High-Throughput Kinetic Analysis for Target-Directed Covalent Ligand Discovery

Angew Chem Int Ed Engl. 2018 May 4;57(19):5257-5261. doi: 10.1002/anie.201711825. Epub 2018 Mar 26.

Abstract

Cysteine-reactive small molecules are used as chemical probes of biological systems and as medicines. Identifying high-quality covalent ligands requires comprehensive kinetic analysis to distinguish selective binders from pan-reactive compounds. Quantitative irreversible tethering (qIT), a general method for screening cysteine-reactive small molecules based upon the maximization of kinetic selectivity, is described. This method was applied prospectively to discover covalent fragments that target the clinically important cell cycle regulator Cdk2. Crystal structures of the inhibitor complexes validate the approach and guide further optimization. The power of this technique is highlighted by the identification of a Cdk2-selective allosteric (type IV) kinase inhibitor whose novel mode-of-action could be exploited therapeutically.

Keywords: Cdk2; covalent inhibition; fragment-based drug discovery; kinetics; protein modification.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cyclin-Dependent Kinase 2 / antagonists & inhibitors*
  • Cyclin-Dependent Kinase 2 / metabolism
  • Cysteine / chemistry
  • Cysteine / pharmacology*
  • Drug Discovery*
  • High-Throughput Screening Assays*
  • Kinetics
  • Ligands*
  • Molecular Structure
  • Protein Kinase Inhibitors / analysis
  • Protein Kinase Inhibitors / chemical synthesis
  • Protein Kinase Inhibitors / pharmacology*
  • Small Molecule Libraries / analysis
  • Small Molecule Libraries / chemical synthesis
  • Small Molecule Libraries / pharmacology*

Substances

  • Ligands
  • Protein Kinase Inhibitors
  • Small Molecule Libraries
  • CDK2 protein, human
  • Cyclin-Dependent Kinase 2
  • Cysteine