Discovery of a Covalent Kinase Inhibitor from a DNA-Encoded Small-Molecule Library × Protein Library Selection

J Am Chem Soc. 2017 Aug 2;139(30):10192-10195. doi: 10.1021/jacs.7b04880. Epub 2017 Jul 20.

Abstract

We previously reported interaction determination using unpurified proteins (IDUP), a method to selectively amplify DNA sequences encoding ligand:target pairs from a mixture of DNA-linked small molecules and unpurified protein targets in cell lysates. In this study, we applied IDUP to libraries of DNA-encoded bioactive compounds and DNA-tagged human kinases to identify ligand:protein binding partners out of 32 096 possible combinations in a single solution-phase library × library experiment. The results recapitulated known small molecule:protein interactions and also revealed that ethacrynic acid is a novel ligand and inhibitor of MAP2K6 kinase. Ethacrynic acid inhibits MAP2K6 in part through alkylation of a nonconserved cysteine residue. This work validates the ability of IDUP to discover ligands for proteins of biomedical relevance.

Publication types

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

MeSH terms

  • DNA / chemistry*
  • Drug Discovery*
  • Humans
  • Ligands
  • MAP Kinase Kinase 6 / antagonists & inhibitors*
  • MAP Kinase Kinase 6 / metabolism
  • Molecular Structure
  • Peptide Library
  • Protein Kinase Inhibitors / chemistry
  • Protein Kinase Inhibitors / pharmacology*
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology*
  • Structure-Activity Relationship

Substances

  • Ligands
  • Peptide Library
  • Protein Kinase Inhibitors
  • Small Molecule Libraries
  • DNA
  • MAP Kinase Kinase 6
  • MAP2K6 protein, human