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Molecular dynamics was used to optimize the droperidol-hERG complex obtained from docking. To accommodate the inhibitor, residues T623, S624, V625, G648, Y652, and F656 did not move significantly during the simulation, while F627 moved significantly. Binding sites in cryo-EM structures and in structures obtained from molecular dynamics simulations were characterized using solvent mapping and Atlas ligands, which were negative images of the binding site, were generated. Atlas ligands were found to be useful for identifying human ether-á-go-go-related potassium channel (hERG) inhibitors by aligning compounds to them or by guiding the docking of compounds in the binding site. A molecular dynamics optimized structure of hERG led to improved predictions using either compound alignment to the Atlas ligand or docking. The structure was also found to be suitable to define a strategy for lowering inhibition based on the proposed binding mode of compounds in the channel.

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We analyzed the influence of calculated physicochemical properties of more than 20,000 compounds on their P-gp and BCRP mediated efflux, microsomal stability, hERG inhibition, and plasma protein binding. Our goal was to provide guidance for designing compounds with desired pharmacokinetic profiles. Our analysis showed that compounds with ClogP less than 3 and molecular weight less than 400 will have high microsomal stability and low plasma protein binding. Compounds with logD less than 2.2 and/or basic pKa larger than 5.3 are likely to be BCRP substrates and compounds with basic pKa less than 5.2 and/or acidic pKa less than 13.4 are less likely to inhibit hERG. Based on these results, compounds with MW < 400, ClogP < 3, basic pKa < 5.2 and acidic pKa < 13.4 are likely to have good bioavailability and low hERG inhibition.

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Phospholipase D enzymes (PLDs) are ubiquitous phosphodiesterases that produce phosphatidic acid (PA), a key second messenger and biosynthetic building block. Although an orthologous bacterial Streptomyces sp. strain PMF PLD structure was solved two decades ago, the molecular basis underlying the functions of the human PLD enzymes (hPLD) remained unclear based on this structure due to the low homology between these sequences. Here, we describe the first crystal structures of hPLD1 and hPLD2 catalytic domains and identify novel structural elements and functional differences between the prokaryotic and eukaryotic enzymes. Furthermore, structure-based mutation studies and structures of inhibitor-hPLD complexes allowed us to elucidate the binding modes of dual and isoform-selective inhibitors, highlight key determinants of isoenzyme selectivity and provide a basis for further structure-based drug discovery and functional characterization of this therapeutically important superfamily of enzymes.

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The calculation of the combined uncertainty of the international estimated short-term intake (IESTI) of ethephon residues in apples is shown as an example. The ethephon residues in apples were reported by the Joint FAO (Food and Agriculture Organization of the United Nations)/WHO (World Health Organization) Meeting on Pesticide Residues (JMPR). The apple consumption data were taken from the IESTI (international short-term intake) calculation template used by the JMPR. The IESTI was calculated with the currently used method (case 2a) and a proposed one recommended by the EFSA (European Food Safety Authority)/RIVM (Dutch National Institute for Public Health) Scientific Workshop co-sponsored by FAO and WHO. In this example, the ratio of IESTIproposed/IESTIcurrent and their combined relative uncertainty are about 2.8, and 1.7, respectively. The larger IESTI and uncertainty obtained with the proposed equation are the consequence of calculation only with the large portion (LP) instead of its combination with unit mass, and the MRL instead of the highest residue (HR). The LP is the major contributor to the combined uncertainty. Both the calculated IESTI and its combined uncertainty depend on the actual food - pesticide residue combination, and should be calculated for each case.

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Maladaptive decision making is associated with several neuropsychiatric disorders, including problem gambling and suicidal behavior. The prevalence of these disorders is higher in men vs women, suggesting gender-dependent regulation of their pathophysiology underpinnings. We assessed sex differences in decision making using the rat version of the Iowa gambling task. Female rats identified the most optimal choice from session 1, whereas male rats from session 5. Male, but not female rats, progressively improved their advantageous option responding and surpassed females. Estrus cycle phase did not affect decision making. To test whether pharmacological manipulations targeting the dopaminergic and stress systems affect decision making in a sex-dependent manner, male and female rats received injections of a dopamine D2 receptor (D2R) antagonist (eticlopride), D2R agonist (quinpirole), corticotropin-releasing factor 1 (CRF1) antagonist (antalarmin), and α2-adrenergic receptor antagonist (yohimbine; used as a pharmacological stressor). Alterations in mRNA levels of D2R and CRF1 were also assessed. Eticlopride decreased advantageous responding in male, but not female rats, whereas quinpirole decreased advantageous responding specifically in females. Yohimbine dose-dependently decreased advantageous responding in female rats, whereas decreased advantageous responding was only observed at higher doses in males. Antalarmin increased optimal choice responding only in female rats. Higher Drd2 and Crhr1 expression in the amygdala were observed in female vs male rats. Higher amygdalar Crhr1 expression was negatively correlated with advantageous responding specifically in females. This study demonstrates the relevance of dopaminergic- and stress-dependent sex differences to maladaptive decision making.

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This study focuses on particle size effect on monomineralic powders recorded using attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy. Six particle size fractions of quartz, feldspar, calcite, and dolomite were prepared (<2, 2-4, 4-8, 8-16, 16-32, and 32-63 µm). It is found that the width, intensity, and area of bands in the ATR FT-IR spectra of minerals have explicit dependence on the particle size. As particle size increases, the intensity and area of IR bands usually decrease while the width of bands increases. The band positions usually shifted to higher wavenumbers with decreasing particle size. Infrared spectra of minerals are the most intensive in the particle size fraction of 2-4 µm. However, if the particle size is very small (<2 µm), due to the wavelength and penetration depth of the IR light, intensity decreases. Therefore, the quantity of very fine-grained minerals may be underestimated compared to the coarser phases. A nonlinear regression analysis of the data indicated that the average coefficients and indices of the power trend line equation imply a very simplistic relationship between median particle diameter and absorbance at a given wavenumber. It is concluded that when powder samples with substantially different particle size are compared, as in regression analysis for modal predictions using ATR FT-IR, it is also important to report the grain size distribution or surface area of samples. The band area of water (3000-3620 cm-1) is similar in each mineral fraction, except for the particles below 2 µm. It indicates that the finest particles could have disproportionately more water adsorbed on their larger surface area. Thus, these higher wavenumbers of the ATR FT-IR spectra may be more sensitive to this spectral interference if the number of particles below 2 µm is considerable. It is also concluded that at least a proportion of the moisture could be very adhesive to the particles due to the band shift towards lower wavenumbers in the IR range of 3000-3620 cm-1.

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AIM: Virtual screening selects compounds that resemble a known modulator or compounds that fit into the binding site of a target protein. Computational solvent mapping defines important chemical features for binding to a target protein. Results/methodology: We have tested the ability to use solvent mapping for generating a 'fake' ligand that is a negative image of the binding site. We used this fake ligand as a query for the program ROCS and to define the search space of the docking programs FRED and HYBRID. CONCLUSION: The fake ligands perform comparably to or better than the ligands from crystal structures across a set of ten targets. Thus, the approach is suitable for guiding virtual screening and hit-to-lead optimization.

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RORγ plays a critical role in controlling a pro-inflammatory gene expression program in several lymphocyte lineages including T cells, γδ T cells, and innate lymphoid cells. RORγ-mediated inflammation has been linked to susceptibility to Crohn's disease, arthritis, and psoriasis. Thus inverse agonists of RORγ have the potential of modulating inflammation. Our goal was to optimize two RORγ inverse agonists: T0901317 from literature and 1 that we obtained from internal screening. We used information from internal X-ray structures to design two libraries that led to a new biaryl series.

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Based on the Hungarian pesticide residues monitoring data of the last five years and the consumption data collected within a 3-day dietary record survey in 2009 (more than 2 million pesticide residue results and almost 5000, 0-101-year-old consumers 3 non-consecutive-day personal fruit and vegetable consumption data), the cumulative acute exposure of organophosphorus pesticide residues was evaluated. The relative potency factor approach was applied, with acephate chosen as index compound. According to our conservative calculation method, applying the measured residues only, the 99.95% of the 99th percentiles of calculated daily intakes was at or below 87 µg/kgbwday, indicating that the cumulative acute exposure of the whole Hungarian population (including all age classes) to organophosphorus compounds was not a health concern.

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Over the past two decades, solvent mapping has emerged as a useful tool for identifying hot spots within binding sites on proteins for drug-like molecules and suggesting properties of potential binders. While the experimental technique requires solving multiple crystal structures of a protein in different solvents, computational solvent mapping allows for fast analysis of a protein for potential binding sites and their druggability. Recent advances in genomics, systems biology and interactomics provide a multitude of potential targets for drug development and solvent mapping can provide useful information to help prioritize targets for drug discovery projects. Here, we review various approaches to computational solvent mapping, highlight some key advances and provide our opinion on future directions in the field.

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The voltage-gated potassium channel encoded by hERG carries a delayed rectifying potassium current (IKr) underlying repolarization of the cardiac action potential. Pharmacological blockade of the hERG channel results in slowed repolarization and therefore prolongation of action potential duration and an increase in the QT interval as measured on an electrocardiogram. Those are possible to cause sudden death, leading to the withdrawals of many drugs, which is the reason for hERG screening. Computational in silico prediction models provide a rapid, economic way to screen compounds during early drug discovery. In this review, hERG prediction models are classified as 2D and 3D quantitative structure-activity relationship models, pharmacophore models, classification models, and structure based models (using homology models of hERG).

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Typical sampling uncertainties were calculated as the average of relative standard deviations (CV) of residues measured in individual crops tested in supervised residue trials and from their pooled variance for crop groups. The relative confidence intervals of the sampling uncertainty for different crops were estimated from the random duplicate composite samples generated with computer modeling from residues in 182 independent primary sample sets, each consisting of 100-320 residue data. The relative 95% confidence intervals were found to be independent from the CV of primary residue data populations; therefore, the calculated values are generally applicable. In view of the potentially serious consequences of underestimated sampling uncertainties, their upper confidence limits are recommended for practical use to verify the compliance of products and for planning statistically based sampling programs. Sampling uncertainties are reported for 24 crop groups and 106 individual crops.

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Aflatoxin M1 (AFM1) contamination in 21,969 milk samples taken in Italy during 2005-08 and 2010 provided the basis for designing an early warning self-control plan. Additionally, 4148 AFM1 data points from the mycotoxin crisis (2003-04) represented the worst case. No parametric function provided a good fit for the skewed and scattered AFM1 concentrations. The acceptable reference values, reflecting the combined uncertainty of AFM1 measured in consignments consisting of milk from one to six farms, ranged from 40 to 16.7 ng kg(-1), respectively. Asymmetric control charts with these reference values, 40 and 50 ng kg(-1) warning and action limits are recommended to assess immediately the distribution of AFM1 concentration in incoming consignments. The moving window method, presented as a worked example including 5 days with five samples/day, enabled verification of compliance of production with the legal limit in 98% of the consignments at a 94% probability level. The sampling plan developed assumes consecutive analyses of samples taken from individual farms, which makes early detection of contamination possible and also immediate corrective actions if the AFM1 concentration in a consignment exceeds the reference value. In the latter case different control plans with increased sampling frequency should be applied depending on the level and frequency of contamination. As aflatoxin B1 increases in feed at about the same time, therefore a coordinated sampling programme performed by the milk processing plants operating in a confined geographic area is more effective and economical then the individual ones. The applicability of the sample size calculation based on binomial theorem and the fast response rate resulting from the recommended sampling plan were verified by taking 1000-10,000 random samples with replacement from the experimental databases representing the normal, moderately and highly contaminated periods. The efficiency of the control plan could be substantially enhanced if the dairy farms used feed with a tolerable level of AFB1.

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The supervised trial datasets (1950), consisting of a minimum of five residue values and selected by the experts of FAO/WHO Joint Meeting on Pesticide Residues for recommending maximum residue levels between 1997 and 2011, were evaluated to obtain information on the typical spread of residue values in individual datasets. The typical relative standard deviation, CV, of field-to-field variation of pesticide residues was about 80%. The spread of residues in datasets is independent from the chemical structure of pesticides, residue level, pre-harvest interval and number of values in the datasets. The CV ranges within the Codex commodity groups and between groups overlapped and their difference were not statistically significant. The number of residues below the limit of quantification (LOQ) affects the CV at various extents depending on the ratio of LOQ/R mean. The combined uncertainty of the highest residue in a dataset significantly affects the CV of the dataset. The lowest and intermediate ones have less influence. The residues in different fields receiving the same treatment vary within large range: 55%, 72%, 78%, 86% and 89% of the 25,766 residues values were, respectively, within 3, 4, 5, 6 and 7 times the median value of the corresponding dataset.

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Alkyne 40, 5-(2-amino-4-chloro-7-((4-methoxy-3,5-dimethylpyridin-2-yl)methyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-2-methylpent-4-yn-2-ol (EC144), is a second generation inhibitor of heat shock protein 90 (Hsp90) and is substantially more potent in vitro and in vivo than the first generation inhibitor 14 (BIIB021) that completed phase II clinical trials. Alkyne 40 is more potent than 14 in an Hsp90α binding assay (IC(50) = 1.1 vs 5.1 nM) as well as in its ability to degrade Her-2 in MCF-7 cells (EC(50) = 14 vs 38 nM). In a mouse model of gastric tumors (N87), 40 stops tumor growth at 5 mg/kg and causes partial tumor regressions at 10 mg/kg (po, qd × 5). Under the same conditions, 14 stops tumor growth only at 120 mg/kg, and does not induce partial regressions. Thus, alkyne 40 is approximately 20-fold more efficacious than 14 in mice.

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PURPOSE: Nanoparticle drug delivery offers a potential solution in the treatment of cancer. Using a heterotopic tumor model for head and neck squamous cell carcinoma (HNSCC), tumors of variable folate binding protein-alpha (FBP-α) have been treated to delineate receptor necessity as well as efficacy and toxicity of folate targeted chemotherapy. MATERIALS AND METHODS: University of Michigan Squamous Cell Carcinoma (UM-SCC) and American Type Culture Collection (ATCC) cell lines were screened using quantitative real-time polymerase chain reaction for FBP-α expression. Acetylated generation 5 dendrimers conjugated to the targeting moiety folic acid and the therapeutic moiety methotrexate were fabricated and administered to severe combined immunodeficiency (SCID) CB-17 mice inoculated with UM-SCC-1, UM-SCC-17B, and UM-SCC-22B cancer cells. Mice were injected with targeted therapy, free methotrexate, or saline control and monitored for drug efficacy and toxicity. RESULTS: Targeted therapy was effective relative to receptor level expression. Targeted therapy could be delivered in molar doses 3 times that of free drug. The treatment of a high folate expression tumor cell population was noted to have increased efficacy over saline (P < .01) and free methotrexate (P = .03) as well as decreased systemic toxicity. CONCLUSIONS: This report represents the first translation of dendrimer-based chemotherapy to HNSCC and underscores its effectiveness as an antitumor agent in human cancer cell lines with lower levels of FBP-α than the in vitro and in vivo models previously reported.

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OBJECTIVE: To investigate the uptake of a poly(amidoamine) dendrimer (generation 5 [G5]) nanoparticle covalently conjugated to polyvalent folic acid (FA) as the targeting ligand into macrophages, and to investigate the activity of an FA- and methotrexate (MTX)-conjugated dendrimer (G5-FA-MTX) as a therapeutic for the inflammatory disease of arthritis. METHODS: In vitro studies were performed in macrophage cell lines and in isolated mouse macrophages to check the cellular uptake of fluorescence-tagged G5-FA nanoparticles, using flow cytometry and confocal microscopy. In vivo studies were conducted in a rat model of collagen-induced arthritis to evaluate the therapeutic potential of G5-FA-MTX. RESULTS: Folate-targeted dendrimer bound and internalized in a receptor-specific manner into both folate receptor ß-expressing macrophage cell lines and primary mouse macrophages. The conjugate G5-FA-MTX acted as a potent antiinflammatory agent and reduced arthritis-induced parameters of inflammation such as ankle swelling, paw volume, cartilage damage, bone resorption, and body weight decrease. CONCLUSION: The use of folate-targeted nanoparticles to specifically target MTX into macrophages may provide an effective clinical approach for antiinflammatory therapy in rheumatoid arthritis.

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A targeted dendrimeric anticancer prodrug, a conjugate of generation 5 (G5) polyamidoamine (PAMAM) dendrimer, folic acid (FA), and methotrexate (MTX), has been successfully synthesized by using a novel "one pot" approach which is simple, reproducible, and feasible for large-scale synthesis. All dendrimer products have been characterized by (1)H NMR, MALDI-TOF, GPC, and HPLC. With this new method, the ratio of FA versus MTX attached to the dendrimer can be easily tuned to achieve the desired therapeutic effect. A new analytical approach for calculating the numbers of FA and MTX attached to the dendrimer has been established. In vitro studies performed on FA receptor-expressing KB cells show that the new conjugate has a similar affinity and cytotoxic potency to G5-FA-MTX synthesized using the traditional multiple-step approach.

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Generation 7 (G7) poly(amidoamine) (PAMAM) dendrimers with amine, acetamide, and carboxylate end groups were prepared to investigate polymer/cell membrane interactions in vitro. G7 PAMAM dendrimers were used in this study because higher-generation of dendrimers are more effective in permeabilization of cell plasma membranes and in the formation of nanoscale holes in supported lipid bilayers than smaller, lower-generation dendrimers. Dendrimer-based conjugates were characterized by (1)H NMR, UV/vis spectroscopy, GPC, HPLC, and CE. Positively charged amine-terminated G7 dendrimers (G7-NH(2)) were observed to internalize into KB, Rat2, and C6 cells at a 200 nM concentration. By way of contrast, neither negatively charged G7 carboxylate-terminated dendrimers (G7-COOH) nor neutral acetamide-terminated G7 dendrimers (G7-Ac) associated with the cell plasma membrane or internalized under similar conditions. A series of in vitro experiments employing endocytic markers cholera toxin subunit B (CTB), transferrin, and GM(1)-pyrene were performed to further investigate mechanisms of dendrimer internalization into cells. G7-NH(2) dendrimers colocalized with CTB; however, experiments with C6 cells indicated that internalization of G7-NH(2) was not ganglioside GM(1) dependent. The G7/CTB colocalization was thus ascribed to an artifact of direct interaction between the two species. The presence of GM(1) in the membrane also had no effect upon XTT assays of cell viability or lactate dehydrogenase (LDH) assays of membrane permeability.

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