Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Kinetic Study on the Reactivity of Azanone (HNO) toward Cyclic C-Nucleophiles.

ABSTRACT: Azanone (HNO) is an elusive electrophilic reactive nitrogen species of growing pharmacological and biological significance. Here, we present a comparative kinetic study of HNO reactivity toward selected cyclic C-nucleophiles under aqueous conditions at pH 7.4. We applied the competition kinetics method, which is based on the use of a fluorescein-derived boronate probe FlBA and two parallel HNO reactions: with the studied scavenger or with O₂ (k = 1.8 × 10⁴ M^-1s^-1). We determined the second-order rate constants of HNO reactions with 13 structurally diverse C-nucleophiles (k = 33-20,000 M^-1s^-1). The results show that the reactivity of HNO toward C-nucleophiles depends strongly on the structure of the scavenger. The data are supported with quantum mechanical calculations. A comprehensive discussion of the HNO reaction with C-nucleophiles is provided.

SUBMITTER: Artelska A

PROVIDER: S-EPMC8657990 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Profiling the Reactivity of Cyclic C-Nucleophiles towards Electrophilic Sulfur in Cysteine Sulfenic Acid.

Project description:Oxidation of a protein cysteine thiol to sulfenic acid, termed S-sulfenylation, is a reversible post-translational modification that plays a crucial role in regulating protein function and is correlated with disease states. The majority of reaction-based small molecule and immunochemical probes used for detecting sulfenic acids are based on the 5,5-dimethyl-1,3-cyclohexanedione (dimedone) scaffold, which is selective, but suffers from low reactivity. In addition, mechanistic details and features that diminish or enhance nucleophile reactivity remain largely unknown. A significant hurdle to resolving the aforementioned issues has been the chemically unstable nature of small-molecule sulfenic acid models. Herein, we report a facile mass spectrometry-based assay and repurposed dipeptide-based model to screen a library of cyclic C-nucleophiles for reactivity with sulfenic acid under aqueous conditions. Observed rate constants for ~100 cyclic C-nucleophiles were obtained and, from this collection, we have identified novel compounds with more than 200-fold enhanced reactivity, as compared to dimedone. The increase in reactivity and retention of selectivity of these C-nucleophiles were validated in secondary assays, including a protein model for sulfenic acid. Together, this work represents a significant step toward developing new chemical reporters for detecting protein S-sulfenylation with superior kinetic resolution. The enhanced rates and varied composition of the C-nucleophiles should enable more comprehensive analyses of the sulfenome and serve as the foundation for reversible or irreversible nucleophilic covalent inhibitors that target oxidized cysteine residues in therapeutically important proteins.

| S-EPMC4724439 | biostudies-literature

Diverse Redoxome Reactivity Profiles of Carbon Nucleophiles.

Project description:Targeted covalent inhibitors have emerged as a powerful approach in the drug discovery pipeline. Key to this process is the identification of signaling pathways (or receptors) specific to (or overexpressed in) disease cells. In this context, fragment-based ligand discovery (FBLD) has significantly expanded our view of the ligandable proteome and affords tool compounds for biological inquiry. To date, such covalent ligand discovery has almost exclusively employed cysteine-reactive small-molecule fragments. However, functional cysteine residues in proteins are often redox-sensitive and can undergo oxidation in cells. Such reactions are particularly relevant in diseases, like cancer, which are linked to excessive production of reactive oxygen species. Once oxidized, the sulfur atom of cysteine is much less reactive toward electrophilic groups used in the traditional FBLD paradigm. To address this limitation, we recently developed a novel library of diverse carbon-based nucleophile fragments that react selectively with cysteine sulfenic acid formed in proteins via oxidation or hydrolysis reactions. Here, we report analysis of sulfenic acid-reactive C-nucleophile fragments screened against a colon cancer cell proteome. Covalent ligands were identified for >1280 S-sulfenylated cysteines present in "druggable" proteins and orphan targets, revealing disparate reactivity profiles and target preferences. Among the unique ligand-protein interactions identified was that of a pyrrolidinedione nucleophile that reacted preferentially with protein tyrosine phosphatases. Fragment-based covalent ligand discovery with C-nucleophiles affords an expansive snapshot of the ligandable "redoxome" with significant implications for covalent inhibitor pharmacology and also affords new chemical tools to investigate redox-regulation of protein function.

| S-EPMC5898444 | biostudies-literature

Carbodiphosphorane mediated synthesis of a triflyloxyphosphonium dication and its reactivity towards nucleophiles.

Project description:A carbodiphosphorane ((Ph3P)2C) mediated synthesis of the first triflyloxyphosphonium dication (12+) bearing two electrophilic sites is presented. Depending on the nucleophile, 12+ reacts selectively either at the sulfur atom of the triflyloxy moiety or at the directly attached phosphorus atom. In substitution reactions at the phosphorus atom the triflyloxy moiety serves as a leaving group and enables the synthesis of rare examples of pseudo-halophosphonium dications.

| S-EPMC5433424 | biostudies-literature

Reactivity of (1-methoxycarbonylpentadienyl)iron(1+) cations with hydride, methyl, and nitrogen nucleophiles.

Project description:The reaction of tricarbonyl and (dicarbonyl)triphenylphosphine (1-methoxycarbonyl-pentadientyl)iron(1+) cations 7 and 8 with methyl lithium, NaBH3CN, or potassium phthalimide affords (pentenediyl)iron complexes 9a-c and 11a-b, while reaction with dimethylcuprate, gave (E,Z-diene)iron complexes 10 and 12. Oxidatively induced-reductive elimination of 9a-c gave vinylcyclopropanecarboxylates 17a-c. The optically active vinylcyclopropane (+)-17a, prepared from (1S)-7, undergoes olefin cross-metathesis with excess (+)-18 to yield (+)-19, a C9-C16 synthon for the antifungal agent ambruticin. Alternatively reaction of 7 with methanesulfonamide or trimethylsilylazide gave (E,E-diene)iron complexes 14d and e. Huisgen [3+2] cyclization of the (azidodienyl)iron complex 14e with alkynes afforded triazoles 25a-e.

| S-EPMC5703425 | biostudies-literature

Reactivity of aziridinomitosene derivatives related to FK317 in the presence of protic nucleophiles.

Project description:The syntheses and reactivity of N-TBDPS and N-trityl protected derivatives of an aziridinomitosene corresponding to FK317 are described. New reactivity patterns were observed for these highly sensitive and functionally dense heterocycles under mild nucleophilic conditions approaching the threshold for degradation. Thus, the silyl or trityl protected aziridinomitosene reacted with Cs(2)CO(3)/CD(3)OD to give isomeric products where substitution occurred at C(10) and C(9a) (mitomycin numbering) providing a CD(3) ether and a CD(3) hemiaminal, respectively. These findings show that heterolysis at C(10) is faster than at aziridine C(1), in contrast to the behavior of typical aziridinomitosenes in the mitomycin series. The labile N-TBDPS hemiaminal and the more stable N-trityl hemiaminal resemble the mitomycin K substitution pattern. A reagent consisting of CsF in CF(3)CH(2)OH/CH(3)CN desilylated a simple N-TBDPS aziridine but caused nucleophilic cleavage at C(1) as well as C(10) without cleavage of the N-TBPDS group in the fully functionalized penultimate aziridinomitosene. The high reactivity of the C(10) carbamate with nucleophiles precludes the use of deprotection methodology that requires N-protonation for fully functionalized aziridinomitosenes in the FK317 series.

| S-EPMC3264803 | biostudies-literature

Multiheterocyclic Motifs via Three-Component Reactions of Benzynes, Cyclic Amines, and Protic Nucleophiles.

Project description:A broadly general, three-component reaction strategy for the construction of compounds containing multiple heterocycles is described. Thermal benzyne formation (by the hexadehydro-Diels-Alder (HDDA) reaction) in the presence of tertiary cyclic amines and a protic nucleophile (HNu) gives, via ring-opening of intermediate ammonium ion/Nu- ion pairs, heterocyclic products. Many reactions are efficient even when the stoichiometric loading of the three reactants approaches unity. Use of HOSO2CF3 as the HNu gives ammonium triflate intermediates, which can then be ring opened by an even wider variety of nucleophiles.

| S-EPMC6344887 | biostudies-literature

Gold(I)-catalyzed amination of allylic alcohols with cyclic ureas and related nucleophiles.

Project description:A 1:1 mixture of [P(t-Bu)(2)-o-biphenyl]AuCl and AgSbF(6) catalyzes the intermolecular amination of allylic alcohols with 1-methylimidazolidin-2-one and related nucleophiles that, in the case of gamma-unsubstituted or gamma-methyl-substituted allylic alcohols, occurs with high gamma-regioselectivity and syn-stereoselectivity.

| S-EPMC2929168 | biostudies-literature

Reactivity of Amine/E(C6F5)3 (E = B, Al) Lewis Pairs toward Linear and Cyclic Acrylic Monomers: Hydrogenation vs. Polymerization.

Project description:This work reveals the contrasting reactivity of amine/E(C6F5)3 (E = B, Al) Lewis pairs toward linear and cyclic acrylic monomers, methyl methacrylate (MMA) and biorenewable ?-methyl-?-methylene-?-butyrolactone (?MMBL). While mixing of 2,2,6,6-tetramethylpiperidine (TMP) and B(C6F5)3 leads to a frustrated Lewis pair (FLP), Et3N reacts with B(C6F5)3 to form disproportionation products, ammonium hydridoborate ionic pair and iminium zwitterion. On the other hand, the stoichiometric reaction of either TMP or Et3N with Al(C6F5)3 leads to clean formation of a classic Lewis adduct (CLA). Neither TMP nor Et3N, when paired with E(C6F5)3, polymerizes MMA, but the Et3N/2B(C6F5)3 pair promotes transfer hydrogenation of MMA to form methyl isobutyrate. In contrast, the amine/E(C6F5)3 pairs promote rapid polymerization of ?MMBL carrying the more reactive exocyclic methylene moiety, achieving full conversion in less than 3 min even at a low catalyst loading of 0.0625 mol %. TMP is more effective than Et3N for the polymerization when paired with either the borane or the alane, while the alane exhibits higher polymerization activity than the borane when paired with Et3N. Overall, the TMP/Al(C6F5)3 system exhibits the highest polymerization activity, achieving a maximum turn-over frequency of 96,000 h-1 at 0.125 mol % of catalyst loading, producing high molecular weight P?MMBL with Mn = 1.29 × 105 g?mol-1.

| S-EPMC6272166 | biostudies-literature

Toward Targeted Kinetic Trapping of Organic-Inorganic Interfaces: A Computational Case Study.

Project description:Properties of inorganic-organic interfaces, such as their interface dipole, strongly depend on the structural arrangements of the organic molecules. A prime example is tetracyanoethylene (TCNE) on Cu(111), which shows two different phases with significantly different work functions. However, the thermodynamically preferred phase is not always the one that is best suited for a given application. Rather, it may be desirable to selectively grow a kinetically trapped structure. In this work, we employ density functional theory and transition state theory to discuss under which conditions such a kinetic trapping might be possible for the model system of TCNE on Cu. Specifically, we want to trap the molecules in the first layer in a flat-lying orientation. This requires temperatures that are sufficiently low to suppress the reorientation of the molecules, which is thermodynamically more favorable for high dosages, but still high enough to enable ordered growth through diffusion of molecules. On the basis of the temperature-dependent diffusion and reorientation rates, we propose a temperature range at which the reorientation can be successfully suppressed.

| S-EPMC8796281 | biostudies-literature

4,6-Dichloro-5-Nitrobenzofuroxan: Different Polymorphisms and DFT Investigation of Its Reactivity with Nucleophiles.

Project description:This research focuses on the X-ray structure of 4,6-dichloro-5-nitrobenzofuroxan 1 and of some of its amino derivatives (4a, 4e, 4g, and 4l) and on DFT calculations concerning the nucleophilic reactivity of 1. We have found that by changing the solvent used for crystallization, it is possible to obtain 4,6-dichloro-5-nitrobenzofuroxan (1) in different polymorphic structures. Moreover, the different torsional angles observed for the nitro group in 1 and in its amino derivatives (4a, 4e, 4g, and 4l) are strictly dependent on the steric hindrance of the substituent at C-4. DFT calculations on the course of the nucleophilic substitution confirm the role of the condensed furoxan ring in altering the aromaticity of the carbocyclic frame, while chlorine atoms strongly influence the dihedral angle and the rotational barrier of the nitro group. These results corroborate previous observations based on experimental kinetic data and give a deep picture of the reaction with amines, which proceeds via a "non-aromatic" nucleophilic substitution.

| S-EPMC8709177 | 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