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Novel Ligands Targeting the DNA/RNA Hybrid and Telomeric Quadruplex as Potential Anticancer Agents

Student thesis: Doctoral ThesisDoctor of Philosophy

Telomeres are repetitive sequences of DNA at the ends of chromosomes that become progressively shorter during cell division, acting as a form of “biological clock” causing cell death once they have reached a certain length. Almost 90% of cancer cells overexpress the enzyme telomerase which can lengthen telomeres and confer immortality to the tumour cells. Thus, telomerase has become an important target for drug discovery in the oncology area, and there is also interest from researchers investigating the aging process. During the catalytic cycle of telomerase, a unique DNA/RNA hybrid duplex (DRH) forms that is typically between 6-11 base pairs long and is key to extending the telomere. There is interest in discovering small drug-like molecules that can recognize and bind to this hybrid duplex to inhibit selectively telomerase, either by stabilizing the structure and thereby preventing telomerase dissociation (a key step in the catalytic cycle) or by sufficiently distorting the hybrid duplex to cause the misalignment of key catalytic groups. This project began by using oligonucleotides representing DNA/RNA hybrid duplex (DRH), telomeric G-quadruplex and control duplex DNA sequences to screen against the National Cancer Institute compound libraries (i.e., Diversity Set II, Mechanistic Set and Natural Product Set) using a high throughput Fluorescent Resonance Energy Transfer (FRET)-based DNA thermal denaturation assay to determine binding affinity and specificity. Thirteen novel chemical scaffold families were identified in the assay, compounds which showed a >5 °C selective stabilization of the DNA/RNA hybrid duplex at a 1 μM ligand concentration. Chemical modifications were then made to these scaffolds to generate focused libraries of analogues to improve selectivity, potency and drug-likeness, and to provide Structure-Activity Relationship (SAR) information. A total of 49 novel molecules were synthesized and then screened against an expanded range of four different nucleic acid constructs including telomeric and DNA/RNA hybrid duplex sequences. A number of compounds showed selective DNA/RNA hybrid stabilization potential with some compounds also showing notable telomeric G-quadruplex stabilization without significant affinity for promoter G-quadruplexes (i.e., c-Kit1, c-Kit-2 and c-Myc) and control duplex DNA sequences. The compounds from library-1 provided DNA/RNA hybrid duplex stabilization in the 0.5-7.2 C range and telomeric G-quadruplex stabilization in the 0.2-6.5 C range at a 1 μM ligand concentration. Molecular modelling and molecular dynamics studies confirmed that the methylene spacer between the benzimidazole and phenylene moieties of molecules within library-1 is perfectly shaped to fit within the DRH sequence. In addition, it was confirmed that minor-groove binding and simultaneous intercalation between the nucleobases of a DNA/RNA hybrid duplex requires a linker of specific length (i.e., an eight methylene spacer as in compound 3.3). Selected compounds were then studied further using a variety of biological techniques to confirm selective telomerase inhibition and cell-based assays to utilize their potential as antitumour agents.
Original languageEnglish
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Award date2016

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