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Bioorthogonal chemistry

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https://www.readbyqxmd.com/read/29338219/pretargeted-immuno-pet-based-on-bioorthogonal-chemistry-for-imaging-egfr-positive-colorectal-cancer
#1
Xudong Shi, Kai Gao, Hao Huang, Ran Gao
Pretargeted immuno-PET imaging based on the bioorthogonal chemistry between 18F-labeled Reppe anhydride derivatives and tetrazine conjugates of the EGFR-specific monoclonal antibodies cetuximab and panitumumab was performed. This pretargeting approach yielded high target-to-nontarget ratios. Furthermore, due to the fast clearance rate of the PET probe, the overall radiation burden to nontarget tissues was also substantially decreased.
January 16, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29327914/mechanistic-evaluation-of-bioorthogonal-decaging-with-trans-cyclooctene-the-effect-of-fluorine-substituents-on-aryl-azide-reactivity-and-decaging-from-the-1-2-3-triazoline
#2
Siddharth Sai Matikonda, Jessica M Fairhall, Franziska Fiedler, Suchaya Sanhajariya, Robert A J Tucker, Sarah Hook, Anna L Garden, Allan B Gamble
Bioorthogonal prodrug activation/decaging strategies need to be selective, rapid and release the drug from the masking group upon activation. The rates of the 1,3-dipolar cycloaddition between a trans-cyclooctene (TCO) and a series of fluorine-substituted azido-PABC self-immolative spacers caging two model drugs, and subsequent release from the 1,2,3-triazoline are reported. As the number of fluorine substituents on the PABC linker increases from one to four, the rate of cycloaddition increases by almost one-order of magnitude...
January 12, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29306675/in-vivo-catalyzed-new-to-nature-reactions
#3
REVIEW
Johannes G Rebelein, Thomas R Ward
Bioorthogonal chemistry largely relies on the use of abiotic metals to catalyze new-to-nature reactions in living systems. Over the past decade, metal complexes and metal-encapsulated systems such as nanoparticles have been developed to unravel the reactivity of transition metals, including ruthenium, palladium, iridium, copper, iron, and gold in biological systems. Thanks to these remarkable achievements, abiotic catalysts are able to fluorescently label cells, uncage or form cytotoxic drugs and activate enzymes in cellulo/vivo...
January 4, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29306547/a-cell-surface-clicked-navigation-system-to-direct-specific-bone-targeting
#4
Young Kim, Zhe Zhang, Jae-Hyuck Shim, Tae Sup Lee, Ching-Hsuan Tung
Cell therapies are promising up-and-coming therapeutic strategies for many diseases. For maximal therapeutic benefits, injected cells have to navigate their way to a designated area, including organ and tissue; unfortunately, the majority of therapeutic cells are currently administered without a guide or homing device. To improve this serious shortcoming, a functionalization method was developed to equip cells with a homing signal. Its application was demonstrated by applying an Azadibenzocyclooctyne-bisphosphonate (ADIBO-BP) and azide paired bioorthogonal chemistry on cells for bone specific homing...
December 26, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29250049/using-click-chemistry-for-visualizing-in-situ-changes-of-translational-activity-in-planktonic-marine-bacteria
#5
Ainara Leizeaga, Margarita Estrany, Irene Forn, Marta Sebastián
A major challenge in microbial ecology is linking diversity and function to determine which microbes are actively contributing to processes occurring in situ. Bioorthogonal non-canonical amino acid tagging (BONCAT) is a promising technique for detecting and quantifying translationally active bacteria in the environment. This technique consists of incubating a bacterial sample with an analog of methionine and using click-chemistry to identify the cells that have incorporated the substrate. Here, we established an optimized protocol for the visualization of protein-synthesizing cells in oligotrophic waters that can be coupled with taxonomic identification using Catalyzed Reporter Deposition Fluorescent in Situ Hybridization...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29240290/bioorthogonal-cycloadditions-with-sub-millisecond-intermediates
#6
Yujia Qing, Gökçe Su Pulcu, Nicolas Bell, Hagan Bayley
Tetrazine- and sydnone-based click chemistries have emerged as important bioconjugation strategies with fast kinetics and N2 or CO2 as the only by-product. Mechanistic studies of these reactions have focused on the initial rate-determining cycloaddition steps. The subsequent N2 or CO2 release from the bicyclic intermediates has been approached mainly through computational studies, which have predicted lifetimes of femtoseconds. In the present study, bioorthogonal cycloadditions involving N2 or CO2 extrusion have been examined experimentally at the single-molecule level by using a protein nanoreactor...
December 14, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29193552/live-cell-protein-sulfonylation-based-on-proximity-driven-n-sulfonyl-pyridone-chemistry
#7
Kazuya Matsuo, Yuki Nishikawa, Marie Masuda, Itaru Hamachi
The development of bioorthogonal approaches for labeling of endogenous proteins under the multimolecular crowding conditions of live cells is highly desirable for the analysis and engineering of proteins without using genetic manipulation. Herein, we report N-sulfonyl pyridone (SP) as a new reactive group for protein sulfonylation. The ligand-directed SP chemistry was able to modify not only purified proteins in vitro, but also endogenous ones on the surface of and inside live cells selectively and rapidly, which allowed to convert endogenous proteins to FRET-based biosensors in situ...
November 28, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29192289/caspase-3-7-specific-metabolic-precursor-for-bioorthogonal-tracking-of-tumor-apoptosis
#8
Man Kyu Shim, Hong Yeol Yoon, Sangmin Lee, Mun Kyeong Jo, Jooho Park, Jong-Ho Kim, Seo Young Jeong, Ick Chan Kwon, Kwangmeyung Kim
Apoptosis is one of the most important intracellular events in living cell, which is a programmed cell death interrelated with caspase enzyme activity for maintaining homeostasis in multicellular organisms. Therefore, direct apoptosis imaging of living cells can provide enormous advantages for diagnosis, drug discovery, and therapeutic monitoring in various diseases. However, a method of direct apoptosis imaging has not been fully validated, especially for live cells in in vitro and in vivo. Herein, we developed a new apoptosis imaging technology via a direct visualization of active caspase-3/-7 activity in living cells...
November 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29177436/designer-trnas-for-efficient-incorporation-of-non-canonical-amino-acids-by-the-pyrrolysine-system-in-mammalian-cells
#9
Robert Serfling, Christian Lorenz, Maja Etzel, Gerda Schicht, Thore Böttke, Mario Mörl, Irene Coin
The pyrrolysyl-tRNA synthetase/tRNAPyl pair is the most versatile and widespread system for the incorporation of non-canonical amino acids (ncAAs) into proteins in mammalian cells. However, low yields of ncAA incorporation severely limit its applicability to relevant biological targets. Here, we generate two tRNAPyl variants that significantly boost the performance of the pyrrolysine system. Compared to the original tRNAPyl, the engineered tRNAs feature a canonical hinge between D- and T-loop, show higher intracellular concentrations and bear partially distinct post-transcriptional modifications...
November 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29171257/stereoselective-synthesis-of-bicyclo-6-1-0-nonene-precursors-of-the-bioorthogonal-reagents-s-tco-and-bcn
#10
Jessica G K O'Brien, Srinivasa R Chintala, Joseph M Fox
The cyclooctyne BCN and the trans-cyclooctene s-TCO are widely used in bioorthogonal chemistry. A bottleneck for their synthesis had been a poorly selective cyclopropanation with ethyl diazoacetate. Here, we describe that low catalyst loadings (0.27 mol%) of Rh2(S-BHTL)4 provides the BCN precursor with 79:21 syn:anti selectivity. The synthesis of the s-TCO precursor was best achieved through a sequence of Rh2(OAc)4 (0.33 mol%) catalyzed cyclopropanation, followed by ester hydrolysis under epimerizing conditions...
November 24, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/29161031/computational-exploration-of-concerted-and-zwitterionic-mechanisms-of-diels-alder-reactions-between-1-2-3-triazines-and-enamines-and-acceleration-by-hydrogen-bonding-solvents
#11
Yun-Fang Yang, Peiyuan Yu, Kendall N Houk
The mechanisms of Diels-Alder reactions between 1,2,3-triazines and enamines have been explored with density functional theory computations. The focus of this work is on the origins of the different reactivities and mechanisms induced by substituents and by hexafluoroisopropanol (HFIP) solvent. These inverse electron-demand Diels-Alder reactions of triazines have wide applications in bioorthogonal chemistry and natural product synthesis. Both concerted and stepwise cycloadditions are predicted, depending on the nature of substituents and solvents...
November 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29147682/synthesis-and-application-of-injectable-bioorthogonal-dendrimer-hydrogels-for-local-drug-delivery
#12
Leyuan Xu, Remy C Cooper, Juan Wang, W Andrew Yeudall, Hu Yang
We developed novel dendrimer hydrogels (DH)s on the basis of bioorthogonal chemistry, in which polyamidoamine (PAMAM) dendrimer generation 4.0 (G4) functionalized with strained alkyne dibenzocyclooctyne (DBCO) via PEG spacer (Mn = 2,000 g/mol) underwent strain-promoted azide-alkyne cycloaddition (SPAAC) with polyethylene glycol bisazide (PEG-BA) (Mn= 20,000 g/mol) to generate a dendrimer-PEG cross-linked network. This platform offers a high degree of functionality and modularity. A wide range of structural parameters including dendrimer generation, degree of PEGylation, loading density of clickable DBCO groups, PEG-BA chain length as well as the ratio of clickable dendrimer to PEG-BA and their concentrations can be readily manipulated to tune chemical and physical properties of DHs...
August 14, 2017: ACS Biomaterials Science & Engineering
https://www.readbyqxmd.com/read/29121649/spatiotemporal-dynamics-of-hsv-genome-nuclear-entry-and-compaction-state-transitions-using-bioorthogonal-chemistry-and-super-resolution-microscopy
#13
Eiki Sekine, Nora Schmidt, David Gaboriau, Peter O'Hare
We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes (HSVEdC). In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid supports that allowed coupling to external capture agents and demonstrated that the vast majority of individual virions contained bioorthogonally-tagged genomes. Using HSVEdC in vivo we reveal novel aspects of the kinetics, localisation, mechanistic entry requirements and morphological transitions of infecting genomes...
November 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29109777/improved-tumor-targeting-and-longer-retention-time-of-nir-fluorescent-probes-using-bioorthogonal-chemistry
#14
Xianghan Zhang, Bo Wang, Na Zhao, Zuhong Tian, Yunpeng Dai, Yongzhan Nie, Jie Tian, Zhongliang Wang, Xiaoyuan Chen
The traditional labeling method for targeted NIR fluorescence probes requires directly covalent-bonded conjugation of targeting domains and fluorophores in vitro. Although this strategy works well, it is not sufficient for detecting or treating cancers in vivo, due to steric hindrance effects that relatively large fluorophore molecules exert on the configurations and physiological functions of specific targeting domains. The copper-free, "click-chemistry"-assisted assembly of small molecules in living systems may enhance tumor accumulation of fluorescence probes by improving the binding affinities of the targeting factors...
2017: Theranostics
https://www.readbyqxmd.com/read/29097747/antibody-pegylation-in-bioorthogonal-pretargeting-with-trans-cyclooctene-tetrazine-cycloaddition-in-vitro-and-in-vivo-evaluation-in-colorectal-cancer-models
#15
Aurélie Rondon, Nancy Ty, Jean-Baptiste Bequignat, Mercedes Quintana, Arnaud Briat, Tiffany Witkowski, Bernadette Bouchon, Claude Boucheix, Elisabeth Miot-Noirault, Jean-Pierre Pouget, Jean-Michel Chezal, Isabelle Navarro-Teulon, Emmanuel Moreau, Françoise Degoul
Bioorthogonal chemistry represents a challenging approach in pretargeted radioimmunotherapy (PRIT). We focus here on mAb modifications by grafting an increase amount of trans-cyclooctene (TCO) derivatives (0 to 30 equivalents with respect to mAb) bearing different polyethylene glycol (PEG) linkers between mAb and TCO (i.e. PEG0 (1), PEG4 (2) and PEG12 (3)) and assessing their functionality. We used colorectal xenograft (HT29/Ts29.2) and peritoneal carcinomatosis (A431-CEA-Luc/35A7) as tumor cells/mAbs models and fluorescent tetrazines (TZ)...
November 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29095606/ex-uno-plura-differential-labeling-of-phospholipid-biosynthetic-pathways-with-a-single-bioorthogonal-alcohol
#16
Timothy W Bumpus, Felice J Liang, Jeremy M Baskin
Imaging approaches that track biological molecules within cells are essential tools in modern biochemistry. Lipids are particularly challenging to visualize, as they are not directly genetically encoded. Phospholipids, the most abundant subgroup of lipids, are structurally diverse and accomplish many cellular functions, acting as major structural components of membranes and as signaling molecules that regulate cell growth, division, apoptosis, cytoskeletal dynamics, and numerous other physiological processes...
November 8, 2017: Biochemistry
https://www.readbyqxmd.com/read/29048718/azido-functionalized-5-cap-analogs-for-preparation-of-translationally-active-mrnas-suitable-for-fluorescent-labeling-in-living-cells
#17
Adam Mamot, Pawel Sikorski, Marcin Warminski, Joanna Kowalska, Jacek Jemielity
The 7-methylguanosine (m7G) cap structure is a unique feature present at the 5' ends of messenger RNAs (mRNAs) that can be subjected to extensive modifications, resulting in alterations to mRNA properties (e.g. translability, susceptibility to degradation). It also can provide molecular tools to study mRNA metabolism. Here, we developed new mRNA 5' cap-based tools that enable the site-specific labeling of RNA at the 5' end using strain-promoted azide-alkyne cycloaddition (SPAAC), i.e. bioorthogonal, copper-free click chemistry, and support the mRNA's basic function in protein biosynthesis...
October 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29044851/a-bifunctional-fluorogenic-rhodamine-probe-for-proximity-induced-bioorthogonal-chemistry
#18
Philipp Werther, Jasper S Möhler, Richard Wombacher
Bioorthogonal reactions have emerged as a versatile tool in life sciences. The inverse electron demand Diels-Alder reaction (DAinv) stands out due to the availability of reactants with very fast kinetics. However, highly reactive dienophiles suffer the disadvantage of being less stable and prone to side reactions. Here, we evaluate the extent of acceleration of rather unreactive but highly stable dienophiles by DNA-templated proximity. To this end, we developed a modular synthetic route for a novel bifunctional fluorogenic tetrazine rhodamine probe that we used to determine the reaction kinetics of various dienophiles in a fluorescence assay...
October 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29040808/independently-tuning-the-biochemical-and-mechanical-properties-of-3d-hyaluronan-based-hydrogels-with-oxime-and-diels-alder-chemistry-to-culture-breast-cancer-spheroids
#19
Alexander E G Baker, Roger Y Tam, Molly S Shoichet
For native breast cancer cell growth to be mimicked in vitro as spheroids, a well-defined matrix that mimics the tumor microenvironment is required. Finding a biomimetic material for 3D cell culture other than Matrigel has challenged the field. Because hyaluronan is naturally abundant in the tumor microenvironment and can be chemically modified, we synthesized a hyaluronan (HA) hydrogel with independently tunable mechanical and chemical properties for 3D culture of breast cancer cells. By modifying HA with distinct bioorthogonal functional groups, its mechanical properties are controlled by chemical cross-linking via oxime ligation, and its biochemical properties are controlled by grafting bioactive peptides via Diels-Alder chemistry...
October 31, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/29022697/improved-photoinduced-fluorogenic-alkene-tetrazole-reaction-for-protein-labeling
#20
Xin Shang, Rui Lai, Xi Song, Hui Li, Wei Niu, Jiantao Guo
The 1,3-dipolar cycloaddition reaction between an alkene and a tetrazole represents one elegant and rare example of fluorophore-forming bioorthogonal chemistry. This is an attractive reaction for imaging applications in live cells that requires less intensive washing steps and/or needs spatiotemporal resolutions. In the present work, as an effort to improve the fluorogenic property of the alkene-tetrazole reaction, an aromatic alkene (styrene) was investigated as the dipolarophile. Over 30-fold improvement in quantum yield of the reaction product was achieved in aqueous solution...
November 15, 2017: Bioconjugate Chemistry
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