Hybrid ligand–alkylating agents targeting telomeric G-quadruplex structures

Dipartimento di Chimica, Università di Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
Organic & Biomolecular Chemistry (Impact Factor: 3.56). 02/2012; 10(14):2798-806. DOI: 10.1039/c2ob06816h
Source: PubMed


The synthesis, physico-chemical properties and biological effects of a new class of naphthalene diimides (NDIs) capable of reversibly binding telomeric DNA and alkylate it through an electrophilic quinone methide moiety (QM), are reported. FRET and circular dichroism assays showed a marked stabilization and selectivity towards telomeric G4 DNA folded in a hybrid topology. NDI-QMs' alkylating properties revealed a good reactivity on single nucleosides and selectivity towards telomeric G4. A selected NDI was able to significantly impair the growth of melanoma cells by causing telomere dysfunction and down-regulation of telomerase expression. These findings points to our hybrid ligand-alkylating NDIs as possible tools for the development of novel targeted anticancer therapies.

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    • "[4]. The human telomere contains 5–15 kb pairs consisting of the repeat unit (TTAGGG) n [3]. These guanine-rich sequences are able to undergo conformational changes to form a higher order DNA structure, consisting of a series of planar G-tetrads, which are then stacked through π–π interactions to form a G-quadruplex [5]. "
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    ABSTRACT: Background: The human telomere contains tandem repeat of (TTAGGG) capable of forming a higher order DNA structure known as G-quadruplex. Porphyrin molecules such as TMPyP4 bind and stabilize G-quadruplex structure. Methods: Isothermal titration calorimetry (ITC), circular dichroism (CD), and mass spectroscopy (ESI/MS), were used to investigate the interactions between TMPyP4 and the Co(III), Ni(II), Cu(II), and Zn(II) complexes of TMPyP4 (e.g. Co(III)-TMPyP4) and a model human telomere G-quadruplex (hTel22) at or near physiologic ionic strength ([Na(+)] or [K(+)] ≈ 0.15 M). Results: The apo-TMPyP4, Ni(II)-TMPyP4, and Cu(II)-TMPyP4 all formed complexes having a saturation stoichiometry of 4:1, moles of ligand per mole of DNA. Binding of apo-TMPyP4, Ni(II)-TMPyP4, and Cu(II)-TMPyP4 is described by a "four-independent-sites model". The two highest-affinity sites exhibit a K in the range of 10(8) to 10(10) M(-1) with the two lower-affinity sites exhibiting a K in the range of 10(4) to 10(5) M(-1). Binding of Co(III)-TMPyP4, and Zn(II)-TMPyP4, is best described by a "two-independent-sites model" in which only the end-stacking binding mode is observed with a K in the range of 10(4) to 10(5) M(-1). Conclusions: In the case of apo-TMPyP4, Ni(II)-TMPyP4, and Cu(II)-TMPyP4, the thermodynamic signatures for the two binding modes are consistent with an "end stacking" mechanism for the higher affinity binding mode and an "intercalation" mechanism for the lower affinity binding mode. In the case of Co(III)-TMPyP4 and Zn(II)-TMPyP4, both the lower affinity for the "end-stacking" mode and the loss of the intercalative mode for forming the 2:1 complexes with hTel22 are attributed to the preferred metal coordination geometry and the presence of axial ligands. General significance: The preferred coordination geometry around the metal center strongly influences the energetics of the interactions between the metallated-TMPyP4 and the model human telomeric G-quadruplex.
    No preview · Article · Sep 2015 · Biochimica et Biophysica Acta
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    • "Nevertheless, there are several other classes of indirect telomerase inhibitors characterized by a remarkable chemical diversity, such as porphyrins, perylene diimides, fluoroquinolones, indoloquinolines , cryptolepines, quindolines, phenanthrolines, triazines, carbazole derivatives, ethidium derivatives, bisamido-anthraquinones , fluorenones, acridones and acridines [29]. Recently, a new class of naphthalene diimides (NDIs), capable of reversibly binding and subsequently alkylating telomeric DNA, has been identified [30]. Phenanthroline derivatives and pyridostatin have been used in several cell-culture studies, in which they have been demonstrated to bind within the cells and disrupt the expression of targeted DNA-quadruplex-forming sequences [31-33]. "
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    ABSTRACT: G-quadruplexes (G4) are non-canonical DNA structures assumed by guanine rich sequences. G4 are stabilized by the presence of cations and are characterized by a high degree of structural polymorphism with different patterns of groove, loop arrangement, strand orientations and stoichiometry. G-rich sequences are over-represented in the promoter regions of many oncogenes as well as at human telomeres, d(TTAGGG) repeats, ranging in size from 3 to 15 kb, involved in protecting chromosomal ends. A specialized enzyme, called telomerase, provides a telomere maintenance mechanism by elongating the end of the G-strand and it is activated in the majority of cancer cells. Therefore there are two general strategies of telomerase targeting in cancer treatment. One is a direct targeting of telomerase to cause its inhibition; the other one is the use of G4 stabilizers which block telomerase access to telomere, thus causing an indirect enzyme inhibition. Here, we evaluated the molecular recognition of some phenanthroline-based ligands against four different experimental models of the human telomeric sequence d[AG3(T2AG3)3] by means of docking simulations. Our theoretical analysis was able to reproduce the experimental affinity measurements, with a linear squared correlation factor r2 equal to 0.719 among all the studied models. These findings highlighted the importance to consider the polymorphism of the DNA G4. Interestingly, this correlation resulted always improved with respect to that of the single folds, with the exception of the parallel structure, thus suggesting a key role of this G4 conformation in the interaction network of the tested binders. Moreover, we identified the moieties of the phenanthroline scaffold directly involved in the complex formation. This allowed to rationalize the improved binding affinity always associated with a bis-phenanthroline system and to explain why a phenanthroline substituted with a pyridine ring is favored with respect to the pyrimidine one.
    Full-text · Article · Jun 2013 · Open Journal of Medicinal Chemistry
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    • "Thus, cross-linking of G-quadruplex is representing a quite promising strategy for its functional and structural study, and development of such G-quadruplex cross-linking agents have aroused wide interests. Previous reported agents were generally confined to telomeric DNAs21222324, besides telomeric sequences, other G-rich sequences are also considerably significant, such as ones in oncogenic promoter regions which have close relationship with gene expression. To best of our knowledge, G-quadruplex cross-linking agents targeting G-rich sequences in oncogenic promoter region through endogenous induction remained to be developed. "
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    ABSTRACT: Existence of G-quadruplex DNA in vivo always attract widespread interest in the field of biology and biological chemistry. We reported our findings for the existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy. Probes for selective G-quadruplex cross-linking was designed and synthesized that show high selectivity for G-quadruplex cross-linking. Further biological studies demonstrated its good inhibition activity against murine melanoma cells. To further investigate if G-quadruplex DNA was formed in vivo and as the target, a derivative was synthesized and pull-down process toward chromosome DNAs combined with circular dichroism and high throughput deep sequencing were performed. Several simulated intracellular conditions, including X. laevis oocytes, Ficoll 70 and PEG, was used to investigate the compound's pure cross-linking ability upon preformed G-quadruplex. Thus, as a potent G-quadruplex cross-linking agent, our strategy provided both valuable evidence of G-quadruplex structures in vivo and intense potential in anti-cancer therapy.
    Full-text · Article · May 2013 · Scientific Reports
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