Revealing the groove binding characteristics of plant growth regulator 3-indoleacetic acid with calf thymus DNA

Elucidating the Interaction of Indole-3-Propionic Acid and Calf Thymus DNA: Multispectroscopic and Computational Modeling Approaches

Indole-3-propionic acid (IPA) is a plant growth regulator with good specificity and long action. IPA may be harmful to human health because of its accumulation in vegetables and fruits. Therefore, in this study, the properties of the interaction between calf thymus DNA (ctDNA) and IPA were systematically explored using multispectroscopic and computational modeling approaches. Analysis of fluorescence spectra showed that IPA binding to ctDNA to spontaneously form a complex was mainly driven by hydrogen bonds and hydrophobic interaction. DNA melting analysis, viscosity analysis, DNA cleavage study, and circular dichroism measurement revealed the groove binding of IPA to ctDNA and showed that the binding did not significantly change ctDNA confirmation. Furthermore, molecular docking found that IPA attached in the A-T rich minor groove region of the DNA. Molecular dynamics simulation showed that DNA and IPA formed a stable complex and IPA caused slight fluctuations for the residues at the binding site. Gel electrophoresis experiments showed that IPA did not significantly disrupt the DNA structure. These findings may provide useful information on the potential toxicological effects and environmental risk assessments of IPA residue in food at the molecular level.

Effects of Processing Conditions and Simulated Digestion In Vitro on the Antioxidant Activity, Inhibition of Xanthine Oxidase and Bioaccessibility of Epicatechin Gallate

The bioactivity and gastrointestinal stability of epicatechin gallate (ECG) may be affected by processing conditions. Results showed that the antioxidant ability and inhibitory activity on xanthine oxidase (XO) of ECG were higher at low pH values. Appropriate microwave and heating treatments improved the antioxidant (the scavenging rate increased from 71.75% to 92.71% and 80.88% under the microwave and heating treatments) and XO inhibitory activity (the inhibitory rate increased from 47.11% to 56.89% and 51.85% at the microwave and heating treatments) of ECG. The treated ECG led to a more compact structure of XO. Moreover, there may be synergistic antioxidant and inhibitory effects between ECG and its degradation products. The bioaccessibility of ECG after simulated digestion was untreated > microwave > heating, and the microwave-treated ECG still had good XO inhibitory activity after digestion. These findings may provide some significant information for the development of functional foods enriched in catechins.

Synthesis, spectral characterization of pyrazole derived Schiff base analogs: molecular dynamic simulation, antibacterial and DNA binding studies

We have synthesized the pyrazole-bearing Schiff base derivatives (5a-5e) and (6a-6h) then the structural confirmation was supported by various spectral analyses. The antibacterial activity of all analogs was screened against bacterial strains Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Klebsiella pneumonieae and Pseudomonas aeruginosa. In comparison to the reference drug ciprofloxacin, the lead analogs 5c and 6c showed potent activity, with MIC values of 64 µg/mL against E. coli and B. subtilis. Compound 5c showed a moderate effect with a MIC value of 128 µg/mL against B. subtilis, P. aeruginosa and K. pneumonieae, while compound 6c was against E. coli and P. aeruginosa. Furthermore, the compounds 5c and 6c displayed groove binding mode towards CT-DNA by absorption, emission, competitive fluorescence studies using EtBr, CD and time-resolved fluorescence studies. Thermodynamic parameters of analogs 5c and 6c with CT-DNA were also calculated at 298, 303 and 308K temperatures by UV-visible spectroscopy. The molecular docking studies give the docking score for all compounds with PDB codes: 1BNA and 2XCT. The MD simulation study of analogs 5c and 6c was also carried out. The pharmacokinetic and ADME properties were calculated for all of the synthesized analogs (5a-5e) and (6a-6h).Communicated by Ramaswamy H. Sarma.

Functionalization of Fe3O4/rGO magnetic nanoparticles with resveratrol and in vitro DNA interaction

Based on the previous research, we found that the magnetic nanocomposite Fe₃O₄/rGO (reduced graphene oxide) has a good drug loading effect. Therefore, in this paper, we studied the positive role of Fe₃O₄/rGO as a drug carrier in the interaction between resveratrol (RES) and calf-thymus DNA (ct-DNA). The fluorescence experiment is used to evaluate by the Stern-Volmer equation, the quenching constant of RES - ct-DNA system with and without Fe₃O₄/rGO decreases with the increasing temperature. It was found the quenching mode of RES - ct-DNA and Fe₃O₄/rGO - RES - ct-DNA systems were all static quenching, but the binding constant of RES -ct-DNA increased from 4.14 ± 0.21 × 10⁴ L mol^-1 to 10.12 ± 0.02 × 10⁴ L mol^-1. It was found that Fe₃O₄/rGO formed a ternary complex with RES and ct-DNA by ultraviolet spectrum (UV-vis), resonance light scattering experiments (RLS) and scanning electron microscope (SEM). Meanwhile, Fourier transform infrared (FT-IR) and circular dichroism (CD) experiments show that Fe₃O₄/rGO and Fe₃O₄/rGO loaded with RES have effect on the secondary structure of ct-DNA and change the conformation of ct-DNA. On the cellular level, the comet assay shows that Fe₃O₄/rGO and Fe₃O₄/rGO - RES could not cause DNA strand break to the mouse hepatocytes after 24 co-incubation. These results confirm that Fe₃O₄/rGO nanocomposites have good application potential, which can be used as a good drug carrier in a wide range of therapeutic methods.

Multi-Spectroscopic and Molecular Simulation Approaches to Characterize the Intercalation Binding of 1-Naphthaleneacetic Acid With Calf Thymus DNA

1-Naphthaleneacetic acid (NAA), having high-quality biological activity and great yield-increasing potential in agricultural production, is a broad-spectrum plant growth regulator. Although NAA is of low toxicity, it can affect the balance of the human metabolism and damage the body if it is used in high quantity for a long time. In this study, the interaction of NAA with calf thymus DNA (ctDNA) was investigated under simulated human physiological acidity (pH 7.4) using fluorescence, ultraviolet-visible absorption, and circular dichroism spectroscopy combined with viscosity measurements and molecular simulation techniques. The quenching of the endogenous fluorescence of NAA by ctDNA, observed in the fluorescence spectrum experiment, was a mixed quenching process that mainly resulted from the formation of the NAA-ctDNA complex. NAA mainly interacted with ctDNA through hydrophobic interaction, and the binding constant and quenching constant at room temperature (298 K) were 0.60 × 10⁵ L mol^-1 and 1.58 × 10⁴ L mol^-1, respectively. Moreover, the intercalation mode between NAA and ctDNA was verified in the analysis of melting point, KI measurements, and the viscosity of ctDNA. The results were confirmed by molecular simulation, and it showed that NAA was enriched near the C-G base of ctDNA. As shown in circular dichroism spectra, the positive peak intensity of ctDNA intensified along with a certain degree of redshift, while the negative peak intensity decreased after binding with NAA, suggesting that the binding of NAA induced the transformation of the secondary structure of ctDNA from B-form to A-form. These researches will help to understand the hazards of NAA to the human body more comprehensively and concretely, to better guide the use of NAA in industry and agriculture.

Epicatechin Gallate as Xanthine Oxidase Inhibitor: Inhibitory Kinetics, Binding Characteristics, Synergistic Inhibition, and Action Mechanism

Epicatechin gallate (ECG) is one of the main components of catechins and has multiple bioactivities. In this work, the inhibitory ability and molecular mechanism of ECG on XO were investigated systematically. ECG was determined as a mixed xanthine oxidase (XO) inhibitor with an IC50 value of 19.33 ± 0.45 μM. The promotion of reduced XO and the inhibition of the formation of uric acid by ECG led to a decrease in O2- radical. The stable ECG-XO complex was formed by hydrogen bonds and van der Waals forces, with the binding constant of the magnitude of 104 L mol-1, and ECG influenced the stability of the polypeptide skeleton and resulted in a more compact conformation of XO. Computational simulations further characterized the binding characteristics and revealed that the inhibitory mechanism of ECG on XO was likely that ECG bound to the vicinity of flavin adenine dinucleotide (FAD) and altered the conformation of XO, hindering the entry of substrate and the diffusion of catalytic products. ECG and allopurinol bound to different active sites of XO and exerted a synergistic inhibitory effect through enhancing their binding stability with XO and changing the target amino acid residues of XO. These findings may provide a theoretical basis for the further application of ECG in the fields of food nutrition and functional foods.