Biophysical and Synthetic Studies of Guanine Quadruplex Binders

Cancer is a group of diseases prevalent in Canada and around the world, and depending on the type of cancer, can be associated with a high death rate. Cancer is considered a genetic disease that results from mutations to normal genes called ‘proto-oncogenes’. Mutations to these proto-oncogenes result in ‘oncogenes’, whose gene expression leads to uncontrolled cell growth and proliferation. The RET oncogene codes for a defective overactive receptor protein located on the cell membrane, which upregulates intracellular growth and proliferation pathways, leading to the progression of various cancers, especially thyroid cancer. Likewise, the c-MYC oncogene is involved with the progression of colon, breast, prostate, cervical, and lung carcinomas. Genome-based regulation of RET and c-MYC has been explored as a potential cancer therapeutic. Normally, genomic deoxyribonucleic acid (DNA) exists in the double-helical structure, but in certain cases, DNA can self-assemble into higher-order architectures called guanine quadruplexes (G4s). By folding in the region that controls gene expression (‘promoter’ region), the G4 has the ability to stall gene expression, thus expanding research has been dedicated to the development of small molecules that can stabilize G4s within the promoter regions of oncogenes. In recent years, the Petitjean Group has made an exciting discovery of a small platinum-based molecule (L) that can bind various G4s with high affinity, and exhibits high quadruplex over duplex selectivity. In the first part of this work, biophysical studies to analyze the binding affinity and stoichiometry of L to G4s are described. Specifically, results from ultraviolet-visible spectroscopy suggest tight binding of L with a telomeric G4 and a 2:1 binder to G4 stoichiometry. Analysis and fitting of fluorescence indicator displacement (FID) assay data suggests similar tight binding between L and the c-MYC-G4. These are detailed in Chapter 2. The tight binding and thus strong stabilization of G4s offered by L is highly promising for future development as an anti-cancer agent. However, a challenge that remains is to specifically target one G4 among the thousands of G4s that can fold in the genome to prevent off-target effects as a potential drug candidate. In the second part of this work, the development of small molecules that can specifically recognize and target the RET oncogene promoter G4 is described. To achieve this specificity, an aminonaphthyridine functionality was incorporated into the design of these small molecules, with the goal for the aminonaphthyridine to interact with structural features unique to the RET-G4, thus enhancing specificity for the RET-G4. Two independent synthesis pathways, the isocyanate and the di-succinimidyl carbonate (DSC) pathway were explored to synthesize dimeric and monomeric targeting molecules, respectively, which are detailed in Chapter 3.

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