Anthracycline binding to DNA

Abstract

Crystallographic methods have been applied to determine the high-resolution structure of the complex formed between the self-complementary oligonucleotide d(TGTACA) and the anthracycline antibiotic 4-epiadriamycin. The complex crystallises in the tetragonal system, space group P4,212 with c1 = 2.802 nm and c = 5.293 nm, and an asymmetric unit consisting of a single D N A strand, one drug molecule and 34 solvent molecules. The refinement converged with an R factor of 0.17 for the 2381 reflections with F a 3oF in the resolution range 0.70-0.14 nm. Two asymmetric units associate such that a distorted B-DNA-type hexanucleotide duplex is formed incorporating two drug molecules that are intercalated at the TpG steps. The amino sugar of 4'-epiadriamycin binds in the minor groove of the duplex and displays different interactions from those observed in previously determined structures. Interactions between the hydrophilic groups of the amino sugar and the oligonucleotidc are all mediated by solvent molecules. Ultraviolet melting measurements and comparison with other anthracycline-DNA complexes suggest that these indirect interactions have a powerful stabilising effect on the complex.Nucleic acids and the proteins that interact with them are primary targets for chemotherapy (Fisher and Aristoff, 1988). The development of new antibiotics and anticancer agents is guided by knowledge of how such compounds interact with specific biochemical targets and thereby exert their influence.Anthracycline antibiotics are of particular interest as potent antitumour agents which bind to both DNA and the DNAbinding protein topoisomerase 11. It has been demonstrated that interactions with DNA are primarily responsible for the biological activity of anthracyclines (Valentini et al., 1985). Despite the fact that these antibiotics have been used clinically for the treatment of ccrtain cancers, they possess serious side effects, most notably cardiotoxicity. It is important to characterise the structures formed betwecn anthracycline antibiotics and DNA in order to understand the precise nature of the molecular intcractions. The structural information may then facilitate the rational design of improved, more selective anticancer, antibiotic or anti-viral agents.The two most-studied anthracyclines are adriamycin and daunomycin. Various methods have been used to study the interactions of these molecules with D N A (Chaires. 1990). Thesc include thooretical studies (Chen ct al., 1985, Pullman, 1987, 1991 and techniques such as DNA footprinting , Skavobogaty et al., 1988a, both of which provide evidence for preferential binding to certain DNA sequences. Of note is thc observation that thesc compounds recognise and bind to three consecutive base pairs. Rcceiitly, a series of X-ray structures have appeared which

The structure of an idarubicin–d(TGATCA) complex at high resolution

“…However, the N2--O9--N3 bonding angle is very acute (45°). It is possible, as pointed out by Leonard et al (1992), that in this geometrical arrangement only one hydrogen bond exists, i.e. between the aglycone 09 and N3.…”

“…The software for data collection and processing was provided by the Molecular Structure Corporation, Texas, USA. The unit-cell dimensions and symmetry indicated isomorphism with d(TGTACA) complexed with 4'-epiadriamycin in P4~2~2 (Leonard et al, 1992) and this structure was used as the starting model for the analysis. Before refinement commenced however, molecular replacement calculations, using the MERLOT package (Fitzgerald, 1988) were carried out on this system to check the space-group enantiomer.…”

“…Before refinement commenced however, molecular replacement calculations, using the MERLOT package (Fitzgerald, 1988) were carried out on this system to check the space-group enantiomer. The translation function was interpretable only in P4~212, so the coordinates from Leonard et al (1992) were used as the starting model. Water molecules were excluded as was the specific hydroxyl O14 and the methoxy 04 groups of the 4'-epiadriamycin chromophore and the 04' atom of the sugar moiety known to be no longer in an equatorial but in an axial position.…”

“…Recent efforts to optimize clinical usefulness whilst diminishing toxicity have led to better tolerated compounds on which attention is now focused. Several X-ray structures of these new drugs complexed with different DNA sequences have already been determined (Gao & Wang, 1991;Leonard, Brown & Hunter, 1992;Langlois d'Estaintot, Gallois, Brown & Hunter, 1992).…”

Intercalation of daunomycin into d(CG)4 oligomer duplex containing G·T mismatches by vibrational circular dichroism and infrared absorption spectroscopy

“…The best documented structures were those containing favorable binding sites. 34,[38][39][40][41] There was only one crystallographic study in which a DNA oligomer containing nonpreferred intercalation sites was examined. 49 To our knowledge there is no published investigation of daunomycin intercalation in DNA containing mismatched base pairs.…”