Abstract
The action of the DNA repair enzyme alkyladenine DNA glycosylase (AAG), as part of the Base Excision Repair pathway, on alkylation-induced DNA damage has been shown in mice to lead to cell death in the retina, spleen, thymus and cerebellum. The action of AAG has also been linked to damage caused by ischaemia/reperfusion (I/R) events in liver, brain and kidney. As a result, small molecule inhibitors of AAG are required for ongoing studies into the biological mechanism of this cellular damage, as well as to become potential drug leads for some types of retinal degeneration, I/R-related tissue damage, or as protective agents for patients undergoing alkylative chemotherapy and showing an increased AAG activity. They could also serve the opposite effect, acting as an alkylating agent (TMZ) sensitiser in paediatric glioblastoma (GBM). Two DNA oligomers, containing etheno-cytidine or an abasic pyrrolidine, are reported in the literature to show potent AAG inhibition in vitro. Unfortunately, their size and the charged nature of DNA chains makes them unsuitable for use as potential drug leads in vivo, as they would show low membrane permeability and face degradation by nucleases. However, the motifs present in these oligomers, together with examination of the enzyme active site, led to the conception of two types of small drug-like pyrrolidine-based inhibitor candidates termed 2-(hydroxymethyl)pyrrolidines and 4-(hydroxymethyl)pyrrolidines. The synthetic routes to these inhibitor candidates have been studied and optimised. That to the 2-(hydroxymethyl)pyrrolidines failed at the final step of attachment of DNA base-mimicking aryl groups. However, five 4-(hydroxymethyl)pyrrolidines nucleoside mimetics were successfully synthesised, bearing imidazole and pyridine groups to represent a DNA base. These were subsequently tested in vitro against AAG in a surface-bound hairpin loop colorimetric DNA oligomer assay. The most promising candidate, (+)-395, showed an IC50 of 157 µM corresponding to a ligand efficiency of 0.37 kcal·mol-1·heavy atom-1. Due to its low molecular weight (197 g·mol-1), this inhibitor constitutes a viable starting point for a future lead optimisation programme.