Thesis advisor: Mary F. Roberts / Thesis advisor: Eranthie Weerapana / Small molecules are of interest both as metabolites in tumor cell biology and as potential therapeutics in the fight against cancer. In this work, small molecules in both roles have been examined. Modulation of tumor cell metabolism holds promise as a strategy to combat cancer, and both glucose and glutamine have been identified as critical fuels for tumor cell growth and proliferation. However, the reason for glutamine addiction is poorly understood. The differential metabolism of glutamine and glucose was therefore examined using ¹³C labeling and NMR-based metabolomics in the VM-M3 tumor cell line, which requires both glucose and glutamine for survival and proliferation. In the course of this study, a novel mammalian metabolite itaconic acid was identified. Itaconic acid was detected in extracts and tissue culture media from the murine macrophage-derived tumor cell lines VM-M3 and RAW 264.7 as well as in primary macrophages. Production and secretion of itaconic acid was increased upon stimulation. LC-MS and NMR based metabolomics studies show that this metabolite is synthesized by the decarboxylation of cis-aconitate from the TCA cycle, and provided evidence for a novel mammalian homologue of the enzyme cis-aconitic decarboxylase. D-3-deoxy diC₈PI is a small molecule of interest as a potential cancer therapeutic. This compound was designed to induce apoptosis in tumor cells by competitively binding to the Akt PH domain and preventing Akt translocation. However, high resolution ³¹P field-cycling studies show that both D-3-deoxy diC₈PI and an inactive analogue L-3,5-dideoxy diC₈PI bind to the same site on the PH domain, which is distinct from the binding site of the ligand diC₈PI(3,4,5)P₃. This makes the aforementioned mechanism of cytotoxicity unlikely. Aggregation of the PH domain in the presence of soluble headgroup IP₆ was also observed, which may be related to a physiological function of this protein and invalidates at least one other binding assay. Investigation into alterations in signaling pathways in the MCF-7 breast cancer cell line showed that D-3-deoxy diC₈PI activates the p38MAPK pathway which results in CREB hyperphosphorylation. However, activation of this pathway appears to be compensatory and unrelated to the mechanism of action. D-3-deoxy diC₈PI also decreases levels of cyclin D1 and cyclin D3, which regulate the progression of the cell cycle. These decreases appear to be occurring at the transcriptional level rather than due to increased proteasomal degradation. The loss of these two proteins does not cause apoptosis in MCF-7 cells, but siRNA knockdown of specifically cyclin D1 inhibits proliferation. This is consistent with the cell cycle arrest observed upon D-3-deoxy diC₈PI treatment in these cells. These findings do not conclusively elucidate the mechanism of cytotoxicity of D-3-deoxy diC₈PI, but provide a characterization of some of its effects in the MCF-7 cell line which may be useful for further studies. / Thesis (PhD) — Boston College, 2012. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Chemistry.