Molecular Recognition of Duplex and Quadruplex DNA by Small Molecules and Its Application for Developing New Anticancer Therapies

Ismail Abdel Karim El Haty


Human telomeres are the end caps of the linear chromosomes and consist of a double stranded DNA and a short single stranded overhang. The later consists of tandem repeats of DNA bases enriched in guanine. Under physiological conditions, telomere can fold up into four stranded intramolecular structure called G-quadruplex in which guanines are connected by Hoogsteen hydrogen bonding. Formation of G-quadruplex was found associated with inhibition of the telomerase enzyme found active in cancer cells. Since telomerase is responsible for elongation of telomeric DNA and subsequently replications of cells, G-quadruplex has become an active target for the development of telomerase inhibitors. Thus, small molecules interact and stabilize G-quadruplex are potential anticancer therapeutic agents. In This dissertation, thymoquinone (TQ), N4-(1-Benzyl-1H-indazol-5-yl)-N6,N6-dimethyl-pyrido-[3,4-d]-pyrimidine-4,6-diamine (GW) and 5-Amino-7-[3-(4-methoxy)phenylpropyl]-2-(2-furyl)-pyrazolo[4,3-e]-1,2,4-triazolo[1,5-c]pyrimidine (SCH) were studied for their binding affinity and selectivity towards telomeric G-quadruplex DNA using UV-Vis absorption, fluorescence, circular dichroism, melting temperature and NMR. In addition to its known anticancer effect, TQ showed high selectivity towards G-quadruplex over duplex DNA. Therefore, it was subjected for further derivatization. Twenty two amino derivatives of thymoquinone analogues were synthesized in one pot reaction at room temperature and their structures were elucidated using IR, NMR, MS and elemental analysis. Binding affinity and selectivity of the synthesized compounds towards G-quadruplex were studied. The results indicated thymoquinone analogues interacted with G-quadruplex DNA. Binding affinities ranged between 5.60x104 and 1.33x107 M-1. TQ8 and TQ6 have shown the best stabilizing effects with a change in melting temperature (ΔTm) of 21 and 10 °C respectively. In addition, the obtained products have shown good selectivity towards G-quadruplex over duplex DNA. Synthesized compounds were also tested against lung, breast, colorectal, prostate, pancreatic, colon and lymphoma cancer cell lines (A549, H1299, MDA-MB-231, MCF-7, HT29, C42B, L3.6pl, MiaPaCa-2, HCT-116 and WSU-FSCCL). TQ8 showed the highest potency among all synthetic analogues. It showed cell viability close to zero relative to control after 48 h against A549, MDA-MB-231 and HT29 cell lines with IC50 of 35.01, 45.14 and 55.81 μM respectively. BQ3, BQ4, BQ6, BQ10 and BQ11 have shown IC50 less than 10 μM for the examined cell lines after 48 h. These results revealed compounds of potential interest as anticancer agents. Furthermore, work will be processed towards the testing in vivo as therapeutic agents.