Screening Of Peptides Research Articles

NF9 peptide specific cytotoxic T lymphocyte clone cross react to Y453F mutation of SARS-CoV-2 virus spike protein

The recognition by cytotoxic T cells (CTLs) is essential for the clearance of SARS-CoV-2 virus-infected cells. Several viral proteins have been described to be recognized by CTLs. Among them, the spike (S) protein is one of the immunogenic proteins. The S protein acts as a ligand for its receptors, and several mutants with different affinities for its cognate receptors have been reported, and certain mutations in the S protein, such as L452R and Y453F, have been found to inhibit the HLA-A24-restricted CTL response. In this study, we conducted a screening of candidate peptides derived from the S protein, specifically targeting those carrying the HLA-A24 binding motif. Among these peptides, we discovered that NF9 (NYNYLYRLF) represents an immunogenic epitope. CTL clones specific to the NF9 peptide were successfully established. These CTL clones exhibited the ability to recognize endogenously expressed NF9 peptide. Interestingly, the CTL clone demonstrated cross-reactivity with the Y453F peptide (NYNYLFRLF) but not with the L452R peptide (NYNYRYRLF). The CTL clone was able to identify the endogenously expressed Y453F mutant peptide. These findings imply that the NF9-specific CTL clone possesses the capability to recognize and respond to the Y453F mutant peptide.

In silico screening of potential plant peptides against the Non-structural proteins of Dengue virus.

Peptides isolated from different sources of plants have the advantages of specificity, lower toxicity, and increased therapeutic effects; hence, it is necessary to search for newer antivirals from plant sources for the treatment of dengue viral infections. In silico screening of selected plant peptides against the non-structural protein 1, NS3 protease domain (NS2B-NS3Pro) with the cofactor and ATPase/Helicase domain (NS3 helicase domain/NS3hel) of Dengue virus was performed. The physicochemical characteristics of the peptides were calculated using Protparam tools, and the allergenicity and toxicity profiles were assessed using allergenFP and ToxinPred, respectively. Among the tested compounds, Ginkbilobin demonstrated higher binding energy against three tested non-structural protein targets. Kalata β-8 demonstrated maximum binding energy against NSP-1 and NSP-2, whereas Circulin A acted against the NSP3 protein of the dengue virus. Hence, the three compounds identified by in silico screening can be tested further for in vitro studies, which could act as potential leads as they are involved in hampering the replication of the dengue virus by interacting with the three prime non-structural proteins.

Solid-phase peptide synthesis in 384-well plates.

Newer solid-phase peptide synthesis and release strategies enable the production of short peptides with high purity, allowing direct screening for desired bioactivity without prior chromatographic purification. However, the maximum number of peptides that can currently be synthesized per microplate reactor is 96, allowing the parallel synthesis of 384 peptides in modern devices that have space for 4 microplate reactors. To synthesize larger numbers of peptides, we modified a commercially available peptide synthesizer to enable the production of peptides in 384-well plates, which allows the synthesis of 1,536 peptides in one run (4× 384 peptides). We report new hardware components and customized software that allowed for the synthesis of 1,536 short peptides in good quantity (average > 0.5μmol), at high concentration (average > 10 mM), and decent purity without purification (average > 80%). The high-throughput peptide synthesis, which we developed with peptide drug development in mind, may be widely used for peptide library synthesis and screening, antibody epitope scanning, epitope mimetic development, or protease/kinase substrate screening.

Identification and virtual screening of novel salty peptides from hydrolysate of tilapia by-product by batch molecular docking.

Tilapia produces a large number of by-products during processing, which contain potentially flavorful peptides. The application of PyRx software enabled batch molecular docking andscreening of 16 potential salty peptides from 189 peptides identified in the enzymaticdigestion of tilapia by-products. According to sensory analysis, all 16 peptides werepredominantly salty with a threshold of 0.256 - 0.379 mmol/L with some sournessand astringency, among which HLDDALR had the highest salty intensity, followedby VIEPLDIGDDKVR, FPGIPDHL, and DFKSPDDPSRH. I addition, moleculardocking results showed these four core peptides with high salt intensity bound to thesalt receptor TRPV1 mainly via van der Waals interactions, hydrogen bonds, andhydrophobic forces; Arg491, Tyr487, VAL441, and Asp708 were the key sites for thebinding of salty peptides to TRPV1. Therefore, the application of batch moleculardocking using PyRx is effective and economical for the virtual screening of saltypeptides.

The cryoprotective effect of Litopenaeus vannamei head-derived peptides and its ice-binding mechanism

Although discarded as waste, shrimp heads are a potential source of antifreeze peptides, which can be used as cryoprotectants in the food industry. Their utilization in frozen foods can help mitigate the negative effects caused by the freezing technique. Litopenaeus vannamei shrimp heads were autolyzed, and the shrimp head autolysate (SHA) was separated via ultra-filtration and ion exchange chromatography. The antifreeze effect of SHA on the biochemical properties of myofibrillar proteins of peeled shrimps during five freeze-thaw cycles was evaluated. Peptide screening was done using the LC-MS/MS technique. A molecular docking (MD) study of the interaction between ice and shrimp head-derived antifreeze peptides was done. Results showed that shrimp-head autolysate has a maximum thermal hysteresis value of 1.84 °C. During the freeze-thaw cycles, the shrimp-head autolysate exhibited an antifreeze effect on frozen peeled shrimps. 1.0 and 3.0%-SHA groups showed significantly lower freeze denaturation than the negative control group. The muscle tissues of SHA-treated groups were not as severely damaged as the negative control group. The molecular docking study revealed that the shrimp head-AFPs bound to ice via hydrogen bonding, and both hydrophilic and hydrophobic amino acid residues were involved in the ice-binding interactions. 6 ice-binding sites were involved in the peptide-ice interaction. Our findings suggest that shrimp head-derived AFPs can be developed into functional additives in frozen foods and add more insights into the existing literature on antifreeze peptides.

Nisin-relevant antimicrobial peptides: synthesis strategies and applications.

Small pentacyclic peptides, represented by nisin, have been successfully utilized as preservatives in the food industry and have evolved into a paradigm for understanding the genetic structure, expression, and control of genes created by lantibiotics. Due to the ever-increasing antibiotic resistance, nisin-relevant antimicrobial peptides have received much attention, which calls for a summarization of their synthesis, modification and applications. In this review, we first provided a timeline of select highlights in nisin biosynthesis and engineering. Then, we outlined the current developments in nisin synthesis. We also provided an overview of the engineering, screening, and production of nisin-relevant antimicrobial peptides based on enzyme alteration, substrate modification, and sequence mining. Furthermore, an updated summary of applications of nisin-relevant antimicrobial peptides has been developed for food applications. Finally, this study offers insights into emerging technologies, limitations and the future development of nisin-relevant antimicrobial peptides for pathogen inhibition, food preservatives, and improved health.

Designing and synthesizing peptide-based quorum sensing modulators.

Quorum sensing (QS) is a density-dependent bacterial communication system that uses small molecules as regulatory modulators. Synthetic changes to these molecules can up-or-down-regulate this system, leading to control of phenotypes, like competence and virulence factor production, that have implications in human health. In this chapter, a methodology for library design and screening of synthetic autoinducing peptides (AIPs) to uncover QS SARs is delineated. Additionally, procedures for the synthesis, purification and analysis of linear and cyclic AIPs are detailed. This includes solutions for potential synthetic challenges including diketopiperazine formation when using N-methyl amino acids and cyclization of peptides containing N-terminal cysteine residues. These procedures have and are currently being applied to develop potent QS modulators in Streptococcus pneumoniae, Bacillus cereus, Streptococcus gordonii and Lactiplantibacillus plantarum.

Screening, separation and identification of metal-chelating peptides for nutritional, cosmetics and pharmaceutical applications.

Metal-chelating peptides, which form metal-peptide coordination complexes with various metal ions, can be used as biofunctional ingredients notably to enhance human health and prevent diseases. This review aims to discuss recent insights into food-derived metal-chelating peptides, the strategies set up for their discovery, their study, and identification. After understanding the overall properties of metal-chelating peptides, their production from food-derived protein sources and their potential applications will be discussed, particularly in nutritional, cosmetics and pharmaceutical fields. In addition, the review provides an overview of the last decades of progress in discovering food-derived metal-chelating peptides, addressing several screening, separation and identification methodologies. Furthermore, it emphasizes the methods used to assess peptide-metal interaction, allowing for better understanding of chemical and thermodynamic parameters associated with the formation of peptide-metal coordination complexes, as well as the specific amino acid residues that play important roles in the metal ion coordination.

In-Silico Screening for Vaccine Candidate Peptides within UPEC-UTI89 Strain against Urinary Tract Infection in Humans

In-Silico Screening for Vaccine Candidate Peptides within UPEC-UTI89 Strain against Urinary Tract Infection in Humans

Screening and molecular dynamics simulation of ACE inhibitory tripeptides derived from milk fermented with Lactobacillus delbrueckii QS306.

Peptides in milk fermented with Lactobacillus delbrueckii QS306 before and after ultrahigh pressure treatment were identified using proteomics. Subsequently, 16 stable tripeptides were screened out based on activity score prediction, PeptideCutter analysis, and hydrophobicity calculations. Among them, WRP, WSR, and YRP showed the best angiotensin-converting enzyme (ACE) inhibitory activity, and their semi-inhibitory concentrations were 46.707, 300.121, and 89.555 μM, respectively. WRP and WSR were competitive inhibitors, whereas YRP was non-competitive. Gastrointestinal simulation revealed that WRP and YRP had better gastrointestinal stability. The values of RMSD, ΔGbind, ΔGpol, and RSMF obtained from molecular dynamics simulation indicated that the interaction of WRP and ACE was stable. Thus, Lactobacillus delbrueckii QS306-fermented milk can serve as an important source of ACE inhibitory peptides both before and after ultrahigh pressure treatment. The strategy of in silico screening, activity evaluation, and molecular dynamics simulation adopted in this study can be applied to the large-scale screening of novel peptides with high ACE inhibitory activity.

Mining Bovine Milk Proteins for DPP-4 Inhibitory Peptides Using Machine Learning and Virtual Proteolysis.

Dipeptidyl peptidase-IV (DPP-4) enzyme inhibitors are a promising category of diabetes medications. Bioactive peptides, particularly those derived from bovine milk proteins, play crucial roles in inhibiting the DPP-4 enzyme. This study describes a comprehensive strategy for DPP-4 inhibitory peptide discovery and validation that combines machine learning and virtual proteolysis techniques. Five machine learning models, including GBDT, XGBoost, LightGBM, CatBoost, and RF, were trained. Notably, LightGBM demonstrated superior performance with an AUC value of 0.92 ± 0.01. Subsequently, LightGBM was employed to forecast the DPP-4 inhibitory potential of peptides generated through virtual proteolysis of milk proteins. Through a series of in silico screening process and in vitro experiments, GPVRGPF and HPHPHL were found to exhibit good DPP-4 inhibitory activity. Molecular docking and molecular dynamics simulations further confirmed the inhibitory mechanisms of these peptides. Through retracing the virtual proteolysis steps, it was found that GPVRGPF can be obtained from β-casein through enzymatic hydrolysis by chymotrypsin, while HPHPHL can be obtained from κ-casein through enzymatic hydrolysis by stem bromelain or papain. In summary, the integration of machine learning and virtual proteolysis techniques can aid in the preliminary determination of key hydrolysis parameters and facilitate the efficient screening of bioactive peptides.

Characterization, mechanisms, structure-activity relationships, and antihypertensive effects of ACE inhibitory peptides: rapid screening from sufu hydrolysate.

This study investigates the characterization, mechanisms of action, structure-activity relationships, and in vivo antihypertensive effects of ACE inhibitory peptides derived from sufu hydrolysate following simulated gastrointestinal digestion. Sufu was enzymatically digested using pepsin, trypsin, and chymotrypsin to mimic gastrointestinal conditions, followed by ultrafiltration to fractionate the peptides based on molecular weight. The fraction under 1 kDa exhibited the highest ACE inhibitory activity. LC-MS/MS analysis identified 119 peptide fragments, with bioinformatics screening highlighting 41 peptides with potential ACE inhibitory properties. Among these, two peptides, AWR and LLR, were selected and synthesized for in vitro validation, displaying IC50 values of 98.04 ± 2.56 μM and 94.01 ± 5.07 μM, respectively. Stability tests showed that both peptides maintained their ACE inhibitory activity across various temperatures and pH levels. Molecular docking and Highest Occupied Molecular Orbital analysis indicated strong binding interactions between these peptides and ACE, with the second-position tryptophan in AWR and the N-terminal leucine in LLR identified as key bioactive sites. These findings were further supported by molecular dynamics simulations, which confirmed the stability of the peptide-ACE complexes. In vivo studies using spontaneously hypertensive rats demonstrated significant reductions in both systolic and diastolic blood pressure, indicating that AWR and LLR have strong antihypertensive potential. This study illustrates that ultrafiltration, combined with LC-MS/MS and bioinformatics analysis, is an effective approach for the rapid screening of ACE inhibitory peptides. These results not only enhance our understanding of sufu-derived peptides but also offer promising implications for hypertension management.

Accessing diverse bicyclic peptide conformations using 1,2,3-TBMB as a linker.

Bicyclic peptides are a powerful modality for engaging challenging drug targets such as protein-protein interactions. Here, we use 1,2,3-tris(bromomethyl)benzene (1,2,3-TBMB) to access bicyclic peptides with diverse conformations that differ from conventional bicyclisation products formed with 1,3,5-TBMB. Bicyclisation at cysteine residues under aqueous buffer conditions proceeds efficiently, with broad substrate scope, compatibility with high-throughput screening, and clean conversion (>90%) for 96 of the 115 peptides tested. We envisage that the 1,2,3-TBMB linker will be applicable to a variety of peptide screening techniques in drug discovery.

A broad-spectrum peptide screening method using an optimized solid-phase extraction and liquid chromatography-high-field asymmetric ion mobility spectrometry-mass spectrometry for doping control in equine urine.

The abuse of prohibited peptide-based drugs with a broad spectrum of chemical characteristics poses a significant concern for the horseracing industry. Recently, there has been a notable increase in positive cases of small-peptide drugs reported in equine and canine sports. In addition to small peptides, large peptides (over 2 kDa) with structural diversity have also entered the market in increasing numbers as drugs for humans and livestock. However, the simultaneous analysis of both small- and large-peptide-based drugs is still challenging. In this study, a screening method was developed to cover 74 analytes, including peptides, their catabolites, and/or their mimetics, with molecular weights ranging from 0.3 kDa to greater than 5 kDa. The simultaneous extraction of both small and large peptides was achieved using a weak cation-exchange solid-phase extraction cartridge with a mixture of different pore sizes (suitable for large peptides), followed by analysis using liquid chromatography high-field asymmetric ion mobility spectrometry tandem mass spectrometry (LC-FAIMS-MS/MS). For method validation, the limits of detection (LoDs), reproducibility, recovery, matrix effect, selectivity, and carryover were evaluated. Remarkably, the LoDs of ∼80% of the analytes were less than or equal to 50 pg ml-1, with the lowest LoD (1 pg ml-1) being observed for selected peptides in horse urine. These results indicate a substantial advancement in achieving comprehensive coverage for both small and large peptides with high sensitivity for the purpose of doping control in horseracing and equestrian sports.

De novo development of small cyclic peptides that are orally bioavailable

Cyclic peptides can bind challenging disease targets with high affinity and specificity, offering enormous opportunities for addressing unmet medical needs. However, as with biological drugs, most cyclic peptides cannot be applied orally because they are rapidly digested and/or display low absorption in the gastrointestinal tract, hampering their development as therapeutics. In this study, we developed a combinatorial synthesis and screening approach based on sequential cyclization and one-pot peptide acylation and screening, with the possibility of simultaneously interrogating activity and permeability. In a proof of concept, we synthesized a library of 8,448 cyclic peptides and screened them against the disease target thrombin. Our workflow allowed multiple iterative cycles of library synthesis and yielded cyclic peptides with nanomolar affinities, high stabilities and an oral bioavailability (%F) as high as 18% in rats. This method for generating orally available peptides is general and provides a promising push toward unlocking the full potential of peptides as therapeutics.

Integration of cloud-based molecular networking and docking for enhanced umami peptide screening from Pixian douban

This study presents an innovative cloud-based approach, using Pixian Douban, a well-known Chinese fermented seasoning, as a case study, to improve the identification of umami peptides and explore their interactions with the T1R1/T1R3 receptor. A feature-based molecular networking method was utilized to rapidly identify a total of eighteen peptides, including seven previously unrecorded ones. Notably, the umami threshold of QIVK in an aqueous solution was determined to be 0.3215 mmol/L, surpassing the majority of peptides reported in the past three years. Molecular docking analysis further revealed the strong binding of QIVK to T1R3 receptor residues through hydrogen bonds, as well as interactions via salt bridges and electrostatic attractions. As a result, this research significantly contributes to the efficient screening of umami peptides and the elucidation of the molecular basis of umami sensory perception in complex food systems.

Peptidomics Screening and Molecular Docking with Umami Receptors T1R1/T1R3 of Novel Umami Peptides from Oyster (Crassostrea gigas) Hydrolysates.

In this study, novel umami peptides were prepared from oyster (Crassostrea gigas) hydrolysates, and their umami mechanisms were investigated. Umami fractions G2 and G3 were isolated by gel filtration chromatography (GFC) and sensory evaluation. The umami scores of the G2 and G3 fractions were 7.8 ± 0.12 and 7.5 ± 0.18, respectively. 36 potential umami peptides with molecular weights below 1500 Da, E and D accounting for >30% of the peptides and iUmami-SCM > 588 were screened by peptidomics. Peptide source analysis revealed that myosin, paramyosin, and sarcoplasmic were the major precursor proteins for these peptides. The electronic tongue results demonstrated that the synthetic peptides DPNDPDMKY and NARIEELEEE possessed an umami characteristic, whereas SIEDVEESRNK and ISIEDVEESRNK possessed a saltiness characteristic. Additionally, molecular docking results indicated that the umami peptide (DPNDPDMKY, NARIEELEEE, SIEDVEESRNK, and ISIEDVEESRNK) binds to H145, S276, H388, T305, Y218, D216, and Q389 residues in the T1R3 taste receptor via a conventional hydrogen bond and a carbon-hydrogen bond. This research provides a new strategy for the screening of umami peptides.

Dual antibacterial mechanism of [K4K15]CZS-1 against Salmonella Typhimurium: a membrane active and intracellular-targeting antimicrobial peptide.

Salmonella genus is a leading cause of food-borne infections with strong public health impact and economic ramifications. The development of antimicrobial resistance added complexity to this scenario and turned the antibiotic drug discovery into a highly important challenge. The screening of peptides has served as a successful discovery platform to design new antibiotic candidates. Motivated by this, the antimicrobial and cytotoxic properties of three cruzioseptins against Salmonella Typhimurium and RAW 264.7 murine macrophage cells, respectively, were investigated. [K4K15]CZS-1 was the most potent antimicrobial peptide identified in the screening step with a minimum inhibitory concentration (MIC) of 16 μg/mL (7.26 μM) and moderate cytotoxicity. From a structural point of view, in vitro and in silico techniques evidenced that [K4K15]CZS-1 is a α-helical cationic antimicrobial peptide. In order to capture mechanistic details and fully decipher their antibacterial action, we adopted a multidimensional approach, including spectroscopy, electron microscopy and omics analysis. In general lines, [K4K15]CZS-1 caused membrane damage, intracellular alterations in Salmonella and modulated metabolic pathways, such as the tricarboxylic acid (TCA) cycle, fatty acid biosynthesis, and lipid metabolism. Overall, these findings provide deeper insights into the antibacterial properties and multidimensional mode of action of [K4K15]CZS-1 against Salmonella Typhimurium. In summary, this study represents a first step toward the screening of membrane-acting and intracellular-targeting peptides as potential bio-preservatives to prevent foodborne outbreaks caused by Salmonella.

Encoding Molecular Docking for Quantum Computers.

Molecular docking is important in drug discovery but is burdensome for classical computers. Here, we introduce Grid Point Matching (GPM) and Feature Atom Matching (FAM) to accelerate pose sampling in molecular docking by encoding the problem into quadratic unconstrained binary optimization (QUBO) models so that it could be solved by quantum computers like the coherent Ising machine (CIM). As a result, GPM shows a sampling power close to that of Glide SP, a method performing an extensive search. Moreover, it is estimated to be 1000 times faster on the CIM than on classical computers. Our methods could boost virtual drug screening of small molecules and peptides in future.

Screening of novel DPP-IV inhibitory peptides derived from bovine milk proteins using a peptide array platform

Dipeptidyl peptidase IV (DPP-IV) has become an important target in the prevention and treatment of diabetes. Although many DPP-IV inhibitory peptides have been identified by a general approach involving the repeated fractionation of food protein hydrolysates, the obtained results have been dependent on the content of each peptide and fractionation conditions. In the present study, a peptide array that provides comprehensive assays of peptide sequences was used to identify novel DPP-IV inhibitory peptides derived from bovine milk proteins; these peptides were then compared with those identified using the general approach. While the general approach identified only known peptides that were abundant in the hydrolysate, the peptide array-based approach identified 10 novel DPP-IV inhibitory peptides, all of which had proline at the second residue from the N-terminus. The proper or combined use of these two approaches, which have different advantages, will enable the efficient development of novel bioactive foods and drugs.