DFG‑1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity

Selectivity
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, noncanonical binding modes that
exclusively target large hydrophobic DFG-1 residues present in many
kinases including PIM, CK1, DAPK, and CLK. By use of the CLK family
as a model, structural and biochemical data revealed that the DFG-1
valine controlled a noncanonical binding mode in CLK1, providing a
rationale for selectivity over the closely related CLK3 which harbors
a smaller DFG-1 alanine. Our data suggest 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.