The cyanomorpholino analogue of antitumor anthracycline doxorubicin possesses an intense potency and differs from the parent compound in cross-resistance and other biological properties. The induction by cyanomorpholinodoxorubicin of both DNA cross-links and strand scission suggests an altered mode of action relative to doxorubicin with a different DNA-interacting capacity. We have co-crystallized 3′-(3-cyano-4-morpholinyl)-3′-desaminodoxorubicin (CMD) with the DNA hexamer d(CGATCG) and have determined the crystal structure at 0.16-nm resolution. The complex crystallizes in the space group P4 1 2 1 2 and is similar to the previously reported anthracycline/DNA structures, with the drug intercalated at the CpG step, forming hydrogen bonds with the guanine residue. The structure reveals that the morpholino moiety has undergone a major rearrangement with loss of the cyano group and opening of the morpholino ring. The compound actually bound to DNA in the complex resembles N-(2-hydroxyethyl)doxorubicin, which was previously identified as a hydrolysis product of CMD. No DNA alkylation has been observed. However, the structure shows that the active site of the morpholino ring, after dissociation of the cyano group, lies in the minor groove in proximity of the A/T base pair. This may indicate that a C/G base pair next to the intercalation site, with NH 2 group in the minor groove, is required for DNA alkylation.Keywords : anthracycline; drug/DNA complex ; anticancer drugs design ; X-ray structure ; DNA intercalation.Anthracycline antibiotics, of which daunomycin (daunorubicin) and adriamycin (doxorubicin) are the best known members, have been widely used as antitumor drugs for over two decades, and adriamycin has been one of the most successful chemotherapeutic agents in clinical use. Since their discovery, a number of studies have suggested that the cytotoxic action of anthracyclines is related to their ability to react with cellular DNA [1]. Though there is no simple relationship between DNAbinding affinity and antitumor activity, structural specificity of these drugs was clearly noted, and it also appeared that an intercalative DNA binding is necessary for drug cytotoxicity [2]. The binding of anthracyclines to DNA has been extensively studied by a variety of biochemical and biophysical methods [3]. Crystallographic data from several three-dimensional structures of DNA-anthracycline complexes have well characterized the molecular interaction between drug and DNA and have established specific sequences as preferred sites of drug intercalation [4Ϫ8].Despite intensive investigation, the mode of action of these drugs is still to be totally understood. Currently, the widely accepted view is that the mechanism of anthracycline cytotoxicity Correspondence to G. Ughetto, Istituto di Strutturistica Chimica 'Giordano Giacomello', C.N.R., Area della Ricerca di Roma, C.P. 10, I-00016 Monterotondo Stazione, Italy Fax: ϩ39 690 672630. E-mail: alex@isc.mlib.cnr.it Abbreviation. CMD, 3′-(3-cyano-4-morpholinyl)-3′-desaminodoxorubicin...