Synthesis and carbonic anhydrase inhibitory properties of amino acid – coumarin/quinolinone conjugates incorporating glycine,alanine and phenylalanine moieties

N-Protected amino acids (Gly, Ala and Phe) were reacted with amino substituted coumarin and quinolinone derivatives, leading to the corresponding N-protected amino acid–coumarin/quinolinone conjugates. The carbonic anhydrase (CA, EC 4.2.1.1) inhibitory activity of the new compounds was assessed against various human (h) isoforms, such as hCA I, hCA II, hCA IV and hCA XII. The quinolinone conjugates were inactive as enzyme inhibitors, whereas the coumarins were ineffective hCA I/II inhibitors (K_Is?>?50?μM) but were submicromolar hCA IV and XII inhibitors, with inhibition constants ranging between 92?nM and 1.19?μM for hCA IV, and between 0.11 and 0.79?μM for hCA XII. These coumarin derivatives, as many others reported earlier, thus show an interesting selective inhibitory profile for the membrane-bound over the cytosolic CA isoforms.     

Honey shows potent inhibitory activity against the bovine testes hyaluronidase

The purpose of this study was to investigate the anti-hyaluronidase activities of honeys from different botanical origins honeys in order to determine their anti-inflammatory properties. The total phenolic contents, total flavonoids and total tannin levels of six types of honey, chestnut, oak, heather, pine, buckwheat and mixed blossom, were determined. Concentration-related inhibition values were tested turbidimetrically on bovine testis hyaluronidase (BTHase) as IC₅₀ (mg/mL). All honeys exhibited various concentration-dependent degrees of inhibition against BTHase. Inhibition values varied significantly depending on honeys’ levels of phenolic contents, flavonoid and tannin. The honeys with the highest anti-hyaluronidase activity were oak, chestnut and heather. In conclusion, polyphenol-rich honeys have high anti-hyaluronidase activity, and these honeys have high protective and complementary potential against hyaluronidase-induced anti-inflammatory failures.     

MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics

Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics.With well-developed algorithms and computational tools for mass spectrometry (MS)¹ data analysis, peptide-based bottom-up proteomics has gained considerable popularity in the field of systems biology (1–9). Nevertheless, the bottom-up approach is suboptimal for the analysis of protein posttranslational modifications (PTMs) and sequence variants as a result of protein digestion (10). Alternatively, the protein-based top-down proteomics approach analyzes intact proteins, which provides a “bird''s eye” view of all proteoforms (11), including those arising from sequence variations, alternative splicing, and diverse PTMs, making it a disruptive technology for the comprehensive analysis of proteoforms (12–24). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for processing data from bottom-up proteomics experiments, the data analysis tools in top-down proteomics remain underdeveloped.The initial step in the analysis of top-down proteomics data is deconvolution of high-resolution mass and tandem mass spectra. Thorough high-resolution analysis of spectra by horn (THRASH), which was the first algorithm developed for the deconvolution of high-resolution mass spectra (25), is still widely used. THRASH automatically detects and evaluates individual isotopomer envelopes by comparing the experimental isotopomer envelope with a theoretical envelope and reporting those that score higher than a user-defined threshold. Another commonly used algorithm, MS-Deconv, utilizes a combinatorial approach to address the difficulty of grouping MS peaks from overlapping isotopomer envelopes (26). Recently, UniDec, which employs a Bayesian approach to separate mass and charge dimensions (27), can also be applied to the deconvolution of high-resolution spectra. Although these algorithms assist in data processing, unfortunately, the deconvolution results often contain a considerable amount of misassigned peaks as a consequence of the complexity of the high-resolution MS and MS/MS data generated in top-down proteomics experiments. Errors such as these can undermine the accuracy of protein identification and PTM localization and, thus, necessitate the implementation of visual components that allow for the validation and manual correction of the computational outputs.Following spectral deconvolution, a typical top-down proteomics workflow incorporates identification, quantitation, and characterization of proteoforms; however, most of the recently developed data analysis tools for top-down proteomics, including ProSightPC (28, 29), Mascot Top Down (also known as Big-Mascot) (30), MS-TopDown (31), and MS-Align+ (32), focus almost exclusively on protein identification. ProSightPC was the first software tool specifically developed for top-down protein identification. This software utilizes “shotgun annotated” databases (33) that include all possible proteoforms containing user-defined modifications. Consequently, ProSightPC is not optimized for identifying PTMs that are not defined by the user(s). Additionally, the inclusion of all possible modified forms within the database dramatically increases the size of the database and, thus, limits the search speed (32). Mascot Top Down (30) is based on standard Mascot but enables database searching using a higher mass limit for the precursor ions (up to 110 kDa), which allows for the identification of intact proteins. Protein identification using Mascot Top Down is fundamentally similar to that used in bottom-up proteomics (34), and, therefore, it is somewhat limited in terms of identifying unexpected PTMs. MS-TopDown (31) employs the spectral alignment algorithm (35), which matches the top-down tandem mass spectra to proteins in the database without prior knowledge of the PTMs. Nevertheless, MS-TopDown lacks statistical evaluation of the search results and performs slowly when searching against large databases. MS-Align+ also utilizes spectral alignment for top-down protein identification (32). It is capable of identifying unexpected PTMs and allows for efficient filtering of candidate proteins when the top-down spectra are searched against a large protein database. MS-Align+ also provides statistical evaluation for the selection of proteoform spectrum match (PrSM) with high confidence. More recently, Top-Down Mass Spectrometry Based Proteoform Identification and Characterization (TopPIC) was developed (http://proteomics.informatics.iupui.edu/software/toppic/index.html). TopPIC is an updated version of MS-Align+ with increased spectral alignment speed and reduced computing requirements. In addition, MSPathFinder, developed by Kim et al., also allows for the rapid identification of proteins from top-down tandem mass spectra (http://omics.pnl.gov/software/mspathfinder) using spectral alignment. Although software tools employing spectral alignment, such as MS-Align+ and MSPathFinder, are particularly useful for top-down protein identification, these programs operate using command line, making them difficult to use for those with limited knowledge of command syntax.Recently, new software tools have been developed for proteoform characterization (36, 37). Our group previously developed MASH Suite, a user-friendly interface for the processing, visualization, and validation of high-resolution MS and MS/MS data (36). Another software tool, ProSight Lite, developed recently by the Kelleher group (37), also allows characterization of protein PTMs. However, both of these software tools require prior knowledge of the protein sequence for the effective localization of PTMs. In addition, both software tools cannot process data from liquid chromatography (LC)-MS and LC-MS/MS experiments, which limits their usefulness in large-scale top-down proteomics. Thus, despite these recent efforts, a multifunctional software platform enabling identification, quantitation, and characterization of proteins from top-down spectra, as well as visual validation and data correction, is still lacking.Herein, we report the development of MASH Suite Pro, an integrated software platform, designed to incorporate tools for protein identification, quantitation, and characterization into a single comprehensive package for the analysis of top-down proteomics data. This program contains a user-friendly customizable interface similar to the previously developed MASH Suite (36) but also has a number of new capabilities, including the ability to handle complex proteomics datasets from LC-MS and LC-MS/MS experiments, as well as the ability to identify unknown proteins and PTMs using MS-Align+ (32). Importantly, MASH Suite Pro also provides visualization components for the validation and correction of the computational outputs, which ensures accurate and reliable deconvolution of the spectra and localization of PTMs and sequence variations.     

A New Type of Anatolian Propolis: Evaluation of Its Chemical Composition,Activity Profile and Botanical Origin

This study was undertaken to analyze the phenolic profiles of 19 propolis samples from Turkey by using a high‐performance thin‐layer chromatographic (HPTLC) method in order to identify their plant origins. Furthermore, their antioxidant and antimicrobial activity profiles were comparatively evaluated. For the appraisal of antioxidant potential, total phenolic (TPC) and total flavonoid contents (TFC) of propolis samples were firstly determined and then their effects on free radicals were evaluated by FRAP, ABTS^.+, CUPRAC, DPPH^. and HPTLC‐DPPH^. methods. Antimicrobial activity of propolis samples against Staphylococcus aureus (ATCC 6538), Pseudomonas aeruginosa (ATCC 15442), Escherichia coli (ATCC 11229) and Candida albicans ATCC 10231 were determined by disc diffusion and broth dilution methods. HPTLC fingerprinting analyses revealed that O‐type (botanical origin from Populus nigra L.) was the primarily available propolis type in Turkey. Moreover, 3‐O‐methylquercetin (3MQ) rich propolis was identified as a new propolis type for the first time. Principal component analysis (PCA) indicated that 3MQ‐type propolis differs from the O‐type. Antioxidant activity studies showed that O‐type of propolis possesses higher antioxidant effect than the other tested propolis types. Quercetin, caffeic acid, caffeic acid phenethyl ester (CAPE) and galangin were determined to contribute significantly to the antioxidant potential of O‐type propolis among others. Propolis extracts exerted moderate antimicrobial activity against the tested microorganisms with MIC values between the ranges of 128–512 μg/mL.     

Quantitative Proteome Analysis of Brain Subregions and Spinal Cord from Experimental Autoimmune Encephalomyelitis Mice by TMT‐Based Mass Spectrometry

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS); its cause is unknown. To understand the pathogenesis of MS, researchers often use the experimental autoimmune encephalomyelitis (EAE) mouse model. Here, the aim is to build a proteome map of the biological changes that occur during MS at the major onset sites—the brain and the spinal cord. Quantitative proteome profiling is performed in five specific brain regions and the spinal cord of EAE and healthy mice with high‐resolution mass spectrometry based on tandem mass tags. On average, 7400 proteins per region are quantified, with the most differentially expressed proteins in the spinal cord (1691), hippocampus (104), frontal cortex (83), cerebellum (63), brainstem (50), and caudate nucleus (41). Moreover, region‐specific and commonly expressed proteins in each region are identified and bioinformatics analysis is performed. Pathway analysis reveals that protein clusters resemble their functions in disease pathogenesis (i.e., by inducing inflammatory responses, immune activation, and cell–cell adhesion). In conclusion, the study provides an understanding of the pathogenesis of MS in the EAE animal model. It is expected that the comprehensive proteome map of the brain and spinal cord can be used to identify biomarkers for the pathogenesis of MS.     

Impacts of dynamic degradation on the morphological and mechanical characterisation of porous magnesium scaffold

Biomechanics and Modeling in Mechanobiology - This study employs a computational approach to analyse the impact of morphological changes on the structural properties of biodegradable porous Mg...     

Tyrosine phosphorylation directs TACE into extracellular vesicles via unconventional secretion

When studying how HIV‐1 Nef can promote packaging of the proinflammatory transmembrane protease TACE (tumor necrosis factor‐α converting enzyme) into extracellular vesicles (EVs) we have revealed a novel tyrosine kinase‐regulated unconventional protein secretion (UPS) pathway for TACE. When TACE was expressed without its trafficking cofactor iRhom allosteric Hck activation by Nef triggered translocation of TACE into EVs. This process was insensitive to blocking of classical secretion by inhibiting endoplasmic reticulum (ER) to Golgi transport, and involved a distinct form of TACE devoid of normal glycosylation and incompletely processed for prodomain removal. Like most other examples of UPS this process was Golgi reassembly stacking protein (GRASP)‐dependent but was not associated with ER stress. These data indicate that Hck‐activated UPS provides an alternative pathway for TACE secretion that can bypass iRhom‐dependent ER to Golgi transfer, and suggest that tyrosine phosphorylation might have a more general role in regulating UPS.      

Modulational Instability,Ion-Acoustic Envelope Solitons,and Rogue Waves in Four-Component Plasmas

Plasma Physics Reports - Modulational instability (MI) of ion-acoustic waves (IAWs) has been theoretically investigated in a plasma system which is composed of inertial warm adiabatic ions,...     

A flavone from the ethyl acetate extract of Leea rubra leaves with DNA damage protection and antineoplastic activity

Among the major constituents of Leea rubra (Family Vitaceae) leaves, phenolic and flavonoind compounds are most important for therapeutic purposes and the plant parts have been used in traditional medicine to treat several diseases for long. Thus, in order to scientifically confirm the traditional uses of the L. rubra leaves, the present study was designed to investigate the efficacy of the isolated flavones against AAPH induced oxidative damage to pUC19 DNA by gel electrophoresis and antineoplastic activity was evaluated on Ehrlich ascites carcinoma (EAC) bearing Swiss albino mice by evaluating percentage inhibition of cell growth, morphological changes of EAC cells and hematological parameters of the mice. The isolation was carried out by column chromatography and structure was revealed by ¹H-NMR and ¹³C NMR. The result shows that, the isolated compound was identified as myricetin 4'-methoxy-3-O-α-l-rhamnopyranoside based on previously reported data. The isolated flavone effectively inhibited AAPH-induced oxidative damage to DNA; because it could inhibit the formation of circular and linear forms of the DNA. In anti-proliferative assay, 76% growth inhibition of EAC cells was observed as compare to the control mice (p<0.05) at a dose 100 mg/kg body weight. Thus the isolated flavone showed great importance as a possible therapeutic agent in preventing oxidative damage to DNA and the chronic diseases caused by such DNA damage, and can also become important in cancer chemotherapy.