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Chemical crystallography

Agnieszka Gunia-Krzyżak, Ewa Żesławska, Florence Bareyre, Wojciech Nitek, Anna M Waszkielewicz, Henryk Marona
A cinnamamide scaffold has been successfully incorporated in several compounds possessing desirable pharmacological activities in central and peripheral nervous system such as anticonvulsant, antidepressant, neuroprotective, analgesic, anti-inflammatory, muscle relaxant, and sedative/hypnotic properties. R,S-(2E)-1-(3-hydroxypiperidin-1-yl)-3-phenylprop-2-en-1-one (KM-608), a cinnamamide derivative, was synthesized, its chemical structure was confirmed by means of spectroscopy and crystallography, additionally thermal analysis showed that it exists in one crystalline form...
January 18, 2017: Chemical Biology & Drug Design
Helge Klare, Jörg M Neudörfl, Simon D Brandt, Elisabeth Mischler, Sigrid Meier-Giebing, Kathrin Deluweit, Folker Westphal, Tim Laussmann
Six collected phenidates, i.e. 4-methylmethylphenidate, 3,4-dichloromethylphenidate, ethylphenidate, 3,4-dichloroethylphenidate, ethylnaphthidate and N-benzyl-ethylphenidate were fully characterized by means of X-ray, NMR, GC-MS, ESI-MS(2) , ATR-FT-IR and GC solid-state IR analysis. Crystallography revealed the exclusive presence of the threo-configuration. Steric crowding induced by N-benzyl substitution at the piperidine moiety prompted an adoption of an unexpected axial positioning of substituents on the piperidine moiety in the crystal state as opposed to the exclusive equatorial positioning encountered in N-unsubstituted phenidate analogs...
January 9, 2017: Drug Testing and Analysis
Feng Yu, Shengbo Yao, Friedhard Römer, Bernd Witzigmann, Tilman Schimpke, Martin Strassburg, Andrey Bakin, Hans Schumacher, Erwin Peiner, Hutomo Suryo Wasisto, Andreas Waag
Vertically aligned GaN nanowire (NW) arrays have attracted a lot of attention because of their potential for novel devices in the fields of optoelectronics and nanoelectronics. In this work, GaN NW arrays have been designed and fabricated by combining suitable nanomachining processes including dry and wet etching. After inductively coupled plasma (ICP) dry reactive ion etching (RIE), the GaN NWs are subsequently treated in wet chemical etching using AZ400K developer (i.e., with an activation energy of 0.69 �� 0...
January 9, 2017: Nanotechnology
Dawid Warszycki, Manuel Rueda, Stefan Mordalski, Kurt Kristiansen, Grzegorz Satała, Krzysztof Rataj, Zdzisław Chilmonczyk, Ingebrigt Sylte, Ruben Abagyan, Andrzej J Bojarski
Despite its remarkable importance in the arena of drug design, serotonin 1A receptor (5-HT1A) has been elusive to the X-ray crystallography community. This lack of direct structural information not only hampers our knowledge regarding the binding modes of many popular ligands (including the endogenous neurotransmitter-serotonin), but also limits the search for more potent compounds. In this paper we shed new light on the 3D pharmacological properties of the 5-HT1A receptor by using a ligand-guided approach (ALiBERO) grounded in the Internal Coordinate Mechanics (ICM) docking platform...
January 18, 2017: Journal of Chemical Information and Modeling
Yuriy V Zatsikha, Cole D Holstrom, Kullapa Chanawanno, Allen J Osinski, Christopher J Ziegler, Victor N Nemykin
The 1,3,7,9-tetraferrocenylazadipyrromethene (3) and the corresponding 1,3,5,7-tetraferrocene aza-BODIPY (4) were prepared via three and four synthetic steps, respectively, starting from ferrocenecarbaldehyde using the chalcone-type synthetic methodology. The novel tetra-iron compounds have ferrocene groups directly attached to both the α- and the β-pyrrolic positions, and the shortest Fe-Fe distance determined by X-ray crystallography for 3 was found to be ∼6.98 Å. These new compounds were characterized by UV-vis, nuclear magnetic resonance, and high-resolution electrospray ionization mass spectrometry methods, while metal-metal couplings in these systems were probed by electro- and spectroelectrochemistry, chemical oxidations, and Mössbauer spectroscopy...
January 5, 2017: Inorganic Chemistry
Jose M Arencibia, Wolfgang Fröhner, Magdalena Krupa, Daniel Pastor-Flores, Piotr Merker, Thomas Oellerich, Sonja Neimanis, Christian Schmithals, Verena Köberle, Evelyn Süß, Stefan Zeuzem, Holger Stark, Albrecht Piiper, Dalibor Odadzic, Jörg O Schulze, Ricardo M Biondi
There is a current and pressing need for improved cancer therapies. The use of small molecule kinase inhibitors and their application in combinatorial regimens represent an approach to personalized targeted cancer therapy. A number of AGC kinases, including atypical Protein Kinase C enzymes (PKCs), are validated drug targets for cancer treatment. Most drug development programs for protein kinases focus on the development of drugs that bind at the ATP-binding site. Alternatively, allosteric drugs have great potential for the development of future innovative drugs...
January 13, 2017: ACS Chemical Biology
Anthony J Metrano, Nadia C Abascal, Brandon Q Mercado, Eric K Paulson, Anna E Hurtley, Scott J Miller
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced...
December 28, 2016: Journal of the American Chemical Society
Cynthia K Holland, Barbara Cascella, Joseph M Jez
In this issue of Cell Chemical Biology, Mori et al. (2016) combine X-ray crystallography and biochemistry to discover a new mechanism for stilbene synthesis in bacteria. The dialkyl-condensing enzyme StlD catalyzes formation of cyclohexanediones using a non-canonical β-ketosynthase active site. Aromatization by StlC completes production of the stilbene product.
December 22, 2016: Cell Chemical Biology
Ivan Polsinelli, Martin Savko, Cecile Rouanet-Mehouas, Lidia Ciccone, Susanna Nencetti, Elisabetta Orlandini, Enrico A Stura, William Shepard
X-ray radiation in macromolecular crystallography can chemically alter the biological material and deteriorate the integrity of the crystal lattice with concomitant loss of resolution. Typical alterations include decarboxylation of glutamic and aspartic residues, breaking of disulfide bonds and the reduction of metal centres. Helical scans add a small translation to the crystal in the rotation method, so that for every image the crystal is shifted to expose a fresh part. On beamline PROXIMA 2A at Synchrotron SOLEIL, this procedure has been tested with various parameters in an attempt to understand how to mitigate the effects of radiation damage...
January 1, 2017: Journal of Synchrotron Radiation
Matthew D Cheeseman, Nicola E A Chessum, Carl S Rye, A Elisa Pasqua, Michael J Tucker, Birgit Wilding, Lindsay E Evans, Susan Lepri, Meirion Richards, Swee Y Sharp, Salyha Ali, Martin Rowlands, Lisa O'Fee, Asadh Miah, Angela Hayes, Alan T Henley, Marissa Powers, Robert Te Poele, Emmanuel De Billy, Loredana Pellegrino, Florence Raynaud, Rosemary Burke, Rob L M van Montfort, Suzanne A Eccles, Paul Workman, Keith Jones
Phenotypic screens, which focus on measuring and quantifying discrete cellular changes rather than affinity for individual recombinant proteins, have recently attracted renewed interest as an efficient strategy for drug discovery. In this article, we describe the discovery of a new chemical probe, bisamide (CCT251236), identified using an unbiased phenotypic screen to detect inhibitors of the HSF1 stress pathway. The chemical probe is orally bioavailable and displays efficacy in a human ovarian carcinoma xenograft model...
December 22, 2016: Journal of Medicinal Chemistry
Matthew Fritz, Caitlin M Quinn, Mingzhang Wang, Guangjin Hou, Xingyu Lu, Leonardus M I Koharudin, Tatyana Polenova, Angela M Gronenborn
NMR chemical shifts are exquisitely sensitive probes for conformation and dynamics in molecules and supramolecular assemblies. Although isotropic chemical shifts are easily measured with high accuracy and precision in conventional NMR experiments, they remain challenging to calculate quantum mechanically, particularly in inherently dynamic biological systems. Using a model benchmark protein, the 133-residue agglutinin from Oscillatoria agardhii (OAA), which has been extensively characterized by us previously, we have explored the integration of X-ray crystallography, solution NMR, MAS NMR, and quantum mechanics/molecular mechanics (QM/MM) calculations for analysis of (13)C(α) and (15)N(H) isotropic chemical shifts...
December 21, 2016: Journal of Physical Chemistry. B
Mikhail Askerka, Gary W Brudvig, Victor S Batista
Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn4O5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen...
December 21, 2016: Accounts of Chemical Research
Asta Zubrienė, Alexey Smirnov, Virginija Dudutienė, David D Timm, Jurgita Matulienė, Vilma Michailovienė, Audrius Zakšauskas, Elena Manakova, Saulius Gražulis, Daumantas Matulis
The goal of rational drug design is to understand structure-thermodynamics correlations in order to predict the chemical structure of a drug that would exhibit excellent affinity and selectivity for a target protein. In this study we explored the contribution of added functionalities of benzenesulfonamide inhibitors to the intrinsic binding affinity, enthalpy, and entropy for recombinant human carbonic anhydrases (CA) CA I, CA II, CA VII, CA IX, CA XII, and CA XIII. The binding enthalpies of compounds possessing similar chemical structures and affinities were found to be very different, spanning a range from -90 to +10 kJ mol(-1) , and are compensated by a similar opposing entropy contribution...
December 21, 2016: ChemMedChem
Eva-Maria Schneeberger, Kathrin Breuker
Ribonucleic acids (RNA) frequently associate with proteins in many biological processes to form more or less stable complex structures. The characterization of RNA-protein complex structures and binding interfaces by nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography, or strategies based on chemical crosslinking, however, can be quite challenging. Herein, we have explored the use of an alternative method, native top-down mass spectrometry (MS), for probing of complex stoichiometry and protein binding sites at the single-residue level of RNA...
December 21, 2016: Angewandte Chemie
Akira Mizuno, Tomoshi Kameda, Tomoki Kuwahara, Hideyuki Endoh, Yoshihiko Ito, Shizuo Yamada, Kimiko Hasegawa, Akihito Yamano, Mizuki Watanabe, Mitsuhiro Arisawa, Satoshi Shuto
Detailed conformational analyses of our previously reported cyclopropane-based peptidomimetics and conformational analysis-driven ligand optimization are described. Computational calculations and X-ray crystallography showed that the characteristic features of cyclopropane function effectively to constrain the molecular conformation in a three-dimensionally diverse manner. Subsequent principal component analysis revealed that the diversity covers the broad chemical space filled by peptide secondary structures in terms of both main-chain and side-chain conformations...
December 21, 2016: Chemistry: a European Journal
Hongwei Liu, Xuan Cheng, Nagarajan Valanoor
Heteroepitaxial nanocrystals are one of the most fundamentally and technologically important classes of materials systems. The correlation between form, dictated by crystallographic features such as growth habit and direction, and function, in terms of the ultimate physio-chemical properties is well established, thus placing an onus on precise synthesis control of nanocrystal morphology. Yet, nanocrystal heteroepitaxy can be a frustrating, time-consuming iterative process, particularly during the initial stages of development...
December 21, 2016: ACS Applied Materials & Interfaces
Michio Yamada, Yukiko Tanabe, Jing-Shuang Dang, Satoru Sato, Naomi Mizorogi, Makoto Hachiya, Mitsuaki Suzuki, Tsuneyuki Abe, Hiroki Kurihara, Yutaka Maeda, Xiang Zhao, Yongfu Lian, Shigeru Nagase, Takeshi Akasaka
We compared the chemical reactivity of D2d(23)-C84 and that of Sc2C2@D2d(23)-C84, both having the same carbon cage geometry, in the photolysis of 2-adamantane-2,3'-[3H]-diazirine, to clarify metal-atom doping effects on the chemical reactivity of the carbon cage. Experimental and computational studies have revealed that the chemical reactivity of the D2d(23)-C84 carbon cage is altered drastically by endohedral Sc2C2 doping. The reaction of empty D2d(23)-C84 with the diazirine under photoirradiation yields two adamantylidene (Ad) adducts...
December 21, 2016: Journal of the American Chemical Society
Juan D Chavez, Jimmy K Eng, Devin K Schweppe, Michelle Cilia, Keith Rivera, Xuefei Zhong, Xia Wu, Terrence Allen, Moshe Khurgel, Akhilesh Kumar, Athanasios Lampropoulos, Mårten Larsson, Shuvadeep Maity, Yaroslav Morozov, Wimal Pathmasiri, Mathew Perez-Neut, Coriness Pineyro-Ruiz, Elizabeth Polina, Stephanie Post, Mark Rider, Dorota Tokmina-Roszyk, Katherine Tyson, Debora Vieira Parrine Sant'Ana, James E Bruce
Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes...
2016: PloS One
María M Quesada-Moreno, Juan Ramón Avilés-Moreno, Juan Jesús López-González, Kane Jacob, Laure Vendier, Michel Etienne, Ibon Alkorta, José Elguero, Rosa M Claramunt
1H-Indazole derivatives exhibit a remarkable property since some of them form chiral supramolecular structures starting from achiral monomers. The present work deals with the study of three perfluorinated 1H-indazoles that resolve spontaneously as conglomerates. These conglomerates can contain either a pure enantiomer (one helix) or a mixture of both enantiomers (both helices) with an enantiomeric excess (e.e.) of one of them. The difficulty of the structural analysis of these types of compounds is thus clear...
January 4, 2017: Physical Chemistry Chemical Physics: PCCP
Marija Petricevic, Lukasz F Sobala, Pearl Z Fernandes, Lluís Raich, Andrew J Thompson, Ganeko Bernardo-Seisdedos, Oscar Millet, Sha Zhu, Matthieu Sollogoub, Jesús Jiménez-Barbero, Carme Rovira, Gideon J Davies, Spencer J Williams
Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools, and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases, members of glycoside hydrolase family 99 (GH99), are interesting targets for inhibitor development as they play key roles in N-glycan maturation and microbiotal yeast mannan degradation, respectively...
January 17, 2017: Journal of the American Chemical Society
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