scholarly journals Controversy of Peptide Cyclization from Tripeptide

Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 389
Author(s):  
Chung-Yin Lin ◽  
Subrata Chakraborty ◽  
Chia-Wei Wong ◽  
Dar-Fu Tai
Keyword(s):  
High Resolution Mass Spectrometry ◽  
High Dilution ◽  
Suberites Domuncula ◽  
Peptide Coupling ◽  
Peptide Cyclization ◽  
Cyclic Hexapeptide ◽  
Naturally Occurring ◽  
Original Target ◽  
Higher Temperature ◽  
Cyclic Tripeptide

The present investigation reports an attempt to synthesize naturally occurring α-cyclic tripeptide cyclo(Gly-l-Pro-l-Glu) 1, [cyclo(GPE)], previously isolated from the Ruegeria strain of bacteria with marine sponge Suberites domuncula. Three linear precursors, Boc-GPE(OBn)2, Boc-PE(OBn)G and Boc-E(OBn)GP, were synthesized using a solution phase peptide coupling protocol. Although cyclo(GPE) 1 was our original target, all precursors were dimerized and cyclized at 0 °C with high dilution to form corresponding α-cyclic hexapeptide, cyclo(GPE(OBn))27, which was then converted to cyclic hexapeptide cyclo(GPE)22. Cyclization at higher temperature induced racemization and gave cyclic tripeptide cyclo(GPDE(OBn)) 9. Structure characteristics of the newly synthesized cyclopeptides were determined using 1H-NMR, 13C-NMR and high-resolution mass spectrometry. The chemical shift values of carbonyls of 2 and 7 are larger than 170 ppm, indicating the formation of a cyclic hexapeptide.

scholarly journals Green resins from renewable resources

2021 ◽  
Author(s):  
Justin J. Kosalka
Keyword(s):  
Phenolic Compounds ◽  
High Resolution Mass Spectrometry ◽  
Dicarboxylic Acids ◽  
13C Nmr Spectroscopy ◽  
One Pot ◽  
1H And 13C Nmr ◽  
X Ray Crystallography ◽  
Naturally Occurring ◽  
One Step ◽  
Acid Catalyzed

This work was aimed at exploring bio-based materials for the purpose of toner production on an industrial scale. Polyester and polyether based resins were prepared in good yields from naturally occurring phenolic compounds with desired thermal and physical properties. Phenols with varying functionality such as guaiacol, eugenol and vanillin along with two synthetically produced phenolic compounds modelling the β-O-4 linkage found in softwood lignins were explored as suitable precursors to synthetic, "green", resins. Phenols were transformed into diols using glycerine carbonate and a base catalyzed reaction. Diols were then polymerized with dicarboxylic acids in an acid catalyzed, transesterfication, reaction. A novel, bio-based polyether was synthesized in one pot, one step polymerization using vanillin. Thermal properties ((Tg) and (Ts) of resulting resins were evaluated. Resulting compounds and polymers were characterized using 1H and 13C NMR spectroscopy, high resolution mass spectrometry, elemental analysis, X-ray crystallography, DSC and GPC.

scholarly journals Natural isotope correction improves analysis of protein modification dynamics

2020 ◽  
Author(s):  
Jörn Dietze ◽  
Alienke van Pijkeren ◽  
Mathias Ziegler ◽  
Marcel Kwiatkowski ◽  
Ines Heiland
Keyword(s):  
Mass Spectrometry ◽  
Protein Modification ◽  
High Resolution Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Stable Isotope Labelling ◽  
Isotope Labelling ◽  
Naturally Occurring ◽  
Natural Isotope ◽  
Experimental Approaches ◽  
Correct Estimation

AbstractStable isotope labelling in combination with high resolution mass spectrometry approaches are increasingly used to analyse both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, none of them is universally applicable for all potential experimental approaches. We here present PICor which has been streamlined for multiple isotope labelling isotopologue correction in proteomics or metabolomics approaches. We demonstrate the importance for accurate measurement of the dynamics of protein modifications, such as histone acetylation.

scholarly journals Natural isotope correction improves analysis of protein modification dynamics

2021 ◽  
Author(s):  
Jörn Dietze ◽  
Alienke van Pijkeren ◽  
Anna-Sophia Egger ◽  
Mathias Ziegler ◽  
Marcel Kwiatkowski ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Modification ◽  
High Resolution Mass Spectrometry ◽  
Accurate Determination ◽  
Mass Spectrometry Data ◽  
Stable Isotope Labelling ◽  
Isotope Labelling ◽  
Naturally Occurring ◽  
Correct Estimation

AbstractStable isotope labelling in combination with high-resolution mass spectrometry approaches are increasingly used to analyze both metabolite and protein modification dynamics. To enable correct estimation of the resulting dynamics, it is critical to correct the measured values for naturally occurring stable isotopes, a process commonly called isotopologue correction or deconvolution. While the importance of isotopologue correction is well recognized in metabolomics, it has received far less attention in proteomics approaches. Although several tools exist that enable isotopologue correction of mass spectrometry data, the majority is tailored for the analysis of low molecular weight metabolites. We here present PICor which has been developed for isotopologue correction of complex isotope labelling experiments in proteomics or metabolomics and demonstrate the importance of appropriate correction for accurate determination of protein modifications dynamics, using histone acetylation as an example.

scholarly journals Green resins from renewable resources

2021 ◽  
Author(s):  
Justin J. Kosalka
Keyword(s):  
Phenolic Compounds ◽  
High Resolution Mass Spectrometry ◽  
Dicarboxylic Acids ◽  
13C Nmr Spectroscopy ◽  
One Pot ◽  
1H And 13C Nmr ◽  
X Ray Crystallography ◽  
Naturally Occurring ◽  
One Step ◽  
Acid Catalyzed

This work was aimed at exploring bio-based materials for the purpose of toner production on an industrial scale. Polyester and polyether based resins were prepared in good yields from naturally occurring phenolic compounds with desired thermal and physical properties. Phenols with varying functionality such as guaiacol, eugenol and vanillin along with two synthetically produced phenolic compounds modelling the β-O-4 linkage found in softwood lignins were explored as suitable precursors to synthetic, "green", resins. Phenols were transformed into diols using glycerine carbonate and a base catalyzed reaction. Diols were then polymerized with dicarboxylic acids in an acid catalyzed, transesterfication, reaction. A novel, bio-based polyether was synthesized in one pot, one step polymerization using vanillin. Thermal properties ((Tg) and (Ts) of resulting resins were evaluated. Resulting compounds and polymers were characterized using 1H and 13C NMR spectroscopy, high resolution mass spectrometry, elemental analysis, X-ray crystallography, DSC and GPC.

scholarly journals Exposing the High Heterogeneity of Circulating Pro B-Type Natriuretic Peptide Fragments in Healthy Individuals and Heart Failure Patients

2020 ◽  
Vol 66 (9) ◽  
pp. 1200-1209 ◽  
Author(s):  
Benno Amplatz ◽  
Bettina Sarg ◽  
Klaus Faserl ◽  
Angelika Hammerer-Lercher ◽  
Johannes Mair ◽  
...  
Keyword(s):  
Heart Failure ◽  
Natriuretic Peptide ◽  
Isotope Labeling ◽  
High Resolution Mass Spectrometry ◽  
Molecular Forms ◽  
Peptide Fragments ◽  
Naturally Occurring ◽  
Current Thinking ◽  
Processing Modes ◽  
Molecular Complexity

Abstract Background The high molecular complexity of variably O-glycosylated and degraded pro B-type natriuretic peptide (proBNP) derived molecular forms challenges current immunoassays. Antibodies used show pronounced differences in cross-reactivities with these circulating fragments, which still need to be better characterized on a molecular level. To pave the way for advanced quantitative assays in the future, it is critical to fully understand these circulating forms. Methods Plasma samples were collected from 8 heart failure (HF) patients and 2 healthy controls. NT-proBNP and proBNP were purified by immunoprecipitation and analyzed by nano-flow liquid chromatography coupled to high-resolution mass spectrometry. Fragments formed during proteolysis in solution digestion were distinguished from naturally occurring peptides by using an 18O stable isotope labeling strategy. Results We detected 16 previously unknown circulating fragments of proBNP peptides (9 of which are located in the N-terminal and 7 in the C-terminal region), revealing a more advanced state of degradation than previously known. Two of these fragments are indicative of either unidentified processing modes or a far-reaching C-terminal degradation (or a combination thereof) of the precursor proBNP. Conclusions Our results further restrict ideal target epitopes for immunoassay antibodies and expand the current thinking of diversity, degradation, and processing of proBNP, as well as the distribution of circulating forms.

scholarly journals Biocontrol of the Food-Borne Pathogens Listeria monocytogenes and Salmonella enterica Serovar Poona on Fresh-Cut Apples with Naturally Occurring Bacterial and Yeast Antagonists

2006 ◽  
Vol 72 (2) ◽  
pp. 1135-1140 ◽  
Author(s):  
Britta Leverentz ◽  
William S. Conway ◽  
Wojciech Janisiewicz ◽  
Maribel Abadias ◽  
Cletus P. Kurtzman ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Salmonella Enterica ◽  
Human Pathogens ◽  
Food Borne Pathogens ◽  
Naturally Occurring ◽  
Food Borne ◽  
Different Temperatures ◽  
Apple Tissue ◽  
Higher Temperature ◽  
Fresh Cut

ABSTRACT Fresh-cut apples contaminated with either Listeria monocytogenes or Salmonella enterica serovar Poona, using strains implicated in outbreaks, were treated with one of 17 antagonists originally selected for their ability to inhibit fungal postharvest decay on fruit. While most of the antagonists increased the growth of the food-borne pathogens, four of them, including Gluconobacter asaii (T1-D1), a Candida sp. (T4-E4), Discosphaerina fagi (ST1-C9), and Metschnikowia pulcherrima (T1-E2), proved effective in preventing the growth or survival of food-borne human pathogens on fresh-cut apple tissue. The contaminated apple tissue plugs were stored for up to 7 days at two different temperatures. The four antagonists survived or grew on the apple tissue at 10 or 25°C. These four antagonists reduced the Listeria monocytogenes populations and except for the Candida sp. (T4-E4), also reduced the S. enterica serovar Poona populations. The reduction was higher at 25°C than at 10°C, and the growth of the antagonists, as well as pathogens, increased at the higher temperature.

scholarly journals Bioactive 3D structures of naturally occurring peptides and their application in drug design

2021 ◽  
Vol 85 (1) ◽  
pp. 24-32
Author(s):  
Yuichi Masuda
Keyword(s):  
Drug Design ◽  
3D Structure ◽  
Amyloid Β ◽  
Cell Membrane Permeability ◽  
Amyloid Β Protein ◽  
Nmr Analysis ◽  
3D Structures ◽  
Cyclic Hexapeptide ◽  
Naturally Occurring ◽  
Turn Structure

Abstract Naturally occurring peptides form unique 3D structures, which are critical for their bioactivities. To gain useful insights into drug design, the relationship between the 3D structure and bioactivity of the peptides has been studied. Solid-state nuclear magnetic resonance (NMR) analysis of the 42-residue amyloid β-protein (Aβ42) suggested the presence of toxic conformers with a turn structure at positions 22 and 23 in the aggregates. Antibodies specific to this turn structure could be utilized for immunotherapy and early diagnosis of Alzheimer's disease. Solution NMR analysis of apratoxin A, a cyclic depsipeptide with potent cytotoxicity, proposed an accurate structural model with an important bend structure, which led to the development of highly active mimetics. X-ray crystal analysis of PF1171F, a cyclic hexapeptide with insecticidal activity, indicated the formation of 4 intramolecular hydrogen bonds, which play an important role in cell membrane permeability of PF1171F.

scholarly journals Determination of the Absolute Configuration of Bioactive Indole-Containing Pyrazino[2,1-b]quinazoline-3,6-Diones and Study of Their In Vitro Metabolic Profile

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5070
Author(s):  
Solida Long ◽  
Izadora L. Furlani ◽  
Juliana M. de Oliveira ◽  
Diana I. S. P. Resende ◽  
Artur M. S. Silva ◽  
...  
Keyword(s):  
Absolute Configuration ◽  
High Performance ◽  
High Resolution Mass Spectrometry ◽  
Liver Microsomes ◽  
Metabolic Studies ◽  
Metabolic Characteristics ◽  
Naturally Occurring ◽  
The Absolute ◽  
First Time

In recent decades, fungi-derived naturally occurring quinazolines have emerged as potential drug candidates. Nevertheless, most studies are conducted for bioactivity assays, and little is known about their absorption, distribution, metabolism, and elimination (ADME) properties. To perform metabolic studies, the synthesis of the naturally occurring quinazolinone, fiscalin B (1), and its chloro derivative, 4-((1H-indol-3-yl)methyl)-8,10-dichloro-1-isobutyl-1,2-dihydro-6H-pyrazino[2,1-b]quinazoline-3,6(4H)-dione (2), disclosed as an antibacterial agent, was performed in a gram scale using a microwave-assisted polycondensation reaction with 22% and 17% yields, respectively. The structure of the non-natural (+)-fiscalin B was established, for the first time, by X-ray crystallography as (1R,4S)-1, and the absolute configuration of the naturally occurring fiscalin B (-)-1 was confirmed by comparison of its calculated and experimental electronic circular dichroism (ECD) spectra as (1S,4R)-1. In vitro metabolic studies were monitored for this class of natural products for the first time by ultra-high-performance liquid chromatography (UHPLC) coupled with high-resolution mass spectrometry (HRMS). The metabolic characteristics of 1 and 2 in human liver microsomes indicated hydration and hydroxylation mass changes introduced to the parent drugs.

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