31P NMR studies on the interaction of morpholinyl anthracyclines and related compounds with d(CGTACG)2. Thermodynamic and kinetic parameters

Abstract

3lp N]V[R spectroscopy has been used to study the intercalation of the anthracyclines doxorubicin 1, daunorubicin 2, 4-demethoxydaunorubicin 3, morpholinodoxorubicin 4, methoxymorpholinodoxorubicin 5 and 9-deoxydaunorubicin 6 with the DNA fragment d(CGTACG)2. The individual phosphate resonances of the oligonucleotide were assigned in the free as well as in the intercalated species. The 3~p chemical shitt vadations allowed us to identify the intercalation sites, which resulted to be the same for all compounds i e. between the terminal CG base-pairs of the helix (two molecules of drug per duplex). The binding coustants, the dissociation rete constants and AG ~ values have been determined in different conditions of ionic strength and temperature. The kinetic constant (ko~) of the slow step of the anthracycline/duplex intercalation process has been directly measured by NOE exchange techniques. Binding constants depend on the ionic strength and on the self-association process so greatly, that their use to study by NMR anthracycline/DNA interactions is questionable. On the contrary, the kof r are not affected by these phenomena and presentan interesting trend for 1~, thus showing that the average lifetime of the drug in the intercalation site appears to be important for determining the cytotoxicity and the antimitotic activity.

Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations

“…It is very encouraging that the minor groove binding is observed in all simulations and our second intercalative trajectory reproduces the binding site observed in both NMR [19,20] and X-ray studies [10,11]. These data combined with previous simulation data [16,[23][24][25] support the applicability of the AMBER force fields in studying DNA-drug binding.…”

“…This 3:1 base pair-drug ratio is also comparable to the experimental value (3.6:1) derived from the binding kinetics data between daunomycin and calf thymus DNA [14]. The sixth system is almost the same as the fifth system except that the DNA sequence d(CGATCG) 2 was replaced with d(CGTACG) 2 [19,20]. The minimal distance from any atom of the solute to the water box wall was set to 10Å for all six systems, leading to 2481, 2348, 2668, 2251, 7811 and 7778 water molecules for the six systems, respectively.…”

“…To probe the detailed dynamics of the intercalation process as well as to validate force fields in direct binding simulations, we constructed two unbound DNA systems with two free doxorubicin drugs using two well-studied DNA fragments [10,11,19,20] (d(CGATCG) 2 and d(CGTACG) 2 ) and conducted six independent binding simulations (three for each construct). At the end of 100 ns, all 12 drug molecules bound to DNA in three modes: end-binding, mini-groove binding and intercalation modes.…”

“…We studied two model DNA sequences (d(CGATCG) 2 and d(CGTACG) 2 ) which have been well studied by X-ray diffraction [10,11] and solution NMR method [19,20]. These experimental studies have shown that both sequences share the same binding sites at CpG sites ( Fig.…”

Structure and Stability of Human Telomeric G-Quadruplex with Preclinical 9-Amino Acridines

“…In order to better understand the specific interaction involved, we performed different NMR titration experiments. A short oligonucleotide, such as ds6, was used in previous studies with intercalating agents [40], [43], [44].…”