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https://www.readbyqxmd.com/read/29792307/putative-vaccine-candidates-and-drug-targets-identified-by-reverse-vaccinology-and-subtractive-genomics-approaches-to-control-haemophilus-ducreyi-the-causative-agent-of-chancroid
#1
Alissa de Sarom, Arun Kumar Jaiswal, Sandeep Tiwari, Letícia de Castro Oliveira, Debmalya Barh, Vasco Azevedo, Carlo Jose Oliveira, Siomar de Castro Soares
Chancroid is a sexually transmitted infection (STI) caused by the Gram-negative bacterium Haemophilus ducreyi The control of chancroid is difficult and the only current available treatment is antibiotic therapy; however, antibiotic resistance has been reported in endemic areas. Owing to recent outbreaks of STIs worldwide, it is important to keep searching for new treatment strategies and preventive measures. Here, we applied reverse vaccinology and subtractive genomic approaches for the in silico prediction of potential vaccine and drug targets against 28 strains of H...
May 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29792109/computational-functional-genomics-based-approaches-in-analgesic-drug-discovery-and-repurposing
#2
Catharina Lippmann, Dario Kringel, Alfred Ultsch, Jörn Lötsch
Persistent pain is a major healthcare problem affecting a fifth of adults worldwide with still limited treatment options. The search for new analgesics increasingly includes the novel research area of functional genomics, which combines data derived from various processes related to DNA sequence, gene expression or protein function and uses advanced methods of data mining and knowledge discovery with the goal of understanding the relationship between the genome and the phenotype. Its use in drug discovery and repurposing for analgesic indications has so far been performed using knowledge discovery in gene function and drug target-related databases; next-generation sequencing; and functional proteomics-based approaches...
May 24, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29791965/searching-for-non-transposable-targets-of-planarian-nuclear-piwi-in-pluripotent-stem-cells-and-differentiated-cells
#3
Makoto Kashima, Kiyokazu Agata, Norito Shibata
Nuclear PIWIs together with their guide RNAs (piRNAs) epigenetically silence various genes including transposons in many organisms. In planarians, the nuclear piwi family gene, DjpiwiB is specifically transcribed in adult pluripotent stem cells (adult PSC, neoblast), but not in differentiated cells. However, the protein accumulates in the nuclei of both neoblasts and their descendant differentiated cells. Interestingly, PIWI(DjPiwiB)-piRNA complexes are indispensable for the repression of transposable genes at the onset of differentiation from neoblasts...
May 23, 2018: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/29791878/computational-design-of-antibodies
#4
REVIEW
Sharon Fischman, Yanay Ofran
Antibody design aims to create new antibodies with biological activity that can be used in therapy and research. Traditional methods for antibody discovery, such as animal immunization and large-scale library screening, generate antibodies that bind to the target of interest, but do not necessarily have the desired functional effect. Computational methods can be utilized as a means to guide the search for biologically relevant antibodies, focusing on specificity and affinity determinants to target a particular region of the antigen...
May 19, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29791798/non-natural-linker-configuration-in-2-6-dipeptidyl-anthraquinones-enhances-the-inhibition-of-tar-rna-binding-annealing-activities-by-hiv-1-nc-and-tat-proteins
#5
Alice Sosic, Irene Saccone, Caterina Carraro, Thomas Kenderdine, Elia Gamba, Giuseppe Caliendo, Angela Corvino, Ferdinando Fiorino, Paola DiVaio, Elisa Magli, Elisa Perissutti, Vincenzo Santagada, Beatrice Severino, Valentina Spada, Daniele Fabris, Francesco Frecentese, Barbara Gatto
The HIV-1 nucleocapsid (NC) protein represents an excellent molecular target for the development of antiretrovirals by virtue of its well-characterized chaperone activities, which play pivotal roles in essential steps of the viral life cycle. Our ongoing search for candidates able to impair NC binding/annealing activities led to the identification of peptidyl-anthraquinones as a promising class of nucleic acid ligands. Seeking to elucidate the inhibition determinants and increase the potency of this class of compounds, we have now explored the effects of chirality in the linker connecting the planar nucleus to the basic side chains...
May 23, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29787234/unfolding-the-mysteries-of-protein-metamorphosis
#6
Acacia F Dishman, Brian F Volkman
Since the proposal of Anfinsen's thermodynamic hypothesis in 1963, our understanding of protein folding and dynamics has gained significant appreciation of its nuance and complexity. Intrinsically disordered proteins, chameleonic sequences, morpheeins, and metamorphic proteins have broadened the protein folding paradigm. Here, we discuss noncanonical protein folding patterns, with an emphasis on metamorphic proteins, and we review known metamorphic proteins that occur naturally and that have been engineered in the laboratory...
May 22, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29786747/microrna-137-dysregulation-predisposes-to-osteoporotic-fracture-by-impeding-alp-activity-and-expression-via-suppression-of-leucine-rich-repeat-containing-g-protein-coupled-receptor-4-expression
#7
Xiangjun Liu, Xiaohui Xu
Osteoporosis is defined as a loss of bone mass and deterioration of its architecture resulting in bone weakness, which becomes prone to fracture. The objective of this study was to investigate the molecular mechanism by which miR-137 can reduce the risk of fracture in patients with osteoporosis. An online miRNA database and a luciferase reporter assay system were used to confirm that leucine-rich repeat-containing G-protein-coupled receptor 4 (LGR4) was the target of miR-137. Real-time PCR and western blot analysis were used to study miR-137 mRNA, the expression of LGR4 mRNA and protein among different groups or cells transfected with a scrambled miRNA control, miR-137 mimic, LGR4 siRNA and miR-137 inhibitor...
May 17, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786430/galaxygpcrloop-template-based-and-ab-initio-structure-sampling-of-the-extracellular-loops-of-g-protein-coupled-receptors
#8
Jonghun Won, Gyu Rie Lee, Hahnbeom Park, Chaok Seok
The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed...
May 22, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29786048/cardiac-hypertrophy-is-positively-regulated-by-microrna-24-in-ratsmicrorna-24
#9
Juan Gao, Min Zhu, Rui-Feng Liu, Jian-Shu Zhang, Ming Xu
Background: MicroRNA-24 (miR-24) plays an important role in heart failure by reducing the efficiency of myocardial excitation-contraction coupling. Prolonged cardiac hypertrophy may lead to heart failure, but little is known about the role of miR-24 in cardiac hypertrophy. This study aimed to preliminarily investigate the function of miR-24 and its mechanisms in cardiac hypertrophy. Methods: Twelve Sprague-Dawley rats with a body weight of 50 ± 5 g were recruited and randomly divided into two groups: a transverse aortic constriction (TAC) group and a sham surgery group...
June 5, 2018: Chinese Medical Journal
https://www.readbyqxmd.com/read/29780359/the-mitotic-and-metabolic-effects-of-phosphatidic-acid-in-the-primary-muscle-cells-of-turbot-scophthalmus-maximus
#10
Tingting Wang, Xuan Wang, Huihui Zhou, Haowen Jiang, Kangsen Mai, Gen He
Searching for nutraceuticals and understanding the underlying mechanism that promote fish growth is at high demand for aquaculture industry. In this study, the modulatory effects of soy phosphatidic acids (PA) on cell proliferation, nutrient sensing, and metabolic pathways were systematically examined in primary muscle cells of turbot ( Scophthalmus maximus ). PA was found to stimulate cell proliferation and promote G1/S phase transition through activation of target of rapamycin signaling pathway. The expression of myogenic regulatory factors, including myoD and follistatin , was upregulated, while that of myogenin and myostatin was downregulated by PA...
2018: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29779788/facilitated-protein-association-via-engineered-target-search-pathways-visualized-by-paramagnetic-nmr-spectroscopy
#11
So Young An, Eun-Hee Kim, Jeong-Yong Suh
Proteins assemble to form functional complexes via the progressive evolution of nonspecific complexes formed by transient encounters. This target search process generally involves multiple routes that lead the initial encounters to the final complex. In this study, we have employed NMR paramagnetic relaxation enhancement to visualize the encounter complexes between histidine-containing phosphocarrier protein and the N-terminal domain of enzyme I and demonstrate that protein association can be significantly enhanced by engineering on-pathways...
May 1, 2018: Structure
https://www.readbyqxmd.com/read/29778427/genomics-driven-approach-for-identification-of-novel-therapeutic-targets-in-salmonella-enterica
#12
Priyanka Gawade, Payel Ghosh
Salmonella enterica is a causative agent of enteric and systemic salmonellosis that affects human and many other animal species. Due to the emergence of drug-resistant strains, available drugs against S. enterica infection are no more effective as before. Thus, there is an urgent need to develop new therapeutic strategies. The current study aims at prioritizing therapeutic targets by an in-silico genomics driven method. The method involves searching proteins of each Salmonella strain for essentiality, virulence and antibiotic-resistance and host-pathogen protein-protein interactions...
May 17, 2018: Gene
https://www.readbyqxmd.com/read/29774127/paf1-complex-interactions-with-setdb1-mediate-promoter-h3k9-methylation-and-transcriptional-repression-of-hoxa9-and-meis1-in-acute-myeloid-leukemia
#13
James Ropa, Nirmalya Saha, Zhiling Chen, Justin Serio, Wei Chen, Dattatreya Mellacheruvu, Lili Zhao, Venkatesha Basrur, Alexey I Nesvizhskii, Andrew G Muntean
The Polymerase Associated Factor 1 complex (PAF1c) is an epigenetic co-modifying complex that directly contacts RNA polymerase II (RNAPII) and several epigenetic regulating proteins. Mutations, overexpression and loss of expression of subunits of the PAF1c are observed in various forms of cancer suggesting proper regulation is needed for cellular development. However, the biochemical interactions with the PAF1c that allow dynamic gene regulation are unclear. We and others have shown that the PAF1c makes a direct interaction with MLL fusion proteins, which are potent oncogenic drivers of acute myeloid leukemia (AML)...
April 24, 2018: Oncotarget
https://www.readbyqxmd.com/read/29771409/mir-299-5p-targets-cell-cycle-to-promote-cell-proliferation-and-progression-of-osteosarcoma
#14
C-L Zhang, L-B Li, C She, Y Xie, D-W Ge, Q-R Dong
OBJECTIVE: Osteosarcoma is a common primary bone tumor with high mortality. MicroRNA (miRNA, miR) is a small RNA with 20-25 nucleotides, which could regulate diverse biological processes by targeting 3'-UTR of gene to degrade it. MiR-299-5p has been reported to participate in the progression of many diseases, but the role in osteosarcoma is still uncertain. The aim of this work was to investigate the expression of miR-299-5p in osteosarcoma and its clinical significance. MATERIALS AND METHODS: The datasets of osteosarcoma miRNA was searched in Gene Expression Omnibus (GEO) datasets, including GSE65071, GSE39040, and GSE39055...
May 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29770277/a-strategy-to-find-novel-candidate-anti-alzheimer-s-disease-drugs-by-constructing-interaction-networks-between-drug-targets-and-natural-compounds-in-medical-plants
#15
Bi-Wen Chen, Wen-Xing Li, Guang-Hui Wang, Gong-Hua Li, Jia-Qian Liu, Jun-Juan Zheng, Qian Wang, Hui-Juan Li, Shao-Xing Dai, Jing-Fei Huang
Background: Alzheimer' disease (AD) is an ultimately fatal degenerative brain disorder that has an increasingly large burden on health and social care systems. There are only five drugs for AD on the market, and no new effective medicines have been discovered for many years. Chinese medicinal plants have been used to treat diseases for thousands of years, and screening herbal remedies is a way to develop new drugs. Methods: We used molecular docking to screen 30,438 compounds from Traditional Chinese Medicine (TCM) against a comprehensive list of AD target proteins...
2018: PeerJ
https://www.readbyqxmd.com/read/29770128/critical-functions-of-region-1-67-and-helix-xiii-in-retaining-the-active-structure-of-nhad-antiporter-in-halomonas-sp-y2
#16
Zhou Yang, Yiwei Meng, Qi Zhao, Bin Cheng, Ping Xu, Chunyu Yang
NhaD-type antiporters are mainly distributed in various Proteobacteria , especially in marine microorganisms and human pathogens. This distribution as well as the pathogenic properties of these strains suggest that these antiporters contribute to the regulation of high osmoregulation and are potential drug targets. Two NhaD homologs, NhaD1 and NhaD2, from the halotolerant and alkaliphilic Halomonas sp. Y2 exhibits similar, high in vitro activity, but remarkably different in vivo functions. To search for critical domains or residues involved in these differences of physiological functions, various chimeras composed of NhaD1 and NhaD2 segments were generated...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29769011/evolving-strategies-for-the-treatment-of-t-cell-lymphoma-a-systematic-review-and-recent-patents
#17
Kamel Laribi, Mustapha Alani, Catherine Truong, Alix Baugier de Materre
OBJECTIVE: Mature T-cell lymphomas are a heterogeneous group of T-cell malignancies with a poor outcome. The discovery of new molecular biomarkers has led to the emergence of new drugs in recent years that target various signaling pathways. METHOD: We examined all pertinent published patents through 2015 that analyzed novel methods for the diagnosis and treatment of T cell lymphoma, as well as related published and unpublished studies. Selection criteria were established before data collection...
May 16, 2018: Recent Patents on Anti-cancer Drug Discovery
https://www.readbyqxmd.com/read/29768255/asiatic-acid-aa-sensitizes-multidrug-resistant-human-lung-adenocarcinoma-a549-ddp-cells-to-cisplatin-ddp-via-downregulation-of-p-glycoprotein-mdr1-and-its-targets
#18
Qilai Cheng, Meixiang Liao, Haibo Hu, Hongliang Li, Longhuo Wu
BACKGROUND/AIMS: P-glycoprotein (P-gp, i.e., MDR1) is associated with the phenotype of multidrug resistance (MDR) and causes chemotherapy failure in the management of cancers. Searching for effective MDR modulators and combining them with anticancer drugs is a promising strategy against MDR. Asiatic acid (AA), a natural triterpene isolated from the plant Centella asiatica, may have an antitumor activity. The present study assessed the reversing effect of AA on MDR and possible molecular mechanisms of AA action in MDR1-overexpressing cisplatin (DDP)-resistant lung cancer cells, A549/DDP...
May 11, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29765332/galectin-9-expression-predicts-favorable-clinical-outcome-in-solid-tumors-a-systematic-review-and-meta-analysis
#19
Xiaoxiang Zhou, Lejia Sun, Dan Jing, Gang Xu, Jinmei Zhang, Li Lin, Jingjing Zhao, Zhuoran Yao, Hongfeng Lin
Background and Objective: Galectin-9 (Gal-9) is one of the galectin family members which are known as proteins with β-galactoside-binding affinity. Accumulative evidence suggest that Gal-9 plays multifaceted roles in tumor biology. However, the prognostic significance of Gal-9 in solid cancer patients remains controversial. The objective of the study was to clarify the prognostic significance of Gal-9 in solid tumors via meta-analysis. Methods: We searched PubMed, Embase and the Cochrane library for studies that report the correlation between Gal-9 expression and prognosis or clinicopathological parameters in solid cancer patients from inception to October 2017, with no language restriction...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29762685/urine-multi-drug-screening-with-gc-ms-or-lc-ms-ms-using-salle-hybrid-ppt-spe
#20
Junhui Lee, Jiwon Park, Ahra Go, Heesung Moon, Sujin Kim, Sohee Jung, Wonjoon Jeong, Heesun Chung
To intoxicated patients in the emergency room, toxicological analysis can be considerably helpful for identifying the involved toxicants. In order to develop a urine multi-drug screening (UmDS) method, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS-MS) were used to determine targeted and unknown toxicants in urine. A GC-MS method in scan mode was validated for selectivity, limit of detection (LOD) and recovery. An LC-MS-MS multiple reaction monitoring (MRM) method was validated for lower LOD, recovery and matrix effect...
May 14, 2018: Journal of Analytical Toxicology
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