Discovery of Pyrazolo[1,5-a]pyrimidine B-Cell Lymphoma 6 (BCL6) Binders and Optimization to High Affinity Macrocyclic Inhibitors

J Med Chem. 2017 May 25;60(10):4386-4402. doi: 10.1021/acs.jmedchem.7b00359. Epub 2017 May 9.

Abstract

Inhibition of the protein-protein interaction between B-cell lymphoma 6 (BCL6) and corepressors has been implicated as a therapeutic target in diffuse large B-cell lymphoma (DLBCL) cancers and profiling of potent and selective BCL6 inhibitors are critical to test this hypothesis. We identified a pyrazolo[1,5-a]pyrimidine series of BCL6 binders from a fragment screen in parallel with a virtual screen. Using structure-based drug design, binding affinity was increased 100000-fold. This involved displacing crystallographic water, forming new ligand-protein interactions and a macrocyclization to favor the bioactive conformation of the ligands. Optimization for slow off-rate constant kinetics was conducted as well as improving selectivity against an off-target kinase, CK2. Potency in a cellular BCL6 assay was further optimized to afford highly selective probe molecules. Only weak antiproliferative effects were observed across a number of DLBCL lines and a multiple myeloma cell line without a clear relationship to BCL6 potency. As a result, we conclude that the BCL6 hypothesis in DLBCL cancer remains unproven.

MeSH terms

  • Cell Line, Tumor
  • Cell Proliferation / drug effects
  • Drug Design
  • Humans
  • Lymphoma, Large B-Cell, Diffuse / drug therapy
  • Molecular Docking Simulation
  • Protein Interaction Maps / drug effects*
  • Proto-Oncogene Proteins c-bcl-6 / antagonists & inhibitors
  • Proto-Oncogene Proteins c-bcl-6 / metabolism*
  • Pyrazoles / chemistry*
  • Pyrazoles / pharmacology*
  • Pyridines / chemistry*
  • Pyridines / pharmacology*

Substances

  • BCL6 protein, human
  • Proto-Oncogene Proteins c-bcl-6
  • Pyrazoles
  • Pyridines
  • pyrazolo(3,4-b)pyridine