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Small molecule structure

Kenji Sugawara, Kohei Honda, Yoshie Reien, Norihide Yokoi, Chihiro Seki, Harumi Takahashi, Kohtaro Minami, Ichiro Mori, Akio Matsumoto, Haruaki Nakaya, Susumu Seino
Insulin secretagogues are used for treatment of type 2 diabetes. We attempted to discover novel small molecules to stimulate insulin secretion by using in silico similarity search using sulfonylureas as query, followed by measurement of insulin secretion. Among 38 compounds selected by in silico similarity search, we found three diphenylsemicarbazides and one quinolone that stimulate insulin secretion. We focused on compound 8 (C8), which had the strongest insulin-secreting effect. Based on the structure-activity relationship of C8-derivatives, we identified diphenylthiosemicarbazide (DSC) 108 as the most potent secretagogue...
2016: PloS One
Gordon G Carmichael
Murine polyomavirus (MPyV) infects mouse cells and is highly oncogenic in immunocompromised hosts and in other rodents. Its genome is a small, circular DNA molecule of just over 5000 base pairs and it encodes only seven polypeptides. While seemingly simply organized, this virus has adopted an unusual genome structure and some unusual uses of cellular quality control pathways that, together, allow an amazingly complex and varied pattern of gene regulation. In this review we discuss how MPyV leverages these various pathways to control its life cycle...
October 17, 2016: Viruses
Tofayel Ahmed, Zhan Yin, Shashi Bhushan
Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit...
October 20, 2016: Scientific Reports
Joshua Bloom, Shan Sun, Yousef Al-Abed
Macrophage migration inhibitory factor (MIF) has emerged as a promising drug target in diseases including sepsis, rheumatoid arthritis, and cancer. MIF has multiple properties that favor development of specific, targeted therapies: it is expressed broadly among human cells, has noted roles in diverse inflammatory and oncological processes, and has intrinsic enzymatic activity amenable to high-throughput screening. Despite these advantages, anti-MIF therapy remains well behind other cytokine-targeted therapeutics, with no small molecules in the pipeline for clinical development and anti-MIF antibodies only recently beginning clinical trials...
October 20, 2016: Expert Opinion on Therapeutic Targets
Siavosh Mahboobi, Bernadette Pilsl, Andreas Sellmer
Chimeric compounds combine the structural features of inhibitors of histone deacetylases (HDACi) and tyrosine kinase inhibitors (TKi), and therefore unite the effects of a dual-targeting strategy in one compound. Here, we describe the generation of such hybrid molecules. Small molecules, known as TKi, are combined with a Zn(2+) chelating motive, preferentially a hydroxamic acid, in addition. The resulting small molecules also can inhibit histone deacetylases, which are dependent on the catalytically active Zn(2+)...
2017: Methods in Molecular Biology
Robyn T Rebbeck, Maram M Essawy, Florentin R Nitu, Benjamin D Grant, Gregory D Gillispie, David D Thomas, Donald M Bers, Razvan L Cornea
Using time-resolved fluorescence resonance energy transfer (FRET), we have developed and validated the first high-throughput screening (HTS) method to discover compounds that modulate an intracellular Ca(2+) channel, the ryanodine receptor (RyR), for therapeutic applications. Intracellular Ca(2+) regulation is critical for striated muscle function, and RyR is a central player. At resting [Ca(2+)], an increased propensity of channel opening due to RyR dysregulation is associated with severe cardiac and skeletal myopathies, diabetes, and neurological disorders...
October 19, 2016: Journal of Biomolecular Screening
Jeroen Aerts, Annelies Laeremans, Laurens Minerva, Kurt Boonen, Budamgunta Harshavardhan, Rudi D'hooge, Dirk Valkenborg, Geert Baggerman, Lutgarde Arckens
The Morris water maze (MWM) spatial learning task has been demonstrated to involve a cognitive switch of action control to serve the transition from an early towards a late learning phase. However, the molecular mechanisms governing this switch are largely unknown. We employed MALDI MS imaging (MSI) to screen for changes in expression of small proteins in brain structures implicated in the different learning phases. We compared mice trained for 3days and 30days in the MWM, reflecting an early and a late learning phase in relation to the acquisition of a spatial learning task...
October 17, 2016: Biochimica et Biophysica Acta
Xiaoyu Zhuang, Bing Zhao, Shu Liu, Fengrui Song, Fengchao Cui, Zhiqiang Liu, Yunqi Li
Misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1) is implicated in the etiology amyotrophic lateral sclerosis (ALS). The use of small molecules may stabilize the spatial structure of SOD1 dimer, thus preventing its dissociation and aggregation. In this study, "native" mass spectrometry (MS) was used to study the non-covalent interactions between SOD1 and flavonoid compounds. MS experiments were performed on a quadruple time-of-flight (Q-ToF) mass spectrometer with an electrospray ionization (ESI) source and T-wave ion mobility...
October 19, 2016: Analytical Chemistry
Aleksandar Antanasijevic, Nicholas J Hafeman, Smanla Tundup, Carolyn Kingsley, Rama K Mishra, Lijun Rong, Balaji Manicassamy, Duncan Wardrop, Michael Caffrey
The viral envelope protein hemagglutinin (HA) plays a critical role in influenza entry and thus is an attractive target for novel therapeutics. The small molecule tert-butylhydroquinone (TBHQ) has previously been shown to bind to HA and inhibit HA-mediated entry with low micromolar potency. However, enthusiasm for the use of TBHQ has diminished due to the compound's antioxidant properties. In this work we show that the antioxidant properties of TBHQ are not responsible for the inhibition of HA-mediated entry...
September 9, 2016: ACS Infectious Diseases
Zhen Yang, Andreas Kappler, Jie Jiang
Humic substances (HS) are redox-active organic compounds with a broad spectrum of molecular sizes and reducing capacities, i.e. number of electrons donated or accepted. However, it is unknown which role the distribution of redox-active functional groups in different molecule sizes plays for HS redox reactions in varying pore sizes micro-environments. We used dialysis experiments to separate bulk humic acids (HA) into low molecular weight fractions (LMWF) and retentate, e.g. the remaining HA in the dialysis bag...
October 19, 2016: Environmental Science & Technology
Irina G Tikhonova
Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors...
October 19, 2016: Handbook of Experimental Pharmacology
Agnieszka Rybarczyk, Paulina Jackowiak, Marek Figlerowicz, Jacek Blazewicz
Since the beginning of the 21st century, an increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins)...
October 19, 2016: Acta Biochimica Polonica
Eiji Yashima, Naoki Ousaka, Daisuke Taura, Kouhei Shimomura, Tomoyuki Ikai, Katsuhiro Maeda
In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described...
October 18, 2016: Chemical Reviews
Sanjay Kumar Dey, Pankaj Prabhakar, Manisha Saini, Toyanji Joseph, B K Thelma, Subir K Maulik, Suman Kundu
OBJECTIVE: To identify novel inhibitors of dopamine beta hydroxylase (DBH) and evaluate their antihypertensive properties in L-NAME induced hypertensive rat model. DESIGN AND METHOD: An experimentally validated computational model for hDBH, built in our lab, was used for structure-based, rational drug-design. The three-dimensional model was used for virtual-screening against small molecule databases from NCI, USA and elsewhere. Identified top hits were then tested in vitro against DBH with known inhibitors nepicastat and disulfiram as controls...
September 2016: Journal of Hypertension
Stephen Harrap
Genetic discovery in blood pressure is generally referenced in relation to protein-coding genes, despite the fact that genes less than 2% of the genome. Recent exploration of the DNA sequences between genes, once called "junk" DNA, has revealed a wealth of transcripts for RNA species that do not encode protein. These non-coding RNAs (ncRNAs) have emerged as dynamic managers of the business of the genome, able to coordinate the expression of genes in time and space to achieve the complexities of normal development and growth...
September 2016: Journal of Hypertension
Christine E Mona, Élie Besserer-Offroy, Jérôme Cabana, Richard Leduc, Pierre Lavigne, Nikolaus Heveker, Éric Marsault, Emanuel Escher
A combination of the CXCR4 inverse agonist T140 with N-terminal CXCL12 oligopeptides has produced the first nanomolar synthetic CXCR4 agonists. In these agonists, the inverse agonistic portion provides affinity whereas the N-terminal CXCL12 sequence induces receptor activation. Several CXCR4 crystal structures exist with either CVX15, an inverse agonist closely related to T140 and IT1t, a small molecule; we therefore attempted to produce another CXCL12 oligopeptide combination with IT1t. For this purpose, a primary amino group was introduced by total synthesis into one of the methyl groups of IT1t, serving as an anchoring point for the oligopeptide graft...
October 18, 2016: Organic & Biomolecular Chemistry
Rane A Harrison, Jia Lu, Martin Carrasco, John Hunter, Anuj Manandhar, Sudershan Gondi, Kenneth D Westover, John R Engen
Structural dynamics of Ras proteins contribute to their activity in signal transduction cascades. Directly targeting Ras proteins with small molecules may rely on movement of a conserved structural motif, switch II. To understand Ras signaling and advance Ras targeting strategies, experimental methods to measure Ras dynamics are required. Here we demonstrate the utility of hydrogen-deuterium exchange mass spectrometry to measure Ras dynamics by studying representatives from two branches of the Ras superfamily, Ras and Rho...
October 14, 2016: Journal of Molecular Biology
Kristian J Tangso, Paulo Henrique C D da Cunha, Patrick T Spicer, Jian Li, Ben J Boyd
Infections arising in hospitalized patients, particularly those who have undergone surgery and are reliant on receiving treatment through biomedical devices, continue to be a rising concern. It is well known that aqueous mixtures of oppositely charged surfactant and polymer molecules can self-assemble to form liquid crystalline structures primarily via electrostatically-driven interactions which have demonstrated great potential as tailored release nanomaterials. Colistin is a re-emerging antibiotic used against multidrug-resistant Gram negative bacteria...
October 17, 2016: ACS Applied Materials & Interfaces
Nis Halland, Jörg Czech, Werngard Czechtizky, Andreas Evers, Markus Follmann, Markus Kohlmann, Herman A Schreuder, Christopher Kallus
Previously disclosed TAFIa inhibitors having a urea zinc-binding motif were used as the starting point for the development of a novel class of highly potent inhibitors having a sulfamide zinc-binding motif. High-resolution X-ray cocrystal structures were used to optimize the structures and reveal a highly unusual sulfamide configuration. A selected sulfamide was profiled in vitro and in vivo and displayed a promising ADMET profile.
October 17, 2016: Journal of Medicinal Chemistry
Arpan Kundu, GiovanniMaria Piccini, Kaido Sillar, Joachim Sauer
For CO and N2 on Mg(2+) sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies...
October 17, 2016: Journal of the American Chemical Society
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