Pharmacophore-based 3D-QSAR as a predictive method for the QSAR analysis on a series of potent and selective inhibitors for three kinases of RTK family

For targets belonging to the same family of receptors, inhibitors often act at more than one biological target and produce a synergistic effect. Separate pharmacophore-based comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were developed from our data-set for the kinase insert domain-containing receptor (KDR), cKit and Flt1 inhibitors. These models showed excellent internal predictability and consistency; validation using test-set compounds yielded a good predictive power for the pIC50-value. The field contour maps (CoMFA and CoMSIA) corresponding to the KDR, cKit and Flt1 kinase subtypes reflected the characteristic similarities and differences between these types. These maps provided valuable information to facilitate structural modifications of the inhibitor to increase selectivity of the KDR over cKit and Flt1.