Importantly, motesanib also inhibited the activity of an activation loop mutant (Y823D) associated with imatinib resistance. Imatinib did not inhibit this mutant at concentrations of up to 3000 nM, suggesting that there are marked differences in how the two inhibitors interact with Kit. We previously solved the structure of motesanib bound to the

VEGFR2 kinase domain at 2.2 Å resolution (PDB Accession Code 3EFL) [19]. This structure superimposes favorably with that of Kit co-crystallized with imatinib (PDB Accession LEE011 chemical structure Code 1T46) [20]. Both inhibitors bind the inactive, auto-inhibited form of the kinases with the backbone of the protein reorganized into the so-called “”DFG-out”" conformation. Based on the structural similarities and the similar

potencies of motesanib against VEGFR2 and Kit, we reasoned that motesanib binds these target kinases in exactly the same fashion. Modeling studies suggest that motesanib engages Kit via three polar interactions and a multitude of van der Waals contacts (Figure RAD001 order 5). In the context of this study, the most important of these interactions are those with threonine 670 via a non-classical CH-O pseudo hydrogen bond and interactions with valine 654 through hydrophobic contacts. The fifteen-fold loss of motesanib activity (5 nM versus 77 nM) noted with the V560D/V654A double mutant, compared with V560 D alone, is rationalized by the loss of two van der Waals contacts with alanine 654 in a similar fashion to that described for imatinib [21, 22]. Figure 5 A model of motesanib bound to the active site of Kit kinase derived from a 2.2 Ångstrom resolution crystal structure of motesanib bound to the active site of VEGFR2 kinase (PDB code 2EFL). Motesanib and imatinib have much diminished activity against the activation loop mutant (D816V). The D816V mutant destabilizes the inactivated form of Kit, in a way that the ability for of the protein to adopt the “”DFG out”"

(inactive) conformation is much reduced or even eliminated; thus, the mutation prevents both motesanib and imatinib from binding to the ATP pocket [23, 24]. The failure to potently inhibit the D816V mutation is a feature of Kit inhibitors in the clinic, with the exception for dasatinib [23, 25, 26], which binds the “”DFG in”", or activated form, of the kinase [27]. However, the ability of motesanib to inhibit the Y823 D mutant suggests that its activity may not be entirely restricted to an inactive protein conformation, or alternatively it may reflect that in contrast to the D816V mutation, the conformational equilibrium of the Y823 D mutant is not shifted permanently to the active conformation. The data from the present study are of translational relevance, supporting evidence indicating that targeted therapy Regorafenib mw molecules with different binding sites and/or mode of action may be required in the treatment of cancers for which mutations are the primary oncogenic event.