Abstract
Chemical biology offers powerful tools that can be used to answer fundamental questions of both biology and chemistry. Biological systems commonly utilize chemicals in order to function properly, such as the use of adenosine triphosphate for energy. The beauty of chemical biology to study complex systems is the ability to take advantage of highly regulated and evolutionarily conserved processes developed and optimized over millions to billions of years to answer underlying questions of the system. Furthermore, chemical biology allows us to discover how these living systems interact with chemicals that are not typically found in nature. Typically, small molecule “probes” are used to capture drug-system interactions, and these probe-modified systems can be enriched from background signal to capture meaningful interactions while minimizing noise.
The drug discovery pipeline relies on billions of dollars of funding and decades of research, and more often than not, results in failure. One of the biggest challenges in drug discovery is understanding what the drug molecule interacts with in very complex living systems. Aspirin, one of the most common drugs in the world, does not have just one protein target. We still do not understand why general anesthesia works or how it functions. Yet these drugs and many more are critical to a variety of therapies. An often-cited reason for failure for a drug to receive FDA-approval and wide-spread usage is off-target toxicity, where drugs can target proteins, fats, or nucleic acids and cause more harm than good.
Chemical biology offers a solution to drug-target discovery by elucidating how complex living systems react to chemicals at a more basic level, such as alterations in the proteome, lipidome, metabolome, etc. Furthermore, chemical biology allows for direct comparison between healthy and diseased living states, which can be useful for ascribing certain cellular markers with disease. By appending a clickable handle onto a drug molecule, probe-modified proteins, lipids, etc. are now able to be enriched for and analyzed, usually by qualitative measurements, such as SDS-PAGE, or by quantitative assessments, such as mass spectrometry. This enrichment and quantitation allows for the analysis of even low-abundance proteins that may contribute to the phenotype of interest.
In chemical biology, covalent probes are often used to study drug-system interactions, as covalent bonds can often be maintained throughout cell lysis and harsh preparatory procedures. Sulfur(VI) Fluoride Exchange (SuFEx) was pioneered by Karl Barry Sharpless, among others, as a water-viable, highly tunable class of covalent chemical probes. The Hsu lab took inspiration from both SuFEx and serine-hydrolase-modifying probes – triazole urea compounds – to develop Sulfur-triazole Exchange (SuTEx) Chemistry. These ancestor probe classes were known to function in biological systems and had been previously used to characterize interactions with such systems. We rationalized that the triazole offered more tunability than a fluoride group, while maintaining an electrophilic sulfur center that proteins could covalently modify. The work presented in this dissertation centers around the study of SuTEx as a chemical probe for tyrosine and lysine residues on proteins.
