to two binding pockets that are in close proximity on TTD and so has the potential to be evolved into more potent inhibitors using a fragment-linking strategy. Our study provides a useful starting point for developing potent chemical probes against UHRF1.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • CCAAT-Enhancer-Binding Proteins / chemistry*
  • CCAAT-Enhancer-Binding Proteins / metabolism*
  • Crystallography, X-Ray
  • Drug Discovery*
  • Histone Code
  • Histones / metabolism
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Molecular Structure
  • Peptide Fragments / metabolism
  • Protein Binding
  • Pyridines / chemistry*
  • Pyridines / metabolism*
  • Pyridines / pharmacokinetics
  • Small Molecule Libraries*
  • Structure-Activity Relationship
  • Tudor Domain*
  • Ubiquitin-Protein Ligases / chemistry*
  • Ubiquitin-Protein Ligases / metabolism*

Substances

  • CCAAT-Enhancer-Binding Proteins
  • Histones
  • Ligands
  • Peptide Fragments
  • Pyridines
  • Small Molecule Libraries
  • 2,4-dimethylpyridine
  • UHRF1 protein, human
  • Ubiquitin-Protein Ligases