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Chemical crystallography

Yilei Wu, Ji-Min Han, Michael Hong, Matthew D Krzyaniak, Anthea K Blackburn, Isurika R Fernando, Dennis D Cao, Michael R Wasielewski, J Fraser Stoddart
The synthesis of stable organic polyradicals is important for the development of magnetic materials. Herein, we report the synthesis, isolation, and characterization of a series of X-shaped pyromellitimide (PI) oligomers (Xn-R, n = 2-4, R = Hex or Ph) linked together by single C-C bonds between their benzenoid cores. We hypothesize that these oligomers might form high-spin states in their reduced forms because of the nearly orthogonal conformations adopted by their PI units. 1H and 13C nuclear magnetic resonance (NMR) spectroscopies confirmed the isolation of the dimeric, trimeric, and tetrameric homologues...
December 7, 2017: Journal of the American Chemical Society
Manuela Crisan, Liliana Halip, Paulina Bourosh, Sergiu Adrian Chicu, Yurii Chumakov
BACKGROUND: Nitroaromatic and chloronitroaromatic compounds have been a subject of great interest in industry and recently in medical-pharmaceutic field. 2-Chloro-4-nitro/2-chloro-5-nitrobenzoic acids and 4-nitrobenzoic acid are promising new agents for the treatment of main infectious killing diseases in the world: immunodeficiency diseases and tuberculosis. RESULTS: New ethanolamine nitro/chloronitrobenzoates were synthesized and characterized by X-ray crystallography, UV-vis, FT-IR and elementary analysis techniques...
December 6, 2017: Chemistry Central Journal
Irina Prokhorova, Roger B Altman, Muminjon Djumagulov, Jaya P Shrestha, Alexandre Urzhumtsev, Angelica Ferguson, Cheng-Wei Tom Chang, Marat Yusupov, Scott C Blanchard, Gulnara Yusupova
Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukaryotic translation remain largely unexplored...
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
Miki Senda, Toshiya Senda
Crystallization has been a bottleneck in the X-ray crystallography of proteins. Although many techniques have been developed to overcome this obstacle, the impurities caused by chemical reactions during crystallization have not been sufficiently considered. Oxidation of proteins, which can lead to poor reproducibility of the crystallization, is a prominent example. Protein oxidization in the crystallization droplet causes inter-molecular disulfide bridge formation, formation of oxidation film, and precipitation of proteins...
December 2, 2017: Biophysical Reviews
Andrew Proudfoot, Dirksen E Bussiere, Andreas Lingel
Structure-based drug design is an integral part of modern day drug discovery and requires detailed structural characterization of protein-ligand interactions, which is most commonly performed by X-ray crystallography. However, the success rate of generating these costructures is often variable, in particular when working with dynamic proteins or weakly binding ligands. As a result, structural information is not routinely obtained in these scenarios, and ligand optimization is challenging or not pursued at all, representing a substantial limitation in chemical scaffolds and diversity...
November 30, 2017: Journal of the American Chemical Society
Chenzhou Hao, Fan Zhao, Hong Yan Song, Jing Guo, Xiaodong Li, Xiaolin Jiang, Ran Huan, Shuai Song, Qiaoling Zhang, Ruifeng Wang, Kai Wang, Yu Pang, Tongchao Liu, Tianqi Lu, Wanxu Huang, Jian Wang, Bin Lin, Zhonggui He, Haitao Li, Feng Li, Dongmei Zhao, Maosheng Cheng
Herein, we report the discovery and characterization of a novel class of PAK4 inhibitors with a quinazoline scaffold. Based on the shape and chemical composition of the ATP-binding pocket of PAKs, we chose a 2, 4-diaminoquinazoline series of inhibitors as a starting point. Guided by X-ray crystallography and a structure-based drug design (SBDD) approach, a series of novel 4-aminoquinazoline-2-carboxamide PAK4 inhibitors were designed and synthesized. The inhibitors' selectivity, therapeutic potency, and pharmaceutical properties were optimized...
November 30, 2017: Journal of Medicinal Chemistry
Li-Cheng Song, Liang Zhu, Fu-Qiang Hu, Yong-Xiang Wang
On the basis of preparation and characterization of [Fe]-H2ase models (2-COCH2-6-HOCH2C5H3N)Fe(CO)2L (A, L = η1-SCOMe; B, L = η1-2-SC5H4N), the chemical reactivities of A and B with various electrophilic and nucleophilic reagents have been investigated, systematically. Thus, when A reacted with 1 equiv of MeCOCl in the presence of Et3N in MeCN to give the η2-SCOMe-coordinated acylation product (2-COCH2-6-MeCO2CH2C5H3N)Fe(CO)2(η2-SCOMe) (1), treatment of A with excess HBF4·Et2O in MeCN gave the cationic MeCN-coordinated complex [(2-COCH2-6-HOCH2C5H3N)Fe(CO)2(MeCN)](BF4) (2)...
November 30, 2017: Inorganic Chemistry
Zhen-Peng Mai, Gang Ni, Yan-Fei Liu, Yu-Huan Li, Li Li, Jia-Yuan Li, De-Quan Yu
Secoheliosphanes A (1) and B (2) and secoheliospholane A (3), possessing an unusual 7,8-seco-jatrophane skeleton and an unprecedented 9,10-seco-7,10-epoxyjatropholane skeleton, respectively, were isolated from the whole plants of Euphorbia helioscopia, along with two biogenetically precursors, a new jatrophane diterpene, 2-epi-euphornin I (4) and a known jatrophane diterpene, euphoscopin A (5). Structures of 1-4 including absolute configurations were elucidated on the basis of spectroscopic data, X-ray crystallography, and chemical conversion...
November 30, 2017: Journal of Organic Chemistry
Jason B Cross
Virtual screening (VS) has become an integral part of the drug discovery process and is a valuable tool for finding novel chemical starting points for GPCR targets. Ligand-based VS makes use of biochemical data for known, active compounds and has been applied successfully to many diverse GPCRs. Recent progress in GPCR X-ray crystallography has made it possible to incorporate detailed structural information into the VS process. This chapter outlines the latest VS techniques along with examples that highlight successful applications of these methods...
2018: Methods in Molecular Biology
Antonella Ciancetta, Kenneth A Jacobson
Recent crystallographic structures of G protein-coupled receptors (GPCRs) have greatly advanced our understanding of the recognition of their diverse agonist and antagonist ligands. We illustrate here how this applies to A2A adenosine receptors (ARs) and to P2Y1 and P2Y12 receptors (P2YRs) for ADP. These X-ray structures have impacted the medicinal chemistry aimed at discovering new ligands for these two receptor families, including receptors that have not yet been crystallized but are closely related to the known structures...
2018: Methods in Molecular Biology
Nathan Sloat, Jui-Wen Liu, Susan J Schroeder
BACKGROUND: The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible non-pseudoknotted RNA structures for RNA sequences. The Swellix program builds on the Crumple program and can include experimental constraints on global RNA structures such as the minimum number and lengths of helices from crystallography, cryoelectron microscopy, or in vivo crosslinking and chemical probing methods...
November 21, 2017: BMC Bioinformatics
Wolfgang Peti, Rebecca Page, Evzen Boura, Bartosz Różycki
The integration of complementary molecular methods (including X-ray crystallography, NMR spectroscopy, small angle X-ray/neutron scattering, and computational techniques) is frequently required to obtain a comprehensive understanding of dynamic macromolecular complexes. In particular, these techniques are critical for studying intrinsically disordered protein regions (IDRs) or intrinsically disordered proteins (IDPs) that are part of large protein:protein complexes. Here, we explain how to prepare IDP samples suitable for study using NMR spectroscopy, and describe a novel SAXS modeling method (ensemble refinement of SAXS; EROS) that integrates the results from complementary methods, including crystal structures and NMR chemical shift perturbations, among others, to accurately model SAXS data and describe ensemble structures of dynamic macromolecular complexes...
2018: Methods in Molecular Biology
Marie-Louise Lemloh, Andreas Verch, Ingrid M Weiss
A ball-milling approach was developed to investigate the constituents of isolated nacre tablets of the gastropod Haliotis glabra in aqueous suspension without additional chemical additives. The obtained particle mixtures were characterized using X-ray crystallography as well as scanning and transmission electron microscopy. Aragonite nanoparticles retained their crystal structure even after 14 h of ball milling. The long-term stability of the particle mixtures varied as a function of the ball-milling duration...
November 2017: Journal of the Royal Society, Interface
Benjamin Cressiot, Sandra J Greive, Wei Si, Tomas C Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw T Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A Antson, Meni Wanunu
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein...
November 15, 2017: ACS Nano
Kevin Burgess, Cory Widdifield, Yang Xu, Cesar Leroy, David L Bryce
A series of fumarate-based organocobalt(I) [CpCo(CO)(fumarate)] catalysts are synthesized and characterized by X-ray crystallography, multinuclear (13C and 59Co) solid-state NMR spectroscopy, and 59Co NQR spectroscopy. Given the dearth of 59Co solid-state NMR studies on Co(I) compounds, the present work constitutes the first systematic characterization of the 59Co electric field gradient and chemical shift tensors for a series of cobalt complexes in this oxidation state. While by X-ray crystallography, the molecular geometry about the Co(I) centre is nearly identical in all compounds studied herein, it is shown that, owing to the 59Co nucleus' large chemical shift range, solid-state NMR experiments can detect small structural differences between the individual organocobalt(I) compounds...
November 9, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Tomas Majtan, Angel L Pey, Paula Gimenez-Mascarell, Luis Alfonso Martínez-Cruz, Csaba Szabo, Viktor Kožich, Jan P Kraus
Classical homocystinuria (HCU) is the most common loss-of-function inborn error of sulfur amino acid metabolism. HCU is caused by a deficiency in enzymatic degradation of homocysteine, a toxic intermediate of methionine transformation to cysteine, chiefly due to missense mutations in the cystathionine beta-synthase (CBS) gene. As with many other inherited disorders, the pathogenic mutations do not target key catalytic residues, but rather introduce structural perturbations leading to an enhanced tendency of the mutant CBS to misfold and either to form nonfunctional aggregates or to undergo proteasome-dependent degradation...
November 10, 2017: Handbook of Experimental Pharmacology
Amanda J Price, Steven Howard, Benjamin D Cons
Fragment-based drug discovery (FBDD) is a technique for identifying low molecular weight chemical starting points for drug discovery. Since its inception 20 years ago, FBDD has grown in popularity to the point where it is now an established technique in industry and academia. The approach involves the biophysical screening of proteins against collections of low molecular weight compounds (fragments). Although fragments bind to proteins with relatively low affinity, they form efficient, high quality binding interactions with the protein architecture as they have to overcome a significant entropy barrier to bind...
November 8, 2017: Essays in Biochemistry
Rob L M van Montfort, Paul Workman
Knowledge of the three-dimensional structure of therapeutically relevant targets has informed drug discovery since the first protein structures were determined using X-ray crystallography in the 1950s and 1960s. In this editorial we provide a brief overview of the powerful impact of structure-based drug design (SBDD), which has its roots in computational and structural biology, with major contributions from both academia and industry. We describe advances in the application of SBDD for integral membrane protein targets that have traditionally proved very challenging...
November 8, 2017: Essays in Biochemistry
Anuj K Sharma, Jason W Schultz, John T Prior, Nigam P Rath, Liviu M Mirica
Positron emission tomography (PET) is emerging as one of the most important diagnostic tools for brain imaging, yet the most commonly used radioisotopes in PET imaging, (11)C and (18)F, have short half-lives, and their usage is thus somewhat limited. By comparison, the (64)Cu radionuclide has a half-life of 12.7 h, which is ideal for administering and imaging purposes. In spite of appreciable research efforts, high-affinity copper chelators suitable for brain imaging applications are still lacking. Herein, we present the synthesis and characterization of a series of bifunctional compounds (BFCs) based on macrocyclic 1,4,7-triazacyclononane and 2,11-diaza[3...
November 7, 2017: Inorganic Chemistry
Ramya Billur, David Ban, T Michael Sabo, Muriel Christine Maurer
Thrombin participates in procoagulation, anticoagulation, and platelet activation. This enzyme contains anion binding exosites, ABE I and ABE II, which attract regulatory biomolecules. As prothrombin is activated to thrombin, pro-ABE I is converted into mature ABE I. Unexpectedly, certain ligands can bind to pro-ABE I specifically. Moreover, knowledge is lacking on changes in conformation and affinity that occur at the individual residue level as pro-ABE I is converted to ABE I. Such changes are transient and failed to be captured by crystallography...
November 7, 2017: Biochemistry
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