Development of Amonafide-Squaramide Conjugates as Efficient DNA Intercalators to Induce DNA Damage and Eventual Anti-cancer Activity

Abstract

Artificially synthesized small molecules that can target double-stranded DNA in living cells and induce cell death form an important part of anti-cancer and anti-tumour therapeutics. In this project, we have successfully synthesized a library of small molecule-based Amonafide-squaramide conjugates 1a-1e, which can serve as efficient DNA intercalators. The compounds were characterized through NMR as well as through their signature photophysical properties in various solvents. Absorbance- based titration with plasmid DNA revealed the binding affinity of all the compounds towards DNA duplex, with 1e showing the highest affinity. Fluorometric titration assay against an EtBr-DNA complex demonstrated the ability of our final compounds to displace EtBr from the complex, proving their intercalative nature. Here, also 1e showed the highest efficiency of EtBr displacement. Gel-based electrophoresis was done to confirm DNA binding and demonstrate the formation of a new DNA-compound complex. Finally, molecular docking was performed with all final derivatives to theoretically prove the formation of an intercalation complex with double-stranded DNA and our compounds, wherein the highest binding affinity of 1e was established further, along with the mode of binding and the π-π interactions and hydrogen bonding of 1e with elements along the DNA backbone.