Advancements in the Preparation of Pyrrole/Imidazole Polyamides and their Application in Gene Knockdown

摘要

Pyrrole/imidazole polyamides are a class of molecules that bind to double-stranded DNA with nanomolar binding affinity, enabling the disruption of transcription factor binding to their target DNA sequence. Polyamides have previously demonstrated the ability to regulate gene expression in vitro and in vivo through inhibition of transcription factor binding. One of the major limitations of polyamide research is the lack of streamlined access to libraries of these compounds.\udThis thesis describes optimized synthetic routes for the preparation of hairpin polyamides. Efforts were made to improve access to monomer units, in addition to the development of a set of standard solid-phase polyamide synthesis conditions, which allowed consistent preparation of hairpin polyamides in high yields and purity. Further to this, a novel fragment-based convergent synthesis has been established to afford hairpin polyamides with crude purities of 85-92%, and with a 3-fold increase in isolated yields compared to existing approaches.\udPolyamides were prepared to bind to DNA sequences located within the transcription factor binding sites in the promoter region of the human ApoB gene, a protein known to be causative of cardiovascular disease. In cellulo analysis of these polyamides using HepG2 cells revealed their localization within the nucleus, a prerequisite for successful pre-transcriptional regulation. It was also discovered that targeting the C/EBP and HNF4 transcription factor binding sites with DNA-binding polyamides resulted in toxicity before concentrations were sufficient for down-regulation of the ApoB gene.\udPolyamides have also been designed to inhibit FUR protein/DNA interactions in the staphylococcus aureus pathogen, with the aim to disrupt homeostasis. Initial results have concluded the tight binding of these polyamides, and biological studies are in progress to validate this as a viable therapeutic avenue.