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Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We chose CDK2 as a model system to study the DFG in-out transition on a target that was thought to have an inaccessible DFG-out conformation. We used site-directed mutagenesis of key residues identified in structural comparisons in conjunction with biochemical and biophysical characterization of the generated mutants. As a result, we identified key residues that facilitate the DFG-out movement, facilitating binding of type II inhibitors. However, surprisingly, we also found that wild type CDK2 is able to bind type II inhibitors. Using protein crystallography structural analysis of the CDK2 complex with an aminopyrimidine-phenyl urea inhibitor (K03861) revealed a canonical type II binding mode and the first available type II inhibitor CDK2 cocrystal structure. We found that the identified type II inhibitors compete with binding of activating cyclins. In addition, analysis of the binding kinetics of the identified inhibitors revealed slow off-rates. The study highlights the importance of residues that may be distant to the ATP binding pocket in modulating the energetics of the DFG-out transition and hence inhibitor binding. The presented data also provide the foundation for a new class of slow off-rate cyclin-competitive CDK2 inhibitors targeting the inactive DFG-out state of this important kinase target.

Original publication

DOI

10.1021/acschembio.5b00398

Type

Journal article

Journal

ACS Chem Biol

Publication Date

18/09/2015

Volume

10

Pages

2116 - 2125

Keywords

Adenosine Triphosphate, Amino Acid Sequence, Binding Sites, Cyclin-Dependent Kinase 2, Cyclins, Drug Design, Humans, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Protein Binding, Protein Conformation, Protein Interaction Domains and Motifs, Protein Kinase Inhibitors