Mechanism- and Structure- Based Development of Small Molecule Inhibitors Against Therapeutically Important Enzymes [electronic resource].

9781088381304

Ann Arbor : ProQuest Dissertations & Theses, 2019.

1 online resource (196 p.)

Access is available to the Yale community.

This thesis describes the work that I have carried out over the course of my graduate studies in the Ellman lab in three different project areas. Chapter 1 and 2 focus on the design, synthesis and biological evaluation of small molecule inhibitors of two medicinally relevant protein targets: protein arginine deiminase 4 (PAD4) and phosphatidylinositol-5-phosphate-4-kinases (PI5P4Ks), respectively. Chapter 3 outlines the development of a GSH-responsive prodrug strategy utilizing a novel class of selenosulfide inhibitors for the inhibition of phosphatase enzymes.Chapter 1 describes an effort to develop a selective mechanism-based inhibitor of PAD4, a Ca2+-dependent enzyme that has been implicated in the pathogenesis of rheumatoid arthritis, inflammatory disorders, and cancers. Inhibitors incorporating privileged nitrogen heterocycle scaffolds were explored, resulting in an indazole-based PAD4 inhibitor with more than 10- to 2000- folds selectivity over the other PAD isozymes. This inhibitor represents the first potent and selective mechanism-based PAD4 inhibitor, and its activity has been demonstrated in a cell-based assay.Chapter 2 discusses the discovery and structure-based development of a novel inhibitor class of PI5P4Kα/β, a therapeutically relevant lipid kinase with poorly defined biological functions. A number of dihydropteridinones were prepared and resulted in the identification of a lead compound that is highly potent and selective against numerous protein kinases as well as other lipid kinases. The rest of the chapter focuses on the application of the lead inhibitor as a chemical tool to probe the roles of PI5P4Kα/β in terminally differentiated muscle cells and in p53-deficient cancer cells. Inhibition of PI5P4Kα/β by the inhibitor was found to perturb cellular energy homeostasis resulting in different responses in muscle and cancer cells. In muscle cells, the energy deficiency leads to increased glucose uptake and consumption. In proliferating p53-null cancer cells, however, the energy deficiency causes transient cell cycle arrest at the G1/S checkpoint.Chapter 3 describes the development and application of a redox-reversible selenosulfide prodrug platform for protein tyrosine phosphatase (PTP) inhibition. This strategy leverages the large difference between intracellular and extracellular GSH levels to deliver the selenosulfide inhibitors into the cells. The selenosulfide inhibitors enable selective active site directed inhibition of the targeted PTP through selenosulfide exchange with the catalytic cysteine residue of the PTP. Active site labeling was rigorously characterized by mass spectrometry methods. As a proof of concept, the selenosulfide pharmacophore was merged with previously identified phosphonic acids-based inhibitors of two therapeutically important PTP targets: the virulence factor mPTPA secreted by Mycobacterium tuberculosis and the central nervous system specific PTP implicated in Alzheimer’s disease, STEP. The lead selenosulfide inhibitors identified for each of these PTP showed potent and selective inhibition over a panel of other phosphatases and a representative cysteine protease. Additionally, the selenosulfide prodrug STEP inhibitor was active in cellular assays.

Dissertations & Theses @ Yale University.

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English

January 17, 2020

Thesis (Ph.D.)--Yale University, 2019.

Yale University. Chemistry.