Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Influence of Substitution on Thiol-Induced Oxanorbornadiene Fragmentation.

ABSTRACT: Oxanorbornadienes (ONDs) undergo facile Michael addition with thiols and then fragment by a retro-Diels-Alder (rDA) reaction, a unique two-step sequence among electrophilic cleavable linkages. The rDA reaction rate was explored as a function of the furan structure, with substituents at the 2- and 5-positions found to be the most influential and the fragmentation rate to be inversely correlated with electron-withdrawing ability. Density functional theory calculations provided an excellent correlation with the experimentally measured OND rDA rates.

SUBMITTER: De Pascalis L

PROVIDER: S-EPMC9020489 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The Influence of Substitution on Thiol-Induced Oxanorbornadiene Fragmentation.

De Pascalis Lucrezia L Yau Mei-Kwan MK Svatunek Dennis D Tan Zhuoting Z Tekkam Srinivas S Houk K N KN Finn M G MG

Organic letters 20210414 9

Oxanorbornadienes (ONDs) undergo facile Michael addition with thiols and then fragment by a retro-Diels-Alder (rDA) reaction, a unique two-step sequence among electrophilic cleavable linkages. The rDA reaction rate was explored as a function of the furan structure, with substituents at the 2- and 5-positions found to be the most influential and the fragmentation rate to be inversely correlated with electron-withdrawing ability. Density functional theory calculations provided an excellent correla ...[more]

PMID: 33851842

Similar Datasets

Modular degradable hydrogels based on thiol-reactive oxanorbornadiene linkers.

Project description:Oxanorbornadiene dicarboxylate (OND) reagents are potent Michael acceptors, the adducts of which undergo fragmentation by retro-Diels-Alder reaction at rates that vary with the substitution pattern on the OND moiety. Rapid conjugate addition between thiol-terminated tetravalent PEG and multivalent ONDs yielded self-supporting hydrogels within 1 min at physiological temperature and pH. Erosion of representative hydrogel formulations occurred with predictable and pH-independent rates on the order of minutes to weeks. These materials could be made non-degradable by epoxidation of the OND linkers without slowing gelation. Hydrogels prepared with OND linkers of equal valence had comparable physical properties, as determined by equilibrium swelling behavior, indicating similar internal network structure. Diffusion and release of entrained cargo varied with both the rate of degradation of PEG-OND hydrogels and the hydrodynamic radius of the entrained species. These results highlight the utility of OND linkers in the preparation of degradable network materials with potential applications in sustained release.

| S-EPMC4415036 | biostudies-literature

Kinetics and mechanisms of thiol-disulfide exchange covering direct substitution and thiol oxidation-mediated pathways.

Project description:SignificanceDisulfides are important building blocks in the secondary and tertiary structures of proteins, serving as inter- and intra-subunit cross links. Disulfides are also the major products of thiol oxidation, a process that has primary roles in defense mechanisms against oxidative stress and in redox regulation of cell signaling. Although disulfides are relatively stable, their reduction, isomerisation, and interconversion as well as their production reactions are catalyzed by delicate enzyme machineries, providing a dynamic system in biology. Redox homeostasis, a thermodynamic parameter that determines which reactions can occur in cellular compartments, is also balanced by the thiol-disulfide pool. However, it is the kinetic properties of the reactions that best represent cell dynamics, because the partitioning of the possible reactions depends on kinetic parameters.Critical issuesThis review is focused on the kinetics and mechanisms of thiol-disulfide substitution and redox reactions. It summarizes the challenges and advances that are associated with kinetic investigations in small molecular and enzymatic systems from a rigorous chemical perspective using biological examples. The most important parameters that influence reaction rates are discussed in detail.Recent advances and future directionsKinetic studies of proteins are more challenging than small molecules, and quite often investigators are forced to sacrifice the rigor of the experimental approach to obtain the important kinetic and mechanistic information. However, recent technological advances allow a more comprehensive analysis of enzymatic systems via using the systematic kinetics apparatus that was developed for small molecule reactions, which is expected to provide further insight into the cell's machinery.

| S-EPMC3613173 | biostudies-literature

Degradable conjugates from oxanorbornadiene reagents.

Project description:Oxanorbornadienedicarboxylate (OND) reagents were explored for purposes of binding and releasing drugs from serum albumins as representative macromolecular carriers. Being highly reactive Michael acceptors, ONDs form adducts with thiols and amines, which then undergo retro-Diels-Alder fragmentation. A study of more than 30 model adducts revealed a number of modifications that can be used to influence adduct stability. For the most reactive OND linkers, the labeling of the single available bovine serum albumin (BSA) cysteine residue was complete within minutes at a mid-micromolar concentration of reactants. While a selectivity of greater than 1000-fold for thiol over amine was observed with model amino acids, the labeling of protein amines with ONDs is fast enough to be practical, as demonstrated by the reaction with thiol-depleted BSA. The OND-amine adducts were found to be up to 15 times more stable than OND-thiol adducts, and to be sensitive to acid by virtue of a stereochemically dependent acceleration of cycloreversion. The release rate of fluorescent cargo from serum albumins was tuned by selecting the coupling partners: the available half-lives ranged from 40 min to 7 days at 37 °C. Such versatility of release profiles from protein carriers, controlled by the nature of the OND linkage, is a useful addition to the drug delivery toolbox.

| S-EPMC3432588 | biostudies-literature

Electrochemical Visualization of Single-Molecule Thiol Substitution with Nanopore Measurement.

Project description:Reactions involving sulfhydryl groups play a critical role in maintaining the structure and function of proteins. However, traditional mechanistic studies have mainly focused on reaction rates and the efficiency in bulk solutions. Herein, we have designed a cysteine-mutated nanopore as a biological protein nanoreactor for electrochemical visualization of the thiol substitute reaction. Statistical analysis of characteristic current signals shows that the apparent reaction rate at the single-molecule level in this confined nanoreactor reached 1400 times higher than that observed in bulk solution. This substantial acceleration of thiol substitution reactions within the nanopore offers promising opportunities for advancing the design and optimization of micro/nanoreactors. Moreover, our results could shed light on the understanding of sulfhydryl reactions and the thiol-involved signal transduction mechanisms in biological systems.

| S-EPMC10885329 | biostudies-literature

Stress Relaxation by Addition-Fragmentation Chain Transfer in Highly Crosslinked Thiol-Yne Networks.

Project description:Radical mediated addition-fragmentation chain transfer of mid-chain allyl sulfide functional groups was utilized to reduce polymerization-induced shrinkage stress in thiol-yne step-growth photopolymerization reactions. In previous studies, the addition-fragmentation of allyl sulfide during the polymerization of a step-growth thiol-ene network demonstrated reduced polymerization stress; however, the glass transition temperature of the material was well below room temperature (~ -20°C). Many applications require super-ambient glass transition temperatures, such as microelectronics and dental materials. Polymerization reactions utilizing thiol-yne functional groups have many of the advantageous attributes of the thiol-ene-based materials, such as possessing a delayed gel-point, resistant to oxygen inhibition, and fast reaction kinetics, while also possessing a high glass transition temperature. Here we incorporate allyl sulfide functional groups into a highly crosslinked thiol-yne network to reduce polymerization-induced shrinkage stress. Simultaneous shrinkage stress and functional group conversion measurements were performed during polymerization using a cantilever-type tensometer coupled with a FTIR spectrometer. The resulting networks were highly crosslinked, possessed super-ambient glass transition temperatures, and exhibited significantly reduced polymerization-induced shrinkage stress when compared with analogous propyl sulfide-containing materials that are incapable of addition-fragmentation.

| S-EPMC3134880 | biostudies-literature

Effects of thiol substitution in deep-eutectic solvents (DESs) as solvents for metal oxides.

Project description:This study deals with an investigation of how substitution of an alcohol group by a thiol group in mixtures of choline chloride with a series of bio-sourceable molecules affects the physico-chemical properties of the mixtures and their ability to dissolve metal oxides. All of the thiol mixtures studied showed a higher affinity and selectivity for late transition metals and the physical properties of the mixtures were improved compared to their alcohol analogues (i.e. lower viscosity, wider liquid range). The metal solubility was assessed via determination of the final concentration of the metal oxides dissolved in thiol mixtures via inductively coupled plasma optical emission spectroscopy (ICP-OES). The thiol function selectively improved the solubilities of the late transition metal oxides (i.e. copper and zinc), which are valuable metals often present as residue in industrial waste. The solubility of iron oxides was much lower than that of the valuable metals, which is a significant benefit in industrial applications. The different solubilization behaviour of metal oxides in the thiol and alcohol mixtures was further investigated via UV-vis absorption and infrared spectroscopy. This study allowed the potential of these deep-eutectic solvents for the selective recovery of metals to be assessed.

| S-EPMC9054895 | biostudies-literature

Factors That Influence Base-Catalyzed Thiol-Ene Hydrogel Synthesis.

Project description:Injectable, localized drug delivery using hydrogels made from ethoxylated trimethylolpropane tri-3-mercaptopropionate (ETTMP) and poly(ethylene glycol) diacrylate (PEGDA) has shown great potential due to these hydrogels' ability to exhibit non-swelling behavior and tunable drug release properties. However, current synthesis methods in the literature suffer from poor ETTMP solubility in water, slow gelation times exceeding 20 min, and a lack of reproducibility. To address these limitations, we have developed a reliable synthesis procedure and conducted a sensitivity analysis of key variables. This has enabled us to synthesize ETTMP-PEGDA hydrogels in a polymer concentration range of 15 to 90 wt% with gelation times of less than 2 min and moduli ranging from 3.5 to 190 kPa. We overcame two synthesis limitations by identifying the impact of residual mercaptopropionic acid and alumina purification column height on gelation time and by premixing ETTMP and PEGDA to overcome low ETTMP solubility in water. Our ETTMP-PEGDA mixture can be stored at -20 °C for up to 2 months without crosslinking, allowing easy storage and shipment. These and previous results demonstrate the potential of ETTMP-PEGDA hydrogels as promising candidates for injectable, localized drug delivery with tunable drug release properties.

| S-EPMC10671550 | biostudies-literature

Populations of metal-glycan structures influence MS fragmentation patterns.

Project description:The structures and collision-induced dissociation (CID) fragmentation patterns of the permethylated glycan Man5GlcNAc2 are investigated by a combination of hybrid ion mobility spectrometry (IMS), mass spectrometry (MS), and MS/MS techniques. IMS analysis of eight metal-adducted glycans ([Man5GlcNAc2 + M](2+), where M = Mn, Fe, Co, Ni, Cu, Mg, Ca, and Ba) shows distinct conformer patterns. These conformers appear to arise from individual metals binding at different sites on the glycan. Fragmentation studies suggest that these different binding sites influence the CID fragmentation patterns. This paper describes a series of separation, activation, and fragmentation studies that assess which fragments arise from each of the different gas-phase conformer states. Comparison of the glycan distributions formed under gentle ionization conditions with those obtained after activation of the gas-phase ions suggests that these conformer binding states also appear to exist in solution.

| S-EPMC4276451 | biostudies-literature

Tandem mass spectrometric characterization of thiol peptides modified by the chemoselective cationic sulfhydryl reagent (4-iodobutyl)triphenylphosphonium--effects of a cationic thiol derivatization on peptide fragmentation.

Project description:Fixed charge chemical modifications on peptides and proteins can impact fragmentation behaviors in tandem mass spectrometry (MS/MS). In this study, we employed a thiol-specific cationic alkylation reagent, (4-iodobutyl)triphenylphosphonium (IBTP), to selectively modify cysteine thiol groups in mitochondrial proteome samples. Tandem mass spectrometric characteristics of butyltriphenylphosphonium (BTP)-modified peptides were evaluated by comparison to their carbamidomethylated (CAM) analogues using a quadrupole time-of-flight (Q-TOF) instrument under low energy collision-induced dissociation (CID) conditions. Introduction of the fixed charge modification resulted in the observation of peptide and fragment (b(n) and y(n)) ions with higher charge states than those observed for CAM-modified analogues. The charged BTP moiety had a significant effect on the neighboring amide bond fragmentation products. A decrease in relative abundances of the product ions at the corresponding cleavage sites was observed compared with those from the CAM-modified derivatives. This effect was particularly noticeable when an Xxx-Pro bond was in the vicinity of a BTP group. We hypothesized that the presence of a phosphonium moiety will reduce the tendency for protonation of the proximal amide bonds in the peptide backbone. Indeed, calculations indicated that proton affinities of backbone amide bonds close to the modified cysteine residues were generally 20-50 kcal/mol lower for BTP-modified peptides than for the unmodified or CAM-modified analogues with the sequence motif -Ala-Cys-Ala(n)-Ala(2)-, -Ala-Cys-Ala(n)-Pro-Ala-, and -Ala-Pro-Ala(n)-Cys-Ala-, n=0-3.

| S-EPMC3187551 | biostudies-literature

Thermally induced fragmentation of nanoscale calcite.

Project description:Calcite nanorods ∼50 nm wide are thermally separated into nanoblocks. The fragmentation is ascribed to the ion diffusion on metastable crystal surfaces at temperatures (∼400 °C) much lower than the melting point. The presence of water molecules enhances the surface diffusion and induces deformation of the nanorods even at ∼60 °C.

| S-EPMC9049556 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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