Study of Topoisomerase IIa inhibitors as potential anti-cancer drugs

Topoisomerase II is an essential enzyme that is required for every process that involves the opening of DNA double helix: it helps to regulate under- and overwinding and removes knots and tangle. In order to carry out its function, topoisomerase II generates transient double stranded breaks in DNA. Vertebrate species encode two types of topoisomerase II: IIα and IIβ. Topoisomerase IIα is essential for cellular proliferation and is typical of the G2/M phase. Each subunits of this homodimeric enzyme is composed of two functionally distinct domains, the ATP-binding domain and the DNA cleavage-religation domain, that require respectivley one ATP molecule and two metal ions (Mg2+). TopoII has been widely exploited as target for anti-tumor drugs. To this aim, we analyzed two classes of compounds, isatin and quinoline thiosemicarbazone derivatives, by means of the molecular docking technique, trying to understand their mechanism of action. Using the Autodock4 software package we investigated the affinity and the binding mode of these compounds in the functional sites of both domains and we compared the results with experimental data obtained in cells and on the pure enzyme in vitro. Copper complexes of both classes of compounds were also studied, which experimentally were found to have a higher inhibitory effect on tumor cells. Despite of the similarity of their chemical structure with that of ATP, the quinoline derivatives and the corresponding copper complexes did not show, in the ATP-binding site, a binding energy comparable with that of the endogenous ligand, nor a preferred position. This led us to exclude this site as competitive binding site for our compounds. For this reasons, we tried to test all the quinoline compounds in the cleavage site, taking into account the presence of a cleaved DNA fragment. The results showed that only copper complexes had good binding energy and clustered conformations, with the metal atom bound to the phosphate group of broken DNA. This suggested us a possible interference on the successive DNA ligation. In addition, we identified the two copper complexes with the greatest affinity, in close agreement with experimental results. The results obtained for isatin derivatives seem to indicate a less favoured binding energy in the cleavage site, even if they still interact with the DNA phosphate group. Docking simulations are still in progress into the ATP-binding site to compare the results.