Discovery of novel inhibitors of histone deacetylase 6: Structure-based virtual screening, molecular dynamics simulation, enzyme inhibition and cell viability assays

Histone deacetylase 6 (HDAC6) contributes to cancer metastasis in several cancers, including triple-negative breast cancer (TNBC)-the most lethal form that lacks effective therapy. Although several efforts have been invested to develop selective HDAC6 inhibitors, none have been approved by the FDA. Toward this goal, existing computational studies used smaller compound libraries and shorter MD simulations. Here, we conducted a structure-based virtual screening of ZINC "Druglike" library containing 17,900,742 compounds using a Glide virtual screening protocol comprising various filters with increasing accuracy. The top 20 hits were subjected to molecular dynamics simulation, MM-GBSA binding energy calculations, and further ADMET prediction. Furthermore, enzyme inhibition assay and cell viability assay were performed on six available compounds from the identified hits. C4 (ZINC000077541942) with a good profile of predicted drug properties was found to inhibit HDAC6 (IC50: 4.7 ± 11.6 μM) with comparative affinity to that of the known HDAC6 selective inhibitor Tubacin (TA) in our experiments. C4 also demonstrated cytotoxic effects against triple-negative breast cancer (TNBC) cell line MDA-MB-231 with EC50 of 40.6 ± 12.7 μM comparable to that of TA (2-20 μM). Therefore, this compound, with pharmacophore features comprising a non-hydroxamic acid zinc-binding group, heteroaromatic linker, and cap group, is proposed as a novel HDAC6 inhibitor.

Note. β—Carotene, α—tocopherol and γ—tocopherol contents in dry legumes. Influence of cooking Nota. Contenido de β—caroteno, α—tocopherol y γ—tocopherol en legumbres secas. Influencia de la cocción

Three essential fat-soluble micronutrients—β-carotene, α-tocopherol and γ-tocopherol-were de termined by HPLC in different varieties of three dry legumes, namely, beans, chick peas and lentils. Their distribution between skin and albumen was also determined. After cooking legumes were found significantly to preserve most of these micronutrients.

Comparison of an acetonitrile extraction/partitioning and “dispersive solid-phase extraction” method with classical multi-residue methods for the extraction of herbicide residues in barley samples

An acetonitrile/partitioning extraction and "dispersive solid-phase extraction (SPE)" method that provides high quality results with a minimum number of steps and a low solvent and glassware consumption was published in 2003. This method, suitable for the analysis of multiple classes of pesticide residues in foods, has been given an acronymic name, QuEChERS, that reflects its major advantages (quick, easy, cheap, effective, rugged, safe). In this work, QuEChERS method, which was originally created for vegetable samples with a high amount of water, was modified to optimise the extraction of a wide range of herbicides in barley. Then, it was compared with known conventional multi-residue extraction procedures such as the Luke method, which was simplified and shortened by eliminating the Florisil clean-up (mini Luke) and the ethyl acetate extraction, which involves a subsequent clean-up by gel permeation chromatography (GPC) and which is the official extraction method used by some of European authorities. Finally, a simple acetone extraction was carried out to check the differences with the other three methods. Extracts were analysed by gas chromatography-time-of-flight mass spectrometry (GC-TOF/MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Mini Luke was significantly more effective for the extraction of non-polar and medium-polar compounds, but the best recoveries for polar compounds were achieved by QuEChERS and ethyl acetate methods. QuEChERS was the only method that provided an overall recovery value of 60-70% for non-, medium- and polar compounds, with some exceptions due to co-eluted matrix interferences. Clean-up by dispersive SPE was effective and did not differ so much with ethyl acetate extracts considering that QuEChERS clean-up step is much easier and less time-consuming. As a conclusion, it resulted to be the most universal extraction method by providing a well-defined phase separation without dilution and achieving acceptable recoveries in average including the extraction of the always difficult acidic herbicides. However, recoveries were not as good as required for validation purposes suggesting that residues are prone to strong matrix interactions in dry samples as barley and further method adaptation incrementing solvent strength, extraction time or more acidic or basic conditions is needed in order to achieve a complete extraction.

Study of different parameters affecting the derivatization of acidic herbicides with trimethylsulfonium hydroxide to make them suitable for gas chromatography analysis

In this study, an orthogonal array design was applied to know the way different parameters affected the derivatization of some herbicides that are commonly applied in the soils. Herbicides formulated as esters have been reported to rapidly hydrolyse, in contact with soil, to their corresponding acids and phenols. What involves is that both forms need to be monitored. Acidic herbicides and phenols cannot be detected by gas chromatography (GC) due to their polarity and low volatility that cause peak asymmetry. Therefore, masking of these polar groups by eliminating the active hydrogen atom with derivatization to their corresponding esters/ethers is needed in order to yield products that possess enhanced volatility and improved GC properties. A lot of derivatization reagents have been proposed but trimethylsulfonium hydroxide (TMSH) was selected due to its easy and quantitative formation of methyl esters/ethers. It was observed that the addition of TMSH promoted not only esterification of acids/phenols but trans-esterification of the original non-hydrolyzed remaining esters to their corresponding methyl ones. As a result, methyl esters/ethers were the final product of both reactions. Different parameters were studied in the statistical design for both TMSH promoted reactions: type of solvent, pH, temperature and time of incubation. The amount of derivatization reagent was calculated to be high enough to ensure the complete derivatization of all compounds present in the sample. The reaction medium was shown as an important factor. The formation of some methyl esters/ethers decreased with increasing time and temperature because trans-esterification, being an equilibrium where the formation of smaller structures is promoted, was not enough shifted. However, the statistical analysis revealed that only the pH of the solution played an important role during the derivatization process. The presence of the anionic form of the acids appeared to be essential for derivatization, being diminished in strong acidic conditions. In addition, pre-heating was shown not to improve derivatization reaction, being easily carried on in the injector port of the GC system.

Volatilisation of triallate as affected by soil texture and air velocity

The rate of volatilisation of the formulated herbicide triallate was investigated in a wind tunnel under controlled wind-speed conditions. An experimental set-up is described which allows the monitoring of wind speed (w.s.), soil-water content, and the temperature of air and soil. A system controlling soil-water content is also described. The influence of air velocity and soil texture was investigated measuring the cumulative volatilisation losses of triallate from soil. The herbicide volatilisation losses after application ranged from 40% at 3 m/s to 53% at 9 m/s for loam soil and from 60% at 3 m/s to 73% at 9 m/s for sandy soil.

Irreversible inhibition of human immunodeficiency virus type 1 integrase by dicaffeoylquinic acids

Human immunodeficiency virus type 1 (HIV-1) and other retroviruses require integration of a double-stranded DNA copy of the RNA genome into the host cell chromosome for productive infection. The viral enzyme, integrase, catalyzes the integration of retroviral DNA and represents an attractive target for developing antiretroviral agents. We identified several derivatives of dicaffeoylquinic acids (DCQAs) that inhibit HIV-1 replication in tissue culture and catalytic activities of HIV-1 integrase in vitro. The specific step at which DCQAs inhibit the integration in vitro and the mechanism of inhibition were examined in the present study. Titration experiments with different concentrations of HIV-1 integrase or DNA substrate found that the effect of DCQAs was exerted on the enzyme and not the DNA. In addition to HIV-1, DCQAs also inhibited the in vitro activities of MLV integrase and truncated variants of feline immunodeficiency virus integrase, suggesting that these compounds interacted with the central core domain of integrase. The inhibition on retroviral integrases was relatively specific, and DCQAs had no effect on several other DNA-modifying enzymes and phosphoryltransferases. Kinetic analysis and dialysis experiments showed that the inhibition of integrase by DCQAs was irreversible. The inhibition did not require the presence of a divalent cation and was unaffected by preassembling integrase onto viral DNA. The results suggest that the irreversible inhibition by DCQAs on integrase is directed toward conserved amino acid residues in the central core domain during catalysis.

High-performance liquid chromatographic determination of benomyl and carbendazim residues in apiarian samples

Simple procedures for the extraction and chromatographic determination of benomyl and carbendazim in honey, bees wax, larvae, bees and pollen are proposed. The fungicides were extracted from honey, larvae and bees using ethyl acetate, while methanol was more suitable for wax and pollen samples. Pollen extracts need a further clean-up step with n-hexane. The determination is carried out by reversed-phase high-performance liquid chromatography (HPLC) with fluorescence detection. The procedures have been applied to the analysis of benomyl on honey and larvae samples from hives whose bees were nourished with artificial food mixed with benomyl.

Determination of the fungicide vinclozolin in honey and bee larvae by solid-phase and solvent extraction with gas chromatography and electron-capture and mass spectrometric detection

Methods for the determination of residual vinclozolin in honey and bee larvae are proposed. The fungicide can be extracted with an n-hexane-acetone (70:30, v/v) mixture, or by passage through ODS cartridges which requires no subsequent clean-up. Vinclozolin is quantified by capillary gas chromatography with electron-capture and mass spectrometric detection. Recoveries from spiked samples exceed 90%, with a relative standard deviation of 3.5-4.5%.

Supercritical fluid extraction of fluvalinate residues in honey. Determination by high-performance liquid chromatography

A method for the analysis of fluvalinate residues in honey from beehives treated with this product to prevent varroatosis is described. The method involves supercritical fluid extraction with carbon dioxide and further analysis by high-performance liquid chromatography on a C18 reversed-phase column, acetonitrile-water (80:20) as mobile phase and detection at 254 nm. This method is simpler than the one in which extraction with organic solvents, thin-layer chromatography and gas chromatography is used.

Bioproduction of an extract from Penicillium funiculosum Thom with activity against Ceratitis capitata and Tetranychus urticae

The bioproduction conditions of a crude extract from a strain of Penicillium funiculosum Thom, which shows activity against Ceratitis capitata and Tetranychus urticae, have been optimized. The efficacy degree was 95% (C. capitata) and 100% (T. urticae), according to Abbot. This is the first report on the pesticide activity of an extract from P. funiculosum against these species. The best yields were obtained when P. funiculosum was grown in Raulin-Thom medium at pH 6.5 with sucrose candy as the carbon source and ammonium sulphate and phosphate as the nitrogen source. Other favourable conditions were static cultures, at 28 degrees C, and in the dark.

Synthesis and antiprotozoal properties of 1,2,6-thiadiazine 1,1-dioxide derivatives

The synthesis and spectroscopical data of 1,2,6-thiadiazine 1,1-dioxides, designed as antiprotozoal agents, are reported. The in vitro trichomonacidal and trypanocidal activities of new compounds and their precursors were evaluated against Trichomonas vaginalis and Trypanosoma cruzi. The chemoprophylactic activity on mice treated with blood infected with T. cruzi and their mortality percentage were tested. Compounds 2 and 8b show a higher chemoprophylactic activity and lower mortality percentage than Nifurtimox used as reference drug.

Isolation and identification of ethisolide as an antibiotic product from Penicillium capsulatum

Ethisolide has been isolated from cultures of Penicillium capsulatum, and its structure determined by means of infrared, mass spectrometry, 1H- and 13C nuclear magnetic resonance. Antibiotic activity against a number of microorganisms is reported.

Flow injection spectrophotometric determination of calcium, phosphate and chloride ions in milk

Flow injection procedures for the determination of calcium, phosphate and chloride ions in milk samples are described. The reactions are based on the formation of coloured complexes and their spectrophotometric monitoring. A sample pre-treatment with acetate buffer was carried out owing to the complexity of the sample matrix. For chloride, a rapid and reliable automated procedure for direct measurement of its content in milk (using a dialyser to eliminate interferences) is also described. After optimizing the sample pre-treatment and flow injection variables, the procedures were applied to commercial milk; the results obtained agreed satisfactorily with those of the reference methods. With 50 mm3 samples, a working range of 0-15 ppm for calcium, 50-150 ppm for phosphate and 5-100 ppm for chloride is covered with a precision of better than 1.1%. The sample throughput was higher than 50 samples h-1. These preliminary experiments are the basis for the automation of the determination of calcium, phosphate and chloride ions using a computer-controlled, self-designed and laboratory-built autoanalyser.

Activity assays of thiadiazine derivatives on Trichomonas vaginalis and amastigote forms of Trypanosoma cruzi

Eight thiadiazine 1,1-dioxide derivatives were evaluated for antitrichomonal and antitrypanosomal activities. In vivo tests were performed on a murine model for trichomoniasis standardized in our laboratory. The capacity of compounds to clear visceral lesions in experimentally infected animals as well as their effects on the mortality time of mice were used as criteria for activity. One of the thiadiazines (compound 7b) showed an efficacy similar to that obtained with the reference drug metronidazole, although higher doses were required. Its toxicity on cell proliferation in tissue culture was moderate. In vitro assays on amastigote forms of Trypanosoma cruzi were carried out using cultures of Vero cells infected with metacyclic trypomastigotes. For one compound (1) trypanocidal activity resembled that of nifurtimox as assessed by microscopic counts of infected and uninfected cells. Unfortunately, this compound showed a high degree of cytotoxicity on Vero cell cultures.

Research for new antichagasic drugs

A series of ten 1-[(5-nitrothenylidene)amino]azoles has been synthesized by the reaction of 5-nitrothiophene-2-carbaldehyde with 1-aminopyrazole, 1-aminoimidazole, 1- and 4- amino-1,2,4-triazoles, 1-aminoindole, 1- and 2-aminoindazoles, 1-aminobenzimidazole and 1- and 2-aminobenzotriazoles. Physical data, spectroscopic characteristics and biological properties of all the derivatives have been examined. The antiprotozoal activity has been tested against Trypanosoma cruzi, comparative to Nifurtimox (Lampit).