Fragment-based ligand design of novel potent inhibitors of tankyrases

J Med Chem. 2013 Jun 13;56(11):4497-508. doi: 10.1021/jm400211f. Epub 2013 Jun 4.

Abstract

Tankyrases constitute potential drug targets for cancer and myelin-degrading diseases. We have applied a structure- and biophysics-driven fragment-based ligand design strategy to discover a novel family of potent inhibitors for human tankyrases. Biophysical screening based on a thermal shift assay identified highly efficient fragments binding in the nicotinamide-binding site, a local hot spot for fragment binding. Evolution of the fragment hit 4-methyl-1,2-dihydroquinolin-2-one (2) along its 7-vector yields dramatic affinity improvements in the first cycle of expansion. A crystal structure of 7-(2-fluorophenyl)-4-methylquinolin-2(1H)-one (11) reveals that the nonplanar compound extends with its fluorine atom into a pocket, which coincides with a region of the active site where structural differences are seen between tankyrases and other poly(ADP-ribose) polymerase (PARP) family members. A further cycle of optimization yielded compounds with affinities and IC50 values in the low nanomolar range and with good solubility, PARP selectivity, and ligand efficiency.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Databases, Factual
  • Drug Stability
  • Humans
  • Ligands
  • Models, Molecular
  • Molecular Structure
  • Protein Binding
  • Quinolines / chemical synthesis*
  • Quinolines / chemistry
  • Solubility
  • Structure-Activity Relationship
  • Tankyrases / antagonists & inhibitors*
  • Tankyrases / chemistry
  • Thermodynamics

Substances

  • Ligands
  • Quinolines
  • TNKS2 protein, human
  • Tankyrases

Associated data

  • PDB/3W5I
  • PDB/41UE
  • PDB/4J21
  • PDB/4J22
  • PDB/4J3L
  • PDB/4J3M
  • PDB/4JIZ