Probing the functions of NEK family kinases

Protein kinases are central to cellular signaling pathways, using ATP as a common substrate to phosphorylate downstream substrate proteins. There are over 500 human protein kinases which, broadly speaking, are specific for either tyrosine or serine/threonine residues. Inhibitors of protein kinases are important tools for dissecting signaling pathways, and are of growing importance in the treatment of disease. Most current kinase inhibitors target the ATP binding site, which is highly druggable, but also highly conserved and so these inhibitors are liable to inhibit more than one human kinase.
The development of highly specific inhibitors is particularly challenging for kinases that belong to families consisting of many highly related members, such as the NEK (Never in Mitosis A-related kinase) family, which comprises 11 members in humans. NEK kinases function in cell division, cilia and DNA repair pathways and these processes involve more than one family member. For example, NEK6, NEK7 and NEK9 mediate mitotic spindle assembly and specific chemical probes that target individual family members are required to dissect their individual functions. Due to conserved features in the active site of NEKs, highly potent and selective inhibitors of individual members of this family have not been discovered.

This proposal aims to develop inhibitors that target NEK family kinases through their ATP binding site or an allosteric site. Kinase inhibitors that act outside the ATP binding pocket, at sites that are less well
conserved, have the potential to be more selective. There are growing efforts to generate allosteric inhibitors of kinases, especially those of therapeutic relevance, but these ideas have not been applied to the NEK family. Here we intend to exploit new approaches to fragment optimization developed in the Nelson group and, for the first time, combine this with high-throughput
crystallography.
The Bayliss group in collaboration with LifeArc recently probed an allosteric pocket on Aurora-A kinase using nanobody- and fragment-based approaches. Structural and biochemical studies
revealed the mechanism of action of these inhibitors, and show that an equivalent pocket is present in NEK family kinases. Crucially, the amino acids that line these pockets are less well
conserved than the ATP binding pockets. Our intention is to create a workflow in which expensive chemistry resources are used sparingly by taking fragment hits forward into new screens that generate diverse sets of related compounds that can themselves be screened. By iterating the synthesis and screening steps, we believe that the compounds will rapidly converge on potent inhibitors.
The project student will integrate biophysical, computational and synthetic approaches to develop ATP-competitive and allosteric NEK inhibitors with clearly defined specificity profiles.