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https://www.readbyqxmd.com/read/28735171/encoding-of-coordination-complexes-with-xml
#1
P Vinoth, P Sankar
An in-silico system to encode structure, bonding and properties of coordination complexes is developed. The encoding is achieved through a semantic XML markup frame. Composition of the coordination complexes is captured in terms of central atom and ligands. Structural information of central atom is detailed in terms of electron status of valence electron orbitals. The ligands are encoded with specific reference to the electron environment of ligand centre atoms. Behaviour of ligands to form low or high spin complexes is accomplished by assigning a Ligand Centre Value to every ligand based on the electronic environment of ligand centre atom...
July 13, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28734207/in-silico-designing-of-therapeutic-protein-enriched-with-branched-chain-amino-acids-for-the-dietary-treatment-of-chronic-liver-disease
#2
Sunil L, Prasanna Vasu
Leucine, isoleucine, and valine are three essential branched-chain amino acids (BCAA) account for 40-45% of total essential amino acids. BCAA stimulates protein synthesis primarily in skeletal muscles, and it can directly transport to circulatory blood stream bypassing the liver. Hence, a protein enriched with BCAA is an important therapeutic target for the dietary treatment of chronic liver disease. The present study is to design a synthetic protein enriched with BCAA and the challenge is to maximize the BCAA content, keeping the balanced ratio of leucine, isoleucine, valine - 2: 1: 1...
July 12, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28734034/protein-features-as-determinants-of-wild-type-glycoside-hydrolase-thermostability
#3
Henrik Marcus Geertz-Hansen, Lars Kiemer, Morten Nielsen, Kiril Stanchev, Nikolaj Blom, Søren Brunak, Thomas Nordahl Petersen
Thermostable enzymes for conversion of lignocellulosic biomass into biofuels have significant advantages over enzymes with more moderate themostability due to the challenging application conditions. Experimental discovery of thermostable enzymes is highly cost intensive, and the development of in-silico methods guiding the discovery process would be of high value. To develop such an in-silico method and provide the data foundation of it, we determined the melting temperatures of 602 fungal glycoside hydrolases from the families GH5, 6, 7, 10, 11, 43 and AA9 (formerly GH61)...
July 22, 2017: Proteins
https://www.readbyqxmd.com/read/28733845/genome-wide-identification-in-silico-characterization-and-expression-analysis-of-zip-like-genes-from-trichomonas-vaginalis-in-response-to-zinc-and-iron
#4
K G Fernández-Martín, M E Alvarez-Sánchez, V E Arana-Argáez, L C Alvarez-Sánchez, J C Lara-Riegos, J C Torres-Romero
Trace elements such as Zinc and Iron are essential components of metalloproteins and serve as cofactors or structural elements for enzymes involved in several important biological processes in almost all organisms. Because either excess or insufficient levels of Zn and Fe can be harmful for the cells, the homeostatic levels of these trace minerals must be tightly regulated. The Zinc regulated transporter, Iron regulated transporter-like Proteins (ZIP) comprise a diverse family, with several paralogues in diverse organisms and are considered essential for the Zn and Fe uptake and homeostasis...
July 21, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28733243/application-of-machine-learning-in-prediction-of-hydrotrope-enhanced-solubilisation-of-indomethacin
#5
Safa A Damiati, Luigi G Martini, Norman W Smith, Jayne M Lawrence, David J Barlow
Systematic in-vitro studies have been conducted to determine the ability of a range of 10 potential hydrotropes to improve the apparent aqueous solubility of the poorly water soluble drug, indomethacin. Solubilisation of the drug in the presence of the hydrotropes was determined experimentally using high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection. These experimental data, together with various known and computed physicochemical properties of the hydrotropes were thereafter used in silico to train an artificial neural network (ANN) to allow for predictions of indomethacin solubilisation...
July 18, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28733203/in-silico-pharmacogenetic-approach-the-natalizumab-case-study
#6
Francesca Cavaliere, Enrico Montanari, Andrew Emerson, Annamaria Buschini, Pietro Cozzini
Natalizumab is a humanized monoclonal antibody to α4β1 integrin and is approved for the treatment of Multiple Sclerosis. In patients there is a great variation in drug response and there is much evidence that genetic contributors play an important role in defining an individual's susceptibility. Natalizumab binds to α4-residues Gln-152, Lys-201, Lys256, and these seem to be essential for its activity. Studies on a range of species in disease model have showed a loss of reactivity when any one of those three residues were different to human...
July 18, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28729949/modeling-the-effect-of-blunt-impact-on-mitochondrial-function-in-cartilage-implications-for-development-of-osteoarthritis
#7
Georgi I Kapitanov, Bruce P Ayati, James A Martin
OBJECTIVE: Osteoarthritis (OA) is a disease characterized by degeneration of joint cartilage. It is associated with pain and disability and is the result of either age and activity related joint wear or an injury. Non-invasive treatment options are scarce and prevention and early intervention methods are practically non-existent. The modeling effort presented in this article is constructed based on an emerging biological hypothesis-post-impact oxidative stress leads to cartilage cell apoptosis and hence the degeneration observed with the disease...
2017: PeerJ
https://www.readbyqxmd.com/read/28729722/structure-based-discovery-of-small-molecule-inhibitors-of-cariogenic-virulence
#8
Qiong Zhang, Bhavitavya Nijampatnam, Zhang Hua, Thao Nguyen, Jing Zou, Xia Cai, Suzanne M Michalek, Sadanandan E Velu, Hui Wu
Streptococcus mutans employs a key virulence factor, three glucosyltransferase (GtfBCD) enzymes to establish cariogenic biofilms. Therefore, the inhibition of GtfBCD would provide anti-virulence therapeutics. Here a small molecule library of 500,000 small molecule compounds was screened in silico against the available crystal structure of the GtfC catalytic domain. Based on the predicted binding affinities and drug-like properties, small molecules were selected and evaluated for their ability to reduce S. mutans biofilms, as well as inhibit the activity of Gtfs...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729681/multiomics-analysis-of-the-giant-triton-snail-salivary-gland-a-crown-of-thorns-starfish-predator
#9
U Bose, T Wang, M Zhao, C A Motti, M R Hall, S F Cummins
The giant triton snail (Charonia tritonis) is one of the few natural predators of the adult Crown-of-Thorns starfish (COTS), a corallivore that has been damaging to many reefs in the Indo-Pacific. Charonia species have large salivary glands (SGs) that are suspected to produce either a venom and/or sulphuric acid which can immobilize their prey and neutralize the intrinsic toxic properties of COTS. To date, there is little information on the types of toxins produced by tritons. In this paper, the predatory behaviour of the C...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728491/catalogic-301c-model-validation-and-improvement
#10
N H Dimitrova, I A Dermen, N D Todorova, K G Vasilev, S D Dimitrov, O G Mekenyan, Y Ikenaga, T Aoyagi, Y Zaitsu, C Hamaguchi
In Europe, REACH legislation encourages the use of alternative in silico methods such as (Q)SAR models. According to the recent progress of Chemical Substances Control Law (CSCL) in Japan, (Q)SAR predictions are also utilized as supporting evidence for the assessment of bioaccumulation potential of chemicals along with read across. Currently, the effective use of read across and QSARs is examined for other hazards, including biodegradability. This paper describes the results of external validation and improvement of CATALOGIC 301C model based on more than 1000 tested new chemical substances of the publication schedule under CSCL...
June 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28727604/preclinical-development-of-ebi-005-an-il-1-receptor-1-inhibitor-for-the-topical-ocular-treatment-of-ocular-surface-inflammatory-diseases
#11
Joseph Kovalchin, Bracken King, Allyson Masci, Elizabeth Hopkins, Jeremy Fry, Jay Hou, Christian Li, Kelly Tenneson, Steve Weber, Gary Wolfe, Kathy Collins, Eric S Furfine
OBJECTIVE: Topical interleukin (IL)-1 receptor (R)1 blockade is therapeutically active in reducing signs and symptoms of dry eye disease. Herein, we describe in vitro and in vivo nonclinical Investigational New Drug (IND)-enabling studies of EBI-005, a novel protein chimera of IL-1β and IL-1 receptor antagonist (IL-1Ra or anakinra) that potently binds IL-1R1 and blocks signaling. These studies provide an assessment of receptor affinity, drug bioavailability, immunogenic response, safety, and tolerability in mice and rabbits...
July 18, 2017: Eye & Contact Lens
https://www.readbyqxmd.com/read/28726847/mapping-genome-wide-transcription-factor-binding-sites-using-dap-seq
#12
Anna Bartlett, Ronan C O'Malley, Shao-Shan Carol Huang, Mary Galli, Joseph R Nery, Andrea Gallavotti, Joseph R Ecker
To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX)...
August 2017: Nature Protocols
https://www.readbyqxmd.com/read/28723478/low-t-cell-receptor-diversity-high-somatic-mutation-burden-and-high-neoantigen-load-as-predictors-of-clinical-outcome-in-muscle-invasive-bladder-cancer
#13
Noura J Choudhury, Kazuma Kiyotani, Kai Lee Yap, Alexa Campanile, Tatjana Antic, Poh Yin Yew, Gary Steinberg, Jae Hyun Park, Yusuke Nakamura, Peter H O'Donnell
BACKGROUND: The success of cancer immunotherapies has highlighted the potent ability of local adaptive immune responses to eradicate cancer cells by targeting neoantigens generated by somatic alterations. However, how these factors interact to drive the natural history of muscle-invasive bladder cancer (MIBC) is not well understood. OBJECTIVE: To investigate the role of immune regulation in MIBC disease progression, we performed massively parallel T-cell receptor (TCR) sequencing of tumor-infiltrating T cells (TILs), in silico neoantigen prediction from exome sequences, and expression analysis of immune-related genes...
October 2016: European Urology Focus
https://www.readbyqxmd.com/read/28723080/an-orthogonal-multi-input-integration-system-to-control-gene-expression-in-escherichia-coli
#14
Fabio Annunziata, Antoni Matyjaszkiewicz, Gianfranco Fiore, Claire Grierson, Lucia Marucci, Mario di Bernardo, Nigel Savery
In many biotechnological applications, it is useful for gene expression to be regulated by multiple signals, as this allows the programming of complex behaviour. Here we implement, in Escherichia coli, a system that compares the concentration of two signal molecules, and tunes GFP expression proportionally to their relative abundance. The computation is performed via molecular titration between an orthogonal σ factor and its cognate anti-σ factor. We use mathematical modelling and experiments to show that the computation system is predictable and able to adapt GFP expression dynamically to a wide range of combinations of the two signals, and our model qualitatively captures most of these behaviours...
July 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28722512/in-silico-and-in-vitro-evaluation-of-two-novel-oximes-k378-and-k727-in-comparison-to-k27-and-pralidoxime-against-paraoxon-ethyl-intoxication
#15
Maria Chaudhry, Muhammad Qaiser Fatmi, Kamil Musilek, Alamdar Hussain, Kamil Kuca, Georg Petroianu, Huba Kalasz, Syed Muhammad Nurulain
Organophosphate (OP) poisoning is a major global health issue; while compounds from this group have been used intensively over the last century, an effective antidote is still lacking. Oxime-type AChE reactivators are used to reactivate the OP inhibited AChE. Pralidoxime is the only US Food and Drug Administration, (FDA) approved oxime for therapeutic use but its efficacy has been disappointing. Two novel oximes (K378 and K727) were investigated in silico and in vitro and compared with an experimental oxime (kamiloxime; K-27) and pralidoxime...
July 19, 2017: Toxicology Mechanisms and Methods
https://www.readbyqxmd.com/read/28722112/in-silico-and-in-vitro-prediction-of-gastrointestinal-absorption-from-potential-drug-eremantholide-c
#16
Tamires G Caldeira, Dênia A Saúde-Guimarães, André B Dezani, Cristina Helena Dos Reis Serra, Jacqueline de Souza
OBJECTIVES: Analysis of the biopharmaceutical properties of eremantholide C, sesquiterpene lactone with proven pharmacological activity and low toxicity, is required to evaluate its potential to become a drug. METHODS: Preliminary analysis of the physicochemical characteristics of eremantholide C was performed in silico. Equilibrium solubility was evaluated using the shake-flask method, at 37.0 °C, 100 rpm during 72 h in biorelevant media. The permeability was analysed using parallel artificial membrane permeability assay, at 37...
July 19, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28720470/molecular-docking-prediction-and-in-vitro-studies-elucidate-anti-cancer-activity-of-phytoestrogens
#17
Shreelekha Dutta, Prashant S Kharkar, Niteshkumar U Sahu, Aparna Khanna
AIM: The study is aimed at evaluating the chemosensitization and apoptotic effect of aglycone rich extracts of dietary phytoestrogens (derived from soybean and flaxseed) on estrogen receptor positive, MCF-7 and estrogen receptor negative, MDA-MB-231 cells. The extracts show potent activity on both the cell lines, hence, in silico studies have been carried out to find the possible reason for their activity. MAIN METHODS: MTT assay was carried to assess chemosensitization effect and activated caspase-3/7 activity was studied using flow-cytometry and western blotting...
July 15, 2017: Life Sciences
https://www.readbyqxmd.com/read/28720135/exploring-anti-malarial-potential-of-fda-approved-drugs-an-in-silico-approach
#18
Gayatri Ramakrishnan, Nagasuma Chandra, Narayanaswamy Srinivasan
BACKGROUND: The critically important issue on emergence of drug-resistant malarial parasites is compounded by cross resistance, where resistance to one drug confers resistance to other chemically similar drugs or those that share mode of action. This aspect requires discovery of new anti-malarial compounds or formulation of new combination therapy. The current study attempts to contribute towards accelerating anti-malarial drug development efforts, by exploring the potential of existing FDA-approved drugs to target proteins of Plasmodium falciparum...
July 18, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#19
Rodrigo Ochoa, María Cecilia Martínez-Pabón, María Adelaida Arismendi-Echeverri, Willer Leandro Rendón-Osorio, Carlos Enrique Muskus-López
Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones...
July 1, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28718641/in-silico-skin-model-a-multiscale-simulation-study-of-drug-transport
#20
Kishore Gajula, Rakesh Gupta, D B Sridhar, Beena Rai
Accurate in-silico models are required to predict the release of drug molecules through skin in order to supplement the in-vivo experiments for faster development/testing of drugs. The upper most layer of the skin, stratum corneum (SC), offers main resistance for permeation of actives. Most of the SC's molecular level models comprise of cholesterol, and phospholipids only, which is far from the reality. In this study we have implemented a multiscale modelling framework to obtain the release profile of three drugs namely Caffeine, Fentanyl and Naphthol through skin SC...
July 18, 2017: Journal of Chemical Information and Modeling
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