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https://www.readbyqxmd.com/read/28527154/structure-based-classification-for-bile-salt-export-pump-bsep-inhibitors-using-comparative-structural-modeling-of-human-bsep
#1
Sankalp Jain, Melanie Grandits, Lars Richter, Gerhard F Ecker
The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline...
May 19, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28527150/development-of-in-silico-protocols-to-predict-structural-insights-into-the-metabolic-activation-pathways-of-xenobiotics
#2
M Kalim A Khan, Salman Akhtar, Jamal M Arif
To establish in silico model to predict the structural insight into the metabolic bioactivation pathway of xenobiotics, we considered two specific and one non-specific mammary procarcinogen [e.g., dibenzo[a,l]pyrene (DBP), 7,12-dimethylbenz[a]anthracene (DMBA), and benzo[a]pyrene (BP)]. The CYP1A1, 1B1, 2C9, 1A2 and 2B6 reported in wet-lab studies to actively metabolize DBP also showed strong binding energies (kcal/mol) of -11.50, -10.67, -10.37, -9.76 and -9.72, respectively, with inhibition constants ranging between 0...
May 19, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28527107/an-immune-related-six-lncrna-signature-to-improve-prognosis-prediction-of-glioblastoma-multiforme
#3
Meng Zhou, Zhaoyue Zhang, Hengqiang Zhao, Siqi Bao, Liang Cheng, Jie Sun
Recent studies have demonstrated the utility and superiority of long non-coding RNAs (lncRNAs) as novel biomarkers for cancer diagnosis, prognosis, and therapy. In the present study, the prognostic value of lncRNAs in glioblastoma multiforme was systematically investigated by performing a genome-wide analysis of lncRNA expression profiles in 419 glioblastoma patients from The Cancer Genome Atlas (TCGA) project. Using survival analysis and Cox regression model, we identified a set of six lncRNAs (AC005013.5, UBE2R2-AS1, ENTPD1-AS1, RP11-89C21...
May 19, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28526475/identification-and-preliminary-structure-activity-relationships-of-1-indanone-derivatives-as-novel-indoleamine-2-3-dioxygenase-1-ido1-inhibitors
#4
Dingding Gao, Yingxia Li
Indoleamine 2,3-dioxygenase 1 (IDO1) plays a vital role in the catabolism of tryptophan along with the kynurenine pathway which is involved in many human diseases including cancer, Alzheimer's disease, etc. In this study, compound 1 bearing a 1-Indanone scaffold was identified as a novel IDO1 inhibitor by structure-based virtual screening, with moderate to good enzymatic and cellular inhibitory activities. Also, surface plasmon resonance analysis validated the direct interaction between compound 1 and IDO1 protein...
May 10, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28525653/predicted-philogeny-secondary-conformational-structure-and-epitope-antigenicity-of-immunological-sequences-in-poultry
#5
L J Lara, A P Peconick, É J Fassani, A M P Júnior, P R B Chalfun, D L Raymundo, T A Barçante, J M de P Barçante
Poultry production is faced with different types of stresses that are responsible for issues of animal welfare as well as for economic losses. Moreover, the immunity decreases when animals are stressed. In silico analyses are important in reducing the cost and in increasing the accuracy of scientific results. A bioinformatics tool was used to perform ontology studies on 15 different immunological sequences of poultry. The mRNA structures and sequences with maximum antigenic residues were also predicted. No homology was found between the sequences of poultry and mammals...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28524201/a-computational-framework-for-distinguishing-direct-versus-indirect-interactions-in-human-functional-protein-protein-interaction-networks
#6
Suyu Mei, Erik K Flemington, Kun Zhang
Recognition of indirect interactions is instrumental to in silico reconstruction of signaling pathways and sheds light on the exploration of unknown physical paths between two indirectly interacting genes. However, very limited computational methods have explicitly exploited the indirect interactions with experimental evidence thus far. In this work, we attempt to distinguish direct versus indirect interactions in human functional protein-protein interaction (PPI) networks via a predictive l2-regularized logistic regression model built on the experimental data...
May 19, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28523927/retinoid-bms411-4-5-5-dimethyl-8-phenyl-5-6-dihydronaphthalen-2-yl-carbonyl-amino-benzoic-acid-a-potential-inhibitor-of-ns5a-protein-of-hepatitis-c-virus-a-candidate-for-combined-therapy-of-hepatitis-c-infection
#7
S Ibrahim, M J Asad, R T Mahmood, F H Wattoo, S Akhter, D Shahwar
Hepatitis C infection is a serious health issue worldwide caused by hepatitis C virus (HCV). There is an urgent need of search for new direct acting antiviral drugs due to the rapid development of drug resistance. The HCV NS5A protein is involved in creating resistance against antiviral therapy and there are also many reports that vitamin A deficiency is associated with non-responsiveness to antiviral treatment in HCV infected patients. So the present in silico study was aimed to find the relation between vitamin A deficiency and the NS5A protein's function in antiviral resistance...
2017: Acta Virologica
https://www.readbyqxmd.com/read/28523647/computational-investigation-of-growth-hormone-receptor-trp169arg-heterozygous-mutation-in-a-child-with-short-stature
#8
William Farias Porto, Felipe Albuquerque Marques, Huri Brito Pogue, Maria Teresinha de Oliveira Cardoso, Maria Gabriela Rodrigues do Vale, Állan da Silva Pires, Octavio Luiz Franco, Sérgio Amorim de Alencar, Robert Pogue
Mutations in the growth hormone receptor (GHR) gene can cause disruption of the growth hormone signaling pathway, resulting in growth deficiency due to growth hormone (GH) resistance. Both recessive and apparently dominant mutations have been described in the literature. In order to shed some light on the molecular mechanism of partial growth hormone resistance caused by heterozygous mutations we performed an in-depth in silico analysis of a mutation found in a girl with a previous diagnosis of idiopathic short stature...
May 18, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28522829/somatic-tumor-mutations-detected-by-targeted-next-generation-sequencing-in-minute-amounts-of-serum-derived-cell-free-dna
#9
Marjolein J A Weerts, Ronald van Marion, Jean C A Helmijr, Corine M Beaufort, Niels M G Krol, Anita M A C Trapman-Jansen, Winand N M Dinjens, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens
The use of blood-circulating cell-free DNA (cfDNA) as 'liquid-biopsy' is explored worldwide, with hopes for its potential in providing prognostic or predictive information in cancer treatment. In exploring cfDNA, valuable repositories are biobanks containing material collected over time, however these retrospective cohorts have restrictive resources. In this study, we aimed to detect tumor-specific mutations in only minute amounts of serum-derived cfDNA by using a targeted next generation sequencing (NGS) approach...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28521820/destabilization-of-the-twist1-e12-complex-dimerization-following-the-r154p-point-mutation-of-twist1-an-in-silico-approach
#10
Charlotte Bouard, Raphael Terreux, Agnès Tissier, Laurent Jacqueroud, Arnaud Vigneron, Stéphane Ansieau, Alain Puisieux, Léa Payen
BACKGROUND: The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues...
May 18, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28521603/in-silico-binding-mechanism-prediction-of-benzimidazole-based-corticotropin-releasing-factor-1-receptor-antagonists-by-quantitative-structure-activity-relationship-molecular-docking-and-pharmacokinetic-parameters-calculation
#11
Neeraj Kumar, Shashank Shekhar Mishra, Chandra Shekhar Sharma, Hamendra Pratap Singh, Sourav Kalra
Despite the various research efforts towards the treatment of stress related disorders, the drug has not yet launched last 20 years. Corticotropin releasing factor-1 receptor antagonists have been point of great interest in stress related disorders. In the present study, we have selected benzazole scaffold based compounds as corticotropin releasing factor-1 antagonists and performed 2D and 3D QSAR studies to identify the structural features to elucidating the binding mechanism prediction. The best 2D QSAR model was obtained through multiple linear regression method with r(2) value of 0...
May 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28521489/identification-of-proteins-with-different-abundance-associated-with-cell-migration-and-proliferation-in-leiomyoma-interstitial-fluid-by-proteomics
#12
Blendi Ura, Federica Scrimin, Cinzia Franchin, Giorgio Arrigoni, Danilo Licastro, Lorenzo Monasta, Giuseppe Ricci
Uterine leiomyoma is the most common female reproductive tract benign tumor. Little is known about protein composition and changes in the leiomyoma interstitial fluid (IF). The present study focused on changes in protein abundance in the IF of leiomyoma. Leiomyoma IFs and adjacent myometrial IFs were obtained and analyzed by two-dimensional electrophoresis (2-DE) coupled with mass spectrometry and western blotting for 2-DE data validation. A total of 25 unique proteins were observed to change significantly (P<0...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28521054/in-silico-prediction-of-drug-induced-liver-injury-based-on-adverse-drug-reaction-reports
#13
Xiang-Wei Zhu, Shao-Jing Li
Drug-induced liver injury (DILI) is a major cause of drug attrition. Currently existing Quantitative Structure-Activity Relationship (QSAR) models have limited predictive capabilities for DILI. Furthermore, their practical applications were limited by lack of new hepatotoxicity data. In this study, we first collected and curated a novel set of 122 DILI-positive and 932 DILI-negative drugs from online adverse drug reports using proportional reporting ratios as the signal detection method. Second, three strategies (under-sampling the majority class, synthetic minority over-sampling technique, and adjusting decision threshold approach) were employed to develop predictive classification models to cope with the unbalanced dataset...
May 17, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28520412/identification-of-the-ferredoxin-binding-site-of-a-ferredoxin-dependent-cyanobacterial-nitrate-reductase
#14
Anurag P Srivastava, Emily P Hardy, James P Allen, Brian J Vaccaro, Michael K Johnson, David B Knaff
An in silico model for the 1:1 ferredoxin (Fd)/nitrate reductase (NR) complex, using the known structure of Synechocystis sp. PCC 6803 Fd and the in silico model of Synechococcus sp. PCC 7942 NR, is used to map the interaction sites that define the interface between Fd and NR. To test the electrostatic interactions predicted by the model complex, five positively charged NR amino acids Arg43, Arg46, Arg197, Lys201 and Lys614; and a negatively charged amino acid, Glu219, were altered using site-directed mutagenesis and characterized by activity measurements, metal analysis and EPR studies...
May 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28520403/integrated-strategy-for-unknown-ei-ms-identification-using-quality-control-calibration-curve-multivariate-analysis-ei-ms-spectral-database-and-retention-index-prediction
#15
Teruko Matsuo, Hiroshi Tsugawa, Hiromi Miyagawa, Eiichiro Fukusaki
Compound identification using unknown electron ionization (EI) mass spectra in gas chromatography coupled with mass spectrometry (GC-MS) is challenging in untargeted metabolomics, natural product chemistry, or exposome research. While the total count of EI-MS records included in publicly or commercially available databases is over 900,000, efficient use of this huge database has not been achieved in metabolomics. Therefore, we proposed a 'four-step' strategy for the identification of biologically significant metabolites using an integrated cheminformatics approach: (i) Quality control calibration curve to reduce background noise, (ii) variable selection by hypothesis testing in principal component analysis for the efficient selection of target peaks, (iii) searching the EI-MS spectral database, and (iv) retention index (RI) filtering in combination with RI predictions...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28518218/comparison-and-optimization-of-in-silico-algorithms-for-predicting-the-pathogenicity-of-sodium-channel-variants-in-epilepsy
#16
Katherine D Holland, Thomas M Bouley, Paul S Horn
OBJECTIVE: Variants in neuronal voltage-gated sodium channel α-subunits genes SCN1A, SCN2A, and SCN8A are common in early onset epileptic encephalopathies and other autosomal dominant childhood epilepsy syndromes. However, in clinical practice, missense variants are often classified as variants of uncertain significance when missense variants are identified but heritability cannot be determined. Genetic testing reports often include results of computational tests to estimate pathogenicity and the frequency of that variant in population-based databases...
May 18, 2017: Epilepsia
https://www.readbyqxmd.com/read/28515570/association-between-hemodynamic-modifications-and-clinical-outcome-of-intracranial-aneurysms-treated-using-flow-diverters
#17
Nikhil Paliwal, Robert J Damiano, Jason M Davies, Adnan H Siddiqui, Hui Meng
Treatment of intracranial aneurysms (IAs) has been revolutionized by the advent of endovascular Flow Diverters (FDs), which disrupt blood flow within the aneurysm to induce pro-thrombotic conditions, and serves as a scaffold for endothelial ingrowth and arterial remodeling. Despite good clinical success of FDs, complications like incomplete occlusion and post-treatment rupture leading to subarachnoid hemorrhage have been reported. In silico computational fluid dynamic analysis of the pre- and post-treated geometries of IA patients can shed light on the contrasting blood hemodynamics associated with different clinical outcomes...
February 11, 2017: Proceedings of SPIE
https://www.readbyqxmd.com/read/28514152/hepatoprotective-properties-of-a-polyphenols-enriched-fraction-from-annona-crassiflora-mart-fruit-peel-against-diabetes-induced-oxidative-and-nitrosative-stress
#18
Allisson B Justino, Mariana N Pereira, Leonardo G Peixoto, Danielle D Vilela, Douglas C Caixeta, Adriele V de Souza, Renata R Teixeira, Heitor C G Silva, Francyelle B R de Moura, Izabela B Moraes, Foued Salmen Espindola
A polyphenols-enriched fraction from Annona crassiflora fruit peel (Ac-Pef) containing chlorogenic acid, (epi)catechin, procyanidin B2 and caffeoyl-glucoside was investigated against hepatic oxidative and nitrosative stress in streptozotocin-induced diabetic rats. Serum biochemical parameters, hepatic oxidative and nitrosative status, glutathione defense system analysis, and in silico assessment of absorption, distribution, metabolism, excretion and toxicity (ADMET) of the main compounds of Ac-Pef were carried out...
May 17, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28513222/the-contribution-of-cyp2c-gene-subfamily-involved-in-epoxygenase-pathway-of-arachidonic-acids-metabolism-to-hypertension-susceptibility-in-russian-population
#19
Alexey Polonikov, Marina Bykanova, Irina Ponomarenko, Svetlana Sirotina, Anna Bocharova, Kseniya Vagaytseva, Vadim Stepanov, Mikhail Churnosov, Olga Bushueva, Maria Solodilova, Yaroslav Shvetsov, Vladimir Ivanov
Numerous studies demonstrated an importance of cytochrome P-450 epoxygenase pathway of arachidonic acids metabolism for the pathogenesis of essential hypertension (EH). The present study was designed to investigate whether common single-nucleotide polymorphisms (SNP) of CYP2C gene subfamily such as CYP2C8 (rs7909236 and rs1934953), CYP2C9 (rs9332242), and CYP2C19 (rs4244285) are associated with susceptibility to EH in Russian population. A total of 816 unrelated Russian individuals comprising 425 EH patients and 391 normotensive controls were included into the study...
May 17, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/28511646/emergence-of-microbial-diversity-due-to-cross-feeding-interactions-in-a-spatial-model-of-gut-microbial-metabolism
#20
Milan J A van Hoek, Roeland M H Merks
BACKGROUND: The human gut contains approximately 10(14) bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn's disease, and make the microbiota more vulnerable to infestation by harmful species, e...
May 16, 2017: BMC Systems Biology
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