Development of novel DNA-binding chemotherapeutic agents based on flavonoid scaffolds of active ingredients isolated from Chinese herbal remedies

Ragazzon, Patricia; Iley, James and Missailidis, Sotiris (2004). Development of novel DNA-binding chemotherapeutic agents based on flavonoid scaffolds of active ingredients isolated from Chinese herbal remedies. In: CNIO Cancer Conference: Structural Biology of Cancer Targets, 19-22 Sep 2004, Madrid, Spain.



Herbal remedies and traditional medicines of ethnic origin have been the source of libraries of active ingredients that have found use in the development of modern medicines for a number of diseases including cancer. Such compounds have shown proven anticancer activity against various cancer cell lines according to the Developmental Therapeutics Programme of the NCI.

This project utilises a group of active ingredients isolated from Traditional Chinese herbal medicines as a scaffold (see figure below), in an attempt to devise molecules that interact with DNA selectively and can act as novel chemotherapeutic agents. The interactions of duplex genomic DNA and synthetic polynucleotides, as well as triplex and tetraplex DNA polymorphs with the unmodified compounds have been studied using different analytical techniques. This study is based on experiments including spectroscopic analysis such as UV, ethidium bromide displacement and thermal denaturation, as well as biological tests like cell viability, flow cytometry, comet assay and topoisomerase I & II assays. This battery of tests ascertained the presence of DNA binding activity for these compounds and provided an estimate of their association constants with the various forms of DNA. These were found to be in the order of 104 M-1 – 105 M-1 depending on the compound and the form of DNA, and provided information on the binding preference of the drug molecules.

Baicalein showed specificity for AT bases and especially pyrimidine triplex and tetraplex formations, and was characterized by activity against the MCF7 breast cancer cell line.

Quercetin showed interaction with tetraplex DNA, purine and pyrimidine triplexes, as well as AT – GC bases and also presented activity against the CCRFCEM leukemia cell line.

Daidzein has low specificity for GC bases, whereas baicalin, puerarin and rutin interact weakly with the various nucleic acid structures. As daidzein is considered a phytoestrogen, it promotes activity where estrogen receptors are located, as was shown by the promotion of growth in MCF7 cell line. In flavonoids, the planarity of the molecule allows the molecule to intercalate between the nucleobases. Furthermore, in the case of quercetin, the hydroxyl groups in R3, R5 and R6 seem to have a strong influence on the interaction with DNA.

Based on these results, we studied further modifications of the molecules and their effect on DNA-binding.We found substitutions on the A and B rings to be important as they increase the binding by an order of magnitude; the position of the B ring is also relevant, in C2 improves the binding, and in C3 decreases it. The absence of the C2-C3 double bond makes a distortion to the planarity of the molecule, which appears to decrease the activity. The acetoxy groups in positions 5 and 7 appear to reduce the binding values. These results, together with molecular modeling; will allow the synthesis of novel molecules that bind selectively to nucleic acids and have improved anticancer activity and pharmacological properties.

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