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Showing 3401 to 3404 of 5186 entries
Published on April 30, 2018
Combining Similarity Searching and Network Analysis for the Identification of Active Compounds.
Abstract: A variety of computational screening methods generate similarity-based compound rankings for hit identification. However, these rankings are difficult to interpret. It is essentially impossible to determine where novel active compounds might be found in database rankings. Thus, compound selection largely depends on intuition and guesswork. Herein, we show that molecular networks can substantially aid in the analysis of similarity-based compound rankings. A series of networks generated for rankings provides visual access to search results and adds chemical neighborhood and context information for reference compounds that are not available in rankings. Network structure is shown to serve as a diagnostic criterion for the likelihood to successfully select active compounds from rankings. In addition, comparison of different networks makes it possible to prioritize alternative similarity measures for search calculations and optimize the enrichment of active compounds in rankings.
Published in April 2018
Thymoquinone ameliorates some endocrine parameters and histological alteration in a rat model of polycystic ovary syndrome.
Abstract: Background: Polycystic ovary syndrome (PCOS) is a common form of the endocrine disease which is associated with metabolic dysfunction. PCOS and type 2 diabetes mellitus are related in multiple aspects and are similar in many pathological features. Anti-diabetic effects of Nigella sativa and protective effects of it on reproductive system have been suggested in some reports. Objective: The aim of current study was to evaluate the effects of thymoquinone, the main components of Nigella sativa, on PCOS model of rats. Materials and Methods: Intraperitoneal injection of estradiol valerate for 25 days was used to induce PCOS in Wistar rats, followed by intraperitoneal administration of 8 and 16 mg/kg thymoquinone for 30 days. Rats were divided into 5 groups; control, sham or PCOS, experiment-1 (PCOS and 8 mg/kg thymoquinone), experiment-2 (PCOS and 16 mg/kg thymoquinone), and metformin (PCOS and metformin administration, 100 mg/kg) groups. All of the animals were subjected to serum biochemical analysis of blood and histopathological study of ovaries. Results: Estradiol valerate induced PCOS while administration of thymoquinone recovered it. The body weight, ovarian morphology, and ovulation had been improved and the serum biochemical parameters including glucose, triglyceride, total cholesterol, low-density lipoprotein, high-density lipoprotein, luteinizing hormone, and follicle stimulating hormone were reversed after thymoquinone intervention. Conclusion: Our data suggest that thymoquinone has improvement effects on an ovarian function and ovulation in the PCOS rat model. Therefore, thymoquinone and Nagilla sativa could be used as a protective agent and as an adjunct treatment in PCOS patients.
Published in April 2018
Comparative Safety of Sulfonylureas and the Risk of Sudden Cardiac Arrest and Ventricular Arrhythmia.
Abstract: OBJECTIVE: To examine the association between individual antidiabetic sulfonylureas and outpatient-originating sudden cardiac arrest and ventricular arrhythmia (SCA/VA). RESEARCH DESIGN AND METHODS: We conducted a retrospective cohort study using 1999-2010 U.S. Medicaid claims from five large states. Exposures were determined by incident use of glyburide, glimepiride, or glipizide. Glipizide served as the reference exposure, as its effects are believed to be highly pancreas specific. Outcomes were ascertained by a validated ICD-9-based algorithm indicative of SCA/VA (positive predictive value approximately 85%). Potential confounding was addressed by adjustment for multinomial high-dimensional propensity scores included as continuous variables in a Cox proportional hazards model. RESULTS: Of sulfonylurea users under study (N = 519,272), 60.3% were female and 34.9% non-Hispanic Caucasian, and the median age was 58.0 years. In 176,889 person-years of sulfonylurea exposure, we identified 632 SCA/VA events (50.5% were immediately fatal) for a crude incidence rate of 3.6 per 1,000 person-years. Compared with glipizide, propensity score-adjusted hazard ratios for SCA/VA were 0.82 (95% CI 0.69-0.98) for glyburide and 1.10 (0.89-1.36) for glimepiride. Numerous secondary analyses showed a very similar effect estimate for glyburide; yet, not all CIs excluded the null. CONCLUSIONS: Glyburide may be associated with a lower risk of SCA/VA than glipizide, consistent with a very small clinical trial suggesting that glyburide may reduce ventricular tachycardia and isolated ventricular premature complexes. This potential benefit must be contextualized by considering putative effects of different sulfonylureas on other cardiovascular end points, cerebrovascular end points, all-cause death, and hypoglycemia.
Published in April 2018
G Protein-Coupled Receptors as Targets for Approved Drugs: How Many Targets and How Many Drugs?
Abstract: Estimates vary regarding the number of G protein-coupled receptors (GPCRs), the largest family of membrane receptors that are targeted by approved drugs, and the number of such drugs that target GPCRs. We review current knowledge regarding GPCRs as drug targets by integrating data from public databases (ChEMBL, Guide to PHARMACOLOGY, and DrugBank) and from the Broad Institute Drug Repurposing Hub. To account for discrepancies among these sources, we curated a list of GPCRs currently targeted by approved drugs. As of November 2017, 134 GPCRs are targets for drugs approved in the United States or European Union; 128 GPCRs are targets for drugs listed in the Food and Drug Administration Orange Book. We estimate that approximately 700 approved drugs target GPCRs, implying that approximately 35% of approved drugs target GPCRs. GPCRs and GPCR-related proteins, i.e., those upstream of or downstream from GPCRs, represent approximately 17% of all protein targets for approved drugs, with GPCRs themselves accounting for approximately 12%. As such, GPCRs constitute the largest family of proteins targeted by approved drugs. Drugs that currently target GPCRs and GPCR-related proteins are primarily small molecules and peptides. Since approximately 100 of the approximately 360 human endo-GPCRs (other than olfactory, taste, and visual GPCRs) are orphan receptors (lacking known physiologic agonists), the number of GPCR targets, the number of GPCR-targeted drugs, and perhaps the types of drugs will likely increase, thus further expanding this GPCR repertoire and the many roles of GPCR drugs in therapeutics.
Published in April 2018
Structural basis for the antiarrhythmic blockade of a potassium channel with a small molecule.
Abstract: The acetylcholine-activated inward rectifier potassium current ( IKACh) is constitutively active in persistent atrial fibrillation (AF). We tested the hypothesis that the blocking of IKACh with the small molecule chloroquine terminates persistent AF. We used a sheep model of tachypacing-induced, persistent AF, molecular modeling, electrophysiology, and structural biology approaches. The 50% inhibition/inhibitory concentration of IKACh block with chloroquine, measured by patch clamp, was 1 muM. In optical mapping of sheep hearts with persistent AF, 1 muM chloroquine restored sinus rhythm. Molecular modeling suggested that chloroquine blocked the passage of a hydrated potassium ion through the intracellular domain of Kir3.1 (a molecular correlate of IKACh) by interacting with residues D260 and F255, in proximity to I228, Q227, and L299. (1)H (15)N heteronuclear single-quantum correlation of purified Kir3.1 intracellular domain confirmed the modeling results. F255, I228, Q227, and L299 underwent significant chemical-shift perturbations upon drug binding. We then crystallized and solved a 2.5 A X-ray structure of Kir3.1 with F255A mutation. Modeling of chloroquine binding to the mutant channel suggested that the drug's binding to the pore becomes off centered, reducing its ability to block a hydrated potassium ion. Patch clamp validated the structural and modeling data, where the F255A and D260A mutations significantly reduced IKACh block by chloroquine. With the use of numerical and structural biology approaches, we elucidated the details of how a small molecule could block an ion channel and exert antiarrhythmic effects. Chloroquine binds the IKACh channel at a site formed by specific amino acids in the ion-permeation pathway, leading to decreased IKACh and the subsequent termination of AF.-Takemoto, Y., Slough, D. P., Meinke, G., Katnik, C., Graziano, Z. A., Chidipi, B., Reiser, M., Alhadidy, M. M., Ramirez, R., Salvador-Montanes, O., Ennis, S., Guerrero-Serna, G., Haburcak, M., Diehl, C., Cuevas, J., Jalife, J., Bohm, A., Lin,Y.-S., Noujaim, S. F. Structural basis for the antiarrhythmic blockade of a potassium channel with a small molecule.
Published in April 2018
Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.
Abstract: Stroke has multiple etiologies, but the underlying genes and pathways are largely unknown. We conducted a multiancestry genome-wide-association meta-analysis in 521,612 individuals (67,162 cases and 454,450 controls) and discovered 22 new stroke risk loci, bringing the total to 32. We further found shared genetic variation with related vascular traits, including blood pressure, cardiac traits, and venous thromboembolism, at individual loci (n = 18), and using genetic risk scores and linkage-disequilibrium-score regression. Several loci exhibited distinct association and pleiotropy patterns for etiological stroke subtypes. Eleven new susceptibility loci indicate mechanisms not previously implicated in stroke pathophysiology, with prioritization of risk variants and genes accomplished through bioinformatics analyses using extensive functional datasets. Stroke risk loci were significantly enriched in drug targets for antithrombotic therapy.
Published in April 2018
Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers.
Abstract: Pharmaceutical interventions can slow aging in animals, and have advantages because their dose can be tightly regulated and the timing of the intervention can be closely controlled. They also may complement environmental interventions like caloric restriction by acting additively. A fertile source for therapies slowing aging is FDA approved drugs whose safety has been investigated. Because drugs bind to several protein targets, they cause multiple effects, many of which have not been characterized. It is possible that some of the side effects of drugs prescribed for one therapy may have benefits in retarding aging. We used computationally guided drug screening for prioritizing drug targets to produce a short list of candidate compounds for in vivo testing. We applied the virtual ligand screening approach FINDSITE(comb) for screening potential anti-aging protein targets against FDA approved drugs listed in DrugBank. A short list of 31 promising compounds was screened using a multi-tiered approach with rotifers as an animal model of aging. Primary and secondary survival screens and cohort life table experiments identified four drugs capable of extending rotifer lifespan by 8-42%. Exposures to 1 microM erythromycin, 5 microM carglumic acid, 3 microM capecitabine, and 1 microM ivermectin, extended rotifer lifespan without significant effect on reproduction. Some drugs also extended healthspan, as estimated by mitochondria activity and mobility (swimming speed). Our most promising result is that rotifer lifespan was extended by 7-8.9% even when treatment was started in middle age.
Published in April 2018
Chemometric and high-resolution mass spectrometry tools for the characterization and comparison of raw and treated wastewater samples of a pilot plant on the SIPIBEL site.
Abstract: Due to its key role in the contamination of natural resources, the assessment of raw and treated wastewater effluents is a current major concern and urges comprehensive analytical methods capable of selectively capturing the chemodiversity of these samples. In this context, the overall objective of this work can be summarized as (i) the assessment of the performance of secondary and tertiary (advanced oxidation) wastewater treatments through multivariate analysis followed by (ii) the comprehensive characterization of wastewater samples based on their spectral fingerprints and a combination of suspect and non-target screening approaches. Several compounds, belonging to different sources of contamination were annotated and/or partially identified: pharmaceuticals, metabolites and transformation compounds, human activity markers, surfactants, and polyethoxy compounds. These results highlight the contribution of filtering and screening tools such as monoisotopic exact mass, mass defect, MS/MS data-dependent acquisitions, isotopic pattern and retention time to the selection, and the identification of environmental contaminants and their metabolites/degradation products. This paper completes the target study conducted in the SIPIBEL site and offers an alternative for the assessment of treatment processes by broadening the spectrum to a larger number of compounds and the correlations between them.
Published on April 27, 2018
A side-effect free method for identifying cancer drug targets.
Abstract: Identifying effective drug targets, with little or no side effects, remains an ever challenging task. A potential pitfall of failing to uncover the correct drug targets, due to side effect of pleiotropic genes, might lead the potential drugs to be illicit and withdrawn. Simplifying disease complexity, for the investigation of the mechanistic aspects and identification of effective drug targets, have been done through several approaches of protein interactome analysis. Of these, centrality measures have always gained importance in identifying candidate drug targets. Here, we put forward an integrated method of analysing a complex network of cancer and depict the importance of k-core, functional connectivity and centrality (KFC) for identifying effective drug targets. Essentially, we have extracted the proteins involved in the pathways leading to cancer from the pathway databases which enlist real experimental datasets. The interactions between these proteins were mapped to build an interactome. Integrative analyses of the interactome enabled us to unearth plausible reasons for drugs being rendered withdrawn, thereby giving future scope to pharmaceutical industries to potentially avoid them (e.g. ESR1, HDAC2, F2, PLG, PPARA, RXRA, etc). Based upon our KFC criteria, we have shortlisted ten proteins (GRB2, FYN, PIK3R1, CBL, JAK2, LCK, LYN, SYK, JAK1 and SOCS3) as effective candidates for drug development.
Published on April 26, 2018
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species.
Abstract: Aspergillus fumigatus and multiple other Aspergillus species cause a wide range of lung infections, collectively termed aspergillosis. Aspergilli are ubiquitous in environment with healthy immune systems routinely eliminating inhaled conidia, however, Aspergilli can become an opportunistic pathogen in immune-compromised patients. The aspergillosis mortality rate and emergence of drug-resistance reveals an urgent need to identify novel targets. Secreted and cell membrane proteins play a critical role in fungal-host interactions and pathogenesis. Using a computational pipeline integrating data from high-throughput experiments and bioinformatic predictions, we have identified secreted and cell membrane proteins in ten Aspergillus species known to cause aspergillosis. Small secreted and effector-like proteins similar to agents of fungal-plant pathogenesis were also identified within each secretome. A comparison with humans revealed that at least 70% of Aspergillus secretomes have no sequence similarity with the human proteome. An analysis of antigenic qualities of Aspergillus proteins revealed that the secretome is significantly more antigenic than cell membrane proteins or the complete proteome. Finally, overlaying an expression dataset, four A. fumigatus proteins upregulated during infection and with available structures, were found to be structurally similar to known drug target proteins in other organisms, and were able to dock in silico with the respective drug.
Showing 3401 to 3404 of 5186 entries