Conformational Selectivity of ITK Inhibitors: Insights from Molecular Dynamics Simulations

Interleukin-2-inducible
T-cell kinase (ITK) regulates
the response
to T-cell receptor signaling and is a drug target for inflammatory
and immunological diseases. Molecules that bind preferentially to
the active form of ITK have low selectivity between kinases, whereas
those that bind preferentially to the inactive form have high selectivity
for ITK. Therefore, computational methods to predict the conformational
selectivity of compounds are required to design highly selective ITK
inhibitors. In this study, we performed absolute binding free-energy
perturbation (ABFEP) simulations for 11 compounds on both active and
inactive forms of ITK, and the calculated binding free energies were
compared with experimental data. The conformational selectivity of
10 of the 11 compounds was correctly predicted using ABFEP. To investigate
the mechanism underlying the stabilization of the active and inactive
structures by the compounds, we performed extensive, conventional
molecular dynamics simulations, which revealed that the compound-induced
stabilization of the P-loop and linkage of conformational changes
in L489, V419, F501, and M410 upon compound binding were critical
factors. A guideline for designing inactive-form binders is proposed
based on these key structural factors. The ABFEP and the created guidelines
are expected to facilitate the discovery of highly selective ITK inhibitors.