Fragment-based Discovery of Modulators of the Aurora-A Kinase

Allosteric inhibition of kinases presents an innovative and potentially selective method of targeting these enzymes for bioactive small molecule development. Contrary to the orthosteric inhibition of highly conserved and defined binding sites, allosteric inhibitors are challenging to develop due to the shallow and flat nature of their binding pockets yet present a desirable target for medicinal chemistry. This thesis focuses on the development of allosteric Aurora-A inhibitors, exploiting standard medicinal chemistry techniques as well as implementing a development workflow that focuses exclusively on productively elaborated fragments from high-throughput microscale arrays.
Chapter 1 gives an overview of Aurora-A kinase structure and function and introduces existing small molecule inhibitors in various stages of development, including allosteric inhibitors and those targeting the Aurora-A/TPX2 protein-protein interaction. Chapter 1 also outlines modern drug discovery practices and focuses on recent methods for the high-throughput and integrated discovery and development of biologically active small molecules.
Chapter 2 describes the design and implementation of three microscale reaction arrays for the activity-directed elaboration of allosteric inhibitors of Aurora-A kinase. Two dirhodium(II) carbenoid reaction arrays were performed, totalling 504 reactions, followed by high-throughput LC-MS analysis of reaction array 1 and purification of productive reactions. The identification of improved bioactive compounds guided the design of the third reaction array, exploiting amide bond formations.Chapter 3 describes the development of a series of fragments based on known allosteric inhibitors of Aurora-A kinase through design and synthesis of a library of fragments. The SAR landscape was initially explored through generation and biological screening of a small library, which was then supplemented with an in silico docking campaign. The combined SAR and docking results were used to design further analogues of elaborated fragments for synthesis and biological screening. Overall, this medicinal chemistry strategy resulted in the expansion of the SAR for the fragment series and led to an increase in biological potency against Aurora-A kinase.