Supramolecular self-assemblies of inverted cucurbit[7]uril with biogenic amines

2019 ◽  
Vol 43 (1) ◽  
pp. 407-412
Author(s):  
Pei-Hui Shan ◽  
Zhi-Rui Zhang ◽  
Dong Bai ◽  
Bing Bian ◽  
Zhu Tao ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Binding Affinity ◽  
Biogenic Amine ◽  
Binding Sites ◽  
Experimental Results ◽  
Binding Interactions ◽  
Strong Binding

The binding interactions between six biogenic amine guests and the iQ[7] host were investigated. The experimental results have revealed that iQ[7] shows strong binding affinity towards five of the studied biogenic amines, but not histamine, and that the binding sites are different depending on the structure of the biogenic amine.

scholarly journals Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

2021 ◽  
Author(s):  
Tomio Iwasaki ◽  
Masashi Maruyama ◽  
Tatsuya Niwa ◽  
Toshiki Sawada ◽  
Takeshi Serizawa
Keyword(s):  
Methyl Methacrylate ◽  
Binding Affinity ◽  
Molecular Simulation ◽  
Dynamics Simulation ◽  
Binding Affinities ◽  
Materials Informatics ◽  
Poly Methyl Methacrylate ◽  
Strong Binding ◽  
Experimental Values ◽  
Pmma Resin

AbstractPeptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

scholarly journals Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution

2013 ◽  
Vol 368 (1632) ◽  
pp. 20130018 ◽  
Author(s):  
Andrea I. Ramos ◽  
Scott Barolo
Keyword(s):  
Transcription Factor ◽  
Binding Affinity ◽  
Binding Sites ◽  
Target Genes ◽  
Gene Activation ◽  
Transcriptional Response ◽  
Morphogen Gradients ◽  
Weak Binding ◽  
Initial Hypothesis

In the era of functional genomics, the role of transcription factor (TF)–DNA binding affinity is of increasing interest: for example, it has recently been proposed that low-affinity genomic binding events, though frequent, are functionally irrelevant. Here, we investigate the role of binding site affinity in the transcriptional interpretation of Hedgehog (Hh) morphogen gradients . We noted that enhancers of several Hh-responsive Drosophila genes have low predicted affinity for Ci, the Gli family TF that transduces Hh signalling in the fly. Contrary to our initial hypothesis, improving the affinity of Ci/Gli sites in enhancers of dpp , wingless and stripe , by transplanting optimal sites from the patched gene, did not result in ectopic responses to Hh signalling. Instead, we found that these enhancers require low-affinity binding sites for normal activation in regions of relatively low signalling. When Ci/Gli sites in these enhancers were altered to improve their binding affinity, we observed patterning defects in the transcriptional response that are consistent with a switch from Ci-mediated activation to Ci-mediated repression. Synthetic transgenic reporters containing isolated Ci/Gli sites confirmed this finding in imaginal discs. We propose that the requirement for gene activation by Ci in the regions of low-to-moderate Hh signalling results in evolutionary pressure favouring weak binding sites in enhancers of certain Hh target genes.

Detection of Biogenic Amine Producer Bacteria in a Typical Italian Goat Cheese

2008 ◽  
Vol 71 (1) ◽  
pp. 205-209 ◽  
Author(s):  
SILVIA BONETTA ◽  
SARA BONETTA ◽  
ELISABETTA CARRARO ◽  
JEAN DANIEL COÏSSON ◽  
FABIANO TRAVAGLIA ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Enterococcus Faecalis ◽  
Biogenic Amine ◽  
Pediococcus Acidilactici ◽  
Bacterial Strains ◽  
Goat Cheese ◽  
Low Concentrations ◽  
Amine Content ◽  
High Concentrations ◽  
Almost All

The aim of this study was to research decarboxylating bacterial strains and biogenic amine content in a typical Italian goat cheese (Robiola di Roccaverano). The study was performed on fresh and ripened samples of goat cheese manufactured from industrial and artisanal producers. Sixty-seven bacterial strains isolated showed decarboxylating activity, and Enterococcus faecalis was the most widespread decarboxylating species in all artisanal and industrial products. Pediococcus acidilactici and Enterococcus malodoratus were also identified as biogenic amine producers in Robiola di Roccaverano cheese. All the E. faecalis strains isolated in this study were able to decarboxylate tyrosine. Tyramine was the most abundant biogenic amine in cheese samples, while histamine was the most widespread. High amounts of these two biogenic amines were found in ripened samples (up to 2,067 mg/kg for tyramine and 1,786 mg/kg for histamine), whereas 2-phenylethylamine and tryptamine were present in almost all ripened cheeses at low concentrations. The detection of strains producing biogenic amines and the high concentrations of tyramine and histamine found in ripened Robiola di Roccaverano could represent a potential risk to the consumer.

scholarly journals Epitope-Based Peptide Vaccine Against Fructose-Bisphosphate Aldolase of Madurella mycetomatis Using Immunoinformatics Approaches

2018 ◽  
Vol 12 ◽  
pp. 117793221880970 ◽  
Author(s):  
Arwa A Mohammed ◽  
Ayman MH ALnaby ◽  
Solima M Sabeel ◽  
Fagr M AbdElmarouf ◽  
Amina I Dirar ◽  
...  
Keyword(s):  
B Cell ◽  
Binding Affinity ◽  
Mhc Class Ii ◽  
Bacterial Infections ◽  
Peptide Vaccine ◽  
Fructose Bisphosphate ◽  
Mhc I ◽  
Strong Binding ◽  
Fructose Bisphosphate Aldolase ◽  
Madurella Mycetomatis

Background: Mycetoma is a distinct body tissue destructive and neglected tropical disease. It is endemic in many tropical and subtropical countries. Mycetoma is caused by bacterial infections ( actinomycetoma) such as Streptomyces somaliensis and Nocardiae or true fungi ( eumycetoma) such as Madurella mycetomatis. To date, treatments fail to cure the infection and the available marketed drugs are expensive and toxic upon prolonged usage. Moreover, no vaccine was prepared yet against mycetoma. Aim: The aim of this study is to predict effective epitope-based vaccine against fructose-bisphosphate aldolase enzymes of M. mycetomatis using immunoinformatics approaches. Methods and materials: Fructose-bisphosphate aldolase of M. mycetomatis sequence was retrieved from NCBI. Different prediction tools were used to analyze the nominee’s epitopes in Immune Epitope Database for B-cell, T-cell MHC class II and class I. Then the proposed peptides were docked using Autodock 4.0 software program. Results and conclusions: The proposed and promising peptides KYLQ show a potent binding affinity to B-cell, FEYARKHAF with a very strong binding affinity to MHC I alleles and FFKEHGVPL that shows a very strong binding affinity to MHC II and MHC I alleles. This indicates a strong potential to formulate a new vaccine, especially with the peptide FFKEHGVPL which is likely to be the first proposed epitope-based vaccine against fructose-bisphosphate aldolase of M. mycetomatis. This study recommends an in vivo assessment for the most promising peptides especially FFKEHGVPL.

scholarly journals Biogenic Amines in Plant-Origin Foods: Are They Frequently Underestimated in Low-Histamine Diets?

Foods ◽  
2018 ◽  
Vol 7 (12) ◽  
pp. 205 ◽  
Author(s):  
Sònia Sánchez-Pérez ◽  
Oriol Comas-Basté ◽  
Judit Rabell-González ◽  
M. Veciana-Nogués ◽  
M. Latorre-Moratalla ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Biogenic Amine ◽  
Plasma Levels ◽  
Diamine Oxidase ◽  
Great Variability ◽  
Plant Origin ◽  
Lower Affinity ◽  
Origin And Evolution ◽  
Histamine Intolerance ◽  
Existing Data

Low-histamine diets are currently used to reduce symptoms of histamine intolerance, a disorder in histamine homeostasis that increases plasma levels, mainly due to reduced diamine-oxidase (DAO) activity. These diets exclude foods, many of them of plant origin, which patients associate with the onset of the symptomatology. This study aimed to review the existing data on histamine and other biogenic amine contents in nonfermented plant-origin foods, as well as on their origin and evolution during the storage or culinary process. The only plant-origin products with significant levels of histamine were eggplant, spinach, tomato, and avocado, each showing a great variability in content. Putrescine has been found in practically all plant-origin foods, probably due to its physiological origin. The high contents of putrescine in certain products could also be related to the triggering of the symptomatology by enzymatic competition with histamine. Additionally, high spermidine contents found in some foods should also be taken into account in these diets, because it can also be metabolized by DAO, albeit with a lower affinity. It is recommended to consume plant-origin foods that are boiled or are of maximum freshness to reduce biogenic amine intake.

Biogenic Amine Index for Freshness Evaluation in Iced Mediterranean Hake (Merluccius merluccius)

2005 ◽  
Vol 68 (11) ◽  
pp. 2433-2438 ◽  
Author(s):  
S. BAIXAS-NOGUERAS ◽  
S. BOVER-CID ◽  
M. T. VECIANA-NOGUÉS ◽  
A. MARINÉ-FONT ◽  
M. C. VIDAL-CAROU
Keyword(s):  
Biogenic Amines ◽  
Biogenic Amine ◽  
Sensory Analysis ◽  
Pelagic Fish ◽  
Point Of View ◽  
Ice Storage ◽  
Complementary Information ◽  
Merluccius Merluccius ◽  
Sensory Data ◽  
Chilling Temperatures

Biogenic amine accumulation was studied during the ice storage of Mediterranean hake. Sensory analysis and counts of Shewanella, Pseudomonas, enterobacteria, psychrotrophic, and mesophilic bacteria provided complementary information on hake spoilage. Putrescine and cadaverine were the main amines accumulated, whereas histamine and tyramine were minor amines but had qualitative interest from the hygienic point of view. Although all biogenic amines were less abundant than in pelagic fish, they may also be used as indicators of freshness and/or spoilage in hake. Cadaverine was the amine best correlated with Shewanella, which was the specific spoilage organism. Therefore, cadaverine may be regarded as the specific spoilage biogenic amine for hake stored at chilling temperatures. However, the biogenic amine index, which considers cadaverine, putrescine, histamine, and tyramine, has several advantages as an indicator of hake quality. Taking into account sensory data, an acceptability limit of the biogenic amine index could be established in 15 to 20 μg/g.

Detection and Quantification of Biogenic Amines in Fermented Food Products Sold in Botswana

2010 ◽  
Vol 73 (9) ◽  
pp. 1703-1708 ◽  
Author(s):  
CLEMENT MAGWAMBA ◽  
MAITSHWARELO IGNATIUS MATSHEKA ◽  
SISAI MPUCHANE ◽  
BERHANU ABEGAZ GASHE
Keyword(s):  
Biogenic Amines ◽  
Biogenic Amine ◽  
High Performance ◽  
Fermented Food ◽  
Allowable Limit ◽  
Fermented Beverages ◽  
Sour Milk ◽  
Mean Concentration ◽  
The U.S ◽  
Detection And Quantification

The incidence and concentrations associated with four important biogenic amines in leading commercial fermented beverages consumed in Botswana were determined using high-performance liquid chromatography. In 87 sorghum brew and 84 sour milk (madila, amasi) samples tested, putrescine was the most prevalent biogenic amine (63 and 61%, respectively), while histamine was the least prevalent (24 and 8%, respectively). Cadaverine was the most frequently detected biogenic amine in 79 of the commercial sour maize beverage (mageu/mahewu) samples tested (found in 70% of the samples), while tyramine was the least detected (occurring in 3% of the samples). In sorghum brew and sour milk, tyramine was found to be the most concentrated (mean concentration of 2.08 mg/100 ml and 3.2 mg/100 ml, respectively), and histamine was found to be the least concentrated (mean concentration of 0.94 mg/100 ml and 0.31 mg/100 ml, respectively). Overall, the biogenic amine concentrations of all three fermented products were within acceptable limits. However, one sorghum brew sample had a histamine content of 5.8 mg/100 ml, which was above the 5.0 mg/100 g allowable limit suggested by the U.S. Food and Drug Administration.

scholarly journals Quantification of Biogenic Amines in 35 Korean Cottage Industry Traditional Gochujang (Fermented Red Pepper Paste) Products

Foods ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2370
Author(s):  
Srinivasan Ramalingam ◽  
Ashutosh Bahuguna ◽  
SeMi Lim ◽  
Ah-ryeong Joe ◽  
Jong-Suk Lee ◽  
...  
Keyword(s):  
Biogenic Amines ◽  
Biogenic Amine ◽  
Red Pepper ◽  
Human Consumption ◽  
Cottage Industry ◽  
Regulatory Authorities

Traditional gochujang is well known for its distinguished flavor and taste. However, the safety of cottage industry gochujang products is uncertain, particularly, in terms of biogenic amine (BA) content which is not yet documented. The present study aimed to determine the level of BAs present in 35 traditional gochujang products nationwide. All gochujang products had considerable amounts of total BAs ranging from 52.95 mg/kg to 176.24 mg/kg. Individually, histamine and tyramine were either not detected or detected up to 16.94 mg/kg and 2.15–52.34 mg/kg, respectively. In all the tested gochujang products, putrescine, spermidine, and spermine were detected in the range of 7.60–56.72 mg/kg, 14.96–36.93 mg/kg, and 4.68–16.31 mg/kg, respectively. A total of 22 and 19 gochujang products had less than 1 mg/kg of cadaverine and histamine, respectively. The findings indicate that all the gochujang products tested herein had BA levels below the suggested toxicity limits recommended by the various regulatory authorities, which reveal that they are safe for human consumption.

scholarly journals The Missing Label Problem: Addressing False Assumptions Improves Ligand-Based Virtual Screening

2019 ◽  
Author(s):  
Lewis Martin ◽  
Michael Bowen
Keyword(s):  
Virtual Screening ◽  
Binding Sites ◽  
Design Theory ◽  
Mapping Function ◽  
True Negative ◽  
Binding Interactions ◽  
Multiple Binding Sites ◽  
A New Technique ◽  
The One ◽  
Machine Readable

<div>Ligand-based virtual screening (LBVS) uses machine readable representations of chemicals to learn a mapping function that can predict binding interactions with protein labels. Because it is highly scalable it is increasingly used in drug development in academic and pharmaceutical contexts. We have identified assumptions commonly used in LBVS that are false, which collectively can be described as the missing label problem. Firstly, many of the binding interactions in the bioactivity databases typically used to train LBVS models have never been tested before, but the absence of a label is interpreted by most models as a true negative. Secondly, many proteins have multiple binding sites with unrelated shapes but the associated ligands are grouped together under the one protein label. These assumptions frustrate the ability of the model to learn a correct mapping function. Here we use statistical techniques to predict values for the missing labels and binding sites and show how this improves the ability of LBVS models to rank ligands correctly. In the process we introduce a new technique for removing bias during model evaluation based on data blocking from experimental design theory. All data and code for analysis and generating figures is publicly available on github (https://github.com/ljmartin/Missing_label_problem).<br></div>

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