Anticoagulant Decapeptide Interacts with Thrombin at the Active Site and Exosite-I

Characterization and preparation of food-derived peptides on improving osteoporosis: A review

Osteoporosis is a systemic bone disease characterized by reduced bone mass and deterioration of the microstructure of bone tissue, leading to an increased risk of fragility fractures and affecting human health worldwide. Food-derived peptides are widely used in functional foods due to their low toxicity, ease of digestion and absorption, and potential to improve osteoporosis. This review summarized and discussed methods of diagnosing osteoporosis, treatment approaches, specific peptides as alternatives to conventional drugs, and the laboratory preparation and identification methods of peptides. It was found that peptides interacting with RGD (arginine-glycine-aspartic acid)-binding active sites in integrin could alleviate osteoporosis, analyzed the interaction sites between these osteogenic peptides and integrin, and further discussed their effects on improving osteoporosis. These may provide new insights for rapid screening of osteogenic peptides, and provide a theoretical basis for their application in bone materials and functional foods.

Peptide composition analysis, structural characterization, and prediction of iron binding modes of small molecular weight peptides from mung bean

Iron supplementation is a proactive approach to limit instances of iron deficiency anemia. This study is based on the enzymatic hydrolysis and fractionation of mung bean proteins (MBPs) followed by the determination of the Fe2+ chelating activities of these peptide-containing fractions. MBP-Fe complex was generated using a chemical chelation method and subsequently characterized. Following Sephadex G15 separation of MBPs, one of the fractions containing 10 different peptides, demonstrated maximum Fe2+ chelating activity of 39.97 ± 0.07 μg/mg. The sequences of these peptides were determined using liquid chromatography-tandem mass spectrometry. The Fe2+ ion content of the MBP-Fe complex was determined using X-ray photoelectron spectroscopy and 80% of the iron was found to be in Fe2+ oxidation state. After iron chelation, there was an increase in the peptide's particle size, with an average value of 550.67 ± 0.70 nm. This increase in size was attributed to the contributions of the amino proline and glycine, which extended the peptides to form the MBP-Fe complex. Finally, molecular docking studies revealed that Fe2+ mainly bound to carboxy-oxygen of glutamate and aspartate residues of mung bean peptides to form MBP-Fe complex. This research could serve as a scientific foundation for the development of dietary iron supplements using plant-derived peptides.

Prospection of Peptide Inhibitors of Thrombin from Diverse Origins Using a Machine Learning Pipeline

Thrombin is a key enzyme involved in the development and progression of many cardiovascular diseases. Direct thrombin inhibitors (DTIs), with their minimum off-target effects and immediacy of action, have greatly improved the treatment of these diseases. However, the risk of bleeding, pharmacokinetic issues, and thrombotic complications remain major concerns. In an effort to increase the effectiveness of the DTI discovery pipeline, we developed a two-stage machine learning pipeline to identify and rank peptide sequences based on their effective thrombin inhibitory potential. The positive dataset for our model consisted of thrombin inhibitor peptides and their binding affinities (KI) curated from published literature, and the negative dataset consisted of peptides with no known thrombin inhibitory or related activity. The first stage of the model identified thrombin inhibitory sequences with Matthew's Correlation Coefficient (MCC) of 83.6%. The second stage of the model, which covers an eight-order of magnitude range in KI values, predicted the binding affinity of new sequences with a log room mean square error (RMSE) of 1.114. These models also revealed physicochemical and structural characteristics that are hidden but unique to thrombin inhibitor peptides. Using the model, we classified more than 10 million peptides from diverse sources and identified unique short peptide sequences (<15 aa) of interest, based on their predicted KI. Based on the binding energies of the interaction of the peptide with thrombin, we identified a promising set of putative DTI candidates. The prediction pipeline is available on a web server.

Absorption characteristics and the effect on vascular endothelial cell permeability of an anticoagulant peptide

In the former report, the casein peptide TKLTEEEKNR (PfCN) exhibits strong thrombin inhibitory activity in vitro. Its absorption capabilities, however, are unclear. Therefore, we studied its absorption characteristics both in vivo and in vitro. PfCN was carried by cells from the apical chamber to the basolateral chamber via active translocation in Caco-2 cells. Meanwhile, it can also be transported by HUVECs. We found that PfCN can be taken up by HUVECs using confocal laser imaging. PfCN has been proven to have good absorption properties in in vivo experiments. After five minutes of oral treatment, PfCN was identified in the blood, peaking at 82.75 ± 36.52 ng/mL in 30 min. And PfCN vanished from the blood circulation after 120 min. According to in vivo experiments, excessive concentrations of PfCN will alter the permeability of HUVECs. As a result, there is a foundation for PfCN application in the food sector. Meanwhile, we also hope this article can give an idea to the researchers who studying the absorption of functional peptides.

Nutritional properties and osteogenic activity of simulated digestion components and peptides from Larimichthys crocea

Fish provides a range of health benefits due to its nutritional and bioactive components. However, the bioactive peptides derived from Larimichthys crocea proteins were not fully investigated, especially the beneficial effects related to bone growth in vitro. In this study, the water extract protein was subjected to the simulated in vitro digestion process, and the osteogenic effect of enzymatic hydrolysate at different digestion stages was evaluated by the proliferation of osteoblast. The protein hydrolyzates of group pepsin treatment for 1 h and pepsin treatment for 2 h showed higher osteogenic activity in vitro. Two peptides including IERGDVVVQDSPSD from pepsin treatment for 1 h and RGDLGIEIPTEK from pepsin treatment for 2 h were identified, which revealed eminent effects in terms of promoting osteoblast proliferation and enhancing ALP activity. Moreover, the available nutrients in the proteins were determined by the molecular weight distribution and free amino acid composition. Those peptides also showed stronger interaction with RGD than integrins. Therefore, the peptides from Larimichthys crocea can be used as an effective ingredient for promoting bone growth in the future.

PM1-loaded recombinant human H-ferritin nanocages: A novel pH-responsive sensing platform for the identification of cancer cells

The aggregation-induced emission (AIE) material has been widely used in biological detection due to their unique property of fluorescing in aggregation state. However, the poor dispersion and biocompatibility limit its application in in vivo real-time imaging. Here, a novel strategy is designed to obtain pH-responsive AIE nanomaterials, working through 4-Undecoxy Tetraphenyl Ethylene Methacrylate (PM1) block, with excellent features (dispersion, biocompatibility, self-reconstruction and cancer specific recognition). The recombinant human H-ferritin (rHuHF) was used to prepare rHuHF-PM1 nanocomposites which effectively supported the dispersion and transfer of PM1 in the biological environment, even making it target tumor cells due to the overexpression of ferritin receptors on tumor cells. To simulate the changes of rHuHF in intracellular lysosomes, particle size and fluorescence of rHuHF-PM1 were analyzed, which reflected the loose structural changes of rHuHF nanocages in weak acid system that facilitated the degradation of macromolecular rHuHF in intracellular lysosomes and following release of PM1. The released PM1 molecules aggregated and emitted brilliant blue fluorescence. Several cell lines, Hela, HT-29, HepG2, L-O2 and HUVEC have all been sensitively detected and distinguished. Accordingly, this nanocage has a potential to be applied to disease diagnosis and provides a novel sensing platform for the identification of cancer.

Anticoagulant Dodecapeptide Suppresses Thrombosis In Vivo by Inhibiting the Thrombin Exosite-I Binding Site

Thrombin is a crucial regulatory serine protease in hemostasis and thrombosis and has been a therapeutic target of thrombotic events. A novel oyster-derived thrombin inhibitory dodecapeptide (IEELEELEAER, P-2-CG) was identified and characterized. P-2-CG prolonged thrombin time from 9.6 s to 23.3 s at 5 mg/mL in vitro. P-2-CG bound to thrombin Exosite-I domain spontaneously. The occupied Exosite-I blocked fibrinogen binding, which prolonged fibrinogen clotting time to 28 s from 18.5 s. Molecule dynamics demonstrated the interaction of P-2-CG and thrombin Exosite-I involved in eight hydrogen bonds and lots of electrostatic forces. The residue Tyr⁷⁶ at thrombin Exosite-I is one critical amino acid for fibrinogen binding. The Glu¹¹ in P-2-CG was bound with Tyr⁷⁶ through strong hydrogen bonds and hydrophobic action. P-2-CG also significantly reduced the mortality of mice that suffered an acute pulmonary embolism induced by thrombin and inhibited mice tail thrombosis induced by κ-carrageenan. The thrombin inhibitory efficiency in vitro and antithrombosis in vivo of P-2-CG provided insight for further applications to serve as an antithrombotic agent.

Antarctic krill-derived peptides with consecutive Glu residues enhanced iron binding, solubility, and absorption

Three peptides containing three glutamic acid (Glu) residues at different positions derived from Antarctic krill were obtained to investigate their iron-binding properties, digestive stability, and effectiveness on enhancing iron solubility and absorption. Results indicated that Fe2+ bound to the carbonyl, carboxyl, or hydroxyl groups of DELEDSLER, EEEFDATR, and DTDSEEEIR at stoichiometric ratios of 0.453, 0.466, and 0.490, respectively. DTDSEEEIR with three consecutive Glu in the middle of the sequence possessed higher iron-binding ability and iron release potential than EEEFDATR with three consecutive Glu in the N-terminal, and DELEDSLER with three discontinuous Glu showed the lowest values. Although EEEFDATR showed remarkably lower digestion stability than DTDSEEEIR, the effect of EEEFDATR-iron on iron solubility and absorption was comparable to that of DTDSEEEIR-iron, but better than that of DELEDSLER-iron and FeSO4. Thus, peptides with consecutive Glu have the potential as an effective iron carrier to improve iron absorption.

Internal cavity amplification of shell-like ferritin regulated with the change of the secondary and tertiary structure induced by PEF technology

In this study, the effect of pulsed electric field (PEF) on apparent morphology and molecular structure of shell-like ferritin obtained from horse spleen was determined by circular dichroic (CD), fluorescence spectroscopy, Raman spectroscopy, cold field emission scanning electron microscopy (CF-SEM) and transmission electron microscopy (TEM), and verified by molecule dynamics (MD) simulation. After PEF treatment, the α-helix content of the samples reached a minimum value at 10 kV/cm, which indicated that the ferritin structure has been partially unfolded. However, the α-helix content peaked again after resting for 2 h at 25 ± 1 °C. This indicated that the PEF-treated ferritin tended to restore its original spherical morphology probably owing to the reversible assembly characteristic of ferritin. In addition, microstructure analysis revealed that ferritin particles aggregated after PEF treatment. Therefore, PEF treatment could induce the "exposure" of hydrophobic amino acids and conversion of disulfide bond configuration, and consequently, regulate the internal cavity stability of ferritin. The research will be beneficial to expand the application of PEF treatment in the modification of protein structure, and provide a theoretical basis for the application of ferritin as a carrier of bioactive molecules in food.