A New Type of DNA Minor-Groove Complex:  Carbazole Dication−DNA Interactions

Abstract

The effect of opportunistic infections (OI) on immune-compromised populations has been known for decades, but the recent AIDS epidemic has sparked renewed interest in the development of new anti-OI agents. The mechanism of action of a series of cationic unfused-aromatic anti-OI drugs is believed to involve binding of the drug to AT sequences in the minor groove of DNA. Some new anti-OI drug candidates have been synthesized with fused aromatic ring systems (e.g. carbazoles) that do not resemble the classical paradigm for minor-groove interactions at AT sequences in DNA. To characterize the DNA interactions of these compounds, we have used UV-vis absorbance, fluorescence, kinetic measurements, and circular dichroism in conjunction with NMR spectroscopy to evaluate the structure of the complexes formed between the carbazoles and DNA. Application of these methods to carbazoles substituted at either the 3,6 or 2,7 positions with cationic imidazoline groups gave conclusive, but very surprising, evidence that both compounds bind strongly in the minor groove at AT DNA sequences. NMR and molecular modeling of the complexes formed between the 3,6- and 2,7-carbazoles and the self-complementary oligomer d(GCGAATTCGC) have been used to establish structural details for the minor-groove complex. These results have been used as constraints for molecular modeling calculations to construct models of the minor-groove-carbazole complexes and to draw conclusions regarding the molecular basis for the effects of substituent position on carbazole-DNA affinities. The surprising result is that the 2,7 carbazole binds in AT sequences with hydrogen bonds involving one imidazoline group and the carbazole NH. The 3,6-carbazole compound binds in a more "classical" model that uses both imidazoline groups for H-bonding while the carbazole NH points out of the minor groove. The carbazoles thus form a new type of DNA minor groove complex and their excellent biological activities indicate that a variety of fused-ring minor-groove binding agents should be investigated.

Molecular Characterization of Recombinant Pneumocystis carinii Topoisomerase I: Differential Interactions with Human Topoisomerase I Poisons and Pentamidine

“…A number of additional classes of biscationic DNA binding compounds have been synthesized and found to demonstrate cytotoxicity against P. carinii in rat models of PCP. These include substituted bisbenzimidazoles linked 2,2Ј through alkyl groups (65), various derivatives of pentamidine (25,64), diarylfurans (8), and carbazoles (60). It has been suggested, on the basis of their cytotoxicity for P. carinii and their minor-groove binding properties (4,20), that some or all of these compounds act by poisoning or inhibiting topoisomerase I or II.…”

Novel linear triaryl guanidines, N-substituted guanidines and potential prodrugs as antiprotozoal agents

“…Structures with rigid frameworks of fused ring systems as linkers for the dicationic groups (e.g. carbazole, benzofuran, benzothiophene, 9H-fluorene, fluorenone, acridine and anthraquinone) were also reported as effective antimicrobial agents [22][23][24][25] and had high DNA minor groove binding affinity and postulated to involve water mediated interactions [26,27].…”

“…Previous studies from our laboratory have demonstrated that guanidine dications display considerable affinity to AT rich sites of the DNA minor groove and possess interesting antiprotozoan activity [25,[28][29][30]. In light of the previous results, we have designed and performed a study aiming at combining the novelty of a rigid rod-like terphenyl framework bearing a bisguanidine.…”

“…Since oral administration is the preferred route of administration, especially for those diseases requiring a prolonged course of treatment, then a prodrug approach is a plausible solution to circumvent the drawback of limited oral absorption. Carbamates were introduced earlier as potential prodrugs for guanidine derivatives [25,[33][34][35]. In this work a number of carbamate derivatives were prepared and evaluated as potential prodrugs for the bis-guanidine series.…”

Introduction of axial chirality in a planar aromatic ligand results in chiral recognition with DNA

“…In searching for a small molecule in which to install a chirality element, we were attracted to the numerous reports of DNA polymorphs binding with substituted carbazoles, resulting in a wide variety of biological activities including anti-protozoal (Tanious et al, 1997;Arafa et al, 2005), G-quadruplex stabilization (Huang et al, 2008), and anti-tumour and anti-infectious activities (Dias et al, 2004;Stover et al, 2009). We recognized that hydroxycarbazole 1 could be dimerized via an oxidative coupling to generate the axially chiral biaryl BICOL (Scheme 1).…”