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  1 / 102710 MEDLINE  
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PMID:28644624
Autor:Sun Z; Wang X; Song J
Endereço:State Key Laboratory of Precision Spectroscopy, School of Physics and Material Science, East China Normal University , Shanghai 200062, China.
Título:Extensive Assessment of Various Computational Methods for Aspartate's pK Shift.
Fonte:J Chem Inf Model; 57(7):1621-1639, 2017 Jul 24.
ISSN:1549-960X
País de publicação:United States
Idioma:eng
Resumo:A series of computational methods for pK shift prediction are extensively tested on a set of benchmark protein systems, aiming at identifying pitfalls and evaluating their performance on high variants. Including 19 ASP residues in 10 protein systems, the benchmark set consists of both residues with highly shifted pK values as well as those varying little from the reference value, with an experimental RMS free energy differences of 2.49 kcal/mol with respect to blocked amino acid, namely the RMS pK shift being 1.82 pK units. The constant pH molecular dynamics (MD), alchemical methods, PROPKA3.1, and multiconformation continuum electrostatics give RMSDs of 1.52, 2.58, 1.37, and 3.52 pK units, respectively, on the benchmark set. The empirical scoring method is the most accurate one with extremely low computational cost, and the pH-dependent model is also able to provide accurate results, while the accuracy of MD sampling incorporating alchemical free energy simulation is prohibited by convergence achievement and the performance of conformational search incorporating multiconformation continuum electrostatics is bad. Former research works did not define statistical uncertainty with care and yielded the questionable conclusion that alchemical methods perform well in most benchmarks. In this work the traditional alchemical methods are thoroughly tested for high variants. We also performed the first application of nonequilibrium alchemical methods to the pK cases.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Proteins); 30KYC7MIAI (Aspartic Acid)


  2 / 102710 MEDLINE  
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PMID:28566580
Autor:Takayama K; Otoguro S; Okada N; Hoshino M; Yagi N; Obata Y
Endereço:Department of Pharmaceutics, Hoshi University.
Título:Determination of Density Distribution of Tablets Using Synchrotron X-ray Computed Tomography.
Fonte:Yakugaku Zasshi; 137(6):757-762, 2017.
ISSN:1347-5231
País de publicação:Japan
Idioma:eng
Resumo:The purpose of this study was to determine the density distribution of scored and round-faced tablets using synchrotron X-ray computed tomography. The tablets were made by direct compression of standard formulations. The density distribution of scored flat-faced tablets was uniform in the whole cross-sectional image. However, the tablet formulated using microcrystalline cellulose (MCC) was very dense at the tip of the score only. It is caused by the poor fluidity of MCC particles. In the case of round-faced tablets, the density in the central section of the tablet was relatively low, compared with those of peripheral areas. These observations correlated well with the results obtained by the finite element method simulation using appropriate material models.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Tablets); 9004-34-6 (Cellulose); OP1R32D61U (microcrystalline cellulose)


  3 / 102710 MEDLINE  
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PMID:28077336
Autor:Jiao YS; Du PF
Endereço:School of Computer Science and Technology, Tianjin University, Tianjin 300350, China.
Título:Predicting protein submitochondrial locations by incorporating the positional-specific physicochemical properties into Chou's general pseudo-amino acid compositions.
Fonte:J Theor Biol; 416:81-87, 2017 Mar 07.
ISSN:1095-8541
País de publicação:England
Idioma:eng
Resumo:Predicting protein submitochondrial locations has been studied for about ten years. A dozen of methods were developed in this regard. Although a mitochondrion has four submitochondrial compartments, all existing studies considered only three of them. The mitochondrial intermembrane space proteins were always excluded in these studies. However, there are over 50 mitochondrial intermembrane space proteins in the recent release of UniProt database. We think it is time to incorporate these proteins in predicting protein submitochondrial locations. We proposed the functional domain enrichment score, which can be used as an enhancement to our positional-specific physicochemical properties method. We constructed a high-quality working dataset from the UniProt database. This dataset contains proteins from all four submitochondrial locations. Proteins with multiple submitochondrial locations are also included. Our method achieved over 70% prediction accuracy for proteins with single location on this dataset. On the M3-317 benchmarking dataset, our method achieved comparable prediction performance to other state-of-the-art methods. Our results indicate that the intermembrane space proteins can be incorporated in predicting protein submitochondrial locations. By evaluating our method with the proteins that have multiple submitochondrial locations, we conclude that our method is capable of predicting multiple submitochondrial locations. This is the first report of ab initio methods that can identify intermembrane space proteins. This is also the first attempt to incorporate proteins with multiple submitochondrial locations. The benchmarking dataset can be obtained by emails to the corresponding author.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Amino Acids); 0 (Proteins)


  4 / 102710 MEDLINE  
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PMID:28768957
Autor:Ismail SAA; El-Anany AM; Ali RFM
Endereço:Biochemistry Department, Faculty of Agriculture, Cairo University.
Título:Regeneration of Used Frying Palm Oil with Coffee Silverskin (CS), CS Ash (CSA) and Nanoparticles of CS (NCS).
Fonte:J Oleo Sci; 66(8):897-905, 2017.
ISSN:1347-3352
País de publicação:Japan
Idioma:eng
Resumo:The present investigation aimed to evaluate the efficiency of coffee silverskin (CS), CS ash (CSA) and nanoparticles of CS (NCS) in regeneration the quality of used frying palm oil. The adsorbents were mixed individually with used frying palm oil at level 4% (w/v) for 60 min. The properties of CS, CSA and NCS adsorbents were studied using (SEM) scanning electron microscopy technique. Some of physico-chemical characteristics of used frying palm oil (UFPO) and UFPO treated with adsorbents were determined. The results showed that the CS ash particles composed of irregular spherical and semispherical grains with deep cavities. The size of particles of CS ash ranged in diameter from 1.1 to 1.7 µm. The morphology of NCS consisted of cluster-type spherical nanoparticles and flakes. The particle size of NCS varies from 0.9 to 1.7 µm. Purification treatments caused marked (p<0.05) increases in the quality parameters of treated oil compared to untreated oil. The treatment of UFPO with 4% of adsorbents caused significant reductions in the content of free fatty acids ranged from 51.2 to 65.0%. The lowest level of peroxide (2.1 meq/kg) was recorded for UFPO treated with 4% of NCS. The highest reductions (72.8; 70.0%) in p-anisidine value were observed in UFPO treated with 4% of CSA and NCS, respectively. Treatment of UFPO with 4% of CS, CSA and NCS significantly lowered the polar content from 13.9% to 6.3, 4.8 and 3.9%, respectively. The results also indicate that CSA and NCS have nearly the same adsorption efficiency in lowering polymer content of UFPO. Filtration treatment of UFPO with 4% of CS, CSA and NCS markedly lowered the viscosity and colour values of treated UFPO.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Aniline Compounds); 0 (Coffee); 0 (Fatty Acids, Nonesterified); 0 (Peroxides); 0 (Plant Oils); 0 (Polymers); 575917SNR4 (4-anisidine); 5QUO05548Z (palm oil)


  5 / 102710 MEDLINE  
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PMID:28361707
Autor:Weng SL; Huang KY; Kaunang FJ; Huang CH; Kao HJ; Chang TH; Wang HY; Lu JJ; Lee TY
Endereço:Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsin-Chu, 300, Taiwan.
Título:Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features.
Fonte:BMC Bioinformatics; 18(Suppl 3):66, 2017 Mar 14.
ISSN:1471-2105
País de publicação:England
Idioma:eng
Resumo:BACKGROUND: Protein carbonylation, an irreversible and non-enzymatic post-translational modification (PTM), is often used as a marker of oxidative stress. When reactive oxygen species (ROS) oxidized the amino acid side chains, carbonyl (CO) groups are produced especially on Lysine (K), Arginine (R), Threonine (T), and Proline (P). Nevertheless, due to the lack of information about the carbonylated substrate specificity, we were encouraged to develop a systematic method for a comprehensive investigation of protein carbonylation sites. RESULTS: After the removal of redundant data from multipe carbonylation-related articles, totally 226 carbonylated proteins in human are regarded as training dataset, which consisted of 307, 126, 128, and 129 carbonylation sites for K, R, T and P residues, respectively. To identify the useful features in predicting carbonylation sites, the linear amino acid sequence was adopted not only to build up the predictive model from training dataset, but also to compare the effectiveness of prediction with other types of features including amino acid composition (AAC), amino acid pair composition (AAPC), position-specific scoring matrix (PSSM), positional weighted matrix (PWM), solvent-accessible surface area (ASA), and physicochemical properties. The investigation of position-specific amino acid composition revealed that the positively charged amino acids (K and R) are remarkably enriched surrounding the carbonylated sites, which may play a functional role in discriminating between carbonylation and non-carbonylation sites. A variety of predictive models were built using various features and three different machine learning methods. Based on the evaluation by five-fold cross-validation, the models trained with PWM feature could provide better sensitivity in the positive training dataset, while the models trained with AAindex feature achieved higher specificity in the negative training dataset. Additionally, the model trained using hybrid features, including PWM, AAC and AAindex, obtained best MCC values of 0.432, 0.472, 0.443 and 0.467 on K, R, T and P residues, respectively. CONCLUSION: When comparing to an existing prediction tool, the selected models trained with hybrid features provided a promising accuracy on an independent testing dataset. In short, this work not only characterized the carbonylated substrate preference, but also demonstrated that the proposed method could provide a feasible means for accelerating preliminary discovery of protein carbonylation.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Amino Acids); 0 (Proteins); 0 (Reactive Oxygen Species); 2ZD004190S (Threonine); 94ZLA3W45F (Arginine); 9DLQ4CIU6V (Proline); K3Z4F929H6 (Lysine)


  6 / 102710 MEDLINE  
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PMID:28686350
Autor:Lilic A; Wei T; Bennici S; Devaux JF; Dubois JL; Auroux A
Endereço:IRCELYON, UMR 5256 CNRS- Université Lyon 1, 2 avenue Albert Einstein, 69626-, Villeurbanne cedex, France.
Título:A Comparative Study of Basic, Amphoteric, and Acidic Catalysts in the Oxidative Coupling of Methanol and Ethanol for Acrolein Production.
Fonte:ChemSusChem; 10(17):3459-3472, 2017 Sep 11.
ISSN:1864-564X
País de publicação:Germany
Idioma:eng
Resumo:The impact of acid/base properties (determined by adsorption microcalorimetry) of various catalysts on the cross-aldolization of acetaldehyde and formaldehyde leading to acrolein was methodically studied in oxidizing conditions starting from a mixture of methanol and ethanol. The aldol condensation and further dehydration to acrolein were carried out on catalysts presenting various acid/base properties (MgO, Mg-Al oxides, Mg/SiO , NbP, and heteropolyanions on silica, HPA/SiO ). Thermodynamic calculations revealed that cross-aldolization is always favored compared with self-aldolization of acetaldehyde, which leads to crotonaldehyde formation. The presence of strong basic sites is shown to be necessary, but a too high amount drastically increases CO production. On strong acid sites, production of acrolein and carbon oxides (CO ) does not increase with temperature. The optimal catalyst for this process should be amphoteric with a balanced acid/base cooperation of medium strength sites and a small amount (<100 µmol g ) of very strong basic sites (Q >150 kJ mol ).
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:3K9958V90M (Ethanol); 7864XYD3JJ (Acrolein); N762921K75 (Nitrogen); Y4S76JWI15 (Methanol)


  7 / 102710 MEDLINE  
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PMID:28834723
Autor:Scott HL; Westerfield JM; Barrera FN
Endereço:Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
Título:Determination of the Membrane Translocation pK of the pH-Low Insertion Peptide.
Fonte:Biophys J; 113(4):869-879, 2017 Aug 22.
ISSN:1542-0086
País de publicação:United States
Idioma:eng
Resumo:The pH-low insertion peptide (pHLIP) is a leading peptide technology to target the extracellular acidosis that characterizes solid tumors. The pHLIP binds to lipid membranes, and responds to acidification by undergoing a coupled folding/membrane insertion process. In the final transmembrane state, the C terminus of pHLIP gets exposed to the cytoplasm of the target cell, providing a means to translocate membrane-impermeable drug cargoes across the plasma membrane of cancer cells. There exists a need to develop improved pHLIP variants to target tumors with greater efficiency. Characterization of such variants typically relies on determining the pK parameter, the pH midpoint of peptide insertion into the lipid bilayer. Here we report that the value of the pK can be strongly dependent on the method used for its determination. Membrane insertion of pHLIP involves at least four intermediate states, which are believed to be linked to the staggered titration of key acidic residues. We propose that some spectroscopic methods are influenced more heavily by specific membrane folding intermediates, and as a result yield different pK values. To address this potential problem, we have devised an assay to independently monitor the environment of the two termini of pHLIP. This approach provides insights into the conformation pHLIP adopts immediately before the establishment of the transmembrane configuration. Additionally, our data indicate that the membrane translocation of the C terminus of pHLIP, the folding step more directly relevant to drug delivery, occurs at more acidic pH values than previously considered. Consequently, such a pK difference could have substantial ramifications for assessing the translocation of drug cargoes conjugated to pHLIP.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Membrane Proteins); 0 (pHLIP protein)


  8 / 102710 MEDLINE  
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PMID:27810561
Autor:Müller J; Martins A; Csábi J; Fenyvesi F; Könczöl Á; Hunyadi A; Balogh GT
Endereço:Compound Profiling Laboratory, Gedeon Richter Plc., Gyömroi út 19-21, Budapest H-1103, Hungary.
Título:BBB penetration-targeting physicochemical lead selection: Ecdysteroids as chemo-sensitizers against CNS tumors.
Fonte:Eur J Pharm Sci; 96:571-577, 2017 Jan 01.
ISSN:1879-0720
País de publicação:Netherlands
Idioma:eng
Resumo:The anticancer potential of ecdysteroids, especially their chemo-sensitizing activity has recently gained a substantial scientific interest. A comprehensive physicochemical profiling was performed for a set of natural or semi-synthetic ecdysteroids (N=37) to identify a lead compound against central nervous system (CNS) tumors. Calculated properties, such as lipophilicity (clogP), topological polar surface area (TPSA), brain-to-plasma ratio (clogBB) along with the measured blood-brain barrier specific in vitro permeability (logP ) were evaluated in parallel. Compounds with the highest CNS-availability predicted (clogBB>0.0 and logP >-6.0) showed moderate to high lipophilicity (clogP=3.89-5.25), relatively low TPSA (94.45Å ), and shared a common apolar 2,3- and 20,22-diacetonide motif (25, 30-33). These ecdysteroids were selected for testing their capacity to sensitize SH-SY5Y neuroblastoma cells to vincristine. All of the five tested compounds exerted a remarkably strong, dose dependent chemo-sensitizing activity: at 2.5-10.0µM ecdysteroids increased the cytotoxic activity of vincristine one to three orders of magnitude in (e.g., from IC =39.5±2.9nM to as low as 0.056±0.03nM). Moreover, analysis of the combination index (CI) revealed outstanding synergism between ecdysteroids and vincristine (CI =0.072-0.444). Thus, based on drug-likeness, physchem character and in vitro CNS activity, compound 25 was proposed as a lead for further in vivo studies.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Antineoplastic Agents); 0 (Ecdysteroids); 0 (Membranes, Artificial)


  9 / 102710 MEDLINE  
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PMID:27742594
Autor:Aeberhard C; Steuer C; Saxer C; Huber A; Stanga Z; Mühlebach S
Endereço:Department of Endocrinology, Diabetes, Clinical Nutrition and Metabolism, Bern University Hospital, University of Bern, Bern, Switzerland. Electronic address: carla.aeberhard@insel.ch.
Título:Physicochemical stability and compatibility testing of levetiracetam in all-in-one parenteral nutrition admixtures in daily practice.
Fonte:Eur J Pharm Sci; 96:449-455, 2017 Jan 01.
ISSN:1879-0720
País de publicação:Netherlands
Idioma:eng
Resumo:BACKGROUND: Parenteral antiepileptic drugs are frequently used in critically ill patients for seizure control therapy or prevention. Many of these patients require additional parenteral nutrition (PN). Therefore, a parallel infusion of the frequently used antiepileptic drug levetiracetam (LEV) is interesting in terms of the restricted i.v. lines (e.g., neonates). The potential interactions of the complex PN admixture with the drug product and the appropriate admixing of a drug at effective dosages require physicochemical lab assessments to obtain specific and reliable pharmaceutical documentation for the intended admixing. AIM: To assess the of compatibility and stability of LEV, a neutral and hydrophilic drug, in commercial all-in-one (AiO) PN admixtures using simple validated tests to provide necessary data in a timely manner and to allow convenient, documented and safe treatment with PN as the drug vehicle. METHODS: Different concentrations of LEV were injected into two different AiO PN admixtures with no further additives. Stability and compatibility tests for the drug and the PN admixtures were performed over seven days at +4°C, +23±1°C and +37°C without light protection. Stability and sample characteristics were observed by visual inspection and the validated light microscope method. Moreover, the pH level of the admixture was checked, as were the concentrations of LEV over time in the PN admixtures, using an established LC-MS/MS method. RESULTS: The stability controls of LEV at different temperatures were within absolute ±20% of the theoretical value in a concentration range of 98.91-117.84% of the initial value. No changes in pH occurred (5.55±0.04) and no microscopic out of specification data or visual changes were observed. The mean value of the largest lipid droplet in each visual field over seven days was 2.4±0.08µm, comparable to that of the drug-free AiO admixture. Samples stored at +37°C showed yellowish discolorations after 96h of storage. CONCLUSION: LEV showed compatibility and stability over seven days in the selected PN admixtures, and the described methods represented a valuable and timely approach to determine the stability and compatibility of the highly hydrophilic, not dissociated LEV in AiO admixtures under conditions of use. Further studies with clinically relevant and representative examples of physicochemically different drug classes are needed.
Tipo de publicação: JOURNAL ARTICLE
Nome de substância:0 (Anticonvulsants); 0 (Fat Emulsions, Intravenous); 230447L0GL (etiracetam); ZH516LNZ10 (Piracetam)


  10 / 102710 MEDLINE  
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PMID:27720897
Autor:Charoenviriyakul C; Takahashi Y; Morishita M; Matsumoto A; Nishikawa M; Takakura Y
Endereço:Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
Título:Cell type-specific and common characteristics of exosomes derived from mouse cell lines: Yield, physicochemical properties, and pharmacokinetics.
Fonte:Eur J Pharm Sci; 96:316-322, 2017 Jan 01.
ISSN:1879-0720
País de publicação:Netherlands
Idioma:eng
Resumo:Exosomes are small membrane vesicles secreted from cells and are expected to be used as drug delivery systems. Important characteristics of exosomes, such as yield, physicochemical properties, and pharmacokinetics, may be different among different cell types. However, there is limited information about the effect of cell type on these characteristics. In the present study, we evaluated these characteristics of exosomes derived from five different types of mouse cell lines: B16BL6 murine melanoma cells, C2C12 murine myoblast cells, NIH3T3 murine fibroblasts cells, MAEC murine aortic endothelial cells, and RAW264.7 murine macrophage-like cells. Exosomes were collected using a differential ultracentrifugation method. The exosomes collected from all the cell types were negatively charged globular vesicles with a diameter of approximately 100nm. C2C12 and RAW264.7 cells produced more exosomes than the other types of cells. The exosomes were labeled with a fusion protein of Gaussia luciferase and lactadherin to evaluate their pharmacokinetics. After intravenous injection into mice, all the exosomes rapidly disappeared from the systemic circulation and mainly distributed to the liver. In conclusion, the exosome yield was significantly different among the cell types, and all the exosomes evaluated in this study showed comparable physicochemical and pharmacokinetic properties.
Tipo de publicação: JOURNAL ARTICLE



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