<p>Aminoglycoside antibiotics are commonly used to treat bacterial infections but are highly susceptible to chemical modification, leading to resistance. Chemical modification can be hindered through the use of small molecule inhibitors that target bacterial enzymes involved in resistance, most notably kinases. Current methods for the discovery of small molecule inhibitors of kinases and related “kinase-like” enzymes are limited in throughput and utilize slow, tedious, and expensive assays. This thesis is focused on the development of highly versatile and scaleable kinase and “kinase-like” screening platforms for the discovery of small molecule inhibitors of these drug targets. The work begins with the validation of a matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) platform utilizing phosphorylation of kanamycin, an aminoglycoside antibiotic, by aminoglycoside phosphotransferase 3ʹIIIa (APH 3ʹIIIa) as a model system. Using a product-to-substrate signal ratio as an internal standard, the assay was used to functionally screen over 200 compounds, combined into mixtures to enhance assay throughput. Moreover, the assay was used to determine inhibitory dissocation constants for newly discovered modulators. Throughput was further increased to a novel dual-kinase assay targeting a bacterial enzyme, APH 3ʹIIIa and a human kinase, protein kinase A (PKA), which was validated using the previous small molecule library. Alternative assay development platforms were also studied using imaging mass spectrometry of reaction microarrays and the fabrication of sol-gel derived bioaffinity chromatography columns. The MS-based kinase assays developed herein are highly amenable to high throughput screening, and have the potential to be extended to other important therapeutic targets.</p> / Doctor of Philosophy (PhD)