Modeling and Biological Investigations of an Unusual Behavior of Novel Synthesized Acridine- Based Polyamine Ligands in the Binding of Double Helix and G-Quadruplex DNA

Three novel 2,7-substituted acridine derivatives were designed and synthesized in order to investigate the effect of this functionalization on their interaction with double stranded and G-quadruplex DNA. A detailed investigation on their binding ability towards both investigated DNA foldings were carried out by means of spectrophotometric, electrophoretic, and computational approaches. The ligands in this study are characterized by an open-chain (L1) or a macrocyclic (L2, L3) framework. The aliphatic amine groups in the macrocycles are joined by ethylenic (L2) or propylenic chains (L3). L1 behaved comparably to the lead compound m-AMSA, efficiently intercalating into ds-DNA but stabilizing G-quadruplex structures poorly, probably due to the modest stabilization effect exerted by its protonated polyamine chains. L2 and L3, containing small polyamine macrocyclic frameworks, are known to adopt a rather bent and rigid conformation, and thus they generally are expected to be sterically impeded to recognize ds-DNA according to an intercalative binding mode. This was confirmed to be true for L3. Nevertheless, we showed that L2 can give rise to efficient π-π and H-bonding interactions with ds-DNA. Additionally, stacking interactions allowed L2 to stabilize theG-quadruplex structure: using the human telomeric sequence, we observed the preferential induction of tetrameric G-quadruplex forms. Thus, the presence of short ethylenic chains seems to be essential for obtaining a correct match between the binding sites of L2 and the nucleobases on both the investigated DNA foldings. Furthermore, current modelling methodologies, including docking and MD simulations and free energy calculations, provide evidence, from a structural point of view, of a different interaction mode of L2 as compared to L3, which could give some clue as to explain the unusual stabilizing ability (L2>L3>L1) of the ligands towards ds-DNA and G-quadruplex that was observed in this study.