High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations

Virtual compound screening using molecular docking is widely used in the discovery of new lead compounds for drug design. However, this method is not completely reliable and therefore unsatisfactory. In this study, we used massive molecular dynamics simulations of protein-ligand conformations obtained by molecular docking in order to improve the enrichment performance of molecular docking. Our screening approach employed the molecular mechanics/Poisson-Boltzmann and surface area method to estimate the binding free energies. For the top-ranking 1,000 compounds obtained by docking to a target protein, approximately 6,000 molecular dynamics simulations were performed using multiple docking poses in about a week. As a result, the enrichment performance of the top 100 compounds by our approach was improved by 1.6–4.0 times that of the enrichment performance of molecular dockings. This result indicates that the application of molecular dynamics simulations to virtual screening for lead discovery is both effective and practical. However, further optimization of the computational protocols is required for screening various target proteins

Effects of clozapine and N-desmethylclozapine on synaptic transmission at hippocampal inhibitory and excitatory synapses

Clozapine is the first atypical antipsychotic, and improves positive and negative symptoms of many patients with schizophrenia resistant to treatment with other antipsychotic agents. Clozapine induces minimal extrapyramidal side effects, but is more often associated with seizures. A large number of studies have been conducted to elucidate pharmacological profiles of clozapine and its major active metabolite, N-desmethylclozapine (NDMC). However, there are only a limited number of electrophysiological studies examining their effects on synaptic transmission. In this study, we examined effects of clozapine and NDMC on synaptic transmission by measuring inhibitory and excitatory postsynaptic currents in rat cultured hippocampal neurons. We found that clozapine and NDMC have qualitatively similar actions. They depressed the inhibitory transmission at 1-30 μM, and the excitatory transmission at 30 μM, the former being much more sensitive. The depression of IPSCs by 30 μM of these drugs was associated with an increase in the paired-pulse ratio. The GABA-induced currents were suppressed by these drugs, but less sensitive than IPSCs. The AMPA-induced currents were slightly potentiated by these drugs at 30 μM. At 30 μM, clozapine and NDMC slightly suppressed Ca2+ and Na+ channels. These results strongly suggest that clozapine and NMDC depress the inhibitory synaptic transmission mainly by antagonizing postsynaptic GABAA receptors, but at higher concentrations additionally by acting on presynaptic site, possibly in part through inhibition of presynaptic Ca2+ and Na+ channels. Preferential depression of inhibitory synaptic transmission by clozapine and NDMC might contribute to therapeutic actions and/or side-effects of clozapine. © 2011 Elsevier B.V. All rights reserved

18. asırda "Hırkai şerif" ziyareti

Taha Toros Arşivi, Dosya No: 120-Saraylar. Not: Gazetenin "Tarihten Sahifeler" köşesinde yayımlanmıştır.İstanbul Kalkınma Ajansı (TR10/14/YEN/0033) İstanbul Development Agency (TR10/14/YEN/0033

精神的ストレスによるアレルギー性気道炎症の増悪

Stress and other psychological factors have long been hypothesized to be associated with asthma symptoms. One of the fundamental features of bronchial asthma is chronic airway inflammation, characteristic of the infiltration and activation of inflammatory cells, such as eosinophils and T lymphocytes. Psychological stress can modulate the inflammatory response through activation of hypothalamus-pituitary-adrenal axis and the sympathetic nervous system increasing the secretion of cortisol and catecholamines. However, the mechanisms linking stress and asthma are not well defined. Therefore, we investigated the effects of psychological stress on asthmatic airway inflammation using a murine model of allergic asthma. Female BALB/c mice and C57BL/6J mice were exposed to restraint stress (RS) during the antigen inhalation, which procedure was repeated 3 times for every seven days. Seven days after the last procedure, the mice were challenged with ovalbumin (OVA), and the airway inflammation was evaluated by the numbers of inflammatory cells in bronchoalveolar lavage fluids. RS significantly increased the numbers of total cells and lymphocytes in BALB/c mice. In C57BL/6J mice, in contrast, the numbers of inflammatory cells were not significantly different between mice exposed and not exposed to RS. Our findings suggest that psychological stress can enhance antigen-induced airway inflammation and, furthermore, that genetic background is involved in the pathogenesis of stress-induced asthma. This model using female BALB/c mice may be useful to elucidate the mechanisms by which psychological stress exacerbates asthma symptoms

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Soil radon (Rn-222) monitoring in a forest site in Fukushima, Japan

Soil radon (Rn-222) has been monitored since August 2013 at three different soil depths on a campus forest of Fukushima University in Japan, where a large amount of fallout nuclides were released by the accident of Fukushima Daiichi Nuclear Power Plant in March 2011. The primary purpose of this study is to evaluate Rn-222 activity level, variability and factors controlling Rn-222 concentration in soil air using data obtained from August to December 2013. Time series of Rn-222 activity concentration showed depth-dependent variability with an equilibrium value (Rn-222(eq)) during this observation period; 7.5, 14 and 23 kBq m(-3) at 0.3, 0.6 and 1.0 m in depth, respectively. Two typhoons passing over the site had a great influence on soil radon level, which was practically used for evaluating effective diffusion coefficient of Rn-222. Transport mechanism of Rn-222 in soil air was considered to be diffusion-controlled with data sets on changing Rn-222 concentration with time in selected cases that showed decreasing (or increasing) Rn-222 concentration with time at every depth. Important factors affecting soil Rn-222 variability are meteorological parameters, low-pressure front passing over the site, and subsequent precipitation. Time lags of decreasing Rn-222 concentration at different depths after rain indicate a certain relationship of Rn-222 level with moving water (and water vapor) in soil. The findings obtained in this study are important to evaluate the fate of fallout nuclides (radiocesium) in contaminated forest sites using soil radon as a tracer of moving soil air

The Arabidopsis cyclin-dependent kinase-activating kinase CDKF;1 is a major regulator of cell proliferation and cell expansion but is dispensable for CDKA activation

Summary Cyclin-dependent kinases (CDKs) play an essential role in cell cycle regulation during the embryonic and post-embryonic development of various organisms. Full activation of CDKs requires not only binding to cyclins but also phosphorylation of the T-loop domain. This phosphorylation is catalysed by CDK-activating kinases (CAKs). Plants have two distinct types of CAKs, namely CDKD and CDKF; in Arabidopsis, CDKF;1 exhibits the highest CDK kinase activity in vitro. We have previously shown that CDKF;1 also functions in the activation of CDKD;2 and CDKD;3 by T-loop phosphorylation. Here, we isolated the knockout mutants of CDKF;1 and showed that they had severe defects in cell division, cell elongation and endoreduplication. No defect was observed during embryogenesis, suggesting that CDKF;1 function is primarily required for post-embryonic development. In the cdkf;1 mutants, T-loop phosphorylation of CDKA;1, an orthologue of yeast Cdc2/Cdc28p, was comparable to that in wild-type plants, and its kinase activity did not decrease. In contrast, the protein level and kinase activity of CDKD;2 were significantly reduced in the mutants. Substitution of threonine-168 with a non-phosphorylatable alanine residue made CDKD;2 unstable in Arabidopsis tissues. These results indicate that CDKF;1 is dispensable for CDKA;1 activation but is essential for maintaining a steady-state level of CDKD;2, thereby suggesting the quantitative regulation of a vertebrate-type CAK in a plant-specific manner

The Arabidopsis cyclin-dependent kinase-activating kinase CDKF;1 is a major regulator of cell proliferation and cell expansion but is dispensable for CDKA activation

Summary Cyclin-dependent kinases (CDKs) play an essential role in cell cycle regulation during the embryonic and post-embryonic development of various organisms. Full activation of CDKs requires not only binding to cyclins but also phosphorylation of the T-loop domain. This phosphorylation is catalysed by CDK-activating kinases (CAKs). Plants have two distinct types of CAKs, namely CDKD and CDKF; in Arabidopsis, CDKF;1 exhibits the highest CDK kinase activity in vitro. We have previously shown that CDKF;1 also functions in the activation of CDKD;2 and CDKD;3 by T-loop phosphorylation. Here, we isolated the knockout mutants of CDKF;1 and showed that they had severe defects in cell division, cell elongation and endoreduplication. No defect was observed during embryogenesis, suggesting that CDKF;1 function is primarily required for post-embryonic development. In the cdkf;1 mutants, T-loop phosphorylation of CDKA;1, an orthologue of yeast Cdc2/Cdc28p, was comparable to that in wild-type plants, and its kinase activity did not decrease. In contrast, the protein level and kinase activity of CDKD;2 were significantly reduced in the mutants. Substitution of threonine-168 with a non-phosphorylatable alanine residue made CDKD;2 unstable in Arabidopsis tissues. These results indicate that CDKF;1 is dispensable for CDKA;1 activation but is essential for maintaining a steady-state level of CDKD;2, thereby suggesting the quantitative regulation of a vertebrate-type CAK in a plant-specific manner