Establishment of a novel tumor neoantigen prediction tool for personalized vaccine design

The personalized neoantigen nanovaccine (PNVAC) platform for patients with gastric cancer we established previously exhibited promising anti-tumor immunoreaction. However, limited by the ability of traditional neoantigen prediction tools, a portion of epitopes failed to induce specific immune response. In order to filter out more neoantigens to optimize our PNVAC platform, we develop a novel neoantigen prediction model, NUCC. This prediction tool trained through a deep learning approach exhibits better neoantigen prediction performance than other prediction tools, not only in two independent epitope datasets, but also in a totally new epitope dataset we construct from scratch, including 25 patients with advance gastric cancer and 150 candidate mutant peptides, 13 of which prove to be neoantigen by immunogenicity test in vitro. Our work lay the foundation for the improvement of our PNVAC platform for gastric cancer in the future.

Wilms' tumor 1 -targeting cancer vaccine: Recent advancements and future perspectives

This mini-review explores recent advancements in cancer vaccines that target Wilms' tumor (WT1). Phase I/II trials of WT1 peptide vaccines have demonstrated their safety and efficacy against various cancers. Early trials employing HLA class I peptides evolved through their combination with HLA class II peptides, resulting in improved clinical outcomes. Additionally, WT1-targeted dendritic cell vaccines have exhibited favorable results. Studies focusing on hematological malignancies have revealed promising outcomes, including long-term remission and extended survival times. The combination of vaccines with immune checkpoint inhibitors has shown synergistic effects. Current preclinical developments are focused on enhancing the effectiveness of WT1 vaccines, underscoring the necessity for future large-scale Phase III trials to further elucidate their efficacy.

Identification of highly conserved Trypanosoma cruzi antigens for the development of a universal serological diagnostic assay

Chagas Disease is an important neglected tropical disease caused by Trypanosoma cruzi. There is no gold standard for diagnosis and commercial serological tests perform poorly in certain locations. By aligning T. cruzi genomes covering parasite genetic and geographic diversity, we identified highly conserved proteins that could serve as universal antigens for improved diagnosis. Their antigenicity was tested in high-density peptide microarrays using well-characterized plasma samples, including samples presenting true infections but discordant serology. Individual and combination of epitopes were also evaluated in peptide-ELISAs. We identified >1400 highly conserved T. cruzi proteins evaluated in microarrays. Remarkably, T. cruzi positive controls had a different epitope recognition profile compared to serologically discordant samples. In particular, multiple T. cruzi antigens used in current tests and their strain-variants, and novel epitopes thought to be broadly antigenic failed to be recognized by discordant samples. Nonetheless, >2000 epitopes specifically recognized by IgGs from both positive controls and discordant samples were identified. Evaluation of selected peptides in ELISA further illustrated the extensive variation in antibody profiles among subjects and a peptide combination could outperform a commercial ELISA, increasing assay sensitivity from 52.3% to 72.7%. Individual variation in antibody profiles rather than T. cruzi diversity appears to be the main factor driving differences in serological diagnostic performance according to geography, which will be important to further elucidate. ELISA with a combination of peptides recognized by a greater number of individuals could better capture infections, and further development may lead to an optimal antigen mixture for a universal diagnostic assay.

A structural atlas of druggable sites on Nav channels

Voltage-gated sodium (Nav) channels govern membrane excitability by initiating and propagating action potentials. Consistent with their physiological significance, dysfunction, or mutations in these channels are associated with various channelopathies. Nav channels are thereby major targets for various clinical and investigational drugs. In addition, a large number of natural toxins, both small molecules and peptides, can bind to Nav channels and modulate their functions. Technological breakthrough in cryo-electron microscopy (cryo-EM) has enabled the determination of high-resolution structures of eukaryotic and eventually human Nav channels, alone or in complex with auxiliary subunits, toxins, and drugs. These studies have not only advanced our comprehension of channel architecture and working mechanisms but also afforded unprecedented clarity to the molecular basis for the binding and mechanism of action (MOA) of prototypical drugs and toxins. In this review, we will provide an overview of the recent advances in structural pharmacology of Nav channels, encompassing the structural map for ligand binding on Nav channels. These findings have established a vital groundwork for future drug development.

Characterization of a novel aspartic protease from Trichoderma asperellum for the preparation of duck blood peptides

A novel aspartic protease gene (TaproA1) from Trichoderma asperellum was successfully expressed in Komagataella phaffii (Pichia pastoris). TaproA1 showed 52.8% amino acid sequence identity with the aspartic protease PEP3 from Coccidioides posadasii C735. TaproA1 was efficiently produced in a 5 L fermenter with a protease activity of 4092 U/mL. It exhibited optimal reaction conditions at pH 3.0 and 50 °C and was stable within pH 3.0-6.0 and at temperatures up to 45 °C. The protease exhibited broad substrate specificity with high hydrolysis activity towards myoglobin and hemoglobin. Furthermore, duck blood proteins (hemoglobin and plasma protein) were hydrolyzed by TaproA1 to prepare bioactive peptides with high ACE inhibitory activity. The IC50 values of hemoglobin and plasma protein hydrolysates from duck blood proteins were 0.105 mg/mL and 0.091 mg/mL, respectively. Thus, the high yield and excellent biochemical characterization of TaproA1 presented here make it a potential candidate for the preparation of duck blood peptides. KEY POINTS: • An aspartic protease (TaproA1) from Trichoderma asperellum was expressed in Komagataella phaffii. • TaproA1 exhibited broad substrate specificity and the highest activity towards myoglobin and hemoglobin. • TaproA1 has great potential for the preparation of bioactive peptides from duck blood proteins.

Direct infusion-multiple reaction monitoring cubed (DI-MRM3) enables widely targeted bi-omics of Colla Corii Asini (Chinese name: Ejiao)

Food authenticity is extremely important and widely targeted bi-omics is a promising pipeline attributing to incorporating metabolomics and peptidomics. Colla Corii Asini (CCA, Ejiao) is one of the most popular tonic edible materials, with counterfeit and adulterated products being widespread. An attempt was devoted to develop a high-throughput and reliable DI-MRM3 program facilitating widely targeted bi-omics of CCA. Firstly, predictive MRM program captured metabolites and peptides in trypsin-digestive gelatins. After data alignment and structure annotation, primary parameters such as Q1 → Q3 → QLIT, CE, and EE were optimized for all 17 metabolites and 34 peptides by online ER-MS. Though a single run merely consumed 6.5 min, great selectivity was reached for each analyte. Statistical results showed that nine peptides contributed to distinguish CCA from other gelatins. After cross-validation with LC-MRM, DI-MRM3 was justified to be reproducible and high-throughput for widely targeted bi-omics of CCA, suggesting a meaningful tool for food authenticity.

Effect of a collagen peptide-fish oil high internal phase emulsion on the printability and gelation of 3D-printed surimi gel inks

The effect of a high internal phase emulsion (HIPE) on three-dimensional-printed surimi gel inks was studied. Increasing the concentration of collagen peptide decreased the particle size of HIPE droplets and improved the viscoelasticity and stability. For example, when the collagen peptide concentration was 5 wt%, the viscoelasticity of the HIPE was high, as indicated by the presence of small and uniform particles, which formed a monolayer in the outer layer of the oil droplets to form stable a HIPE. A HIPE was used as the filling material to fill the surimi gel network, which reduced the porosity of the network. Surimi protein and peptides have dual emulsifying effects on the stabilization of oil. After adding the emulsion, the texture, gel properties and rheological properties of the surimi were reduced, and its printing adaptability was improved. This study provides new ideas for the production of surimi and its application in 3D printing.

Nanozyme-assisted molecularly imprinted polymer-based indirect competitive ELISA for the detection of marine biotoxin

Saxitoxin (STX), which is produced by certain dinoflagellate species, is a type of paralytic shellfish poisoning toxin that poses a serious threat to human health and the environment. Therefore, developing a technology for the convenient and cost-effective detection of STX is imperative. In this study, we developed an affinity peptide-imprinted polymer-based indirect competitive ELISA (ic-ELISA) without using enzyme-toxin conjugates. AuNP/Co3O4@Mg/Al cLDH was synthesized by calcining AuNP/ZIF-67@Mg/Al LDH, which was obtained by combining AuNPs, ZIF-67, and flower-like Mg/Al LDH. This synthesized nanozyme exhibited high catalytic activity (Km = 0.24 mM for TMB and 132.5 mM for H2O2). The affinity peptide-imprinted polymer (MIP) was imprinted with an STX-specific template peptide (STX MIP) on a multi-well microplate and then reacted with an STX-specific signal peptide (STX SP). The interaction between the STX SP and MIP was detected using a streptavidin-coated nanozyme (SA-AuNP/Co3O4@Mg/Al cLDH). The developed MIP-based ic-ELISA exhibited excellent selectivity and sensitivity, with a limit of detection of 3.17 ng/mL (equivalent: 0.317 μg/g). Furthermore, the system was validated using a commercial ELISA kit and mussel tissue samples, and it demonstrated a high STX recovery with a low coefficient of variation. These results imply that the developed ic-ELISA can be used to detect STX in real samples.

Advances of nanoparticle derived from food in the control of α-dicarbonyl compounds-A review

α-Dicarbonyl compounds (α-DCs) are predominantly generated through the thermal processing of carbohydrate and protein-rich food. They are pivotal precursors to hazard formation, such as advanced glycation end products (AGEs), acrylamide, and furan. Their accumulation within the body will be genotoxicity and neurotoxicity. Recently, significant advancements have been made in nanotechnology, leading to the widespread utilization of nanomaterials as functional components in addressing the detrimental impact of α-DCs. This review focuses on the control of α-DCs through the utilization of nanoparticle-based functional factors, which were prepared by using edible components as resources. Four emerging nanoparticles are introduced including phenolic compounds-derived nanoparticle, plant-derived nanoparticle, active peptides-derived nanoparticle, and functional minerals-derived nanoparticle. The general control mechanisms as well as the recent evidence pertaining to the aforementioned aspects were also discussed, hoping to valuable helpful references for the development of innovative α-DCs scavengers and identifying the further scope of research.

High-throughput method for Peptide mapping and Amino acid sequencing for Calcitonin Salmon in Calcitonin Salmon injection using Ultra High Performance Liquid Chromatography - High Resolution Mass Spectrometry (UHPLC-HRMS) with the application of Bioinformatic tools

BACKGROUND

Tandem mass spectrometry (MS/MS) can provide direct and accurate sequence characterization of synthetic peptide drugs, and peptide drug products including side chain modifications in the Peptide drugs. This article explains a step-by-step guide to developing a high-throughput method using high resolution mass spectrometry for characterization of Calcitonin Salmon injection containing high proportion of UV-active excipients.

METHODS

The major challenge in the method development of Amino acid sequencing and Peptide mapping was presence of phenol in drug product. Phenol is a UV-active excipient and reacts with both Dithiothreitol (DTT) and Trypsin. Hence Calcitonin Salmon was extracted from the Calcitonin Salmon injection using solid phase extraction after the extraction, Amino acid sequencing and peptide mapping study was performed. Upon incubation of Calcitonin Salmon with Trypsin and DTT, digested fragments were generated which were separated by mass compatible reverse phase chromatography and the molecular mass of each fragment was determined using HRMS.

RESULTS

A reverse phase chromatographic method was developed using UHPLC-HRMS for the determination of direct mass, peptide mapping and to determine the amino acid sequencing in the Calcitonin Salmon injection. The method was found Specific and fragments after trypsin digest are well resolved from each other and the molecular mass of each fragment was determined using HRMS. Sequencing was performed using automated identification of b and y ions annotation and identifications based on MS/MS spectra using Biopharma finder and Proteome discoverer software.

CONCLUSION

Using this approach 100% protein coverage was obtained and protein was identified as Calcitonin Salmon and the observed masses of tryptic digest of peptide was found similar with theoretical masses. The method can be used for both UV and MS based Peptide mapping and whereas the UV based peptide mapping method can be used as identification test for Calcitonin Salmon drug substance and drug product in quality control.

A multiplex UPLC-MS/MS method for the quantification of three PD-L1 checkpoint inhibitors, atezolizumab, avelumab, and durvalumab, in human serum

BACKGROUND AND AIM

To support pharmacokinetic studies, a multiplex UPLC-MS/MS assay was developed and validated to quantify PD-L1 checkpoint inhibitors atezolizumab, avelumab, and durvalumab in serum.

METHODS

A bottom-up sample pre-treatment procedure was developed to determine atezolizumab, avelumab, and durvalumab in serum. This procedure consisted of (1) precipitation of the monoclonal antibody with ammonium sulfate, (2) reduction with dithiothreitol, (3) denaturation with methanol, and (4) tryptic digestion of the protein. The unique signature peptides resulting after sample pre-treatment of the antibodies were measured using UPLC-MS/MS with a total run time of 11 minutes. The clinical application was evaluated by analyzing 114 atezolizumab patient samples.

RESULTS

The developed method was found to be accurate and precise for all three analytes over a concentration range of 3.00-150 µg/mL. No endogenous interference was present in serum samples. Cross-interference experiments showed no cross-analyte interference and acceptable cross-internal standard interference. In addition, no substantial carry-over was observed. The stable isotopically labeled signature peptides were most effective in compensating for matrix effects. Recovery based on back-calculated concentrations of calibration standards and quality control samples was found to be high. The analytes were stable for at least three freeze-thaw cycles, for 42 hours at processing conditions, for at least two days at 2-8°C in the final extract, for five days before re-injection analysis at 4°C, and long-term for at least 11 months at -70°C. The assay was tested for its applicability in clinical practice. For this purpose, 114 atezolizumab patient samples were measured.

CONCLUSION

A multiplex UPLC-MS/MS assay was developed and validated to quantify atezolizumab, avelumab, and durvalumab in human serum. The applicability of this method was demonstrated by the analysis of clinical atezolizumab samples. The method is suitable to support clinical pharmacokinetic studies involving atezolizumab, avelumab, or durvalumab.

Quantification of endogenous Angiotensin 1-10, 1-9, 1-8, 1-7, and 1-5 in human plasma using micro-UHPLC-MS/MS: Outlining the importance of the pre-analytics for reliable results

Angiotensin peptides (ANGs) play a central role in the renin-angiotensin-aldosterone system, rendering them interesting biomarkers associated with hypertension. Precise quantification of circulating ANGs holds the potential to assess the activity of angiotensin-converting enzyme (ACE), a key protease targeted by widely prescribed drugs, namely ACE inhibitors. This ability could pave the way for personalised medicine, offering insights into the prescription of inhibitors targeting either the proteases or the receptors within the system. Despite recent developments in liquid chromatography-mass spectrometry (LC-MS) methods for measuring circulating ANG concentrations, comprehensive stability studies of ANGs in human plasma are absent in the literature, raising concerns about the reliability of measured concentrations and their link to clinical conditions. To address this critical gap, we conducted an exhaustive evaluation of the pre-analytical stability of ANG1-10, ANG1-9, ANG1-8, ANG1-7, and ANG1-5. By employing surfactants to mitigate non-specific adsorption and a dedicated mix of protease inhibitors to limit protease activity, we established an MS-based assay for these five peptides. We used this method to quantify circulating concentrations of ANGs in the plasma of 11 healthy donors and 3 patients under kidney dialysis. Our findings revealed that ANG1-10 and ANG1-8 circulate at concentrations ranging from 1 to 10 pM in healthy subjects and exhibit a high degree of correlation. Notably, ANG1-9, ANG1-7, and ANG1-5 were undetectable in any of the 14 patients, despite a sub-picomolar limit of detection. This strikingly contrasts with the reference concentrations reported in the literature, which typically fall within the picomolar range. In light of these discrepancies, we strongly advocate for rigorous pre-analytical considerations and comprehensive stability studies to ensure reliable results. We emphasise the pivotal role of heightened pre-analytical awareness within the clinical chemistry community, and we hope for continued growth in this critical area.

Analysing polypeptide antibiotics residues in animal muscle tissues: The crucial role of HRMS

A confirmatory method for the determination of polypeptide antibiotics (bacitracin, colistin, and polymyxin B) in muscle samples has been developed. Extraction is performed with acidified methanol, and a clean-up step by solid-phase extraction with polymeric cartridges is applied. Separation by ultra-high performance liquid chromatography (UHPLC) is carried out using a solid core C18 column and gradient elution with water/acetonitrile containing 0.2% formic acid. High-resolution mass spectrometry (HRMS) (Q-Orbitrap) detection using different working modes has proved to be highly advantageous in eliminating interfering signals from endogenous matrix components. The analytical method has been successfully validated according to Commission Regulation 2021/808/EU and is currently used in a public health laboratory involved in veterinary medicines residue surveillance activities.

Monomeric pilose antler peptide improves depression-like behavior in mice by inhibiting FGFR3 protein expression

ETHNOPHARMACOLOGICAL RELEVANCE

It has been found that pilose antler peptide has an antidepressant effect on depression. However, the exact molecular mechanism of its antidepressant effect is still unclear.

AIM OF THE STUDY

The study sought to determine the impact of monomeric pilose antler peptide (PAP; sequence LVLVEAELRE) on depression as well as investigate potential molecular mechanisms.

MATERIALS AND METHODS

Chronic unexpected mild stress (CUMS) was used to establish the model, and the effect of PAP on CUMS mice was detected by the behavioral test. The influence of PAP on neuronal cells and dendritic spine density was observed by immunofluorescence and Golgi staining. FGFR3 and the CaMKII-associated pathway were identified using quantitative real-time polymerase chain reaction, and Western blot analysis was utilized to measure their proteins and gene expression levels. Molecular docking and microscale thermophoresis were applied to detect the binding of PAP and FGFR3. Finally, the effect of FGFR3's overexpression on PAP treatment of depression was detected.

RESULTS

PAP alleviated the changes in depressive behavior induced by CUMS, promoted the growth of nerve cells, and the density of dendritic spines was increased to its original state. PAP therapy successfully downregulated the expression of FGFR3 and ERK1/2 while upregulating the expression of CREB, BDNF, and CaMKII.

CONCLUSION

Based on the current research, PAP has a therapeutic effect on depression brought on by CUMS by inhibiting FGFR3 expression and enhancing synaptic plasticity.

Rapid and label-free A2 peptide epitope decorated CoFe2O4-C60 nanocomposite-based electrochemical immunosensor for detecting Visceral Leishmaniasis

Diagnosis of Visceral Leishmaniasis is challenging due to the shared clinical features with malaria, typhoid, and tuberculosis. A CoFe2O4-C60 nanocomposite-based immunosensor decorated with a sensitive A2 peptide antigen was fabricated to detect anti-A2 antibodies for application in visceral leishmaniasis diagnosis. The flame-synthesised nanocomposite was characterised using Fourier Transform Infrared spectroscopy (FTIR), X-ray diffraction spectroscopy (XRD), Scanning electron microscopy (SEM), Energy dispersive X-ray spectroscopy (EDX), Raman spectroscopy and electrochemical impedance spectroscopy (EIS) techniques. N terminated specific A2 peptide epitope antigen (NH2-QSVGPLSVGP-OH) was synthesised and characterised by high-performance liquid chromatography (HPLC) and liquid chromatography-mass spectroscopy (LC-MS). Using EDC/NHS, A2 peptide antigen (Apg) was immobilised on the CoFe2O4-C60-modified electrode. The performance of the immunosensor, Apg-CoFe2O4-C60NP/GCE, was evaluated by testing its ability to detect varying concentrations of anti-A2 antibody solution in PBS and spiked serum with 1 mM [Fe(CN)6]3-/4- in 0.01 M PBS (pH 7.4) as supporting electrolyte. using differential pulse voltammetry. The immunosensor showed excellent reproducibility and a linear range of 10-10-10-1 µg/mL, with an experimental detection limit of 30.34 fg/mL. These results suggest that the fabricated sensor has great potential as a tool for diagnosing visceral leishmaniasis.

Carboxymethyl cellulose and carboxymethyl chitosan-based composite nanogel as a stable delivery vehicle for oyster peptides: Characterization, absorption and transport mechanism

An oyster peptide (OPs)-loaded composite nanogel based on carboxymethyl cellulose and carboxymethyl chitosan (CMC@CMCS@OPs) was prepared, and the characterization, absorption and transport mechanism were further investigated. CMC@CMCS@OPs, a dense spherical microstructure with a diameter of ∼64 nm, which enhanced the thermal and digestive stabilities of individual OPs and improved its retention rate of hypoglycemic activity in vitro. The swelling response and in-vitro release profiles showed that CMC@CMCS@OPs could help OPs achieve targeted and controlled release in the intestine. In addition, CMC@CMCS@OPs had no cytotoxicity on Caco-2 cells, and its apparent permeability coefficients increased 4.70-7.45 times compared with OPs, with the absorption rate increased by 129.38 %. Moreover, the transcytosis of CMC@CMCS@OPs nanogel occurred primarily through the macropinocytosis pathway, endocytosis pathway and intestinal efflux transporter-mediated efflux. Altogether, these results suggested that CMC@CMCS@OPs nanogel could be as an effective OPs delivery device for enhancing its stability and absorption.

Small but powerful: RALF peptides in plant adaptive and developmental responses

Plants live in a highly dynamic environment and require to rapidly respond to a plethora of environmental stimuli, so that to maintain their optimal growth and development. A small plant peptide, rapid alkalization factor (RALF), can rapidly increase the pH value of the extracellular matrix in plant cells. RALFs always function with its corresponding receptors. Mechanistically, effective amount of RALF is induced and released at the critical period of plant growth and development or under different external environmental factors. Recent studies also highlighted the role of RALF peptides as important regulators in plant intercellular communications, as well as their operation in signal perception and as ligands for different receptor kinases on the surface of the plasma membrane, to integrate various environmental cues. In this context, understanding the fine-print of above processes may be essential to solve the problems of crop adaptation to various harsh environments under current climate trends scenarios, by genetic means. This paper summarizes the current knowledge about the structure and diversity of RALF peptides and their roles in plant development and response to stresses, highlighting unanswered questions and problems to be solved.

Bovine serum albumin uptake and polypeptide disaggregation studies of hypoglycemic ruthenium(II) uracil Schiff-base complexes

Our prior studies have illustrated that the uracil ruthenium(II) diimino complex, [Ru(H3ucp)Cl(PPh3)] (1) (H4ucp = 2,6-bis-((6-amino-1,3-dimethyluracilimino)methylene)pyridine) displayed high hypoglycemic effects in diet-induced diabetic rats. To rationalize the anti-diabetic effects of 1, three new derivatives have been prepared, cis-[Ru(bpy)2(urdp)]Cl2 (2) (urdp = 2,6-bis-((uracilimino)methylene)pyridine), trans-[RuCl2(PPh3)(urdp)] (3), and cis-[Ru(bpy)2(H4ucp)](PF6)2 (4). Various physicochemical techniques were utilized to characterize the structures of the novel ruthenium compounds. Prior to biomolecular interactions or in vitro studies, the stabilities of 1-4 were monitored in anhydrous DMSO, aqueous phosphate buffer containing 2% DMSO, and dichloromethane (DCM) via UV-Vis spectrophotometry. Time-dependent stability studies showed ligand exchange between DMSO nucleophiles and chloride co-ligands of 1 and 3, which was suppressed in the presence of an excess amount of chloride ions. In addition, the metal complexes 1 and 3 are stable in both DCM and an aqueous phosphate buffer containing 2% DMSO. In the case of compounds 2 and 4 with no chloride co-ligands within their coordination spheres, high stability in aqueous phosphate buffer containing 2% DMSO was observed. Fluorescence emission titrations of the individual ruthenium compounds with bovine serum albumin (BSA) showed that the metal compounds interact non-discriminately within the protein's hydrophobic cavities as moderate to strong binders. The metal complexes were capable of disintegrating mature amylin amyloid fibrils. In vivo glucose metabolism studies in liver (Chang) cell lines confirmed enhanced glucose metabolism as evidenced by the increased glucose utilization and glycogen synthesis in liver cell lines in the presence of complexes 2-4.

Development of an insulin-like growth factor-1 certified reference material by SI-traceable isotope-dilution mass spectrometry

In this study, an insulin-like growth factor-1 (IGF-1) certified reference material (CRM) was developed by the National Institute of Metrology (NIM), and two different principles for evaluating the IGF-1 CRM were established. After optimisation of the acid hydrolysis conditions (110 °C, 36 h), quantitative determination of peptide purity, and chromatographic separation and mass spectrometric detection, amino acid analysis-based high-performance liquid chromatography combined with isotope-dilution tandem mass spectrometry (AAA-HPLC-IDMS/MS) and peptide analysis-based HPLC-IDMS/MS (Peptide-HPLC-IDMS/MS) were used for certified value assignment; the results obtained were 136.28 and 135.01 μg/g, respectively, which were in good agreement. These results were subjected to the normal distribution test, outlier test, and method consistency test. The homogeneity and stability of the reference materials were also examined, and the uncertainty introduced in the experimental process was calculated. The final certified value was (136 ± 15) μg g-1 (k = 2). The CRM was found to be stable for at least six months when stored at -70 °C and for 7 d when stored at higher temperatures (-20 °C, 4 °C, 25 °C, or 40 °C). The CRM is expected to be used as a primary calibrator for quality control in biopharmaceutical production and clinical diagnostics.

Pseudomonas weihenstephanensis through the iron metabolism pathway promotes in situ spoilage capacity of prepared beef steaks during cold storage

In this study, we evaluated the histomorphology, reactive oxygen species (ROS), protein degradation, and iron metabolism characteristics and differential expression analysis of genes for siderophores synthesis and protease secretion in prepared beef steaks inoculated alone or co-inoculated with P. weihenstephanensis, B. thermotrichothrix and M. caseolyticus at 4 °C for 12 days. The results showed that the P. weihenstephanensis was the key bacteria that degraded protein in the process of prepared beef steaks spoilage, which led to protein oxidation by promoting ferritin degradation to release free iron and inducing ROS accumulation. The highest expression of FpvA and AprE was detected in the P. weihenstephanensis group by comparing qRT-PCR of the different inoculation groups. Both qRT-PCR and Western blot revealed that ferritin heavy polypeptide and ferritin light chain polypeptide gene and protein expressions were significantly higher in the P. weihenstephanensis inoculation group compared to the other inoculation groups. Results suggested that FpvA and AprE might play roles in meat spoilage and were potential positional, physiological and functional candidate genes for improving the quality traits of prepared beef steaks. This work may provide insights on controlling food quality and safety by intervening in spoilage pathways targeting iron carrier biosynthesis or protease secretion genes.

Photo-sensitive peptide inducing targeted cross-linking in a one-step and reagent-, enzyme- and antibody-free detection of SARS-Cov-2 marker protein

Modern biosensing technology plays a crucial role in combating the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). However, the associated assays remain costly, considering their extensive daily use. In response, we developed a simplified one-step SARS-CoV-2 protease assay that reduces both time and financial expenses. This approach eliminates the need for extra reagents, enzymes, or antibodies. The simplification involves a photo-sensitive Bengal red-tagged substrate peptide, allowing specific cross-linking upon protease-substrate recognition. This process forms a di-tyrosine product with a distinctive fluorescence signal readout, enabling the detection of SARS-CoV-2 in patient serum samples. This method anticipates a major reduction in assay costs in the near future.

Nanogel delivery systems for cationic peptides: More than a 'One Size Fits All' solution

Self-assembled hyaluronic acid-based nanogels are versatile drug carriers due to their biodegradable nature and gentle preparation conditions, making them particularly interesting for delivery of peptide therapeutics. This study aims to elucidate the relation between peptide structure and encapsulation in a nanogel. Key peptide properties that affect encapsulation in octenyl succinic anhydride-modified hyaluronic acid nanogels were identified as we explored the effect on nanogel characteristics using 12 peptides with varying charge and hydrophobicity. The size and surface properties of the microfluidics-assembled peptide-loaded nanogels were evaluated using dynamic light scattering, laser Doppler electrophoresis, and small angle neutron scattering. Additionally, the change in peptide secondary structure upon encapsulation in nanogels, their release from the nanogels, and the in vitro antimicrobial activity were assessed. In conclusion, the more hydrophobic peptides showed stronger binding to the nanogel carrier and localized internally rather than on the surface of the nanogel, resulting in more spherical nanogels with smoother surfaces and slower release profiles. In contrast, cationic and hydrophilic peptides localized at the nanogel surface resulting in fluffier nanogel structures and quick and more complete release in biorelevant medium. These findings emphasize that the advantages of nanogel delivery systems for different applications depend on the therapeutic peptide properties.

Electrochemical detection of bacterial endotoxin lipopolysaccharide (LPS) on gold electrode modified with DAL-PEG-DK5-PEG-OH - Antimicrobial peptide conjugate

This work describes fabrication of gold electrodes modified with peptide conjugate DAL-PEG-DK5-PEG-OH that enables ultra-sensitive detection of lipopolysaccharide (LPS) isolated from the reference strain of Escherichia coli O26:B6. The initial step of the established procedure implies immobilization of the fully protected DAL-PEG-DK5-PEG-OH peptide on the surface of the gold electrode previously modified by cysteamine. Then side chain- and Fmoc-deprotection was performed in situ on the electrode surface, followed by its incubation in 1 % of BSA solution to block non-specific bindings sites before LPS detection. The efficiency of the modification was confirmed by X-ray Photoelectron Spectroscopy (XPS) measurements. Additionally, the cyclic voltammetry (CV) and electrochemical impendance spectroscopy (EIS) were employed to monitor the effectiveness of each step of the modification. The obtained results confirmed that the presence of the surface-attached covalently bound peptide DAL-PEG-DK5-PEG-OH enables LPS detection by means of CV technique within the range from 5 × 10-13 to 5 × 10-4 g/mL in PBS solution. The established limit of detection (LOD) for EIS measurements was 4.93 × 10-21 g/mL with wide linear detection range from 5 × 10-21 to 5 × 10-14 g/mL in PBS solution. Furthermore, we confirmed the ability of the electrode to detect LPS in a complex biological samples, like mouse urine and human serum. The effectiveness of the electrodes in identifying LPS in both urine and serum matrices was confirmed for samples containing LPS at both 2.5 × 10-15 g/mL and 2.5 × 10-9 g/mL.

Assembling Ag2S quantum dots onto peptide nanosheet as a biomimetic two-dimensional nanoplatform for synergistic near infrared-II fluorescent imaging and photothermal therapy of tumor

Fluorescent bioimaging and photothermal therapy (PTT) techniques have potential significance in cancer diagnosis and treatment and have been widely applied in biomedical and practical clinical trials. This study proposes the molecular design and biofabrication of a two-dimensional (2D) nanoplatform, exhibiting promising prospects for synergistic bioimaging and PTT of tumors. First, biocompatible 2D peptide nanosheets (PNSs) were designed and prepared through peptide self-assembly. These served as a support matrix for assembling polyethylene glycol-modified Ag2S quantum dots (PEG-Ag2SQDs) to form a 2D nanoplatform (PNS/PEG-Ag2SQDs) with unique fluorescent and photothermal properties. The designed 2D nanoplatform not only showed improved photothermal efficacy and an elevated photothermal conversion efficiency of 52.46 %, but also demonstrated significant lethality against tumors in both in vitro and in vivo cases. Additionally, it displays excellent imaging effects in the near-infrared II region, making it suitable for synergistic fluorescent imaging-guided PTT of tumors. This study not only provides a facile approach for devising and synthesizing 2D peptide assemblies but also presents new biomimetic strategies to create functional 2D organic/inorganic nanoplatforms for biomedical applications.

An α-helical peptide-based plasmonic biosensor for highly specific detection of α-synuclein toxic oligomers

BACKGROUND

α-Synuclein (αS) aggregation is the main neurological hallmark of a group of neurodegenerative disorders, collectively referred to as synucleinopathies, of which Parkinson's disease (PD) is the most prevalent. αS oligomers are elevated in the cerebrospinal fluid (CSF) of PD patients, standing as a biomarker for disease diagnosis. However, methods for early PD detection are still lacking. We have recently identified the amphipathic 22-residue peptide PSMα3 as a high-affinity binder of αS toxic oligomers. PSMα3 displayed excellent selectivity and reproducibility, binding to αS toxic oligomers with affinities in the low nanomolar range and without detectable cross-reactivity with functional monomeric αS.

RESULTS

In this work, we leveraged these PSMα3 unique properties to design a plasmonic-based biosensor for the direct detection of toxic oligomers under label-free conditions.

SIGNIFICANCE AND NOVELTY

We describe the integration of the peptide in a lab-on-a-chip plasmonic platform suitable for point-of-care measurements of αS toxic oligomers in CSF samples in real-time and at an affordable cost, providing an innovative biosensor for PD early diagnosis in the clinic.

Renoprotective effects of laxative linaclotide: Inhibition of acute kidney injury and fibrosis in a rat model of renal ischemia-reperfusion

Ischemia-reperfusion (I/R) leads to tissue damage in transplanted kidneys, resulting in acute kidney injury (AKI) and chronic graft dysfunction, which critically compromises transplant outcomes, such as graft loss. Linaclotide, a guanylate cyclase C agonist clinically approved as a laxative, has recently been identified to exhibit renoprotective effects in a chronic kidney disease (CKD) model. This study evaluates the therapeutic effects of linaclotide on AKI triggered by I/R in a rat model with an initial comparison with other laxatives. Here, we show that linaclotide administration resulted in substantial reduction in serum creatinine levels, reflective of enhanced renal function. Histological examination revealed diminished tubular damage, and Sirius Red staining confirmed less collagen deposition, collectively indicating preserved structural integrity and mitigation of fibrosis. Further analysis demonstrated lowered expression of TGF-β and associated fibrotic markers, α-SMA, MMP2, and TIMP1, implicating the downregulation of the fibrogenic TGF-β pathway by linaclotide. Furthermore, one day after I/R insult, linaclotide profoundly diminished macrophage infiltration and suppressed critical pro-inflammatory cytokines such as TNF, IL-1β, and IL-6, signifying its potential to disrupt initial inflammatory mechanisms integral to AKI pathology. These findings suggest that linaclotide, with its established safety profile, could extend its benefits beyond gastrointestinal issues and potentially serve as a therapeutic intervention for organ transplantation. Additionally, it could provide immediate and practical insights into selecting laxatives for managing patients with AKI or CKD, regardless of the cause, and for those receiving dialysis or transplant therapy.

Fatty acids-modified liposomes for encapsulation of bioactive peptides: Fabrication, characterization, storage stability and in vitro release

The fragile membranes of liposomes limit their application by the food industry. In this study, we hypothesized that interactions between fatty acids with different chain lengths and phospholipids might enhance liposome stability. Decanoic acid modified liposomes (Lipo-DA) and stearic acid modified liposomes (Lipo-SA) were fabricated for encapsulation of hydrophilic peptides. Fluorescence spectroscopy and FTIR analysis showed molecular interactions existed between alkyl chains and phospholipids, resulting in greater compactness and hydrophobicity of the membranes in Lipo-DA and Lipo-SA. This led to a reduction in melting point characterized by differential scanning calorimetry analysis. Lipo-DA and Lipo-SA could delay the release of hydrophilic peptides compared with unmodified liposomes in simulated digestion. Moreover, Lipo-DA showed better stability during storage, while Lipo-SA exhibited precipitation, resulting in the lowest peptide retention. Our study showed that decanoic acid is suitable to enhance the stability of liposomes, although this approach has yet to be tested in food products.

Volatile compounds, gamma-glutamyl-peptides and free amino acids as biomarkers of long-ripened protected designation of origin Coppa Piacentina

Coppa Piacentina is an Italian protected designation of origin (PDO) dry-cured product obtained from the muscle of pork neck and ripened for at least six months. Metabolomics- and volatilomics-based strategies, combined with a chemical characterization of free amino acids were applied to identify biomarkers of long-ripened Coppa Piacentina PDO. Long ripening induced a significantly increase of total free amino acids, mainly represented by glutamic acid, involved in the umami taste perception. Untargeted metabolomics, performed using UHPLC-HRMS, allowed to identify 32 putative gamma-glutamyl-peptides, known as main contributors to the kokumi taste. Unsupervised and supervised multivariate statistics observed a clear modification of these peptides over the ripening, with gamma-glutamyl-peptides which significantly increased in long-ripened samples. A volatilomics-based strategy, conducted with GCxGC-MS, was then performed, and 93 different compounds were identified, with aldehyde and ketones deriving from the lipid auto-oxidation which increased according to ripening.

Dry-heat-induced phosphoserine-specific fragmentation of ovalbumin

When subjected to dry-heating, egg white ovalbumin, a phosphoglycoprotein, undergoes fragmentation and forms soluble aggregates. We investigated the mechanisms of dry-heat-induced fragmentation of ovalbumin. SDS-PAGE analysis showed that ovalbumin fragmented into five polypeptides, and their amount increased over 6 h of dry-heat treatment at 120 °C. The fragments contained fewer or no phosphoserine, compared with that in crude ovalbumin. Liquid chromatography-tandem mass spectrometry analysis of tryptic digests revealed that the fragmentation sites were located on phosphoserine residues, S68 and S344. During fragmentation, the phosphoserine residues underwent conversion into dehydroalanine residues, which were subsequently hydrolyzed. The nitrogen from the dehydroalanine became a newly formed terminal amide group on the N-terminal fragment, while the remaining molecule predominantly formed a new terminal pyruvoyl group. Furthermore, the fragments were incorporated into monomers or soluble aggregates of ovalbumin via covalent and non-covalent bonds. This study demonstrated a novel mechanism for dry-heat-induced fragmentation of phosphoproteins.

Multiphase reactions of proteins in the air: Oligomerization, nitration and degradation of bovine serum albumin upon ambient exposure

Proteins in atmospheric aerosol can react with atmospheric pollutants such as ozone (O3) and nitrogen dioxide (NO2) in the atmosphere via the reactions of oxidation, nitration, and cross-linking etc. Currently, the reactions have been more thoroughly studied in the laboratory but rarely investigated in the ambient environment. In this study, we used bovine serum albumin (BSA) as the model protein to conduct the exposure experiment in the ambient environment in southern China, an area with increasing oxidative capacity, to investigate the reactions of proteins in the atmosphere. We observed the occurrence of oligomerization, nitration and degradation of BSA upon exposure. The mass fraction of BSA monomer decreased by 5.86 ± 1.61% after exposure and those of dimers, trimers and higher oligomers increased by 1.04 ± 0.49%, 1.37 ± 0.74% and 3.40 ± 1.06%, respectively. Simultaneously, the nitration degrees of monomers, dimers, trimers and higher oligomers increased by 0.42 ± 0.15%, 0.53 ± 0.15%, 0.55 ± 0.28% and 2.15 ± 1.01%, respectively. The results show that oligomerization was significantly affected by O3 and temperature and nitration was jointly affected by O3, temperature and relative humidity, indicating the important role of atmospheric oxidants in the atmospheric reactions of protein. Atmospheric degradation of BSA was observed with the release of free amino acids (FAAs) such as glycine, alanine, serine and methionine. Glycine was the dominant FAA with a molar yield ranging from ∼8% to 33% for BSA. The estimated stoichiometric coefficient (α) of glycine is 10-7-10-6 for the degradation of BSA upon O3. Our observation suggests the occurrence of protein reactions in the oxidative ambient environment, leading to the production of nitrated products, oligomers and low molecular weight products such as peptides and FAAs. This study may deepen the current understanding of the atmospheric reaction mechanisms and reveal the influence of environmental factors in the atmosphere.

An electrochemical biosensor for the amplification of thrombin activity by perylene-mediated photoinitiated polymerization

BACKGROUND

Thrombin, a coagulation system protease, is a key enzyme involved in the coagulation cascade and has been developed as a marker for coagulation disorders. However, the methods developed in recent years have the disadvantages of complex operation, long reaction time, low specificity and sensitivity. Meanwhile, thrombin is at a lower level in the pre-disease period. Therefore, to accurately diagnose the disease, it is necessary to develop a fast, simple, highly sensitive and specific method using signal amplification technology.

RESULTS

We designed an electrochemical biosensor based on photocatalytic atom transfer radical polymerization (photo-ATRP) signal amplification for the detection of thrombin. Sulfhydryl substrate peptides (without carboxyl groups) are self-assembled to the gold electrode surface via Au-S bond and serve as thrombin recognition probes. The substrate peptide is cleaved in the presence of thrombin to generate -COOH, which can form a carboxylate-Zr(IV)-carboxylate complex via Zr(IV) and initiator (α-bromophenylacetic acid, BPAA). Subsequently, an electrochemical biosensor was prepared by introducing polymer chains with electrochemical signaling molecules (ferrocene, Fc) onto the electrode surface by photocatalytic (perylene, Py) mediated ATRP using ferrocenylmethyl methacrylate (FMMA) as a monomer. The concentration of thrombin was evaluated by the voltammetric signal generated by square wave voltammetry (SWV), and the result showed that the biosensor was linear between 1.0 ng/mL ∼ 10 fg/mL, with a lower detection limit of 4.0 fg/mL (∼0.1 fM). Moreover, it was shown to be highly selective for thrombin activity in complex serum samples and for thrombin inhibition screening.

SIGNIFICANCE

The biosensor is an environmentally friendly and economically efficient strategy while maintaining the advantages of high sensitivity, anti-interference, good stability and simplicity of operation, which has great potential for application in the analysis of complex samples.

Novel technologies uncover novel 'anti'-microbial peptides in Hydra shaping the species-specific microbiome

The freshwater polyp Hydra uses an elaborate innate immune machinery to maintain its specific microbiome. Major components of this toolkit are conserved Toll-like receptor (TLR)-mediated immune pathways and species-specific antimicrobial peptides (AMPs). Our study harnesses advanced technologies, such as high-throughput sequencing and machine learning, to uncover a high complexity of the Hydra's AMPs repertoire. Functional analysis reveals that these AMPs are specific against diverse members of the Hydra microbiome and expressed in a spatially controlled pattern. Notably, in the outer epithelial layer, AMPs are produced mainly in the neurons. The neuron-derived AMPs are secreted directly into the glycocalyx, the habitat for symbiotic bacteria, and display high selectivity and spatial restriction of expression. In the endodermal layer, in contrast, endodermal epithelial cells produce an abundance of different AMPs including members of the arminin and hydramacin families, while gland cells secrete kazal-type protease inhibitors. Since the endodermal layer lines the gastric cavity devoid of symbiotic bacteria, we assume that endodermally secreted AMPs protect the gastric cavity from intruding pathogens. In conclusion, Hydra employs a complex set of AMPs expressed in distinct tissue layers and cell types to combat pathogens and to maintain a stable spatially organized microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.

Naturally sourced amphiphilic peptides as paclitaxel vehicles for breast cancer treatment

The marketed paclitaxel (PTX) formulation Taxol relies on the application of Cremophor EL as a solubilizer. The major drawback of Taxol is its hypersensitivity reactions and a pretreatment of anti-allergic drugs is a necessity. Therefore, developing an efficient and safe delivery vehicle is a solution to increase PTX treatment outcomes with minimal adverse effects. In this work, we prepared the amphiphilic peptides (termed AmP) from soybean proteins using a facile two-step method. AmP could efficiently solubilize PTX by self-assembling into mixed micelles with D-α-tocopherol polyethylene glycol succinate (TPGS), a common pharmaceutical expedient (PTX@TPGS-AmP). The intravenously administrated PTX@TPGS-AmP exhibited a slow clearance (0.24 mL·(min·kg)-1) and an enhanced AUC (41.4 μg.h/mL), manifesting a 3.6-fold increase compared to Taxol. In a murine 4T1 tumor model, PTX@TPGS-AmP displayed a superior antitumor effect over Taxol. Importantly, safety assessment showed a high biocompatibility of AmP and an i.v. dose up to 2500 mg/kg led to no observable abnormalities in the mice. In summary, the AmP presents a new green and easily-prepared amphiphilic biomaterial, with promising potential as a pharmaceutical excipient for drug delivery.

Evaluation of primary and secondary oxidation products in fish oil-in-water emulsions: Effect of metal-complexing peptides and protein hydrolysates

A novel approach consisting of preselection of peptides using bioinformatics tool followed by final selection using Surface Plasmon Resonance (SPR) - an efficient technique to investigate metal complexing properties of peptides/hydrolysates - was developed. Selected pea hydrolysates and synthetic metal chelating peptides potentially present in pea hydrolysates were investigated for their ability to inhibit the lipid oxidation in emulsions composed of 5 % w/w fish oil and stabilized with Tween® 20. Results indicated that addition of peptides/hydrolysates did not impact the physical stability of emulsions and led to lower level of lipid hydroperoxides. Moreover, peptide KGKSR inhibited the generation of 1-penten-3-ol and hexanal to the same level as ethylenediaminetetraacetic acid (EDTA) did and the formation of 2 ethyl-furan was lower than when EDTA was added. Peptide GRHRQKHS showed same concentration of hexanal as EDTA thus confirming efficacy of using SPR for selecting peptides/hydrolysates to use as antioxidants in emulsions.

Molecular insights into nanoplastics-peptides binding and their interactions with the lipid membrane

Micro- and nanoplastics have become a significant concern, due to their ubiquitous presence in the environment. These particles can be internalized by the human body through ingestion, inhalation, or dermal contact, and then they can interact with environmental or biological molecules, such as proteins, resulting in the formation of the protein corona. However, information on the role of protein corona in the human body is still missing. Coarse-grain models of the nanoplastics and pentapeptides were created and simulated at the microscale to study the role of protein corona. Additionally, a lipid bilayer coarse-grain model was reproduced to investigate the behavior of the coronated nanoplastics in proximity of a lipid bilayer. Hydrophobic and aromatic amino acids have a high tendency to create stable bonds with all nanoplastics. Moreover, polystyrene and polypropylene establish bonds with polar and charged amino acids. When the coronated nanoplastics are close to a lipid bilayer, different behaviors can be observed. Polyethylene creates a single polymeric chain, while polypropylene tends to break down into its single chains. Polystyrene can both separate into its individual chains and remain aggregated. The protein corona plays an important role when interacting with the nanoplastics and the lipid membrane. More studies are needed to validate the results and to enhance the complexity of the systems.

Abrogation and homeostatic restoration of IgE responses by a universal IgE allergy CTL vaccine-The three signal self/non-self/self (S/NS/S) theory

Natural IgE cytotoxic peptides (nECPs), which are derived from the constant domain of the heavy chain of human IgE producing B cells via endoplasmic reticulum (ER) stress, are decorated onto MHC class 1a molecules (MHCIa) as unique biomarkers for CTL (cytotoxic T lymphocyte)-mediated immune surveillance. Human IgE exhibits only one isotype and lacks polymorphisms; IgE is pivotal in mediating diverse, allergen-specific allergies. Therefore, by disrupting self-IgE tolerance via costimulation, the CTLs induced by nECPs can serve as universal allergy vaccines (UAVs) in humans to dampen IgE production mediated by diverse allergen-specific IgE-secreting B cells and plasma cells expressing surface nECP-MHCIa as targets. The study herein has enabled the identification of nECPs, A32 and SP-1/SP-2 nonameric natural peptides produced through the correspondence principle. Vaccination using nECP induced nECP-specific CTL that profoundly suppressed human IgE production in vitro as well as chimeric human IgE production in human IgE/HLA-A2.01/HLA-B7.02 triple transgenic rodents. Furthermore, nECP-tetramer-specific CTLs were found to be converted into CD4 Tregs that restored IgE competence via the homeostatic principle, mediatepred by SREBP-1c suppressed DCs. Thus, nECPs showed causal efficacy and safety as UAVs for treating categorically type I hypersensitivity IgE-mediated allergies. The applied vaccination concept presented provides the foundation to unify, integrate through a singular class of tetramer-specific TCR clonotypes for regulaing human IgE production. The three signal theory pertains to mechanisms of three cells underlying central tolerance (S), breaking self tolerance (NS) and regaining peripheral tolerance (S) via homeostasis concerning nECP as an efficacious and safe UAV to treat type I IgE-mediated hypersensitivity. The three signal theory impirically extended, may be heuritic for immuno-regulation of adaptive immune repertoire in general.

Polyglutamine disorders: Pathogenesis and potential drug interventions

Polyglutamine/poly(Q) diseases are a group nine hereditary neurodegenerative disorders caused due to abnormally expanded stretches of CAG trinucleotide in functionally distinct genes. All human poly(Q) diseases are characterized by the formation of microscopically discernable poly(Q) positive aggregates, the inclusion bodies. These toxic inclusion bodies are responsible for the impairment of several cellular pathways such as autophagy, transcription, cell death, etc., that culminate in disease manifestation. Although, these diseases remain largely without treatment, extensive research has generated mounting evidences that various events of poly(Q) pathogenesis can be developed as potential drug targets. The present review article briefly discusses the key events of disease pathogenesis, model system-based investigations that support the development of effective therapeutic interventions against pathogenesis of human poly(Q) disorders, and a comprehensive list of pharmacological and bioactive compounds that have been experimentally shown to alleviate poly(Q)-mediated neurotoxicity. Interestingly, due to the common cause of pathogenesis, all poly(Q) diseases share etiology, thus, findings from one disease can be potentially extrapolated to other poly(Q) diseases as well.

Molecular targets of cisplatin in HeLa cells explored through competitive activity-based protein profiling strategy

Cisplatin is widely used as anticancer drugs, and DNA is considered as the main target. Considering its high affinity towards cysteines and the important role of cystine containing proteins, we applied a competitive activity-based protein profiling strategy to identify protein cysteines that bind with cisplatin in HeLa cells. Living cells were treated with cisplatin at cytotoxic concentrations, then the protein was extracted. After labeling with desthiobiotin iodoacetamide (DBIA) probe, protein was precipitated, digested and isotopically labeled, subsequently the peptides were combined, and the biotinylated cysteine-containing peptides were enriched and quantified by LC-MS/MS. A total of 3571 peptides which originated from 1871 proteins were identified using the DBIA probe. Among them, 46 proteins were screened as targets, including proteins that have been identified as binding proteins by previous study. A novel cisplatin target, calpain-1 (CAPN1), was identified and validated as binding with cisplatin in vitro.

CD4+ T Cells From Individuals With Type 1 Diabetes Respond to a Novel Class of Deamidated Peptides Formed in Pancreatic Islets

The β-cell plays a crucial role in the pathogenesis of type 1 diabetes, in part through the posttranslational modification of self-proteins by biochemical processes such as deamidation. These neoantigens are potential triggers for breaking immune tolerance. We report the detection by LC-MS/MS of 16 novel Gln and 27 novel Asn deamidations in 14 disease-related proteins within inflammatory cytokine-stressed human islets of Langerhans. T-cell clones responsive against one Gln- and three Asn-deamidated peptides could be isolated from peripheral blood of individuals with type 1 diabetes. Ex vivo HLA class II tetramer staining detected higher T-cell frequencies in individuals with the disease compared with control individuals. Furthermore, there was a positive correlation between the frequencies of T cells specific for deamidated peptides, insulin antibody levels at diagnosis, and duration of disease. These results highlight that stressed human islets are prone to enzymatic and biochemical deamidation and suggest that both Gln- and Asn-deamidated peptides can promote the activation and expansion of autoreactive CD4+ T cells. These findings add to the growing evidence that posttranslational modifications undermine tolerance and may open the road for the development of new diagnostic and therapeutic applications for individuals living with type 1 diabetes.

ARTICLE HIGHLIGHTS

Potential use of yeast protein in terms of biorefinery, functionality, and sustainability in food industry

A growing demand for sustainable, alternative protein sources that are nutrient-dense, such as microorganisms, and insects, has gradually evolved. When paired with effective processing techniques, yeast cells contain substantial substances that could supply the population's needs for food, medicine, and fuel. This review article explores the potential of yeast proteins as a sustainable and viable alternative to animal and plant-based protein sources. It highlights the various yeast protein extraction methods including both mechanical and non-mechanical methods. The application of nanoparticles is one example of the fast-evolving technology used to damage microbial cells. SiO2 or Al2O3 nanoparticles break yeast cell walls and disrupt membranes, releasing intracellular bioactive compounds. Succinylation of yeast protein during extraction can increase yeast protein extraction rate, lower RNA concentration, raise yeast protein solubility, increase amino acid content, and improve yeast protein emulsification and foaming capabilities. Combining physical and enzymatic extraction methods generates the most representative pool of mannose proteins from yeast cell walls. Ethanol or isoelectric precipitation purifies mannose proteins. Mannoproteins can be used as foamy replacement for animal-derived components like egg whites due to their emulsification, stability, and foaming capabilities. Yeast bioactive peptide was separated by ultrafiltration after enzymatic hydrolysis of yeast protein and has shown hypoglycemic, hypotensive, and oxidative action in vitro studies. Additionally, the review delves into the physicochemical properties and stability of yeast-derived peptides as well as their applications in the food industry. The article infers that yeast proteins are among the promising sources of sustainable protein, with a wide range of potential applications in the food industry.

In vitro caries-preventive effect of a mineralization-promoting peptide combined with fluoride gel on sound primary teeth

BACKGROUND

Mineralization-promoting peptide-3 (MPP3) is a new biomimetic remineralization agent.

AIM

To assess the remineralization efficiency of MPP3, either alone or in combination with fluoride gel.

DESIGN

The samples were divided into four groups: control, 1.23% fluoride gel, 10% MPP3 gel, and 1.23% fluoride gel + 10% MPP3. Following the application of remineralization agents (4 min), the samples remained in a pH-cycling model (37°C, 4 weeks). Microhardness, microcomputed tomography (micro-CT), polarized light microscopy (PLM), and field emission scanning electron microscopy (FE-SEM) analysis were conducted. RM-ANOVA, one-way ANOVA, and intraclass correlation coefficient (ICC) were used for statistical analysis, and a significance level of p < .05 was employed.

RESULTS

Mineralization-promoting peptide 3 and fluoride gel + MPP3 increased the microhardness of the enamel compared with initial values in each group (p < .05). Mineralization-promoting peptide 3 successfully maintained the mineral density of enamel, although the cariogenic pH-cycling and PLM results indicated that the lesion depth (μm) was significantly lower in the fluoride gel + MPP3 group (27.0336 ± 12.53650) than in the control group (37.3907 ± 12.76002, p < .05).

CONCLUSION

The combined use of MPP3 with fluoride gel enhanced the caries-protective and mineralization-promoting effects of fluoride. Mineralization-promoting peptide 3 may be a potential agent that can be employed to improve the physical properties of enamel.

Alternative Renin-Angiotensin System

The renin-angiotensin system is the most important peptide hormone system in the regulation of cardiovascular homeostasis. Its classical arm consists of the enzymes, renin, and angiotensin-converting enzyme, generating angiotensin II from angiotensinogen, which activates its AT1 receptor, thereby increasing blood pressure, retaining salt and water, and inducing cardiovascular hypertrophy and fibrosis. However, angiotensin II can also activate a second receptor, the AT2 receptor. Moreover, the removal of the C-terminal phenylalanine from angiotensin II by ACE2 (angiotensin-converting enzyme 2) yields angiotensin-(1-7), and this peptide interacts with its receptor Mas. When the aminoterminal Asp of angiotensin-(1-7) is decarboxylated, alamandine is generated, which activates the Mas-related G-protein-coupled receptor D, MrgD (Mas-related G-protein-coupled receptor type D). Since Mas, MrgD, and the AT2 receptor have opposing effects to the classical AT1 receptor, they and the enzymes and peptides activating them are called the alternative or protective arm of the renin-angiotensin system. This review will cover the historical aspects and the current standing of this recent addition to the biology of the renin-angiotensin system.

A SILAC-based accurate quantification of shrimp allergen tropomyosin in complex food matrices using UPLC-MS/MS

The carryover of trace allergens in complex food matrices poses challenges for detection techniques. Here, we demonstrate an accurate UPLC-MS/MS quantification assay for the shrimp allergen tropomyosin with a full-length isotope-labelled recombinant tropomyosin (TM-I) internal standard in complex food matrices. The TM-I, expressed based on the SILAC technique, exhibited a high isotope labelling ratio (>99%), purity, and alignment with the natural sequence. This method determined the tropomyosin ranging from 0.2 to 100 ng/mL. Mean recoveries ranged from 89 to 116%, with intra- and inter-day RSDs below 12%, for three signature peptides across three types of commercially processed food matrices. The limits of quantitation were 1 μg/g in pop food and sauce, and 10 μg/g in surimi product, respectively. This study supports the use of recombinant full-length isotope-labelled proteins rather than stable-isotope labelling peptides as internal standards to achieve more accurate quantitation of food allergens as the digestion error is corrected.

Qualification of a LC-HRMS platform method for biosimilar development using NISTmab as a model

Biosimilars are a cost-effective alternative to biopharmaceuticals, necessitating rigorous analytical methods for consistency and compliance. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) is a versatile tool for assessing key attributes, encompassing molecular mass, primary structure, and post-translational modifications (PTMs). Adhering to ICH Q2R1, we validated an LC-HRMS based peptide mapping method using NISTmab as a reference. The method validation parameters, covering system suitability, specificity, accuracy, precision, robustness, and carryover, were comprehensively assessed. The method effectively differentiated the NISTmab from similar counterparts as well as from artificially introduced spiked conditions. Notably, the accuracy of mass error for NISTmab specific complementarity determining region peptides was within a maximum of 2.42 parts per million (ppm) from theoretical and the highest percent relative standard deviation (%RSD) observed for precision was 0.000219 %. It demonstrates precision in sequence coverage and PTM detection, with a visual inspection of total ion chromatogram approach for variability assessment. The method maintains robustness when subjected to diverse storage conditions, encompassing variations in column temperature and mobile phase composition. Negligible carryover was noted during the carryover analysis. In summary, this method serves as a versatile platform for multiple biosimilar development by effectively characterizing and identifying monoclonal antibodies, ultimately ensuring product quality.

An Insulin-Chromogranin A Hybrid Peptide Activates DR11-Restricted T Cells in Human Type 1 Diabetes

Hybrid insulin peptides (HIPs) formed through covalent cross-linking of proinsulin fragments to secretory granule peptides are detectable within murine and human islets. The 2.5HIP (C-peptide-chromogranin A [CgA] HIP), recognized by the diabetogenic BDC-2.5 clone, is a major autoantigen in the nonobese diabetic mouse. However, the relevance of this epitope in human disease is currently unclear. A recent study probed T-cell reactivity toward HIPs in patients with type 1 diabetes, documenting responses in one-third of the patients and isolating several HIP-reactive T-cell clones. In this study, we isolated a novel T-cell clone and showed that it responds vigorously to the human equivalent of the 2.5HIP (designated HIP9). Although the responding patient carried the risk-associated DRB1*04:01/DQ8 haplotype, the response was restricted by DRB1*11:03 (DR11). HLA class II tetramer staining revealed higher frequencies of HIP9-reactive T cells in individuals with diabetes than in control participants. Furthermore, in DR11+ participants carrying the DRB4 allele, HIP9-reactive T-cell frequencies were higher than observed frequencies for the immunodominant proinsulin 9-28 epitope. Finally, there was a negative correlation between HIP9-reactive T-cell frequency and age at diagnosis. These results provide direct evidence that this C-peptide-CgA HIP is relevant in human type 1 diabetes and suggest a mechanism by which nonrisk HLA haplotypes may contribute to the development of β-cell autoimmunity.

ARTICLE HIGHLIGHTS

Sensitization with Fungal Protease Allergen Establishes Long-Lived, Allergenic Th Cell Memory in the Lung

Allergic asthma is a chronic inflammatory disease that affects millions of individuals worldwide. Exposure to allergens produced by a variety of otherwise harmless microbes, including fungi, predisposes individuals to immunopathologic disease upon subsequent encounters with allergen. We developed a mouse model that employs a purified protease produced by Aspergillus (Asp f 13) to investigate the contributions of CD4+ Th cells to recurrent lung inflammation. Notably, memory CD4+ T cells enhanced the eosinophil response of sensitized/rechallenged animals. In addition, memory CD4+ T cells maintained allergenic features, including expression of GATA-binding protein 3 and IL-5. Th2 memory T cells persisted in the peribronchiolar interstitium of the lung and expressed markers of tissue residence, such as CD69, CCR8, and IL-33R. Lastly, we identified a peptide epitope contained within Asp f 13 and generated a peptide-MHC class II tetramer. Using these tools, we further demonstrated the durability and exquisite sensitivity of memory T cells in promoting lung eosinophilia. Our data highlight important features of memory T cells that strengthen the notion that memory T cells are principal drivers of eosinophilic disease in murine models of allergic sensitization and episodic airway inflammation.

A simple polyarginine membrane electrochemical sensor for the determination of MDMA and MDA

In this study, a simple electrochemical sensor based on l-arginine membrane (P-L-arg/GCE) was developed for rapid and sensitive detection of MDMA and MDA. A polyarginine membrane was obtained through one-step direct electropolymerization, which provides more reaction sites for the analyte and improves the sensitivity of the sensor. Following the optimized selection parameters, the MDMA detection range was established at 1.0 × 10-7∼3.5 × 10-5 mol L-1, with a detection limit of 3.3 × 10-8 mol L-1. Similarly, the detection range for MDA was established at 1.0 × 10-7∼5.3 × 10-5 mol L-1 with a detection limit of 3.3 × 10-8 mol L-1. Additionally, the potential oxidation mechanism of MDMA and MDA during the REDOX process was analyzed by cyclic voltammetry. Furthermore, the proposed sensor exhibited superior selectivity, excellent reproducibility, and satisfactory stability. The proposed sensors can be used for reliable monitoring of MDMA or MDA in human urine and hair samples, respectively, and it has acceptable analytical reliability and enormous potential for practical applications.

Oriented docking of the template for improved imprinting efficiency toward peptide with modifications

Molecular imprinting polymers (MIPs) are synthetic receptors as biomimetic materials for various applications ranging from sensing to separation and catalysis. However, currently existing MIPs are stuck to some of the issues including the longer preparation steps and poor performance. In this report, a facile and one-pot strategy by integrating the in-situ growth of magnetic nanoparticles and reversed phase microemulsion oriented molecularly imprinting strategy to develop magnetic molecular imprinted nanocomposites was proposed. Through self-assembling of the template, it brought up highly ordered and uniform arrangement of the imprinting structure, which offered faster adsorption kinetic as adsorption equilibrium was achived within 15 min, higher adsorption capacity (Qmax = 48.78 ± 1.54 μmol/g) and high affinity (Kd = 127.63 ± 9.66 μM) toward paradigm molecule-adenosine monophosphate (AMP) compared to the conventional bulk imprinting. The developed MIPs offered better affinity and superior specificity which allowed the specific enrichment toward targeted phosphorylated peptides from complex samples containing 100-fold more abundant interfering peptides. Interestingly, different types of MIPs can be developed which could targetly enrich the specific phosphorylated peptides for mass spectrometry analysis by simply switching the templates, and this strategy also successfully achieved imprinting of macromolecular peptides. Collectively, the approach showed broad applicability to target specific enrichment from metabolites to phosphorylated peptides and providing an alternative choice for selective recognition and analysis from complex biological systems.

Solvent effect on the detection of peptides and proteins by nanoelectrospray ionization mass spectrometry: Anomalous behavior of aqueous 2-propanol

To investigate the solvent effect on the detection of peptides and proteins, nanoelectrospray mass spectra were measured for mixtures of 1 % acetic acid and 5 × 10-6 M gramicidin S (G), ubiquitin (U), and cytochrome c (C) in water (W), methanol (MeOH), 1-propanol (1-PrOH), acetonitrile (AcN), and 2-propanol (2-PrOH). Although doubly protonated G (G2+) and multiply protonated U (Un+) and C (Cn+) were readily detected with a wide range of mixing ratios of W solutions for MeOH, 1-PrOH, and AcN, Cn+ was totally suppressed for the solutions with mixing ratios (v/v) of W/2-PrOH (50/50) and (70/30). However, denatured Cn+ started to be detected with W/2-PrOH (90/10) together with Gn+ (n = 1, 2) and native Un+ (n = 6-8). At the mixing ratio of W/2-PrOH (95/5), native Cn+ (n = 7-10) together with Gn+ (n = 1, 2) and native Un+ (n = 6-8) were detected with high ion intensities. The use of W/2-PrOH (95/5) is profitable because it enables the detection of native proteins with high detection sensitivities.