Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-XL and BCL-2

J Med Chem. 2021 May 13;64(9):5447-5469. doi: 10.1021/acs.jmedchem.0c01771. Epub 2021 Apr 27.

Abstract

The BCL-2 family of proteins (including the prosurvival proteins BCL-2, BCL-XL, and MCL-1) is an important target for the development of novel anticancer therapeutics. Despite the challenges of targeting protein-protein interaction (PPI) interfaces with small molecules, a number of inhibitors (called BH3 mimetics) have entered the clinic and the BCL-2 inhibitor, ABT-199/venetoclax, is already proving transformative. For BCL-XL, new validated chemical series are desirable. Here, we outline the crystallography-guided development of a structurally distinct series of BCL-XL/BCL-2 inhibitors based on a benzoylurea scaffold, originally proposed as α-helix mimetics. We describe structure-guided exploration of a cryptic "p5" pocket identified in BCL-XL. This work yields novel inhibitors with submicromolar binding, with marked selectivity toward BCL-XL. Extension into the hydrophobic p2 pocket yielded the most potent inhibitor in the series, binding strongly to BCL-XL and BCL-2 (nanomolar-range half-maximal inhibitory concentration (IC50)) and displaying mechanism-based killing in cells engineered to depend on BCL-XL for survival.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antineoplastic Agents / chemistry*
  • Antineoplastic Agents / metabolism
  • Antineoplastic Agents / pharmacology
  • Binding Sites
  • Biphenyl Compounds / chemistry
  • Biphenyl Compounds / metabolism
  • Cell Line
  • Cell Survival / drug effects
  • Crystallography, X-Ray
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Inhibitory Concentration 50
  • Mice
  • Molecular Dynamics Simulation
  • Nitrophenols / chemistry
  • Nitrophenols / metabolism
  • Piperazines / chemistry
  • Piperazines / metabolism
  • Protein Binding
  • Proto-Oncogene Proteins c-bcl-2 / antagonists & inhibitors*
  • Proto-Oncogene Proteins c-bcl-2 / genetics
  • Proto-Oncogene Proteins c-bcl-2 / metabolism
  • Structure-Activity Relationship
  • Sulfonamides / chemistry
  • Sulfonamides / metabolism
  • Surface Plasmon Resonance
  • Urea / analogs & derivatives*
  • Urea / metabolism
  • Urea / pharmacology
  • bcl-X Protein / antagonists & inhibitors*
  • bcl-X Protein / genetics
  • bcl-X Protein / metabolism

Substances

  • ABT-737
  • Antineoplastic Agents
  • Biphenyl Compounds
  • Nitrophenols
  • Piperazines
  • Proto-Oncogene Proteins c-bcl-2
  • Sulfonamides
  • bcl-X Protein
  • Urea