CRYSTAL-STRUCTURE OF A COVALENT DNA DRUG ADDUCT - ANTHRAMYCIN BOUND TO C-C-A-A-C-G-T-T-G-G AND A MOLECULAR EXPLANATION OF SPECIFICITY

A 2.3-Angstrom, X-ray crystal structure analysis has been carried out on the antitumor drug anthramycin, covalently bound to a ten base pair DNA double helix of sequence C-C-A-A-C-G-T-T-G-G. One drug molecule s its within the minor groove at each end of the helix, covalently bound through its C11 position to the N2 amine of the penultimate guanine o f the chain. The stereochemical conformation is C11S, C11aS. The natur al twist of the anthramycin molecule in the C11aS conformation matches the twist of the minor groove as it winds along the helix; a C11aR dr ug would only fit into a left-handed helix. The C11S attachment is rou ghly equatorial to the overall plane of the molecule, whereas a C11R a ttachment would be axial and would obstruct the fitting of the drug in to the groove. The six-membered ring of anthramycin points toward the 3' end of the chain to which it is covalently attached or toward the e nd of the helix. The acrylamide tail attached to the five-membered rin g extends back along the minor groove toward the center of the helix, binding in a manner reminiscent of netropsin or distamycin. The drug-D NA complex is stabilized by hydrogen bonds from C9-OH, N10, and the en d of the acrylamide tail to base pair edges on the floor of the minor groove. The origin of anthramycin specificity for three successive pur ines arises not from specific hydrogen bonds but from the low twist an gles adopted by purine-purine steps in a B-DNA helix. Binding of anthr amycin induces a low twist at T-G in the T-G-G sequence of this DNA-dr ug complex, by comparison with the structure of the free DNA. The orig in of anthramycin's preference for adenines flanking the alkylated gua nine arises from a netropsin-like fitting of the acrylamide tail into the minor groove.