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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
#1
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/28734205/identification-of-mycobacterium-tuberculosis-enoyl-acyl-carrier-protein-reductase-inhibitors-a-combined-in-silico-and-in-vitro-analysis
#2
Mohsin Y Lone, Mohd Athar, Vivek K Gupta, Prakash C Jha
Mycobacterium tuberculosis (Mtb), had developed evolutionary changes in its genome to adapt for survival and thereby generated multi-drug resistant strains. However, novel drug targets that remained unchanged for their biochemical role has impressed the research community to target such proteins. The comprehensive analysis of multiple protein targets has influenced us to make a consensus structural rule exploited by pharmacophore and other allied techniques from a large repository of protein structures. In this pursuit, we made a retrospective analysis of pharmacophores mapped from the tuberculosis structural proteome and identified unique patterns that can be employed for the novel molecules design...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28733595/how-cholesteryl-ester-transfer-protein-can-also-be-a-potential-triglyceride-transporter
#3
Venkat R Chirasani, Sanjib Senapati
CETP transfers cholesteryl esters (CEs) and triglycerides (TGs) between different lipoproteins and came in limelight as a drug-target against CVD. In the search for detailed mechanism of lipid transfer through CETP, enormous effort is devoted employing crystallographic, cryo-EM, and Molecular Dynamics (MD) studies. However, these studies primarily focused on CE-bound CETP structure and CE transfer mechanism. With the reported correlation that CETP looses significant CE transfer activity upon inhibiting TG transfer, it is of tremendous importance to understand the structure and dynamics of TG-bound CETP...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28732368/meta-analysis-of-micrornas-expression-in-head-and-neck-cancer-uncovering-association-with-outcome-and-mechanisms
#4
Joshua Lubov, Mariana Maschietto, Iman Ibrahim, Alex Mlynarek, Michael Hier, Luiz Paulo Kowalski, Moulay A Alaoui-Jamali, Sabrina Daniela da Silva
Head and neck squamous cell carcinoma (HNSCC) is often diagnosed at advanced stages, incurring significant high mortality and morbidity. This review explored the risk stratification of miRNAs, and investigated the impact of miRNA networking in HNSCC prognostication. We performed a meta-analysis and a systematic literature search on online databases for papers published prior to December 1, 2016. The list of miRNAs was uploaded to MetacoreTM to construct a protein-protein interaction network, which was used to identify targets of the miRNAs and potential drugs...
July 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732158/deleterious-consequences-of-udp-galactopyranose-mutase-inhibition-for-nematodes
#5
Valerie J Winton, Alexander M Justen, Helen Deng, Laura L Kiessling
Parasitic nematodes pose a serious threat to agriculture, livestock, and human health. Increasing resistance to anti-parasitic agents underscores the need to replenish our anthelmintic arsenal. The non-pathogenic Caenorhabditis elegans, which serves as an effective model of parasitic helminths, has been used to search for new anthelmintic leads. We previously reported small-molecule inhibitors of the essential C. elegans protein UDP-galactopyranose mutase (UGM or Glf). This enzyme is required for the generation of galactofuranose (Galf)-containing glycans and is needed in nematodes for proper cuticle formation...
July 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28726736/protozoadb-2-0-a-trypanosoma-brucei-case-study
#6
Rodrigo Jardim, Diogo Tschoeke, Alberto M R Da Vila
Over the last decade new species of Protozoa have been sequenced and deposited in GenBank. Analyzing large amounts of genomic data, especially using Next Generation Sequencing (NGS), is not a trivial task, considering that researchers used to deal or focus their studies on few genes or gene families or even small genomes. To facilitate the information extraction process from genomic data, we developed a database system called ProtozoaDB that included five genomes of Protozoa in its first version. In the present study, we present a new version of ProtozoaDB called ProtozoaDB 2...
July 20, 2017: Pathogens
https://www.readbyqxmd.com/read/28719833/in-silico-search-of-inhibitors-of-streptococcus-mutans-for-the-control-of-dental-plaque
#7
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/28716134/detecting-protein-variants-by-mass-spectrometry-a-comprehensive-study-in-cancer-cell-lines
#8
Javier A Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C Boutros, Thomas Kislinger
BACKGROUND: Onco-proteogenomics aims to understand how changes in a cancer's genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-spectrometry (MS) datasets, as traditional proteomic analyses only identify proteins from a reference sequence database. METHODS: We established proteomic workflows to detect peptide variants within MS datasets. We used a combination of publicly available population variants (dbSNP and UniProt) and somatic variations in cancer (COSMIC) along with sample-specific genomic and transcriptomic data to examine proteome variation within and across 59 cancer cell-lines...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28713998/identification-of-micrornas-in-acute-respiratory-distress-syndrome-based-on-microrna-expression-profile-in-rats
#9
Yinghui Guan, Xiang Jin, Xingang Liu, Yuanping Huang, Man Wang, Xiaodan Li
Acute respiratory distress syndrome (ARDS) remains a severe disease associated with an ~40% mortality rate and as many as 200,000 new cases annually. MicroRNAs (miRNAs) have important roles in gene regulation and cancer development. The present study aimed to identify the potential roles of miRNAs in the pathogenesis and progression of ARDS. The miRNA expression profile of the GSE57223 dataset was downloaded from the Gene Expression Omnibus database. Following data normalization, differentially expressed miRNAs were identified using the t‑test method...
July 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28710287/rna-search-engines-empower-the-bacterial-intranet
#10
REVIEW
Tom Dendooven, Ben F Luisi
RNA acts not only as an information bearer in the biogenesis of proteins from genes, but also as a regulator that participates in the control of gene expression. In bacteria, small RNA molecules (sRNAs) play controlling roles in numerous processes and help to orchestrate complex regulatory networks. Such processes include cell growth and development, response to stress and metabolic change, transcription termination, cell-to-cell communication, and the launching of programmes for host invasion. All these processes require recognition of target messenger RNAs by the sRNAs...
July 14, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28707666/-identification-of-proteins-associated-with-transcription-factors-hoxa9-and-e2a-pbx1-by-tandem-affinity-purification
#11
E A Shestakova, M Boutin, S Bourassa, E Bonneil, J J Bijl
Chimeric transcription factor E2A-PBX1 induces the development of acute lymphoblastic B-cell leukemia in children. Using a transgenic mouse model, we previously demonstrated that homeobox (HOX) gene HOXA9 genetically interact with E2A-PBX1 gene in the development of B-cell leukemia in mice. HOXA9 itself is a potent oncogene resulting in myeloid leukemia when overexpressed, which is strongly accelerated by its collaborator Meis1. HOX, PBX1 and MEIS1 proteins have been shown to form hetero dimeric or trimeric complexes in different combinations...
May 2017: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28706532/identification-of-single-nucleotide-polymorphic-loci-associated-with-biomass-yield-under-water-deficit-in-alfalfa-medicago-sativa-l-using-genome-wide-sequencing-and-association-mapping
#12
Long-Xi Yu
Alfalfa is a worldwide grown forage crop and is important due to its high biomass production and nutritional value. However, the production of alfalfa is challenged by adverse environmental factors such as drought and other stresses. Developing drought resistance alfalfa is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. In the present study, we used genotyping-by-sequencing and genome-wide association to identify marker loci associated with biomass yield under drought in the field in a panel of diverse germplasm of alfalfa...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28705213/the-therapeutic-landscape-of-hiv-1-via-genome-editing
#13
REVIEW
Alexander Kwarteng, Samuel Terkper Ahuno, Godwin Kwakye-Nuako
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1...
July 14, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28702565/identifying-the-common-genetic-networks-of-adr-adverse-drug-reaction-clusters-and-developing-an-adr-classification-model
#14
Youhyeon Hwang, Min Oh, Giup Jang, Taekeon Lee, Chihyun Park, Jaegyoon Ahn, Youngmi Yoon
Adverse drug reactions (ADRs) are one of the major concerns threatening public health and have resulted in failures in drug development. Thus, predicting ADRs and discovering the mechanisms underlying ADRs have become important tasks in pharmacovigilance. Identification of potential ADRs by computational approaches in the early stages would be advantageous in drug development. Here we propose a computational method that elucidates the action mechanisms of ADRs and predicts potential ADRs by utilizing ADR genes, drug features, and protein-protein interaction (PPI) networks...
July 12, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28702009/crm1-inhibitors-for-antiviral-therapy
#15
REVIEW
Cynthia Mathew, Reena Ghildyal
Infectious diseases are a major global concern and despite major advancements in medical research, still cause significant morbidity and mortality. Progress in antiviral therapy is particularly hindered by appearance of mutants capable of overcoming the effects of drugs targeting viral components. Alternatively, development of drugs targeting host proteins essential for completion of viral lifecycle holds potential as a viable strategy for antiviral therapy. Nucleocytoplasmic trafficking pathways in particular are involved in several pathological conditions including cancer and viral infections, where hijacking or alteration of function of key transporter proteins, such as Chromosome Region Maintenance1 (CRM1) is observed...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28700469/microarray-analysis-of-copy-number-variations-and-gene-expression-profiles-in-prostate-cancer
#16
Yuping Han, Xuefei Jin, Hongyan Li, Kaichen Wang, Ji Gao, Lide Song, Yanting Lv
BACKGROUND: This study aimed to identify potential prostate cancer (PC)-related variations in gene expression profiles. METHODS: Microarray data from the GSE21032 dataset that contained the whole-transcript and exon-level expression profile (GSE21034) and Agilent 244K array-comparative genomic hybridization data (GSE21035) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and copy-number variations (CNVs) were identified between PC and normal tissue samples...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28700230/ligq-a-webserver-to-select-and-prepare-ligands-for-virtual-screening
#17
Leandro Gabriel Radusky, Sergio Ruiz Carmona, Carlos Modenutti, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A Marti
Virtual screening is a powerful methodology to search for new small molecule inhibitors against a desired molecular target. Usually, it involves evaluating thousand of compounds (derived from large databases) in order to select a set of potential binders that will be tested in the wet-lab. The number of tested compounds is directly proportional to the cost, and thus the best possible set of ligands is the one with the highest number of true binders, for the smallest possible compound set size. Therefore, methods that are able to trim down large universal datasets enriching them in potential binders are highly appreciated...
July 12, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28699823/the-gmz2-malaria-vaccine-from-concept-to-efficacy-in-humans
#18
Michael Theisen, Bright Adu, Benjamin Mordmüller, Subhash Singh
GMZ2 is a recombinant protein consisting of conserved domains of GLURP and MSP3, two asexual blood-stage antigens of Plasmodium falciparum, and is designed with the aim of mimicking naturally acquired anti-malarial immunity. The rationale for combining these two antigens is based on a series of immune epidemiological studies from geographically diverse malaria endemic regions; functional in vitro studies; and pre-clinical studies in rodents and New World monkeys. GMZ2 adjuvanted with alhydrogel® (alum) was well tolerated and immunogenic in three phase 1 studies...
July 12, 2017: Expert Review of Vaccines
https://www.readbyqxmd.com/read/28699535/protein-kinases-as-targets-for-opisthorchis-viverrini-associated-cholangiocarcinoma-therapy
#19
Watcharin Loilome, Hasaya Dokduang
Protein kinases are enzymes that catalyze the transfer of phosphate from ATP to the serine/threonine or tyrosine residues of target molecules. These are key important mediators in a signaling cascade involved in several biological processes. Dysregulation of their activity has been found in various tumors. From our increased understanding of kinase structure and activation mechanisms there emerged new strategies for targeting kinase in cancer treatment. Nowadays, kinase specific inhibitors are developed and widely used for clinical cancer treatment...
July 10, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28698171/natural-compounds-for-the-treatment-of-psoriatic-arthritis-a-proposal-based-on-multi-targeted-osteoclastic-regulation-and-on-a-preclinical-study
#20
Shiqiang Deng, Jianwen Cheng, Jinmin Zhao, Felix Yao, Jiake Xu
BACKGROUND: Psoriatic arthritis (PsA) is a chronic inflammatory arthritis affecting approximately 2% to 3% of the population globally, and is characterized by both peripheral articular manifestations and axial skeletal involvement. Conventional therapies for PsA have not been fully satisfactory, though natural products (NPs) have been shown to be highly effective and represent important treatment options for psoriasis. PsA is a multigenic autoimmune disease with both environmental and genetic factors contributing to its pathogenesis...
July 11, 2017: JMIR Research Protocols
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