Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Readily Accessible Ambiphilic Cyclopentadienes for Bioorthogonal Labeling.

ABSTRACT: A new class of bioorthogonal reagents based on the cyclopentadiene scaffold is described. The diene 6,7,8,9-tetrachloro-1,4-dioxospiro[4,4]nona-6,8-diene (a tetrachlorocyclopentadiene ketal, TCK) is ambiphilic and self-orthogonal with remarkable stability. The diene reacts rapidly with a trans-cyclooctene and an endo-bicyclononyne, but slowly with dibenzoazacyclooctyne (DIBAC), allowing for tandem labeling studies with mutually orthogonal azides that react rapidly with DIBAC. TCK analogues are synthesized in three steps from inexpensive, commercially available starting materials.

SUBMITTER: Levandowski BJ

PROVIDER: S-EPMC6314806 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Readily Accessible Ambiphilic Cyclopentadienes for Bioorthogonal Labeling.

Levandowski Brian J BJ Gamache Raymond F RF Murphy Jennifer M JM Houk K N KN

Journal of the American Chemical Society 20180515 20

A new class of bioorthogonal reagents based on the cyclopentadiene scaffold is described. The diene 6,7,8,9-tetrachloro-1,4-dioxospiro[4,4]nona-6,8-diene (a tetrachlorocyclopentadiene ketal, TCK) is ambiphilic and self-orthogonal with remarkable stability. The diene reacts rapidly with a trans-cyclooctene and an endo-bicyclononyne, but slowly with dibenzoazacyclooctyne (DIBAC), allowing for tandem labeling studies with mutually orthogonal azides that react rapidly with DIBAC. TCK analogues are s ...[more]

PMID: 29712423

Similar Datasets

Readily accessible multifunctional fluorous emulsions.

Project description:Strategies for the facile fabrication of nanoscale materials and devices represent an increasingly important challenge for chemists. Here, we report a simple, one-pot procedure for the formation of perfluorocarbon emulsions with defined functionalization. The fluorous core allows for small molecules containing a fluorous tail to be stabilized inside the emulsions. The emulsions can be formed using a variety of hydrophilic polymers resulting in an array of sizes (90 nm to >1 micron) and surface charges (-95 mV to 65 mV) of fluid particles. The surface of the emulsions can be further functionalized, covalently or non-covalently, through in situ or post-emulsion modification. The total preparation time is 30 minutes or less from commercially available reagents without specialized equipment. We envision these emulsions to be applicable to both biological and materials systems.

| S-EPMC6020120 | biostudies-literature

Functionally Diverse Nylon-3 Copolymers from Readily Accessible ?-Lactams.

Project description:A new family of ?-lactams is described that enables anionic ring-opening polymerization (AROP) to prepare nylon-3 materials bearing diverse appended functionality, including carboxylic acid, thiol, hydroxyl and secondary amine groups. Nylon-3 copolymers generated with the new ?-lactams are shown to display distinctive self-assembly behavior and biological properties.

| S-EPMC3551626 | biostudies-literature

Generating Multibillion Chemical Space of Readily Accessible Screening Compounds.

Project description:An approach to the generation of ultra-large chemical libraries of readily accessible ("REAL") compounds is described. The strategy is based on the use of two- or three-step three-component reaction sequences and available starting materials with pre-validated chemical reactivity. After the preliminary parallel experiments, the methods with at least ∼80% synthesis success rate (such as acylation - deprotection - acylation of monoprotected diamines or amide formation - click reaction with functionalized azides) can be selected and used to generate the target chemical space. It is shown that by using only on the two aforementioned reaction sequences, a nearly 29-billion compound library is easily obtained. According to the predicted physico-chemical descriptor values, the generated chemical space contains large fractions of both drug-like and "beyond rule-of-five" members, whereas the strictest lead-likeness criteria (the so-called Churcher's rules) are met by the lesser part, which still exceeds 22 million.

| S-EPMC7593547 | biostudies-literature

Enantiomerically enriched tris(boronates): readily accessible conjunctive reagents for asymmetric synthesis.

Project description:The catalytic enantioselective diboration of vinyl boronate esters furnishes chiral tris(boronates) in a selective fashion. Subsequent deborylative alkylation occurs in a diastereoselective fashion, both for intermolecular and intramolecular processes.

| S-EPMC5539535 | biostudies-other

Asymmetric NHC-catalyzed synthesis of ?-fluoroamides from readily accessible ?-fluoroenals.

Project description:The scope of the NHC-redox amidation has been expanded to include a variety of ?,?-unsaturated aldehydes, including ?-fluoro ?,?-unsaturated aldehydes which give rise to enantioenriched ?-fluoroamides in good to excellent yield and enantioselectivity (up to 97% ee). Enantioenriched amines may be elaborated to either diastereomer of the product in high diastereoselectivity (up to 99:1). Functionalization of the amide products to amines and fluorohydrins is also demonstrated with retention of enantioenrichment at the fluorine stereocenter.

| S-EPMC4205762 | biostudies-literature

Readily accessible sp3-rich cyclic hydrazine frameworks exploiting nitrogen fluxionality.

Project description:Increased molecular complexity correlates with improved chances of success in the drug development process. Here, a strategy for the creation of sp3-rich, non-planar heterocyclic scaffolds suitable for drug discovery is described that obviates the need to generate multiple stereogenic centers with independent control. Asymmetric transfer hydrogenation using a tethered Ru-catalyst is used to efficiently produce a range of enantiopure cyclic hydrazine building blocks (up to 99% ee). Iterative C-N functionalization at the two nitrogen atoms of these compounds produces novel hydrazine and hydrazide based chemical libraries. Wide chemical diversification is possible through variation in the hydrazine structure, use of different functionalization chemistries and coupling partners, and controlled engagement of each nitrogen of the hydrazine in turn. Principal Moment of Inertia (PMI) analysis of this small hydrazine library reveals excellent shape diversity and three-dimensionality. NMR and crystallographic studies confirm these frameworks prefer to orient their substituents in three-dimensional space under the control of a single stereogenic center through exploitation of the fluxional behavior of the two nitrogen atoms.

| S-EPMC7069508 | biostudies-literature

Readily accessible fluorescent probes for sensitive biological imaging of hydrogen peroxide.

Project description:Hydrogen peroxide is a major component of oxygen metabolism in biological systems that, when present in high concentrations, can lead to oxidative stress in cells. Noninvasive molecular imaging of H(2)O(2) using fluorogenic systems represents an effective way to detect and measure the accumulation of this metabolite. Herein, we detail the development of robust H(2)O(2)-sensitive fluorescent probes using a boronic ester trigger appended to the fluorophore through a benzyl ether linkage. A major advantage of the probes presented here is their synthetic accessibility, with only one step needed to generate the probes on the gram scale. The sensitivity of the probes was evaluated in simulated physiological conditions, showing micromolar sensitivity to H(2)O(2). The probes were tested in biological model systems, demonstrating effective imaging of unstimulated, endogenous H(2)O(2) levels in RAW 264.7 cells and murine brain tissue.

| S-EPMC3689009 | biostudies-literature

Creation of readily accessible and orally active analogue of cortistatin a.

Project description:Syntheses of structurally simplified analogues of cortistatin A (1), a novel antiangiogenic steroidal alkaloid from Indonesian marine sponge, and their biological activities were investigated. The analogues were designed by considering the 3-D structure of 1. Compound 30, in which the isoquinoline moiety was appended to the planar tetracyclic core structure, showed potent antiproliferative activity against human umbilical vein endothelial cells (HUVECs) together with high selectivity and also showed in vivo antiangiogenic activity and significant antitumor effect by oral administration.

| S-EPMC4025756 | biostudies-literature

Readily accessible shape-memory effect in a porous interpenetrated coordination network.

Project description:Shape-memory effects are quite well-studied in general, but there is only one reported example in the context of porous materials. We report the second example of a porous coordination network that exhibits a sorbate-induced shape-memory effect and the first in which multiple sorbates, N2, CO2 and CO promote this effect. The material, a new threefold interpenetrated pcu network, [Zn2(4,4'-biphenyldicarboxylate)2(1,4-bis(4-pyridyl)benzene)]n (X-pcu-3-Zn-3i), exhibits three distinct phases: the as-synthesized ? phase; a denser-activated ? phase; and a shape-memory ? phase, which is intermediate in density between the ? and ? phases. The ? phase is kinetically stable over multiple adsorption/desorption cycles and only reverts to the ? phase when heated at >400 K under vacuum. The ? phase can be regenerated by soaking the ? phase in N,N'-dimethylformamide. Single-crystal x-ray crystallography studies of all three phases provide insight into the shape-memory phenomenon by revealing the nature of interactions between interpenetrated networks. The ? and ? phases were further investigated by in situ coincidence powder x-ray diffraction, and their sorption isotherms were replicated by density functional theory calculations. Analysis of the structural information concerning the three phases of X-pcu-3-Zn-3i enabled us to understand structure-function relationships and propose crystal engineering principles for the design of more examples of shape-memory porous materials.

| S-EPMC5922793 | biostudies-literature

Isocyanides: Promising Functionalities in Bioorthogonal Labeling of Biomolecules.

Project description:Isocyanides have drawn increasing attention in biological applications due to their attractive properties and unique reactivities, which can undergo various reactions, such as multicomponent reactions, α-addition reactions, [4 + 1] cycloaddition reactions, and the reaction scope keeps expanding. In addition to acting as reactants for the preparation of structurally interesting and diverse N-heterocycles or peptidomimetics, this type of functionality may be a good choice in the labeling and modulation of biomolecules due to the high biocompatibility and small size to minimize modifications on the parent molecule. It has been demonstrated that isocyanides can participate in biomolecule labeling through three strategies, including the two-component bioorthogonal reaction, multicomponent reaction, and metal chelation. Among them, the isocyanide-tetrazine reaction has been better studied recently, augmenting the potency of isocyanide as a bioorthogonal handle. This review will focus on the recent progress in isocyanide chemistry for labeling of biomolecules. Meanwhile, methods to introduce isocyano groups into biomacromolecules are also described to facilitate wider applications of this unique functionality.

| S-EPMC8117350 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data