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In silico

Hugo de Almeida, Vincent Leroux, Flávia Nader Motta, Philippe Grellier, Bernard Maigret, Jaime M Santana, Izabela Marques Dourado Bastos
We have previously demonstrated that the secreted prolyl oligopeptidase of Trypanosoma cruzi (POPTc80) is involved in the infection process by facilitating parasite migration through the extracellular matrix. We have built a 3D structural model where POPTc80 is formed by a catalytic α/β-hydrolase domain and a β-propeller domain, and in which the substrate docks at the inter-domain interface, suggesting a "jaw opening" gating access mechanism. This preliminary model was refined by molecular dynamics simulations and next used for a virtual screening campaign, whose predictions were tested by standard binding assays...
October 21, 2016: Journal of Computer-aided Molecular Design
Duthika M Mallawaaratchy, Susannah Hallal, Ben Russell, Linda Ly, Saeideh Ebrahimkhani, Heng Wei, Richard I Christopherson, Michael E Buckland, Kimberley L Kaufman
Extracellular vesicles (EVs) play key roles in glioblastoma (GBM) biology and represent novel sources of biomarkers that are detectable in the peripheral circulation. Despite this notionally non-invasive approach to assess GBM tumours in situ, a comprehensive GBM EV protein signature has not been described. Here, EVs secreted by six GBM cell lines were isolated and analysed by quantitative high-resolution mass spectrometry. Overall, 844 proteins were identified in the GBM EV proteome, of which 145 proteins were common to EVs secreted by all cell lines examined; included in the curated EV compendium (Vesiclepedia_559; http://microvesicles...
October 21, 2016: Journal of Neuro-oncology
Yanfeng Zhang, Yong Xu, Wei Fang, Xiaotang Wang, Zemin Fang, Yazhong Xiao
A taxonomic study was carried out on a Gram-stain negative, rod-shaped, non-flagellated, and facultatively anaerobic bacterial strain designated as strain SF-16(T), which was isolated from an unidentified starfish in Sanya, China. Strain SF-16(T) was found to be 5.0-7.0 μm long, and oxidase and catalase positive. Cell growth was observed at pH 6.0-8.5 (optimum, 7.0-8.0), temperatures of 10-41 °C (optimum, 25-30 °C), and salinities of 0-12 % (optimum, 3.0-6.0 %). The predominant fatty acids (>20 %) were found to be C18:1 ω7c and/or C18:1 ω6c (summed feature 8)...
October 21, 2016: Antonie Van Leeuwenhoek
Marie Umber, Rose-Marie Gomez, Suzia Gélabale, Lydiane Bonheur, Claudie Pavis, Pierre-Yves Teycheney
The complete genome sequence of Dioscorea bacilliform TR virus (DBTRV) was determined. The closest relatives of DBTRV are Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform RT virus 1 (DBRTV1). Specific primers were designed and used to determine the prevalence of DBTRV in a yam germplasm collection. It was found that this virus infects Dioscorea alata and D. trifida plants in Guadeloupe and French Guyana. DTRBV was not detected in any of the tested D. cayenensis-rotundata accessions. In silico analysis provided evidence for the presence of DBTRV-like endogenous sequences in the genome of D...
October 21, 2016: Archives of Virology
Su Hui Seong, Anupom Roy, Hyun Ah Jung, Hee Jin Jung, Jae Sue Choi
ETHNOPHARMACOLOGICAL RELEVANCE: Pueraria lobata root was used to treat wasting-thirst regarded as diabetes mellitus and was included in the composition of Okcheonsan, which is prescribed for thirst-waste in traditional Chinese medicine. AIM OF THE STUDY: The objective of this study was to evaluate the anti-diabetic potential of the root of Pueraria lobata and its constituents via protein tyrosine phosphatase 1B (PTP1B) and α-glucosidase inhibitory activities. MATERIALS AND METHODS: In this study, anti-diabetic activities of the 70% ethanolic (EtOH) extract from P...
October 18, 2016: Journal of Ethnopharmacology
Dimitrios Spiliotopoulos, Amedeo Caflisch
We review the results of fragment-based high-throughput docking to the N-terminal bromodomain of BRD4 and the CREBBP bromodomain. In both docking campaigns the ALTA (anchor-based library tailoring) procedure was used to reduce the size of the initial library by selecting for flexible docking only the molecules that contain a fragment with favorable predicted binding energy. Ranking by a force field-based energy with solvation has resulted in small-molecule hits with low-micromolar affinity and favorable ligand efficiency...
March 2016: Drug Discovery Today. Technologies
Christina Gutierrez Bracamontes, Rebecca Lopez-Valdez, Ramadevi Subramani, Arunkumar Arumugam, Sushmita Nandy, Venkatesh Rajamanickam, Vignesh Ravichandran, Rajkumar Lakshmanaswamy
Early parity reduces the risk of breast cancer in women while nulliparity and late parity increase the risk of breast cancer. In order to translate this protection to women where early pregnancy is not feasible, much work has focused on understanding how parity confers protection against breast cancer, the molecular mechanisms by which this occurs is still not well understood. Healthy parous and nulliparous women were recruited for this study. We assessed serum protein profiles of early parous, late parous, and nulliparous women using the Phospho Explorer antibody array...
October 19, 2016: Oncotarget
Pradipta Ranjan Rauta, Sarbani Ashe, Debasis Nayak, Bismita Nayak
Virulence-related outer membrane proteins (Omps) are expressed in bacteria (Gram-negative) such as V. cholerae and are vital to bacterial invasion in to eukaryotic cell and survival within macrophages that could be best candidate for development of vaccine against V. cholerae. Applying in silico approaches, the 3-D model of the Omp was developed using Swiss model server and validated byProSA and Procheck web server. The continuous stretch of amino acid sequences 26mer: RTRSNSGLLTWGDKQTITLEYGDPAL and 31mer: FFAGGDNNLRGYGYKSISPQDASGALTGAKY having B-cell binding sites were selected from sequence alignment after B cell epitopes prediction by BCPred and AAP prediction modules of BCPreds...
October 12, 2016: Computational Biology and Chemistry
Vineetha Mandlik, Sohan Patil, Ramanamurthy Bopanna, Sudipta Basu, Shailza Singh
Cutaneous leishmaniasis affects nearly 0.7 to 1.3 million people annually. Treatment of this disease is difficult due to lack of appropriate medication and the growing problem of drug resistance. Natural compounds such as coumarins serve as complementary therapeutic agents in addition to the current treatment modalities. In this study, we have performed an in-silico screening of the coumarin derivatives and their anti-leishmanial properties has been explored both in-vitro and in-vivo. One of the compounds (compound 2) exhibited leishmanicidal activity and to further study its properties, nanoliposomal formulation of the compound was developed...
2016: PloS One
Kerstin Reuter, Alexander Biehl, Laurena Koch, Volkhard Helms
Translation of mRNA sequences into proteins typically starts at an AUG triplet. In rare cases, translation may also start at alternative non-AUG codons located in the annotated 5' UTR which leads to an increased regulatory complexity. Since ribosome profiling detects translational start sites at the nucleotide level, the properties of these start sites can then be used for the statistical evaluation of functional open reading frames. We developed a linear regression approach to predict in-frame and out-of-frame translational start sites within the 5' UTR from mRNA sequence information together with their translation initiation confidence...
October 2016: PLoS Computational Biology
Dorimar Stiz, Adriana Campos, Ana Lúcia Tasca Gois Ruiz, João Ernesto de Carvalho, Rogério Corrêa, Valdir Cechinel-Filho
This work describes the antiproliferative potential of 14 cyclic imides (methylphtalimides, carboxylic acid phtalimides and itaconimides) against several human cancer cell lines. The antiproliferative effect was evaluated using the sulforhodamine B assay. Although some compounds from methylphtalimide and carboxylic acid phtalimide classes exhibited a selective antiproliferative activity, the itaconimides (11-14) exhibited the best results, especially compound 14, which presented a TGI (concentration that produces total growth inhibition) value of 0...
October 21, 2016: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
Anna J MacDonald, Stephen D Sarre
Taxon-specific DNA tests are applied to many ecological and management questions, increasingly using environmental DNA (eDNA). eDNA facilitates non-invasive ecological studies, but introduces additional risks of bias and error. For effective application, PCR primers must be developed for each taxon and validated in each system. We outline a nine step framework for the development and validation of taxon-specific primers for eDNA analysis in ecological studies, involving reference database construction, phylogenetic evaluation of the target gene, primer design, primer evaluation in silico, and laboratory evaluation of primer specificity, sensitivity, and utility...
October 21, 2016: Molecular Ecology Resources
Gianluigi Franci, Federica Sarno, Angela Nebbioso, Lucia Altucci
Epigenetic modifications are functionally involved in gene expression regulation. In particular, histone posttranslational modifications play a crucial role in functional chromatin organization. Several drugs able to inhibit or stimulate some families of proteins involved in epigenetic histone regulation have been found, a number of which are FDA-approved for the treatment of cutaneous T-cell lymphoma or are in phase I/II/III clinical trials for solid tumors. Although some protein families, such as histone deacetylases and their inhibitors, are well characterized, our understanding of histone lysine demethylases is still incomplete...
October 21, 2016: Epigenetics: Official Journal of the DNA Methylation Society
Pierre E Affaticati, Shao-Bo Dai, Panwajee Payongsri, Helen C Hailes, Kai Tittmann, Paul A Dalby
The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation...
October 21, 2016: Scientific Reports
Shaher Bano Mirza, Ramin Ekhteiari Salmas, M Qaiser Fatmi, Serdar Durdagi
The Klotho is known as lifespan enhancing protein involved in antagonizing the effect of Wnt proteins. Wnt proteins are stem cell regulators, and uninterrupted exposure of Wnt proteins to the cell can cause stem and progenitor cell senescence, which may lead to aging. Keeping in mind the importance of Klotho in Wnt signaling, in silico approaches have been applied to study the important interactions between Klotho and Wnt3 and Wnt3a (wingless-type mouse mammary tumor virus (MMTV) integration site family members 3 and 3a)...
October 21, 2016: Journal of Enzyme Inhibition and Medicinal Chemistry
Arathi Kizhedath, Simon Wilkinson, Jarka Glassey
Biopharmaceuticals, monoclonal antibody (mAb)-based therapeutics in particular, have positively impacted millions of lives. MAbs and related therapeutics are highly desirable from a biopharmaceutical perspective as they are highly target specific and well tolerated within the human system. Nevertheless, several mAbs have been discontinued or withdrawn based either on their inability to demonstrate efficacy and/or due to adverse effects. Approved monoclonal antibodies and derived therapeutics have been associated with adverse effects such as immunogenicity, cytokine release syndrome, progressive multifocal leukoencephalopathy, intravascular haemolysis, cardiac arrhythmias, abnormal liver function, gastrointestinal perforation, bronchospasm, intraocular inflammation, urticaria, nephritis, neuropathy, birth defects, fever and cough to name a few...
October 20, 2016: Archives of Toxicology
Barbara Maciejewska, Bartosz Roszniowski, Akbar Espaillat, Agata Kęsik-Szeloch, Grazyna Majkowska-Skrobek, Andrew M Kropinski, Yves Briers, Felipe Cava, Rob Lavigne, Zuzanna Drulis-Kawa
Lytic bacteriophages and phage-encoded endolysins (peptidoglycan hydrolases) provide a source for the development of novel antimicrobial strategies. In the present study, we focus on the closely related (96 % DNA sequence identity) environmental myoviruses vB_KpnM_KP15 (KP15) and vB_KpnM_KP27 (KP27) infecting multidrug-resistant Klebsiella pneumoniae and Klebsiella oxytoca strains. Their genome organisation and evolutionary relationship are compared to Enterobacter phage phiEap-3 and Klebsiella phages Matisse and Miro...
October 21, 2016: Applied Microbiology and Biotechnology
Beata Powroźnik, Karolina Słoczyńska, Krzysztof Marciniec, Paweł Zajdel, Elżbieta Pękala
Purpose: Determination of the mutagenic potential of new biologically active compounds is of great concern for preliminary toxicity testing and drug development. Methods: The mutagenic and antimutagenic effects of some quinoline- and isoquinolinesulfonamide analogs of aripiprazole (1-8), which display potent antidepressant, anxiolytic, and antipsychotic properties, were evaluated using the Vibrio harveyi assay and OSIRIS Property Explorer software. Additionally, the Ames test was used as the reference. Results: In silico prediction showed that compounds 5 (N-(3-(4-(2,3- dichlorophenyl)piperazin-1-yl)propyl)quinoline-7-sulfonamide) and 6 (N-(4-(4-(2,3- Dichlorophenyl)piperazin-1-yl)butyl)quinoline-7-sulfonamide) trigger a mutagenic structural alert...
September 2016: Advanced Pharmaceutical Bulletin
Oihane Irazoki, Jesús Aranda, Timo Zimmermann, Susana Campoy, Jordi Barbé
In addition to its role in DNA damage repair and recombination, the RecA protein, through its interaction with CheW, is involved in swarming motility, a form of flagella-dependent movement across surfaces. In order to better understand how SOS response modulates swarming, in this work the location of RecA and CheW proteins within the swarming cells has been studied by using super-resolution microscopy. Further, and after in silico docking studies, the specific RecA and CheW regions associated with the RecA-CheW interaction have also been confirmed by site-directed mutagenesis and immunoprecipitation techniques...
2016: Frontiers in Microbiology
N C N Perera, G I Godahewa, Jehee Lee
Mitogen-activated protein kinase (MAPK) is involved in the regulation of cellular events by mediating signal transduction pathways. MAPK1 is a member of the extracellular-signal regulated kinases (ERKs), playing roles in cell proliferation, differentiation, and development. This is mainly in response to growth factors, mitogens, and many environmental stresses. In the current study, we have characterized the structural features of a homolog of MAPK1 from disk abalone (AbMAPK1). Further, we have unraveled its expressional kinetics against different experimental pathogenic infections or related chemical stimulants...
October 17, 2016: Fish & Shellfish Immunology
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