Calories from carbohydrates: energetic contribution of the carbohydrate moiety of rebeccamycin to DNA binding and the effect of its orientation on topoisomerase I inhibition

Background: Only a few antitumor drugs inhibit the DNA breakage-reunion rea ction catalyzed by topoisomerase. One is the camptothecin derivative topote can that has recently been used clinically. Others are the glycosylated ant ibiotic rebeccamycin and its synthetic analog NB-506, which is presently in phase I of clinical trials. Unlike the camptothecins, rebeccamycin-type co mpounds bind to DNA. We set out to elucidate the molecular basis of their i nteraction with duplex DNA, with particular emphasis on the role of the car bohydrate residue. Results: We compared the DNA-binding and topoisomerase-I-inhibition activit ies of two isomers of rebeccamycin that contain a galactose residue attache d to the indolocarbazole chromophore via an alpha (axial) or a beta (equato rial) glycosidic linkage. The modification of the stereochemistry of the ch romophore-sugar linkage results in a marked change of the DNA-binding and t opoisomerase I poisoning activities. The inverted configuration at the C-1' of the carbohydrate residue abolishes intercalative binding of the drug to DNA thereby drastically reducing the binding affinity. Consequently, the a lpha isomer has lost the capacity to induce topoisomerase-I-mediated cleava ge of DNA. Comparison with the aglycone allowed us to determine the energet ic contribution of the sugar residue. Conclusions: The optimal interaction of rebeccamycin analogs with DNA is co ntrolled to a large extent by the stereochemistry of the sugar residue. The results clarify the role of carbohydrates in stereospecific drug-DNA inter actions and provide valuable information for the rational design of new reb eccamycin-type antitumor agents.