The experimental and theoretical QM/MM study of interaction of chloridazon herbicide with ds-DNA

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.

Monitoring of glyphosate-DNA interaction and synergistic genotoxic effect of glyphosate and 2,4-dichlorophenoxyacetic acid using an electrochemical biosensor

Glyphosate (GLY) is a broad-spectrum herbicide used worldwide to control broadleaf sedge, and grass weeds to control non-specific vegetation. Although it was evaluated as non-toxic agent in 20th century, its carcinogenic and genotoxic potential has being intensively investigated all over the world in the last decade. Moreover, the combination of GLY and 2,4-dichlorophenoxyacetic acid (2,4-D) has been widely applied. Although genotoxicity of GLY has been evaluated in vivo studies, there is no report in the literature for the monitoring of in vitro biointeraction of GLY and double stranded DNA, or how effect the combination of GLY and 2,4-D onto DNA. Herein, an electrochemical biosensor platform was developed for detection of the pesticide-DNA interaction by using disposable pencil graphite electrodes (PGEs). First, voltammetric detection of the interaction between GLY and DNA was investigated and the electrochemical characterization of the interaction was achieved. Taking a step further, the synergistic genotoxic effect of the mixture of GLY and 2,4-dichlorophenoxyacetic acid (2,4-D) or the mixture of their herbicide forms onto DNA could be monitored. This effect was concentration dependent, and the herbicide of GLY or the use of mixture of herbicides of GLY and 2,4-D had more genotoxic effect than analytical grade of the active molecules, GLY and 2,4-D. The single-use PGEs provided to fabricate robust, eco-friendly and time saver recognition platform for monitoring of herbicide-DNA interaction with the sensitive and reliable results. It is expected that this study will lead to be designed miniaturized lab-on-a chip platforms for on-line analysis of the pesticide-nucleic acid interactions.

Assessment of binding interaction dihydromyricetin and myricetin with bovine lactoferrin and effects on antioxidant activity

The binding interactions of bovine lactoferrin (BLF) with two flavonoids dihydromyricetin (DMY) and myricetin (MY) were investigated by the multi-spectroscopic, microscale thermophoresis (MST) techniques, molecular docking, and then their antioxidant activities were studied by detection of free radical scavenging activity against DPPH. Results of UV-vis and fluorescence spectroscopies showed that DMY/MY and BLF formed the ground state complex through the static quenching mechanism. Moreover, MY with more planar stereochemical structure had higher affinity for BLF than DMY with twisted stereochemical structure, according to the binding constant (K_b), free energy change (ΔG°), dissociation constant (K_d) and donor-acceptor distance (r). Thermodynamic parameters revealed that hydrogen bond and van der Waals force were major forces in the formation of BLF-DMY complex, while hydrophobic interactions played major roles in the formation of BLF-DMY complex. The circular dichroism (CD) study indicated that MY induced more conformational change in BLF than DMY. Furthermore, molecular modeling provided insights into the difference of binding interactions between BLF and two flavonoids. Finally, the radical scavenging activity assays indicated the presence of BLF delayed the decrease in antioxidant capacities of two flavonoids. These results were helpful to understand the binding mechanism and biological effects of non-covalent BLF-flavonoid interaction.

Monodisperse cobalt(II) based metal-organic coordination polymer beads as a sorbent for solid-phase extraction of chlorophenoxy acid herbicides prior to their quantitation by HPLC

Metal-organic coordination polymer beads (MOCBs) are described for use as a sorbent for solid-phase extraction of chlorophenoxy herbides. By applying regulation of Co(II) ions, micro-sized monodisperse MOCBs were obtained through the microwave heating. The MOCBs-based method displays excellent extraction efficiency towards chlorophenoxy herbicides, specifically of 2-chlorophenoxyacetic acid, 4-chlorophenoxyacetic acid, 4-chloromethylphenoxyacetic acid, 2,4-dichlorophenoxyacetic acid, 2,4,5-trichlorophenoxyacetic acid and 2-(2,4-dichlorophenoxy)propionic acid. Following extraction, the herbicides were eluted with 8% formic acid in methanol and quantified by HPLC. The method, when applied to analyze spiked cereals, exhibits a wide linear range (from 0.6 to 1000 ng g^-1) and low limits of quantification (ranging from 0.10 to 0.25 ng g^-1). For a single column, the inter-day and intra-day precisions, expressed as the relative standard deviation are in the range of 2.5-6.8%. The batch-to-batch reproducibility (for n = 3) is <4.6%. For spiked cereal samples, relative recoveries are very good (90.3-102.3%, for n = 4). The extraction efficiency of MOCBs remains unchanged after reusing for 40 times. Graphical abstractSchematic presentation of Co(II)-doped metal-organic coordination polymer beads (Co(II)@MOCB) using for solid-phase extraction (SPE).

Synthesis, characterization and DNA binding studies of a new ibuprofen-platinum(II) complex

The study is focused on the synthesis of a novel complex of ibuprofen and Platinum(II). The formation of the product was characterized through analytical tools including Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance, ultraviolet-visible spectroscopy, mass spectrometry as well as density functional theory. Using the continuous variation method, the stoichiometry of Pt(HIb)₂(Cl)₂ binding on DNA (ct-DNA) determines as a single class of binding. Based on the results of Stern-Volmer analysis on the fluorescence quenching data, the quenching mechanism was determined to be static in nature. The studies indicated that the complex could bind DNA molecules via groove binding for four major reasons. Initially, the complex-DNA binding constant determined based on spectrophotometric data were found to be comparable to those of groove-binding drugs. In addition, the competitive fluorimetric based on the applications of Hoechst 33258 proved the ability of Pt(HIb)₂(Cl)₂ to displace with Hoechst in its DNA-bounded form, reflecting the competition between Pt(HIb)₂(Cl)₂ and Hoechst for groove binding. Further, no considerable changes were observed in the intensity of the methylene blue (MB)-DNA system after adding the Pt(HIb)₂(Cl)₂ complex, reflecting the stability of MB molecules in the DNA helix and a non-intercalative bonds of Pt(HIb)₂(Cl)₂ interaction on DNA. Finally, minor changes in the viscosity of DNA in the presence of Pt(HIb)₂(Cl)₂, indicated that changes in the length of DNA in the presence of the complex are negligible, supporting the assumption of DNA groove-binding. Also induced CD spectral changes and docking simulations were in favor of the groove mechanism for the Pt(HIb)₂(Cl)₂-DNA binding.Communicated by Ramaswamy H. Sarma.

Synthesis of a 3,4-Disubstituted 1,8-Naphthalimide-Based DNA Intercalator for Direct Imaging of Legionella pneumophila

The development of organic molecules to target nucleic acid is an active area of research at the interface of chemistry and biochemistry, which involves DNA binding, nuclear imaging, and antitumor studies. These molecules bind with DNA through covalent interactions, electrostatic interactions, or intercalation. However, they are less permeable to membrane, and they have a significant cytotoxicity, which limits their application under in vivo conditions. In the present work, various mono- and disubstituted 1,8-naphthalimides-based derivatives (S-12, S-13, S-15, and S-21) have been synthesized and characterized through various spectroscopic techniques. Among these, 3-amino-4-bromo-1,8-naphthalimide (S-15) was found to have an attractive water solubility and act as a nuclear imaging agent. The spectroscopic absorption and emission data showed that S-15 has a strong affinity for salmon sperm DNA with a binding constant of 6.61 × 10⁴ M^-1, and the ratiometric fluorescence intensity (I ₄₈₉/I ₅₅₂) of S-15 has a linear relationship in the 0-50 μM range of DNA concentrations. It intercalates with DNA through the hydrophobic planar naphthalimide core as confirmed through cyclic voltammetry, circular dichroism, ¹H NMR titration, and thermal denaturation studies. Positively charged amine groups also participate in H-bonding with the bases and backbone of DNA. The S-15 intercalator showed a large Stokes shift and photostability, which made it attractive for direct imaging of Legionella pneumophila, without the need for a prior membrane permeabilization.

Coffee consumption and risk of nonmelanoma skin cancer: a dose-response meta-analysis

Several epidemiological studies have evaluated the associations between coffee consumption and the risk of skin cancer; however, the results were not conclusive. This systematic review and meta-analysis of the cohort and case-control studies was carried out to determine the association between coffee intake and the risk of nonmelanoma skin cancer. Studies were identified by searching the PubMed and MEDLINE databases (to November 2015). Study-specific risk estimates were pooled under the random-effects model. We separately estimated the relative risk of the three conditions, for exposure to different doses of coffee consumption, kind of study design, and analysis restricted to the basal cell carcinoma type. The summary relative risks for nonmelanoma skin cancer were 0.96 [95% confidence interval (CI): 0.92-0.99] for one cup of coffee, 0.92 (95% CI: 0.88-0.97) for one to two cups of coffee, 0.89 (95% CI: 0.86-0.93) for two to three cups of coffee, and 0.81 (95% CI: 0.77-0.85) for more than three cups of coffee per day, respectively. This meta-analysis suggested that caffeinated coffee might have chemopreventive effects against basal cell carcinoma dose dependently. However, other prospective studies are warranted to confirm these effects.

Two DNA binding modes of a zinc-metronidazole and biological evaluation as a potent anti-cancer agent

A complex of metronidazole (MTZ) with zinc ion was synthesized and characterized by UV-Vis, Fourier transform infrared (FT-IR), ¹H-NMR, X-ray crystallography and thermal gravimetric-differential thermal analysis (TG-DTA). The cytotoxicity effect of the synthesized complex investigated over SKNMC, A549, MCF-7, and MCDK cell lines and the results have shown that it has high cytotoxic potential over cancer cell lines. In order to clarify the mechanism of cell cytotoxicity, the oxidative stress and binding of the complex to the calf thymus-DNA studied by evaluating the intrinsic binding constant and defining thermodynamic parameters of complex over the DNA accompanying with in silico molecular modeling method. For this purpose, the complex optimized at the B3LYP/LANL2DZ level and docked over the DNA structure. The results revealed that the metronidazole-zinc complex interacted with DNA via hydrogen binding and electrostatic interaction to the minor groove region and phosphate backbone of DNA, respectively.

The evaluation of Cr-curcumin-DNA complexation by experimental and theoretical approaches

Chromium(III) chloride mediates DNA-DNA cross-linking. Some chromium complexes promote programmed cell death in specific ligand environment through binding to DNA. One strategy that can be supposed for reduction of Cr³⁺ binding affinity to DNA is using curcumin as a chelator. In the current study, the [Cr(Curcumin)(EtOH)₂](NO₃)₂ (CCC) was synthesized and characterized by UV/Vis, FT-IR, CHN and spectrophotometric titration techniques. The mole ratio plot revealed a 1:1 complex between Cr³⁺ and curcumin in solution. Binding interaction of this complex with calf thymus-DNA (CT-DNA) was investigated using UV/Vis, circular dichroism (CD), FT-IR and cyclic voltammetry. The intrinsic binding constants of CCC with DNA, measured by UV/Vis and cyclic voltammetry, were 1.60 × 10⁵ and 1.13 × 10⁵, respectively. The thermodynamic studies showed that the reaction is enthalpy and entropy favoured. CD analysis revealed that only Λ-CCC interacts with DNA and Δ-CCC form has no tendency towards DNA. Based on FT-IR studies, it was understood that CCC interacts with DNA via minor groove binding. The docking simulation was carried out for finding the binding mode of CCC to DNA, too. All of data demonstrated that the curcumin significantly reduced the affinity of Cr³⁺ to the DNA and the form of Δ-CCC has no interaction with DNA.

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.

Binding mode of triazole derivatives as aromatase inhibitors based on docking, protein ligand interaction fingerprinting, and molecular dynamics simulation studies

Aromatase inhibitors (AIs) as effective candidates have been used in the treatment of hormone-dependent breast cancer. In this study, we have proposed 300 structures as potential AIs and filtered them by Lipinski's rule of five using DrugLito software. Subsequently, they were subjected to docking simulation studies to select the top 20 compounds based on their Gibbs free energy changes and also to perform more studies on the protein-ligand interaction fingerprint by AuposSOM software. In this stage, anastrozole and letrozole were used as positive control to compare their interaction fingerprint patterns with our proposed structures. Finally, based on the binding energy values, one active structure (ligand 15) was selected for molecular dynamic simulation in order to get information for the binding mode of these ligands within the enzyme cavity. The triazole of ligand 15 pointed to HEM group in aromatase active site and coordinated to Fe of HEM through its N4 atom. In addition, two π-cation interactions was also observed, one interaction between triazole and porphyrin of HEM group, and the other was 4-chloro phenyl moiety of this ligand with Arg115 residue.

Proposed binding mechanism of galbanic acid extracted from Ferula assa-foetida to DNA

Recently, galbanic acid (GA), a sesquiterpenoid coumarin, has been introduced as an apoptotic and geno/cytotoxicity agent. In the present study, GA has been extracted from Ferula assa-foetida, a native medicinal plant in Iran, and characterized by ¹H NMR, mass spectroscopy. Additionally, spectroscopic studies have been performed in order to investigate its DNA-interaction mode. The electrochemical behavior of GA has been studied by cyclic voltammetry (CV) in various scan rates. In neutral media (pH=7.3) one irreversible cathodic peak was obtained at -1.46 V, while in higher scan rates an irreversible one was determined at -1.67 V. According to the voltametric data GA can be easily reduced by 2e^-/2H⁺ mechanism at hanging mercury drop electrode (HMDE). The interaction of GA with ct-DNA was evaluated by CV, differential pulse voltammetry (DPV), enhancement fluorescence, UV-Vis, FT-IR spectroscopy and molecular docking. The molecular docking study shows that the GA interacts to DNA on partial intercalation mode via DNA groove binding and forms a complex by van der Waals and electroastatic interactions. In addition, the thermodynamic parameters of GA-DNA complex were investigated with ΔH°, ΔS° and ΔG° values of 15.81KJmol^-1, 133.95Jmol^-1 and -23.10KJmol^-1, respectively. All data revealed that the GA is binding to DNA by van der Waals and electrostatic interactions through the partial intercalations from the DNA's grooves.

Grandivittin as a natural minor groove binder extracted from Ferulago macrocarpa to ct-DNA, experimental and in silico analysis

Ferulago macrocarpa (Fenzl) Boiss., is an endemic medicinal herb of Iran. In this study a dihydrofuranocoumarin called grandivittin (GRA) was separate and purified from Ferulago macrocarpa (Fenzl) Boiss, and characterized by (1)H NMR and Mass spectroscopic methods. The electrochemical behavior of GRA was evaluated by cyclic voltammetry (CV). The interaction of GRA with calf thymus double strand deoxyribonucleic acid (ct-DNA), was evaluated by CV, differential pulse voltammetry (DPV), fluorescence, UV-Vis, FT-IR and molecular modeling methods. The thermodynamic parameters of GRA-DNA complex were measured and reported as: ΔH = 15.04 kJ mol(-1), ΔS = 105.54 J mol(-1) and ΔG = -15.62 kJ mol(-1). Docking simulation was performed to investigate the probable binding mode of GRA to various DNA, too. The polymerase extension study was performed using real-time PCR to confirm the inhibitory effect of GRA on polymerase extension activity as a mirror of binding to ct-DNA. However, all data showed that the grooves binding especially minor groove between GRA and ct-DNA is more predominant rather than other binding modes.

Separation and quantitative determination of cinacalcet metabolites in urine sample using RP-HPLC after derivation with a fluorescent labeling reagent

In this investigation, a novel strategy for separation and quantitative determination of four metabolites of cinacalcet (M2a-Glu, M2b-Glu, M7-Gly, and M8-Gly) in human urine is suggested. The analytical assay is based on a pre-column derivation procedure of cinacalcet metabolites with 1-pyrenyldiazomethane (PDAM) as a fluorescent labeling reagent, and subsequently separation and quantitative determination with reverse-phase high-performance liquid chromatography (RP-HPLC) coupled with a fluorescence detector. Metabolites were separated on a Microsorb-MV 100-5 C18 chromatography column (250×4.6mm, 5μm) using acetate buffer (pH 3.5):methanol (30:70 v/v) as mobile phase at a flow rate of 1.0mLmin(-1). The method was fully validated in terms of linearity (r(2)>0.996; 1-10ngmL(-1)), precision (both intra-day and inter-day; RSD<6.2%), accuracy (92-110%), specificity, robustness (0.15%<RSD<4.1%), limits of detection (5×10(-4) to 3×10(-3)ngmL(-1)) and quantification (2×10(-3) to 1×10(-2)ngmL(-1)). According to the results, the proposed method can be useful in the routine analysis for the determination of cinacalcet metabolites in urine samples.

Interaction of ruthenium(ii) antitumor complexes with d(ATATAT)2 and d(GCGCGC)2: a theoretical study

We have investigated the interaction of three ruthenium(ii) complexes with d(ATATAT)₂ and d(GCGCGC)₂ sequences by using the molecular docking and quantum mechanics/molecular mechanics (QM/MM) hybrid method.

Proposed model for binding of permethrin and deltamethrin insecticides with ct-DNA, a structural comparative study

In this work, the interaction of two synthetic pyrethroid insecticides, permethrin (PER) and deltamethrin (DEL), with ct-DNA has been studied by cyclic voltammetry (CV), circular dichroism (CD), competitive fluorescence, atomic force microscopy (AFM), UV-vis spectroscopy, thermodynamic measurements, Fourier-transform infra-red (FT-IR), high performance liquid chromatography (HPLC) and two-layered ONIOM (our N-layered integrated molecular orbital+molecular mechanics) (DFT B3LYP, 6-31++G(d, p):UFF) molecular modeling methods. The last four methods were also utilized to study the binding of DEL with DNA. The results revealed that the PER may interact through partial intercalation and groove binding process while the PER only interacts through groove binding. Finally, the insecticides structure effect on interaction is discussed.

Proposed model for in vitro interaction between fenitrothion and DNA, by using competitive fluorescence, (31)P NMR, (1)H NMR, FT-IR, CD and molecular modeling

In this work we proposed a model for in vitro interaction of fenitrothion (FEN) with calf thymus-DNA by combination of multispectroscopic and two dimensional molecular modeling (ONIOM) methods. The circular dichroism results showed that FEN changes the conformation of B-DNA and caused some changes to C-DNA form. The FT-IR results confirmed a partial intercalation between FEN and edges of all base pairs. The competitive fluorescence, using methylene blue as fluorescence probe, in the presence of increasing amounts of FEN, revealed that FEN is able to release the non-intercalated methylene blue from the DNA. The weak chemical shift and peak broadening of (1)H NMR spectrum of FEN in the presence of DNA confirmed a non-intercalation mode. The (31)P NMR showed that FEN interacts more with DNA via its -NO2 moiety. The ONIOM, based on the hybridization of QM/MM (DFT, 6.31++G (d,p)/UFF) methodology, was also performed by Gaussian 2003 package. The results revealed that the interaction is base sequence dependent, and FEN interacts more with AT base sequences.

A three-layer ONIOM model for the outside binding of cationic porphyrins and nucleotide pair DNA

In this work we investigated the outside binding mode between a cationic porphyrin and a nucleotide pair of DNA, adenine-thymine and guanine-cytosine, in a supramolecular assembly. We used two structural models (semi-extended, extended) that differ in the size of porphyrin, two kinds of theoretical methods: a three layer ONIOM (B3LYP/6-31G(d)/PM3/UFF), and DFT B3LYP/6-31G(d,p), and three cationic porphyrins. ONIOM method was first tested on the semi-extended model that was calculated in four environments: gas phase, solution phase using an explicit solvent model (H(2)O), in the presence of a sodium cation (Na(+)) and in both (H(2)O + Na(+)). From interaction energy results, we found that the affinity of the cationic substituent by the adenine nucleotide is favored upon the thymine nucleotide. The extended model that considers the whole porphyrin was applied in the gas phase to the four nucleotides. All the cationic porphyrins showed affinity by the nucleotides in the order adenine > guanine > thymine > cytosine. The interaction energy values for outside binding showed a strong porphyrin-nucleotide interaction (≈-90 kcal mol(-1)), that slightly varies between the nucleotides suggesting that this kind of cationic porphyrin has a little selectivity for some of them. We also found that the effect of the nature of the cationic substituent (chain length) in the porphyrin on the outside binding is small (≈2-13 kcal mol(-1)). Coherence between the results showed that ONIOM is a useful tool to get a reasonable molecular geometry to be used as a starting point in calculations of density functional theory.