Search

An unprecedented and direct PS‐MS (paper spray ionization mass spectrometry) method was proposed for the detection of native peptides, that is, glutathiones (GSHs), homoglutathiones (hGSHs), and phytochelatins (PCs), in basil (Ocimum basilicum L.) roots before and after cadmium exposure. The roots were submitted to cold maceration followed by sonication with formic acid as the extractor solvent for sample preparation. PS‐MS was used to analyze such extracts in the positive mode, and the results allowed for the detection of several GSHs, hGSHs, and PCs. Some of these PCs were not distinguished in the control samples, that is, basil roots not exposed to cadmium. Other PCs were noticed in both types of roots, uncontaminated and cadmium‐contaminated, but the intensities were higher in the former samples. Moreover, long‐time exposure to cadmium stimulated the formation of some of these PCs and their cadmium complexes. The results, therefore, provided some crucial insights into the defense mechanism of plants against an external stress condition due to exposure to a toxic heavy metal. The present study represents a promising alternative to investigate other crucial physiological processes in plants submitted to assorted stress conditions. [ABSTRACT FROM AUTHOR]

We developed a simple, paper‐based device that enables sensitive detection by mass spectrometry (MS) without solid phase extraction or other sample preparation. Using glass fiber filter papers within a 3D printed holder, the device employs electrokinetic manipulations to stack, separate, and desalt charged molecules on paper prior to spray into the MS. Due to counter‐balanced electroosmotic flow and electrophoresis, charged analytes stack on the paper and desalting occurs in minutes. One end of the paper strip was cut into a sharp point and positioned near the inlet of a MS. The stacked analyte bands move toward the paper tip with the EOF where they are ionized by paper spray. The device was applied to analysis of PFAS in tap water with sub part‐per‐trillion detection limits in less than ten minutes with no sample pretreatment. Analysis of opioids in urine also occurs in minutes. The crucial parameters to enable stacking, separation, and MS ionization of both positively and negatively charged analytes were determined and optimized. Experimental and computational modeling studies confirm the electrokinetic stacking and analyte transport mechanisms. On‐paper separations were carried out by stacking analyte bands at different locations depending on their electrophoretic mobility, achieving baseline separation in some cases. [ABSTRACT FROM AUTHOR]

We developed a simple, paper‐based device that enables sensitive detection by mass spectrometry (MS) without solid phase extraction or other sample preparation. Using glass fiber filter papers within a 3D printed holder, the device employs electrokinetic manipulations to stack, separate, and desalt charged molecules on paper prior to spray into the MS. Due to counter‐balanced electroosmotic flow and electrophoresis, charged analytes stack on the paper and desalting occurs in minutes. One end of the paper strip was cut into a sharp point and positioned near the inlet of a MS. The stacked analyte bands move toward the paper tip with the EOF where they are ionized by paper spray. The device was applied to analysis of PFAS in tap water with sub part‐per‐trillion detection limits in less than ten minutes with no sample pretreatment. Analysis of opioids in urine also occurs in minutes. The crucial parameters to enable stacking, separation, and MS ionization of both positively and negatively charged analytes were determined and optimized. Experimental and computational modeling studies confirm the electrokinetic stacking and analyte transport mechanisms. On‐paper separations were carried out by stacking analyte bands at different locations depending on their electrophoretic mobility, achieving baseline separation in some cases. [ABSTRACT FROM AUTHOR]

Biased and accelerated molecular simulations (BAMS) are widely used tools to observe relevant molecular phenomena occurring on time scales inaccessible to standard molecular dynamics, but evaluation of the physical time scales involved in the processes is not directly possible from them. For this reason, the problem of recovering dynamics from such kinds of simulations is the object of very active research due to the relevant theoretical and practical implications of dynamics on the properties of both natural and synthetic molecular systems. In a recent paper [A. Rapallo et al., J. Comput. Chem. 42, 586–599 (2021)], it has been shown how the coupling of BAMS (which destroys the dynamics but allows to calculate average properties) with Extended Diffusion Theory (EDT) (which requires input appropriate equilibrium averages calculated over the BAMS trajectories) allows to effectively use the Smoluchowski equation to calculate the orientational time correlation function of the head–tail unit vector defined over a peptide in water solution. Orientational relaxation of this vector is the result of the coupling of internal molecular motions with overall molecular rotation, and it was very well described by correlation functions expressed in terms of weighted sums of suitable time-exponentially decaying functions, in agreement with a Brownian diffusive regime. However, situations occur where exponentially decaying functions are no longer appropriate to capture the actual dynamical behavior, which exhibits persistent long time correlations, compatible with the so called subdiffusive regimes. In this paper, a generalization of EDT will be given, exploiting a fractional Smoluchowski equation (FEDT) to capture the non-exponential character observed in the relaxation of intramolecular distances and molecular radius of gyration, whose dynamics depend on internal molecular motions only. The calculation methods, proper to EDT, are adapted to implement the generalization of the theory, and the resulting algorithm confirms FEDT as a tool of practical value in recovering dynamics from BAMS, to be used in general situations, involving both regular and anomalous diffusion regimes. [ABSTRACT FROM AUTHOR]

Biotoxins are ranges of toxic substances produced by animals, plants, and microorganisms, which could contaminate foods during their production, processing, transportation, or storage, thus leading to foodborne illness, even food terrorism. Therefore, proposing simple, rapid, and effective detection methods for ensuring food free from biotoxin contamination shows a highly realistic demand. Aptamers are single-stranded oligonucleotides obtained from the systematic evolution of ligands by performing exponential enrichment (SELEX). They can specifically bind to wide ranges of targets with high affinity; thus, they have become important recognizing units in safety monitoring in food control and anti-terrorism. In this paper, we reviewed the technical points and difficulties of typical aptamer screening processes for biotoxins. For promoting the understanding of food control in the food supply chain, the latest progresses in rapid optical detection of biotoxins based on aptamers were summarized. In the end, we outlined some challenges and prospects in this field. We hope this paper could stimulate widespread interest in developing advanced sensing systems for ensuring food safety. [ABSTRACT FROM AUTHOR]

With the vigorous development of the petroleum industry, improving the efficiency of oil and gas exploitation has become an important issue. Temperature-sensitive materials show great potential for application in the development and production of oil and gas fields due to their unique temperature-responsive properties. This paper reviews the application of temperature-sensitive materials in oil and gas drilling and introduces the characteristics of three types of temperature-sensitive materials: N-substituted acrylamide polymers, amphiphilic block copolymers, and peptides. Because these materials can change their physical state at specific temperatures, this paper discusses in detail the role of various temperature-sensitive materials as plugging agent, thickener, oil displacing agent, flocculant, and tackifier in oil and gas field operations, as well as the mechanism of action and performance of temperature-sensitive materials in practical oil and gas drilling operations. As we have not yet seen relevant similar literature, this paper aims to discuss the innovative application of temperature-sensitive materials in the oil and gas drilling process, and at the same time points out the problems in the current research and applications as well as future development directions. Through analysis and comparison, we provide an efficient and environmentally friendly materials selection option for the petroleum industry in order to promote the progress and sustainable development of oil and gas extraction processes. [ABSTRACT FROM AUTHOR]

A commentary of the paper 'Humanin variant P3S is associated with longevity in APOE4 carriers and resists APOE4‐induced brain pathology' that appeared recently in Aging Cell. The possible association of a mitochondrial haplogroup with a disease is frequently discussed. The Humanin peptide encoded by the mtDNA has been shown to play an important regulatory role in cell metabolism. There are variants of Humanin caused by different mutations and it is known that the potent form of Humanin, termed S14G, is found naturally in the people of haplogroup U6a7a1a because they have the mutation m.A2672G; however it has not been shown that having this mutation is indeed beneficial. In their paper, the authors suggest that the mitochondrial DNA mutation, m.C2639T, may be beneficial in people who are in haplogroup N1b and also carry APOE4. The mutation changes the common form of Humanin to Humanin P3S. In the study, the researchers looked at a group of Ashkenazi women who were over the age of 95, and found that a higher proportion of them carried APOE4, suggesting that Humanin P3S protected them against the adverse effects of APOE4. A study in a mouse model supported this finding by showing treatment with Humanin P3S reduced APOE4‐induced brain pathology. In the world population, there are about 500,000 Ashkenazi in haplogroup N1b, predominantly in the subgroup N1b1b1; and there are about 9.5 million non‐Ashkenazi people with the mutation m.C2639T and are therefore also in haplogroup N1b and have Humanin P3S. However, the researchers have yet to show Humanin P3S is of benefit in non‐Ashkenazi people. This paper raises the possibility of a therapeutic use of Humanin P3S in the treatment of Alzheimer's disease. [ABSTRACT FROM AUTHOR]

A single amino acid in a peptide sequence can play an important role to tune the self‐assembly and hydrogelation behaviour. Here, a C‐terminal cysteine‐containing ultrashort peptide hydrogelator forms hydrogel through non‐covalent and covalent interactions. Interestingly, the hydrogel is insoluble in water and buffer solutions at different pH values (1‐13) and is thixotropic and injectable. In recent years, removing dyes from contaminated water has become a significant concern because of the shortage of freshwater resources. Therefore, the adsorption of dyes through a reliable, straightforward, nontoxic, cheap, and environmentally friendly adsorbent has become a popular topic. Hence, the hydrogelator was exploited to remove organic dyes from wastewater, harnessing its applicability in the gel phase and solid supports (filter paper and cotton). [ABSTRACT FROM AUTHOR]

[Display omitted] • A novel dual-functional probe FAHK was design and synthesized based on copper peptide backbone. • FAHK showed sequential response towards Cu2+/Hg2+ and S2− via fluorescent and colorimetric methods. • The detection limit of 37.1 nM for Cu2+, 20.8 nM for Hg2+ and 0.27 μM/0.12 μM for S2−, respectively. • FAHK has low toxicity and was successfully used to image Cu2+, Hg2+ and S2− in living cells. • Test strips of FAHK were prepared for rapid and visual detection for Cu2+, Hg2+ and S2− with naked eye. In this study, a novel peptide-based fluorescent and colorimetric dual-functional probe (FAHK) was designed and synthesized by simulating the structure of copper peptide. FAHK exhibited high selectivity and rapid response to Cu2+ and Hg2+ with two non-fluorescence ensembles FAHK- Cu2+ and FAHK- Hg2+ formation by the 2:1 coordination mode, and the limits of detection for Cu2+ and Hg2+ were 37.1 nM and 20.8 nM, respectively. FAHK showed a naked eye colorimetric response for Cu2+ and Hg2+ in an aqueous solutions under visible light. As two new promising cascade probes, FAHK- Cu2+ and FAHK- Hg2+ ensemble were used for sequential selective recognition of S2− according to the displacement approach with fluorescence "turn-on" response and colorimetric change, and the limit of detection were 0.27 μM (FAHK -Cu2+ ensemble) and 0.12 μM (FAHK -Hg2+ ensemble) for S2−, which were well below the safety level the H 2 S standard in drinking waters (14.8 µM, WHO guidelines). What' more, in view of low toxicity and biocompatibility, the potential application of FAHK in biological systems was demonstrated via living cells imaging. More importantly, FAHK could also be made into the paper test strips for visual detection of Cu2+, Hg2+ and S2− with the naked eye under 365 nm UV light and visible light, which suggested that better portability and operation simplicity that is favourable for on-site analysis. [ABSTRACT FROM AUTHOR]

Peptide therapeutics play an increasingly important role in modern drug discovery. Improving the pharmacokinetic profile of bioactive peptides has been effectively achieved with chemical modifications, especially macrocyclisation reactions. Consequently, there is a great demand for highly constrained compounds such as bicyclic peptides. In our previous research, we introduced peptide–bismuth bicycles and peptide–arsenic bicycles as new classes of constrained peptides. In this work, we extend our peptide bicyclisation strategy towards antimony. Similar to arsenic and bismuth, antimony(III) selectively binds to three cysteine residues in peptides, enabling the in situ formation of stable bicycles. The bicyclisation reaction occurs instantaneously under biocompatible conditions at physiological pH. Antimony–peptide bicycles remain largely intact in the presence of the common metal chelator ethylenediaminetetraacetic acid (EDTA) and the main endogenous thiol competitor glutathione (GSH). Furthermore, when challenged with bismuth(III) from water-soluble gastrodenol (bismuth tripotassium dicitrate), antimony–peptide bicycles convert into the corresponding bismuth–peptide bicycle, highlighting the superior thiophilicity of bismuth over other pnictogens. Our study further expands the toolbox of peptide multicyclisation with main group elements previously underexplored in chemical biology. Cyclic peptide drugs are important therapeutics. Previously, bismuth and arsenic were introduced to create peptide bicycles by binding three cysteines. Now, antimony complements this set of elements to form stable bicyclic peptides. These remain stable in the presence of a common metal chelator and glutathione. Bismuth outcompetes antimony as the core atom in peptide bicycles. (Image credit: Lani Davies.) This article belongs to the 10th Anniversary Collection of RACI and AAS Award papers. [ABSTRACT FROM AUTHOR]

Tannery solid waste (TSW) contains 70–90% collagen by weight. The rapid extraction of collagen while preserving its original and unique triple-helical conformation has proved challenging. In this paper, an ionic liquid-synergistic dissolution and regeneration (IL-SDR) method was developed based on a TBAH/DMSO/H2O ternary (TDH) solvent for the rapid recovery of collagen from TSW under mild conditions. A solubility of 10.25% TSW and a collagen recovery yield of 51.2% were achieved in 30 minutes at room temperature. The original triplet helical conformation and the molecular weight of the collagen product were retained, confirmed via FT-IR, circular dichroism, and matrix-assisted laser desorption/ionization time-of-flight analysis. SEM was used to verify that dense and uniform pores could be formed within collagen by adjusting the DMSO content, and cytotoxicity and moisture retention tests demonstrated that the collagen produced via the IL-SDR process is comparable to natural collagen used in cosmetic and skincare applications. Moreover, the TDH solvent demonstrated excellent reproducibility across five cycles, achieving consistent solubility varying from 9.71% to 11.04%. EPR and 1H NMR showed that the OH– in TBAH induced the generation of DMSO˙ free radicals in the TDH solvent, and these radicals were indispensable for the dissolution of TSW. The DMSO content was positively correlated with the concentration of free radicals. A synergistic dissolution mechanism was proposed: DMSO˙ free radicals preferentially cleaved the terminal peptide chains, causing the collagen molecules to be exposed to DMSO. Subsequently, DMSO disrupted the original hydrogen bond network within the collagen molecules. Then, TBAH and DMSO formed hydrogen bonds with the collagen molecules, stabilizing the dissolved collagen and preventing the reformation of the hydrogen bond network between collagen molecules. This work provides an avenue for low-temperature and rapid dissolution of TSW, and reveals an in-depth, atypical dissolution mechanism for collagen-based materials during the IL-SDR process. [ABSTRACT FROM AUTHOR]

The average content of casein in yak milk is 40.2 g/L. Casein can be degraded by enzymatic digestion or food processing to produce abundant degradation peptides. International researchers have studied the degradation peptides of yak milk casein by using multiple techniques and methods, such as in vitro activity tests, cellular experiments, proteomics, bioinformatics, etc., and found that the degradation peptides have a wide range of functional activities that are beneficial to the human body, such as angiotensin-converting enzyme (ACE) inhibitory, antioxidant, anti-inflammatory, antidiabetic, antimicrobial, anticancer, and immunomodulatory activities, etc., and it has been proved that the types and strengths of functional activities are closely related to the structural characteristics of the peptides. This paper describes the characteristics of yak milk proteins, the functional activities, and mechanism of action of degraded peptides. Based on the types of functional activities of yak milk casein degradation peptides, we classified and elucidated the effects of structural factors, such as peptide molecular weight, peptide length, amino acid sequence, physicochemical properties, electrical charge, hydrophobicity, spatial conformation, chain length, and the type of enzyme on these activities. It reveals the great potential of yak milk casein degradation peptides as functional active peptide resources and as auxiliary treatments for diseases. It also provides important insights for analyzing yak casein degradation peptide activity and exploring high-value utilization. [ABSTRACT FROM AUTHOR]

Background: Current markers for monitoring of Celiac disease (CD) and outcome after gluten-free diet (GFD) are limited. Urinary gluten immunogenic peptide (UGIP) has been shown to correlate with gluten intake and mucosal damage in CD. Hence our study objective was to review the evidence of efficacy of UGIP as a biomarker for CD Method: This systematic review was conducted using standards outlined in the PRISMA statement. Databases including PubMed, ProQuest, EBSCOHost, and Google Scholar were searched for relevant studies (randomized controlled trials (RCTs) and observational) up to March 2023. Newcastle Ottawa Scale and Cochrane Risk of Bias were used to assess the quality of included papers. Result: T: Literature search identified 85 studies, and after assessment of eligibility, eight studies were eventually reviewed. UGIP concentration was found to correlate with degree of mucosal damage of CD (Marsh II-III). Although three observational studies found a correlation between gluten intake and UGIP concentration, two RCTs did not find UGIP reliable for determining GFD adherence. In addition, UGIP concentrations did not correlate with antibody titers and clinical symptoms. Conclusion: UGIP may be useful for predicting degree of mucosal damage in CD. However, further studies are needed to evaluate its role in GFD adherence. [ABSTRACT FROM AUTHOR]

Simple Summary: Functional studies of neuropeptides are of great significance in revealing the neuroendocrine regulation mechanism in crustaceans, and in guiding and developing artificial regulation techniques in economic species. In this paper, we investigated the effect of a crustacean neuropeptide corazonin (Crz) on ecdysteroid synthesis based on the high expression of Crz receptor in the Y-organ, the main site of ecdysteroid synthesis. By using Crz treatment and CrzR silencing, we found that Crz/CrzR signaling could cause up-regulation of ecdysteroid synthesis genes and an increase in ecdysteroid levels both in vitro and in vivo. In addition, it was also observed that Crz/CrzR signaling affects the expression level of ecdysis-triggering hormones. Our results provide new insights into the understanding of Crz function in crustaceans. The neuropeptide corazonin (Crz) exerts diverse physiological effects in insects, yet its role in crustaceans remains elusive. The abundant expression of Crz receptor (CrzR) in the Y-organs of several crustaceans suggests a potential involvement of Crz in regulating ecdysteroid synthesis. In this study, we examined the effects of PtCrz on ecdysteroid synthesis during the molting period of Portunus trituberculatus through PtCrz treatments and PtCrzR silencing. Our results showed that PtCrz peptide stimulates ecdysteroid levels and the gene expression involved in ecdysteroidogenesis both in vitro and in vivo, whereas dsPtCrzR treatments had opposite effects on ecdysteroid levels and associated gene expression. Thus, our study suggests that PtCrz may modulate ecdysteroid synthesis via Y-organ-expressed PtCrzR. Furthermore, we also discovered the involvement of PtCrz/PtCrzR signaling in regulating PtETH expression. Notably, the inhibitory effect of dsPtCrzR on ecdysteroid synthesis or PtETH expression can be reversed by PtCrz treatment, suggesting the potential existence of multiple receptors for PtCrz. This study provides new insights into the function of crustacean Crz and, for the first time, elucidates the presence of a neuropeptide that can stimulate ecdysteroid synthesis in crustaceans. [ABSTRACT FROM AUTHOR]

The process of synthesizing radionuclide-coupled drugs, especially shutdown technology that links bipotent chelators with biomolecules, utilizes traditional coupling reactions, including emerging click chemistry; these reactions involve different drawbacks, such as complex and cumbersome reaction steps, long reaction times, and the use of catalysts at various pH values, which can negatively impact the effects of the chelating agent. To address the above problems in this study, This research designed a novel bipotent chelator coupled with peptides. In the present study, dichloromethane was used as a solvent, and the reaction was conducted at room temperature for 12 h. A one-step ring-opening method was employed to introduce the coupling functional group of tridentate amide acid. The coupling materials consisted of the amino active site of the peptide and diethylene glycol anhydride. In this paper, this study explored the reactions between different equivalents of acid anhydride coupled to the peptide (peptide sequence: HLRKLRKR) and determined that the maximum conversion of the peptide feedstock was 87%. To determine the selectivity of the reaction sites in this polypeptide, This study identified the peptide sequence at the reaction site using nuclear magnetic resonance (NMR) and liquid chromatography–mass spectrometry (LC-MS). For the selected peptide, the first reactive site was on the terminal amino group, followed by the amino group on the tetra- and hepta-lysine side chains. The tridentate amic acid framework functions as a chelating agent, capable of binding a range of lanthanide ions. This significantly reduces and optimizes the time and cost associated with synthesizing radionuclide-coupled drugs. [ABSTRACT FROM AUTHOR]

Objective: Lantibiotics are a family of bacterial antimicrobial peptides synthesized by ribosomes, that undergo post-translational modification to form lanthionine (Lan) and methyllanthionine (MeLan) residues. Lantibiotics are currently considered promising agents for combating antibiotic-resistant bacterial infections. This paper presents a biotechnological method for obtaining two components of the lantibiotic lichenicidin from Bacillus licheniformis B-511, Lchα and Lchβ. Such a system has the potential to facilitate the production of not only lichenicidin, but also other lantibiotics, including two-component ones, and also to enable the study of their biosynthesis and the activity and substrate specificity of modifying enzymes. Methods: The developed system is based on heterologous coexpression of the genes of Lchα and Lchβ precursors with the genes of their corresponding modifying enzymes in the cytoplasm of Escherichia coli BL21(DE3). Subsequent steps included immobilized metal affinity chromatography of the His-tagged hybrid peptide under denaturing conditions, cyanogen bromide cleavage in acidic medium, and final purification using reverse-phase HPLC. Results and Discussion: The system was employed for the expression and purification of lantibiotics, resulting in the successful isolation of the β-component of lichenicidin in high yield (approximately 4 mg/L of culture). This purified beta component exhibited structural and functional characteristics comparable to its natural counterpart, which was purified from the natural producer. However, the yield of the mature α-component of lichenicidin in such a system was significantly lower. Conclusions: The work presents a biotechnological method for obtaining recombinant two-component lantibiotic lichenicidin, which has proven to be particularly effective in the case of Lchβ. The developed method can also be applied to the production of other promising lantibiotics and their further research. [ABSTRACT FROM AUTHOR]

Context: The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)—leucine (Leu/L) and isoleucine (Ile/I)—as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the chirality indices of various nanotubes are given, depending on the chirality of the initial dipeptides—the results obtained are consistent with the law of changes in the type of chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed. Method: The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree–Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree–Fock (RHF) and in the unrestricted Hartree–Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak–Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO − EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package. [ABSTRACT FROM AUTHOR]

Cation‐π interactions, often found in protein assemblies, are characterized by favorable electrostatic interactions between an aromatic π‐electron surface and a positively charged species. There are evidences that reveal the importance of cation‐π interactions between arginine and aromatic residues in protein structure and function. In this paper, the effect of cation‐π interactions on the aggregation propensity of peptides derived from human islet polypeptide (hIAPP) was explored using UV resonance Raman and fluorescence spectroscopy. By employing an analog of hIAPP22–29 in which Phe‐23 is replaced with tryptophan (NWGAILSS), we were able to demonstrate an increase in the amyloidogenic propensity of this mutant in the presence of Zn2+ that is attributable to cation‐π interactions. In contrast, no cation‐π interactions were observed when the cationic F23R analog of hIAPP22–29 (NRGAILSS) was allowed to interact with NWGAILSS. From these observations, it was surmised that in these peptides, the dominant interaction between arginine and tryptophan involves the π‐cloud of the guanidino group and the indole ring, not cation‐π interactions. The spectroscopic data, supported by density functional theory‐based simulation results, suggest that arginine‐tryptophan interaction involves π‐π stacking where the guanidino group is oriented parallel to the indole ring. These hydrophobic interactions, coupled with the hydrotropic effect of the guanidine functionality of arginine, led to a delay in the aggregation kinetics of NWGAILSS. These unique interactions were further exploited to design a peptide inhibitor of full‐length amylin self‐assembly. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has tested the technical, scientific, and industrial resources of all countries worldwide. Faced with the absence of pharmacological strategies against the disease, an effective plan for vaccinating against SARS-CoV-2 has been essential. Due to the lack of production means and necessary infrastructure, only a few nations could adequately confront this pathogen with a production, storage, and distribution scheme in place. This disease has become endemic in many countries, especially in those that are developing, thus necessitating solutions tailored to their reality. In this paper, we propose an in silico method to guide the design towards a thermally stable, universal, efficient, and safe COVID-19 vaccine candidate against SARS-CoV-2 using bioinformatics, immunoinformatics, and molecular modeling approaches for the selection of antigens with higher immunogenic potential, incorporating them into the surface of the M13 phage. Our work focused on using phagemid display as peptide array for neutralizing antibodies (PdPANA). This alternative approach might be useful during the vaccine development process, since it could bring improvements in terms of costeffectiveness in production, durability, and ease of distribution of the vaccine under less stringent thermal conditions compared to existing methods. Our results suggest that in the heavily glycosylated region of SARS-CoV-2 Spike protein (aa 344–583), from its inter-glycosylated regions, useful antigenic peptides can be obtained to be used in M13 phagemid display system. PdPANA, our proposed method might be useful to overcome the classic shortcoming posed by the phage-display technique (i.e., the time-consuming task of in vitro screening through great sized libraries with non-useful recombinant proteins) and obtain the most ideal recombinant proteins for vaccine design purposes. [ABSTRACT FROM AUTHOR]

The process of oxidation is believed to be mainly responsible for different chronic diseases and the deterioration of food by reducing shelf life. Antioxidants are known to scavenge various free radicals like hydroxyl radicals, and peroxyl radicals, and also inhibit lipid peroxidation. An increasing number of peptides and hydrolysates possessing antioxidant capacity have been characterized by soybean and other soy-based products. Due to their high protein content, soybeans, and other soy products are considered to be a great source for generating antioxidative peptides using enzymatic hydrolysis or microbial fermentation. This paper focuses on the recent advances in soy-derived antioxidative peptides, especially the methods for producing the peptides, evaluating the antioxidant capacity in vitro and in vivo, and purifying and identifying the most active peptide fraction and the factors influencing their antioxidant activity. • Soybean and soy-based products hold significant potential as rich sources of antioxidative peptides. • This paper provides a comprehensive summary of bioactive peptides, with a particular focus on those derived from soybean. • The review explores the structure-activity relationship of soybean peptides, shedding light on their functional properties. • Further research is necessary to explore and optimize the utilization of these bioactive peptides for various applications. [ABSTRACT FROM AUTHOR]

Bacillus anthracis is a fatal biological warfare agent, with a mortality rate of almost 100% when the bacteria are inhaled. Therefore, developing a biosensor for rapidly detecting B. anthracis spores in the ambient air is critical. Conventional techniques tend to be time-consuming, labor-intensive, and require highly trained personnel, thereby preventing rapid onsite detection. Moreover, low-cost, stable probes are required for continuous monitoring of multiple airborne targets. This study presents a paper-based electrochemical peptide sensor for rapid, label-free, sensitive, and economical quantification of liquid-borne and airborne Bacillus subtilis spores, widely used nonpathogenic B. anthracis simulant spores. These sensors were fabricated using wax printing on Whatman filter paper along with stencil-printed carbon paste electrodes and Ag/AgCl ink, as well as subsequent peptide (NHFLPKV) immobilization. These low-cost quickly fabricated sensors were characterized by differential pulse voltammetry and could detect spore concentrations as low as 6.9 × 102 colony-forming units (CFU) mL-1 in 30 min with high specificity towards the spores and stability. Furthermore, spore concentrations were determined from air samples obtained using the BioSampler, which demonstrated that these measurements agreed with those using the plate-counting assay; therefore, the surface proteins of the spores were intact through sampling with the BioSampler. These paper-based peptide sensors can be used for onsite rapid and continuous airborne spore-monitoring systems. • The first study to use a peptide-immobilized electrochemical paper-based sensor for detection of whole bacteria. • Rapid, label-free, sensitive, and economical quantification of airborne B. subtilis spores is presented. • The sensors detected spore concentrations as low as 6.9 × 102 CFU/mL in 30 min with low-cost and fast fabrication. • Measurements of air-sampled spores agreed with those using the plate-counting assay. • The surface proteins of the spores were intact through sampling with the BioSampler. [ABSTRACT FROM AUTHOR]

Background: Pheochromocytoma is a rare disease, and its familial occurrence is quite uncommon. The aim of this paper is to report a three-generation phenotypical expression of a case familial occurrence of pheochromocytoma. Case presentation: A 25-year-old female, with a history of adrenalectomy for pheochromocytoma, arrived at the shock room during her third pregnancy with an adrenergic crisis and hypoglycemia. To prevent perinatal complications, the patient was stabilized and the newborn was delivered through a Kerr-type cesarean section. A detailed history revealed that the paternal grandfather of the patient had an unilateral pheochromocytoma, whereas her paternal uncle had a bilateral pheochromocytoma. Additionally, a brother of the patient presented a unilateral pheochromocytoma. Amplicons for PCR assays were designed to span the protein-coding segments of the three Von Hippel–Lindau (VHL) exons, and the PCR products were sequenced using the Sanger method. In the trace of exon 3, we detected in the sample of the proband a heterozygous guanine to adenine transition (NM_000551.4 c. 552G > A) within the protein-coding segment of exon 3 of the VHL gene, which leads to a substitution of the arginine residue at position 161 by a glutamine residue in the encoded peptide (NP_000542.1p.R161Q). This mutation was absent in two unaffected daughters. Conclusion: A VHL mutation was suspected and confirmed in this family that was not transmitted to a fourth generation. This case illustrates the importance of molecular genetics methodologies to assist genetic counseling in cases of pheochromocytoma where familial aggregation is presumed. [ABSTRACT FROM AUTHOR]

In recent years, heavy metal pollution has become increasingly prominent, severely damaging ecosystems and biodiversity, and posing a serious threat to human health. However, the results of current methods for heavy metal restoration are not satisfactory, so it is urgent to find a new and effective method. Peptides are the units that make up proteins, with small molecular weights and strong biological activities. They can effectively repair proteins by forming complexes, reducing heavy metal ions, activating the plant's antioxidant defense system, and promoting the growth and metabolism of microorganisms. Peptides show great potential for the remediation of heavy metal contamination due to their special structure and properties. This paper reviews the research progress in recent years on the use of peptides to remediate heavy metal pollution, describes the mechanisms and applications of remediation, and provides references for the remediation of heavy metal pollution. [ABSTRACT FROM AUTHOR]

This paper presents the initial exploration of the free radical scavenging capabilities of peptides derived from protein hydrolysates (PPH) obtained from Zingiber cassumunar rhizomes (Phlai). To replicate the conditions of gastrointestinal digestion, a combination of pepsin and pancreatin proteolysis was employed to generate these hydrolysates. Subsequently, the hydrolysate underwent fractionation using molecular weight cut-off membranes at 10, 5, 3, and 0.65 kDa. The fraction with a molecular weight less than 0.65 kDa exhibited the highest levels ABTS, DPPH, FRAP, and NO radical scavenging activity. Following this, RP-HPLC was used to further separate the fraction with a molecular weight less than 0.65 kDa into three sub-fractions. Among these, the F5 sub-fraction displayed the most prominent radical-scavenging properties. De novo peptide sequencing via quadrupole-time-of-flight-electron spin induction-mass spectrometry identified a pair of novel peptides: Asp-Gly-Ile-Phe-Val-Leu-Asn-Tyr (DGIFVLNY or DY-8) and Ile-Pro-Thr-Asp-Glu-Lys (IPTDEK or IK-6). Database analysis confirmed various properties, including biological activity, toxicity, hydrophilicity, solubility, and potential allergy concerns. Furthermore, when tested on the human adenocarcinoma colon (Caco-2) cell line, two synthetic peptides demonstrated cellular antioxidant activity in a concentration-dependent manner. These peptides were also assessed using the FITC Annexin V apoptosis detection kit with PI, confirming the induction of apoptosis. Notably, the DY-8 peptide induced apoptosis, upregulated mRNA levels of caspase-3, -8, and -9, and downregulated Bcl-2, as confirmed by real-time quantitative polymerase chain reaction (RT-qPCR). Western blot analysis indicated increased pro-apoptotic Bax expression and decreased anti-apoptotic Bcl-2 expression in Caco-2 cells exposed to the DY-8 peptide. Molecular docking analysis revealed that the DY-8 peptide exhibited binding affinity with Bcl-2, Bcl-xL, and Mcl-1, suggesting potential utility in combating colon cancer as functional food ingredients. [ABSTRACT FROM AUTHOR]

A relaxin‐like gonad‐stimulating peptide (RGP), Aso‐RGP, featuring six cysteine residues, was identified in the Crown‐of‐Thorns Starfish (COTS, Acanthaster cf. solaris) and initially produced through recombinant yeast expression. This method yielded a single‐chain peptide with an uncleaved C‐peptide (His Tag) and suboptimal purity. Our objective was to chemically synthesize Aso‐RGP in its mature form, comprising two chains (A and B) and three disulfide bridges, omitting the C‐peptide. Furthermore, we aimed to synthesize a newly identified relaxin‐like peptide, Aso‐RLP2, from COTS, which had not been previously synthesized. This paper reports the first total chemical synthesis of Aso‐RGP and Aso‐RLP2. Aso‐RGP synthesis proceeded without major issues, whereas the A‐chain of Aso‐RLP2, in its reduced and unfolded state with two free thiols, presented considerable challenges. These were initially marked by "messy" RP‐HPLC profiles, typically indicative of synthesis failure. Surprisingly, oxidizing the A‐chain significantly improved the RP‐HPLC profile, revealing the main issue was not synthesis failure but the peptide's aggregation tendency, which initially obscured analysis. This discovery highlights the critical need to account for aggregation in peptide synthesis and analysis. Ultimately, our efforts led to the successful synthesis of both peptides with purities exceeding 95 %. [ABSTRACT FROM AUTHOR]

Peptides, both natural and synthetic, are well suited for a wide range of purposes and offer versatile applications in different fields such as biocatalysts, injectable hydrogels, tumor treatment, and drug delivery. The research of the better part of the cited papers was conducted using various database platforms such as MetalPDB. The rising prominence of therapeutic peptides encompasses anticancer, antiviral, antimicrobial, and anti-neurodegenerative properties. The metals Na, K, Mg, Ca, Fe, Mn, Co, Cu, Zn, and Mo are ten of the twenty elements that are considered essential for life. Crucial for understanding the biological role of metals is the exploration of metal-bound proteins and peptides. Aside from essential metals, there are other non-essential metals that also interact biologically, exhibiting either therapeutic or toxic effects. Irregularities in metal binding contribute to diseases like Alzheimer's, neurodegenerative disorders, Wilson's, and Menkes disease. Certain metal complexes have potential applications as radiopharmaceuticals. The examination of these complexes was achieved by preforming UV–Vis, IR, EPR, NMR spectroscopy, and X-ray analysis. This summary, although unable to cover all of the studies in the field, offers a review of the ongoing experimentation and is a basis for new ideas, as well as strategies to explore and gain knowledge from the extensive realm of peptide-chelated metals and biotechnologies. [ABSTRACT FROM AUTHOR]

Honey is a natural product that is used by a large number of people because of its distinctive compositional constituents, which have a considerable impact on its market value. The distinctive combination of amino acids and sugars found in honey's composition, along with its peptide content, could potentially provide several benefits to human health. During the past few years, cutting-edge techniques have been developed and used for the purpose of investigating, identifying, and characterizing peptides that are produced from honey bees. Therefore, the purpose of this review is to examine current trends and technological advancements in the study of honey bee-derived peptides, focusing on innovative and cutting-edge methods. Furthermore, this review explores various attributes of honey and its components, including the honey bee-derived peptide defensin-1. In addition, this review investigates various methods for separating and purifying peptides, as well as the factors that affect these methods. Additionally, defensin-1, a peptide produced by honey bees, is discussed along with its antioxidant and antimicrobial capabilities. In addition, this review focuses on cutting-edge and innovative omic methods used to study honey bee peptides, as well as the significance of artificial intelligence tools in their investigation. Consequently, the review paper delves into various significant obstacles faced by researchers and scientists studying honey bee peptides, while also offering an extensive range of fascinating opportunities and possibilities for future research for those interested in groundbreaking discoveries in this area. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance, particularly the emergence of resistant strains in fungal pathogens, has become a pressing global health concern. Antifungal peptides (AFPs) have shown great potential as a promising alternative therapeutic strategy due to their inherent antimicrobial properties and potential application in combating fungal infections. However, the identification of antifungal peptides using experimental approaches is time-consuming and costly. Hence, there is a demand to propose fast and accurate computational approaches to identifying AFPs. This paper introduces a novel multi-view feature learning (MVFL) model, called AFP-MVFL, for accurate AFP identification, utilizing multi-view feature learning. By integrating the sequential and physicochemical properties of amino acids and employing a multi-view approach, the AFP-MVFL model significantly enhances prediction accuracy. It achieves 97.9%, 98.4%, 0.98, and 0.96 in terms of accuracy, precision, F1 score, and Matthews correlation coefficient (MCC), respectively, outperforming previous studies found in the literature. [ABSTRACT FROM AUTHOR]

According to data from the World Health Organization (WHO), cancer is considered to be one of the leading causes of death worldwide, and new therapeutic approaches, especially improved novel cancer treatment regimens, are in high demand. Considering that many chemotherapeutic drugs tend to have poor pharmacokinetic profiles, including rapid clearance and limited on-site accumulation, a combined approach with tumor-homing peptide (THP)-functionalized magnetic nanoparticles could lead to remarkable improvements. This is confirmed by an increasing number of papers in this field, showing that the on-target peptide functionalization of magnetic nanoparticles improves their penetration properties and ensures tumor-specific binding, which results in an increased clinical response. This review aims to highlight the potential applications of THPs in combination with magnetic carriers across various fields, including a pharmacoeconomic perspective. [ABSTRACT FROM AUTHOR]

Bicyclic peptides have attracted the interest of pharmaceutical companies because of their remarkable properties, putting them on a new path in medicine. Their conformational rigidity improves proteolytic stability and leads to rapid penetration into tissues via any possible route of administration. Moreover, elimination of renal metabolism is of great importance, for example, for people with a history of liver diseases. In addition, each ring can function independently, making bicyclic peptides extremely versatile molecules for further optimization. In this paper, we compared the potentiometric and spectroscopic properties studied by UV–vis, MCD, and EPR of four synthetic analogues of the bi-cyclic peptide c(PKKHP-c(CFWKTC)-PKKH) (BCL). In particular, we correlated the structural and spectral properties of complexes with coordinating abilities toward Cu(II) ions of MCL1 (Ac-PKKHPc(CFWKTC)PKKH-NH2) that contains the unbinding cycle and N- and C-terminal linear parts with two histidine residues, one per part; two monocyclic ligands containing one histidine residue, both in the N-terminal position, i.e., MCL2 (Ac-PKKHPc(CFWKTC)PKKS-NH2) and in the C-terminal position, i.e., MCL3 (Ac-PKKSPc(CFWKTC)PKKH-NH2), respectively; and the linear structure LNL (Ac-PKKHPSFWKTSPKKH-NH2). Potentiometric results have shown that the bicyclic structure promotes the involvement of the side chain imidazole donors in Cu(II) binding. On the other hand, the results obtained for the mono-cyclic analogues lead to the conclusion that the coordination of the histidine moiety as an anchoring group is promoted by its location in the peptide sequence further from the nonbinding cycle, strongly influencing the involvement of the amide donors in Cu(II) coordination. [ABSTRACT FROM AUTHOR]

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding motifs. Based on the discovery, we make the preprocessing and coding closer to the natural biological process. Besides, due to the input being based on multiple types of features and the attention module focused on the BiGRU hidden layer, TripHLApan has learned more sequence level binding information. The application of transfer learning strategies ensures the accuracy of prediction results under special lengths (peptides in length 8) and model scalability with the data explosion. Compared with the current optimal models, TripHLApan exhibits strong predictive performance in various prediction environments with different positive and negative sample ratios. In addition, we validate the superiority and scalability of TripHLApan's predictive performance using additional latest data sets, ablation experiments and binding reconstitution ability in the samples of a melanoma patient. The results show that TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines. TripHLApan is publicly available at https://github.com/CSUBioGroup/TripHLApan.git. [ABSTRACT FROM AUTHOR]

In the age of information technology and the additional computational search tools and software available, this systematic review aimed to identify potential therapeutic targets for obesity, evaluated in silico and subsequently validated in vivo. The systematic review was initially guided by the research question "What therapeutic targets have been used in in silico analysis for the treatment of obesity?" and structured based on the acronym PECo (P, problem; E, exposure; Co, context). The systematic review protocol was formulated and registered in PROSPERO (CRD42022353808) in accordance with the Preferred Reporting Items Checklist for Systematic Review and Meta-Analysis Protocols (PRISMA-P), and the PRISMA was followed for the systematic review. The studies were selected according to the eligibility criteria, aligned with PECo, in the following databases: PubMed, ScienceDirect, Scopus, Web of Science, BVS, and EMBASE. The search strategy yielded 1142 articles, from which, based on the evaluation criteria, 12 were included in the systematic review. Only seven these articles allowed the identification of both in silico and in vivo reassessed therapeutic targets. Among these targets, five were exclusively experimental, one was exclusively theoretical, and one of the targets presented an experimental portion and a portion obtained by modeling. The predominant methodology used was molecular docking and the most studied target was Human Pancreatic Lipase (HPL) (n = 4). The lack of methodological details resulted in more than 50% of the papers being categorized with an "unclear risk of bias" across eight out of the eleven evaluated criteria. From the current systematic review, it seems evident that integrating in silico methodologies into studies of potential drug targets for the exploration of new therapeutic agents provides an important tool, given the ongoing challenges in controlling obesity. [ABSTRACT FROM AUTHOR]

Simple Summary: Cancer Metastasis has been mostly misunderstood and underestimated by the general public regarding cancer deaths. The aims and objectives of the present report was to more fully describe the scientific activities and components that are involved in the malignant cell's fulfillment of the metastatic process and to impress the readership that metastasis is the major cause on all cancer deaths. The paper proceeds to enumerate and describe certain factors that contribute to cancer cell proliferation and subsequent metastasis such as; (a) calcium levels, (b) multiple cell membrane channels, and (c) the chemokine/receptor system. These latter components could serve to provide ideal molecular targets for possible future peptide therapeutic applications in treating cancer patients. Metastasis (Met) largely contributes to the major cause of cancer deaths throughout the world, rather than the growth of the tumor mass itself. The present report brings together several of the pertinent contributors to cancer growth and metastatic processes from an activity standpoint. Such biological activities include the following: (1) cell adherence and detachment; (2) cell-to-cell contact; (3) contact inhibition; (4) the cell interfacing with the extracellular matrix (ECM); (5) tumor cell-to-stroma communication networks; (6) chemotaxis; and (7) cell membrane potential. Moreover, additional biochemical factors that contribute to cancer growth and metastasis have been shown to comprise the following: (a) calcium levels in the extracellular matrix and in intracellular compartments; (b) cation voltage and ATP-regulated potassium channels; (c) selective and non-selective cation channels; and (d) chemokines (cytokines) and their receptors, such as CXCL12 (SDF-1) and its receptor/binding partner, CXCR4. These latter molecular components represent a promising group of an interacting and synchronized set of candidates ideal for peptide therapeutic targeting for cancer growth and metastasis. Such peptides can be obtained from naturally occurring proteins such as alpha-fetoprotein (AFP), an onco-fetal protein and clinical biomarker. [ABSTRACT FROM AUTHOR]

Background: About 15% to one third of migraineurs experience aura symptoms. Aura is a reversible focal neurological phenomenon involving visual, sensory, speech, and motor symptoms that usually precede migraine pain. Monoclonal antibodies against calcitonin-related peptide (anti- CGRP mAbs) are effective in preventing chronic and episodic migraine, but little is known about their effectiveness on specifically preventing migraine with aura. Methods: This is a pilot prospective observational cohort study, aiming at evaluating the effectiveness and safety of Erenumab, Fremanezumab or Galcanezumab for the treatment of migraine aura. We enrolled 14 patients at the Headache Centre of University Federico II of Naples. Duration of follow-up was 12 months. We assessed mean monthly days with aura symptoms, with or without subsequent headache, as well as mean monthly days with headache and mean monthly MIDAS score, by reviewing standardized paper patient headache diaries every three months. Results: A significant decrease in mean monthly aura days was observed throughout the observation period (median baseline: 13, interquartile range: 4–16; after 12 months: 1, interquartile range: 0–3, p < 0.001). We observed a statistically significant decrease in mean monthly headache days as well (median baseline 21, interquartile range: 16–30; after 12 months: 5, interquartile range: 4–7, p < 0.001). During the 12-month treatment period, none of the 14 patients reported mild or serious adverse events. Conclusion: Our findings suggest that anti-CGRP mAbs are highly effective in migraine with aura, both in reducing mean monthly aura days and mean monthly days with headache. [ABSTRACT FROM AUTHOR]

INTRODUCTION: One of the main allergens in soybeans is glycinin, which seriously impacts the normal lives of allergic people. Previous studies have confirmed that thermal processing and thermal processing combined with ultrahigh‐pressure processing could significantly reduce the antigenicity of glycinin. The dominant antigen region of acidic peptide chain A2 of G2 subunit was located by phage display experiment. METHODS: In this paper, overlapping peptides and alanine substitution techniques were used to explore the key amino acids that significantly affect the antigenicity of A2 peptide chain. The purity of peptide 1, peptide 2 and peptide 3 was identified by mass spectrometry and high‐performance liquid chromatography, and the results showed that the purity of the synthesized overlapping peptide was more than 90%. SDS‐PAGE showed that the peptide was successfully coupled with bovine serum albumin. The antigenicity of the coupling peptide was tested by ELISA and Dot‐Blot, and the allergenicity was detected by reacting with the serum of patients with soybean globulin allergy. CONCLUSION: The results showed that peptide 3 has stronger antigenicity and sensitization. Alanine substitution technology allowed one to perform site‐directed mutagenesis on peptide 3. Dot‐Blot and ELISA tests showed that D259, E260, E261, Q263 and C266 may be the key amino acids that significantly affect the antigenicity of peptide 3. The research presented is of great significance for correctly guiding the production of safe food and preventing the occurrence of food allergic diseases. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Styrene-maleic acid (SMA) and similar amphiphilic copolymers are known to cut biological membranes into lipid nanoparticles/nanodiscs containing membrane proteins apparently in their relatively native membrane lipid environment. Our previous work demonstrated that membrane raft microdomains resist such disintegration by SMA. The use of SMA in studying membrane proteins is limited by its heterogeneity and the inability to prepare defined derivatives. In the present paper, we demonstrate that some amphiphilic peptides structurally mimicking SMA also similarly disintegrate cell membranes. In contrast to the previously used copolymers, the simple peptides are structurally homogeneous. We found that their membrane-disintegrating activity increases with their length (reaching optimum at 24 amino acids) and requires a basic primary structure, that is, (XXD)n, where X represents a hydrophobic amino acid (optimally phenylalanine), D aspartic acid, and n is the number of repeats of these triplets. These peptides may provide opportunities for various well-defined potentially useful modifications in the study of membrane protein biochemistry. Our present results confirm a specific character of membrane raft microdomains. [ABSTRACT FROM AUTHOR]

Vigna bean and common bean have received much attention from the functional food and nutraceutical aspects. Upon hydrolysis of beans protein, bioactive peptides from various conditions are produced, with health-promoting properties and a broad spectrum of biological activities, offering nutraceutical or therapeutic potential. There have been few comprehensive investigations into improving the bioactivity and functionality of peptides from vigna and common beans. Therefore, this article describes the key parameters impacting bean derived peptide bioactivity, as well as approaches to improve it. This paper includes a review of papers indicating the stability of peptides obtained from beans under simulated gastrointestinal digestion conditions, as well as some insights into the mechanisms of action of those peptides and their relationship with structure. This review outlines important criteria for rationally designing and selecting bean bioactive peptides with intact structure and therapeutic potential in vivo. This study could be beneficial when conducting future investigations on vigna and common bean protein hydrolysates in vitro or in vivo and the knowledge gained could help with the incorporation of these new bean peptides into functional foods. [ABSTRACT FROM AUTHOR]

Next-generation single-molecule protein sequencing technologies have the potential to significantly accelerate biomedical research. These technologies offer sensitivity and scalability for proteomic analysis. One auspicious method is fluorosequencing, which involves: cutting naturalized proteins into peptides, attaching fluorophores to specific amino acids, and observing variations in light intensity as one amino acid is removed at a time. The original peptide is classified from the sequence of light-intensity reads, and proteins can subsequently be recognized with this information. The amino acid step removal is achieved by attaching the peptides to a wall on the C-terminal and using a process called Edman Degradation to remove an amino acid from the N-Terminal. Even though a framework (Whatprot) has been proposed for the peptide classification task, processing times remain restrictive due to the massively parallel data acquisicion system. In this paper, we propose a new beam search decoder with a novel state formulation that obtains considerably lower processing times at the expense of only a slight accuracy drop compared to Whatprot. Furthermore, we explore how our novel state formulation may lead to even faster decoders in the future. Author summary: Proteomic analyses frequently rely on mass spectrometry, a method characterized by its limited dynamic range, potentially overlooking low-abundant proteins. To address this limitation, single-molecule protein sequencing methods offer a solution. Fluorosequencing is a cutting-edge single-molecule protein sequencing method, which can distinguish peptides or protein molecules massively parallelly. This method has attracted interest from investors, as evidenced by the recent funding of Erisyon, a company developing this technology. This technique contains a challenging classification task: determining the original peptide sequence from light-intensity observations obtained after several Edman cycles. A classifier based on a combination of k Nearest Neighbors (kNN) with Hidden Markov Models (HMM) had been shown to have close-to-optimal accuracy with tractable complexity. We propose in this paper a new algorithm that reduces computation time significantly at the expense of a slight reduction in accuracy compared to state-of-the-art method. [ABSTRACT FROM AUTHOR]

In this paper, we report an open system consisting of three self-replicating peptides, in which peptide 1 inhibits the duplex template of peptide 2, peptide 2 inhibits duplex 3, and peptide 3 inhibits duplex 1 to complete the negative feedback loop. This interacting chemical network yields oscillations in the concentrations of all species over time and establishes a possible mechanism for pre-biotic chemical systems organization. The first focus of our analysis is the effect of altering rates of duplex formation and inhibition on oscillations. We then examine the autocatalytic rate constant in the symmetric and asymmetric cases. [ABSTRACT FROM AUTHOR]

The atomistic description of the folding process of a structureless chain of amino acids to a functioning protein is still considered to be a challenge for computational biophysics. An in-depth understanding of protein-folding can be achieved through atomistic dynamics accounting for the solvent effects, combined with the theoretical description of conformational changes in shorter polypeptide chains. The present paper studies the folding transitions in short polypeptide chains consisting of 11 alanine residues in explicit solvent employing all-atom molecular dynamics. The multiple observed folding ↔ unfolding events of the peptide are interpreted as a dynamic process and rationalised through the analysis of the potential energy surface of the system. It is demonstrated that alanine polypeptide folding dynamics is governed by the backbone dihedral angles and involves the formation of spontaneously folded α -helices which emerge and live for ca. 1–20 picoseconds. The helical content within the polypeptide at different temperatures was quantified through a statistical mechanics approach, which showed a reasonable agreement with the results of molecular dynamics simulations and experiments performed for alanine-rich peptides. [ABSTRACT FROM AUTHOR]

Obesity is a global health concern with limited treatment options due to side effects and limited efficacy. Bioactive peptides (BAPs) derived from food proteins have shown promise as safe and effective anti-obesity agents by regulating adipocyte differentiation through various signaling pathways. BAPs derived from milk, eggs, fish, and marine sources have been extensively studied for their anti-obesity effects in vitro and in vivo. These peptides can alter gut hormones and appetite to regulate energy balance while decreasing adipogenesis and increasing adipocyte apoptosis. This paper provides a comprehensive overview of the studies investigating the potency of BAPs in managing obesity. It focuses on their ability to modulate adipogenesis and regulate appetite and lipid metabolism. Key findings and Conclusions: BAPs derived from various food sources such as milk, eggs, fish, and marine byproducts have the potential to act as anti-obesity agents. These peptides have been shown to be able to regulate adipogenesis, lipid metabolism, and appetite control through different mechanisms, making them promising candidates for developing functional foods or nutraceuticals for obesity prevention and management. This paper also highlights the advantages of using BAPs over conventional anti-obesity drugs, such as their safety, natural origin, and lower risk of adverse effects. Further research and development in this field can lead to the identification and utilization of specific BAPs with optimized efficacy and minimal side effects, ultimately contributing to the development of novel anti-obesity therapies. [Display omitted] • Various food proteins as potential source of bioactive peptides is summarized. • Bioactive peptides derived from food is promising anti-obesity agent. • In vitro and in vivo experiment proven an anti-obesity activity through various mechanism. • Food derived bioactive peptides are prospective for development of functional foods or nutraceuticals. [ABSTRACT FROM AUTHOR]

Dipeptidyl Peptidase IV (DPP-IV) inhibitory peptides are attracting increasing attention, owing to their potential role in glycemic regulation by preventing the inactivation of incretins. However, few reviews have summarized the current understanding of DPP-IV inhibitory peptides and their knowledge gaps. This paper reviews the production, identification and structure-activity relationships (SAR) of DPP-IV inhibitory peptides. Importantly, their bioavailability and hypoglycemic effects are critically discussed. Unlike the traditional method to identifying peptides after separation step by step, the bioinformatics approach identifies peptides via virtual screening that is more convenient and efficient. In addition, the bioinformatics approach was also used to investigate the SAR of peptides. Peptides with proline (Pro) or alanine (Ala) residue at the second position of N-terminal are exhibit strong DPP-IV inhibitory activity. Besides, the bioavailability of DPP-IV inhibitory peptides is related to their gastrointestinal stability and cellular permeability, and in vivo studies showed that the glucose homeostasis has been improved by these peptides. Especially, the intestinal transport of DPP-IV inhibitory peptides and cell biological assays used to evaluate their potential role in glycemic regulation are innovatively summarized. For further successful development of DPP-IV inhibitory peptides in glycemic regulation, future study should elucidate their SAR and in vivo hypoglycemic effects. [ABSTRACT FROM AUTHOR]

Background: Viral infections have been the main health issue in the last decade. Antiviral peptides (AVPs) are a subclass of antimicrobial peptides (AMPs) with substantial potential to protect the human body against various viral diseases. However, there has been significant production of antiviral vaccines and medications. Recently, the development of AVPs as an antiviral agent suggests an effective way to treat virus-affected cells. Recently, the involvement of intelligent machine learning techniques for developing peptide-based therapeutic agents is becoming an increasing interest due to its significant outcomes. The existing wet-laboratory-based drugs are expensive, time-consuming, and cannot effectively perform in screening and predicting the targeted motif of antiviral peptides. Methods: In this paper, we proposed a novel computational model called Deepstacked-AVPs to discriminate AVPs accurately. The training sequences are numerically encoded using a novel Tri-segmentation-based position-specific scoring matrix (PSSM-TS) and word2vec-based semantic features. Composition/Transition/Distribution-Transition (CTDT) is also employed to represent the physiochemical properties based on structural features. Apart from these, the fused vector is formed using PSSM-TS features, semantic information, and CTDT descriptors to compensate for the limitations of single encoding methods. Information gain (IG) is applied to choose the optimal feature set. The selected features are trained using a stacked-ensemble classifier. Results: The proposed Deepstacked-AVPs model achieved a predictive accuracy of 96.60%%, an area under the curve (AUC) of 0.98, and a precision-recall (PR) value of 0.97 using training samples. In the case of the independent samples, our model obtained an accuracy of 95.15%, an AUC of 0.97, and a PR value of 0.97. Conclusion: Our Deepstacked-AVPs model outperformed existing models with a ~ 4% and ~ 2% higher accuracy using training and independent samples, respectively. The reliability and efficacy of the proposed Deepstacked-AVPs model make it a valuable tool for scientists and may perform a beneficial role in pharmaceutical design and research academia. [ABSTRACT FROM AUTHOR]

Simple Summary: This review mainly focuses on epigenetic changes in a few selective genes associated with insulin insensitivity in the periphery and how this peripheral insulin insensitivity is linked with impaired signaling of insulin in the brain, thus causing Alzheimer's disease. DNA methylation and histone modifications are the focus of this review, with primary importance given to DNA methylation. Moreover, there has been a focus shift from the amyloid β hypothesis to epigenetic mechanisms. Furthermore, we discuss the advanced drug delivery systems that can be used for the delivery of drugs targeting the brain during Alzheimer's disease. The advanced drug delivery systems discussed in this paper are nanoparticles, vesicular systems, network systems and dendrimers, hydrogel-based systems, and biologics. Alzheimer's disease (AD) is a neurodegenerative condition that predominantly affects the hippocampus and the entorhinal complex, leading to memory lapse and cognitive impairment. This can have a negative impact on an individual's behavior, speech, and ability to navigate their surroundings. AD is one of the principal causes of dementia. One of the most accepted theories in AD, the amyloid β (Aβ) hypothesis, assumes that the buildup of the peptide Aβ is the root cause of AD. Impaired insulin signaling in the periphery and central nervous system has been considered to have an effect on the pathophysiology of AD. Further, researchers have shifted their focus to epigenetic mechanisms that are responsible for dysregulating major biochemical pathways and intracellular signaling processes responsible for directly or indirectly causing AD. The prime epigenetic mechanisms encompass DNA methylation, histone modifications, and non-coding RNA, and are majorly responsible for impairing insulin signaling both centrally and peripherally, thus leading to AD. In this review, we provide insights into the major epigenetic mechanisms involved in causing AD, such as DNA methylation and histone deacetylation. We decipher how the mechanisms alter peripheral insulin signaling and brain insulin signaling, leading to AD pathophysiology. In addition, this review also discusses the need for newer drug delivery systems for the targeted delivery of epigenetic drugs and explores targeted drug delivery systems such as nanoparticles, vesicular systems, networks, and other nano formulations in AD. Further, this review also sheds light on the future approaches used for epigenetic drug delivery. [ABSTRACT FROM AUTHOR]

The aim of the paper was to develop chitosan-coated nanoliposomes for carrying bioactive peptides derived from hydrolyzed shrimp waste (SW) with chitosan coating (concentrations of 0, 0.5 and 1% W/ V). The study involved producing SW hydrolysates using protease enzymes from Bacillus salsus bacteria, followed by investigating the physicochemical, antioxidant, and antimicrobial properties of the peptide-loaded nanoliposomes. The dispersion index ranged from 0.17 to 0.65, and the particle size varied from 500 to 685 nm. Increasing the chitosan concentration to 1% significantly increased the particle size (P < 0.05). The Zeta potential of the nanoliposomes became positive as the chitosan concentration increased, starting from − 47.73 mV and reaching + 36.40 mV. The highest encapsulation efficiency (84.67%) was observed in nanoliposomes with 1% chitosan, while uncoated liposomes had the lowest encapsulation efficiency (44%). Scanning electron microscopy (SEM) revealed that the nanoparticles exhibited homogeneous, spherical, and cluster-shaped structures with smooth surfaces. Chitosan coating enhanced the stability of the peptides in simulated stomach and intestinal environments, with higher stability observed at higher chitosan concentrations (P < 0.05). Chitosan-coated nanoliposomes exhibited higher antioxidant and antimicrobial activities compared to uncoated nanoliposomes. Increasing the chitosan concentration resulted in greater inhibition of free radicals (DPPH and ABTS free radical activities increased significantly in nanoliposomes with 1% chitosan compared to uncoated samples: 32.56–70.28% and 41.58–80.28% respectively) and enhanced antimicrobial properties (P < 0.05). In conclusion, coating hydrolyzed SW with nanoliposomes and chitosan improved the structural, physicochemical, antioxidant, and antimicrobial properties of the peptides, making them suitable for direct application in food products requiring antioxidant and antimicrobial effects. [ABSTRACT FROM AUTHOR]

Synthetic therapeutic peptides are a complex and popular class of pharmaceuticals. In recent years, peptides with proven therapeutic activity have gained significant interest in the market. The determination of synthetic peptide enantiomeric purity plays a critical role in the evaluation of the quality of the medicine. Since racemization is one of the most common side reactions occurring in AAs or peptides, enantiomeric impurities such as D‐isomers can form during the peptide synthesis or can be introduced from the starting materials (e.g., AAs). The therapeutic effect of a synthetic or semi‐synthetic bioactive peptide molecule depends on its AA enantiomeric purity and secondary/tertiary structure. Therefore, the enantiomeric purity determination for synthetic peptides is supportive for interpreting unwanted therapeutic effects and determining the quality of synthetic peptide therapeutics. However, enantiomeric purity analysis encounters formidable analytical challenges during chromatographic separation, as D/L isomers have identical physical–chemical properties except stereochemical configuration. To ensure peptides AA stereochemical configuration whether in the free or bound state, sensitive and reproducible quantitative analytical method is mandatory. In this regard, numerous analytical techniques were emerged for the quantification of D‐isomeric impurities in synthetic peptides, but still, very few reports are available in the literature. Thus, the purpose of this paper is to provide an overview of the importance, regulatory requirements, and various analytical methods used for peptide enantiomeric purity determination. In addition, we discussed the available literature in terms of enantiomeric impurity detection, common hydrolysis procedural aspects, and different analytical strategies used for sample preparation. [ABSTRACT FROM AUTHOR]

Preeclampsia (PE) is a unique pregnancy disorder affecting women across the world. It is characterized by the new onset of hypertension with coexisting end-organ damage. Although the disease has been known for centuries, its exact pathophysiology and, most importantly, its prevention remain elusive. The basis of its associated molecular changes has been attributed to the placenta and the hormones regulating its function. One such hormone is chromogranin A (CgA). In the placenta, CgA is cleaved to form a variety of biologically active peptides, including catestatin (CST), known inter alia for its vasodilatory effects. Recent studies indicate that the CST protein level is diminished both in patients with hypertension and those with PE. Therefore, the aim of the present paper is to review the most recent and most relevant in vitro, in vivo, and clinical studies to provide an overview of the proposed impact of CST on the molecular processes of PE and to consider the possibilities for future experiments in this area. [ABSTRACT FROM AUTHOR]

Background: Endometrial receptivity (ER), a pivotal event for successful embryo implantation, refers to the capacity of endometrium to allow the adhesion of the trophectoderm of the blastocyst to endometrial cells. In this paper, we set to elucidate whether the peptides encoded by lncRNAs could influence trophoblast cells' adhesion to endometrial cells. Methods: WGCNA construction and bioinformatics were used to find out the ER-related lncRNAs with coding potential. Protein analysis was done by immunoblotting and immunofluorescence (IF) microscopy. CCK-8 and Calcein-AM/PI double staining assays were employed to evaluate cell viability. The effect of the peptide on trophoblast spheroids' adhesion to endometrial cells was evaluated. The RNA sequencing (RNA-seq) analysis was applied to identify downstream molecular processes. Results: lncRNA LINC00339 was found to be related to ER development and it had been predicted to have protein-coding potential. LINC00339 had high occupancy of ribosomes and was confirmed to encode a 49-aa peptide (named LINC00339-205-49aa). LINC00339-205-49aa could promote the attachment of JAR trophoblast spheroids to Ishikawa endometrial cells in vitro. LINC00339-205-49aa also upregulated the expression of E-cadherin in Ishikawa cells. Mechanistically, MAPK and PI3K-Akt signaling pathways were involved in the modulation of LINC00339-205-49aa, which were activated by LINC00339-205-49aa in Ishikawa cells. Conclusion: These data demonstrate that a previously uncharacterized peptide encoded by lncRNA LINC00339 has the ability to enhance JAR trophoblast spheroids' adhesion to Ishikawa endometrial cells, highlighting a new opportunity for the development of drugs to improve ER. [ABSTRACT FROM AUTHOR]

Effective drug delivery is essential for cancer treatment. Drug delivery systems, which can be tailored to targeted transport and integrated tumor therapy, are vital in improving the efficiency of cancer treatment. Peptides play a significant role in various biological and physiological functions and offer high design flexibility, excellent biocompatibility, adjustable morphology, and biodegradability, making them promising candidates for drug delivery. This paper reviews peptide-mediated drug delivery systems, focusing on self-assembled peptides and peptide–drug conjugates. It discusses the mechanisms and structural control of self-assembled peptides, the varieties and roles of peptide–drug conjugates, and strategies to augment peptide stability. The review concludes by addressing challenges and future directions. [ABSTRACT FROM AUTHOR]