Saminadin et al (2000) Eur. J. Biol. - Release of the cyano moiety in the crystal structure of N‐cyanomethyl‐N‐(2‐methoxyethyl)‐daunomycin complexed with d (CGATCG) (original) (raw)

Anthracycline binding to DNA. High-resolution structure of d(TGTACA) complexed with 4'-epiadriamycin

European Journal of Biochemistry, 1992

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.

Structure of daunomycin complexed to d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy

European Journal of Medicinal Chemistry, 2006

The anthracycline antibiotic daunomycin, having four fused rings and an amino sugar, is being used in the treatment of acute leukemia. Binding to DNA is generally believed to be essential for its activity. We have studied the interaction of daunomycin with DNA hexamer sequence d-(TGATCA) 2 by titrating up to two drug molecules per duplex using nuclear magnetic resonance spectroscopy. The solution structure of 2:1 drug to DNA complex based on two dimensional nuclear Overhauser enhancement (NOE) spectroscopy and molecular dynamics calculations has been studied. The change in conformation of drug molecule on binding to DNA, deoxyribose conformation and glycosidic bond rotation has been obtained. The absence of sequential NOE connectivities at d-T1pG2 and d-C5pA6 sites shows that the drug chromophore intercalates between these two base pairs. This is substantiated by intermolecular NOEs observed between nucleotide base protons and aromatic ring protons of drug molecule. A set of 17 intermolecular NOE interactions allowed the structure to be derived by restrained molecular dynamics simulations, which have been compared with that obtained by X-ray analysis. Several specific interactions between the drug and DNA protons are found to stabilize the formation of drug-DNA complex.

Interactions of antitumor drug daunomycin with DNA in solution and at the surface

Bioelectrochemistry and Bioenergetics, 1998

The interaction of the antitumor drug daunomycin with double-stranded ds calf thymus DNA was studied in solution and at the Ž . electrode surface by means of cyclic voltammetry and particularly by constant-current chronopotentiometric stripping analysis CPSA Ž . with the carbon paste electrodes CPE . As a result of intercalation of this drug between the base pairs in dsDNA, the CPSA daunomycin peak d decreased and a new more positive shoulder d appeared. This shoulder was attributed to the oxidation of the drug intercalated in b Ž . DNA. Under the same conditions almost no changes in the DNA peak G due to oxidation of guanine residues were observed. It was ox Ž . shown that daunomycin adheres strongly to the bare CPE resisting washing so that a daunomycin-modified electrode can be easily prepared. Daunomycin immobilized at CPE interacted with DNA on immersion of the modified electrode into the dsDNA solution, Ž showing a decrease of peak d and a well-separated peak d instead of the shoulder which resulted from the interaction of DNA with b . daunomycin in solution . When the DNA-modified CPE was immersed into a daunomycin solution the peak G increased in dependence ox on daunomycin concentration or on the time of interaction of daunomycin with dsDNA at the electrode surface. Such changes in peak G ox were observed only at submicromolar concentrations of daunomycin. At higher daunomycin concentrations or at longer interaction time intervals a daunomycin peak appeared, which was substantially smaller and more positive than the peak of free daunomycin. The increase of the DNA peak G was attributed to interaction of daunomycin from the side of the DNA double helix not contacting the electrode ox surface. Such binding may induce changes in the DNA structure including bending of the DNA molecule which may result in the increase of peak G . Our results thus suggest that the interaction of daunomycin with DNA anchored at the surface may significantly differ from ox that with DNA in solution. The prospects of using of electroanalytical methods in studies of DNA-drug interactions are discussed. q 1998 Elsevier Science S.A.

Binding of saframycin A, a heterocyclic quinone anti-tumor antibiotic to DNA as revealed by the use of the antibiotic labeled with [ 14C]tyrosine or [ 14C]cyanide

Journal of Biological Chemistry

Saframycin A is an antitumor antibiotic structuraIly characterized by twin heterocyclic quinone skeletons and a-cyanoamine moiety. The binding of saframycin A to DNA was investigated using the antibiotic labeled at different positions. Heterocyclic quinone skeletons were biosynthetically labeled with [14CJtyrosine. The cyano residue of saframycin A was specifically labeled as a result of the reaction of [14C]cyanide with a derivative of saframycins, decyanosaframycin A, in the culture filtrate. When calf thymus DNA was incubated with ['4C]tyrosine-labeled saframycin A in the presence of dithiothreitol, radioactivities were progressively recovered from DNA fraction. In contrast, saframycin A in the absence of dithiothreitol was completely devoid of reactivity toward DNA. When ['4C]cyanide-labeled saframycin A was reacted with DNA, however, none of the radioactivity was associated with DNA. The release of cyano residue from the antibiotic was triggered by the reduction. Thus, conversion of quinone to hydroquinone skeletons as well as conversion of a-cyanoamine to immonium or a-carbinolamine is the consequence of the reduction. The fact that dithiothreitol-inducible binding of saframycin A to DNA was blocked by the addition of excess cyanide indicates that immonium or a-carbinolamine is the actual species involved in the interaction with DNA. The striking similarities between saframycin A and anthramycin in regard to the mode of binding to DNA are discussed.

High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA 1 1 Edited by I. Tinoco

Journal of Molecular Biology, 1997

The three-dimensional solution structure of duocarmycin SA in complex with d-(G 1 ACTAATTGAC 11 )Á d-(G 12 TCATTAGTC 22 ) has been determined by restrained molecular dynamics and relaxation matrix calculations using experimental NOE distance and torsion angle constraints derived from 1 H NMR spectroscopy. The ®nal input data consisted of a total of 858 distance and 189 dihedral angle constraints, an average of 46 constraints per residue. In the ensemble of 20 ®nal structures, there were no distance constraint violations >0.06 A Ê or torsion angle violations >0.8 . The average pairwise root mean square deviation (RMSD) over all 20 structures for the binding site region is 0.57 A Ê (average RMSD from the mean: 0.39 A Ê ). Although the DNA is very B-like, the sugar-phosphate backbone torsion angles b, e, and z are distorted from standard values in the binding site region. The structure reveals site-speci®c bonding of duocarmycin SA at the N3 position of adenine 19 in the AT-rich minor groove of the duplex and binding stabilization via hydrophobic interactions. Comparisons have been made to the structure of a closely related complex of duocarmycin A bound to an AT-rich DNA duplex. These results provide insights into critical aspects of the alkylation site selectivity and source of catalysis of the DNA alkylating agents, and the unusual stability of the resulting adducts.

DNA interactions of 2-pyrrolinodoxorubicin, a distinctively more potent daunosamine-modified analogue of doxorubicin

Biochemical Pharmacology, 2011

Please cite this article as: Stepankova J, Studenovsky M, Malina J, Kasparkova J, Liskova B, Novakova O, Ulbrich K, Brabec V, DNA interactions of 2pyrrolinodoxorubicin, a distinctively more potent daunosamine-modified analog of doxorubicin, Biochemical Pharmacology (2010),

High resolution solution structure of a DNA duplex alkylated by the antitumor agent duocarmycin SA

Journal of Molecular Biology, 1997

The three-dimensional solution structure of duocarmycin SA in complex with d-(G 1 ACTAATTGAC 11)Á d-(G 12 TCATTAGTC 22) has been determined by restrained molecular dynamics and relaxation matrix calculations using experimental NOE distance and torsion angle constraints derived from 1 H NMR spectroscopy. The ®nal input data consisted of a total of 858 distance and 189 dihedral angle constraints, an average of 46 constraints per residue. In the ensemble of 20 ®nal structures, there were no distance constraint violations >0.06 A Ê or torsion angle violations >0.8. The average pairwise root mean square deviation (RMSD) over all 20 structures for the binding site region is 0.57 A Ê (average RMSD from the mean: 0.39 A Ê). Although the DNA is very B-like, the sugar-phosphate backbone torsion angles b, e, and z are distorted from standard values in the binding site region. The structure reveals site-speci®c bonding of duocarmycin SA at the N3 position of adenine 19 in the AT-rich minor groove of the duplex and binding stabilization via hydrophobic interactions. Comparisons have been made to the structure of a closely related complex of duocarmycin A bound to an AT-rich DNA duplex. These results provide insights into critical aspects of the alkylation site selectivity and source of catalysis of the DNA alkylating agents, and the unusual stability of the resulting adducts.

Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA

Journal of Biomolecular Structure and Dynamics, 2004

Daunomycin is a widely used antibiotic of the anthracycline family. In the present study we reveal the structural properties and important intercalator-DNA interactions by means of molecular dynamics. As most of the X-ray structures of DNA-daunomycin intercalated complexes are short hexamers or octamers of DNA with two drug molecules per doublehelix we calculated a self complementary 14-mer oligodeoxyribonucleotide duplex d(CGCGCGATCGCGCG) 2 in the B-form with two putative intercalation sites at the 5´-CGA-3´ step on both strands. Consequently we are able to look at the structure of a 1:1 complex and exclude crystal packing effects normally encountered in most of the X-ray crystallographic studies conducted so far. We performed different 10 to 20 ns long molecular dynamics simulations of the uncomplexed DNA structure, the DNA-daunomycin complex and a 1:2 complex of DNA-daunomycin where the two intercalator molecules are stacked into the two opposing 5´-CGA-3´ steps. Thereby-in contrast to X-ray structures-a comparison of a complex of only one with a complex of two intercalators per doublehelix is possible. The chromophore of daunomycin is intercalated between the 5´-CG-3´ bases while the daunosamine sugar moiety is placed in the minor groove. We observe a flexibility of the dihedral angle at the glycosidic bond, leading to three different positions of the ammonium group responsible for important contacts in the minor groove. Furthermore a distinct pattern of B I and B II around the intercalation site is induced and stabilized. This indicates a transfer of changes in the DNA geometry caused by intercalation to the DNA backbone.