Excited state proton transfer of natural flavonoids and their chromophores in duplex and tetraplex DNAs

Oxygen Atom from Carbonyl Group as an Important Binding Agent to the G-Quadruplex - Study Case of Flavonoids

In the field of anticancer therapy study it is of great interest to find effective G-quadruplex ligands which may be of potential use in medical treatment or cancer prevention. Since among the compounds of natural origin, flavonoids have attracted notable attention because of their unique properties and promising therapeutic applications, an interesting question was to identify the flavonoid structural features that could provide effective binding properties toward G-quadruplex. By using electrospray ionization mass spectrometry, followed by the survival yield method, it has been shown that the flavonoid molecules which contain an available C4=O carbonyl group form more stable adducts with G-tetrads than the other ones. Molecular docking has shown that C4=O carbonyl group can be a source of hydrogen bonds and/or π-stacking interactions. Therefore, the flavonoid molecules which contain an available C4=O carbonyl group can be regarded as good binders of G-quadruplexes.

Binding of Quercetin Derivatives toward G-Tetrads as Studied by the Survival Yield Method

Recently, much interest has been devoted to finding effective G-quadruplex ligands, both of synthetic or natural origins, which may be of potential use in the field of cancer therapy. Among compounds of natural origin, a common flavonol quercetin has attracted notable attention. Yet, only a modest number of papers have been concerned with a comparison of quercetin conjugates binding to G-quadruplexes. In this study, we applied the survival yield (SY) method in order to compare the stability of G-tetrad complexes with quercetin and its conjugates, namely, 3-O-glycosides and O-methylated conjugates. According to the determined values of Ecomδ50, flavonol glycosides bind most effectively with G-tetrads, whereas, among flavonols, 3-O-methylquercetin makes the most effective bonds. Because the aglycone structure is of crucial importance for biological processes, 3-O-methylquercetin seems to be a suitable candidate for anticancer therapeutics, and the extracts from the plants, which contain high amounts of 3-O-methylquercetin or its glycosides, should be considered as interesting materials for preparation of pharmaceuticals or dietary supplements.

Exploring Glycosylated Soy Isoflavones Affinities toward G-tetrads as Studied by Survival Yield Method

Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G+Na]⁺ ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G+Na]⁺ interaction in the gas phase was determined from E_com50 - the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G+Na]⁺ interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.

7-Hydroxyflavone Alleviates Myocardial Ischemia/Reperfusion Injury in Rats by Regulating Inflammation

Inflammation is the primary pathological process of myocardial ischemia/reperfusion injury (MI/RI). 7-Hydroxyflavone (HF), a natural flavonoid with a variety of bioactivities, plays a crucial role in various biological processes. However, its cardioprotective effects and the underlying mechanisms of MI/RI have not been investigated. This study aimed to explore whether pretreatment with HF could attenuate MI/RI-induced inflammation in rats and investigate its potential mechanisms. The results showed that pretreatment with HF could significantly improve the anatomic data and electrocardiograph parameters, reduce the myocardial infarct size, decrease markers of myocardial injury (aspartate transaminase, creatine kinase, lactate dehydrogenase, and cardiac troponin I), inhibit inflammatory cytokines (IL-1β, IL-6, and TNF-α), suppress oxidative stress, and recover the architecture of the cardiomyocytes. The cardioprotective effect of HF was connected with the regulation of the MAPK/NF-κB signaling pathway. What is more, molecular docking was carried out to prove that HF could be stably combined with p38, ERK1/2, JNK, and NF-κB. In summary, this is a novel study demonstrating the cardioprotective effects of HF against MI/RI in vivo. Consequently, these results demonstrate that HF can be considered a promising potential therapy for MI/RI.

Theoretical Insights into Excited-State Intermolecular Proton Transfers of 2,7-Diazaindole in Water Using a Microsolvation Approach

The detailed excited-state intermolecular proton transfer (ESInterPT) mechanism of 2,7-diazaindole with water wires consisting of either one or two shells [2,7-DAI(H₂O)_n; n = 1-5] has been theoretically explored by time-dependent density functional theory using microsolvation with an implicit solvent model. On the basis of the excited-state potential energy surfaces along the proton transfer (PT) coordinates, among all 2,7-DAI(H₂O)_n, the multiple ESInterPT of 2,7-DAI(H₂O)₂₊₃ through the first hydration shell (inner circuit) is the most easy process to occur with the lowest PT barrier and a highly exothermic reaction. The lowest PT barrier resulted from the outer three waters pushing the inner circuit waters to be much closer to 2,7-DAI, leading to the enhanced intermolecular hydrogen-bonding strength of the inner two waters. Moreover, on-the-fly dynamic simulations show that the multiple ESInterPT mechanism of 2,7-DAI(H₂O)₂₊₃ is the triple PT in a stepwise mechanism with the highest PT probability. This solvation effect using microsolvation and dynamic simulation is a cost-effect approach to reveal the solvent-assisted multiple proton relay of chromophores based on excited-state proton transfer.

Influence of position of hydroxyl group of flavonoids on their binding with single stranded polyriboadenylic acid: A spectroscopic evaluation

Single stranded polyriboadenylic acid [poly (rA)] has been accepted widely as a suitable drug target owing to its vital role in the development of cancer since it controls gene expression during cell growth and differentiation. The biological properties of poly (rA) depend on its structural morphology. Pharmacologically active flavonoids can act as suitable binders to poly (rA) and significantly change its biophysical properties. Different factors favour flavonoid-poly (rA) binding. In our present work we have explored the role played by the position of hydroxyl groups in the flavonoids namely 3, 5, 6 and 7 hydroxyflavones in their course of interaction with poly (rA). A range of spectroscopic experiments reveal that 3HF binds best to poly (rA) among the four chosen flavonoids. This is probably due to the presence of a hydroxyl group in '3' position that enables it to exhibit ESIPT phenomenon which is missing for the other used flavonoids.

Influence of a 4'-substituent on the efficiency of flavonol-based fluorescent indicators of β-glycosidase activity

This article presents novel fluorescent probes, based on the excited-state intramolecular proton transfer (ESIPT) phenomenon and flavonols, sensitive to the action of specific glycosidases. 4'-Substituted flavonols were synthesized, using various approaches, and glycosylated with d-glucose, N-acetyl-d-glucosamine and d-glucuronic acid. Evaluation of the β-glycosidase activities was performed in neutral and acidic pH. In all the cases examined, an acidic environment accelerated enzymatic hydrolysis. It was demonstrated that the 4'-chloroflavonyl glycosides of all sugars tested, both in neutral and acidic pH, are the ones most sensitive to the presence of hydrolase. In turn, 4'-dimethylaminoflavonyl glucoside is not sensitive to glucosidase action at all. Generally, the rate of enzymatic hydrolysis increases as the electron-withdrawing nature of the 4'-substituent increases. An exception is the trifluoromethyl group which, in spite of having the most favourable Hammett constant, does not contribute enough to increase the rate of hydrolysis of its glucoside. The presented experimental results are supported by the electrostatic potential (ESP) analysis and related to the mechanisms of glycoside bond enzymatic hydrolysis.

Spectroscopic Study on Pseudomonas Aeruginosa Biofilm in the Presence of the Aptamer-DNA Scaffolded Silver Nanoclusters

We report the effectiveness of silver nanocluster (Ag-NC) against the biofilm of Pseudomonas aeruginosa (PA). Two DNA aptamers specific for PA and part of their sequences were chosen as templates for growing the Ag-NC. While circular dichroism (CD) studies determined the presence of secondary structures, UV/Vis absorption, and fluorescence spectroscopic studies confirmed the formation of the fluorescent Ag-NC on the DNA templates. Furthermore, mesoscopic physics-based partial wave spectroscopy (PWS) was used to analyze the backscattered light signal that can detect the degree of nanoscale mass density/refractive index fluctuations to identify the biofilm formation, comparatively among the different aptamers with respect to the control sample. The importance of the secondary structure of the aptamer DNA in targeting, successfully binding with the cells and delivering the Ag-NC, is evidenced by the decrease in disorder strength (L_d) of the Ag-NC treated samples compared to the untreated PA cells, which showed the abundance of higher L_d in the PWS studies. The higher L_d value attributed to the higher mass density fluctuations and the formation of biofilm. We envision this study to open a new avenue in using a powerful optical microscopic technique like PWS in detection, and DNA aptamer enclosed silver nanoclusters to prevent biofilms for opportunist pathogens like Pseudomonas aeruginosa.

Preferential targeting cancer-related i-motif DNAs by the plant flavonol fisetin for theranostics applications

The relationship of i-motif DNAs with cancer has prompted the development of specific ligands to detect and regulate their formation. Some plant flavonols show unique fluorescence and anti-cancer properties, which suggest the utility of the theranostics approach to cancer therapy related to i-motif DNA. We investigated the effect of the plant flavonol, fisetin (Fis), on the physicochemical property of i-motif DNAs. Binding of Fis to the i-motif from the promoter region of the human vascular endothelial growth factor (VEGF) gene dramatically induced the excited state intramolecular proton transfer (ESIPT) reaction that significantly enhanced the intensity of the tautomer emission band of Fis. This unique response was due to the coincidence of the structural change from i-motif to the hairpin-like structure which is stabilized via putative Watson-Crick base pairs between some guanines within the loop region of the i-motif and cytosines in the structure. As a result, the VEGF i-motif did not act as a replication block in the presence of Fis, which indicates the applicability of Fis for the regulation of gene expression of VEGF. The fluorescence and biological properties of Fis may be utilised for theranostics applications for cancers related to a specific cancer-related gene, such as VEGF.

Graphene oxide as selective transporter of flavonols for physiological target DNA: A two-color fluorescence approach

Our study determines the selectivity of graphene oxide (GO) to recognize its ligands (e.g. flavonoids) in facilitating the binding with their respective cellular targets. The polyhydroxy phenolic compounds, flavonoids, have a broad spectrum of therapeutic activities with high potency and low systemic toxicity. Despite the vast medicinal importance, their bioavailability is low. In this exploratory study, GO has been used as the transporter of three flavonols fisetin (3, 7, 3', 4'-OH flavone), quercetin (3, 5, 7, 3', 4'-OH flavone), and morin (3, 5, 7, 2', 4'-OH flavone) for the physiological target DNA. Calf thymus DNA is chosen as the model physiological target. Characterization of GO is performed using FTIR, Raman and dynamic light scattering (DLS) spectroscopy. The strong absorption peak at 1730 cm-1 indicated the presence of carbonyl groups (C=O) at the edges of GO. The presence of sp3 carbons due to oxidation of sp2 carbons in GO is further proved by Raman spectroscopy. DLS provided the average size of the GO particles to be ~9 μm. The dual luminescence behavior of the flavonols has been used in this study for the noninvasive sensing of the GO-flavonol and GO-flavonol-DNA interactions; as well as for the selectivity of GO for one flavonol over other in transferring the ligand to DNA. Furthermore, circular dichroism (CD) indicated that the optical activity of GO undergoes drastic change when conjugated with flavonols. Molecular modeling corroborated the findings from the binding studies. GO provides high promise as facilitators for drug delivery.

Exploring the preferential interaction of quercetin with VEGF promoter G-quadruplex DNA and construction of a pH-dependent DNA-based logic gate

The plant flavonoid quercetin (Que) binds more efficiently to VEGF G-quadruplex DNA (G4–DNA) compared to double stranded DNA as well as other G4–DNAs.

Targeting G-quadruplex DNA and B-DNA with a natural alkaloid: a comparative spectroscopic study

Different modes of binding of natural alkaloid harmine with G-quadruplex DNA and B-DNA: key roles in molecular recognition.

Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues

We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.