Simultaneous incorporations of two anticancer drugs into DNA: The structures of formaldehyde-cross-linked adducts of daunorubicin-d(CG(araC)GCG) and doxorubicin-d(CA(araC)GTG) complexes at high resolution

Anthracycline antibiotics (notably daunorubicin (DAU) and doxorubicin (DOX)) and nucleoside analog arabinosylcytosine (araC or ^aC) are important anticancer drugs. They are sometimes used together in the treatment of certain cancers. Both classes of compounds act by blocking DNA replication and transcription. To probe whether both drugs can be incorporated simultaneously into DNA and the possible structural consequences, we carried out x-ray diffraction analyses of the complexes between DAU/DOX and araC-containing DNA hexamers cross-linked with formaldehyde. The crystal structures were determined to high resolution (DAU-CG^aCGCG, 1.2 Å, space group P4₁2₁2, R = 0.182, 3275 reflections; DOX-CA^aCGTG, 1.5 Å, space group C2, R = 0.175, 3359 reflections), and they are similar to those of the previously studied DAU- and DOX-DNA complexes, despite different crystal packings. Two DAU/DOX molecules intercalate at both ends of the helix with their amino sugars in the minor groove. As in the structure of DAU-CGCGCG (Wang, A. H.-J., Gao, Y.-G., Liaw, Y.-C., and Li, Y. K. (1991) Biochemistry 30, 3812-3815), a covalent methylene bridge (from formaldehyde) between the N³′ of daunosamine and the N² of the guanine is formed in both adducts. In DOX-CA^aCGTG, the two halves are slightly different with a root-mean-square deviation of 0.322 Å between them. The O¹⁴ hydroxyls of the intercalated DOXs are within hydrogen bond distances to the O^2P atoms of the A2p(^aC3) and A8p(^aC9) steps. The O²′-hydroxyl group from araC does not affect the binding of DAU-DOX or the conformation of the drug-DNA complexes. The results suggest that three major drug modifications on DNA, i.e., intercalation, covalent bond formation, and nucleoside analog incorporation, can coexist in the same DNA molecule without difficulty. When they occur in close proximity in DNA, they may provide an additive inhibitory effect for the target enzymes.