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Chembiochem: a European Journal of Chemical Biology

Chao Wang, Xinbo Song, Yi Xiao
Genetically encoded technologies provide methods for specific labeling and imaging of proteins, which is essential for the understanding of their subcellular localization and function. Herein, we employ naphthalimide, an efficient two-photon fluorophore, to develop O6-benzylguanine (BG) derivatives for specific labeling of subcellular proteins and fluorescent imaging through the SNAP-tag. The three naphthalimide-BG derivatives, TNI-BG, QNI-BG and ONI-BG are conveniently synthesized through modular "click chemistry" with high yields...
June 20, 2017: Chembiochem: a European Journal of Chemical Biology
Emeline Richard, C Pifferi, M Fiore, Eric Samain, Audrey Le Gouellec, Sébastien Fort, Olivier Renaudet, Bernard Priem
A conjugatable form of the tumour-associated carbohydrate antigen sialyl-Tn (Neu5Ac-alfa-2,6-GalNAc) was efficiently produced in Escherichia coli. Metabolically engineered E. coli strains overexpressing the 6-sialyl-transferase gene of Photobacterium sp. and CMP-Neu5Ac synthetase genes of Neisseria meningitidis were cultivated at high density in presence of GalNAc-alfa-propargyl as the exogeneous acceptor. The target disaccharides, which were produced on the scale of several hundred milligrams, were then conjugated using CuAAC click chemistry to a fully synthetic and immunogenic scaffold with the aim to create a candidate anticancer vaccine...
June 20, 2017: Chembiochem: a European Journal of Chemical Biology
Gabriella Perell, Rachel Staebell, Mehrdad Hairani, Alessandro Cembran, William Charles Krause Pomerantz
Thioethers, sulfoxides, and sulfonium ions, despite diverse physicochemical properties, all engage in non-covalent interactions with proteins. Thioether-containing macrocycles are also attracting attention as protein-protein interaction (PPI) inhibitors. Here we use a model PPI between -helical MLL and KIX to evaluate oxidation effects on sulfur-containing macrocycle structure, stability, and protein affinity. Desolvation effects from varied polarity states were evaluated computationally and experimentally at the side chain, amino acid and peptide level...
June 19, 2017: Chembiochem: a European Journal of Chemical Biology
Yu Sherry Jiang, Apollo Stacy, Marvin Whiteley, Andrew D Ellington, Sanchita Bhadra
It is inherently difficult to quantitate nucleic acid analytes with most isothermal amplification assays. We have now developed loop-mediated isothermal amplification (LAMP) reactions in which competition between defined numbers of 'false' and 'true' amplicons leads to order of magnitude quantitation via a single end-point determination. These thresholded LAMP reactions were successfully used to directly and quantitatively estimate the numbers of nucleic acids in complex biospecimens, including directly from cells and in sewage, with the values obtained closely correlating with qPCR quantitations...
June 19, 2017: Chembiochem: a European Journal of Chemical Biology
Martin J Ross, Insiya Fidai, James Allan Cowan
New therapeutics for the targeting of the hepatitis C virus have been released in recent years. Although these therapies are less prone to resistance, they are still administered in cocktails as a combination of drugs targeting various aspects of the viral life cycle. Herein, we aim to contribute to an arsenal of new HCV therapeutics by targeting HCV internal ribosomal entry sequence (IRES) RNA via development of catalytic metallodrugs that function to degrade rather than inhibit the target molecule. Based on a previously characterized HCV IRES stem-loop IIb RNA-targeting metallopeptide Cu-GGHYrFK (1-Cu), an all L-analogue (3-Cu) and a series of additional complexes with single alanine substitutions in the targeting domain were prepared and screened to determine the influence each amino acid side-chain on RNA localization and recognition, and catalytic reactivity toward the RNA...
June 19, 2017: Chembiochem: a European Journal of Chemical Biology
Maciej A Walczak, Feng Zhu
Chemical synthesis of oligosaccharides has reached the stage where access to highly complex structures is becoming a reality. The recent synthesis of a 92-mer oligosaccharide is a record-breaking achievement of preparative carbohydrate chemistry and creates opportunities to study complex biological phenomena with atomic precision not previously available.
June 19, 2017: Chembiochem: a European Journal of Chemical Biology
Stephan Hinderlich, Rudolf Tauber, Carolyn R Bertozzi, Christian P R Hackenberger
A creative pioneer: Werner Reutter (1937-2016) was a scientist who both made fundamental discoveries in glycobiology and reached out to disciplines beyond his core field. Many of his former colleagues and students will remember his desire to exchange research ideas, which ultimately contributed to the birth of new research fields.
June 16, 2017: Chembiochem: a European Journal of Chemical Biology
Zhan-Yi Sun, Pu-Guang Chen, Yan-Fang Liu, Lei Shi, Bo-Dou Zhang, Jun-Jun Wu, Yu-Fen Zhao, Yong-Xiang Chen, Yan-Mei Li
Immunotherapy has become one of the most promising therapies for the treatment of diseases. Chemical molecule immunostimulants and nanomaterial immunostimulant systems are indispensable for the activation of the immune system in cancer immunotherapy. Here we report a strategy of self-assembled nano-immunostimulant (SANI) for synergistic immune activation. Three immunostimulants self-assembled into nanoparticles through electrostatic interactions. SANI showed strong synergistic immunostimulation in macrophages...
June 15, 2017: Chembiochem: a European Journal of Chemical Biology
Maria Taskova, Anna Mantsiou, Kira Astakhova
The main objective of this work is an update on synthetic nucleic acid analogues and nano-assemblies as tools in gene therapy. In particular, we describe in detail the synthesis and properties of peptide-oligonucleotide conjugates, POCs, which according to us and others have high potential in research and as therapeutics. The exploration of POCs has already led to fruitful results in the treatment of neurological diseases, lung disorders, cancer, leukemia, viral and bacterial infections. However, delivery and in vivo stability are the major barriers to the clinical application of POCs and other analogues that still have to be overcome...
June 14, 2017: Chembiochem: a European Journal of Chemical Biology
Ji Luo, Jessica Torres-Kolbus, Jihe Liu, Alexander Deiters
We genetically encoded three new caged tyrosine analogues with improved photochemical properties by using an engineered pyrrolysyl-tRNA synthetase/tRNACUA pair in bacterial and mammalian cells. We applied the new tyrosine analogues to the photoregulation of firefly luciferase by caging its key tyrosine residue, Tyr340, and observed excellent off-to-on light switching. This reporter was then used to evaluate the activation rates of the different light-removable protecting groups in live cells. We identified the nitropiperonyl caging group as an excellent compromise between incorporation efficiency and photoactivation properties...
June 13, 2017: Chembiochem: a European Journal of Chemical Biology
Matthias Knop, Roxana Lemnaru, Florian P Seebeck
The formylglycine-generating enzyme (FGE) recognizes proteins with a specific cysteine containing six amino-acid motif and converts this cysteine to formylglycine. The resulting aldehyde function provides a unique handle for selective protein labeling. We have identified two mutations in FGE from Thermomonospora curvata that increase this catalytic efficiency by more than 40-fold. The resulting activity, the stability and ease of recombinant production make this FGE variant a practical reagent for in vitro protein engineering...
June 12, 2017: Chembiochem: a European Journal of Chemical Biology
Katharina Veith, Maria Martinez Molledo, Yasser Almeida Hernandez, Inokentijs Josts, Julius Nitsche, Christian Löw, Henning Tidow
A crucial bottleneck in membrane protein structural biology is the difficulty in identifying a detergent that can maintain the stability and functionality of integral membrane proteins (IMPs). Detergents are poor membrane mimics and their common use in membrane protein crystallography may be one reason for the challenges in obtaining high-resolution crystal structures of many IMP families. Lipid-like peptides (LLPs) have detergent-like properties and have been proposed as alternatives for the solubilization of GPCRs and other membrane proteins...
June 11, 2017: Chembiochem: a European Journal of Chemical Biology
Shahriar Mobashery, Mijoon Lee, Dusan Hesek, Elena Lastochkin, Bill Boggess, David A Dik
The major constituent of bacterial cell wall is peptidoglycan, which in its crosslinked form is a polymer of considerable complexity that encases the entire bacterium. A functional cell wall is indispensable for the survival of the organism. There are several dozens of enzymes that assemble and disassemble the peptidoglycan dynamically within each bacterial generation. Understanding of the nature of these transformations is critical knowledge on these events. Octasaccharide peptidoglycans were prepared and studied with seven recombinant cell-wall-active enzymes (SltB1, MltB, RlpA, mutanolysin, AmpDh2, AmpDh3 and PBP5)...
June 7, 2017: Chembiochem: a European Journal of Chemical Biology
Chris Meier, Katharina Pahnke
The design of a bioreversible protected, lipophilic sugar nucleotide as a potential membrane-permeable precursor of adenosine diphosphate ribose (ADPR) is described. ADPR is the most potent activator of the TRPM2 ion channel. Membrane permeable, lipophilic derivatives of ADPR are of great interest as tools to study the mechanism of TRPM2. The approach described herein was based on our recently disclosed 'DiPPro' and 'TriPPPro'-prodrug approaches developed for the intracellular delivery of nucleotides. A lipophilic, bioreversible masked ADPR-analog was prepared in high yields containing an enzymatically cleavable 4-pentanoyloxybenzyl (PB)-mask at the phosphate moiety next to the 5'-position of adenosine as well as O-acetyl groups...
June 6, 2017: Chembiochem: a European Journal of Chemical Biology
Bohao Cheng, Hiromu Kashida, Naohiko Shimada, Atsushi Maruyama, Hiroyuki Asanuma
We report a photo-driven DNA strand displacement by using 2', 6'-dimethylazobenzene-tethered strand and poly(L-lysine)-graft-dextran (PLL-g-Dex) as a chaperone. Rapid strand displacement was reversibly induced by UV and visible light irradiation without any toehold portion. To further improve the method, we also optimized the concentration of PLL-g-Dex and the equivalence of photoresponsive strand. Optimally, 64% strand displacement was reversibly induced by alternating UV and visible light irradiation.
June 6, 2017: Chembiochem: a European Journal of Chemical Biology
Shweta Ganapati, Stephanie D Grabitz, Steven Murkli, Flora Scheffenbichler, Maira I Rudolph, Peter Y Zavalij, Matthias Eikermann, Lyle Isaacs
We measured the affinity of five molecular container compounds (Calabadion 1 and 2, CB[7], sulfocalix[4]arene and HP-β-CD) toward seven drugs of abuse in homogenous aqueous solution at physiological pH by various (1H NMR, UV/Vis, ITC) binding assays and find that they span from less than 102 to over 108 M-1. X-ray crystal structures of CB[7]*methamphetamine and 1*methamphetamine are reported. We find that 2, but not CB[7], is able to ameliorate the hyperlocomotive activity of rats treated with methamphetamine...
June 6, 2017: Chembiochem: a European Journal of Chemical Biology
Joseph Cowell, Matthew Buck, Ali H Essa, Rebecca Clarke, Waldemar Vollmer, Daniela Vollmer, Catharien Hilkens, John Isaacs, Michael J Hall, Joe Gray
Biotinylation of amines is widely used to conjugate biomolecules, but the resulting label is either non-removable or removal leaves a tag on the molecule of interest, affecting downstream processes. We present here a set of reagents (RevAmines) that allow traceless, reversible biotinylation under biologically-compatible, mild conditions. Release following avidin-based capture is achieved through the cleavage of a (2-(alkylsulfonyl)ethyl) carbamate linker under mild conditions (200 mM ammonium bicarbonate, pH 8, 16 - 24 h, r...
June 5, 2017: Chembiochem: a European Journal of Chemical Biology
Xiaoyu Zhang, Shiqiang Zhang, Seung Baek, Michael D Best
Cell surface glycoproteins are commonly aberrant in disease and act as biomarkers that facilitate diagnostics. MUC1 is a prominent example exhibiting truncated glyscosylation in cancer. We present a boronic acid microplate assay for sensitive and high-throughput detection of such glycoproteins. Here, the immobilization of biotinboronic acid 1 onto streptavidin plates generates a multivalent surface for glycoprotein recruitment and detection. We first validated the binding properties of 1 in solution through titrations with alizarin dye...
June 2, 2017: Chembiochem: a European Journal of Chemical Biology
Seergazhi G Srivatsan, Sudeshna Manna, Cornelia H Panse, Vyankat A Sontakke, Sarangamath Sangamesh
Development of biophysical systems that enable the understanding of the structure and ligand-binding properties of G-quadruplex forming nucleic acid sequences in cells or models mimicking cellular environment would be highly beneficial in advancing GQ-directed therapeutic strategies. Here, we describe the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H-Telo) DNA and RNA repeats in a cell-like confined environment using conformation-sensitive fluorescent nucleoside probes and a widely used cellular model, AOT (aerosol OT, bis(2-ethylhexyl) sodium sulfosuccinate) reverse micelles (RM)...
June 1, 2017: Chembiochem: a European Journal of Chemical Biology
Siqi Zheng, Xinyuan Fan, Jie Wang, Jingyi Zhao, Peng Chen
The interference from endogenous signaling enzymes represents a major hurdle for building orthogonal signaling cascade inside cells, particularly among the close related isoforms within an enzyme family. Here we employed the genetically-encoded chemical decaging strategy to build orthogonal-activated kinase isoforms, with the endogenous counterparts temporally disabled by an extracellular-delivered bacterial effector. This approach eliminated the potential interference from other kinase isoforms as well as the endogenous kinases, which allowed the specific, gain-of-function report of mitogen activated protein kinase kinase 1 (MEK1) activity as opposed to MEK2 with high temporal resolution...
May 31, 2017: Chembiochem: a European Journal of Chemical Biology
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