Binding properties of pendimethalin herbicide to DNA: multispectroscopic and molecular docking approaches

Interaction between antidepressant drug trazodone with double-stranded DNA: Multi-spectroscopic and computational analysis

Trazodone (TZD) is an antidepressant drug used to treat major depressive and sleeping disorders. Elevated doses of trazodone are associated with central nervous system depression, which manifests as nausea, drowsiness, confusion, vertigo, exhaustion, etc. To develop a clinically viable active pharmaceutical compound with minimal adverse effects, it is imperative to possess a comprehensive knowledge of the drug's action mechanism on DNA. Hence, we investigate the mode of interaction between trazodone and DNA utilizing various spectroscopic and computational techniques. Studies using UV-vis titration showed that the DNA and trazodone have an effective interaction. The magnitude of the Stern-Volmer constant (KSV) has been calculated to be 5.84 × 106 M-1 by the Lehrer equation from a steady-state fluorescence study. UV-vis absorption, DNA melting, dye displacement, and circular dichroism studies suggested that trazodone binds with DNA in minor grooves. Molecular docking and molecular dynamic simulation demonstrated that the TZD-DNA system was stable, and the mode of binding was minor groove. Furthermore, ionic strength investigation demonstrates that DNA and trazodone do not have a substantial electrostatic binding interaction.

Copper-mediated cyclization of thiosemicarbazones leading to 1,3,4-thiadiazoles: Structural elucidation, DFT calculations, in vitro biological evaluation and in silico evaluation studies

Cancer's global impact necessitates innovative and less toxic treatments. Thiosemicarbazones (TSCs), adaptable metal chelators, offer such potential. In this study, we have synthesized N (4)-substituted heterocyclic TSCs from syringaldehyde (TSL1, TSL2), and also report the unexpected copper-mediated cyclization of the TSCs to form thiadiazoles (TSL3, TSL4), expanding research avenues. This work includes extensive characterization and studies such as DNA/protein binding, molecular docking, and theoretical analyses to demonstrate the potential of the as-prepared TSCs and thiadiazoles against different cancer cells. The DFT results depict that the thiadiazoles exhibit greater structural stability and reduced reactivity compared to the corresponding TSCs. The docking results suggest superior EGFR inhibition for TSL3 with a binding constant value of - 6.99 Kcal/mol. According to molecular dynamics studies, the TSL3-EGFR complex exhibits a lower average RMSD (1.39 nm) as compared to the TSL1-EGFR complex (3.29 nm) suggesting that both the thiadiazole and thiosemicarbazone examined here can be good inhibitors of EGFR protein, also that TSL3 can inhibit EGFR better than TSL1. ADME analysis indicates drug-likeness and oral availability of the thiadiazole-based drugs. The DNA binding experiment through absorption and emission spectroscopy discovered that TSL3 is more active towards DNA which is quantitatively calculated with a Kb value of 4.74 × 106 M-1, Kq value of 4.04 × 104 M-1and Kapp value of 5 × 106 M-1. Furthermore, the BSA binding studies carried out with fluorescence spectroscopy showed that TSL3 shows better binding capacity (1.64 × 105 M-1) with BSA protein. All the compounds show significant cytotoxicity against A459-lung, MCF-7-breast, and HepG2-liver cancer cell lines; TSL3 exhibits the best cytotoxicity, albeit less effective than cisplatin. Thiadiazoles demonstrate greater cytotoxicity than the TSCs. Overall, the promise of TSCs and thiadiazoles in cancer research is highlighted by this study. Furthermore, it unveils unexpected copper-mediated cyclization of the TSCs to thiadiazoles.

Intercalation of anticancer drug Palbociclib with calf-thymus DNA: new insights from molecular spectroscopic, molecular dynamic simulations and cleavage studies

The interaction between the anti-cancer drug Palbociclib (PAL) and calf-thymus DNA (CT-DNA) was investigated using various biophysical techniques in a physiological buffer (pH 7.4). It was found that PAL intercalated into the base pairs of CT-DNA as evidenced from the results of UV-Vis, fluorescence, circular dichroism (CD), competitive binding assay with ethidium bromide (EB) and Hoechst 33258, KI quenching study, the effect of denaturing agent and viscosity measurements. The magnitude of binding constants (106 M-1) at different temperatures suggested strong binding between PAL and CT-DNA during complexation. The observed ΔHo > 0 and ΔSo > 0 indicated that the binding process is primarily driven by hydrophobic interactions. Molecular docking studies indicated partial intercalation of pyridopyrimidine ring between the base pairs of DNA. Free energy surface (FES) analysis derived from metadynamics simulation studies revealed the PAL-induced cleavage of DNA, which was confirmed by gel electrophoresis experiments.Communicated by Ramaswamy H. Sarma.

High-throughput method for screening pendimethalin-degrading bacteria from one microbial bank

The extensive use of chemical pesticides, such as herbicides, has resulted in significant environmental pollution. Microbial degradation represents a crucial approach for managing this pesticide-associated pollution, with enrichment culturing serving as a method for isolating pesticide-degrading microorganisms. However, the efficiency of this strategy is limited, often yielding only a few isolated strains. In this study, a new mineral salt medium (MSM) was developed, and a high-throughput method was used for screening pendimethalin-degrading bacteria by measuring the bacterial growth in the MSM. The utilization of this method resulted in the isolation of 56 pendimethalin-degrading bacteria from approximately 2000 bacterial strains, including 37 Bacillus spp., 10 Alcaligenes spp., 5 Pseudomonas spp., and other 4 strains identified for the first time as pendimethalin-degrading strains. This method may hold promise not only for isolating bacterial strains capable of degrading other pesticides but also for facilitating the utilization of the substantial bacterial strains stored in bacterial banks.

Insight into the binding interactions of fluorenone-pendent Schiff base with calf thymus DNA

A novel fluorenone appended Schiff base (L) has been synthesized and utilized for studying the binding interactions with Calf Thymus DNA (ct-DNA). The mechanism of binding with ct-DNA was explored by employing various spectroscopic techniques viz. UV-Vis absorption spectroscopy, fluorescence emission spectroscopy, gel-electrophoresis, circular dichroism (CD), melting studies, viscosity arrays and molecular modelling methodology. The interpretation of UV-vis absorbance spectra pointed to binding of L within minor groove of ct-DNA with the binding constant of K_b = 0.15 × 10⁴ M^-1. Dye-displacement studies with Rhodamine-B (RhB) and Ethylene Bromide (EB) in fluorescence spectroscopy verified the groove binding mode of interaction between L and ct-DNA. Melting studies, circular dichroism, and viscosity studies further elucidated the binding modes of L with ct-DNA. Thermodynamic variable measurements taken at various temperatures such as ΔG^⁰, ΔH^⁰, and ΔS^⁰ revealed that hydrophobic forces played a significant role in the binding process. The meticulous computational interaction demonstrated by molecular docking confirmed the minor groove binding of L with ct-DNA.

Binding studies of sertraline hydrochloride with CT-DNA using experimental and computational techniques

Sertraline Hydrochloride (STH) is an antidepressant drug that belongs to the selective serotonin reuptake inhibitor family (SSRIs), which inhibits serotonin uptake in presynaptic nerve fibers. The use of these medications without a legitimate prescription might result in adverse effects, and in rare circumstances, death. The interaction mechanism and binding mode of STH with duplex DNA were extensively investigated using spectroscopic and modeling techniques at different temperatures. The hypochromic shift of the absorption spectra of STH on binding with CT-DNA indicated groove binding. Fluorescence spectroscopic studies showed that CT-DNA quenches the fluorescence intensity of STH through a static quenching mechanism. The thermodynamic parameters indicated that the complex formation was spontaneous, and enthalpy driven. The competitive displacement binding study revealed that STH displaced DAPI from the minor groove of DNA. Molecular docking and molecular dynamics simulations also revealed that the complex was stable over 150 ns and that STH preferred the minor groove of DNA. The binding energy of the stable conformations were evaluated through MM/PBSA methods. A comparison of the bound poses at different timescales showed minor changes in STH structure upon DNA binding. Furthermore, a structural analysis of CT-DNA indicated that STH induced changes in the sugar-phosphate backbone had an impact on the minor groove's width which are in agreement with the CD spectroscopic results. This study provides a better understanding of STH binding with duplex DNA.

A closer look at the mode of binding of drug pemetrexed with CT-DNA

The interaction of antifolate drug Pemetrexed (PEM) with CT-DNA has been studied by UV-Vis, fluorescence and circular dichroism spectroscopic techniques. The results of these spectroscopic studies in combination with viscosity measurements, voltammetric and KI quenching studies suggested a less-common mode of binding of PEM with CT-DNA i.e. neither intercalation nor groove binding. Thus, metadynamic (MD) simulation is utilized to decipher the nature of binding of PEM with CT-DNA. Analysis of free energy surfaces obtained in MD simulation, reveals that PEM binds to the 3'- and 5'-ends of the DNA molecule. The thermodynamics of the interaction has been investigated by isothermal titration calorimetric experiment. The analysis shows that PEM binds with CT-DNA strongly with a binding constant of 2.6x109 M-1 and the process is found to be spontaneous (ΔG - 12.84 kcal/mol). Further, positive values of enthalpy (ΔH 6.09 cal/mol) and entropy (ΔS 43.1 cal/mol) changes indicate that the binding is an enthalpically unfavourable and, instead, entropically driven process.Communicated by Ramaswamy H. Sarma.

Dinitroaniline herbicides: a comprehensive review of toxicity and side effects on animal non-target organisms

The widespread use of herbicides has increased concern about the hazards and risks to animals living in terrestrial and aquatic ecosystems. A comprehensive understanding of their effective action at different levels of biological organization is critical for establishing guidelines to protect ecosystems and human health. Dinitroanilines are broad-spectrum pre-emergence herbicides currently used for weed control in the conventional agriculture. They are considered extremely safe agrochemicals because they act specifically on tubulin proteins and inhibit shoot and root growth of plants. However, there is a lack of toxicity information regarding the potential risk of exposure to non-target organisms. The aim of the present review is to focus on side effects of the most commonly used active ingredients, e.g. pendimethalin, oryzalin, trifluralin and benfluralin, on animal non-target cells of invertebrates and vertebrates. Acute toxicity varies from slightly to high in terrestrial and aquatic species (i.e. nematodes, earthworms, snails, insects, crustaceans, fish and mammals) depending on the species-specific ability of tested organisms to adsorb and discharge toxicants. Cytotoxicity, genotoxicity and activation of oxidative stress pathways as well as alterations of physiological, metabolic, morphological, developmental and behavioural traits, reviewed here, indicate that exposure to sublethal concentrations of active ingredients poses a clear hazard to animals and humans. Further research is required to evaluate the molecular mechanisms of action of these herbicides in the animal cell and on biological functions at multiple levels, from organisms to communities, including the effects of commercial formulations.

Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA

Remdesivir (REM) is an antiviral drug, which exercises its effect by targeting specifically RNA-dependent RNA polymerase. The interaction of REM with calf thymus DNA (CT-DNA) was investigated by multi-spectroscopic techniques (UV-Vis, fluorescence, circular dichroism and ³¹P NMR) in combination with different biophysical experiments and metadynamics simulation studies. UV-Vis and fluorescence spectroscopic analysis indicated formation of a complex between REM and CT-DNA, whose binding constant is in the order of 10⁴ M^-1. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 shown that REM binds to CT-DNA via intercalation mode. Significant alteration in the band due to base stacking pairs at 274 nm in the circular dichroism spectrum, appreciable increase in relative viscosity of the biomolecule upon binding with REM and the results of potassium iodide quenching studies confirmed that REM intercalates into the base pairs of CT-DNA. Thermodynamic parameters revealed that the binding of REM to CT-DNA is a spontaneous process (ΔG⁰ < 0) and the main force which holds them together in the REM/CT-DNA complex is electrostatic interaction (ΔH⁰ < 0 and ΔS⁰ > 0). The up-field shift in the ³¹P NMR signal of REM on interaction with CT-DNA suggested that phenyl ring adjacent to the phosphate moiety of REM may involve in the intercalation process. This is well supported by the analysis of free energy surface landscape derived from metadynamics simulation studies.

Current status of pesticide effects on environment, human health and it's eco-friendly management as bioremediation: A comprehensive review

Pesticides are either natural or chemically synthesized compounds that are used to control a variety of pests. These chemical compounds are used in a variety of sectors like food, forestry, agriculture and aquaculture. Pesticides shows their toxicity into the living systems. The World Health Organization (WHO) categorizes them based on their detrimental effects, emphasizing the relevance of public health. The usage can be minimized to a least level by using them sparingly with a complete grasp of their categorization, which is beneficial to both human health and the environment. In this review, we have discussed pesticides with respect to their global scenarios, such as worldwide distribution and environmental impacts. Major literature focused on potential uses of pesticides, classification according to their properties and toxicity and their adverse effect on natural system (soil and aquatic), water, plants (growth, metabolism, genotypic and phenotypic changes and impact on plants defense system), human health (genetic alteration, cancer, allergies, and asthma), and preserve food products. We have also described eco-friendly management strategies for pesticides as a green solution, including bacterial degradation, myco-remediation, phytoremediation, and microalgae-based bioremediation. The microbes, using catabolic enzymes for degradation of pesticides and clean-up from the environment. This review shows the importance of finding potent microbes, novel genes, and biotechnological applications for pesticide waste management to create a sustainable environment.

Decrypting the interaction pattern of Piperlongumine with calf thymus DNA and dodecamer d(CGCGAATTCGCG)2 B-DNA: Biophysical and molecular docking analysis

The mechanisms of interaction of DNA with pharmacological molecules are critical to understanding their therapeutic actions on physiological systems. Piperlongumine is widely studied for its anticancer potential. Multi-spectrometry, calorimetry and in silico studies were employed to study the interaction of piperlongumine and calf thymus DNA. UV-Vis spectroscopy illustrated a hyperchromic pattern in spectra of the calf thymus DNA-piperlongumine complex, while fluorescent quenching was observed in emission spectral studies. Competitive displacement assay demonstrated higher displacement and binding constant for DNA-rhodamine B complex by piperlongumine than DNA-methylene blue complex. Differential scanning calorimetry presented non-significant changes in melting temperature and molecular docking presented the precise interaction site of piperlongumine with calf thymus DNA at minor groove. Further, piperlongumine treatment did not result in pBluescript KS plasmid DNA cleavage as revealed from the DNA topology assay. All these experiments confirmed the binding of piperlongumine with DNA through minor groove binding mode.

Elimination of Pendimethalin in Integrated Rice and Procambarus clarkii Breeding Models and Dietary Risk Assessments

This study investigated elimination of the herbicide pendimethalin using an integrated rice and Procambarus clarkii breeding model of indoor and outdoor (pond culture) exposure tests. The pendimethalin levels in 484 samples from the primary rice and P. clarkii integrated breeding areas in Hubei province were monitored, and dietary risk assessments of pendimethalin were calculated. Pendimethalin was quantified using high-performance liquid chromatography tandem mass spectrometry, and detection levels were linear in the range of 1.0 to 10.0 μg/L, and peak areas were positively correlated with concentration, with a correlation coefficient of 0.9996. Recoveries ranged from 86.9 to 103.5%, and the limit of quantitation was 2.5 × 10⁻⁴ μg/L in water, and 1 × 10⁻² μg/kg in tissues, sediments, and waterweeds. The dissipation rate of pendimethalin in tissues and water followed first-order kinetics, with half-lives of 0.51–5.64 d. In 484 samples taken from aquaculture farms, pendimethalin was detected in 8.67% of the samples at levels in the range of 1.95 to 8.26 μg/kg in Hubei province from 2018 to 2020. The maximum residue limit of pendimethalin in P. clarkii has not been established in China, but our dietary risk assessments indicated that consumption of P. clarkii from integrated rice farms was acceptable.

Spectroscopic and theoretical evidences for the surface binding of voglibose drug with DNA

Binding of voglibose (VOG), an alpha glucosidase inhibitor, with CT-DNA has been investigated using various spectroscopic techniques including UV-Vis, fluorescence and circular dichroism (CD) coupled with relative viscosity. Isothermal titration calorimetric studies have been used to calculate the thermodynamic parameters such as ΔH (0.0188 cal/mol), ΔS (63.3 cal/mol/K) and ΔG (-18.8 kcal/mol), which reveal that the binding is a spontaneous process and hydrophobic and H-bonding interactions play major roles in the binding process. Effect of ionic strength confirms the existence of hydrophobic interaction between VOG and CT-DNA. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 suggest that VOG possibly binds on the surface of CT-DNA. Viscosity measurements also disclose that the binding could be mainly surface binding. Corroborating the experimental observations, metadynamics molecular simulation studies confirm that VOG binding on the surface of the DNA molecule through hydrophobic interactions and direct and water molecule mediated H-bonding.

Exploring the binding characteristics of febuxostat, an inhibitor of xanthine oxidase with calf thymus DNA: Multi-spectroscopic methodologies and molecular docking

In this paper, the interacting characteristics of febuxostat (FBST), an inhibitor of xanthine oxidase for treating gout patients with hyperuricemia with calf thymus DNA (ctDNA) was investigated through multi-spectroscopic methodologies combined with theoretical calculation for understanding the interacting mode on ctDNA, affinity with ctDNA, interacting forces, as well as the alteration in the conformation of ctDNA after interacting FBST The experimental results demonstrated that interacting FBST with ctDNA formed 1:1 complex, the association constant was 913 M^-1 at 298 K, suggesting the affinity of FBST on ctDNA was very weak, the interacting mode of FBST on ctDNA was groove binding, and it inserted into the minor groove with rich A-T region of ctDNA. Based on the results of the thermodynamic analysis and theoretical calculation, it can be inferred that the dominated interacting forces between FBST and ctDNA were van der Waals forces and hydrogen bond. And, interacting FBST with ctDNA was a spontaneous, enthalpy-driven, and exothermic process because of ΔG⁰ < 0, ΔH⁰ < 0, and |ΔH⁰| > T|ΔS⁰|. The results of the circular dichroism (CD) measurements indicated the conformation of ctDNA was weakly disturbed after interacting with FBST but still maintained B-conform. The studied results offer significant insight into further clarifying whether it has genotoxicity.

Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol^-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.

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.

Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies

Buprofezin (BUP) is an insecticide which belongs to the thiadiazine structural family and known to damage DNA in mice. Though its toxic effect on human is not known clearly, understanding the mechanism of interaction of BUP with DNA can prove useful when required. Multi-spectroscopic experiments such as UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR coupled with viscosity measurements, urea effect and voltametric studies were performed to ascertain the mode of binding of BUP with calf thymus DNA (CT-DNA). Analysis of UV-Vis and fluorescence spectra indicated the formation of a complex between BUP and CT-DNA. Other experiments such as competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, effect of urea, CD, voltammetric studies and ¹H NMR spectral analysis suggested that BUP intercalates into the base pairs of CT-DNA. All these results revealed that the binding mode of BUP with CT-DNA should be intercalation and the binding constant is in the order of 10⁴ M^-1. The ΔH^o < 0 and ΔS^o < 0 suggested that H-bonding or van der Waals force was the main binding force between BUP and CT-DNA. The proposed mode of binding of BUP with CT-DNA has been visualized using in silico molecular docking and metadynamics simulation studies, which showed that the phenyl ring of BUP binds to CT-DNA via π-π stacking interaction in addition to H-bond formation.Communicated by Ramaswamy H. Sarma.

The new psychoactive substances 25H-NBOMe and 25H-NBOH induce abnormal development in the zebrafish embryo and interact in the DNA major groove

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25H-NBOMe and 25H-NBOH recreational drugs induces abnormal formation in zebrafish embryos.

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Biophysical and theoretical studies indicate that these drugs have affinity for the DNA major groove.

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The toxicity observed in the zebrafish embryos and DNA interaction may be correlated.

Toxicological effects of 25H-NBOMe and 25H-NBOH recreational drugs on zebrafish embryos and larvae at the end of 96 h exposure period were demonstrated. 25H-NBOH and 25H-NBOMe caused high embryo mortality at 80 and 100 µg mL⁻¹, respectively. According to the decrease in the concentration tested, lethality decreased while non-lethal effects were predominant up to 10 and 50 µg mL⁻¹ of 25H-NBOH and 25H-NBOMe, respectively, including spine malformation, egg hatching delay, body malformation, otolith malformation, pericardial edema, and blood clotting. We can disclose that these drugs have an affinity for DNA in vitro using biophysical spectroscopic assays and molecular modeling methods. The experiments demonstrated that 25H-NBOH and 25H-NBOMe bind to the unclassical major groove of ctDNA with a binding constant of 27.00 × 10⁴ M⁻¹ and 5.27 × 10⁴ M⁻¹, respectively. Furthermore, these interactions lead to conformational changes in the DNA structure. Therefore, the results observed in the zebrafish embryos and DNA may be correlated.

Study the interaction between juglone and calf thymus DNA by spectroscopic and molecular docking techniques

Juglone (Jug) is one of the main active substances of Cortex Juglandis Mandshuricae in a folk anti-cancer prescription. Previously, there were few studies on its interaction with DNA and mechanism of action. The present paper studied, the mechanism of action between Jug and calf thymus DNA (ctDNA) by fluorescence spectroscopy, together with ethidium bromide (EB) fluorescence probe, UV-vis absorption spectroscopy, salt effect and ctDNA melting point (T_m) experiment, resonance scattering spectroscopy and molecular docking under the simulated human physiological conditions. The experimental findings indicated that Jug quiescently quenched the fluorescence of EB-ctDNA system, characteristic absorption peak intensity of ctDNA presented a decolorization effect after the interaction of ctDNA and Jug, the interaction with ctDNA enhanced of Jug resonance scattering peak and generated new resonance scattering peak, the salt exerted less effect on the interaction between Jug and ctDNA molecules, and the interaction with Jug increased the T_m value of ctDNA by 5.0 °C The binding constant (K_A) between Jug and ctDNA was 2.12 × 10⁵ L/mol (310 K) and the number of binding sites (n) was about 1. The interaction between Jug and ctDNA was an entropically driven spontaneous and endothermic process. The results of molecular docking further showed that the naphthoquinone plane was embedded in the region between the two TA bases in the ctDNA groove, and the 5'-hydroxyl and 4-naphthoquinone groups extended to the outside of the ctDNA double helix.

Assessment of cytotoxicity in gills of fish Labeo rohita reared in untreated and treated sewage water

The unregulated discharge of untreated municipal sewage water to the natural water bodies is a major threat to the aquatic ecosystems. In the present study, the fingerlings of Labeo rohita were exposed to treated sewage water and 1/10^th of LC₅₀ and 1/20^th of LC₅₀ of untreated sewage water (UT) obtained from sewage water treatment plant, Ludhiana, India. After determining 96-h LC₅₀ value of UT, fingerlings were divided into four groups: control, treated, 1/10^th of LC₅₀ UT and 1/20^th of LC₅₀ UT and exposed for a period of 2 months. Our study revealed that 1/10^th LC₅₀ UT and 1/20^th LC₅₀ UT groups had significant reduction in body weight, total body length, standard body length and gills somatic index in comparison with the control and treated groups. Histopathological alterations in cellular structure of gills such as ruptured primary lamellae, broken secondary lamellae, distorted chloride cells and goblet cells, missing lamellae and disintegrated lamellar epithelium were also observed in 1/10^th LC₅₀ UT and 1/20^th LC₅₀ UT groups. A significantly high frequency of micronucleated (MN) cells was observed in 1/10^th LC₅₀ UT and 1/20^th LC₅₀ UT groups along with the presence of binucleated cells (BN), elongated nuclei (EN) and nuclear buds in gill cells. Genotoxic nature of UT was further confirmed from significantly high values of genetic damage index (GDI) and percentage (%) DNA damage in gill cells of fingerlings exposed to sub-lethal concentrations of UT. The study concluded that untreated sewage water has potential to induce anatomical and physiological defects in gills cells and the severity of toxicity increases with the increase in duration of exposure.

Pendimethalin-based herbicide impairs cellular immune response and haemocyte morphology in a beneficial ground beetle

Herbicides have become the most commonly applied agrochemicals in agroecosystems. Thus, basic knowledge of their physiological effects on insects is needed, especially for understanding their impact on beneficial insect species. In this study, we evaluated the effect of a pendimethalin-based herbicide (PND) on the cellular immune response of the carabid beetle Harpalus (Pseudoophonus) rufipes (De Geer 1774) (Coleoptera, Carabidae), acting as biocontrol agent in agroecosystems. Total and differential haemocyte counts and phagocytosis assay, performed by injecting in vivo carboxylate-modified polystyrene latex beads, were measured in beetles exposed to a recommended field dose (4L per ha) of PND to evaluate the exposure effects over the time. The pattern of haemocyte subpopulations and the decrease of the phagocytic index after the exposure to PND suggested a lowering of P. rufipes ability to face an infection performing a cell-mediated response. PND was also found to cause cytotoxic effects on the haemocyte ultrastructure. Ultrastructural alterations such as irregular shape, large vacuolization of the cytoplasm, and condensation of marginated chromatin were recorded from 2d of exposure. The loss of RER, Golgi apparatus, mitochondria integrity and the swelling of the outer nuclear membrane found in some haemocytes suggested an interference of PND with the membrane permeability. Results indicated that the exposure to PND impairs the distribution, morphology and physiological functions of haemocytes causing a decrease of P. rufipes immunocompetence. Moreover, the sensitivity to herbicide exposure makes this species a suitable model and a useful bioindicator for monitoring exposure effects on non-target species. This study provides useful information to protect and preserve biodiversity of insects in agroecosystems.

A DNA small molecular probe with increasing K+ concentration promoted selectivity

DNA small molecular probe study was considered as a promising approach to achieve DNA related disease diagnosis. Most related reports were performed under specific salinity. Herein, 4-imino-3-(pyridin-2-yl)-4H-quinolizine-1-carbonitrile (IPQC) was generated via a facile procedure with high yield (85%). It is found that IPQC could act as a universal probe for most tested ssDNA, dsDNA and G4 DNA in low [K+] concentration (less than 20 mM). However, IPQC showed highly selective G4 DNA binding via UV-vis and fluorescence response in increasing [K+] (e.g., 150 mM) conditions. The ion atmosphere effects are instructive for DNA probe exploration. This provides guidance for the design, selection and optimization of the probes for target DNA sensing.

Genotoxic and epigenetic effects of diuron in the Pacific oyster: in vitro evidence of interaction between DNA damage and DNA methylation

Recently, research has contributed to better knowledge on the occurrence of pesticides in coastal water by identifying frequently detected substances, their concentration range and their acute and chronic toxicity for organisms. Pesticide pollution is of particular concern in France due to important agricultural activities and presence of several exoreic catchment areas that vehicle pesticides up to coastal waters, impacting non-target marine species. Several ecotoxicology questions remain to be addressed concerning the long-term effects of chronic pesticide exposure and the mechanisms involved in adaptation to chemical stress. In the present study, we brought new insights on the genetic and epigenetic effects of the herbicide diuron in oyster genitors. During gametogenesis, we exposed Crassostrea gigas to environmentally realistic herbicide concentrations (0.2-0.3 μg L^-1 during two 7-day periods at half-course and end of gametogenesis). Diuron exposure was shown to decrease global DNA methylation and total methyltransferase activity in whole oyster tissue; this is consistent with the previous observation of a significant decrease in DNMT1 gene expression. Diuron effect seemed to be tissue-specific; hypermethylation was detected in the digestive gland, whereas diuron exposure had no effect on gill and gonad tissue. The genotoxicity of diuron was confirmed by the detection of one adduct in gonad DNA. By using in vitro approaches and human DNMT1 (DNMT1 has not been purified yet in bivalves), the presence of DNA lesions (adduct, 8-oxodGuo) was shown to interfere with DNMT1 activity, indicating a complex interaction between DNA damage and DNA methylation. Based on our results, we propose mechanisms to explain the effect of diuron exposure on DNA methylation, a widespread epigenetic mark.

Heavy metal pollution and risk assessment by the battery of toxicity tests

The current study was carried out on dominant fish Oreochromis niloticus and water collected from the polluted Yamuna River, Agra, India. The heavy metals in water, recorded as follows: Fe > Mn > Zn > Cu > Ni > Cr > Cd and all were found to be above the prescribed limits. According to metal pollution index, exposed muscle (49.86), kidney (47.68) and liver (45.26) have been recorded to have higher bioaccumulation. The blood biochemical analysis of exposed O. niloticus indicated significant increase in activities of aspartate aminotransferase (+ 343.5%), alkaline phosphatase (+ 673.6%), alanine aminotransferase (+ 309.1%), and creatinine (+ 494.3%) over the reference. However, a significant decrease in albumin (A): globulins (G) ratio (− 87.86%) was observed. Similarly, the exposed fish also showed significant increase in total leucocyte count (+ 121%), differential leucocyte count, respiratory burst (+ 1175%), and nitric oxide synthase (+ 420%). The histological examination of liver and kidney showed tissue injury. Moreover, micronuclei (0.95%), kidney shaped nuclei (1.2%), and lobed nuclei (0.6%) along with DNA damage in the form of mean tail length in the liver (20.7 µm) and kidney (16.5 µm) was observed in the exposed O. niloticus. Potential health risk assessments based on estimated daily intake, target hazard quotient, hazard index, and target cancer risk indicated health risks associated with the consumption of these contaminated fishes. In conclusion, the present study showed that exposure to heavy metals contaminated water can alter immunological response; induce histopathological alterations and DNA damage in the studied fish. The consumption of this contaminated water or fish could have serious impact on human health.

DNA-Targeted NO Release Photoregulated by Green Light

A novel molecular hybrid has been designed and synthesized in which acridine orange (AO) is covalently linked to an N-nitrosoaniline derivative through an alkyl spacer. Photoexcitation of the AO antenna with the highly biocompatible green light results in intense fluorescence emission and triggers NO detachment from the N-nitroso appendage via an intramolecular electron transfer. The presence of the AO moiety encourages the binding with DNA through both external and partially intercalative fashions, depending on the DNA:molecular hybrid molar ratio. Importantly, this dual-mode binding interaction with the biopolymer does not preclude the NO photoreleasing performances of the molecular hybrid, permitting NO to be photogenerated nearby DNA with an efficiency similar to that of the free molecule. These properties make the presented compound an intriguing candidate for fundamental and potential applicative research studies where NO delivery in the DNA proximity precisely regulated by harmless green light is required.

Studies on conformational changes induced by binding of pendimethalin with human serum albumin

Pendimethalin (PND) is a widely used herbicide in modern means of agricultural practices. So, its toxic residues exist extensively in the environment and can enter human body. Therefore, the in vitro interaction of PND with human serum albumin (HSA) has been explored by employing various biophysical, molecular docking and dynamics simulation studies as well as enzyme kinetics to unravel its binding mechanism. The binding constant of the PND-HSA complex was about 10⁴ M^-1 using Fluorescence quenching spectra. The negative value of Gibbs free energy change (ΔG⁰ = -32.0 kJ mol^-1) indicates this interaction is a spontaneous process. A large negative ΔH⁰ and positive ΔS⁰ suggests that hydrophobic interactions and H-bonding are involved in the binding process of PND with HSA. The binding of PND can cause conformational and micro-environmental changes in HSA molecule, as shown by various biophysical and molecular dynamics simulation studies. The site marker competition and molecular docking and simulation experiments affirmed that the binding of PND to HSA occurs at or near site I. Esterase-like activity of HSA exhibited decline in the presence of PND revealed the direct involvement of Lys199 of subdomain IIA (Sudlow's site I) in the binding process.

Study on the substitution effects of zinc benzoate terpyridine complexes on photoluminescence, antiproliferative potential and DNA binding properties

Six zinc(II) complexes, [Zn(OCOPh)₂L^R] (R = 1, 2, 3, 4, 5, 6) were synthesized by the reaction of zinc benzoate and six para-substituted 4-phenyl-terpyridine complexes and their structures were confirmed by elemental analysis, FT-IR, ¹H NMR and X-ray single crystal diffraction analysis. Their photoluminescent properties in solid and in solutions of DMSO were studied. Three human cancer cell lines were used for antiproliferative potential: human lung cancer cell line (A549), human esophageal cancer cell line (Eca-109) and human breast cancer cell line (MCF-7). The results have shown that these zinc complexes have good inhibitory effects on cancer cells, which are better than that of the commonly used clinical drug cisplatin. The ability of the complexes to binding to CT-DNA was studied by UV spectroscopy and fluorescence titration, while the interaction between the complexes and CT-DNA, AT6, GC6 short-chain DNA sequences and G-quadruplex were analyzed by circular dichroism (CD). It is found that these complexes can bind to DNA, and the binding mode is mainly intercalator. The docking of the complexes with the DNA fragment was simulated using molecular docking software. All the results clearly display that the substituents at these ligands of the complexes have the substitution effects on the properties of photoluminescence, antiproliferative potential and DNA binding study.

Continuous Agrochemical Treatments in Agroecosystems Can Modify the Effects of Pendimethalin-Based Herbicide Exposure on Immunocompetence of a Beneficial Ground Beetle

Herbicide application for pest control can negatively affect soil biodiversity, mainly acting on species that are involved in ecosystem service. In this study, field and laboratory trials were designed to assay herbicide exposure effects on the constitutive immunity of Harpalus (Pseudoophonus) rufipes (De Geer, 1774), a beneficial carabid species that inhabits croplands. The circulating hemocytes (THCs) and plasmatic levels of basal and total phenoloxidase (PO), as well as lysozyme-like enzyme activities, were measured as markers of exposure. In laboratory tests, the exposure to realistic field doses of pendimethalin-based herbicides for two, seven and 21 days caused a reduction in enzyme activities in beetles from organic crops. In beetles from conventional fields, the THCs and total PO activity decreased significantly at two and seven days after the initial exposure, though no effects were recorded on basal PO and lysozyme like-enzyme activities. These differences in enzyme activities and THCs indicate that the interference of pendimethalin with immune parameters clearly depends on both the different field conditions from which the population comes and the cumulative effects of repeated applications over the time.

Spectroscopic investigations on DNA binding profile of two new naphthyridine carboxamides and their application as turn-on fluorescent DNA staining probes

Two new 10-methoxydibenzo[b,h][1,6]naphthyridine-2-carboxamide derivatives (R1 and R2) have been synthesized and characterized using different spectral techniques. The binding of these probes with DNA was investigated using spectral (Electronic, fluorescence, ¹H NMR and circular dichroism) and molecular docking studies. These probes exhibited a strong fluorescence around 440 nm upon excitation around 380 nm. Electronic and competitive fluorescence titration studies, in HEPES [(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)] buffer/dimethyl sulfoxide (pH 7.4) medium, suggest that these probes bind strongly to DNA, which is substantiated by ¹H NMR study. The binding constants are calculated to be 5.3 × 10⁷ and 6.8 × 10⁶ M^-1 for R1 and R2, respectively. From the results of spectral studies, it is proposed that the mechanism of binding of these probes with DNA is through minor groove binding mode, which is further confirmed by circular dichroism and molecular docking studies. Initial cell viability screening using MTT (3-[4,5-methylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay shows that normal Vero cells are viable towards these probes at nano molar concentration, which is the concentration range employed in the present study for DNA staining (IC₅₀ in the order of 0.023 mM). The enhancement in fluorescence intensity of these probes upon binding with DNA enables the staining of DNA in agarose gel in gel electrophoresis experiment. The sensitivity of these probes is comparable with that of ethidium bromide and DNA amounts as low as 4 nano gram are detectable.Communicated by Ramaswamy H. Sarma.

Groove binding between ferulic acid and calf thymus DNA: spectroscopic methodology combined with chemometrics and molecular docking studies

Ferulic acid (FA), a dietary phenolic acid compound, is proved to possess numerous biological activities. Hence, this study was devoted to explore the interaction between FA and calf thymus DNA (ctDNA) by UV - vis absorption, fluorescence, circular dichroism (CD) spectroscopy combined with multivariate curve resolution-alternating least-squares (MCR - ALS) and molecular docking studies. The concentration curves and the pure spectra of compositions (FA, ctDNA and FA - ctDNA complex) were obtained by MCR - ALS approach to verify and monitor the interaction of FA with ctDNA. The groove binding mode between FA and ctDNA was confirmed by the results of melting analysis, viscosity measurements, single-stranded DNA experiments, and competitive studies. The binding constant of FA - ctDNA complex was 4.87 × 10⁴ L mol^-1 at 298 K. The values of enthalpy (ΔH°) and entropy (ΔS°) changes in the interaction were -16.24 kJ mol^-1 and 35.02 J mol^-1 K^-1, respectively, indicating that the main binding forces were hydrogen bonds and hydrophobic interactions. The result of CD spectra suggested that a decrease in right-handed helicity of ctDNA was induced by FA and the DNA conformational transition from the B-form to the A-form. The results of docking indicated that FA binding with ctDNA in the minor groove. These findings may be conducive to understand the interaction mechanism of FA with ctDNA and the pharmacological effects of FA. Communicated by Ramaswamy H. Sarma[Formula: see text].

Exploring the binding interaction of Maillard reaction by-product 5-hydroxymethyl-2-furaldehyde with calf thymus DNA

BACKGROUND

5-Hydroxymethyl-2-furaldehyde (5-HMF), a by-product of the Maillard reaction, usually present in fried and baked food, may cause potential harm to the human body. Here, the interaction between 5-HMF and calf thymus DNA (ctDNA) under physiological buffer (pH 7.4) was studied using multi-spectroscopic methods combined with multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics and molecular simulation techniques.

RESULTS

The concentration profiles and pure spectra of the three components (5-HMF, ctDNA and 5-HMF-ctDNA complex) were extracted from highly overlapping spectra using MCR-ALS analysis, which verified the formation of 5-HMF-ctDNA complex. The binding constant being of the order of 10³  L mol^-1 at four temperatures (292, 298, 304 and 310 K) indicated a weak affinity in the binding of 5-HMF to ctDNA. The binding interaction was mainly driven by hydrogen bonds and van der Waals forces. Viscosity analysis, melting assay, ionic strength effect and competitive fluorescence studies ascertained that 5-HMF bound to ctDNA through groove binding, and it tended to bind to guanine-cytosine rich region of ctDNA which was characterized using Fourier transform infrared spectra and molecular docking. Circular dichroism spectral analysis and DNA cleavage assays indicated that the ctDNA conformation was altered from B to A form and 5-HMF caused DNA damage at higher concentration.

CONCLUSIONS

The results suggested that 5-HMF bound to ctDNA through groove binding and caused DNA damage. This research may contribute to understand the binding mechanism of 5-HMF to ctDNA and to the assessment of the toxicological effect of 5-HMF in biological processes. © 2018 Society of Chemical Industry.

Determination of the DNA binding properties of a novel PARP inhibitor MK-4827 with calf-thymus DNA by molecular simulations and detailed spectroscopic investigations

The binding interaction of niraparib (MK-4827), a poly(ADP-ribose) polymerase inhibitor, with calf thymus deoxyribonucleic acid (ctDNA) has been explored by various theoretical and experimental techniques.

Pendimethalin-induced oxidative stress, DNA damage and activation of anti-inflammatory and apoptotic markers in male rats

Male Wistar rats were exposed to herbicide, pendimethalin (PND) at varying oral doses of 62.5, 125 and 250 mg/kg b.w. for 14 days. Toxiological effects were assessed in terms of oxidative stress, DNA damage, histopathological alterations and induction of anti-inflammatory and apoptotic responses linked Bax, Bcl-2, IFN-γ, TNF-α and caspase-3 gene expression. In comparison with respective untreated controls, all exposure groups of PND exhibited significant changes in the oxidative stress markers (protein carbonylation and lipid peroxidation) and antioxidant defenses (GSH, SOD, CAT and GST) in liver and kidney tissues. The histopathological changes including leucocyte infiltration, pyknotic nuclei, necrosis, large bowman’s space, shrinked renal cortex, were observed in the liver and kidney tissues of PND exposed rats. Significant DNA damage was recorded through comet assay in liver and kidney cells of treated animals as compared to control. Alteration in anti-inflammatory and apoptotic genes expression determined by RT-PCR, revealed the activation of intrinsic apoptotic pathway(s) under the PND induced cellular stress. A pronounced increase in Bax expression, caspase-3 activities and decreased Bcl-2 expressions were also associated with PND-induced apoptosis. Data from this study suggests that PND induces cellular toxicity and genetic perturbations which can alter the normal cellular and physiological functioning in rats.

Binding studies of guggulsterone-E to calf thymus DNA by multi-spectroscopic, calorimetric and molecular docking studies

Guggulsterone, a sterol found in plants is used as an ayurvedic medicine for many diseases such as obesity, internal tumors, ulcers etc. E and Z are two isoforms of guggulsterone, wherein guggulsterone-E (GUGE) has also been shown to have anticancer potential. Most of the anticancer drugs target nucleic acids. Therefore, we studied the mode of interaction between ctDNA and GUGE using UV-Vis, fluorescence and CD spectroscopy, isothermal calorimetry along with molecular docking studies. Hoechst 3325, ethidium bromide and rhodamine-B displacement experiments confirms that GUGE binds in the minor groove of DNA. ITC results further suggest these interactions to be feasible and spontaneous with hydrogen bond formation and van der waals interactions. Lastly, molecular docking also suggests GUGE to be a minor groove binder interacting through a single hydrogen bond formation between OH group of GUGE and nitrogen (N3) of adenosine (A6).

Deciphering the mechanism of interaction of edifenphos with calf thymus DNA

Edifenphos is an important organophosphate pesticide with many antifungal and anti-insecticidal properties but it may cause potential hazards to human health. In this work, we have tried to explore the binding mode of action and mechanism of edifenphos to calf thymus DNA (CT-DNA). Several experiments such as ultraviolet-visible absorption spectra and emission spectroscopy showed complex formation between edifenphos and CT-DNA and low binding constant values supporting groove binding mode. These results were further confirmed by circular dichroism (CD), CT-DNA melting studies, viscosity measurements, density functional theory and molecular docking. CD study suggests that edifenphos does not alter native structure of CT-DNA. Isothermal calorimetry reveals that binding of edifenphos with CT-DNA is enthalpy driven process. Competitive binding assay and effect of ionic strength showed that edifenphos binds to CT-DNA via groove binding manner. Hence, edifenphos is a minor groove binder preferably interacting with A-T regions with docking score -6.84kJ/mol.