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Small molecule structure

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https://www.readbyqxmd.com/read/28340334/advances-in-phase-plate-cryo-em-imaging-of-dna-and-nucleosomes
#1
Eugene Y D Chua, Sara Sandin
Contrast in electron cryo-microscopy (cryo-EM) is limited by the weak phase and radiation sensitive nature of biologic samples embedded in vitrified ice. We have recently shown that a new contrast enhancement technique utilizing the Volta phase plate can be combined with single particle analysis to determine the structure of a small chromatin complex, the nucleosome core particle, at near-atomic resolution. Here, we discuss advantages and limitations of the technique in terms of data collection, particle detection, and visualization of individual DNA molecules and higher-order chromatin structure...
February 7, 2017: Nucleus
https://www.readbyqxmd.com/read/28339120/accessing-structurally-diverse-near-infrared-cyanine-dyes-for-folate-receptor-targeted-cancer-cell-staining
#2
Sandra G König, Roland Krämer
Folate receptor (FR) targeting is one of the most promising strategies for the development of small-molecule based cancer imaging agents since the FR is highly overexpressed on the surface of many cancer cell types. FR-targeted conjugates of NIR emissive cyanine dyes are in advanced clinical trials for fluorescence-guided surgery and are valuable research tools for optical molecular imaging in animal models. Only a small number of promising conjugates has been evaluated so far. Analysis of structure-performance relations to identify critical factors modulating the performance of targeted conjugates is essential for successful further optimization...
March 24, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28338896/rapid-evolution-of-microrna-loci-in-the-brown-algae
#3
J Mark Cock, Fuli Liu, Delin Duan, Simon Bourdareau, Agnieszka Lipinska, Susana M Coelho, James E Tarver
Stringent searches for microRNAs (miRNAs) have so far only identified these molecules in animals, land plants, chlorophyte green algae, slime molds and brown algae. The identification of miRNAs in brown algae was based on analysis of a single species, the filamentous brown alga Ectocarpus sp. Here we have used deep sequencing of small RNAs and a recently published genome sequence to identify miRNAs in a second brown alga, the kelp Saccharina japonica. S. japonica possesses a large number of miRNAs (117) and these miRNAs are highly diverse, falling into 98 different families...
March 3, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338680/real-time-molecular-scale-observation-of-crystal-formation
#4
Roy E Schreiber, Lothar Houben, Sharon G Wolf, Gregory Leitus, Zhong-Ling Lang, Jorge J Carbó, Josep M Poblet, Ronny Neumann
How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28338621/optimized-4-5-diarylimidazoles-as-potent-selective-inhibitors-of-protein-kinase-ck1%C3%AE-and-their-structural-relation-to-p38%C3%AE-mapk
#5
Jakob Halekotte, Lydia Witt, Chiara Ianes, Marc Krüger, Mike Bührmann, Daniel Rauh, Christian Pichlo, Elena Brunstein, Andreas Luxenburger, Ulrich Baumann, Uwe Knippschild, Joachim Bischof, Christian Peifer
The involvement of protein kinase CK1δ in the pathogenesis of severe disorders such as Alzheimer's disease, amyotrophic lateral sclerosis, familial advanced sleep phase syndrome, and cancer has dramatically increased interest in the development of effective small molecule inhibitors for both therapeutic application and basic research. Unfortunately, the design of CK1 isoform-specific compounds has proved to be highly complicated due to the existence of six evolutionarily conserved human CK1 members that possess similar, different, or even opposite physiological and pathophysiological implications...
March 24, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28337938/optimization-and-development-of-antidiabetic-phytosomes-by-box-benhken-design
#6
Sushila Rathee, Anjoo Kamboj
Researchers have extensively reviewed on herbs and natural products for their marked clinical efficacy in some recent years, however maximum of the newly discovered bioactive constituents offer poor bioavailability due to their large size molecules or to their poor miscibility with oils and lipids, thereby limiting their ability to pass across the lipid-rich outer membranes of the enterocytes of the small intestine (Mukherjee and Wahile, 2006). Phytosomes are more bioavailable as compared to herbal extracts owing to their enhanced capacity to cross the bio-membranes and thus reaching the systemic circulation...
March 24, 2017: Journal of Liposome Research
https://www.readbyqxmd.com/read/28337127/nlrp3-inflammasome-in-neurological-diseases-from-functions-to-therapies
#7
REVIEW
Limin Song, Lei Pei, Shanglong Yao, Yan Wu, You Shang
Neuroinflammation has been identified as a causative factor of multiple neurological diseases. The nucleotide-binding oligomerization domain-, leucine-rich repeat- and pyrin domain-containing 3 (NLRP3) inflammasome, a subcellular multiprotein complex that is abundantly expressed in the central nervous system (CNS), can sense and be activated by a wide range of exogenous and endogenous stimuli such as microbes, aggregated and misfolded proteins, and adenosine triphosphate, which results in activation of caspase-1...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28336865/synthesis-optical-and-structural-properties-of-copper-sulfide-nanocrystals-from-single-molecule-precursors
#8
Peter A Ajibade, Nandipha L Botha
We report the synthesis and structural studies of copper sulfide nanocrystals from copper (II) dithiocarbamate single molecule precursors. The precursors were thermolysed in hexadecylamine (HDA) to prepare HDA-capped CuS nanocrystals. The optical properties of the nanocrystals studied using UV-visible and photoluminescence spectroscopy showed absorption band edges at 287 nm that are blue shifted, and the photoluminescence spectra show emission curves that are red-shifted with respect to the absorption band edges...
February 4, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28336064/novel-fluorescence-based-biosensors-incorporating-unnatural-amino-acids
#9
Wei Niu, Jiantao Guo
Fluorescent proteins of different colors are useful probes to study protein structure and function, and to investigate cellular events and conditions. Large efforts have focused on engineering new properties into fluorescent proteins via rational design and directed evolution. In addition to applications in imaging of protein expression level and subcellular localization, fluorescent proteins have been increasingly engineered to act as biosensors to track concentrations of small-molecule metabolites, enzyme activities, and protein conformational changes in living cells...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28335888/second-and-third-generation-drugs-for-immuno-oncology-treatment-the-more-the-better
#10
REVIEW
Wolfram C M Dempke, Klaus Fenchel, Peter Uciechowski, Stephen P Dale
Recent success in cancer immunotherapy (anti-CTLA-4, anti-PD1/PD-L1) has confirmed the hypothesis that the immune system can control many cancers across various histologies, in some cases producing durable responses in a way not seen with many small-molecule drugs. However, only less than 25% of all patients do respond to immuno-oncology drugs and several resistance mechanisms have been identified (e.g. T-cell exhaustion, overexpression of caspase-8 and β-catenin, PD-1/PD-L1 gene amplification, MHC-I/II mutations)...
March 2017: European Journal of Cancer
https://www.readbyqxmd.com/read/28335409/the-formyl-peptide-receptors-diversity-of-ligands-and-mechanism-for-recognition
#11
REVIEW
Hui-Qiong He, Richard D Ye
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors...
March 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335208/the-influence-of-fluorination-on-nano-scale-phase-separation-and-photovoltaic-performance-of-small-molecular-pc71bm-blends
#12
Zhen Lu, Wen Liu, Jingjing Li, Tao Fang, Wanning Li, Jicheng Zhang, Feng Feng, Wenhua Li
To investigate the fluorination influence on the photovoltaic performance of small molecular based organic solar cells (OSCs), six small molecules based on 2,1,3-benzothiadiazole (BT), and diketopyrrolopyrrole (DPP) as core and fluorinated phenyl (DFP) and triphenyl amine (TPA) as different terminal units (DFP-BT-DFP, DFP-BT-TPA, TPA-BT-TPA, DFP-DPP-DFP, DFP-DPP-TPA, and TPA-DPP-TPA) were synthesized. With one or two fluorinated phenyl as the end group(s), HOMO level of BT and DPP based small molecular donors were gradually decreased, inducing high open circuit voltage for fluorinated phenyl based OSCs...
April 21, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28333549/ksr-as-a-therapeutic-target-for-ras-dependent-cancers
#13
Beth K Neilsen, Danielle E Frodyma, Robert E Lewis, Kurt W Fisher
Targeting downstream effectors required for oncogenic Ras signaling is a potential alternative or complement to the development of more direct approaches targeting Ras in the treatment of Ras-dependent cancers. Areas covered: Here we review literature pertaining to the molecular scaffold Kinase Suppressor of Ras (KSR) and its role in promoting signals critical to tumor maintenance. We summarize the phenotypes in knockout models, describe the role of KSR in cancer, and outline the structure and function of the KSR1 and KSR2 proteins...
March 23, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/28332831/layer-by-layer-assembly-of-amine-reactive-multilayers-using-an-azlactone-functionalized-polymer-and-small-molecule-diamine-linkers
#14
Yashira M Zayas-Gonzalez, Benjamin J Ortiz, David M Lynn
We report the reactive layer-by-layer assembly of amine-reactive polymer multilayers using an azlactone-functionalized polymer and small-molecule diamine linkers. This approach yields crosslinked polymer/linker-type films that can be further functionalized, after fabrication, by treatment with functional primary amines, and provides opportunities to incorporate other useful functionality that can be difficult to introduce using other polyamine building blocks. Films fabricated using poly(2-vinyl-4,4-dimethylazlactone) (PVDMA) and three model non-degradable aliphatic diamine linkers yielded reactive thin films that were stable upon incubation in physiologically relevant media...
March 23, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28330354/scanning-tunneling-microscopy-study-of-thin-ptcdi-films-on-ag-si-111-%C3%A2-3-%C3%A3-%C3%A2-3
#15
C Emanuelsson, H M Zhang, E Moons, L S O Johansson
3,4,9,10-perylene tetracarboxylic diimide molecules were evaporated onto a Ag/Si(111)-√3 × √3 surface and studied by scanning tunneling microscopy/spectroscopy and low energy electron diffraction (LEED). The growth mode was characterized as layer-by-layer growth with a single molecular unit cell in a short range order. The growth of the first two monolayers involves a molecule/substrate superstructure and a molecule/molecule superstructure. At higher coverages, the molecules in each layer were found to align so that unit cells are on top of each other...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330340/cooperative-enhancement-of-the-nonlinear-optical-response-in-conjugated-energetic-materials-a-td-dft-study
#16
Andrew E Sifain, Loza F Tadesse, Josiah A Bjorgaard, David E Chavez, Oleg V Prezhdo, R Jason Scharff, Sergei Tretiak
Conjugated energetic molecules (CEMs) are a class of explosives with high nitrogen content that posses both enhanced safety and energetic performance properties and are ideal for direct optical initiation. As isolated molecules, they absorb within the range of conventional lasers. Crystalline CEMs are used in practice, however, and their properties can differ due to intermolecular interaction. Herein, time-dependent density functional theory was used to investigate one-photon absorption (OPA) and two-photon absorption (TPA) of monomers and dimers obtained from experimentally determined crystal structures of CEMs...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28327441/structure-based-design-synthesis-and-biological-evaluation-of-amino-phosphonate-derivatives-as-human-glucokinase-activators
#17
Nanda Kumar Yellapu, Ravendra Babu Kilaru, Nagaraju Chamarthi, Sarma Pvgk, Bhaskar Matcha
Glucokinase (GK) is a potential therapeutic target of type 2 diabetes and GK activators (GKAs) represent a promising class of small organic molecules which enhance GK activity. Based on the configuration and conformation of the allosteric site of GK, we have designed a novel class of amino phosphonate derivatives in order to develop potent GKAs. The QSAR model developed using numerous descriptors revealed its potential with the best effective statistical values of RMSE=1.52 and r(2)=0.30. Moreover, application of this model on the present test set GKAs proved to be worthy to predict their activities as a better linear relationship was observed with RMSE=0...
March 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28326635/structure-enabled-discovery-of-a-stapled-peptide-inhibitor-to-target-the-oncogenic-transcriptional-repressor-tle1
#18
Sally McGrath, Marcello Tortorici, Ludovic Drouin, Savade Solanki, Lewis Vidler, Isaac Westwood, Peter Gimeson, Rob vanMontfort, Swen Hoelder
TLE1 is an oncogenic transcriptional co-repressor that exerts its repressive effects through binding of transcription factors. Inhibition of this protein-protein interaction represents a putative cancer target but no small molecule inhibitors have been published for this challenging interface. In this manuscript, we report the structure enabled design and synthesis of a constrained peptide inhibitor of TLE1. Our design featured introduction of a four carbon atom linker into the peptide epitope found in many TLE1 binding partners...
March 22, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28324509/human-telomeric-g-quadruplex-structures-and-g-quadruplex-interactive-compounds
#19
Clement Lin, Danzhou Yang
G-quadruplexes are noncanonical secondary structures formed in DNA sequences containing consecutive runs of guanines. It has been shown that the 3' G-rich single-stranded overhangs of human telomeres can form G-quadruplex structures, and the human telomeric DNA G-quadruplexes are considered attractive targets for anticancer drugs. G-quadruplex-interactive compounds have been shown to inhibit telomerase access as well as telomere capping. Nuclear magnetic resonance (NMR) spectroscopy is a powerful method in determining the G-quadruplex structures under physiologically relevant conditions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28322731/the-substitution-of-proline-168-favors-bax-oligomerization-and-stimulates-its-interaction-with-luvs-and-mitochondria
#20
Lilit Simonyan, Alexandre Légiot, Ioan Lascu, Grégory Durand, Marie-France Giraud, Cécile Gonzalez, Stéphen Manon
Bax is a major player in the apoptotic process, being at the core of the mitochondria permeabilization events. In spite of the major recent advances in the knowledge of Bax organization within the membrane, the precise behavior of the C-terminal helix α9 remains elusive, since it was absent from the resolved structure of active Bax. The Proline 168 (P168) residue, located in the short loop between α8 and α9, has been the target of site-directed mutagenesis experiments, with conflicting results. We have produced and purified a recombinant mutant Bax-P168A, and we have compared its behavior with that of wild-type Bax in a series of tests on Large Unilamellar Vesicles (LUVs) and isolated mitochondria...
March 16, 2017: Biochimica et Biophysica Acta
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