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

Abstract

A 2.3-A 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 sits within the minor groove at each end of the helix, covalently bound through its C11 position to the N2 amine of the penultimate guanine of the chain. The stereochemical conformation is C11S, C11aS. The natural twist of the anthramycin molecule in the C11aS conformation matches the twist of the minor groove as it winds along the helix; a C11aR drug would only fit into a left-handed helix. The C11S attachment is roughly equatorial to the overall plane of the molecule, whereas a C11R attachment would be axial and would obstruct the fitting of the drug into 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 end of the helix. The acrylamide tail attached to the five-membered ring extends back along the minor groove toward the center of the helix, binding in a manner reminiscent of netropsin or distamycin. The drug-DNA complex is stabilized by hydrogen bonds from C9-OH, N10, and the end of the acrylamide tail to base pair edges on the floor of the minor groove. The origin of anthramycin specificity for three successive purines arises not from specific hydrogen bonds but from the low twist angles adopted by purine-purine steps in a B-DNA helix. Binding of anthramycin induces a low twist at T-G in the T-G-G sequence of this DNA-drug complex, by comparison with the structure of the free DNA. The origin of anthramycin's preference for adenines flanking the alkylated guanine arises from a netropsin-like fitting of the acrylamide tail into the minor groove.

From Anthramycin to Pyrrolobenzodiazepine (PBD)‐Containing Antibody–Drug Conjugates (ADCs)

“…Molecules with the ( R )‐stereochemistry at C11a are not isohelical with the DNA minor groove, causing them to sterically clash with the groove wall 13, 35. Examples of PBDs with the incorrect ( R )‐stereochemistry at C11a have been synthesized and, as predicted, do not possess significant DNA‐binding affinity or cytotoxicity 36.…”

Crystal structures of nucleic acids and their drug complexes

“…The complex with the decamer d(CCAACGTTG*G) has two anthramycin molecules bound per duplex 144 ( Fig. 25), with each lying in a narrowed region of the minor groove.…”

Molecular Replacement Using DNA Helical Symmetry

“…Kopka et al (1994) However, it is not immediately clear from Fig. 5 whether the single peak representing the pileup from aligned helices 6 and 7' is to be found at (v, w) = (0, ~) or at (½, ½) that is, whether the single peak occurs at the upper left and right corners of the map, or whether it is obscured by the set of fringes in the center.…”

“…These ideas were tested with the other crystalline DNA-anthramycin complex, Ant-2. This form adopts the familiar trigonal space group P3221, but with a completely different crystal packing (Kopka et aL, 1994). Double helices no longer are stacked in endless rods parallel to the ab plane.…”