Synthesis of novel anti-inflammatory peptides derived from the amino-acid sequence of the bioactive protein SV-IV

ILeukin10Pred: A Computational Approach for Predicting IL-10-Inducing Immunosuppressive Peptides Using Combinations of Amino Acid Global Features

Simple Summary

Interleukin-10 is a cytokine that exhibits potent anti-inflammatory characteristics that play an essential role in limiting the host’s immune response to pathogens and regulating the growth or differentiation of various immune cells. Moreover, interleukin-10 prediction via conventional approaches is time-consuming and labor-intensive. Hence, researchers are inclined towards an alternative approach to predict interleukin-10-inducing peptides. Additionally, numerous in silico tools are available to predict T cell epitopes. These methods generally follow a direct or indirect approach where they directly predict cytotoxic T-lymphocyte epitopes rather than major histocompatibility complex binders or indirectly predict single components of the T cell recognition pathway. However, very few studies are available that address cytokine-specific predictions. Our research utilized a computer-aided approach to develop a model to predict IL-10-inducing peptides. This study outperformed the existing state-of-the-art method and achieved an accuracy of 87.5% and Matthew’s correlation coefficient (MCC) of 0.755 on the hybrid feature types and outperformed an existing state-of-the-art method based on dipeptide compositions that achieved an accuracy of 81.24% and an MCC value of 0.59. Therefore, our model is promising to assist in predicting immunosuppressive peptides that induce interleukin-10 cytokines.

Abstract

Interleukin (IL)-10 is a homodimer cytokine that plays a crucial role in suppressing inflammatory responses and regulating the growth or differentiation of various immune cells. However, the molecular mechanism of IL-10 regulation is only partially understood because its regulation is environment or cell type-specific. In this study, we developed a computational approach, ILeukin10Pred (interleukin-10 prediction), by employing amino acid sequence-based features to predict and identify potential immunosuppressive IL-10-inducing peptides. The dataset comprises 394 experimentally validated IL-10-inducing and 848 non-inducing peptides. Furthermore, we split the dataset into a training set (80%) and a test set (20%). To train and validate the model, we applied a stratified five-fold cross-validation method. The final model was later evaluated using the holdout set. An extra tree classifier (ETC)-based model achieved an accuracy of 87.5% and Matthew’s correlation coefficient (MCC) of 0.755 on the hybrid feature types. It outperformed an existing state-of-the-art method based on dipeptide compositions that achieved an accuracy of 81.24% and an MCC value of 0.59. Our experimental results showed that the combination of various features achieved better predictive performance..

Evaluation of Anti-Inflammatory and Atheroprotective Properties of Wheat Gluten Protein Hydrolysates in Primary Human Monocytes

Bioactive protein hydrolysates have been identified in several sources as possible agents in the prevention and treatment of many diseases. A wheat gluten (WG) concentrate was hydrolyzed by Alcalase under specific conditions. The resulting hydrolysates were evaluated by in vitro cell-free experiments leading to the identification of one bioactive WG protein hydrolysate (WGPH), which was used at 50 and 100 μg/mL on primary human monocytes. Reactive oxygen species (ROS) and nitrite levels and RT-qPCR and ELISA techniques were used to analyze the functional activity of WGPH. Our results showed that WGPH hydrolyzed in 45 min (WGPH45A) down-regulated gene expression of Interleukin (IL)-1β, IL-6, IL-17, and Interferon gamma (IFNγ) and reduced cytokine release in lipopolysaccharide (LPS)-stimulated monocytes. In addition, WGPH45A down-regulated gene-related to atherosclerotic onset. Our results suggest that WGPH45A has a potent anti-inflammatory and atheroprotective properties, reducing the expression of gene-related inflammation and atherosclerosis that could be instrumental in maintaining cardiovascular homeostasis.

Legume Proteins as a Promising Source of Anti-Inflammatory Peptides

Legume proteins are precursors of bioactive components, such as peptides. In the present paper, different types of legume as sources of bioactive peptides and hydrolysates are considered and discussed based on their anti-inflammatory effect. Peptides with anti-inflammatory activity were included from in vitro and in vivo studies. Current strategies for obtaining bioactive peptides, as well as their structure and impact on health, were also reviewed. It was discovered that peptides derived from legume protein, mainly soybean and bean, can regulate several inflammatory markers, which include prostaglandin E2 (PGE2), nitric oxide (NO), inducible nitric oxide synthase (iNOS), cyclooxygenase 2 (COX- 2), cytokines, and chemokines. So far, lunasin, VPY and γ-glutamyl peptides have been identified with anti-inflammatory activity but their mechanisms have not been fully elucidated. Furthermore, it is necessary to gather more information about hydrolysates containing peptides and single peptides with antiinflammatory activity. Considering the wide diversity, legume may be promising components to produce peptides efficient to ameliorate inflammatory disorders.

Food-derived bioactive peptides and their role in ameliorating hypertension and associated cardiovascular diseases

Non-communicable diseases including cardiovascular diseases (CVDs) and associated metabolic disorders are responsible for nearly 40 million deaths globally per year. Hypertension or high blood pressure (BP) is one of the primary reasons for the development of CVDs. A healthy nutritional strategy complementing with physical activity can substantially reduce high BP and prevent the occurrence of CVD-associated morbidity and mortality. Bioactive peptides currently are the next wave of the promising bench to clinic options for potential targeting chronic and acute health issues including hypertension. Peptides demonstrating anti-inflammatory, anti-oxidant, and angiotensin-converting enzyme-I inhibitory activity are widely studied for the amelioration of hypertension and associated CVDs. Isolating these potent bioactive peptides from different food sources is a promising endeavor toward nutraceutical based dietary management and prevention of hypertension. Understanding the pathophysiology of hypertension and the action mechanisms of the bioactive peptides would complement in designing and characterizing more potent peptides and suitable comprehensive dietary plans for the prevention of hypertension and associated CVDs.

PreAIP: Computational Prediction of Anti-inflammatory Peptides by Integrating Multiple Complementary Features

Numerous inflammatory diseases and autoimmune disorders by therapeutic peptides have received substantial consideration; however, the exploration of anti-inflammatory peptides via biological experiments is often a time-consuming and expensive task. The development of novel in silico predictors is desired to classify potential anti-inflammatory peptides prior to in vitro investigation. Herein, an accurate predictor, called PreAIP (Predictor of Anti-Inflammatory Peptides) was developed by integrating multiple complementary features. We systematically investigated different types of features including primary sequence, evolutionary and structural information through a random forest classifier. The final PreAIP model achieved an AUC value of 0.833 in the training dataset via 10-fold cross-validation test, which was better than that of existing models. Moreover, we assessed the performance of the PreAIP with an AUC value of 0.840 on a test dataset to demonstrate that the proposed method outperformed the two existing methods. These results indicated that the PreAIP is an accurate predictor for identifying AIPs and contributes to the development of AIPs therapeutics and biomedical research. The curated datasets and the PreAIP are freely available at http://kurata14.bio.kyutech.ac.jp/PreAIP/.

Prediction of anti-inflammatory proteins/peptides: an insilico approach

Background

The current therapy for inflammatory and autoimmune disorders involves the use of nonspecific anti-inflammatory drugs and other immunosuppressant, which are often accompanied with potential side effects. As an alternative therapy, anti-inflammatory peptides are recently being exploited as anti-inflammatory agents for treatment of various inflammatory diseases such as Alzheimer’s disease and rheumatoid arthritis. Thus, understanding the correlation between amino acid sequence and its potential anti-inflammatory property is of great importance for the discovery of novel and efficient anti-inflammatory peptide-based therapeutics.

Methods

In this study, we have developed a prediction tool for the classification of peptides as anti-inflammatory epitopes or non anti-inflammatory epitopes. The training was performed using experimentally validated epitopes obtained from Immune epitope database and analysis resource database. Different sequence-based features and their hybrids with motif information were employed for development of support vector machine-based machine learning models. Similarly, machine learning models were also constructed using random forest.

Results

The composition and terminal residue conservation analysis of peptides revealed the dominance of leucine, serine, tyrosine and arginine residues in anti-inflammatory epitopes as compared to non anti-inflammatory epitopes. Similarly, the anti-inflammatory epitopes specific motifs were found to be rich in hydrophobic and polar residues. The hybrid of tripeptide composition-based support vector machine model and motif yielded the best performance on 10-fold cross validation with an accuracy of 78.1% and MCC of 0.58. The same displayed an accuracy of 72% and MCC of 0.45 on validation dataset, rejecting any possibility of over-fitting. The tripeptide composition-based random forest model displayed an accuracy of 0.8 and MCC of 0.59 on 10-fold cross validation, however, the accuracy (0.68) and MCC (0.31) was lower as compared to support vector machine model on validation dataset. Thus, the support vector machine model is implemented as the default model and an additional option of using the random forest model is provided.

Conclusion

The prediction models along with tools for epitope mapping and similarity search have been provided as a web server which is freely accessible at http://metagenomics.iiserb.ac.in/antiinflam/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12967-016-1103-6) contains supplementary material, which is available to authorized users.

Heterogenous turnover of sperm and seminal vesicle proteins in the mouse revealed by dynamic metabolic labeling

Plasticity in ejaculate composition is predicted as an adaptive response to the evolutionary selective pressure of sperm competition. However, to respond rapidly to local competitive conditions requires dynamic modulation in the production of functionally relevant ejaculate proteins. Here we combine metabolic labeling of proteins with proteomics to explore the opportunity for such modulation within mammalian ejaculates. We assessed the rate at which proteins are synthesized and incorporated in the seminal vesicles of male house mice (Mus musculus domesticus), where major seminal fluid proteins with potential roles in sperm competition are produced. We compared rates of protein turnover in the seminal vesicle with those during spermatogenesis, the timing of which is well known in mice. The subjects were fed a diet containing deuterated valine ([(2)H(8)]valine) for up to 35 days, and the incorporation of dietary-labeled amino acid into seminal vesicle- or sperm-specific proteins was assessed by liquid chromatography-mass spectrometry of samples recovered from the seminal vesicle lumen and cauda epididymis, respectively. Analyses of epididymal contents were consistent with the known duration of spermatogenesis and sperm maturation in this species and in addition revealed evidence for a subset of epididymal proteins subject to rapid turnover. For seminal vesicle proteins, incorporation of the stable isotope was evident from day 2 of labeling, reaching a plateau of labeling by day 24. Hence, even in the absence of copulation, the seminal vesicle proteins and certain epididymal proteins demonstrate considerable turnover, a response that is consonant with the capacity to rapidly modulate protein production. These techniques can now be used to assess the extent of phenotypic plasticity in mammalian ejaculate production and allocation according to social and environmental cues of sperm competition.

Deletion of androgen receptor in the smooth muscle of the seminal vesicles impairs secretory function and alters its responsiveness to exogenous testosterone and estradiol

The seminal vesicles (SVs), like much of the male reproductive tract, depend on androgen-driven stromal-epithelial interactions for normal development, structure, and function. The primary function of the SVs is to synthesize proteins that contribute to the seminal plasma and this is androgen dependent. However, the cell-specific role for androgen action in adult SVs remains unclear. This study analyzed the SV in mice with targeted ablation of androgen receptors specifically in smooth muscle cells (PTM-ARKO) to determine in vivo whether it is androgen action in a subset of the SV stroma, the smooth muscle cells, that drives epithelial function and identity. These mice have significantly smaller SVs in adulthood with less smooth muscle and reduced epithelial cell height. Less epithelial cell proliferation was observed in adult PTM-ARKO SVs, compared with controls, and production of seminal proteins was reduced, indicating global impairment of epithelial cell function in PTM-ARKO SVs. None of these changes could be explained by altered serum testosterone or estradiol concentrations. We also demonstrate altered SV responsiveness to exogenous testosterone and estradiol in PTM-ARKO mice, indicating that smooth muscle androgen receptors may limit the SV epithelial proliferative response to exogenous estrogens. These results therefore demonstrate that the smooth muscle cells play a vital role in androgen-driven stromal-epithelial interactions in the SV, determining epithelial cell structure and function as well as limiting the SV epithelial proliferative response to exogenous estrogens.

The N-terminal 1-16 peptide derived in vivo from protein seminal vesicle protein IV modulates alpha-thrombin activity: potential clinical implications

We have previously shown that seminal vesicle protein IV (SV-IV) and its 1-70 N-terminal fragment have anti-inflammatory activity and modulate anti-thrombin III (AT) activity. Moreover, mass spectrometry analysis of purified SV-IV has shown that the protein was found to be highly heterogeneous and 14% of the total SV-IV molecules are truncated forms, of particular interest the 1-16, 1-17, and 1-18 peptides. In this work we report experimental data which demonstrate that the 1-16 peptide (P1-16) possesses a marked effect on the AT activity by preventing the formation of the thrombin-AT complex. We found that the formation of thrombin-AT complex is markedly decreased in the presence of P1-16 used at equimolar concentration with thrombin as evaluated with SDS-PAGE. We also monitored the conformational changes of thrombin in the presence of different P1-16 concentrations, and calculated the K(d) of thrombin/P1-16 system by circular dichroism technique. The probable interaction sites of P1-16 with thrombin have been also evaluated by molecular graphics and computational analyses. These results have potential implications in the treatment of sterility and thrombotic diseases.

Comparative proteomics reveals evidence for evolutionary diversification of rodent seminal fluid and its functional significance in sperm competition

During insemination, males of internally fertilizing species transfer a complex array of seminal fluid proteins to the female reproductive tract. These proteins can have profound effects on female reproductive physiology and behavior and are thought to mediate postcopulatory sexual selection and intersexual conflict. Such selection may cause seminal fluid to evolve rapidly, with potentially important consequences for speciation. Here we investigate the evolution of seminal fluid proteins in a major mammalian radiation, the muroid rodents, by quantifying diversity in seminal fluid proteome composition for the first time across a broad range of closely related species. Using comparative proteomics techniques to identify and cross-match proteins, we demonstrate that rodent seminal fluid is highly diverse at the level of both proteomes and individual proteins. The striking interspecific heterogeneity in seminal fluid composition revealed by our survey far exceeds that seen in a second proteome of comparable complexity, skeletal muscle, indicating that the complement of proteins expressed in seminal fluid may be subject to rapid diversification. We further show that orthologous seminal fluid proteins exhibit substantial interspecific variation in molecular mass. Because this variation cannot be attributed to differential glycosylation or radical differences in termination sites, it is strongly suggestive of rapid amino acid divergence. Sperm competition is implicated in generating such divergence for at least one major seminal fluid protein in our study, SVS II, which is responsible for copulatory plug formation via transglutaminase-catalyzed cross-linking after insemination. We show that the molecular mass of SVS II is positively correlated with relative testis size across species, which could be explained by selection for an increased number of cross-linking sites involved in the formation of the copulatory plug under sperm competition.

Adaptive evolution in rodent seminal vesicle secretion proteins

Proteins involved in reproductive fitness have evolved unusually rapidly across diverse groups of organisms. These reproductive proteins show unusually high rates of amino acid substitutions, suggesting that the proteins have been subject to positive selection. We sought to identify seminal fluid proteins experiencing adaptive evolution because such proteins are often involved in sperm competition, host immunity to pathogens, and manipulation of female reproductive physiology and behavior. We performed an evolutionary screen of the mouse prostate transcriptome for genes with elevated evolutionary rates between mouse and rat. We observed that secreted rodent prostate proteins evolve approximately twice as fast as nonsecreted proteins, remarkably similar to findings in the primate prostate and in the Drosophila male accessory gland. Our screen led us to identify and characterize a group of seminal vesicle secretion (Svs) proteins and to show that the gene Svs7 is evolving very rapidly, with many amino acid sites under positive selection. Another gene in this group, Svs5, showed evidence of branch-specific selection in the rat. We also found that Svs7 is under selection in primates and, by using three-dimensional models, demonstrated that the same regions have been under selection in both groups. Svs7 has been identified as mouse caltrin, a protein involved in sperm capacitation, the process responsible for the timing of changes in sperm activity and behavior, following ejaculation. We propose that the most likely explanation of the adaptive evolution of Svs7 that we have observed in rodents and primates stems from an important function in sperm competition.

In vitro stimulatory effect of anti-apoptotic seminal vesicle protein 4 on purified peroxidase enzymes

The enzymatic activities of purified horseradish peroxidase, selenium-dependent glutathione peroxidase, thyroid peroxidase and myeloperoxidase, but not that of lactoperoxidase, were markedly enhanced when added into a reaction mixture containing 5 mum native seminal vesicle protein 4, a major protein secreted from rat seminal vesicle epithelium. A further increase of horseradish peroxidase activity was obtained using Ser58-phosphorylated or acetylated seminal vesicle protein 4. The activating effect of native seminal vesicle protein 4 was highest (about 60-fold) on horseradish peroxidase when 4-chloro-1-naphtol was used as the electron donor substrate. The main kinetics parameters of the stimulatory effect on horseradish peroxidase were evaluated and the enzyme-electron donor substrate interaction was investigated by HPLC and electrospray-MS. A native seminal vesicle protein 4/4-chloro-1-naphtol noncovalent adduct was detected when the protein and 4-chloro-1-naphtol were present in the appropriate molar ratio in the horseradish peroxidase-catalyzed reaction. By contrast, no adducts were formed between native seminal vesicle protein 4 and horseradish peroxidase. This native seminal vesicle protein 4/4-chloro-1-naphtol interaction might underlie the native seminal vesicle protein 4-induced horseradish peroxidase stimulation. Furthermore, native seminal vesicle protein 4 was shown by spectrophotometric and electrospray-MS analysis to interact with NADPH, an electron donor substrate of the selenium-dependent glutathione peroxidase/glutathione reductase redox system, with formation of an adduct between them. Although further investigation is required to elucidate the mechanism of adduct formation, this interaction, probably by promoting the release of the NADPH electrons required for glutathione disulphide reduction, could explain the stimulatory effect of seminal vesicle protein 4 on mammalian peroxidases possibly involved in its physiological function on the selenium-dependent glutathione peroxidase/glutathione reductase system. The biological significance of these properties of native seminal vesicle protein 4 might be related to its ability to downregulate reactive oxygen species and oxidative stress-induced apoptosis.

SV-IV Peptide1-16 reduces coagulant power in normal Factor V and Factor V Leiden

Native Factor V is an anticoagulant, but when activated by thrombin, Factor X or platelet proteases, it becomes a procoagulant. Due to these double properties, Factor V plays a crucial role in the regulation of coagulation/anticoagulation balance.

Factor V Leiden (FVL) disorder may lead to thrombophilia. Whether a reduction in the activation of Factor V or Factor V Leiden may correct the disposition to thrombophilia is unknown. Therefore we tested SV-IV Peptide 1–16 (i.e. a peptide derived by seminal protein vescicle number IV, SV-IV) to assess its capacity to inhibit the procoagulant activity of normal clotting factor V or Factor V Leiden (FVL). We found that SV-IV protein has potent anti-inflammatory and immunomodulatory properties and also exerts procoagulant activity. In the present work we show that the SV-IV Peptide 1–16, incubated with plasma containing normal Factor V or FVL plasma for 5 minutes reduces the procoagulant capacity of both substances. This is an anticoagulant effect whereas SV-IV protein is a procoagulant. This activity is effective both in terms of the coagulation tests, where coagulation times are increased, and in terms of biochemical tests conducted with purified molecules, where Factor X activation is reduced.

Peptide 1–16 was, in the pure molecule system, first incubated for 5 minutes with purified Factor V then it was added to the mix of phosphatidylserine, Ca2⁺, Factor X and its chromogenic molecule Chromozym X. We observed a more than 50% reduction in lysis of chromogenic molecule Chromozym X by Factor Xa, compared to the sample without Peptide 1–16. Such reduction in Chromozym X lysis, is explained with the reduced activation of Factor X by partial inactivation of Factor V by Peptide 1–16. Thus our study demonstrates that Peptide 1–16 reduces the coagulation capacity of Factor V and Factor V Leiden in vitro, and, in turn, causes factor X reduced activation.

Protein SV-IV promotes nitric oxide production not associated with apoptosis in murine macrophages

SV-IV (seminal vesicle protein no. 4) is a potent immunomodulatory and anti-inflammatory secretory protein (Mr 9758) produced in large amounts by the rat seminal vesicle epithelium. Here we show that this protein possesses the ability to upregulate in J774 macrophages the expression of the gene coding for the inducible nitric oxide synthase (iNOS). The increase in NO production consequent on the marked enhancement of iNOS activity was not associated with apoptotic damage of the SV-IV-treated cells. In the same experimental model, however, LPS induced upregulation of iNOS coupled with an increase in NO production and marked apoptotic death. Differences in the ability of SV-IV and LPS to control the life/ death signal balance in target cells via trans-membrane activation of apoptotic (mediated by TNF-alpha and NO/iNOS system) and anti-apoptotic (mediated by bcl-2, c-myc, etc.) pathways are suggested to be the basis of the apoptotic fate of the experimentally treated cells. In addition, considering the important role played by NO in the process of mammalian reproduction, SV-IV may be involved in the fine tuning of NO concentration in the female genital tract mucosa via an SV-IV-mediated control of iNOS gene expression in local macrophages.