Biased multicomponent reactions to develop novel bromodomain inhibitors

J Med Chem. 2014 Nov 13;57(21):9019-27. doi: 10.1021/jm501120z. Epub 2014 Oct 31.

Abstract

BET bromodomain inhibition has contributed new insights into gene regulation and emerged as a promising therapeutic strategy in cancer. Structural analogy of early methyl-triazolo BET inhibitors has prompted a need for structurally dissimilar ligands as probes of bromodomain function. Using fluorous-tagged multicomponent reactions, we developed a focused chemical library of bromodomain inhibitors around a 3,5-dimethylisoxazole biasing element with micromolar biochemical IC50. Iterative synthesis and biochemical assessment allowed optimization of novel BET bromodomain inhibitors based on an imidazo[1,2-a]pyrazine scaffold. Lead compound 32 (UMB-32) binds BRD4 with a Kd of 550 nM and 724 nM cellular potency in BRD4-dependent lines. Additionally, compound 32 shows potency against TAF1, a bromodomain-containing transcription factor previously unapproached by discovery chemistry. Compound 32 was cocrystallized with BRD4, yielding a 1.56 Å resolution crystal structure. This research showcases new applications of fluorous and multicomponent chemical synthesis for the development of novel epigenetic inhibitors.

Publication types

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

MeSH terms

  • Alkanesulfonic Acids / chemistry
  • Azepines / pharmacology
  • Cell Cycle Proteins
  • Cell Line, Tumor
  • Crystallography, X-Ray
  • Fluorocarbons / chemistry
  • Gene Expression Regulation
  • Humans
  • Imidazoles / chemical synthesis*
  • Imidazoles / pharmacology
  • Inhibitory Concentration 50
  • Isoxazoles / chemistry*
  • Ligands
  • Models, Molecular
  • Nuclear Proteins / antagonists & inhibitors*
  • Nuclear Proteins / chemistry
  • Pyrazines / chemical synthesis*
  • Pyrazines / pharmacology
  • Pyridines / chemical synthesis
  • Small Molecule Libraries / chemical synthesis
  • Structure-Activity Relationship
  • Transcription Factors / antagonists & inhibitors*
  • Transcription Factors / chemistry

Substances

  • Alkanesulfonic Acids
  • Azepines
  • BRD4 protein, human
  • Cell Cycle Proteins
  • Fluorocarbons
  • Imidazoles
  • Isoxazoles
  • Ligands
  • N-(tert-butyl)-2-(4-(3,5-dimethylisoxazol-4-yl)phenyl)imidazo(1,2-a)pyrazin-3-amine
  • Nuclear Proteins
  • Pyrazines
  • Pyridines
  • Small Molecule Libraries
  • Transcription Factors
  • perfluorooctane sulfonic acid

Associated data

  • PDB/4WIV
  • PDB/BRD4