Mutual Conformational Adaptation of Both Ligand and Receptor in Antitumor Drug-DNA Complexes

Abstract

Many antitumor/anticancer drugs bind and interact with DNA double helix to exert their biological activities. The consequence of the binding process is that both the drug and the DNA molecule change their conformations to accommodate each other to optimize the binding interactions. Two series of drug-DNA complexes associated with intercalator and minor-groove binder, with their structures derived from the high resolution x-ray diffraction analysis, are used to illustrate this concept of mutual conformational adaptation between ligand and receptor. Anthracylcine drugs, including daunomycin, adriamycin and nogalamycin, intercalate between CpG base pairs using the aglycone chromophore with its elongated direction almost perpendicular to the Cl’-Cl’ vector of the neighboring base pairs. Around the anthracycline intercalator, DNA stretches the two complementary backbones in a different manner to move the base pairs 6.8 A apart. On the one side, the dC changes the e/ζ combinatory torsion angles to ~[-100°/180°], while keeping the glycosyl χ angle near high anti range [-90°]. On the other side, all torsion angles are maintained close to those of B-DNA with the exception of the glycosyl χ angle changing to normal anti range [ca. -150°]. All sugar puckers are in the C2’- endo family. Daunomycin and adriamycin adjust the glycosyl ether linkage (between ring A and amino sugar) torsion angle such that the amino sugar fits better in the minor groove. In contrast, nogalamycin has a gentle bend in the long direction of the aglycone chromophore, bringing the aminoglucose and nogalose closer to each other. In the minor groove binding drug-DNA dodecamer complexes, there is a wide range of backbone torsion angles in the DNA molecules despite the uniform narrow minor groove width associated with the central AT sequences. Drug molecules (netropsin, distamycin and Hoechst 33258) exhibit sufficient flexibility and adjust their conformations to follow the contour surface of the right-handed B-DNA minor groove.