keyword
MENU ▼
Read by QxMD icon Read
search

Crystallography

keyword
https://www.readbyqxmd.com/read/29332299/similarity-search-combined-with-docking-and-molecular-dynamics-for-novel-hache-inhibitor-scaffolds
#1
Nadia Melo Borges, Geraldo Rodrigues Sartori, Jean F R Ribeiro, Josmar R Rocha, João B L Martins, Carlos A Montanari, Ricardo Gargano
The main purpose of this study was to address the performance of virtual screening methods based on ligands and the protein structure of acetylcholinesterase (AChE) in order to retrieve novel human AChE (hAChE) inhibitors. In addition, a protocol was developed to identify novel hit compounds and propose new promising AChE inhibitors from the ZINC database with 10 million commercially available compounds. In this sense, 3D similarity searches using rapid overlay of chemical structures and similarity analysis through comparison of electrostatic overlay of docked hits were used to retrieve AChE inhibitors from collected databases...
January 13, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/29329326/utilization-of-peptide-phage-display-to-investigate-hotspots-on-il-17a-and-what-it-means-for-drug-discovery
#2
Joey P Ting, Frances Tung, Stephen Antonysamy, Stephen Wasserman, Spencer B Jones, Feiyu F Zhang, Alfonso Espada, Howard Broughton, Michael J Chalmers, Michael E Woodman, Holly A Bina, Jeffrey A Dodge, Jordi Benach, Aiping Zhang, Christopher Groshong, Danalyn Manglicmot, Marijane Russell, Sepideh Afshar
To date, IL-17A antibodies remain the only therapeutic approach to correct the abnormal activation of the IL-17A/IL-17R signaling complex. Why is it that despite the remarkable success of IL-17 antibodies, there is no small molecule antagonist of IL-17A in the clinic? Here we offer a unique approach to address this question. In order to understand the interaction of IL-17A with its receptor, we combined peptide discovery using phage display with HDX, crystallography, and functional assays to map and characterize hot regions that contribute to most of the energetics of the IL-17A/IL-17R interaction...
2018: PloS One
https://www.readbyqxmd.com/read/29329277/synthesis-structural-characterization-antimicrobial-activity-and-in-vitro-biocompatibility-of-new-unsaturated-carboxylate-complexes-with-2-2-bipyridine
#3
Gina Vasile Scăețeanu, Mariana Carmen Chifiriuc, Coralia Bleotu, Crina Kamerzan, Luminiţa Măruţescu, Constantin G Daniliuc, Cătălin Maxim, Larisa Calu, Rodica Olar, Mihaela Badea
The synthesis, structural characterization, cytotoxicity, and antimicrobial properties of four new complexes formed by employing acrylate anion and 2,2'-bipyridine are reported herein. X-ray crystallography revealed the trinuclear nature of [Mn₃(2,2'-bipy)₂(C₃H₃O₂)₆] (1), meanwhile complexes with general formula [M(2,2'-bipy)(C₃H₃O₂)₂(H₂O)x]∙yH₂O ((2) M: Ni, x = 1, y = 0; (3) M: Cu, x = 1, y = 0; (4) M: Zn, x = 0, y = 1; 2,2'-bipy: 2,2'-bipyridine; C₃H₃O₂: acrylate anion) were shown to be mononuclear...
January 12, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29329269/design-synthesis-and-safener-activity-of-novel-methyl-r-n-benzoyl-dichloroacetyl-thiazolidine-4-carboxylates
#4
Li-Xia Zhao, Hao Wu, Yue-Li Zou, Qing-Rui Wang, Ying Fu, Chun-Yan Li, Fei Ye
A series of novel methyl (R)-N-benzoyl/dichloroacetyl-thiazolidine-4-carboxylates were designed by active substructure combination. The title compounds were synthesized using a one-pot route from l-cysteine methyl ester hydrochloride, acyl chloride, and ketones. All compounds were characterized by IR, ¹H NMR, 13C NMR, and HRMS. The structure of 4q was determined by X-ray crystallography. The biological tests showed that the title compounds protected maize from chlorimuron-ethyl injury to some extent. The ALS activity assay showed that the title compounds increased the ALS activity of maize inhibited by chlorimuron-ethyl...
January 12, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29327921/the-nature-and-reactivity-of-ferryl-heme-in-compounds-i-and-ii
#5
Peter C E Moody, Emma L Raven
Aerobic organisms have evolved to activate oxygen from the atmosphere, which allows them to catalyze the oxidation of different kinds of substrates. This activation of oxygen is achieved by a metal center (usually iron or copper) buried within a metalloprotein. In the case of iron-containing heme enzymes, the activation of oxygen is achieved by formation of transient iron-oxo (ferryl) intermediates; these intermediates are called Compound I and Compound II. The Compound I and II intermediates were first discovered in the 1930s in horseradish peroxidase, and it is now known that these same species are used across the family of heme enzymes, which include all of the peroxidases, the heme catalases, the P450s, cytochrome c oxidase, and NO synthase...
January 12, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29323880/photoactivated-in-vitro-anticancer-activity-of-rhenium-i-tricarbonyl-complexes-bearing-water-soluble-phosphines
#6
Sierra C Marker, Samantha N MacMillan, Warren R Zipfel, Zhi Li, Peter C Ford, Justin J Wilson
Fifteen water-soluble rhenium compounds of the general formula [Re(CO)3(NN)(PR3)]+, where NN is a diimine ligand and PR3 is 1,3,5-triaza-7-phosphaadamantane (PTA), tris(hydroxymethyl)phosphine (THP), or 1,4-diacetyl-1,3,7-triaza-5-phosphabicylco[3.3.1]nonane (DAPTA), were synthesized and characterized by multinuclear NMR spectroscopy, IR spectroscopy, and X-ray crystallography. The complexes bearing the THP and DAPTA ligands exhibit triplet-based luminescence in air-equilibrated aqueous solutions with quantum yields ranging from 3...
January 11, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29323636/an-optimized-method-for-3d-fluorescence-co-localization-applied-to-human-kinetochore-protein-architecture
#7
Aussie Suzuki, Sarah K Long, Edward D Salmon
Two-color fluorescence co-localization in 3D (three-dimension) has the potential to achieve accurate measurements at the nanometer length scale. Here, we optimized a 3D fluorescence co-localization method that uses mean values for chromatic aberration correction to yield the mean separation with ~10 nm accuracy between green and red fluorescently labeled protein epitopes within single human kinetochores. Accuracy depended critically on achieving small standard deviations in fluorescence centroid determination, chromatic aberration across the measurement field, and coverslip thickness...
January 11, 2018: ELife
https://www.readbyqxmd.com/read/29323171/new-anti-inflammatory-guaianes-from-the-atlantic-hydrotherm-derived-fungus-graphostroma-sp-mccc-3a00421
#8
Siwen Niu, Chun-Lan Xie, Jin-Mei Xia, Zhu-Hua Luo, Zongze Shao, Xian-Wen Yang
Nine new guaianes (graphostromanes A-I, 1-9) were isolated from the deep-sea-derived fungus Graphostroma sp. MCCC 3A00421, along with four known ones (10-13). The relative configurations were established mainly by detailed analysis of the NMR and HRESIMS data, while the absolute configurations were assigned using the X-ray crystallography and modified Mosher's method. All isolates were evaluated for their inhibitory effects against lipopolysaccharide (LPS)-induced nitric oxide (NO) production in RAW264.7 macrophages...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29323112/signaling-ammonium-across-membranes-through-an-ammonium-sensor-histidine-kinase
#9
Tobias Pflüger, Camila F Hernández, Philipp Lewe, Fabian Frank, Haydyn Mertens, Dmitri Svergun, Manfred W Baumstark, Vladimir Y Lunin, Mike S M Jetten, Susana L A Andrade
Sensing and uptake of external ammonium is essential for anaerobic ammonium-oxidizing (anammox) bacteria, and is typically the domain of the ubiquitous Amt/Rh ammonium transporters. Here, we report on the structure and function of an ammonium sensor/transducer from the anammox bacterium "Candidatus Kuenenia stuttgartiensis" that combines a membrane-integral ammonium transporter domain with a fused histidine kinase. It contains a high-affinity ammonium binding site not present in assimilatory Amt proteins. The levels of phosphorylated histidine in the kinase are coupled to the presence of ammonium, as conformational changes during signal recognition by the Amt module are transduced internally to modulate the kinase activity...
January 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29322425/production-of-recombinant-killer-immunoglobulin-like-receptors-for-crystallography-and-luminex-based-assays
#10
Phillip Pymm, Julian P Vivian
The killer immunoglobulin-like receptors (KIR) are a highly diverse family of cell-surface receptors that are of importance to the effector function of Natural Killer cells. KIR have been implicated in the detection and clearance of malignantly transformed cells and in the immune-control of viruses including HIV, HCV and CMV. Recently, the mismatching of donor and recipient KIR has been demonstrated to improve success of hematopoietic stem cell transplantation treatments of leukemias. Due to the high degree of diversity amongst the KIR, a number of strategies are required for the production of recombinant protein for medical, biochemical and structural applications...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29319704/multiply-trapped-3-trans-pt-pr3-2-c-triple-bond-length-as-m-dash-cc6h4x-2-conformers-in-rigid-media
#11
Gabriel Marineau-Plante, Frank Juvenal, Adam Langlois, Daniel Fortin, Armand Soldera, Pierre D Harvey
The complexes (R = Me, Et, Bu; X = H, SMe) exhibit well-defined multi-exponential emissions (2-4 components) in the solid state at 77 and 298 K and in 2MeTHF glasses at 77 K due to multiple frozen conformers exhibiting variable dihedral angles formed by the PtP2C2 and C6H4 planes. The demonstration was made using X-ray crystallography at various temperatures where different sites are present in the samples, and using geometry optimization (DFT computations) where various stable conformers are noted.
January 10, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29318309/synthesis-crystal-structures-molecular-docking-and-mao-b-inhibitory-activity-of-transition-metal-complexes-derived-from-2-4-pyridin-2-yl-piperazin-1-yl-acetic-acid
#12
Yan-Jie Ren, Jin-Long Zhu, Li-Xin Zhang, Yin-Xiang Xu, Shao-Song Qian
Three new complexes derived from 2-(4-(pyridin-2-yl)piperazin-1-yl)acetic acid (HL), [M(L)2(H2O)2] where M = CuII (1), ZnII (2) and CdII (3), have been synthesized and characterized by IR spectroscopy, elemental analysis and X-ray crystallography. The inhibitory activity of these three complexes against MAO-B was tested in vitro, and the molecular docking experiments were also carried out to rationalize their binding models. Both the experimental and docking simulation results indicated that complex 1 has the best inhibitory activity with IC50 value being 6...
December 2017: Acta Chimica Slovenica
https://www.readbyqxmd.com/read/29314830/x-ray-structures-of-the-proprotein-convertase-furin-bound-with-substrate-analog-inhibitors-reveal-substrate-specificity-determinants-beyond-the-s4-pocket
#13
Sven O Dahms, Kornelia Hardes, Torsten Steinmetzer, Manuel E Than
The proprotein convertase (PC) furin is a highly specific serine protease modifying and thereby activating proteins in the secretory pathway by proteolytic cleavage. Its substrates are involved in many diseases including cancer and infections caused by bacteria and viruses. Understanding furin's substrate specificity is of crucial importance for the development of pharmacologically applicable inhibitors. Using protein X-ray crystallography we investigated the extended substrate binding site of furin in complex with three peptide derived inhibitors at up to 1...
January 9, 2018: Biochemistry
https://www.readbyqxmd.com/read/29311713/towards-high-throughput-gpcr-crystallography-in-meso-soaking-of-adenosine-a2a-receptor-crystals
#14
Prakash Rucktooa, Robert K Y Cheng, Elena Segala, Tian Geng, James C Errey, Giles A Brown, Robert M Cooke, Fiona H Marshall, Andrew S Doré
Here we report an efficient method to generate multiple co-structures of the A2A G protein-coupled receptor (GPCR) with small-molecules from a single preparation of a thermostabilised receptor crystallised in Lipidic Cubic Phase (LCP). Receptor crystallisation is achieved following purification using a low affinity "carrier" ligand (theophylline) and crystals are then soaked in solutions containing the desired (higher affinity) compounds. Complete datasets to high resolution can then be collected from single crystals and seven structures are reported here of which three are novel...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29306330/papain-like-cysteine-proteases-in-carica-papaya-lineage-specific-gene-duplication-and-expansion
#15
Juan Liu, Anupma Sharma, Marie Jamille Niewiara, Ratnesh Singh, Ray Ming, Qingyi Yu
BACKGROUND: Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases structurally related to papain, play important roles in plant development, senescence, and defense responses. Papain, the first cysteine protease whose structure was determined by X-ray crystallography, plays a crucial role in protecting papaya from herbivorous insects. Except the four major PLCPs purified and characterized in papaya latex, the rest of the PLCPs in papaya genome are largely unknown...
January 6, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29304282/dual-allosteric-inhibition-of-shp2-phosphatase
#16
Michelle Fodor, Edmund Price, Ping Wang, Hengyu Lu, Andreea Argintaru, Zhouliang Chen, Meir Glick, Huai-Xiang Hao, Mitsunori Kato, Robert Koenig, Jonathan R LaRochelle, Gang Liu, Eric McNeill, Dyuti Majumdar, Gisele A Nishiguchi, Lawrence B Perez, Gregory Paris, Christopher M Quinn, Timothy Ramsey, Martin Sendzik, Michael David Shultz, Sarah L Williams, Travis Stams, Stephen C Blacklow, Michael G Acker, Matthew J LaMarche
SHP2 is a cytoplasmic protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell proliferation, differentiation, and survival. Recently we reported an allosteric mechanism of inhibition that stabilizes the auto-inhibited conformation of SHP2. SHP099 (1) was identified and characterized as a moderately potent, orally bioavailable, allosteric small molecule inhibitor, which binds to a tunnel-like pocket formed by the confluence of three domains of SHP2. In this report, we describe further screening strategies that enabled the identification of a second, distinct small molecule allosteric site...
January 5, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29303494/substituent-position-effect-on-the-crystal-structures-of-n-phenyl-2-phthalimidoethanesulfonamide-derivatives
#17
Resul Sevinçek, Duygu Barut Celepci, Serap Köktaş Koca, Özlem Akgül, Muittin Aygün
In order to determine the impact of different substituents and their positions on intermolecular interactions and ultimately on the crystal packing, unsubstituted N-phenyl-2-phthalimidoethanesulfonamide, C16H14N2O4S, (I), and the N-(4-nitrophenyl)-, C16H13N3O6S, (II), N-(4-methoxyphenyl)-, C16H16N3O6S, (III), and N-(2-ethylphenyl)-, as the monohydrate, C18H18N2O4S·H2O, (IV), derivatives have been characterized by single-crystal X-ray crystallography. Sulfonamides (I) and (II) have triclinic crystal systems, while (III) and (IV) are monoclinic...
January 1, 2018: Acta Crystallographica. Section C, Structural Chemistry
https://www.readbyqxmd.com/read/29303250/we-fret-so-you-don-t-have-to-new-models-of-the-lipoprotein-lipase-dimer
#18
Cassandra K Hayne, Hayretin Yumerefendi, Lin Cao, Jacob W Gauer, Michael J Lafferty, Brian Kuhlman, Dorothy A Erie, Saskia B Neher
Lipoprotein lipase (LPL) is a dimeric enzyme that is responsible for clearing triglyceride-rich lipoproteins from the blood. Although LPL plays a key role in cardiovascular health, an experimentally derived three-dimensional structure has not been determined. Such a structure would aid in understanding mutations in LPL that cause familial LPL deficiency in patients and help in the development of therapeutic strategies to target LPL. A major obstacle to structural studies of LPL is that LPL is an unstable protein that is difficult to produce in the quantities needed for nuclear magnetic resonance or crystallography...
January 5, 2018: Biochemistry
https://www.readbyqxmd.com/read/29303183/electron-sponge-from-naphthalenediimide-viologen-conjugates-water-stable-highly-electron-deficient-polyions-with-1-v-potential-window
#19
Jyoti Shukla, M R Ajayakumar, Yogendra Kumar, Pritam Mukhopadhyay
We report a new class of multi-electron acceptors by integrating for the first time multiple π-cations at the naphthalenediimide-core. These polyions present a remarkably low-lying LUMO with water stability, seven-redox states in a narrow window of ∼1 V and excellent reversibility. Extended conjugation is manifest in mixed valence states with NIR absorption. X-ray crystallography revealed appealing multiple anion-π interactions.
January 5, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29300483/unexpected-diffusion-anisotropy-of-carbon-dioxide-in-the-metal-organic-framework-zn2-dobpdc
#20
Alexander C Forse, Miguel I Gonzalez, Rebecca L Siegelman, Velencia J Witherspoon, Sudi Jawahery, Rocio Mercado, Phillip J Milner, Jeffrey D Martell, Berend Smit, Bernhard Blümich, Jeffrey R Long, Jeffrey A Reimer
Metal-organic frameworks are promising materials for energy-efficient gas separations, but little is known about the diffusion of adsorbates in materials featuring one-dimensional porosity at the nanoscale. An understanding of the interplay between framework structure and gas diffusion is crucial for the practical application of these materials as adsorbents or in mixed-matrix membranes, since the rate of gas diffusion within the adsorbent pores impacts the required size (and therefore cost) of the adsorbent column or membrane...
January 4, 2018: Journal of the American Chemical Society
keyword
keyword
110093
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"