High-Field NMR and Restrained Molecular Modeling Studies on a DNA Heteroduplex Containing a Modified Apurinic Abasic Site in the Form of Covalently Linked 9-Aminoellipticine

Abstract

Two-dimensional NMR methods were used to model the possible solution structure of an intercalative complex of 9-aminoellipticine (Aell), a polycyclic pyridocarbazolamine, covalently bound to an apurinic ring-opened deoxyribose site of a duplex DNA fragment in the reduced Schiff base form. The required oligonucleotide single strand containing covalently attached aminoellipticine was obtained by reductive amination in the presence of sodium cyanoborohydride. The combined NMR-energy minimization methods were employed to refine the model structures of two distinct forms, intrahelical and extrahelical, of a control 9-mer duplex DNA, d(CGTG.dr.GTGC).d(GCACTCACG), which contains an apurinic site positioned opposite a dT residue on the complementary strand. The model structure of an aminoellipticine conjugate with the same DNA sequence, derivatized via the aforementioned covalent attachment, was also obtained by incorporating intermolecular drug-DNA and intra- and internucleotide NOE-derived proton-proton distance estimates as restraints in energy minimization routines. The indole ring system of aminoellipticine, which is inserted at the apurinic site, intercalates between and is parallel to flanking GC base pairs. The pyridinic ring of aminoellipticine, in protonated form, also stacks between cytidine and thymidine bases on the complementary strand, which is consistent with the observation that the normal sequential NOE connectivity at the 5'-C13-T14 step is broken and indeed diverted through the ellipticine moiety, e.g., C13-Aell-T14 connectivities through the Aell-H4/C5Me protons. Interestingly, the partial stacking of the pyridinic ring is observed only between the 5'-CT step vs an adjacent 5'-TC step, owing to inherently weak stacking interactions associated with the former. In the absence of any potential groups that can participate in electrostatic or hydrogen-bonding interactions with the nucleic acid, pi-pi stacking and hydrophobic contacts at the intercalation site appear to be the important factors in determining stability and conformation of the aminoellipticine-DNA conjugate. Stacking interactions in such a bistranded intercalative complexation of aminoellipticine apparently govern the formation of a single intrahelical form of a right-handed B-type DNA duplex. The overall structural features lead us to propose working models for an enzyme-like DNA cleavage activity of 9-aminoellipticine and the observed inhibition of the AP endonuclease-dependent DNA excision-repair pathway.

The mechanism of cytotoxicity and DNA adduct formation by the anticancer drug ellipticine in human neuroblastoma cells

“…Chemotherapy-induced cell cycle arrest was shown to result from DNA damages caused by a variety of chemotherapeutics. In the case of ellipticine, it was suggested that the prevalent DNA-mediated mechanisms of their antitumor, mutagenic and cytotoxic activities are (i) intercalation into DNA [4,13], and (ii) inhibition of DNA topoisomerase II activity [4,[14][15][16].…”

Molecular Mechanisms of Antineoplastic Action of an Anticancer Drug Ellipticine

“…Furthermore, the polycyclic aromatic character of the molecule may, moreover, result in tight interactions with appropriately conformed hydrophobic regions in DNA. Interactions between the methyl groups of the drug and the thymine bases at the intercalation site appear important in determining the orientational preferences of the drug [11][12] . The mechanism of ellipticine action as the inhibitor of topoisomerase II has also been extensively studied [13][14][15] .…”

The Anticancer Drug Ellipticine Is a Potent Inducer of Rat Cytochromes P450 1A1 and 1A2, Thereby Modulating Its Own Metabolism

“…It was suggested that the prevalent mechanisms of their antitumor, mutagenic, and cytotoxic activities are 1) intercalation into DNA (Auclair, 1987;Singh et al, 1994), and 2) inhibition of DNA topoisomerase II activity (Auclair, 1987;Fossé et al, 1992;Froelich-Ammon et al, 1995). Ellipticine and its metabolite 9-hydroxyellipticine also cause selective inhibition of p53 protein phosphorylation in several human cancer cell lines (Sugikawa et al, 1999), and this correlates with their cytotoxic activity.…”