Structure-based development of anticancer drugs: Complexes of NAD(P)H : quinone oxidoreductase 1 with chemotherapeutic quinones

Background: NAD(P)H:quinone acceptor oxidoreductase (QR1) protects animal c ells from the deleterious and carcinogenic effects of quinones and other el ectrophiles. Remarkably, the same enzyme activates cancer prodrugs that bec ome cytotoxic only after two-electron reduction. QR1's ability to bioactiva te quinones and its elevated expression in many human solid tumors makes th is protein an excellent target for enzyme-directed drug development. Until now, structural analysis of the mode of binding of chemotherapeutic compoun ds to QR1 was based on model building using the structures of complexes wit h simple substrates; no structure of complexes of QR1 with chemotherapeutic prodrugs had been reported. Results: Here we report the high-resolution crystal structures of complexes of QR1 with three chemotherapeutic prodrugs: RH1, a water-soluble homolog of dimethylaziridinylbenzoquinone; EO9, an aziridinylindolequinone; and ARH 019, another aziridinylindolequinone. The structures, determined to resolut ions of 2.0 Angstrom, 2.5 Angstrom, and 1.86 Angstrom, respectively, were r efined to R values below 21 % with excellent geometry. Conclusions: The structures show that compounds can bind to QR1 in more tha n one orientation. Surprisingly, the two aziridinylindolequinones bind to t he enzyme in different orientations. The results presented here reveal two new factors that must be taken into account in the design of prodrugs targe ted for activation by QR1: the enzyme binding site is highly plastic and ch anges to accommodate binding of different substrates, and homologous drugs with different substituents may bind to QR1 in different orientations. Thes e structural insights provide important clues for the optimization of chemo therapeutic compounds that utilize this reductive bioactivation pathway.