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https://www.readbyqxmd.com/read/29139199/in-silico-ligand-based-modeling-of-hbace-1-inhibitors
#1
Govindan Subramanian, Gennady Poda
Alzheimer's disease (AD) is a chronic neurodegenerative disease affecting more than 30 million people worldwide. Development of small molecule inhibitors of human β-secretase 1 (hBACE-1) is being the focus of pharmaceutical industry for the past 15-20 years. Here, we successfully applied multiple ligand-based in silico modeling techniques to understand the inhibitory activities of a diverse set of small molecule hBACE-1 inhibitors reported in the scientific literature. Strikingly, the use of only a small subset of 230 (13%) molecules allowed us to develop quality models that performed reasonably well on the validation set of 1476 (87%) inhibitors...
November 15, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/29138116/in-silico-identification-of-genes-involved-in-chronic-metabolic-acidosis
#2
Ishfaq A Sheikh, Adeel Malik, Sameera F M AlBasri, Mohd A Beg
AIMS: Chronic metabolic acidosis (CMA) refers to increased plasma acidity due to disturbed acid-base equilibrium in human body. CMA leads to many dysfunctions including disorders of intestinal metabolism and barrier functions. The human body responds to these intestinal dysfunctions by creating a compensatory mechanism at genomic level in intestinal epithelial cells. This study was to identify the molecular pathways involved in metabolic dysfunction and compensatory adaptations in intestinal epithelium during CMA...
November 11, 2017: Life Sciences
https://www.readbyqxmd.com/read/29138086/eugenol-derivatives-prospectively-inhibit-l-asparaginase-a-heady-target-protein-of%C3%A2-salmonella-typhimurium
#3
Archana Vimal, Anubhuti Jha, Awanish Kumar
Salmonella typhimurium is the causative agent of severe human infections and mortality throughout the world. Pacing advent of new resistance mechanisms in this microorganism exists, rendering treatment of infectious disease difficult. Ciprofloxacin is no longer considered the first choice of antimicrobial agent due to the emergence of resistance. Therefore, the need for scenario is to find out novel drug target and its potential inhibitor to fight against this pathogen. The present study was undertaken to find out a novel drug target and its inhibitor for improving the current therapeutic methods for treating Salmonella infections...
November 11, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29137627/prevalence-of-current-patterns-and-predictive-trends-of-multidrug-resistant-salmonella-typhi-in-sudan
#4
Ayman A Elshayeb, Abdelazim A Ahmed, Marmar A El Siddig, Adil A El Hussien
BACKGROUND: Enteric fever has persistence of great impact in Sudanese public health especially during rainy season when the causative agent Salmonella enterica serovar Typhi possesses pan endemic patterns in most regions of Sudan - Khartoum. OBJECTIVES: The present study aims to assess the recent state of antibiotics susceptibility of Salmonella Typhi with special concern to multidrug resistance strains and predict the emergence of new resistant patterns and outbreaks...
November 14, 2017: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/29137601/random-walks-on-mutual-microrna-target-gene-interaction-network-improve-the-prediction-of-disease-associated-micrornas
#5
Duc-Hau Le, Lieven Verbeke, Le Hoang Son, Dinh-Toi Chu, Van-Huy Pham
BACKGROUND: MicroRNAs (miRNAs) have been shown to play an important role in pathological initiation, progression and maintenance. Because identification in the laboratory of disease-related miRNAs is not straightforward, numerous network-based methods have been developed to predict novel miRNAs in silico. Homogeneous networks (in which every node is a miRNA) based on the targets shared between miRNAs have been widely used to predict their role in disease phenotypes. Although such homogeneous networks can predict potential disease-associated miRNAs, they do not consider the roles of the target genes of the miRNAs...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29135043/a-framework-for-ecological-risk-assessment-of-metal-mixtures-in-aquatic-systems
#6
Charlotte Nys, Tina Van Regenmortel, Colin R Janssen, Koen Oorts, Erik Smolders, Karel A C DE Schamphelaere
Although metal mixture toxicity has been studied relatively intensely, there is no general consensus yet on how to incorporate metal mixture toxicity into aquatic risk assessment. Here, we combined existing data on chronic metal mixture toxicity at the species level with species-sensitivity-distribution (SSD)-based in-silico metal mixture risk predictions at the community-level for mixtures of Ni, Zn, Cu, Cd and Pb, in order to develop a tiered risk assessment scheme for metal mixtures in freshwater. Generally, independent action (IA) predicts chronic metal mixture toxicity at the species level most accurately, while concentration addition (CA) is the most conservative model...
November 14, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/29134756/development-of-predictive-qsar-models-of-4-thiazolidinones-antitrypanosomal-activity-using-modern-machine-learning-algorithms
#7
Anna Kryshchyshyn, Oleg Devinyak, Danylo Kaminskyy, Philippe Grellier, Roman Lesyk
This paper presents novel QSAR models for the prediction of antitrypanosomal activity among thiazolidines and related heterocycles. The performance of four machine learning algorithms: Random Forest regression, Stochastic gradient boosting, Multivariate adaptive regression splines and Gaussian processes regression have been studied in order to reach better levels of predictivity. The results for Random Forest and Gaussian processes regression are comparable and outperform other studied methods. The preliminary descriptor selection with Boruta method improved the outcome of machine learning methods...
November 14, 2017: Molecular Informatics
https://www.readbyqxmd.com/read/29134712/characterization-of-forced-degradation-products-of-canagliflozine-by-lc-qtof-ms-ms-and-in-silico-toxicity-predictions
#8
Shandilya Mahamuni Baira, Pradipbhai D Kalariya, Rakesh Nimbalkar, Prabha Garg, R Srinivas, M V N Kumar Talluri
RATIONALE: Forced degradation studies are useful for better understanding of the stability of active pharmaceutical ingredients and drugs and to generate information about drug degradation pathways and formation of degradation products (DPs). Identification of DPs plays a vital role in establishing the safety and therapeutic benefit of the drug. METHODS: Canagliflozin (CAN) was subjected to different stress conditions as per ICH guidelines (Q1A R2). All the DPs and the drug were well separated on Aquity CSH C18 (100 × 2...
November 14, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29134420/co-localization-and-interaction-of-pax5-with-iba1-in-brain-of-mice
#9
Shashank Kumar Maurya, Rajnikant Mishra
The Pax5, a B-cell-Specific Activator Protein (BSAP) and redox-sensitive transcription factor, is expressed in the immune-privileged brain, B-lymphocytes, lymph nodes and spleen. PAX5-mediated immune pathway has also been described in the progression of Glioblastoma multiforme. However, the status of Pax5 and its role in brain immunity are not yet elucidated. In silico analysis of Pax5 interacting proteins predicts its interaction with proteins of cell proliferation, differentiation of hematopoietic cells, neurogenesis and several cell signalling pathways...
November 13, 2017: Cellular and Molecular Neurobiology
https://www.readbyqxmd.com/read/29133956/network-inference-from-glycoproteomics-data-reveals-new-reactions-in-the-igg-glycosylation-pathway
#10
Elisa Benedetti, Maja Pučić-Baković, Toma Keser, Annika Wahl, Antti Hassinen, Jeong-Yeh Yang, Lin Liu, Irena Trbojević-Akmačić, Genadij Razdorov, Jerko Štambuk, Lucija Klarić, Ivo Ugrina, Maurice H J Selman, Manfred Wuhrer, Igor Rudan, Ozren Polasek, Caroline Hayward, Harald Grallert, Konstantin Strauch, Annette Peters, Thomas Meitinger, Christian Gieger, Marija Vilaj, Geert-Jan Boons, Kelley W Moremen, Tatiana Ovchinnikova, Nicolai Bovin, Sakari Kellokumpu, Fabian J Theis, Gordan Lauc, Jan Krumsiek
Immunoglobulin G (IgG) is a major effector molecule of the human immune response, and aberrations in IgG glycosylation are linked to various diseases. However, the molecular mechanisms underlying protein glycosylation are still poorly understood. We present a data-driven approach to infer reactions in the IgG glycosylation pathway using large-scale mass-spectrometry measurements. Gaussian graphical models are used to construct association networks from four cohorts. We find that glycan pairs with high partial correlations represent enzymatic reactions in the known glycosylation pathway, and then predict new biochemical reactions using a rule-based approach...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133212/quantitative-and-systems-pharmacology-2-in-silico-polypharmacology-of-g-protein-coupled-receptor-ligands-via-network-based-approaches
#11
Zengrui Wu, Weiqiang Lu, Weiwei Yu, Tianduanyi Wang, Weihua Li, Guixia Liu, Hankun Zhang, Xiufeng Pang, Jin Huang, Mingyao Liu, Feixiong Cheng, Yun Tang
G protein-coupled receptors (GPCRs) are the largest super family with more than 800 membrane receptors. Currently, over 30% of the approved drugs target human GPCRs. However, only approximately 30 human GPCRs have been resolved three-dimensional crystal structures, which limits traditional structure-based drug discovery. Recent advances in network-based systems pharmacology approaches have demonstrated powerful strategies for identifying new targets of GPCR ligands. In this study, we proposed a network-based systems pharmacology framework for comprehensive identification of new drug-target interactions on GPCRs...
November 10, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/29133159/highly-conserved-exposed-immunogenic-peptides-of-omp34-against-acinetobacter-baumannii-an-innovative-approach
#12
Abolfazl Jahangiri, Iraj Rasooli, Parviz Owlia, Abbas Ali Imani Fooladi, Jafar Salimian
Omp34, also known as Omp34kDa or Omp33-36 is a virulence factor associated with A. baumannii metabolic fitness or its adherence and invasion to human epithelial cells. This protein is also introduced as a specific antigen which could induce strong antibody responses. In the present in silico study, recent vaccine design strategies such as 'antigen minimization' and 'high epitope density' were invoked to design a soluble immunogen with higher antigenicity. As an advantage, the tools employed in the current study are easily available...
November 10, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29133047/discovery-of-new-potent-molecular-entities-able-to-inhibit-mpges-1
#13
Simone Di Micco, Stefania Terracciano, Vincenza Cantone, Katrin Fischer, Andreas Koeberle, Antonio Foglia, Raffaele Riccio, Oliver Werz, Ines Bruno, Giuseppe Bifulco
mPGES-1, a glutathione-dependent membrane protein is involved in the last step of PGE2 production and has been well recognized as a strategic target for the development of anti-inflammatory and anti-cancer agents. It has been proven to selectively control the PGE2 levels induced by inflammatory stimuli, with neither affecting PGE2 constitutively produced, nor homeostatic prostanoids, so that its modulation can represent a better strategy to control PGE2 related disorders, compared to the use of the classical anti-inflammatory drugs, endowed with severe side effects...
October 23, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29132146/identification-of-unique-neoantigen-qualities-in-long-term-survivors-of-pancreatic-cancer
#14
Vinod P Balachandran, Marta Łuksza, Julia N Zhao, Vladimir Makarov, John Alec Moral, Romain Remark, Brian Herbst, Gokce Askan, Umesh Bhanot, Yasin Senbabaoglu, Daniel K Wells, Charles Ian Ormsby Cary, Olivera Grbovic-Huezo, Marc Attiyeh, Benjamin Medina, Jennifer Zhang, Jennifer Loo, Joseph Saglimbeni, Mohsen Abu-Akeel, Roberta Zappasodi, Nadeem Riaz, Martin Smoragiewicz, Z Larkin Kelley, Olca Basturk, Mithat Gönen, Arnold J Levine, Peter J Allen, Douglas T Fearon, Miriam Merad, Sacha Gnjatic, Christine A Iacobuzio-Donahue, Jedd D Wolchok, Ronald P DeMatteo, Timothy A Chan, Benjamin D Greenbaum, Taha Merghoub, Steven D Leach
Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8(+) T-cell infiltrates, but neither alone, stratified patients with the longest survival...
November 8, 2017: Nature
https://www.readbyqxmd.com/read/29132026/integrated-omics-analysis-of-root-preferred-genes-across-diverse-rice-varieties-including-japonica-and-indica-cultivars
#15
Sunok Moon, Anil Kumar Nalini Chandran, Yun-Shil Gho, Sun-A Park, Sung-Ryul Kim, Yo-Han Yoo, Ki-Hong Jung
Plant root systems play essential roles in developmental processes, such as the absorption of water and inorganic nutrients, and structural support. Gene expression is affected by growth conditions and the genetic background of plants. To identify highly conserved root-preferred genes in rice across diverse growth conditions and varieties, we used two independent meta-anatomical expression profiles based on a large collection of Affymetrix and Agilent 44K microarray data sets available for public use. We then identified 684 loci with root-preferred expression, which were validated with in silico analysis using both meta-expression profiles...
October 26, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29127258/homozygous-mutation-in-cep19-a-gene-mutated-in-morbid-obesity-in-bardet-biedl-syndrome-with-predominant-postaxial-polydactyly
#16
Esra Yıldız Bölükbaşı, Sara Mumtaz, Muhammad Afzal, Ute Woehlbier, Sajid Malik, Aslıhan Tolun
BACKGROUND: Bardet-Biedl syndrome (BBS) is a ciliopathy with extensive phenotypic variability and genetic heterogeneity. We aimed to discover the gene mutated in a consanguineous kindred with multiple cases of a BBS phenotype. METHODS: SNP genotype data were used for linkage analysis and exome sequencing to identify mutations. Modelling and in silico analysis were performed to predict mutation severity. RESULTS: Patients had postaxial polydactyly plus variable other clinical features including rod-cone dystrophy, obesity, intellectual disability, renal malformation, developmental delay, dental anomalies, speech disorder and enlarged fatty liver...
November 10, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29126163/identification-of-novel-cancer-biomarkers-of-prognostic-value-using-specific-gene-regulatory-networks-grn-a-novel-role-of-rad51ap1-for-ovarian-and-lung-cancers
#17
Dimple Chudasama, Valeria Bo, Marcia Hall, Vladimir Anikin, Jeyarooban Jeyaneethi, Jane Gregory, George Pados, Allan Tucker, Amanda Harvey, Ryan Pink, Emmanouil Karteris
To date, microarray analyses have led to the discovery of numerous individual "molecular signatures" associated with specific cancers. However, there are serious limitations for the adoption of these multi-gene signatures in the clinical environment for diagnostic or prognostic testing as studies with more power need to be carried out. This may involve larger richer cohorts and more advanced analyses.In this study, we conduct analyses -based on GRN- to reveal distinct and common biomarkers across cancer types...
November 8, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29126020/mechanistic-insight-in-potential-dual-role-of-sinigrin-against-helicoverpa-armigera
#18
Aniruddha R Agnihotri, Chaitanya V Hulagabali, Anmol S Adhav, Rakesh S Joshi
The adverse effect of glucosinolates on diverse phytophagous insects is well documented, but its impact on insect physiology has remained enigmatic. Here we report insights into detrimental effects of plant glucosinolate molecule, sinigrin, on Helicoverpa armigera growth and development. In-silico screening of multiple glucosinolates predicted sinigrin as one of the potential inhibitor of H. armigera cathepsin B and L. Insects fed on sinigrin containing diet showed significantly reduced growth (20-30%), delayed pupation (10-15%), decreased fecundity (50-80%) and developmental abnormalities...
November 7, 2017: Phytochemistry
https://www.readbyqxmd.com/read/29124899/simeprevir-oxidative-degradation-product-molecular-modeling-in-silico-toxicity-and-resolution-by-synchronous-spectrofluorimetry
#19
Khalid A M Attia, Nasr M El-Abasawi, Ahmed El-Olemy, Ahmed Serag
In this article, one of the potential degradation products of the novel antiviral drug simeprevir was isolated and characterized by means of infrared (IR) and mass spectrometry. Moreover, comparative molecular docking, ADMET (absorption, distribution, metabolism, excretion - toxicity) and insilico toxicity prediction studies were applied to evaluate the activity of simeprevir and its degradation product. Furthermore,a simple, accurate and selective second derivative synchronous spectrofluorimetric method was developed for the determination of simeprevir in the presence of its oxidative degradation product...
November 10, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/29122004/identification-and-characterization-of-serovar-independent-immunogens-in-actinobacillus-pleuropneumoniae
#20
Fabio Antenucci, Cyrielle Fougeroux, Janine T Bossé, Zofia Magnowska, Camille Roesch, Paul Langford, Peter Johannes Holst, Anders Miki Bojesen
Despite numerous actions to prevent disease, Actinobacillus pleuropneumoniae (A. pleuropneumoniae) remains a major cause of porcine pleuropneumonia, resulting in economic losses to the swine industry worldwide. In this paper, we describe the utilization of a reverse vaccinology approach for the selection and in vitro testing of serovar-independent A. pleuropneumoniae immunogens. Potential immunogens were identified in the complete genomes of three A. pleuropneumoniae strains belonging to different serovars using the following parameters: predicted outer-membrane subcellular localization; ≤ 1 trans-membrane helices; presence of a signal peptide in the protein sequence; presence in all known A...
November 9, 2017: Veterinary Research
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