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1.
J Chem Phys ; 160(21)2024 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-38842492

RESUMO

Both sugars and lipids are important biomolecular building blocks with exceptional conformational flexibility and adaptability to their environment. Glycolipids bring together these two molecular components in the same assembly and combine the complexity of their conformational landscapes. In the present study, we have used selective double resonance vibrational spectroscopy, in combination with a computational approach, to explore the conformational preferences of two glycolipid models (3-0-acyl catechol and guaiacol α-D-glucopyranosides), either fully isolated in the gas phase or controlled interaction with a single water molecule. We could identify the preferred conformation and structures of the isolated and micro-hydrated species and evidence of the presence of a strong water pocket, which may influence the conformational flexibility of such systems, even in less controlled environments.

2.
Chembiochem ; : e202400097, 2024 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-38703401

RESUMO

A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.

3.
Chemistry ; 28(59): e202201543, 2022 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-35818782

RESUMO

Arylborinic acids represent new, efficient, and underexplored hydrogen peroxide-responsive triggers. In contrast to boronic acids, two concomitant oxidative rearrangements are involved in the complete oxidation of these species, which might represent a major limitation for an efficient effector (drug or fluorophore) release. Herein, a comprehensive study of H2 O2 -mediated unsymmetrical arylborinic acid oxidation to investigate the factors that could selectively guide their oxidative rearrangement is described. The o-CF3 substituent was found to be an excellent directing group allowing a complete regioselectivity on borinic acid models. This result was successfully applied to synthesizing new borinic acid-based fluorogenic probes, which exclusively release the fluorescent moiety upon H2 O2 treatment. These compounds maintained their superior kinetic properties compared to boronic acids, thus further enhancing the potential of arylborinic acids as valuable new H2 O2 -sensitive triggers.


Assuntos
Ácidos Borínicos , Peróxido de Hidrogênio , Oxirredução , Ácidos Borônicos , Estresse Oxidativo
4.
Org Biomol Chem ; 20(9): 1974-1981, 2022 03 02.
Artigo em Inglês | MEDLINE | ID: mdl-35179161

RESUMO

Trehalose-based probes are useful tools that allow the detection of the mycomembrane of mycobacteria through the metabolic labeling approach. Trehalose analogues conjugated to fluorescent probes can be used, and other probes are functionalized with a bioorthogonal chemical reporter for a two-step labeling approach. The synthesis of such trehalose-based probes mainly relies on the desymmetrization of natural trehalose using a large number of regioselective protection-deprotection steps to differentiate the eight hydroxyl groups. Herein, in order to avoid these time-consuming steps, we reinvestigated our previously reported tandem protocol mediated by FeCl3·6H2O, with the aim of modifying the ratio of the products to allow the challenging desymmetrization of the C2-symmetrical disaccharide trehalose. We demonstrate the usefulness of this method in providing easy access to trehalose analogues with a bioorthogonal moiety or a fluorophore in C-2, and also present their use in a one-step and two-step labeling approach, either of which can be used to study the mycomembrane in live mycobacteria.


Assuntos
Antibacterianos/farmacologia , Membrana Celular/efeitos dos fármacos , Cloretos/farmacologia , Corynebacterium/efeitos dos fármacos , Compostos Férricos/farmacologia , Trealose/farmacologia , Antibacterianos/síntese química , Antibacterianos/química , Cloretos/química , Compostos Férricos/química , Testes de Sensibilidade Microbiana , Trealose/síntese química , Trealose/química
5.
Proc Natl Acad Sci U S A ; 118(50)2021 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-34873034

RESUMO

Hydrogen peroxide (H2O2) is responsible for numerous damages when overproduced, and its detection is crucial for a better understanding of H2O2-mediated signaling in physiological and pathological processes. For this purpose, various "off-on" small fluorescent probes relying on a boronate trigger have been prepared, and this design has also been involved in the development of H2O2-activated prodrugs or theranostic tools. However, this design suffers from slow kinetics, preventing activation by H2O2 with a short response time. Therefore, faster H2O2-reactive groups are awaited. To address this issue, we have successfully developed and characterized a prototypic borinic-based fluorescent probe containing a coumarin scaffold. We determined its in vitro kinetic constants toward H2O2-promoted oxidation. We measured 1.9 × 104 m-1⋅s-1 as a second-order rate constant, which is 10,000-fold faster than its well-established boronic counterpart (1.8 m-1⋅s-1). This improved reactivity was also effective in a cellular context, rendering borinic acids an advantageous trigger for H2O2-mediated release of effectors such as fluorescent moieties.

6.
Chem Commun (Camb) ; 55(87): 13074-13077, 2019 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-31588930

RESUMO

In this study, we report the first synthesis of an alkyne-based trehalose monomycolate probe containing a ß-hydroxylated fatty acid and an α-branched chain similar to those of the natural mycolic acid. We demonstrate its utility for the labeling of the mycomembrane of Corynebacteria as well as for the study of mycoloyltransferases.


Assuntos
Aciltransferases/análise , Membrana Celular/química , Corynebacterium/enzimologia , Corantes Fluorescentes/química , Ácidos Micólicos/química , Aciltransferases/metabolismo , Membrana Celular/metabolismo , Corynebacterium/citologia , Corantes Fluorescentes/síntese química , Estrutura Molecular , Ácidos Micólicos/síntese química
7.
Chemphyschem ; 18(19): 2812-2823, 2017 Oct 06.
Artigo em Inglês | MEDLINE | ID: mdl-28547843

RESUMO

The fragmentation mechanisms of prototypical disaccharides have been studied herein by coupling tandem mass spectrometry (MS) with collisional chemical dynamics simulations. These calculations were performed by explicitly considering the collisions between the protonated sugar and the neutral target gas, which led to an ensemble of trajectories for each system, from which it was possible to obtain reaction products and mechanisms without pre-imposing them. The ß-aminoethyl and aminopropyl derivatives of cellobiose, maltose, and gentiobiose were studied to observe differences in both the stereochemistry and the location of the glycosidic linkage. Chemical dynamics simulations of MS/MS and MS/MS/MS were used to suggest some primary and secondary fragmentation mechanisms for some experimentally observed product ions. These simulations provided some new insights into the fundamentals of the unimolecular dissociation of protonated sugars under collisional induced dissociation conditions.


Assuntos
Dissacarídeos/química , Simulação de Dinâmica Molecular , Prótons , Configuração de Carboidratos , Espectrometria de Massas em Tandem
8.
Angew Chem Int Ed Engl ; 53(24): 6184-7, 2014 Jun 10.
Artigo em Inglês | MEDLINE | ID: mdl-24764235

RESUMO

The umpolung of glycals with samarium diiodide offers a simple route to novel carbohydrate-derived nucleophilic reagents in a single step using a readily available reductant. The corresponding allyl samarium reagent that arises from the hexose series reacts with ketones at the C3 position with high stereoselectivity; carbon-carbon bond formation takes place only anti to the substituent at the C4 position of the dihydropyran ring. For the sialic acid series, the completely regio- and stereoselective coupling process of the samarium reagent occurs at the anomeric carbon atom and provides a new approach to the α-C-glycosides of N-acetyl neuraminic acid.


Assuntos
Iodetos/química , Samário/química , Ácidos Siálicos/química , Estrutura Molecular
10.
Carbohydr Res ; 342(12-13): 1974-82, 2007 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-17466287

RESUMO

The conformational behavior of two C-glycosyl analogues of the sialyl-Tn antigen has been determined by a combination of NMR methods and molecular mechanics calculations. Both compounds show a major solution conformation that is drastically different from the major one of the natural compound.


Assuntos
Antígenos Glicosídicos Associados a Tumores/química , Ácido N-Acetilneuramínico/química , Configuração de Carboidratos , Dissacarídeos/química , Glicosilação , Espectroscopia de Ressonância Magnética , Modelos Moleculares , Conformação Molecular , Soluções
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