Dual Src/Abl inhibitor SKI-606 binding mode in BCR-ABL kinase hypothesized on the basis of molecular docking studies

Background SKI-606 is a novel 4-anilino-3-quinolinecarbonitrile Src and Abl kinase inhibitor. SKI-606 has been shown to be a potent antiproliferative and proapoptotic agent when tested on Bcr-Abl-positive cell lines. The remarkable efficacy of SKI-606 against chronic myeloid leukemia (CML) cells in culture was mirrored by its activity in vivo against CML xenografts: K562 tumors regressed in nude mice when SKI-606 was administered per os once daily over a 5-day period. The crystal structure of the Bcr-Abl kinase domain in complex with SKI-606 has not yet been determined and the mode of binding of this inhibitor is therefore unknown. Moreover, there are currently no published data on the ability of SKI-606 to bind and efficiently inhibit the Bcr-Abl mutants known to confer resistance to imatinib. Aims In this study, we used a molecular docking approach to a) determine SKI-606 binding mode to the wild-type (wt) form of the Bcr-Abl kinase; b) hypothesize SKI-606 binding mode to the more frequent, clinically relevant Bcr-Abl mutants known not to be inhibited by imatinib; c) predict which novel mutant forms might emerge and interfere with SKI-606 binding. Methods Modelling of the human Abl kinase was performed with the program Modeller v7.7 (http://salilab.org/modeller) adopting the highly related Mus musculus Abl homologue as a template structure (PDB: 1OPJ, 0.175nm resolution). Chemsketch (http://www.acdlabs.com) was used to build a three-dimensional model of SKI-606. Flexible docking of the ligand to the protein was performed with Autodock v3.0 (http://www.scripps.edu/mb/olson). Results We first docked SKI-606 on Bcr-Abl with the activation loop in the active (open) and inactive (closed) conformation (the latter is the one to which imatinib binds). According to our results, the interaction between SKI-606 and Bcr-Abl seems to be more stable when the activation loop is in the inactive conformation. The consequent structural study of SKI-606 modeled into wt-Bcr-Abl ATP binding site highlighted the variant residues located within a spherical environment of 0.5nm centered on SKI-606: Y253, T315 and F359 (residues numbered according to ABL exon Ia splice variant). The binding of SKI-606 to the eight Bcr-Abl mutants which are most frequently implicated in clinical resistance to imatinib mesylate was also studied: G250E, Y253H, E255K, T315I, M351T, F359V, H396R. Our results indicated that SKI-606 retains the ability of efficiently binding all the above mentioned Bcr-Abl variants with the exception of the T315I mutant. Finally, we identified six potential residues around SKI-606 that, if mutated, could potentially be able to interfere with the SKI-606/Bcr-Abl interaction: a) the charged residues K271, D381 and H361; b) the hydrophobic/aliphatic residues V299, A380 and M318. Conclusions Pre-clinical data suggest that SKI-606 is a promising second-generation kinase inhibitor with potent antiproliferative and proapoptotic effects on CML cells. Our docking experiments indicate that SKI-606 may prove effective in imatinib-resistant patients since it is expected to retain the ability to bind several Bcr-Abl mutant forms. A phase I trial is about to start in CML and Philadelphia-positive acute lymphoblastic leukemia.