My graduate research focuses on the development of small molecule probes or inhibitors that can be used in diverse sets of applications.In chapter 1, I present a new biochemical probe called AP3B that crosslinks and biotinylates nucleic acids. The compound was inspired by a commercially available probe but designed to have better affinity for and reactivity with DNA double helixes. I show that the new crosslinker is more efficient at crosslinking DNA in vitro. AP3B also biotinylates nucleic acids in cells better than the commercially available alternative. In chapter 2, I synthesized a new APT2 inhibitor KW5129. Our lab had previously shown APT2 to be a potential therapeutic target for treating colitis. In this work I attempted to synthesize an APT2 selective covalent inhibitor. Though was met limited success, I synthesized the non-covalent inhibitor KW5129 and show that it is nearly 9 times more potent in vitro than the compound it was inspired by, ML349. KW5129 also alleviates dextran sodium sulfate induced inflammation in mice. The Lin lab has previously synthesized the highly potent SIRT2 selective inhibitor, TM. However, TM’s utility is limited by its poor water solubility. I synthesized thioamide and thiourea derivatives of TM that have benzodiazepinedione moieties which improve the water solubility of these compounds. In chapter 3, I present the compound NH-C1-10 as our latest generation SIRT2 inhibitor. I show that NH-C1-10 is an effective SIRT2 selective inhibitor that has broad cytotoxicity in cancer cells and hinders pancreatic cancer tumor progression in mouse xenografts. In chapter 4, I present the design and synthesis of several quaternary ammonium containing protein crosslinkers that can be applied for crosslinking mass spectrometry. I identify multiple ways in which using quaternary ammoniums could overcome some of the short comings associated with the well-known crosslinker DSBSO. I show that my crosslinkers work well to both crosslink proteins and identify crosslinked peptides using mass spectrometry. Since this project is still ongoing, future directions are presented including how the crosslinkers are being applied in collaborative projects and how we aim to develop a method for removing dead end crosslinks prior to MS analysis.