Application of a Combined Peptidomics and In Silico Approach for the Identification of Novel Dipeptidyl Peptidase-IV-Inhibitory Peptides in In Vitro Digested Pinto Bean Protein Extract

The conventional approach in bioactive peptides discovery, which includes extensive bioassay-guided fractionation and purification processes, is tedious, time-consuming and not always successful. The recently developed bioinformatics-driven in silico approach is rapid and cost-effective; however, it lacks an actual physiological significance. In this study a new integrated peptidomics and in silico method, which combines the advantages of the conventional and in silico approaches by using the pool of peptides identified in a food hydrolysate as the starting point for subsequent application of selected bioinformatics tools, has been developed. Pinto bean protein extract was in vitro digested and peptides were identified by peptidomics. The pool of obtained peptides was screened by in silico analysis and structure–activity relationship modelling. Three peptides (SIPR, SAPI and FVPH) were selected as potential inhibitors of the dipeptidyl-peptidase-IV (DPP-IV) enzyme by this integrated approach. In vitro bioactivity assay showed that all three peptides were able to inhibit DPP-IV with the tetra-peptide SAPI showing the highest activity (IC50 = 57.7 μmol/L). Indeed, a new possible characteristic of peptides (i.e., the presence of an S residue at the N-terminus) able to inhibit DPP-IV was proposed.

Sensitive and Robust LC-MS/MS Assay to Quantify 25-Hydroxyvitamin D in Leftover Protein Extract from Dried Blood Spots

Neonatal dried blood spots (DBS) provide a remarkable resource for biobanks. These microsamples can provide information related to the genetic correlates of disease and can be used to quantify a range of analytes, such as proteins and small molecules. However, after routine neonatal screening, the amount of DBS sample available is limited. To optimize the use of these samples, there is a need for sensitive assays which are integrated across different analytic platforms. For example, after DNA extraction, protein extracts are available for additional analyses. We describe a sensitive and robust LC-MS/MS method for 25-hydroxyvitamin D2 and 25-hydroxyvitamin D3 optimized for leftover protein extracts from DBS, which has excellent recovery, precision, and accuracy.

ADP-ribosyl transferase activity and gamma radiation cytotoxicity of Pseudomonas aeruginosa exotoxin A

This work explores the ADP-ribosyltransferase activity of Pseudomonas (P.) aeruginosa exotoxin A using the guanyl hydrazone derivative, nitrobenzylidine aminoguanidine (NBAG) and the impact of gamma radiation on its efficacy. Unlike the conventional detection methods, NBAG was used as the acceptor of ADP ribose moiety instead of wheat germ extract elongation factor 2. Exotoxin A was extracted from P. aeruginosa clinical isolates and screened for toxA gene using standard PCR. NBAG was synthesized using aminoguanidine bicarbonate and 4-nitrobenzaldehyde and its identity has been confirmed by UV, FTIR, Mass and 13C-NMR spectroscopy. The ADP-ribosyl transferase activity of exotoxin A on NBAG in the presence of Nicotinamide adenine dinucleotide (NAD+) was recorded using UV spectroscopy and HPLC. In vitro ADP-ribosyl transferase activity of exotoxin A protein extract was also explored by monitoring its cytotoxicity on Hep-2 cells using sulforhodamine B cytotoxicity assay. Bacterial broths were irradiated at 5, 10, 15, 24 Gy and exotoxin A protein extract activity were assessed post exposure. Exotoxin A extract exerted an ADP-ribosyltransferase ability which was depicted by the appearance of a new ʎmax after the addition of exotoxin A to NBAG/NAD+ mixture, fragmentation of NAD+ and development of new peaks in HPLC chromatograms. Intracellular enzyme activity was confirmed by the prominent cytotoxic effects of exotoxin A extract on cultured cells. In conclusion, the activity of Exotoxin A can be monitored via its ADP-ribosyltransferase activity and low doses of gamma radiation reduced its activity. Therefore, coupling radiotherapy with exotoxin A in cancer therapy should be carefully monitored.

Discovery and initial characterization of YloC, a novel endoribonuclease in Bacillus subtilis

Bacillus subtilis genome is predicted to encode numerous ribonucleases, including four 3’ exoribonucleases that have been characterized to some extent. A strain containing gene knockouts of all four known 3’ exoribonucleases is viable, suggesting that one or more additional RNases remain to be discovered. A protein extract from the quadruple RNase mutant strain was fractionated and RNase activity was followed, resulting in identification of an enzyme activity catalyzed by the YloC protein. YloC is an endoribonuclease and is a member of the highly conserved “YicC family” of proteins that is widespread in bacteria. YloC is a metal-dependent enzyme that catalyzes cleavage of single-stranded RNA, preferentially at U residues, and exists in an oligomeric form, most likely a hexamer. As such, YloC shares some characteristics with the SARS-CoV Nsp15 endoribonuclease. While the in vivo function of YloC in B. subtilis is yet to be determined, YloC was found to act similarly to YicC in an Escherichia coli in vivo assay that assesses decay of the small RNA, RyhB. Thus, YloC may play a role in small RNA regulation.

In vitro and in vivo genotoxicity and cytotoxicity analysis of protein extract from Aplysina fulva sponges

This study evaluated the physicochemical and morphological properties of a marine sponge protein extract (PE) using scanning electron microscopy (SEM), Energy dispersive X-ray spectroscopy (EDS), analysis of mass loss and pH and in vitro and in vivo. Scanning electron microscopy showed that PE fibers present a granular aspect and irregular structure and the element carbon followed by oxygen was detected in the EDS analysis. Moreover, a 29% of mass loss was observed after 14 days and the pH slightly modified after 14 days. Cell viability of fibroblast cells (L929) of control and PE at a concentration of 25% demonstrated higher values compared to the groups. Osteoblast cell viability of PE at 25 and 50% was significantly higher. Comet assay on day 1 showed higher values for PE at 25%. In addition, in vivo experiments demonstrated that in the treated animals, the bone defects were filled with biomaterial particles, granulation tissue and some areas of newly formed bone. Furthermore, similar immunoexpression of Runx-2 and Cox-2 was observed. Taken together, all results suggest that PE is biocompatible, present non-citotoxicity in the in vitro studies (at the lower concentration) and in the in vivo studies and it can be considered as an alternative source of collagen for tissue engineering proposals.

IAF, QGF, and QDF Peptides Exhibit Cholesterol-Lowering Activity through a Statin-like HMG-CoA Reductase Regulation Mechanism: In Silico and In Vitro Approach

In this study, in silico approaches are employed to investigate the binding mechanism of peptides derived from cowpea β-vignin and HMG-CoA reductase. With the obtained information, we designed synthetic peptides to evaluate their in vitro enzyme inhibitory activity. In vitro, the total protein extract and <3 kDa fraction, at 5000 µg, support this hypothesis (95% and 90% inhibition of HMG-CoA reductase, respectively). Ile-Ala-Phe, Gln-Gly-Phe, and Gln-Asp-Phe peptides were predicted to bind to the substrate binding site of HMGCR via HMG-CoAR. In silico, it was established that the mechanism of HMG-CoA reductase inhibition largely entailed mimicking the interactions of the decalin ring of simvastatin and via H-bonding; in vitro studies corroborated the predictions, whereby the HMG-CoA reductase activity was decreased by 69%, 77%, and 78%, respectively. Our results suggest that Ile-Ala-Phe, Gln-Gly-Phe, and Gln-Asp-Phe peptides derived from cowpea β-vignin have the potential to lower cholesterol synthesis through a statin-like regulation mechanism.

Characterisation of black soldier fly larva protein before and after conjugation by the Maillard reaction

Black soldier fly has been proposed as an alternative protein source sustainable for both food and feed due to its nutritional composition. The functional properties of this protein can be improved by inducing the Maillard reaction (MR) in protein-sugar mixtures. This study focused on the conjugation and characterisation of black soldier fly larvae (BSFL) proteins and conjugates. The defatted BSFL larvae were subjected to protein extraction at an alkaline pH. The protein extract was then conjugated with glucose. The BSFL protein and glucose were mixed at (2:1 w/w, pH 9), incubated at 50, 70, and 90 °C for 30, 60, 90 and 120 min. The products obtained were then characterised and compared. The changes were confirmed by universal attenuated total reflectance Fourier-transform infrared spectroscopy (UATR-FTIR), scanning electron microscopy, thermal gravimetric analysis and differential scanning calorimetry. UATR-FTIR combined with principal component analysis monitored the protein-sugar conjugates, to show the structural difference among heated proteins and conjugates. The heating treatments resulted in the unfolding and reduction of the protein molecule aggregation. The protein extract from the larvae was rich in protein content (67±0.78%) and displayed good essential amino acids (EAA) in sufficient quantities to meet the dietary requirements for humans. The EAA quantities of the conjugates decreased due to the MR treatment. The conjugates showed a significant decrease in the lysine content as a function of reaction temperature and time at 90 °C and 120 min, respectively. FTIR indicated that the amide I and II bands of the protein were altered by the MR. The increased Tmax (the temperature at which decomposition is completed) demonstrated that the conjugation of the protein with glucose improved the thermal stability, remarkably. These results suggested that MR with glucose can be a promising way to improve the thermal properties of BSFL protein.