Developing Spindlin1 small-molecule inhibitors by using protein microarrays

Nat Chem Biol. 2017 Jul;13(7):750-756. doi: 10.1038/nchembio.2377. Epub 2017 May 15.

Abstract

The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence for the 'druggability' of epigenetic effector molecules. The small-molecule probe UNC1215 prevents methyl-dependent protein-protein interactions by engaging the aromatic cage of MBT domains and, with lower affinity, Tudor domains. Using a library of tagged UNC1215 analogs, we screened a protein-domain microarray of human methyllysine effector molecules to rapidly detect compounds with new binding profiles with either increased or decreased specificity. Using this approach, we identified a compound (EML405) that acquired a novel interaction with the Tudor-domain-containing protein Spindlin1 (SPIN1). Structural studies facilitated the rational synthesis of SPIN1 inhibitors with increased selectivity (EML631-633), which engage SPIN1 in cells, block its ability to 'read' H3K4me3 marks and inhibit its transcriptional-coactivator activity. Protein microarrays can thus be used as a platform to 'target-hop' and identify small molecules that bind and compete with domain-motif interactions.

MeSH terms

  • Benzamides / chemical synthesis
  • Benzamides / chemistry
  • Benzamides / pharmacology*
  • Cell Cycle Proteins / antagonists & inhibitors*
  • Cell Cycle Proteins / chemistry
  • Dose-Response Relationship, Drug
  • Humans
  • Microtubule-Associated Proteins / antagonists & inhibitors*
  • Microtubule-Associated Proteins / chemistry
  • Models, Molecular
  • Molecular Structure
  • Phosphoproteins / antagonists & inhibitors*
  • Phosphoproteins / chemistry
  • Piperidines / chemical synthesis
  • Piperidines / chemistry
  • Piperidines / pharmacology*
  • Protein Array Analysis*
  • Small Molecule Libraries / chemical synthesis
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*
  • Structure-Activity Relationship

Substances

  • Benzamides
  • Cell Cycle Proteins
  • Microtubule-Associated Proteins
  • Phosphoproteins
  • Piperidines
  • Small Molecule Libraries
  • UNC1215
  • spindlin

Associated data

  • PubChem-Substance/333497403
  • PubChem-Substance/333497414
  • PubChem-Substance/333497423
  • PubChem-Substance/333497424
  • PubChem-Substance/333497425
  • PubChem-Substance/333497426
  • PubChem-Substance/333497427
  • PubChem-Substance/333497428
  • PubChem-Substance/333497429
  • PubChem-Substance/333497404
  • PubChem-Substance/333497405
  • PubChem-Substance/333497406
  • PubChem-Substance/333497407
  • PubChem-Substance/333497408
  • PubChem-Substance/333497409
  • PubChem-Substance/333497410
  • PubChem-Substance/333497411
  • PubChem-Substance/333497412
  • PubChem-Substance/333497413
  • PubChem-Substance/333497415
  • PubChem-Substance/333497416
  • PubChem-Substance/333497417
  • PubChem-Substance/333497418
  • PubChem-Substance/333497419
  • PubChem-Substance/333497420
  • PubChem-Substance/333497421
  • PubChem-Substance/333497422