Development of Potent and Selective Bivalent Inhibitors for Protein Kinases Utilizing Phage Display

Abstract

Protein kinases function as key regulators in a variety of signaling pathways by executing the phosphorylation of a variety of protein substrates. Perturbation in the activity of numerous proteins kinases has been implicated in a large number of diseases including cancer, diabetes, inflammation and neurological disorders. Therefore, selective modulation of kinase activity is highly desirable for the dissection of complex signaling pathways and substantiating therapeutic targets. To develop potent and selective inhibitors for an array of kinases, our group has developed a fragment based bivalent methodology utilizing phage display. The strategy involves an ATP active site targeted small molecule which directs the selection of cyclic peptides, from a phage displayed library, on the target kinase surface through coiled coil interactions. The selected cyclic peptides can be conjugated to the ATP mimetic to generate bivalent inhibitors. In this thesis, I have expanded the scope of the bivalent phage-display selection approach. To interrogate the generality of this approach, we targeted several kinases from different groups within the human kinome using the staurosporine warhead. Fyn and PDGFRβ represented the tyrosine kinase group and CLK2 and Pim-1 kinases represented the CMGC and CaMK groups respectively. The selections against these four kinases did not result in potent inhibitors though they provided an avenue for the refinement of the bivalent phage-display approach as well as method development. Application of this methodology to AKT2 in the AGC family resulted in bivalent inhibitors which were interrogated for their selectivity and mode of action. The bivalent strategy was further explored for its utility to target inactive kinases, and success was achieved against AKT1. Finally, we demonstrated the modularity of ATP site targeted ligand by carrying out a selection against STK33 kinase using a new small molecule warhead, sunitinib. This resulted in potent and selective bivalent inhibitors for STK33. The use of different ATP site targeting molecules potentially increases the number of targetable kinases with our strategy. In all the selections, the identified cyclic peptides inhibited the kinase and showed a non-competitive mode of inhibition with respect to the kinase substrate. This suggests that the selected peptides do not target the substrate site and possibly bind to unidentified pockets on the kinase surface, which potentially provides new methods to target kinases outside the traditional ATP binding cleft. The strategy may prove to be a robust method to discover new allosteric sites on kinases as well as other proteins. The potent and selective bivalent inhibitors obtained by our strategy have the potential to provide insight towards the design of new non-ATP targeted approaches for inhibiting protein kinases and elucidating their specific functions.