The
antitumor drug NB-506, which is currently undergoing phase I/II clinical trials, contains
a DNA-intercalating indolocarbazole chromophore substituted with a
glucose residue. In addition to interacting with
DNA, the
drug stabilizes the
topoisomerase I-
DNA covalent complex. To reinforce the
DNA binding and anti-
topoisomerase I activities of
NB-506, an analogue containing a new substituent on the
naphthalimide ring F was synthesized. The N-formylamino group of
NB-506 has been replaced with a more hydrophilic group, N-bis(hydroxymethyl)methylamino. In this study we show that the incorporation of a longer substituent on the N6 position effectively reinforces both the interaction with
DNA and the capacity of the
drug to maintain the integrity of the
topoisomerase I-
DNA covalent complexes. The strength and the mode of binding of the drugs to
DNA were studied by complementary biophysical techniques including absorption, fluorescence, and circular and linear dichroism. Various biochemical procedures were applied to investigate the effects on human
topoisomerase I using plasmid
DNA as well as restriction fragments. The
drug binding sites and the positions of the
topoisomerase I-mediated cleavage sites were mapped with
nucleotide resolution using footprinting and sequencing techniques. Cytotoxicity measurements performed with various human
cancer cell lines (HCT-116, DLD-1, MKN-45) indicate that the newly designed
drug is 3 to 4 times more toxic to colon and
gastric cancer cells than
NB-506. Therefore, the results suggest that the antitumor activity of indolocarbazole-based drugs can be enhanced by incorporating
DNA and/or
topoisomerase I reactive groups. They also support the hypothesis that the substituent on the
imide nitrogen on the F ring of
NB-506 has direct interaction with the molecular target. The study helps to define the structure-activity relationships in the indolocarbazole series of
antitumor agents targeting
topoisomerase I.