Recent Computer-Aided Studies on Herbicides: A Short Review.

Current industrial herbicides have a negative impact on the environment and have widespread resistance, so computational studies on their properties, elimination, and overcoming resistance can be helpful. On the other hand, developing new herbicides, especially bioherbicides, is slow and costly. Therefore, computational studies that guide the design and search for new herbicides that exist in various plant sources, can alleviate the pain associated with the many obstacles. This review summarizes for the first time the most recent studies on both aspects of herbicides over 10 years.

New Facts on the Antimicrobial Essential Oil of Satureja kitaibelii.

The objective of the present study was to assess the difference in antimicrobial activity of Satureja kitaibelii Wierzb. ex Heuff. essential oil at three growth stages. In addition, using statistical and chemometric tools, we tried to explain why the essential oil from a certain vegetation stage shows the highest antimicrobial activity. S. kitaibelii essential oils demonstrated minimum inhibitory concentration values from 160 to 10000 µg mL-1 , and minimum microbicidal concentration values from 630 to 20000 µg mL-1 . Geraniol, borneol, limonene and p-cymene are the dominant compounds of S. kitaibelii essential oil. The most abundant compound, geraniol, possesses antimicrobial activity in a range of MIC values from 40 to 5000 µg mL-1 and MMC values from 80 to 10000 µg mL-1 . The highest activity of essential oil for all tested strains of microorganisms was recorded in November. Results of statistical analysis indicate that the percentage of dominant compounds of essential oils does not affect the antibacterial activity of essential oils. Chemometric analyses leads to the conclusion that borneol, spathulenol, caryophyllene oxide and limonene can be the main contributors to the antibacterial activity of essential oil from November and that their mutual ratio is important. These results may represent a new methodological approach for future research on essential oils.

In Silico Investigation of Selected Pesticides and Their Determination in Agricultural Products Using QuEChERS Methodology and HPLC-DAD.

In this study, we considered some pesticides as active substances within formulations for the protection of plant-based food in the Republic of Serbia in silico, because these pesticides have not often been investigated in this way previously, and in an analytical way, because there are not very many available fast, cheap, and easy methods for their determination in real agricultural samples. Seven pesticides were detected in selected agricultural products (tomatoes, cucumbers, peppers, and grapes) using the QuEChERS methodology and HPLC-DAD. Standard curves for the investigated pesticides (chlorantraniliprole, methomyl, metalaxyl, thiacloprid, acetamiprid, emamectin benzoate, and cymoxanil) show good linearity, with R2 values from 0.9785 to 0.9996. The HPLC-DAD method is fast, and these pesticides can be determined in real spiked samples in less than 15 min. We further characterized the pesticides we found in food based on physicochemical properties and molecular descriptors to predict the absorption, distribution, metabolism, elimination, and toxicity (ADMET) of the compounds. We summarized the data supporting their effects on humans using various computational tools to determine their potential adverse effects. The results of our prediction study show that all of the selected pesticides considered in this study have good oral bioavailability, and those with high toxicity, therefore, could be harmful to human health. Chlorantraniliprole was shown in a molecular docking study as a good starting point for a new Alzheimer's disease drug candidate.

Molecular Docking Assessment of Cathinones as 5-HT2AR Ligands: Developing of Predictive Structure-Based Bioactive Conformations and Three-Dimensional Structure-Activity Relationships Models for Future Recognition of Abuse Drugs.

Commercially available cathinones are drugs of long-term abuse drugs whose pharmacology is fairly well understood. While their psychedelic effects are associated with 5-HT2AR, the enclosed study summarizes efforts to shed light on the pharmacodynamic profiles, not yet known at the receptor level, using molecular docking and three-dimensional quantitative structure-activity relationship (3-D QSAR) studies. The bioactive conformations of cathinones were modeled by AutoDock Vina and were used to build structure-based (SB) 3-D QSAR models using the Open3DQSAR engine. Graphical inspection of the results led to the depiction of a 3-D structure analysis-activity relationship (SAR) scheme that could be used as a guideline for molecular determinants by which any untested cathinone molecule can be predicted as a potential 5-HT2AR binder prior to experimental evaluation. The obtained models, which showed a good agreement with the chemical properties of co-crystallized 5-HT2AR ligands, proved to be valuable for future virtual screening campaigns to recognize unused cathinones and similar compounds, such as 5-HT2AR ligands, minimizing both time and financial resources for the characterization of their psychedelic effects.

Chemometric Approach to the Composition of Flavonoid Compounds and Phenolic Acids and Antioxidant Potential of Artemisia Species from Different Habitats.

Four Artemisia species from Serbia were selected for the study: A. annua L., A. absinthium L., A. vulgaris L. and A. scoparia Waldst. et Kit. because of the proven excellent action in treating certain medical conditions and diseases. A. absinthium L., A. vulgaris L., A. annua L. and A. scoparia Waldst. et Kit. collected from different habitats across Serbia (48 samples in total) were studied from the statistical aspect considering the phenolic and flavonoid contents, compositions, and antioxidant activities of methanol extracts in correlation with the soil type. The components were identified using HPLC (High Performance Liquid Chromatography), while antioxidant activities were determined by seven assays (TP (Total phenolic content), TF (Total flavonoid content), DPPH (2,2-diphenyl-1-picrylhydrazyl) radical-based, ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) radical cation-based, FRAP (Ferric Reducing Antioxidant Power), TRP (Total Reducing Power), and CUPRAC (Cupric Reducing Antioxidant Capacity). The results were processed using five statistical methods (PCA (Principal Component Analysis), ANOVA (Analysis of Variance), MANOVA (Multivariate analysis of variance), DA (Discriminant analysis), and AHC (Agglomerative Hierarchical Clustering)). Principal component analysis enabled very well separation of the analyzed Artemisia species based on the content of total phenolics, total flavonoids, and the values obtained from antioxidant tests, but not on the individual compounds identified and quantified by HPLC. The MANOVA analyses showed that for A. scoparia and A. annua there was a significant effect of soil type on the total phenolics, total flavonoids, and antioxidant tests. In contrast, for A. vulgaris and A. absinthium, that effect was not significant. Additional MANOVA analyses showed a significant effect of soil type on phenolic and flavonoid compounds in the case of A. vulgaris, A. annua, and A. absinthium. The overall correct classification rate of all samples of four investigated Artemisia species by the discriminant analysis was 81.25 % using the training sample and 72.92 % the cross-validation results based on TP, TF, and antioxidant tests, but a much lower based on selected compounds identified and quantified by HPLC. MANOVA analyses based on particular Artemisia species show that soil is a significant factor affecting the measurable variables.

Computational Studies on Selected Macrolides Active against Escherichia coli Combined with the NMR Study of Tylosin A in Deuterated Chloroform.

Although many antibiotics are active against Gram-positive bacteria, fewer also show activity against Gram-negative bacteria. Here, we present a combination of in silico (electron ion-interaction potential, molecular docking, ADMET), NMR, and microbiological investigations of selected macrolides (14-membered, 15-membered, and 16-membered), aiming to discover the pattern of design for macrolides active against Gram-negative bacteria. Although the conformational studies of 14-membered and 15-membered macrolides are abundant in the literature, 16-membered macrolides, and their most prominent representative tylosin A, have received relatively little research attention. We therefore report the complete 1H and 13C NMR assignment of tylosin A in deuterated chloroform, as well as its 3D solution structure determined through molecular modelling (conformational search) and 2D ROESY NMR. Additionally, due to the degradation of tylosin A in deuterated chloroform, other species were also detected in 1D and 2D NMR spectra. We additionally studied the anti-bacterial activity of tylosin A and B against selected Gram-positive and Gram-negative bacteria.

The Targeted Pesticides as Acetylcholinesterase Inhibitors: Comprehensive Cross-Organism Molecular Modelling Studies Performed to Anticipate the Pharmacology of Harmfulness to Humans In Vitro.

Commercially available pesticides were examined as Mus musculus and Homo sapiens acetylcholinesterase (mAChE and hAChE) inhibitors by means of ligand-based (LB) and structure-based (SB) in silico approaches. Initially, the crystal structures of simazine, monocrotophos, dimethoate, and acetamiprid were reproduced using various force fields. Subsequently, LB alignment rules were assessed and applied to determine the inter synaptic conformations of atrazine, propazine, carbofuran, carbaryl, tebufenozide, imidacloprid, diuron, monuron, and linuron. Afterwards, molecular docking and dynamics SB studies were performed on either mAChE or hAChE, to predict the listed pesticides' binding modes. Calculated energies of global minima (Eglob_min) and free energies of binding (∆Gbinding) were correlated with the pesticides' acute toxicities (i.e., the LD50 values) against mice, as well to generate the model that could predict the LD50s against humans. Although for most of the pesticides the low Eglob_min correlates with the high acute toxicity, it is the ∆Gbinding that conditions the LD50 values for all the evaluated pesticides. Derived pLD50 = f(∆Gbinding) mAChE model may predict the pLD50 against hAChE, too. The hAChE inhibition by atrazine, propazine, and simazine (the most toxic pesticides) was elucidated by SB quantum mechanics (QM) DFT mechanistic and concentration-dependent kinetic studies, enriching the knowledge for design of less toxic pesticides.

A preliminary evaluation of influence of body mass index on in vitro fertilization outcome in non-obese endometriosis patients.

BACKGROUND/AIMS: Obese and overweight women experience a lower probability for pregnancy after IVF. However, despite the increasing prevalence of obesity, the large majority of infertile women are non-obese. One of the most common indications for IVF is endometriosis. Thought-provoking inverse correlation has been established between BMI and endometriosis. Lower BMI is a risk factor for development of endometriosis and a predictive factor for severe endometriosis. Since severe endometriosis carries lower reproductive chances, even after IVF, we preliminary tested a hypothesis that higher BMI among non-obese endometriosis patients improves IVF outcomes. METHODS: Preliminary retrospective observational cross-sectional study was performed in women with endometriosis as a sole infertility cause who underwent IVF. During analyzed period we performed 2782 IVF procedures. In order to achieve highly homogenous study sample and to eliminate almost all confound factors that could lead to bias, we implemented strict study criteria. The number of eligible subjects was 156 and they were divided into underweight, normal weight and overweight groups. Primary outcomes were number of retrieved oocytes, good quality oocytes, embryos, and the rates of biochemical, clinical and ongoing pregnancies. For group comparisons, we used parametric test, analysis of variance, and non-parametric tests (Kruskal-Wallis test, Chi-square test). Logistic regression and General linear model was used to assess correlation between BMI and dependent variables (outcome and stimulation duration) when adjusted for age. RESULTS: Endometriosis as a single infertility factor among IVF couples had prevalence of 5.61%. Underweight women accounted for 10.26%, normal weight 71.15% and overweight 18.59% of study population. Significant differences were not found in number of retrieved oocytes (p = 0.880), good quality oocytes (p = 0.476), obtained embryos (p = 0.706), and biochemical (p = 0.298), clinical (p = 0.770) and ongoing (p = 0.822) pregnancy rates between study groups. CONCLUSION: Although preliminary results do not support our hypothesis, increase in BMI did not adversely affect the outcome of IVF in non-obese endometriosis patients, which is in contrast to literature data as regards general population of infertile women undergoing IVF. Prospective studies with large number of patients with endometriosis or prospective case-control studies should address these issues and provide more comprehensive counseling of infertile endometriosis patients regarding achievement of optimal BMI prior to IVF with the intention of achievement higher pregnancy rates.

Broad-spectrum of antimicrobial properties of commercial wines from different Vitis vinifera L. varieties.

Fifteen commercial wines produced from international and autochthonic varieties of Vitis vinifera L. cultivation of different Balkan winegrowing subregions were studied for their antimicrobial activity against six Gram-positive (Clostridium perfringens, Bacillus subtilis, Staphylococcus aureus, Listeria inocua, Sarcina lutea and Micrococcus flavus) and six Gram-negative (Escherichia coli, Pseudomonas aeruginosa, Salmonella enteritidis, Shigella sonnei, Klebsiella pneumonia and Proteus vulgaris) bacteria. The concentrations and types of phenolic compounds responsible for antibacterial activity in wines were investigated by HPLC and spectroscopic methods. The correlation between amounts of phenolics and antibacterial activities of investigated wines were studied by application of statistical (PCA, factor and cluster) analyses. This study gives the possibility to predict the biological quality of the wine from the same cluster towards bacteria without "wet" analysis. Obtained results can to be useful both to wine producers for the formation of market price of wine, and to wine consumers in choosing quality red wine with high content of polyphenols.

Enhancement of the properties of a drug by mono-deuteriation: reduction of acid-catalysed formation of a gut-motilide enol ether from 8-deuterio-erythromycin B.

Erythromycin B is structurally very similar to erythromycin A, and also shares its clinically important antibacterial activity. Its potential advantage is that it is much more stable to acid. Both compounds are susceptible to 6-9-enol ether formation, involving loss of a proton from C-8. The enol ethers lack antibacterial activity and can give rise to unpleasant gut motilide side-effects. Our previous work on degradation kinetics revealed that the formation of erythromycin B enol ether from erythromycin B is subject to a large deuterium isotope effect. We therefore synthesized 8-d-erythromycin B (in 87% yield) in the hope that acid-catalysed enol ether formation would be reduced, relative to erythromycin B. In a range of microbiological and biochemical assays, deuteriation did not appear to compromise the efficacy of the drug. Degradation studies showed, however, that incorporation of deuterium into erythromycin B reduces (though does not completely suppress) enol ether formation, providing the possibility of using a facile mono-deuteriation to reduce the gut motilide side-effects of the drug.

Statistical characteristics of selected elements in vegetables from Kosovo.

Zinc, copper, iron, chromium and cobalt are essential elements for human health, showing toxicity only in high concentrations, while lead and cadmium are extremely toxic even as traces. Therefore, it is important to monitor the contents of toxic metals in vegetables. Large number of vegetables is grown and used in nutrition, in Kosovo. The concentrations of selected elements in vegetables (radish, onion, garlic and spinach) from Kosovo were determined using ICP-OES method. Oral intake of metals and health risk index were calculated. Statistical analysis indicated numerous positive correlations between concentrations of selected elements in vegetables. As a result of principal component analysis, 15 new variables were obtained which were characterized by eigenvalues. The sequence of health quotients for the heavy metals followed the decreasing order Zn = Mn > Pb > Cu > Ni > Fe > Cd > Co > Cr. The health quotients for all investigated heavy metals were below 1 (one), which is considered safe. The vegetables from Kosovo are mainly safe for use in everyday diet.

Creation of products made from honey based on the content of elements determined by ICP-OES.

People of different age can consume honey, but the taste is often not accepted easily. Therefore, products made from honey with a pleasant taste and high nutritional and health benefits are highly demanded on the market. Honey is a bioindicator of environmental pollution. Certain plants are known as high accumulators of toxic elements. Here on the example of three honey-based prototypes, with sesame, shelled pumpkin, sunflower seeds, plums, walnut, almond, hazel, and cinnamon as minor ingredients, we demonstrated the creation of new products putting the accent on the content of toxic and potentially toxic elements, usually treated as irrelevant in making products. Nineteen elements (Al, B, Ba, Ca, Cd, Co, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, P, Pb, Se, Si, and Zn) were determined by ICP-OES after oven-based and wet digestion methods in blossom honey and prototypes samples. Among the investigated elements, the most abundant element in blossom honey for the products and the investigated products was potassium in most cases. Investigated honey (used for the products) and two of the products contain small quantities of toxic and potentially toxic elements. However, the second product, containing besides honey two accumulators of toxic metals (sesame, sunflower seeds), shows higher values for toxic elements. Therefore, the ICP-OES analysis can be a good step in making new products with high nutritional and health values but almost free from toxic and potentially toxic elements.

Pregnancy outcomes and newborn characteristics in women with follicular fluid thyroid autoantibodies undergoing assisted reproduction.

Background: Higher levels of thyroid autoantibodies in follicular fluid (FF) of thyroid autoimmunity (TAI) positive women are strongly correlated with serum levels and may have effect on the post-implantation embryo development. Literature highlights that levothyroxine (LT4) treatment may attenuate the risk of adverse pregnancy outcomes. The aim of the study was to estimate the pregnancy and newborn outcomes in women with FF thyroid autoantibodies undergoing assisted reproductive technology (ART). Methods: The study population included 24 women with confirmed clinical pregnancy, 8 TAI positive and 16 TAI negative women. LT4 supplementation was applied in 20.8% patients, TAI positive. Results: Pregnancy outcomes were: twin pregnancy rate 41.7%, early miscarriage rate 8.3%, late miscarriage rate 4.2%, preterm birth rate 16.7%, term birth rate 70.8%, live birth rate 96.0%. There was significant difference in serum and in FF TgAbs (p< 0.001)between the groups according to TAI, while serum fT3 was lower in the group with TAI (p = 0.047). Serum P4 was higher in LT4 treated group (p = 0.005), with TAI, and newborns in this group had higher birth weight (p = 0.001) and height (p = 0.008). Maternal complications occurred in 23.8% of patients. No congenital malformations in newborns were noted. Conclusions: Thyroid autoantibodies present in FF may have an effect on the post-implantation embryo development, but have no effect on further course of pregnancy. The special benefit of LT4 treatment for successful ART outcome was demonstrated for newborn anthropometric parameters.

Selected Derivatives of Erythromycin B-In Silico and Anti-Malarial Studies.

Erythromycin A is an established anti-bacterial agent against Gram-positive bacteria, but it is unstable to acid. This led to an evaluation of erythromycin B and its derivatives because these have improved acid stability. These compounds were investigated for their anti-malarial activities, by their in silico molecular docking into segments of the exit tunnel of the apicoplast ribosome from Plasmodium falciparum. This is believed to be the target of the erythromycin A derivative, azithromycin, which has mild anti-malarial activity. The erythromycin B derivatives were evaluated on the multi-drug (chloroquine, pyrimethamine, and sulfadoxine)-resistant strain K1 of P. falciparum for asexual growth inhibition on asynchronous culture. The erythromycin B derivatives were identified as active in vitro inhibitors of asexual growth of P. falciparum with low micro-molar IC50 values after a 72 h cycle. 5-Desosaminyl erythronolide B ethyl succinate showed low IC50 of 68.6 µM, d-erythromycin B 86.8 µM, and erythromycin B 9-oxime 146.0 µM on the multi-drug-resistant K1 of P. falciparum. Based on the molecular docking, it seems that a small number of favourable interactions or the presence of unfavourable interactions of investigated derivatives of erythromycin B with in silico constructed segment from the exit tunnel from the apicoplast of P. falciparum is the reason for their weak in vitro anti-malarial activities.

Synthesis and bioluminescence-inducing properties of autoinducer (S)-4,5-dihydroxypentane-2,3-dione and its enantiomer.

The autoinducer (4S)-4,5-dihydroxypentane-2,3-dione ((S)-DPD, AI-2) facilitates chemical communication, termed 'quorum sensing', amongst a wide range of bacteria, The synthesis of (S)-DPD is challenging in part due to its instability. Herein we report a novel synthesis of (S)-DPD via (2S)-2,3-O-isopropylidene glyceraldehyde, through Wittig, dihydroxylation and oxidation reactions, with a complimentary asymmetric synthesis to a key precursor. Its enantiomer (R)-DPD, was prepared from d-mannitol via (2R)-2,3-O-isopropylideneglyceraldehyde. The synthesized enantiomers of DPD have AI-2 bioluminescence-inducing properties in the Vibrio harveyi BB170 strain.

Hamilton anxiety scale (HAMA) in infertile women with endometriosis and its correlation with magnesium levels in peritoneal fluid.

BACKGROUND: Endometriosis is a complex disease that can result in substantial morbidity, including chronic pain, dysmenorrhea and dyspareunia. There are contradictory reports regarding the connection between acute and chronic stress and magnesium levels in body fluids. SUBJECTS AND METHODS: A prospective study included 87 patients undergoing laparoscopy. The study group included 40 women with endometriosis and the control group consisted of 47 women with other causes of infertility. The levels of fright were determined using HAMA scale. The measurements of Mg levels were performed using biochemical analyzer "Monarch Plus". RESULTS: One day before the operation, HAMA score was 9.54+/-7.34 in the women with endometriosis, and 6.69+/-5.51 in the women without endometriosis. The morning before the operation, HAMA score was 8.64 +/- 8.10 in the women with endometriosis, and 4.29+/-2.29 in the women without endometriosis. The second postoperative day, HAMA score was 8.96+/-7.60 in the women with endometriosis and 6.92+/-5.16 in the women without endometriosis. Higher HAMA score in the women with endometriosis, in comparison with the control group, in all three time periods has been found, but the differences were not statistically significant (p>0.05). A negative correlation between the concentration of Mg in peritoneal fluid and HAMA score was found in the control group (p<0.01). CONCLUSIONS: In infertile women without endometriosis a correlation between Mg concentration in peritoneal fluid and HAMA score was found. No such correlation was found in the women with endometriosis, possibly due to a systemic disorder in endometriosis that might affect Mg transport through the cell membrane.

Author Correction: Influence of the magnetic field on bandgap and chemical composition of zinc thin films prepared by sparking discharge process.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Influence of the magnetic field on bandgap and chemical composition of zinc thin films prepared by sparking discharge process.

We examine the influence of the magnetic field on the chemical reaction of nitrogen and carbon dioxide in sparking electric discharge of zinc wires. Samples are prepared on Indium Tin Oxide (ITO) and quartz substrates in the form of thin films at 0 T, 0.2 T and 0.4 T. Different chemical composition of thin-films prepared by sparking discharge was obtained and verified by XPS, Raman and Cyclic voltammetry. Carbon dioxide conversion to carbonates was observed for zinc sparked in CO2 and nitrogen affecting crystallization of thin films was confirmed by XRD. Synthesis route for thin-film preparation used in this study is electric sparking discharge, convenient for fast ionization of metal and gasses. Band gap energy of thin films prepared by this method was starting from 2.81 eV and 4.24 eV, with the lowest band gaps prepared on ITO in 0.4 T. Dynamic mobility analysis (DMA) indicates smaller particles are fabricated by discharging zinc wires in a higher magnetic field. Nitridification of zinc nanoparticles occurred on 0.2 Tesla magnetic field strength and it was detectable even after XPS ion gun etching. Carbonation and nitridification of zinc thin films by sparking wires inside the magnetic field to observe the effect of the magnetic field on bandgap and chemical composition are confirmed by XPS.

Free and bound state structures of 6-O-methyl homoerythromycins and epitope mapping of their interactions with ribosomes.

The solution and solid state conformations of several 6-O-methyl homoerythromycins 1-4 were studied using a combination of X-ray crystallography, NMR spectroscopy and molecular modelling calculations. In the solid state 1 was found to exist as the two independent molecules with similar structures termed 3-endo-folded-out. In solution a significant conformational flexibility was noticed especially in the C2 to C5 region. The compounds 1 and 2 unlike 14-membered macrolides adopted the 3-endo-folded-out conformation while 3 and 4 existed in the classical folded-out conformation. TrNOESY and STD experiments showed that 1 and 2 bound to the Escherichia coli ribosome while 3 and 4, lacking the cladinose sugar, did not exhibit binding activities, this being in accordance with biochemical data. The bound conformations were found to be very similar to the free ones, some small differences were observed and discussed. The STD experiments provided evidence on binding epitopes. The structural parts of 1 and 2 in close contact with ribosome were similar, however the degree of saturation transfer was higher for 2. The differences between tr-NOE data and STD enhancements in 1 and 2 arouse as a consequence of structural changes upon binding and a closer proximity of 2 to the ribosome surface. An understanding of the molecular mechanisms involved in the interaction of macrolides with ribosomes can help in developing strategies aiming at design of potential inhibitors.