DFG-1 residue controls inhibitor binding mode and affinity providing a basis for rational design of kinase inhibitor selectivity

Abstract

ABSTRACTSelectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, non-canonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK and CLK. Using the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a non-canonical binding mode in CLK1, providing a rational for selectivity over the closely-related CLK3 which harbors a smaller DFG-1 alanine. Our data suggests that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.Competing Interest StatementThe authors have declared no competing interest.ABBREVIATIONSCLKCdc2 like kinasePIMProviral insertion in murine kinaseACVR1Activin receptor type IDAPKdeath-associated protein kinaseDYRKdual specificity tyrosine-phosphorylation-regulated kinasesDRAKDAP kinase-related apoptosis-inducing protein kinasesCKcasein kinaseRETProto-oncogene tyrosine-protein kinase receptor RetCDK2Cyclin-dependent kinase 2DFG motiftripeptide Asp-Phe-Gly motifVIAK motifvaline-isoleucine-alanine-lysine motif.View Full Text