Structure of daunomycin complexed to d-TGATCA by two-dimensional nuclear magnetic resonance spectroscopy (original) (raw)
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Journal of the American Chemical Society, 2012
Atomic-scale molecular dynamics and free energy calculations in explicit aqueous solvent are used to study the complex mechanism by which a molecule can intercalate between successive base pairs of the DNA double helix. We have analyzed the intercalation pathway for the anticancer drug daunomycin using two different methods: metadynamics and umbrella sampling. The resulting free energy pathways are found to be consistent with one another and point, within an equilibrium free energy context, to a three-step process. Daunomycin initially binds in the minor groove of DNA. An activated step then leads to rotation of the drug, coupled with DNA deformation that opens a wedge between the base pairs, bends DNA toward the major groove, and forms a metastable intermediate that resembles structures seen within the interfaces between DNA and minorgroove-binding proteins. Finally, crossing a small free energy barrier leads to further rotation of daunomycin and full intercalation of the drug, reestablishing stacking with the flanking base pairs and straightening the double helix.
Aromatic ring derivative molecules like daunomycin, epiadriamycin and adriamycin are anticancerous anthracycline drugs that are obtained from Streptomyces peucetius strains of bacteria through the process of fermentation.These drugs a r e e ff e c t i v e i n t h e t r e a t m e n t o f a c u t e lymphoblastic leukemia, and myelogenous leukemia. These drugs intercalate in the major groove and minor groove of various DNA sequences and inhibit the replication of DNA during the S-phase of cell cycle. The structure of these drugs consists of a planar, hydrophobic tetracycline ring structure linked to a sugar moiety with a glycosidic bond linkage. The anthracycline d e r i v a t i v e h a s f o u r f u s e d r i n g s (AD). Epiadriamycin molecule has 4' hydroxyl (OH) group inversion on the sugar moiety as compared to Adriamycin and Daunomycin molecules. There are various forces between drug-DNA complexes such as electrostatic forces, hydrogen bonds, hydrophobic effects, salt bridges, and dispersion forces. Electrostatic forces depend upon the concentration of salt solutions as the concentration increases, the electrostatic force decreases. The electrostatic forces vary where there is a presence of water and or its absence and the forces are much ABSTRACT The anticancer drugs like adriamycin,epiadriamycin and daunomycin intercalate with different sequences of DNA and provide hindrance to the replication of DNA in cancerous cells by interacting with DNA gyrase, DNA helicase and DNA topoisomerase which help in the winding and unwinding of DNA respectively. The drugs bind in the major groove and minor groove of DNA according to the base specificity of nucleotides in DNA. Various forces that help in the stabilization of drug with DNA are electrostatic forces like salt bridges, dipole forces like hydrogen bonds, entropic forces like hydrophobic effect, base stacking forces like dispersion forces. Adriamycin has a higher affinity, cooperativity and conformational stability during binding to poly(dA.dT) than epiadriamycin and daunomycin Further studies were done to study the binding of daunomycin, adriamycin, and epiadriamycin to hexanucleotide sequence d-CGATCG by absorption and fluorescence measurements and energy minimization studies were done with AMBER force field to study the hydrogen binding interactions between drug and DNA sequence. In addition to these studies,the affinity of binding of hexanucleotide sequences like d-CGATCA, and dCGTACA to drugs adriamycin, epiadriamycin and daunomycin was studied and compared with d-CGATCG sequence. Sugar moiety in drug molecules interacts more strongly with d-CGATCA than with d-CGTACA due to the formation of direct hydrogen bonds between d-CGATCA and not in altered nucleotide conformation sequence d-CGTACA. In sequence d-CGATCG interaction with drug epiadriamycin, the 4'hydroxyl group is inverted in the sugar molecule as compared to the adriamycin drug where the 4-hydroxyl group position helps in the formation of hydrogen bonds with adenine N atom in the DNA hexanucleotide sequence d-CGATCG.
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.
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.
Self-Association of the Anionic Form of the DNA-Binding Anticancer Drug Mithramycin
The Journal of Physical Chemistry B, 2008
The aqueous-phase self-association of mithramycin (MTR), an aureolic acid anticancer antibiotic, has been studied using different spectroscopic techniques such as absorption, fluorescence, circular dichroism, and 1 H nuclear magnetic resonance spectroscopy. Results from these studies indicate self-association of the anionic antibiotic at pH 8.0 over a concentration range from micromolar to millimolar. These results could be ascribed to the following steps of self-association: M + M / M 2 , M 2 + M / M 3 , and M 3 + M / M 4 , where M, M 2 , M 3 , and M 4 represent the monomer, dimer, trimer, and tetramer of mithramycin, respectively. Dynamic light scattering and isothermal titration calorimetry studies also support aggregation. In contrast, an insignificant extent of self-association is found for the neutral drug (at pH 3.5) and the [(MTR) 2 Mg 2+ ] complex (at pH 8.0). Analysis of 2D NMR spectra of 1 mM MTR suggests that the sugar moieties play a role in the self-association process. Self-association of the drug might occur either via hydrophobic interaction of the sugar residues among themselves or water-mediated hydrogen bond formation between sugar residue(s). On the other hand, absence of a significant upfield shift of the aromatic protons from 100 µM to 1 mM MTR suggests against the possibility of stacking interactions between the aromatic rings as a stabilizing force for the formation of the dimer and higher oligomers.
Biopolymers, 1990
We present the results of free energy perturbation/molecular dynamics studies on 3-DNA . daunomycin and 3-DNA . 9-aminoacridine complexes as well as on B-DNA itself in order to calculate the free energy differences between complexes having different base pair sequences. The results generally reproduce the trends observed experimentally, i.e., preferences of acridine and daunomycin to bind to a specific base sequence in the DNA. This is encouraging, given the simplicity of the molecular mechanicaI/dynamical model in which solvent is not explicitly included.