A Qualified Success: Discovery of a New Series of ATAD2 Bromodomain Inhibitors with a Novel Binding Mode Using High-Throughput Screening and Hit Qualification

J Med Chem. 2019 Aug 22;62(16):7506-7525. doi: 10.1021/acs.jmedchem.9b00673. Epub 2019 Aug 9.


The bromodomain of ATAD2 has proved to be one of the least-tractable proteins within this target class. Here, we describe the discovery of a new class of inhibitors by high-throughput screening and show how the difficulties encountered in establishing a screening triage capable of finding progressible hits were overcome by data-driven optimization. Despite the prevalence of nonspecific hits and an exceptionally low progressible hit rate (0.001%), our optimized hit qualification strategy employing orthogonal biophysical methods enabled us to identify a single active series. The compounds have a novel ATAD2 binding mode with noncanonical features including the displacement of all conserved water molecules within the active site and a halogen-bonding interaction. In addition to reporting this new series and preliminary structure-activity relationship, we demonstrate the value of diversity screening to complement the knowledge-based approach used in our previous ATAD2 work. We also exemplify tactics that can increase the chance of success when seeking new chemical starting points for novel and less-tractable targets.

MeSH terms

  • ATPases Associated with Diverse Cellular Activities / antagonists & inhibitors*
  • ATPases Associated with Diverse Cellular Activities / chemistry
  • ATPases Associated with Diverse Cellular Activities / metabolism
  • Biophysical Phenomena
  • Catalytic Domain
  • DNA-Binding Proteins / antagonists & inhibitors*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Drug Design*
  • Drug Discovery / methods*
  • High-Throughput Screening Assays / methods*
  • Humans
  • Models, Molecular
  • Molecular Structure
  • Protein Binding / drug effects
  • Protein Domains*
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / metabolism
  • Small Molecule Libraries / pharmacology*


  • DNA-Binding Proteins
  • Small Molecule Libraries
  • ATAD2 protein, human
  • ATPases Associated with Diverse Cellular Activities