Interactions of flavones and related compounds with nucleic acids.

This project focused on a group of active ingredients isolated from herbal medicines, most of them flavonoids, as a foundation for the development of new anticancer drugs. Interactions between these compounds and genomic DNA, synthetic polynucleotides, or higher order DNA isoforms (triple and quadruple helical forms) have been studied using a range of physicochemical and biological techniques. The studies demonstrated that flavonoids and isoflavonoids bind to the various nucleic acid forms with weak or moderate affinities and no significant specificity, apart from quercetin that demonstrated a differential binding for G-quadruplex structures. Rational drug design has been subsequently employed to elucidate the mode of binding and novel compounds have been synthesized in order to provide precise structure-activity related studies and result in a second generation of chemotherapeutic anticancer agents with improved properties. Interaction with DNA is thought to involve the planar ring structures. The double bond of the O in C4 in a flavone scaffold gives planarity to the molecule, and this allows the molecule to intercalate between the bases in the different nucleic acid structures. The comparison between flavone, flavanone and isoflavonoid indicates that the position of the B ring and the double bond in the C ring are important for the interactions with DNA. Introduction of nitrogen in the ring did not improve the binding but tertiary amines improved binding 100 fold. Introduction of sulfur produced two binding constants. Position 7 in the A ring of the flavones is extremely relevant for the binding to the nucleic acids, but substitutions in the B ring did not improve the binding. Methoxylation or acetoxylation in positions 5 and 7 decreased the affinity for DNA. Novel compounds were tested for their specificity against different DNA isoforms and their anticancer activity in various tumour cell lines

Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform

Virtual Screening is an increasingly attractive way to discover new small molecules with potential medicinal value. We introduce a novel strategy that integrates use of the molecular docking software Surflex with experimental validation by the method of competition dialysis. This integrated approach was used to identify ligands that selectively bind to the triplex DNA poly(dA)-[poly(dT)]2. A library containing ∼2 million ligands was virtually screened to identify compounds with chemical and structural similarity to a known triplex intercalator, the napthylquinoline MHQ-12. Further molecular docking studies using compounds with high structural similarity resulted in two compounds that were then demonstrated by competition dialysis to have a superior affinity and selectivity for the triplex nucleic acid than MHQ-12. One of the compounds has a different chemical backbone than MHQ-12, which demonstrates the ability of this strategy to ‘scaffold hop’ and to identify small molecules with novel binding properties. Biophysical characterization of these compounds by circular dichroism and thermal denaturation studies confirmed their binding mode and selectivity. These studies provide a proof-of-principle for our integrated screening strategy, and suggest that this platform may be extended to discover new compounds that target therapeutically relevant nucleic acid morphologies

Microwave assisted synthesis of novel bis-flavone dimers as new anticancer agents

In this study we describe a microwave based click chemistry method used to prepare a family of novel bis-flavone dimers. The substituted 7-hydroxy and 4’-hydroxy flavonoids were linked through a triazole ring. The compounds were easily synthesized and purified in high yields. The bis-flavonoids were tested on different cell lines including HCT116, HepG2, MCF7 and MOLT-4. Several analogues showed to have anticancer activity with IC50 values in the range of 20-60 µM. Flavonoids are known for their anticancer properties and this method provides the basis for new medicinal structures

A 2-step synthesis of Combretastatin A-4 and derivatives as potent tubulin assembly inhibitors

A series of combretastatin derivatives were designed and synthesised by a two-step stereoselective synthesis by use of Wittig olefination followed by Suzuki cross-coupling. Interestingly, all new compounds (2a-2i) showed potent cell-based antiproliferative activities in nanomolar concentrations. Among the compounds, 2a, 2b and 2e were the most active across three cancer cell lines. In addition, these compounds inhibited the polymerisation of tubulin in vitro more efficiently than CA-4. They caused cell cycle arrest in G2/M phase further confirming their ability to inhibit tubulin polymerisation

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

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

Structure-activity studies of the binding of the flavonoid scaffold to DNA

Background: Flavonoids have been shown to have a wide variety of biological activities and proven to be good scaffolds for the design of DNA-binding agents as anticancer therapeutics. Materials and Methods: In structure-activity relationship studies, flavonoid derivatives were designed and synthesised through various organic synthesis protocols, resulting in novel or previously described molecules. These were studied by UV-Vis absorbance and fluorescence spectroscopy as well as competition dialysis for their binding to DNA isoforms. Their cytotoxic potential was assessed using MTS assays on MCF-7 breast cancer and CCRFCEM leukaemia cell lines. Results and Conclusion: Introduction of moieties such as chloride, nitrogen, acetoxy and methoxy groups did not help to improve binding affinity, but introduction of tertiary amines improved the binding 1,000-fold due to an improved interaction of the compound with the nucleic acid; replacement of oxygen by sulphur increased the binding 7-fold, possibly because sulphur being less electronegative than oxygen would allow the electrons of the molecule to interact more strongly with the nucleic acid. Inhibition of growth by 50% (IG50) values were moderate in breast and leukaemia cancer cell lines possibly due to the flavonoids interacting with other cellular components besides the nucleic acids

The characterisation of flavone-DNA isoform interactions as a basis for anticancer drug development

Background: The interactions of small molecules with nucleic acids are of considerable interest for the design of novel anticancer compounds. The physical properties and sequence specificity observed in the interactions between a group of flavonoids with proven antitumour activity and various nucleic acid structures are summarised. Materials and Methods: UV and fluorescence spectroscopy, together with competition dialysis, were used to assess the affinity of the drugs for the nucleic acid structures in the presence or absence of different metal ions. The effect of these compounds on breast and leukaemia cancer cell lines was evaluated using MTS and COMET assays and flow cytometry. Results and Conclusion: The flavonoids studied are weak duplex DNA-binding ligands and the binding of flavonoids to DNA is affected by metal ions. Baicalein and quercetin display stronger affinity for triplex and quadruplex than for double-stranded DNA and offer interesting scaffolds for the design of novel, high order DNA-binding agents

Tetraplex DNA specific ligands based on the fluorenone-carboxamide scaffold

A series of fluorenone-carboxamide compounds was analyzed with regard to DNA binding properties by UV spectroscopy and competition dialysis methods. The morpholino derivative 10 provided interesting results in terms of affinity and specificity toward the DNA G-tetraplex structures. Interactions against this target were evaluated by a comparative molecular modeling study in agreement with the experimental data, proposing a model for the rational design of new agents with potent and selective DNA tetraplex binding properties