Fragment-based hit discovery and characterization of the RNA-related protein UHMK1 (U2AF Homology motif kinase 1)

Abstract

Fragment-based Hit Discovery (FBHD) is a new and effective tool for the discovery of lead molecules both in industry and academia and is responsible for the development of several FDA-approved drugs. Its strategy of screening libraries of very small molecules allows for covering a vast chemical space with fewer compounds, which permits an accelerated and cheaper method for drug design when compared to traditional high throughput methods. In parallel, it is important to add crystallography as an approach to co-crystalize the hits with the target protein and thus learn how the spatial organization can allow chemical expansion of fragments. Here, we're employing Weak-affinity Chromatography coupled to Mass Spectrometer (WAC-MS), an emergent tool for FBHD, where proteins of interest are purified in the lab and bound to a stationary phase in a column. Next, many small molecules are eluted through the phase according to its weak binding. WAC-MS allows the identification of kinetics of chemical groups at low concentrations while maintaining high sensitivity and low ligand consumption. It is, then, an ideal method to screen hits for understudied targets, in our case RNA-regulating proteins, as U2AF homology motif kinase 1 (UHMK1). UHMK1 is a protein with a unique combination of a kinase domain and an RNA recognition motif (RRM) and is related to cell cycle progression, division and migration, and also RNA splicing and local translation. Its expression is upregulated in many types of cancer and although this data links UHMK1 to the cancer process, molecular details to mechanistically explain its role in cancer and are lacking. Exploring the UHMK1 ligands and better understanding the UHMK1 structure may be a new therapeutic strategy for targeting the spliceosome. This study and experimental approach will be expanded to other protein kinases.