In all living organisms,
protein kinases regulate various cell
signaling events through phosphorylation. The phosphorylation occurs
upon transferring an ATP’s terminal phosphate to a target residue.
Because of the central role of protein kinases in several proliferative
pathways, point mutations occurring within the kinase’s ATP-binding
site can lead to a constitutively active enzyme, and ultimately, to
cancer. A select set of these point mutations can also make the enzyme
drug resistant toward the available kinase inhibitors. Because of
technical and economical limitations, rapid experimental exploration
of the impact of these mutations remains to be a challenge. This underscores
the importance of kinase–ligand binding affinity prediction
tools that are poised to measure the efficacy of inhibitors in the
presence of kinase mutations. To this end, here, we compare the performances
of six web-based scoring tools (DSX-ONLINE, KDEEP, HADDOCK2.2, PDBePISA,
Pose&Rank, and PRODIGY-LIG) in assessing the impact of kinase
mutations on their interactions with their inhibitors. This assessment
is carried out on a new structure-based BINDKIN benchmark we compiled.
BINDKIN contains wild-type and mutant structure pairs of kinase–inhibitor
complexes, together with their corresponding experimental binding
affinities (in the form of IC50, K
d, and K
i). The performance of
various web servers over BINDKIN shows that they cannot predict the
binding affinities (ΔGs) of wild-type and mutant
cases directly. Still, they could catch whether a mutation improves
or worsens the ligand binding (ΔΔGs)
where the highest Pearson’s R correlation
coefficient is reached by DSX-ONLINE over the K
i dataset. When homology models are used instead of K
i-associated crystal structures, DSX-ONLINE
loses its predictive capacity. These results highlight that there
is room to improve the available scoring functions to estimate the
impact of protein kinase point mutations on inhibitor binding. The
BINDKIN benchmark with all related results is freely accessible online
().