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Organic & Biomolecular Chemistry

Brittany A Riggle, Mara L Greenberg, Yanfei Wang, Rebecca F Wissner, Serge D Zemerov, E James Petersson, Ivan J Dmochowski
We present the first cryptophane-based "turn-on" (129)Xe NMR biosensor, employing a peptide-functionalized cryptophane to monitor the activation of calmodulin (CaM) protein in solution. In the absence of CaM binding, interaction between the peptide and cryptophane completely suppresses the hyperpolarized (129)Xe-cryptophane NMR signal. Biosensor binding to Ca(2+)-activated CaM produces the expected (129)Xe-cryptophane NMR signal.
October 23, 2017: Organic & Biomolecular Chemistry
Miguel Macias-Contreras, Kirsten L Daykin, J Tyler Simmons, John R Allen, Zachary S Hooper, Michael W Davidson, Lei Zhu
Photoinduced electron transfer (PeT)-type fluorescent molecular switches are often applied in ion-selective sensors. Zinc-targeting sensors that contain an anilino-based electron donor (aka, the PeT 'switch') have multiple advantages over those with an aliphatic amino switch. In addition to the lower pKa value of an aniline than that of a comparably substituted aliphatic amine, which reduces the interference of pH on the spectral properties of the attached fluorophore, the oxidation potentials of anilino groups are lower than those of aliphatic amino counterparts, which make them better electron donors in PeT...
October 20, 2017: Organic & Biomolecular Chemistry
S B Yeldell, B K Ruble, I J Dmochowski
Single cell transcriptomics provides a powerful discovery tool for identifying new cell types and functions as well as a means to probe molecular features of the etiology and treatment of human diseases, including cancer. However, such analyses are limited by the difficulty of isolating mRNA from single cells within biological samples. We recently introduced a photochemical method for isolating mRNA from single living cells, Transcriptome In Vivo Analysis (TIVA). The TIVA probe is a "caged" polyU : polyA oligonucleotide hairpin designed to enter live tissue, where site-specific activation with 405 nm laser reveals the polyU-biotin strand to bind mRNA in a target cell, enabling subsequent mRNA isolation and sequencing...
October 20, 2017: Organic & Biomolecular Chemistry
Javier Ramos-Soriano, M Carmen de la Fuente, Noelia de la Cruz, Rute C Figueiredo, Javier Rojo, José J Reina
The high-mannose oligosaccharide (or its corresponding Man9 epitope) is the most abundant structure present in pathogen envelope glycoproteins. These glycans play a key role in the pathogenesis of several pathogens and also in the communication with the immune system. Understanding the mechanism of action of these glycans requires the access to pure and chemically well-defined structures in reasonable amounts. The synthesis of these complex branched oligosaccharides is not trivial and few syntheses are reported in the literature with several synthetic and purification steps and low overall yields...
October 20, 2017: Organic & Biomolecular Chemistry
Lihan Zhu, Haiyan Yuan, Jingping Zhang
A comprehensive density functional theory investigation was employed to disclose the effect of reaction conditions on the mechanism and effective anion relay sequence of a NaH promoted non-Brook rearrangement of benzaldehyde and 1-cinnamoylcyclopropanecarboxamides. Two main mechanisms were explored under four different reaction conditions: Na(+)-assisted and nH2O-Na(+), 2H2O-DMSO-Na(+), and Na(+)-DMSO co-assisted, and the difference relies on the reaction sequence between the concerted ring-opening and recyclization and electrophilic addition...
October 20, 2017: Organic & Biomolecular Chemistry
S Mirabella, G Fibbi, C Matassini, C Faggi, A Goti, F Cardona
A dual synthetic strategy to afford 2-substituted trihydroxypiperidines is disclosed. The procedure involved Grignard addition either to a carbohydrate-derived aldehyde or to a nitrone derived thereof, and took advantage of an efficient ring-closure reductive amination strategy in the final cyclization step. An opposite diastereofacial preference was demonstrated in the nucleophilic attack to the two electrophiles, which would finally produce the same piperidine diastereoisomer as the major product. However, use of a suitable Lewis acid in the Grignard addition to the nitrone allowed reversing the selectivity, giving access to 2-substituted piperidines with the opposite configuration at C-2...
October 20, 2017: Organic & Biomolecular Chemistry
Nicolai Krogh, Martin Kongsbak-Wismann, Carsten Geisler, Henrik Nielsen
Sequencing-based profiling of ribose methylations is a new approach that allows for experiments addressing dynamic changes on a large scale. Here, we apply such a method to spliceosomal snRNAs present in human whole cell RNA. Analysis of solid tissue samples confirmed all previously known sites and demonstrated close to full methylation at almost all sites. Methylation changes were revealed in biological experimental settings, using T cell activation as an example, and in the T cell leukemia model, Jurkat cells...
October 19, 2017: Organic & Biomolecular Chemistry
Jyoti Chauhan, Tania Luthra, Rambabu Gundla, Antonio Ferraro, Ulrike Holzgrabe, Subhabrata Sen
Natural products are the source of innumerable pharmaceutical drug candidates and also form an important aspect of herbal remedies. They are also a source of various bioactive compounds. Herein we have leveraged the structural attributes of several natural products in building a library of architecturally diverse chiral molecules by harnessing R-tryptophan as the chiral auxiliary. It is converted to its corresponding methyl ester 1 which in turn provided a bevy of 1-aryl-tetrahydro-β-carbolines 2a-d, which were then converted to chiral compounds via a diversity oriented synthetic strategy (DOS)...
October 19, 2017: Organic & Biomolecular Chemistry
Sanjiv O Tomer, Hemant P Soni
We have experimentally demonstrated that by 'locking' the molecular conformation through the introduction of a double or triple bond in the center of a symmetric diol, enzymatic monoesterification can be achieved selectively. The enzyme Candida antarctica lipase B, generally used for the transesterification of diols, can be effectively used for the monoesterification of symmetrical diols in an unbuffered system also. By varying the chain length of a carboxylic acid moiety, we have established that optimum selectivity and efficiency can be achieved in the range of 4...
October 18, 2017: Organic & Biomolecular Chemistry
Rubén Ruiz-González, Francesca Setaro, Òscar Gulías, Montserrat Agut, Uwe Hahn, Tomás Torres, Santi Nonell
In the present study we describe the synthesis, photophysical properties and the photoinactivation performance against representative microorganisms of two families of cationic dendrimeric phthalocyanines as potential photosensitisers. Four charged dendrimeric compounds varying in their degree of ionicity (4 or 8 positive charges) and the coordinating metal (zinc or ruthenium) are compared and assessed as potential photosensitising agents in terms of their antimicrobial activity.
October 18, 2017: Organic & Biomolecular Chemistry
Li Zhang, Yewen Fang, Xiaoping Jin, Housan Xu, Ruifeng Li, Hao Wu, Bin Chen, Yiming Zhu, Yi Yang, Zongming Tian
A general and robust protocol for the synthesis of terminal α-substituted vinylphosphonates via Suzuki coupling of α-bromovinylphosphonates with organotrifluoroborates has been successfully developed. This method features a broad substrate scope, great functional group compatibilities, and easy scale-up ability. In addition to easy access of nucleophiles, a straightforward synthesis of electrophiles was also realized with diethyl α-bromoethenylphosphonate as the starting material. With a combination of Pd2(dba)3/SPhos as the catalyst, a range of α-alkyl, aryl, heteroaryl, and alkynyl substituted ethenylphosphonates could be nicely accessed under mild conditions...
October 18, 2017: Organic & Biomolecular Chemistry
K Ermanis, K E B Parkes, T Agback, J M Goodman
A large-scale optimisation of density functional theory (DFT) conditions for computational NMR structure elucidation has been conducted by systematically screening the DFT functionals and statistical models. The extended PyDP4 workflow was tested on a diverse and challenging set of 42 biologically active and stereochemically rich compounds, including highly flexible molecules. MMFF/mPW1PW91/M06-2X in combination with a 2 Gaussian, 1 region statistical model was capable of identifying the correct diastereomer among up to an upper limit of 32 potential diastereomers...
October 18, 2017: Organic & Biomolecular Chemistry
Zhigang Wu, Yunpeng Liu, Lei Li, Xiu-Feng Wan, He Zhu, Yuxi Guo, Mohui Wei, Wanyi Guan, Peng George Wang
N-Glycans are normally involved in crucial physiological and disease processes by interactions with glycan-binding proteins. So far structurally defined N-glycans have been good candidates for glycan binding study. Herein, a class of homogeneous asymmetric N-glycans was synthesized by coupling glycan-oxazoline and N-glycans using EndoM N175Q catalyzed quick glycan extension. Branch-biased binding and spacial inhibition caused by the bulky group on the other branch of N-glycan were observed in glycan protein interactions involving lectins and these glycans by glycan microarray study...
October 18, 2017: Organic & Biomolecular Chemistry
Krishanthi P Jayasundera, Tim G W Engels, David J Lun, Maulik N Mungalpara, Paul G Plieger, Gareth J Rowlands
The synthesis of three planar chiral pseudo-gem disubstituted [2.2]paracyclophane-derived P,N-pre-ligands is reported along with preliminary results of their activity in the amination of aryl bromides and chlorides. The pseudo-gem aminophosphines were capable of mediating the coupling reaction at a loading of 1 mol%.
October 18, 2017: Organic & Biomolecular Chemistry
Przemysław Krawczyk, Beata Jędrzejewska, Piotr Cysewski, Tomasz Janek
In this study, a new oxazolone derivative 4-{N,N-bis[2-phenyl-4-benzylidene-1,3-oxazol-5(4H)-one]amino}benzaldehyde (PB3) was synthesized and investigated as a fluorescent dye. The spectroscopic properties in different solvents were thoroughly studied. The experimental data were supported by quantum-chemical calculations using density functional theory. Measurements and theoretical calculations showed that the PB3 dye is characterized by non-monotonic solvatochromism, a strongly polar charge transfer excited state, a large Stokes' shift, a high fluorescence quantum yield and a high fluorescence lifetime...
October 18, 2017: Organic & Biomolecular Chemistry
Steven Moerkerke, Volodymyr Malytskyi, Lionel Marcélis, Johan Wouters, Ivan Jabin
Artificial receptors able to recognize efficiently chemical species bearing a quaternary ammonium group have potential applications in the fields of biological and environmental analyses. A possible biomimetic strategy for the elaboration of such receptors consists of associating in close proximity a polyaromatic cavity with a polar binding site. Herein, we show that bis-calix[6]arene 1 behaves as a heteroditopic receptor that can bind biologically relevant quaternary ammonium ions and zwitterions. This host can selectively extract carbamylcholine G3 from water, opening the way for the sensing of this acetylcholine agonist...
October 18, 2017: Organic & Biomolecular Chemistry
O Ries, P M G Löffler, A Rabe, J J Malavan, Stefan Vogel
The fusion of biomembranes with release of encapsulated content in a controlled way is crucial for cell signaling, endo- and exocytosis and intracellular trafficking. Programmable fusion of liposomes and an efficient mixing of their contents have the potential to enable the study of chemical and enzymatic processes in a confined environment and under crowded conditions outside biological systems. We report on DNA-controlled fusion of lipid bilayer membranes using lipid-nucleic acid conjugates (LiNAs) to mediate lipid and content mixing of liposomes...
October 18, 2017: Organic & Biomolecular Chemistry
Yuki Osumi, Chengwei Liu, Michal Szostak
The palladium-catalyzed Suzuki-Miyaura cross-coupling of N-acylsuccinimides as versatile acyl-transfer reagents via selective amide N-C bond cleavage is reported. The method is user-friendly since it employs commercially-available, air-stable reagents and catalysts. The cross-coupling is enabled by half-twist of the amide bond in N-acylsuccinimides. These highly effective, crystalline acyl-transfer reagents present major advantages over perpendicularly twisted N-acylglutarimides, including low price of the succinimide activating ring, selective metal insertion under redox neutral conditions and high stability of the amide bond towards reaction conditions...
October 17, 2017: Organic & Biomolecular Chemistry
Chihiro Maeda, Takumi Todaka, Tomomi Ueda, Tadashi Ema
Carbazole-based BODIPY dimers 2a-g were synthesized via direct arylation. They showed red-shifted solid-state fluorescence spectra as compared with the corresponding monomer. In addition, unsymmetrical dimers 2d, 2f, and 2g with two different substituents showed red fluorescence with improved quantum yields in the solid state.
October 17, 2017: Organic & Biomolecular Chemistry
Emil Lindbäck, Óscar Lopéz, Ådne Tobiesen, José G Fernández-Bolaños, Magne O Sydnes
The preparation of a novel type of iminosugar including a hydrazide imide moiety is described. The sugar hydrazide imides (3S,4S,5R,6R)-1-amino-3,4,5-trihydroxy-6-(hydroxymethyl)-2-iminopiperidine acetate and (3S,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)-2-imino-1-(methylamino)piperidine acetate presented here behave as inhibitors of α/β-glucosidases in the low micromolar concentration range. The former inhibitor displays a pH-dependent inhibition of β-glucosidase. The N-methylated counterpart behaves as an anomer-selective competitive micromolar inhibitor of α-glucosidase...
October 17, 2017: Organic & Biomolecular Chemistry
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