Amide Isosteres of Lexitropsins: Synthesis, DNA Binding Characteristics and Sequence Selectivity of Thioformyldistamycin

Abstract

The synthesis and properties of an amide isostere of the antibiotic distamycin, thioformyldistamycin 3 is described. Compound 3 exists predominantly in the E conformation of the thioamide group in freshly prepared DMSO solution but is converted into the Z form, predicted by molecular mechanics to be more stable, on standing for 24 h. The coalescence temperature in DMSO is 110 degrees C by 1H-NMR. The thioformyl moiety of 3 is resistant to both peptidase action and acid treatment. Complementary strand MPE footprinting on a EcoRI/Hind III restriction fragment of pBR322 DNA demonstrated that either E or Z forms of 3 give a single set of footprints very similar to that of the parent antibiotic with strongest protection at TAAG and TATTAT with moderately strong protection at ATTT and AAAA. The strength of binding of 3 and distamycin from delta Tm measurements to either poly.d(AT) or calf thymus DNA is comparable. Molecular modeling predicted a preferred conformation for 3 wherein the C = S bond has a torsional angle of 110 degrees with the pyrrole ring. The energy difference between this conformation and the E form is less than 1 kcal/mole. In contrast the E-form has an energy 17.3 kcal/mole greater than the Z and a value of 26.3 kcal/mole was calculated for the energy barrier between the two isomers.

Biological activity and DNA Sequence Specificity of Synthetic Carbamoyl Analogues of Distamycin

“…In common with distamycin and other minor groove binders, the lack of binding of the drugs to GC-containing sequences in DNA can be attributed to steric clashes with the guanine exocyclic 2-amino group projecting into the minor groove of DNA. The footprinting data are fully consistent with previous studies showing that the terminal forrnamido group can be replaced with other entities such as a thioformyl group (Zimmermann et al, 1991;Singh et al, 1992) without markedly affecting the capacity of the ligand to recognize preferentially AT-rich sequences in DNA. Early studies on distamycin analogues showed that an increase in the number of N-methylpyrrolecarboxamide residues generally correlates with an increase in the affinity of the drug for DNA as well as its antiviral activity (Zimmer et al, 1972;Chandra et al, 1972;Kotler & Becker, 1972).…”

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

“…Thioformyldistamycin, being a flexible ligand, assumes a slightly twisted conformation to curve along the DNA helix and thereby achieves a snug fit. The conformation of the thioformyl end of the ligand is only slightly different from the energy-minimized conformation of the free ligand itself (Zimmermann et al, 1991). In this arrangement the amide groups of the ligand are in close proximity to several potential hydrogen-bond acceptor sites in the DNA strands.…”

“…One key issue concerning the biological potency, however, pertains to the stability of such peptidic ligands toward hydrolytic and/or enzymatic degradation. In order to circumvent this problem, we recently reported the synthesis and peptidase stability of an analog of distamycin A, obtained by replacing the formyl end group by a thioformyl group (Zimmermann et al 1991). This report is an extension of that study and provides detailed information on the DNA binding characteristics of thioformyldistamycin, elucidated from its interaction with a synthetic decadeoxynucleotide d(CGCAATTGCG)2.…”

“…An important extension of these efforts with particular relevance to their biological potency is to overcome the inherent susceptibility of the terminal amide groups in these amido ligands toward cellular degradation. To this end, we recently reported on an isosteric thioamide surrogate of distamycin A, which shows DNA binding footprints similar to that of the parent molecule and is stable toward add and enzymatic hydrolysis (Zimmermann et al, 1991). We now report the details of the high-field -NMR study of interactions between thioformyldistamytin and a synthetic decadeoxynucleotide sequence.…”

Solution Structure Studies of the Cobalt Complex of a Bleomycin Functional Model Bound to d(CGCAATTGCG)2 by Two-Dimensional Nuclear Magnetic Resonance Methods and Restrained Molecular Dynamics Simulation

“…In order to gain insight into the interaction of bleomycin with DNA, we have designed and synthesized a series of functional model compounds (36)(37)(38)(39) of bleomycin through conjugation of the simplified metal-chelating subunit AMPHIS (40,41) [methyl [[[2-(2-aminoethyl)amino]methyl]pyridinyl]-6-carboxylhistidinate] with oligo(N-methylpyrrole) lexitropsin (26,(42)(43)(44)(45) residues which are recognized as sequence-selective DNA minor groove binding moieties (46)(47)(48). It has been assumed, but hitherto has not been proven, that metal ions are coordinated at the AMPHIS site and that the oligo(Nmethylpyrrole) moiety of the AMPHIS-lexitropsin hybrid would provide DNA affinity and sequence selectivity, directing the metal binding moiety to sites differing from those of bleomycin.…”