Antitumor Activity, X-ray Crystal Structure, and DNA Binding Properties of Thiocoraline A, a Natural Bisintercalating Thiodepsipeptide

Abstract

The marine natural product thiocoraline A displayed approximately equal cytotoxic activity at nanomolar concentrations in a panel of 12 human cancer cell lines. X-ray diffraction analyses of orthorhombic crystals of this DNA-binding drug revealed arrays of docked pairs of staple-shaped molecules in which one pendent hydroxyquinoline chromophore from each cysteine-rich molecule appears intercalated between the two chromophores of a facing molecule. This arrangement is in contrast to the proposed mode of binding to DNA that shows the two drug chromophores clamping two stacked base pairs, in agreement with the nearest-neighbor exclusion principle. Proof of DNA sequence recognition was obtained from both classical DNase I footprinting experiments and determination of the melting temperatures of several custom-designed fluorescently labeled oligonucleotides. A rationale for the DNA-binding behavior was gained when models of thiocoraline clamping a central step embedded in several octanucleotides were built and studied by means of unrestrained molecular dynamics simulations in aqueous solution.

Relevance of the Fanconi anemia pathway in the response of human cells to trabectedin

“…1B as well as the more recently characterized AGA triplet for which only one hydrogen bond is possible (34,35). The consistently high increment in melting temperature of dsDNA (average DT m z 20jC) was at least 2-fold greater than that brought about by a tight-binding bisintercalating agent such as echinomycin or thiocoraline (23) and was essentially identical after 15 min or 24 h of incubation in the whole range of drug/DNA ratios studied (1:10 to 1:1). The extra DNA stabilization was very similar for all the duplexes that embedded one of the preferred binding sequences in the central triplet irrespective of the number of hydrogen bonds (Fig.…”

“…The raw data recovered from the instrument for each plate consisted of an array of FAM fluorescence values for each of the 96 wells at each temperature. A complete analysis was then carried out using an in-house Visual Basic Application running on Microsoft Excel (23).…”

“…The thermal stability of different duplex oligodeoxynucleotides, each containing a unique binding site for trabectedin in the central region, was assessed by means of a previously reported method based on molecular beacons (23). These duplexes encompass the two-hydrogenbond-compliant purine-G-C and pyrimidine-G-G combinations shown in Fig.…”

“…Because of the reported structural characteristics of trabectedin-DNA adducts (2) we decided to investigate the extent to which a single drug molecule is able to stabilize dsDNA using a highly sensitive fluorescence-based melting assay (23). Increases in the thermal stability of the double helix suggested that trabectedin might mimic the cellular effects induced by ICL drugs.…”

Myoblast Cell Interaction with Polydopamine Coated Liposomes

“…(Fig. 7b), suggesting that the presence of PDA and the used coating thickness did not significantly hinder the activity and release of TC, a compound which acts by unwinding negatively supercoiled double-stranded DNA and binding to DNA by bisintercalation [32].…”