keyword
MENU ▼
Read by QxMD icon Read
search

Bioorthogonal chemistry

keyword
https://www.readbyqxmd.com/read/28218446/in-situ-bioorthogonal-metabolic-labeling-for-fluorescence-imaging-of-virus-infection-in-vivo
#1
Hong Pan, Wen-Jun Li, Xiang-Jie Yao, Ya-Yun Wu, Lan-Lan Liu, Hua-Mei He, Ren-Li Zhang, Yi-Fan Ma, Lin-Tao Cai
Optical fluorescence imaging is an important strategy to explore the mechanism of virus-host interaction. However, current fluorescent tag labeling strategies often dampen viral infectivity. The present study explores an in situ fluorescent labeling strategy in order to preserve viral infectivity and precisely monitor viral infection in vivo. In contrast to pre-labeling strategy, mice are first intranasally infected with azide-modified H5N1 pseudotype virus (N3 -H5N1p), followed by injection of dibenzocyclooctyl (DBCO)-functionalized fluorescence 6 h later...
February 20, 2017: Small
https://www.readbyqxmd.com/read/28215631/posttranscriptional-chemical-labeling-of-rna-by-using-bioorthogonal-chemistry
#2
REVIEW
Jerrin Thomas George, Seergazhi G Srivatsan
Recent developments in RNA labeling technology have provided viable tools to analyze RNA synthesis, processing and function in cell-free and cellular environments. Notably, emerging methodologies based on posttranscriptional chemical labeling by using bioorthogonal chemistry have enabled the visualization and profiling of exogenous and endogenous RNA transcripts. In this review, we first give an overview of different RNA labeling strategies based on chemical as well as genetically encoded systems. Subsequently, we provided a detailed discussion on methodologies that have been developed to introduce various bioorthogonal reactive groups into RNA transcripts, which are compatible for posttranscriptional functionalization...
February 16, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28194834/steering-siglec-sialic-acid-interactions-on-living-cells-using-bioorthogonal-chemistry
#3
Christian Büll, Torben Heise, Niek van Hilten, Johan F A Pijnenborg, Victor Bloemendal, Lotte Gerrits, Esther D Kers-Rebel, Tina Ritschel, Martijn H den Brok, Gosse J Adema, Thomas J Boltje
Sialic acid sugars that terminate cell-surface glycans form the ligands for the sialic acid binding immunoglobulin-like lectin (Siglec) family, which are immunomodulatory receptors expressed by immune cells. Interactions between sialic acid and Siglecs regulate the immune system, and aberrations contribute to pathologies like autoimmunity and cancer. Sialic acid/Siglec interactions between living cells are difficult to study owing to a lack of specific tools. Here, we report a glycoengineering approach to remodel the sialic acids of living cells and their binding to Siglecs...
February 14, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28183600/injectable-dextran-hydrogels-fabricated-by-metal-free-click-chemistry-for-cartilage-tissue-engineering
#4
Xiaoyu Wang, Zihan Li, Ting Shi, Peng Zhao, Kangkang An, Chao Lin, Hongwei Liu
Injectable dextran-based hydrogels were prepared for the first time by bioorthogonal click chemistry for cartilage tissue engineering. Click-crosslinked injectable hydrogels based on cyto-compatible dextran (Mw=10kDa) were successfully fabricated under physiological conditions by metal-free alkyne-azide cycloaddition (click) reaction between azadibenzocyclooctyne-modified dextran (Dex-ADIBO) and azide-modified dextran (Dex-N3). Gelation time of these dextran hydrogels could be regulated in the range of approximately 1...
April 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28166295/correction-a-99mtc-labelled-tetrazine-for-bioorthogonal-chemistry-synthesis-and-biodistribution-studies-with-small-molecule-trans-cyclooctene-derivatives
#5
Alyssa Vito, Hussain Alarabi, Shannon Czorny, Omid Beiraghi, Jeff Kent, Nancy Janzen, Afaf R Genady, Salma A Al-Karmi, Stephanie Rathmann, Zoya Naperstkow, Megan Blacker, Lisset Llano, Paul J Berti, John F Valliant
[This corrects the article DOI: 10.1371/journal.pone.0167425.].
2017: PloS One
https://www.readbyqxmd.com/read/28139910/cell-selective-bioorthogonal-metabolic-labeling-of-rna
#6
Kim Nguyen, Michael Fazio, Miles Kubota, Sarah Nainar, Chao Feng, Xiang Li, Scott X Atwood, Timothy W Bredy, Robert C Spitale
Stringent chemical methods to profile RNA expression within discrete cellular populations remains a key challenge in biology. To address this issue, we developed a chemical-genetic strategy for metabolic labeling of RNA. Cell-specific labeling of RNA can be profiled and imaged using bioorthogonal chemistry. We anticipate that this platform will provide the community with a much-needed chemical toolset for cell-type specific profiling of cell-specific transcriptomes derived from complex biological systems.
February 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28137568/drug-target-identification-using-an-itraq-based-quantitative-chemical-proteomics-approach-based-on-a-target-profiling-study-of-andrographolide
#7
J Wang, Y K Wong, J Zhang, Y-M Lee, Z-C Hua, H-M Shen, Q Lin
Identifying the cellular binding targets of drugs and other bioactive small molecules is a crucial step for understanding their molecular mechanisms of action as well as potential off-target effects. The field of chemical proteomics is an emerging discipline in chemical biology using synthetic chemistry and high-throughput detection techniques to study small molecule-protein interactions. In this chapter, we describe a quantitative chemical proteomics protocol combining bioorthogonal click chemistry and quantitation by isobaric tags for relative and absolute quantification (iTRAQ) to identify the specific binding targets of drugs and bioactive small molecules such as natural products...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28130882/direct-intracellular-delivery-of-cell-impermeable-probes-of-protein-glycosylation-using-nanostraws
#8
Alexander Minyi Xu, Derek Schawn Wang, Peyton Shieh, Yuhong Cao, Nick Melosh
Bioorthogonal chemistry is an effective tool for measuring metabolic pathways and cellular activity, yet its use is currently limited due to the difficulty of introducing probes past the cell membrane and into the cytoplasm, especially as more complex probes are desired. Here we present a simple and minimally perturbative technique to deliver functional probes of glycolysylation into cells using a nanostructured "nanostraw" delivery system. Nanostraws provide large scale intracellular access to cells through fluidic conduits that remain small enough to minimize cell perturbation...
January 28, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28094987/crystal-engineering-of-self-assembled-porous-protein-materials-in-living-cells
#9
Satoshi Abe, Hiroyasu Tabe, Hiroshi Ijiri, Keitaro Yamashita, Kunio Hirata, Kohei Atsumi, Takuya Shimoi, Masaki Akai, Hajime Mori, Susumu Kitagawa, Takafumi Ueno
Crystalline porous materials have been investigated for development of important applications in molecular storage, separations, and catalysis. The potential of protein crystals is increasing as they become better understood. Protein crystals have been regarded as porous materials because they present highly ordered 3D arrangements of protein molecules with high porosity and wide range of pore sizes. However, it remains difficult to functionalize protein crystals in living cells. Here, we report that polyhedra, a natural crystalline protein assembly of polyhedrin monomer (PhM) produced in insect cells infected by cypovirus, can be engineered to extend porous networks by deleting selected amino acid residues located on the intermolecular contact region of PhM...
February 9, 2017: ACS Nano
https://www.readbyqxmd.com/read/28074503/bioorthogonal-diversification-of-peptides-through-selective-ruthenium-ii-catalyzed-c-h-activation
#10
Alexandra Schischko, Hongjun Ren, Nikolaos Kaplaneris, Lutz Ackermann
Methods for the chemoselective modification of amino acids and peptides are powerful techniques in biomolecular chemistry. Among other applications, they enable the total synthesis of artificial peptides. In recent years, significant momentum has been gained by exploiting palladium-catalyzed cross-coupling for peptide modification. Despite major advances, the prefunctionalization elements on the coupling partners translate into undesired byproduct formation and lengthy synthetic operations. In sharp contrast, we herein illustrate the unprecedented use of versatile ruthenium(II)carboxylate catalysis for the step-economical late-stage diversification of α- and β-amino acids, as well as peptides, through chemo-selective C-H arylation under racemization-free reaction conditions...
January 11, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28034806/targeting-the-extracellular-matrix-of-ovarian-cancer-using-functionalized-drug-loaded-lyophilisomes
#11
Sophieke C H A van der Steen, René Raavé, Sjoerd Langerak, Laurens van Houdt, Sander M J van Duijnhoven, Sanne A M van Lith, Leon F A G Massuger, Willeke F Daamen, William P Leenders, Toin H van Kuppevelt
Epithelial ovarian cancer is characterized by a high mortality rate and is in need for novel therapeutic avenues to improve patient outcome. The tumor's extracellular matrix ("stroma") offers new possibilities for targeted drug-delivery. Recently we identified highly sulfated chondroitin sulfate (CS-E) as a component abundantly present in the ovarian cancer extracellular matrix, and as an novel target for anti-cancer therapy. Here, we report on the functionalization of drug-loaded lyophilisomes (albumin-based biocapsules) to specifically target the stroma of ovarian carcinomas with the potential to eliminate cancer cells...
December 26, 2016: European Journal of Pharmaceutics and Biopharmaceutics
https://www.readbyqxmd.com/read/28027640/hydrogels-for-therapeutic-delivery-current-developments-and-future-directions
#12
Sytze J Buwalda, Tina Vermonden, Wim E Hennink
Hydrogels are attractive materials for the controlled release of therapeutics because of their capacity to embed biologically active agents in their water-swollen network. Recent advances in organic and polymer chemistry, bioengineering and nanotechnology have resulted in several new developments in the field of hydrogels for therapeutic delivery. In this Perspective, we present our view on the state-of-the-art in the field, thereby focusing on a number of exciting topics, including bioorthogonal cross-linking methods, multicomponent hydrogels, stimuli-responsive hydrogels, nanogels, and the release of therapeutics from 3D printed hydrogels...
January 10, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28004799/controlled-orientation-of-active-sites-in-a-nanostructured-multienzyme-complex
#13
Sung In Lim, Byungseop Yang, Younghan Jung, Jaehyun Cha, Jinhwan Cho, Eun-Sil Choi, Yong Hwan Kim, Inchan Kwon
Multistep cascade reactions in nature maximize reaction efficiency by co-assembling related enzymes. Such organization facilitates the processing of intermediates by downstream enzymes. Previously, the studies on multienzyme nanocomplexes assembled on DNA scaffolds demonstrated that closer interenzyme distance enhances the overall reaction efficiency. However, it remains unknown how the active site orientation controlled at nanoscale can have an effect on multienzyme reaction. Here, we show that controlled alignment of active sites promotes the multienzyme reaction efficiency...
December 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27998071/characterization-of-the-artemisinin-binding-site-for-translationally-controlled-tumor-protein-tctp-by-bioorthogonal-click-chemistry
#14
Weichao Li, Yiqing Zhou, Guanghui Tang, Youli Xiao
Despite the fact that multiple artemisinin-alkylated proteins in Plasmodium falciparum have been identified in recent studies, the alkylation mechanism and accurate binding site of artemisinin-protein interaction have remained elusive. Here, we report the chemical-probe-based enrichment of the artemisinin-binding peptide and characterization of the artemisinin-binding site of P. falciparum translationally controlled tumor protein (TCTP). A peptide fragment within the N-terminal region of TCTP was enriched and found to be alkylated by an artemisinin-derived probe...
December 21, 2016: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/27992180/fast-diazaborine-formation-of-semicarbazide-enables-facile-labeling-of-bacterial-pathogens
#15
Anupam Bandyopadhyay, Samantha Cambray, Jianmin Gao
Bioorthogonal conjugation chemistry has enabled the development of tools for the interrogation of complex biological systems. Although a number of bioorthogonal reactions have been documented in literature, they are less ideal for one or several reasons including slow kinetics, low stability of the conjugated product, requirement of toxic catalysts, and side reactions with unintended biomolecules. Herein we report a fast (>10(3) M(-1) s(-1)) and bioorthogonal conjugation reaction that joins semicarbazide to an aryl ketone or aldehyde with an ortho-boronic acid substituent...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27965173/clickecm-development-of-a-cell-derived-extracellular-matrix-with-azide-functionalities
#16
S M Ruff, S Keller, D E Wieland, V Wittmann, G E M Tovar, M Bach, P J Kluger
: In vitro cultured cells produce a complex extracellular matrix (ECM) that remains intact after decellularization. The biological complexity derived from the variety of distinct ECM molecules makes these matrices ideal candidates for biomaterials. Biomaterials with the ability to guide cell function are a topic of high interest in biomaterial development. However, these matrices lack specific addressable functional groups, which are often required for their use as a biomaterial. Due to the biological complexity of the cell-derived ECM, it is a challenge to incorporate such functional groups without affecting the integrity of the biomolecules within the ECM...
December 10, 2016: Acta Biomaterialia
https://www.readbyqxmd.com/read/27960310/co-opting-a-bioorthogonal-reaction-for-oncometabolite-detection
#17
Thomas T Zengeya, Julie M Garlick, Rhushikesh A Kulkarni, Mikayla Miley, Allison M Roberts, Youfeng Yang, Daniel R Crooks, Carole Sourbier, W Marston Linehan, Jordan L Meier
Dysregulated metabolism is a hallmark of many diseases, including cancer. Methods to fluorescently detect metabolites have the potential to enable new approaches to cancer detection and imaging. However, fluorescent sensing methods for naturally occurring cellular metabolites are relatively unexplored. Here we report the development of a chemical approach to detect the oncometabolite fumarate. Our strategy exploits a known bioorthogonal reaction, the 1,3-dipolar cycloaddition of nitrileimines and electron-poor olefins, to detect fumarate via fluorescent pyrazoline cycloadduct formation...
December 14, 2016: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/27936007/a-99mtc-labelled-tetrazine-for-bioorthogonal-chemistry-synthesis-and-biodistribution-studies-with-small-molecule-trans-cyclooctene-derivatives
#18
Alyssa Vito, Hussain Alarabi, Shannon Czorny, Omid Beiraghi, Jeff Kent, Nancy Janzen, Afaf R Genady, Salma A Al-Karmi, Stephanie Rathmann, Zoya Naperstkow, Megan Blacker, Lisset Llano, Paul J Berti, John F Valliant
A convenient strategy to radiolabel a hydrazinonicotonic acid (HYNIC)-derived tetrazine with 99mTc was developed, and its utility for creating probes to image bone metabolism and bacterial infection using both active and pretargeting strategies was demonstrated. The 99mTc-labelled HYNIC-tetrazine was synthesized in 75% yield and exhibited high stability in vitro and in vivo. A trans-cyclooctene (TCO)-labelled bisphosphonate (TCO-BP) that binds to regions of active calcium metabolism was used to evaluate the utility of the labelled tetrazine for bioorthogonal chemistry...
2016: PloS One
https://www.readbyqxmd.com/read/27882694/fused-bicyclic-caspase-1-inhibitors-assembled-by-copper-free-strain-promoted-alkyne-azide-cycloaddition-spaac
#19
Linghui Qian, Chong-Jing Zhang, Ji'en Wu, Shao Q Yao
Challenges exist in the development of potent and selective small-molecule inhibitors against caspase-1. Herein, by making use of the copper-free strain-promoted alkyne-azide cycloaddition (SPAAC) reaction between difluorinated cyclooctynes (DIFOs) and various azide-containing compounds, we showed for the first time that potential caspase-1 inhibitors could be rapidly synthesized. The resulting fused bicyclic compounds structurally resembled the central portion (P2 -P3 ) of Pralnacasan (a well-known small molecule caspase-1 inhibitor), with diversity at the P4 -position of the parental inhibitor conveniently installed from the azide component...
November 24, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27862410/fluorogenic-behaviour-of-the-hetero-diels-alder-ligation-of-5-alkoxyoxazoles-with-maleimides-and-their-applications
#20
Kévin Renault, Laurie-Anne Jouanno, Antoine Lizzul-Jurse, Pierre-Yves Renard, Cyrille Sabot
Fluorogenic reactions are largely underrepresented in the toolbox of chemoselective ligations despite their tremendous potential, particularly in chemical biology and biochemistry. In this respect, we have investigated in full detail the fluorescence behaviour of the azaphthalamide, a scaffold which is generated through a hetero-Diels-Alder reaction of 5-alkoxyoxazole and maleimide derivatives under mild conditions that are compatible with, among others, peptide chemistry. The scope and limitations of such a fluorogenic labelling strategy were examined through four distinct applications, which target enzymatic activities or bioorthogonal reactions...
December 19, 2016: Chemistry: a European Journal
keyword
keyword
39357
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"