Structure-Based Design of γ-Carboline Analogues as Potent and Specific BET Bromodomain Inhibitors

J Med Chem. 2015 Jun 25;58(12):4927-39. doi: 10.1021/acs.jmedchem.5b00613. Epub 2015 Jun 16.

Abstract

Small-molecule inhibitors of bromodomain and extra terminal proteins (BET), including BRD2, BRD3, and BRD4 proteins have therapeutic potential for the treatment of human cancers and other diseases and conditions. In this paper, we report the design, synthesis, and evaluation of γ-carboline-containing compounds as a new class of small-molecule BET inhibitors. The most potent inhibitor (compound 18, RX-37) obtained from this study binds to BET bromodomain proteins (BRD2, BRD3, and BRD4) with Ki values of 3.2-24.7 nM and demonstrates high selectivity over other non-BET bromodomain-containing proteins. Compound 18 potently and selectively inhibits cell growth in human acute leukemia cell lines harboring the rearranged mixed lineage leukemia 1 gene. We have determined a cocrystal structure of 18 in complex with BRD4 BD2 at 1.4 Å resolution, which provides a solid structural basis for the compound's high binding affinity and for its further structure-based optimization. Compound 18 represents a promising lead compound for the development of a new class of therapeutics for the treatment of human cancer and other conditions.

Publication types

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

MeSH terms

  • Antineoplastic Agents / chemistry*
  • Antineoplastic Agents / pharmacology*
  • Carbolines / chemistry*
  • Carbolines / pharmacology*
  • Cell Cycle Proteins
  • Cell Line, Tumor
  • Crystallography, X-Ray
  • Humans
  • Leukemia / drug therapy
  • Leukemia / metabolism
  • Molecular Docking Simulation
  • Nuclear Proteins / antagonists & inhibitors*
  • Nuclear Proteins / metabolism
  • Protein-Serine-Threonine Kinases / antagonists & inhibitors*
  • Protein-Serine-Threonine Kinases / metabolism
  • RNA-Binding Proteins / antagonists & inhibitors*
  • RNA-Binding Proteins / metabolism
  • Transcription Factors / antagonists & inhibitors*
  • Transcription Factors / metabolism

Substances

  • Antineoplastic Agents
  • BRD2 protein, human
  • BRD3 protein, human
  • BRD4 protein, human
  • Carbolines
  • Cell Cycle Proteins
  • Nuclear Proteins
  • RNA-Binding Proteins
  • Transcription Factors
  • gamma-carboline
  • Protein-Serine-Threonine Kinases