A proton-NMR study of the DNA binding characteristics of thioformyldistamycin, an amide isosteric lexitropsin

Abstract

The interaction of thioformyldistamycin, an amide isostere of the naturally occurring antibiotic distamycin A, with a self-complementary decadeoxynucleotide duplex, d(CGCAATTGCG)2, has been examined using a variety of high-field 1H-NMR techniques. The ligand exhibits two forms in solution arising from geometric isomerism due to restricted rotation around the thioformamide bond. Only the thermodynamically more stable Z-form is shown to bind to the oligonucleotide along its minor groove at the central 5'-AATT segment with the end groups of the ligand extending into the flanking GC regions but without any close contact at the amidinium terminus. Cross-peaks involving characteristic intra- and interresidue proton connectivities in the 2D experiments (COSY and NOESY) were employed to assign individual resonances of both strands in the asymmetric DNA-drug complex. The solution structure of the complex was constructed by molecular mechanics calculations based upon initial estimates of drug-DNA NOE contacts and further refined through energy minimization. These results complement previous structural studies on distamycin and other lexitropsins with oligonucleotides. The exchange of the ligand between two equivalent binding sites on the DNA sequence was estimated to occur at 40 s-1 with a free energy of activation of 16.5 kcal.mol-1 at 321-326 K. There was no evidence of formation of a 2:1 drug-oligomer complex, in contrast to the case of the natural product, which is attributed to steric demands of the larger sulfur atom.

Solution structure of a highly stable DNA duplex conjugated to a minor groove binder

“…The minor groove binding drugs netropsin (22), distamycin (23) and their structural analogs (24)(25) have been reported to bind isohelically into the AT-rich minor groove of the DNA double helix, owing to their crescent-shaped structure. These molecules have planar N-pyrrole moieties and fit edge-on into the minor groove, replacing the spine of hydration and follow the natural curvature of the DNA.…”

Crystal Structure of the DNA Decamer d(CGCAATTGCG) Complexed with the Minor Groove Binding Drug Netropsin

“…A number of studies of ligands bound to the decamer d(CGCAATTGCG) have been undertaken using NMR spectroscopy. Lexitropsins form 1:1 complexes with the decamer (Singh et al, 1992;Kumar et al, 1991), as does Hoechst 33258 (Kumar et al, 1992), by noncovalent binding within the minor groove of the DNA duplex. In addition to (Fregeau et al, 1995).…”

A Crystallographic and Spectroscopic Study of the Complex between d(CGCGAATTCGCG)2 and 2,5-Bis(4-guanylphenyl)furan, an Analogue of Berenil. Structural Origins of Enhanced DNA-Binding Affinity

“…As the number of complexes between DNA and minor groove binding ligands that have been solved by X-ray crystallography (Kopka et al, 1985;Coll et al, 1989;Brown et al, 1990Brown et al, , 1992Gao et al, 1993;Tabernero et al, 1993;Nunn et al, 1994;Goodsell et al, 1995) and NMR (Klevit et al, 1986;Patel & Shapiro, 1986;Lee et al, 1988;Pelton & Wemmer, 1989;Kumar et al, 1990Kumar et al, , 1991Parkinson et al, 1990;Searle & Embrey, 1990;Fede et al, 1991;Singh et al, 1992;Jenkins et al, 1993;Sriram et al, 1994) increases, it is becoming possible to identify structural considerations that govern observed patterns of sequence selectivity and affinity. Some of these factors are relatively self-evident, such as the requirement for overall shape complementarity between the ligand and the minor groove surface (isohelicity) (Goodsell & Dickerson, 1986) and for complementarity in hydrogen-bonding and electrostatic characteristics (Zakrzewska et al, 1987) between the ligand and a DNA binding site.…”