The binding orientation of a norindenoisoquinoline in the topoisomerase I-DNA cleavage complex is primarily governed by π-π stacking interactions

High level ab initio quantum chemical studies have shown that the binding orientations of topoisomerase I (top1) inhibitors such as camptothecins and indenoisoquinolines are primarily governed by pi-pi stacking. However, a recently discovered norindenoisoquinoline antitumor compound was observed by X-ray crystallography to adopt a "flipped" orientation (relative to indenoisoquinolines), which facilitates the formation of a characteristic hydrogen bond with the Arg364 of top1 in its binding with the top I-DNA complex. This observation raises the possibility that hydrogen bonding between the norindenoisoquinoline nitrogen and the Arg364 side chain of top1 might be responsible for the "flip". It also brings into question whether pi-pi, stacking, as opposed to hydrogen bonding, is primarily responsible for the binding orientations of indenoisoquinolines and norindenoisoquinolines. In this study, the forces responsible for the binding orientation of a norindenoisoquinoline in the DNA cleavage site were systematically investigated using MP2 methods. The theoretical calculation of the preferred binding orientation based solely on pi-pi stacking was completely consistent with the actual orientation observed by X-ray crystallography, indicating that the binding of the norindenoisoquinoline in the top1-DNA complex is mainly governed by pi-pi stacking forces and that the "flip" can occur independently from hydrogen bonding.