A comparative study of fragment screening methods on the p38α kinase: new methods, new insights

J Comput Aided Mol Des. 2011 Jul;25(7):677-87. doi: 10.1007/s10822-011-9454-9. Epub 2011 Jul 6.

Abstract

The stress-activated kinase p38α was used to evaluate a fragment-based drug discovery approach using the BioFocus fragment library. Compounds were screened by surface plasmon resonance (SPR) on a Biacore(™) T100 against p38α and two selectivity targets. A sub-set of our library was the focus of detailed follow-up analyses that included hit confirmation, affinity determination on 24 confirmed, selective hits and competition assays of these hits with respect to a known ATP binding site inhibitor. In addition, functional activity against p38α was assessed in a biochemical assay using a mobility shift platform (LC3000, Caliper LifeSciences). A selection of fragments was also evaluated using fluorescence lifetime (FLEXYTE(™)) and microscale thermophoresis (Nanotemper) technologies. A good correlation between the data for the different assays was found. Crystal structures were solved for four of the small molecules complexed to p38α. Interestingly, as determined both by X-ray analysis and SPR competition experiments, three of the complexes involved the fragment at the ATP binding site, while the fourth compound bound in a distal site that may offer potential as a novel drug target site. A first round of optimization around the remotely bound fragment has led to the identification of a series of triazole-containing compounds. This approach could form the basis for developing novel and active p38α inhibitors. More broadly, it illustrates the power of combining a range of biophysical and biochemical techniques to the discovery of fragments that facilitate the development of novel modulators of kinase and other drug targets.

Publication types

  • Comparative Study

MeSH terms

  • Binding Sites
  • Bridged Bicyclo Compounds / chemistry
  • Drug Discovery / methods*
  • Drug Evaluation, Preclinical / methods
  • Humans
  • Ligands
  • Mitogen-Activated Protein Kinase 14 / chemistry*
  • Molecular Conformation
  • Peptide Fragments / chemistry
  • Protein Binding
  • Small Molecule Libraries / chemistry*
  • Surface Plasmon Resonance / methods
  • Triazoles / chemistry*
  • X-Ray Diffraction

Substances

  • Bridged Bicyclo Compounds
  • Ligands
  • Peptide Fragments
  • Small Molecule Libraries
  • Triazoles
  • Mitogen-Activated Protein Kinase 14