A small organic compound enhances the religation reaction of human topoisomerase I and identifies crucial elements for the religation mechanism.

The different steps of the human topoisomerase I catalytic cycle have been analyzed in the presence of a pentacyclic-diquinoid synthetic compound. The experiments indicate that it efficiently inhibits the cleavage step of the enzyme reaction, well fitting into the catalytic site. Surprisingly the compound, when incubated with the binary topoisomerase-DNA cleaved complex, helps the enzyme to remove itself from the cleaved DNA and close the DNA gap increasing the religation rate. The compound also induces the religation of the stalled enzyme-camptothecin-DNA ternary complex. Analysis of the molecule docked over the binary complex, together with its chemical properties, suggests that the religation enhancement is due to the presence on the compound of a couple of oxygens that act as hydrogen acceptors. This property facilitates the deprotonation of the 5' DNA end, suggesting that this is the limiting step in the topoisomerase religation mechanism.