Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling.

The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.

Novel isoxazole polycyclic aromatic hydrocarbons as DNA-intercalating agents.

The third generation of isoxazole polycyclic aromatic hydrocarbons, acting as DNA-intercalator agents and possessing the binding constants in the range 10(4)-10(5) M(-1), in order to easily diffuse targeting remotely implanted tumors, has been synthesized in good yields according to the 1,3-dipolar cycloaddition methodology. The structure of the obtained cycloadducts has been determined by NOE experiments and supported by computational studies at PM3 level. All the obtained compounds have been tested for their in vitro cytotoxic activity and the most potent of them, (3RS,5SR)-2-benzyl-N,N-dimethyl-3-(pyren-1-yl)isoxazolidine-5-carboxamide (7d), showed an IC(50) of 4 µM upon the human lung cancer (A-549) cells. Moreover, compound 7d showed binding constant for the intercalation with calf thymus DNA, poly-d(AT)(2) and poly-d(GC)(2) of 1.7 × 10(5) M(-1), 1.6 × 10(5) M(-1) and 0.3 × 10(5) M(-1), respectively. Biological and docking studies showed that, in vitro, these compounds complex by intercalation between base pairs, approaching the DNA from its minor groove with a preference for the AT nucleobases pairs.