title: Targeting DNA with novel diphenylcarbazoles.
abstract: Double-stranded DNA is a therapeutic target for a variety of anticancer and antimicrobial drugs. Noncovalent interactions of small molecules with DNA usually occur via intercalation of planar compounds between adjacent base pairs or minor-groove recognition by extended crescent-shaped ligands. However, the dynamic and flexibility of the DNA platform provide a variety of conformations that can be targeted by structurally diverse compounds. Here, we propose a novel DNA-binding template for construction of new therapeutic candidates. Four bisphenylcarbazole derivatives, derived from the combined molecular architectures of known antitumor bisphenylbenzimidazoles and anti-infectious dicationic carbazoles, have been designed, and their interaction with DNA has been studied by a combination of biochemical and biophysical methods. The substitutions of the bisphenylcarbazole core with two terminal dimethylaminoalkoxy side chains strongly promote the interaction with DNA, to prevent the heat denaturation of the double helix. The deletion or the replacement of the dimethylamino-terminal groups with hydroxyl groups strongly decreased DNA interaction, and the addition of a third cationic side chain on the carbazole nitrogen reinforced the affinity of the compound for DNA. Although the bi- and tridentate molecules both derive from well-characterized DNA minor-groove binders, the analysis of their binding mode by means of circular and linear dichroism methods suggests that these compounds form intercalation complexes with DNA. Negative-reduced dichroism signals were recorded in the presence of natural DNA and synthetic AT and GC polynucleotides. The intercalation hypothesis was validated by unwinding experiments using topoisomerase I. Prominent gel shifts were observed with the di- and trisubstituted bisphenylcarbazoles but not with the uncharged analogues. These observations, together with the documented stacking properties of such molecules (components for liquid crystals), prompted us to investigate their binding to the human telomeric DNA sequence by means of biosensor surface plasmon resonance. Under conditions favorable to G4 formation, the title compounds showed only a modest interaction with the telomeric quadruplex sequence, comparable to that measured with a double-stranded oligonucleotide. Their sequence preference was explored by DNase I footprinting experiments from which we identified a composite set of binding sequences comprising short AT stretches and a few other mixed AT/GC blocks with no special AT character. The variety of the binding sequences possibly reflects the coexistence of distinct positioning of the chromophore in the intercalation sites. The bisphenylcarbazole unit represents an original pharmacophore for DNA recognition. Its branched structure, with two or three arms suitable to introduce a structural diversity, provides an interesting scaffold to built molecules susceptible to discriminate between the different conformations of nucleic acids.
authors.affiliation: INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, 59045 Lille, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Dias
authors.forename: Ulrich
authors.initials: U
authors.lastname: Jacquemard
authors.forename: Brigitte
authors.initials: B
authors.lastname: Baldeyrou
authors.forename: Christelle
authors.initials: C
authors.lastname: Tardy
authors.forename: Amélie
authors.initials: A
authors.lastname: Lansiaux
authors.forename: Pierre
authors.initials: P
authors.lastname: Colson
authors.forename: Farial
authors.initials: F
authors.lastname: Tanious
authors.forename: W David
authors.initials: WD
authors.lastname: Wilson
authors.forename: Sylvain
authors.initials: S
authors.lastname: Routier
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Mérour
authors.forename: Christian
authors.initials: C
authors.lastname: Bailly
mesh_terms: D001483:Base Sequence; D002227:Carbazoles / Q000138:chemical synthesis / Q000633:toxicity*; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry*; D026942:DNA Topoisomerases / Q000737:chemistry; D003850:Deoxyribonuclease I; D016503:Drug Delivery Systems / Q000379:methods*; D006576:Heterocyclic Compounds, 4 or More Rings / Q000138:chemical synthesis / Q000633:toxicity*; D006358:Hot Temperature; D006801:Humans; D007364:Intercalating Agents / Q000633:toxicity*; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D011067:Poly dA-dT / Q000737:chemistry; D011089:Polydeoxyribonucleotides / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet; D020349:Surface Plasmon Resonance
chemical_list: D002227:Carbazoles; D006576:Heterocyclic Compounds, 4 or More Rings; D007364:Intercalating Agents; D011089:Polydeoxyribonucleotides; D011067:Poly dA-dT; C019530:poly(dC-dG); D004247:DNA; D003850:Deoxyribonuclease I; D026942:DNA Topoisomerases