Changes in 13C NMR chemical shifts of DNA as a tool for monitoring drug interactions

Interaction of human telomeric G-quadruplex DNA with thymoquinone: a possible mechanism for thymoquinone anticancer effect

BACKGROUND

Thymoquinone (TQ) has been documented to possess chemo-preventive and chemotherapeutic antitumor effects. Studies reported that TQ inhibits the growth of cancer cells in animal models, culture and xenografted tumors. Molecular mechanisms underlying these anticancer effects were attributed to inductions of cell cycle arrest, apoptosis, oxidative damage of cellular macromolecules, blockade of tumor angiogenesis and inhibitions in migration, invasion and metastasis of cancer cells. On the other hand, human telomere DNA plays a role in regulating genes' transcriptions. It folds up into G-quadruplex structures that inhibit telomerase enzyme over-expressed in cancerous cells. Molecules that selectively stabilize G-quadruplex are potential anticancer agents. Therefore, this work aimed to explore the interaction of TQ with G-quadruplex DNA as a possible underlying mechanism for the anticancer effect of TQ.

METHODS

Interactions of TQ with telomeric G-quadruplex (5'-AGGG(TTAGGG)3-3') and duplex DNAs were studied using UV-vis, fluorescence, circular dichroism, liquid and solid NMR (1H and 13C), melting temperature and docking simulation.

RESULTS

Changes in UV-vis, CD, fluorescence, 1H NMR and 13C NMR, spectra as well as melting temperatures and docking simulations provided evidences for TQ's interactions with G-quadruplex. TQ was found to interact with G-quadruplex on two binding sites adjacent to the TTA loop with binding constants 1.80×10(5) and 1.12×10(7) M(-1). Melting temperatures indicated that TQ stabilized G-quadruplex by 5.6 °C and destabilized ct-DNA by 5.1 °C. Selectivity experiment indicated that TQ is preferentially binding to G-quadruplex over duplex with selectivity coefficients of 2.80-3.33×10(-3). Results suggested an intercalation binding mode based on π-π stacking.

CONCLUSION

Our results propose that TQ can possibly act as a G-quadruplex DNA stabilizer and subsequently contribute to the inhibition of telomerase enzyme and cancer's proliferation.

GENERAL SIGNIFICANCE

Our results represent a change in the paradigms reported for structural features of G-quadruplex's stabilizers and anticancer mechanisms of TQ.

N- versus O-alkylation: utilizing NMR methods to establish reliable primary structure determinations for drug discovery

A classic synthetic issue that remains unresolved is the reaction that involves the control of N- versus O-alkylation of ambident anions. This common chemical transformation is important for medicinal chemists, who require predictable and reliable protocols for the rapid synthesis of inhibitors. The uncertainty of whether the product(s) are N- and/or O-alkylated is common and can be costly if undetermined. Herein, we report an NMR-based strategy that focuses on distinguishing inhibitors and intermediates that are N- or O-alkylated. The NMR strategy involves three independent and complementary methods. However, any combination of two of the methods can be reliable if the third were compromised due to resonance overlap or other issues. The timely nature of these methods (HSQC/HMQC, HMBC. ROESY, and (13)C shift predictions) allows for contemporaneous determination of regioselective alkylation as needed during the optimization of synthetic routes.

Changes in drug 13C NMR chemical shifts as a tool for monitoring interactions with DNA

The antibiotic drug, netropsin, was complexed with the DNA oligonucleotide duplex [d(GGTATACC)]2 to monitor drug 13C NMR chemical shifts changes. The binding mode of netropsin to the minor groove of DNA is well-known, and served as a good model for evaluating the relative sensitivity of 13C chemical shifts to hydrogen bonding. Large downfield shifts were observed for four resonances of carbons that neighbor sites which are known to form hydrogen bond interactions with the DNA minor groove. Many of the remaining resonances of netropsin exhibit shielding or relatively smaller deshielding changes. Based on the model system presented here, large deshielding NMR shift changes of a ligand upon macromolecule binding can likely be attributed to hydrogen bond formation at nearby sites.

Random coil carbon chemical shifts of deoxyribonucleic acids

The sequence and temperature effects on random coil DNA carbon chemical shifts have been investigated using sixteen 17-nucleotide sequences. Temperature effect correction parameters have been determined for the aromatic C6/C8 carbons and the deoxyribose C1', C2', and C3' carbons. The carbon chemical shifts of a specific nucleotide in a random coil sequence have been shown to depend mainly on the type of its nearest neighbors. A carbon chemical shift database containing all 64 different types of triplets has been established for predicting random coil DNA carbon chemical shifts. The use of this triplet database for carbon chemical shift predictions shows good accuracy with experimental data, with root-mean-square deviations of 0.09, 0.10, 0.10, and 0.10 ppm and correlation coefficients of 0.999, 0.996, 0.978, and 0.974 for C6/C8, C1', C2', and C3', respectively.