Studies on the interaction of a synthetic nitro-flavone derivative with DNA: A multi-spectroscopic and molecular docking approach

Complexation of Flavonoids: Spectral Phenomena, Regioselectivity, Interplay with Charge and Proton Transfer

The review compiles information on the spectral classification of flavonoids, the changes in their electronic structure upon complex formation, and the manifestation of these changes in the absorption and emission spectra. Part of the review is devoted to the regioselectivity of the complex formation process, including types of complexation sites, the structure of chelates and 'open' complexes, and the correlation between the structure of complexes and their spectral properties. The interplay between complex formation and other processes occurring in flavonoids during electronic excitation is also considered, such as intramolecular inter-fragment charge transfer (ICT) and intramolecular proton transfer (ESIPT). The review also contains systematic data on the study of regioselectivity and spectral properties of flavone complexes, obtained by the author and their colleagues over the past decades.

Investigation of the binding behavior of bioactive 7-methoxyflavone to human serum albumin by coupling multi-spectroscopic with computational approaches

The natural flavonoids with bioactivity as secondary plant metabolites are mostly found in fruits, vegetables, tea and herbs, the distribution and bioavailability of which in vivo depends on the interaction and successive binding with carrier proteins in the systemic circulation. In this paper, the binding behavior of bioactive 7-methoxyflavone (7-MF) with human serum albumin (HSA) was studied with the aid of the combination of multi-spectroscopic methods, molecular docking and molecular dynamic simulation. The results of multi-spectroscopic experiments revealed that 7-MF interacted with HSA predominantly via fluorescence static quenching and the microenvironment around the fluorophore Trp residues in HSA became more hydrophilicity with the binding of 7-MF. Thermodynamic analysis demonstrated that hydrogen bonds and van der Waals forces played a dominant role in stabilizing the HSA-7-MF complex. Moreover, the docking experiment and molecular dynamic simulation further confirmed that 7-MF could enter the active cavity of HSA and caused more stable conformation and change of secondary structure of HSA through forming hydrogen bond. The exploration of the mechanism of 7-MF binding to HSA lights a new avenue to understand the stability, transport and distribution of 7-MF and 7-MF may hold great potential to be extended as a promising alternative of dietary supplements or pharmaceutical agents.

Evaluation of Docking Machine Learning and Molecular Dynamics Methodologies for DNA-Ligand Systems

DNA is a molecular target for the treatment of several diseases, including cancer, but there are few docking methodologies exploring the interactions between nucleic acids with DNA intercalating agents. Different docking methodologies, such as AutoDock Vina, DOCK 6, and Consensus, implemented into Molecular Architect (MolAr), were evaluated for their ability to analyze those interactions, considering visual inspection, redocking, and ROC curve. Ligands were refined by Parametric Method 7 (PM7), and ligands and decoys were docked into the minor DNA groove (PDB code: 1VZK). As a result, the area under the ROC curve (AUC-ROC) was 0.98, 0.88, and 0.99 for AutoDock Vina, DOCK 6, and Consensus methodologies, respectively. In addition, we proposed a machine learning model to determine the experimental ∆T_m value, which found a 0.84 R² score. Finally, the selected ligands mono imidazole lexitropsin (42), netropsin (45), and N,N′-(1H-pyrrole-2,5-diyldi-4,1-phenylene)dibenzenecarboximidamide (51) were submitted to Molecular Dynamic Simulations (MD) through NAMD software to evaluate their equilibrium binding pose into the groove. In conclusion, the use of MolAr improves the docking results obtained with other methodologies, is a suitable methodology to use in the DNA system and was proven to be a valuable tool to estimate the ∆T_m experimental values of DNA intercalating agents.

Synthesize and multi-spectroscopic studies of zinc-naproxen nanodrug as DNA intercalator agent

The zinc-naproxen complex as a nano-drug (NanoD) was synthesized successfully via fast and effective ultrasound-assisted processes. The chemicophysical properties of the NanoD were determined using FT-IR, XRD, SEM, and EDX mapping analyses. The results confirmed the formation of the 55 nm NanoD laminates. The interaction of the obtained NanoD with calf thymus deoxyribonucleic acid (CT-DNA) was studied as well. Structural and topography changes of DNA in interaction with the NanoD were investigated by atomic force microscopy (AFM). The results of electronic absorption spectroscopy, the DNA-viscosity studies, and competition fluorescence spectroscopy showed that CT-DNA binds to the NanoD through the intercalative binding mode. The data of AFM analysis indicated swollen CT-DNA upon interaction with the NanoD. The in vitro investigation of cytotoxicity of the NanoD on HT-29 and Hep G2 cancer cells demonstrated high cytotoxicity activity of the NanoD than that of cisplatin in HT-29 cell line, especially at lower concentrations.

A375 melanoma cells are sensitized to cisplatin-induced toxicity by a synthetic nitro-flavone derivative 2-(4-Nitrophenyl)-4H-chromen-4-one through inhibition of PARP1

BACKGROUND

Cisplatin has been extensively used in therapeutics for its broad-spectrum anticancer activity and frequently used for the treatment of solid tumors. However, it presents several side-effects and several cancers develop resistance. Combination therapy of cisplatin with poly (ADP-ribose) polymerase 1 (PARP1) inhibitors has been effective in increasing its efficacy at lower doses.

METHODS AND RESULTS

In this work, we have shown that the nitro-flavone derivative, 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO), can improve the sensitivity of cancer cells to cisplatin through inhibition of PARP1. The effect of 4NCO on cisplatin toxicity was studied through combination therapy in both exponential and density inhibited A375 melanoma cells. Combination index (CI) was determined from isobologram analysis. The mechanism of cell killing was assessed by lactate dehydrogenase (LDH) assay. Temporal nicotinamide adenine dinucleotide (NAD⁺) assay was done to show the inhibition of PARP1. We also performed in silico molecular modeling studies to know the binding mode of 4NCO to a modeled PARP1-DNA complex containing cisplatin-crosslinked adduct. The results from both in silico and in cellulo studies confirmed that PARP1 inhibition by 4NCO was most effective in sensitizing A375 melanoma cells to cisplatin. Isobologram analysis revealed that 4NCO reduced cell viability both in exponential and density inhibited A375 cells synergistically. The combination led to cell death through apoptosis.

CONCLUSION

The synthetic nitro-flavone derivative 4NCO effectively inhibited the important nuclear DNA repair enzyme PARP1 and therefore, could complement the DNA-damaging anticancer drug cisplatin in A375 cells and thus, could act as a potential adjuvant to cisplatin in melanoma therapy.

Studies to explore the UVA photosensitizing action of 9-phenylacridine in cells by interaction with DNA

Acridine and its derivatives are well known for their DNA binding properties. In this report, we present our findings on evaluating different binding parameters of the interaction of 9-phenylacridine (ACPH) with DNA. Absorption spectroscopic studies including standard and reverse titration, the effects of ionic strength and temperature on titration, and Job plot analysis were done to calculate the binding constant and determine the different thermodynamic parameters and stoichiometry of the binding. Spectrofluorimetry and circular dichroism (CD) spectral titration were also utilized to confirm these findings. The results indicated that ACPH binds to DNA reversibly through non-electrostatic interactions by hydrogen bonding and van der Waals interactions. The binding constant and the number of binding sites were of the order 10³ M^-1 and ≈2, respectively with a binding stoichiometry of 1:4. The binding of ACPH with DNA was spontaneous, exothermic and enthalpy-driven. The extent of uptake of ACPH in B16 melanoma cells was estimated. As this compound absorbs in the UVA region, the effect of treatment with ACPH prior to UVA exposure was assessed to evaluate its phototoxicity in these cells. Our results indicated that the binding to DNA enhanced damage to sensitize cells to killing through apoptosis. Our findings indicated its potential to act as a photosensitizer.

Investigation of biological activity of nickel (II) complex with naproxen and 1,10-phenanthroline ligands

After the accidental discovery of cis-platinum, extensive attempts have centralized on the rational design of metallic compounds for cancer treatment. Here a solvent-dependent complex of nickel (II) with 1,10-phenanthroline and naproxen, [Ni(1,10-phenanthroline)(naproxen)₂(solvent)], solvent = 83% H₂O and 17% EtOH in the crystal structure, has been synthesized and specified by the X-ray structure analysis. It's in vitro DNA binding was inspected by the multispectroscopic methods and gel electrophoresis. The data of DNA-viscosity and competition fluorimetric test by methylene blue (MB) and Hoechst 33258 confirm groove binding mode of the complex to CT-DNA. Comparison of the results of this binding study with previous work revealed that the mode of binding of small compounds to DNA is highly influenced by the structure of the compounds. The DNA cleavage potency of the complex was appraised by the agarose gel electrophoretic and it was found that the complex does not have any momentous cleavage potency on the pUC18 plasmid DNA. The cytotoxicity of the complex on HT 29, HepG2 and HEK-293 cell lines by MTT method indicates that %inhibition of the complex on HT 29 is better than HepG2, compared with cisplatin drug. On HEK-293 cells, %inhibition growth of normal cells of the complex is less than cisplatin. Flow cytometry analysis of the complex on the HT 29 cells indicated the apoptosis cell death. RT-PCR studies revealed down-regulation of BCL2 expression, while the expression of BAX, caspase 3 and BAX/BCL2 genes was up-regulated in HT 29 cells by the complex. HighlightsA solvent-dependent nickel (II) with naproxen and 1,10-phenanthroline with aqueous solubility was synthesized and characterized.All experimental results indicate a groove mode of binding of the complex to CT-DNA.Potential biological characteristics confirmed that the complex is a promising candidate as anticancer agent.Communicated by Ramaswamy H. Sarma.

Increasing DNA binding affinity of doxorubicin by loading on Fe3O4 nanoparticles: A multi-spectroscopic study

Magnetic Fe₃O₄ nanoparticles were synthesized successfully by co-precipitation method and characterized using XRD, SEM and EDS analyses. Then doxorubicin (DOX, a known anticancer drug) was loaded onto nanoparticles. In vitro DNA interaction of free DOX and loaded DOX onto Fe₃O₄ nanoparticles (DOX-Fe₃O₄) was investigated by DNA-viscosity measurements, UV-visible and fluorescence spectroscopies. The obtained values for binding constant of DOX and DOX-Fe₃O₄ compounds from UV-visible spectroscopies were 0.04 × 10⁵ and 0.68 × 10⁵ L mol^-1, respectively, which confirms DOX-Fe₃O₄ compound have a stronger interaction with CT-DNA compared to DOX. Considerable changes on viscosity of the compounds recommended that their binding mode with CT-DNA is intercalative binding. Fluorescence intensity of DOX and DOX-Fe₃O₄ was quenched via static process by regular addition of CT-DNA. Thermodynamic parameters suggest that Van der Waals forces and hydrogen bonding for DOX and electrostatic forces for DOX-Fe₃O₄ are predominantly responsible for interaction with CT-DNA. Competition fluorescence studies were done by Hoechst 33258 as a well-known groove binder and ethidium bromide (EtBr) as a known intercalator probe. Percentage of displacement for EtBr-DNA complex with DOX and DOX-Fe₃O₄ was 39% and 61%, and for Hoechst-DNA complex was 9% and 5%, respectively. These results confirmed that both compounds are intercalator binders, although DOX-Fe₃O₄ with a further 22% displacement is a stronger intercalator binder than DOX. The stronger interaction of DOX-Fe₃O₄ compared to DOX suggests that the current system can be used as a new and effective way to targeted therapy of anticancer drugs.

Insight into the binding of a synthetic nitro-flavone derivative with human poly (ADP-ribose) polymerase 1

Flavones are important bioactive compounds, many of which are effective in cancer therapy for their ability to target enzymes related to DNA repair and cell proliferation. In this report, the interaction of a synthetic nitroflavone, 2,4-nitrophenylchromen-4-one (4NCO) with human poly (ADP-ribose) polymerase 1 (hPARP1) was investigated to explore its inhibitory action. Its interaction with hPARP1 was compared with that of other inhibitors through molecular docking studies. Further insight into the 4NCO-hPARP1 interaction was obtained from competitive docking and molecular dynamic simulation studies. In silico mutagenesis studies and per-residue interaction energy calculations were carried out. Quantitative Structure Activity Relationship analysis was also performed to calculate its predictive percent inhibitory activity. Our results indicated that 4NCO exhibited competitive mode of binding to hPARP1. It formed a stable interaction with the protein thereby hindering any further molecular interaction to render it inactive with a predictive inhibition of 96%. It also had good ADMET properties and showed best Autodock binding free energy values compared to other known inhibitors. 4NCO showed good hPARP1 inhibitory properties with higher bioavailability and lower probability of getting effluxed. Development of inhibitors against hPARP1 is important for cell proliferative disorders, where 4NCO can be predicted as a potential new drug.

CAPE-pNO2 Inhibited the Growth and Metastasis of Triple-Negative Breast Cancer via the EGFR/STAT3/Akt/E-Cadherin Signaling Pathway

Overexpressed epidermal growth factor receptor (EGFR) and overactivated epithelial-mesenchymal transition (EMT) in triple-negative breast cancer (TNBC) can enhance tumorigenesis and tumor recurrence and metastasis. Caffeic acid p-nitro-phenethyl ester (CAPE-pNO₂) has various pharmacological activities in our previous research, but its effect on metastasis and growth of TNBC has not been studied. In this study, Caffeic acid phenethyl ester (CAPE) was as a positive control. in vitro, MTT, Transwell, wound healing, colony formation and cell adhesion assays were performed to examine the effect on viability, invasion, migration, colony formation and adhesion of MDA-MB-231 cells by CAPE-pNO₂, the results indicated that CAPE-pNO₂ significantly dose-dependently inhibited metastasis of MDA-MB-231 cells (p < 0.05). in vivo, TNBC xenograft mice were established by subcutaneously injected with MDA-MB-231 cells, and they were used to estimate the effect on metastasis and growth of CAPE-pNO₂ after 38 days of treatment. HE staining and TUNEL staining were carried out in tumor tissues, results showed that CAPE-pNO₂ obviously suppressed the tumor growth, induced cells apoptosis (p < 0.01) and decreased pulmonary and splenic metastatic tumor cells. The results of IHC demonstrated that the VEGFA and Ki-67 proteins expression were downregulated (p < 0.01) in tumor tissues. Furthermore, western blot analysis was used to quantify key metastasis- and growth-associated proteins expression in vitro and in vivo, the results suggested that CAPE-pNO₂ downregulated the proteins expression of p-EGFR, p-STAT3, p-Akt, MMP-2, MMP-9, Survivin, and key EMT-related proteins (Vimentin and N-cadherin) (p < 0.01), and increased the expression of E-cadherin (p < 0.01) in vivo and in vitro. Besides, CAPE-pNO₂ had a similar effect as erlotinib in regulating the EGFR downstream proteins in EGF-induced MDA-MB-231cells. Collectively, these results indicated that CAPE-pNO₂ possessed inhibitory effect on the growth and metastasis of TNBC may via the EGFR/STAT3/Akt/E-cadherin signaling pathway, and CAPE-pNO₂ is better than CAPE in inhibiting growth and metastasis.

Synthetic flavonoids with antimicrobial activity: a review

The emergence of drug-resistant microbes left us with a great need for new antimicrobial agents. Flavonoids, with their wide range of biological activities, are good candidates in this respect. Although naturally occurring flavonoids are the most studied ones, semi-synthetic or synthetic flavonoids have proven to have great potential, inhibiting and even killing microbes at concentrations below 1 μg ml^-1 . The substitution pattern of these flavonoids often includes hydroxy groups, halogens or other heteroatomic rings, such as pyridine, piperidine or 1,3-dithiolium cations. However, the great variety in substituents makes it difficult to draw any definitive conclusion regarding their structure-activity relationship.