Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Iron-Binding and Anti-Fenton Properties of Novel Amino Acid-Derived Cyclic Imide Dioximes.

ABSTRACT: We present a novel route for the preparation of amino acid-derived cyclic imide dioxime derivatives. Readily accessible amino acids were conveniently converted to their corresponding cyclic imide dioximes in simple synthetic steps. The aim of this work was to describe and compare the iron-chelating and antioxidant properties of synthesized compounds in relation to their molecular structure, and in particular, which of those features are essential for iron(II)-chelating ability. The glutarimide dioxime moiety has been established as an iron(II)-binding motif and imparts potent anti-Fenton properties to the compounds. Compound 3 was shown to strongly suppress hydroxyl radical formation by preventing iron cycling via Fe-complexation. These findings provide insights into the structural requirements for achieving anti-Fenton activity and highlight the potential use of glutarimide dioximes as antioxidants.

SUBMITTER: Mravljak J

PROVIDER: S-EPMC6826749 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Iron-Binding and Anti-Fenton Properties of Novel Amino Acid-Derived Cyclic Imide Dioximes.

Mravljak Janez J Jakopin Žiga Ž

Antioxidants (Basel, Switzerland) 20191011 10

We present a novel route for the preparation of amino acid-derived cyclic imide dioxime derivatives. Readily accessible amino acids were conveniently converted to their corresponding cyclic imide dioximes in simple synthetic steps. The aim of this work was to describe and compare the iron-chelating and antioxidant properties of synthesized compounds in relation to their molecular structure, and in particular, which of those features are essential for iron(II)-chelating ability. The glutarimide d ...[more]

PMID: 31614461

Similar Datasets

Iron-binding and anti-Fenton properties of baicalein and baicalin.

Project description:Baicalein and baicalin, the major bioactive compounds found in the Chinese herb Scutellaria baicalensis, have been shown to be effective against cancer, bacterial infections and oxidative stress diseases. However, little is known about their mechanisms of action. To probe whether iron homeostasis modulation may play a role in their bioactivity, we have investigated their iron binding characteristics under physiologically relevant conditions. A 2:1 baicalein-ferrous complex was readily formed in 20mM phosphate buffer, pH 7.2, with a binding constant approximately 2-9 x 10(11)M(-2), whereas a 1:1 baicalein-ferric complex was formed, under the same conditions, with an apparent binding constant approximately 1-3 x 10(6)M(-1). Baicalein appears to bind the ferrous ion more strongly than ferrozine, a well known iron(II) chelator. Using (1) H NMR and Zn(2+) and Ga(3+) as probes, the iron-binding site on baicalein was elucidated to be at the O6/O7 oxygen atoms of the A-ring. No binding was observed for baicalin under the same NMR conditions. Furthermore, baicalein strongly inhibits the Fe-promoted Fenton chemistry via a combination of chelation and radical scavenging mechanism while baicalin can provide only partial protection against radical damage. These results indicate that baicalein is a strong iron chelator under physiological conditions and hence may play a vital role in modulating the body's iron homeostasis. Modulation of metal homeostasis and the inhibition of Fenton chemistry may be one of the possible mechanisms for herbal medicine.

| S-EPMC2659571 | biostudies-literature

Positron Binding and Annihilation Properties of Amino Acid Systems.

Project description:Despite the fact that the positron annihilation has been used in biomedical applications, the detailed mechanism of the positron annihilation on biological molecules remains poorly understood so far. In this work, we investigated the positron binding and positron annihilation properties for both global minimum and hydrogen-bonded structures of 20 amino acid molecules using the multicomponent molecular orbital method. By regression analysis, we confirmed that positron affinity can increase with an increase of the permanent dipole moment of the parent amino acids as reported in previous studies, while the annihilation rate linearly increases with respect to the square root of positron affinity. By the one-particle property analyses for probabilities of electron-positron contacts, we found that delocalization characteristics of both electrons and positrons play key roles to enhance the positron annihilation rate arising from both the valence electrons in σ- and π-type molecular orbitals from 2p atomic orbitals but not from the highest occupied molecular orbital electrons, particularly for comparatively weakly bound positronic amino acid systems.

| S-EPMC8581980 | biostudies-literature

Synthesis of amino acid-derived cyclic acyl amidines for use in beta-strand peptidomimetics.

Project description:The acyl amidine represented by the 4,5-dihydro-2(3H)-pyrazinone ring system 2 is isosteric to the vinylogous amide of the 1,2-dihydro-3(6H)-pyridinone 1, but its assembly from separate amine and amide components enables ready incorporation of an amino acid side chain with correct regio- and stereochemistry. beta-Strand peptidomimetics incorporating amino acid analogues based on 2 have recently been shown to be potent, protease-resistant ligands to a PDZ protein-interaction domain. Two routes to the protected dipeptide analogue 3 are described.

| S-EPMC2536638 | biostudies-literature

Antimicrobial Properties of Amino-Acid-Derived N-Heterocyclic Carbene Silver Complexes.

Project description:Complexes {Ag[NHCMes,R]}n (R = H, 2a; Me, 2b and 2b'; iPr, 2c; iBu, 2d), were prepared by treatment of imidazolium precursor compounds [ImMes,R] (2-(3-mesityl-1H-imidazol-3-ium-1-yl)acetate, 1a, (S)-2-alkyl(3-mesityl-1H-imidazol-3-ium-1-yl)acetate, 1b-d, and (R)-2-methyl(3-mesityl-1H-imidazol-3-ium-1-yl)acetate, 1b', with Ag2O under appropriate conditions. They were characterised by analytical, spectroscopic (IR, 1H, and 13C NMR and polarimetry), and X-ray methods (2a). In the solid state, 2a is a one-dimensional coordination polymer, in which the silver(I) cation is bonded to the carbene ligand and to the carboxylate group of a symmetry-related Ag[NHCMes,H] moiety. The coordination environment of the silver centre is well described by the DFT study of the dimeric model {Ag[NHCMes,H]}2. The antimicrobial properties of these complexes were evaluated versus Gram-negative bacteria E. coli and P. aeruginosa. From the observed MIC and MBC values (minimal inhibitory concentration and minimal bactericidal concentration, respectively), complex 2b' showed the best antimicrobial properties (eutomer), which were significantly better than those of its enantiomeric derivative 2b (distomer). Additionally, analysis of MIC and MBC values of 2a-d reveal a clear structure-antimicrobial effect relationship. Antimicrobial activity decreases when the steric properties of the R alkyl group in {Ag[NHCMes,R]}n increase.

| S-EPMC9024828 | biostudies-literature

Basic amino acid residues of human eosinophil derived neurotoxin essential for glycosaminoglycan binding.

Project description:Human eosinophil derived neurotoxin (EDN), a granule protein secreted by activated eosinophils, is a biomarker for asthma in children. EDN belongs to the human RNase A superfamily possessing both ribonucleolytic and antiviral activities. EDN interacts with heparin oligosaccharides and heparin sulfate proteoglycans on bronchial epithelial Beas-2B cells. In this study, we demonstrate that the binding of EDN to cells requires cell surface glycosaminoglycans (GAGs), and the binding strength between EDN and GAGs depends on the sulfation levels of GAGs. Furthermore, in silico computer modeling and in vitro binding assays suggest critical roles for the following basic amino acids located within heparin binding regions (HBRs) of EDN 34QRRCKN39 (HBR1), 65NKTRKN70 (HBR2), and 113NRDQRRD119 (HBR3) and in particular Arg35, Arg36, and Arg38 within HBR1, and Arg114 and Arg117 within HBR3. Our data suggest that sulfated GAGs play a major role in EDN binding, which in turn may be related to the cellular effects of EDN.

| S-EPMC3794821 | biostudies-literature

Structural evidence of the species-dependent albumin binding of the modified cyclic phosphatidic acid with cytotoxic properties.

Project description:Cyclic phosphatidic acids (cPAs) are naturally occurring, very active signalling molecules, which are involved in several pathological states, such as cancer, diabetes or obesity. As molecules of highly lipidic character found in the circulatory system, cPAs are bound and transported by the main extracellular lipid binding protein-serum albumin. Here, we present the detailed interactions between human serum albumin (HSA) and equine serum albumin (ESA) with a derivative of cPA, 1-O-myristoyl-sn-glycerol-2,3-cyclic phosphorodithioate (Myr-2S-cPA). Initial selection of the ligand used for the structural study was made by the analysis of the therapeutically promising properties of the sulfur containing analogues of cPA in respect to the unmodified lysophospholipids (LPLs). Substitution of one or two non-bridging oxygen atoms in the phosphate group with one or two sulfur atoms increases the cytotoxic effect of cPAs up to 60% on the human prostate cancer (PC) cells. Myr-2S-cPA reduces cancer cell viability in a dose-dependent manner, with IC50 value of 29.0 ?M after 24 h incubation, which is almost 30% lower than IC50 of single substituted phosphorothioate cPA. Although, the structural homology between HSA and ESA is big, their crystal complexes with Myr-2S-cPA demonstrate significantly different mode of binding of this LPL analogue. HSA binds three molecules of Myr-2S-cPA, whereas ESA only one. Moreover, none of the identified Myr-2S-cPA binding sites overlap in both albumins.

| S-EPMC5293571 | biostudies-literature

Conformation and anion binding properties of cyclic hexapeptides containing L-4-hydroxyproline and 6-aminopicolinic acid subunits.

Project description:Two cyclic hexapeptides containing alternating all R and all S configured Ll-(4R/S)-hydroxyproline and 6-aminopicolinic acid subunits are presented, and the influence of the hydroxyl groups on the solubility, conformation, and receptor properties is investigated. Cyclopeptide 2, containing the natural 4R configured hydroxyproline, adopts a conformation similar to that of the unsubstituted peptide 1, which is able to bind anions such as halides and sulfate in aqueous solution. 2 also interacts with these anions, but whereas 1 forms sandwich type 2:1 complexes, in which the anion is bound by two cyclopeptide moieties, 2 forms 1:1 complexes. The stabilities of the halide and sulfate complexes of 2 range between 10(0) and 10(2) M(-1) in 80% D(2)O/CD(3)OD. Complex formation is detectable even in water, but with slightly smaller stability constants. Using this information a quantitative evaluation of the stability of the 2:1 complexes of 1, for which overall stability constants in the order 10(4) to 10(5) M(-2) in 80% D(2)O/CD(3)OD were observed, was made. In contrast to 2, the conformation of 3, containing the non-natural 4S configured hydroxyproline, is strongly affected by the presence of the hydroxyl groups. In d(6)-DMSO and methanol/water mixtures a slow conformational equilibrium between two C(3)-symmetrical conformers is observed, and 3 is thus much less preorganized for anion binding than either 1 or 2.

| S-EPMC122733 | biostudies-literature

Amino acid properties conserved in molecular evolution.

Project description:That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

| S-EPMC4072533 | biostudies-literature

Stepwise N-H Bond Formation From N<sub>2</sub>-Derived Iron Nitride, Imide and Amide Intermediates to Ammonia.

Project description:Reduction of N2 to ammonia in nature and in electrocatalysis takes place through 1-proton/1-electron steps, motivating efforts to experimentally study the steps during proton/electron transfer to well-characterized N2-derived species with bridging nitrides. We report here the protonation and reduction reactions of an N2-derived iron bis(nitride) complex (Rodriguez et al., Science, 2011, 334, 780). We isolate and definitively characterize triiron imido and amido intermediates that lie along the path to ammonia formation, and Mössbauer spectroscopy shows the oxidation level of iron atoms in these mixed-valence clusters. The first two H atoms add to one of the two nitrides of the bis(nitride) complex, and the proton-coupled electron transfer in the second step can be concerted or stepwise depending on the sources of protons and electrons. The characterization of partially protonated nitrides and their mechanisms of formation are expected to guide efforts to convert N2 to ammonia with mild acids.

| S-EPMC5207225 | biostudies-literature

Investigation of major amino acid residues of anti-norfloxacin monoclonal antibodies responsible for binding with fluoroquinolones.

Project description:It is important to understand the amino acid residues that govern the properties of the binding between antibodies and ligands. We studied the binding of two anti-norfloxacins, anti-nor 132 and anti-nor 155, and the fluoroquinolones norfloxacin, enrofloxacin, ciprofloxacin, and ofloxacin. Binding cross-reactivities tested by an indirect competitive enzyme-linked immunosorbent assay indicated that anti-nor 132 (22-100%) had a broader range of cross-reactivity than anti-nor 155 (62-100%). These cross-reactivities correlated with variations in the numbers of interacting amino acid residues and their positions. Molecular docking was employed to investigate the molecular interactions between the fluoroquinolones and the monoclonal antibodies. Homology models of the heavy chain and light chain variable regions of each mAb 3D structure were docked with the fluoroquinolones targeting the crucial part of the complementarity-determining regions. The fluoroquinolone binding site of anti-nor 155 was a region of the HCDR3 and LCDR3 loops in which hydrogen bonds were formed with TYR (H:35), ASN (H:101), LYS (H:106), ASN (L:92), and ASN (L:93). These regions were further away in anti-nor 132 and could not contact the fluoroquinolones. Another binding region consisting of HIS (L:38) and ASP (H:100) was found for norfloxacin, enrofloxacin, and ciprofloxacin, whereas only ASP (H:100) was found for ofloxacin.

| S-EPMC8387498 | 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