Peptide Docking Research Articles

Short Link N Modulates Inflammasome Activity in Intervertebral Discs Through Interaction with CD14.

Intervertebral disc degeneration and pain are associated with the nucleotide-binding domain, leucine-rich repeat, and pyrin domain-containing 3 (NLRP3) inflammasome activation and the processing of interleukin-1 beta (IL-1β). Activation of thehm inflammasome is triggered by Toll-like receptor stimulation and requires the cofactor receptor cluster of differentiation 14 (CD14). Short Link N (sLN), a peptide derived from link protein, has been shown to modulate inflammation and pain in discs in vitro and in vivo; however, the underlying mechanisms remain elusive. This study aims to assess whether sLN modulates IL-1β and inflammasome activity through interaction with CD14. Disc cells treated with lipopolysaccharides (LPS) with or without sLN were used to assess changes in Caspase-1, IL-1β, and phosphorylated nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB). Peptide docking of sLN to CD14 and immunoprecipitation were performed to determine their interaction. The results indicated that sLN inhibited LPS-induced NFκB and Caspase-1 activation, reducing IL-1β maturation and secretion in disc cells. A significant decrease in inflammasome markers was observed with sLN treatment. Immunoprecipitation studies revealed a direct interaction between sLN and the LPS-binding pocket of CD14. Our results suggest that sLN could be a potential therapeutic agent for discogenic pain by mitigating IL-1β and inflammasome activity within discs.

Decoding of the saltiness enhancement taste peptides from Jinhua ham and its molecular mechanism of interaction with ENaC/TMC4 receptors

This study focused on unlocking the potential of Jinhua ham-derived peptides (JHP) for enhancing saltiness. JHP (<3 kDa) was obtained through ultrafiltration and desalting, reducing the salt content by 96 %. Four peptide fractions (JHP-P1/P2/P3/P4) were isolated using Sephadex G-25 gel filtration and anion-exchange chromatography. Sensory evaluation and electronic tongue analysis revealed that JHP-P2 (0.5 mg/mL) exhibited the highest saltiness which could replace four-fold NaCl salinity. Three peptides (DL, FMSALF, and HVRRK) identified by UPLC-QTOF-MS/MS were simulated with salty taste receptors ENaC/TMC4. Results indicated that Ser84 and Phe89 of ENaC and Asn404 and Lys567 of TMC4 are crucial for peptide docking related to salty taste. Molecular dynamics simulations showed that the three peptides bind to the TMC4 and ENaC through van der Waals forces, electrostatic interactions, and hydrogen bonds. These findings establish a robust theoretical foundation for salt reduction strategies and provide novel insights into the potential applications of Jinhua ham.

Identification and Molecular Docking of ACE Inhibitory Peptides Derived from Sodium Substituted Cheddar Cheese

Identification and Molecular Docking of ACE Inhibitory Peptides Derived from Sodium Substituted Cheddar Cheese

In Silico Analysis and Molecular Docking of Human Antimicrobial Peptides for Targeting Monkeypox Virus: Potential Therapeutic Implications of Histatin 5 Peptide

Background: Monkeypox, a viral zoonotic disease akin to smallpox, has posed significant public health challenges, particularly in Africa. Recent outbreaks, including those in India, underscore the global threat it poses. Objective: In this study, we explore a novel approach to combat monkeypox virus (MPXV) infection by targeting its surface proteins, crucial for viral entry and fusion. Methods: Employing advanced computational techniques, we predict and refine the 3D structures of MPXV surface proteins and human antimicrobial peptides (hAMPs), specifically Histatin 1, 3, and their cleaved product, Histatin 5 (HIS 5). Further, molecular docking was carried out for MPXV surface proteins with hAMP HIS using HDOCK and Cluspro 2.0. Protein-peptide interactions were analyzed using PdbSum. Finally, the physicochemical properties of HIS peptides were determined using CamSol. Results: Our findings suggest HIS 5 as a potential therapeutic peptide against MPXV, warranting further investigation through in vitro and in vivo studies. result: Compared to HIS 1 and 3, HIS 5 has higher solubility, an estimated half-life, cell permeability, stability, and a good docking score. Hence, based on the physicochemical properties of HIS 5, it may be used as a novel potential therapeutic peptide against MPXV. Conclusion: This study sheds light on the efficacy of the HIS family in targeting MPXV and advocates for continued exploration of HIS 5's antiviral effects.

Exploring Novel Umami Peptides from Bovine Bone Soups Using Nano-HPLC-MS/MS and Molecular Docking.

In this study, umami peptides were screened and characterized from bovine bone soups manufactured via atmospheric and high-pressure boiling. Peptide fractions with molecular weights less than 3 kDa were selected for peptide sequencing using LC-MS/MS, the toxicity prediction of the umami peptides was carried out by using an website, and the peptides were screened according to the binding energy, i.e., three peptides including YDAELS, TDVAHR, and ELELQ were selected. The three umami peptides were further synthesized, and their umami thresholds were determined through sensory evaluation and electronic tongue analysis, ranging from 0.375 to 0.75 mg/mL. All three peptides exhibited a significant synergistic taste enhancement effect when combined with MSG (monosodium glutamate) solution. The molecular docking of the umami peptides with the T1R1/T1R3 receptor revealed the mechanism of umami presentation, and the main interaction forces between the three umami peptides and the receptor were hydrogen bonding, electrostatic interactions, and hydrophobic interactions.

In-silico binding affinity of a phage display library screened novel peptide against various FABPs.

In accordance to the American Heart Association (AHA), cardiovascular diseases (CVDs) are the leading cause of death around the globe, causing more than 19.1million deaths in 2020. Heart-type fatty acid binding protein (H-FABP) is required for the metabolism of fatty acids (FA) inside cardiomyocytes is reported as a biomarker for myocardial damage. As early as one hour after an Acute myocardial infarction (AMI), H-FABP can be used to detect myocardial ischemia. Thus, H-FABP based detection can reduce the burden on the emergency department. A peptide-based detection system can provide point-of-care diagnostics for CVDs. There is a lot of research being done on peptide-based detection, and it has a lot of potential to help with unmet medical diagnostic needs. A twelve (12) amino acid peptide has been discovered using Phage Display Library Screening. The affinity of peptide with H-FABP and other FABPs has been done using molecular docking and ADMET profile has been done. Molecular docking of small peptides against the target protein can play a crucial role in recognizing peptide binding sites and poses. The docking study was done using the HDOCK server and the visualization of the docked complex was done using Pymol and UCSF chimera. The molecular simulation study of three protein-peptide complexes were done which also validated the binding affinity of peptide with the proteins. The RMSD, RMSF and radius of gyration are also analyzed. The results indicate that H-FABP shows higher level of binding interaction with the peptide having bond length ranging from 2.3 to 3.4 Å. The screened peptide is suitable for H-FABP binding and can be used for prognosis purposes in the heart ischemic conditions.

Purification, Structural Characterization, and Anticandidal Activity of a Chitin-Binding Peptide with High Similarity to Hevein and Endochitinase Isolated from Pepper Seeds.

With the emergence of multidrug-resistant microorganisms, microbial agents have become a serious global threat, affecting human health and various plants. Therefore, new therapeutic alternatives, such as chitin-binding proteins, are necessary. Chitin is an essential component of the fungal cell wall, and chitin-binding proteins exhibit antifungal activity. In the present study, chitin-binding peptides isolated from Capsicum chinense seeds were characterized and evaluated for their in vitro antimicrobial effect against the growth of Candida and Fusarium fungi. Proteins were extracted from the seeds and subsequently the chitin-binding proteins were separated by chitin affinity chromatography. After chromatography, two fractions, Cc-F1 (not retained on the column) and Cc-F2 (retained on the column), were obtained. Electrophoresis revealed major protein bands between 6.5 and 26.6kDa for Cc-F1 and only a ~ 6.5kDa protein band for Cc-F2, which was subsequently subjected to mass spectrometry. The protein showed similarity with hevein-like and endochitinase and was then named Cc-Hev. Data are available via ProteomeXchange with identifier PXD054607. Next, we predicted the three-dimensional structure of the peptides and performed a peptide docking with (NAG)3. Subsequently, growth inhibition assays were performed to evaluate the ability of the peptides to inhibit microorganism growth. Cc-Hev inhibited the growth of C. albicans (up to 75% inhibition) and C. tropicalis (100% inhibition) and induced a 65% decrease in cell viability for C. albicans and 100% for C. tropicalis. Based on these results, new techniques to combat fungal diseases could be developed through biotechnological applications; therefore, further studies are needed.

A Multi-Angle Approach to Predict Peptide-GPCR Complexes: The N/OFQ-NOP System as a Successful AlphaFold Application Case Study.

With nearly 700 structures solved and a growing number of customized structure prediction algorithms being developed at a fast pace, G protein-coupled receptors (GPCRs) are an optimal test case for validating new approaches for the prediction of receptor active state and ligand bioactive conformation complexes. In this study, we leveraged the availability of hundreds of peptide GPCRs in the active state and both classical homology and artificial intelligence (AI) based protein modeling combined with docking and AI-based peptide structure prediction approaches to predict the nociceptin/orphanin FQ-NOP receptor active state complex (N/OFQ-NOPa). The In Silico generated hypotheses were validated via the design, synthesis, and pharmacological characterization of novel linear N/OFQ(1-13)-NH2 analogues, leading to the discovery of a novel antagonist (3B; pKB = 6.63) bearing a single ring-constrained residue in place of the Gly2-Gly3 motif of the N/OFQ message sequence (FGGF). While the experimental validation was ongoing, the availability of the Cryo-EM structure of the predicted complex enabled us to unambiguously validate the generated hypotheses. To the best of our knowledge, this is the first example of a peptide-GPCR complex predicted with atomistic accuracy (full complex Cα RMSD < 1.0 Å) and of the N/OFQ message moiety being successfully modified with a rigid scaffold.

A computational approach to identifying peptide inhibitors againstWhite Spot Syndrome Virus: Targeting the virus envelope protein

The white spot syndrome virus (WSSV), a rapidly replicating and highly lethal pathogen that targets Penaeid shrimp, has emerged as one of the most widespread viruses globally due to its high virulence. With effective chemotherapeutics still unavailable, the pursuit of novel and viable strategies against WSSV remains a crucial focus in the field of shrimp farming. The envelope proteins of WSSV are essential for virus entry, serving as excellent targets for the development of antiviral therapeutics. Novel strategies in the design of inhibitory peptides, especially those targeting envelope protein (VP28) located on the surface of the virus particle, play a critical role as a significant virulence factor during the early stages of inherent WSSV infection in shrimp. In this direction, the current computational study focused on identifying self-inhibitory peptides from the hydrophobic membrane regions of the VP28 protein, employing peptide docking and molecular dynamics simulation (MDS) approaches. Such inhibitory peptides could be useful building blocks for the rational engineering of inhibitory therapeutics since they imitate the mechanism of binding to homologous partners used by their origin domain to interact with other molecules. The N-terminal sequence of VP28 has been reported as the potential site for membrane interactions during the virus entry. Moreover, drug delivery systems mediated by chitosan and gold nanoparticles are being developed to enhance the therapeutic efficacy of anti-viral peptides. These systems can increase the solubility, stability, and selectivity of peptides, possessing better qualities than conventional delivery methods. This computational study on self-inhibitory peptides could be a valuable resource for further in vitro and in vivo studies on anti-viral therapeutics in the aquaculture industry.

PepBinding: A Workflow for Predicting Peptide Binding Structures by Combining Peptide Docking and Peptide Gaussian Accelerated Molecular Dynamics Simulations.

Predicting protein-peptide interactions is crucial for understanding peptide binding processes and designing peptide drugs. However, traditional computational modeling approaches face challenges in accurately predicting peptide-protein binding structures due to the slow dynamics and high flexibility of the peptides. Here, we introduce a new workflow termed "PepBinding" for predicting peptide binding structures, which combines peptide docking, all-atom enhanced sampling simulations using the Peptide Gaussian accelerated Molecular Dynamics (Pep-GaMD) method, and structural clustering. PepBinding has been demonstrated on seven distinct model peptides. In peptide docking using HPEPDOCK, the peptide backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures ranged from 3.8 to 16.0 Å, corresponding to the medium to inaccurate quality models according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. The Pep-GaMD simulations performed for only 200 ns significantly improved the docking models, resulting in five medium and two acceptable quality models. Therefore, PepBinding is an efficient workflow for predicting peptide binding structures and is publicly available at https://github.com/MiaoLab20/PepBinding.

In silico Molecular Docking of Cyclic Peptides against TEM-1 Beta-Lactamases for Effective Antimicrobial Drug Development

Targeting the class A Beta lactamases Omega loop is an ideal way to combat drug resistance because of its significant role in the catalytic activity and deacylation process inhibition. Therefore, the molecular docking approach with computerized peptide-based in silico screening has been applied for the identification of inhibitors of TEM-type βLs. Among the subjected 105 peptides, Chrombacin (-47.8 KJ/mol), Gassericin A (-35.7 KJ/mol), Duramycin (-34.1 KJ/mol), Brevinin-1DYa (-34.0 KJ/mol), Amoebapore A (-31.2 KJ/mol), Mundticin ATO6 (-29.0 KJ/mol), Lactocyclicin Q (-26.3 KJ/mol), Cinnamycin (-25.9 KJ/mol showed highest binding energy. Among the peptides that showed the highest docking score Elafin, Cinnamycin, Duramycin interacted with Lys 73 of the α domain of catalytic residues of TEM-1 Beta lactamases, whereas Taromycin A, Gassericin A interacted with Lys 234 of the β domain, depicting a strong inhibition and also exhibited desirable physicochemical properties. Hence further in vitro examination of these cyclic peptides against the resistant strains is warranted to help design further novel inhibitors based on their scaffolds and also for the development of an effective drug combination regime.

In-silico screening of missense nsSNPs in Delta-opioid receptor protein and their restoring tendency on MCRT interaction; focusing on dynamic nature

Delta-opioid receptor protein (OPRD1) is one of the potential targets for treating pain. The presently available opioid agonists are known to cause unnecessary side effects. To discover a novel opioid agonist, our research group has synthesized a chimeric peptide MCRT and proved its potential activity through in vivo analysis. Non-synonymous SNPs (nsSNPs) missense mutations affect the functionality and stability of proteins leading to diseases. The current research was focused on understanding the role of MCRT in restoring the binding tendency of OPRD1 nsSNPs missense mutations on dynamic nature in comparison with Deltorphin-II and morphiceptin. The deleterious effects of nsSNPs were analyzed using various bioinformatics tools for predicting structural, functional, and oncogenic influence. The shortlisted nine nsSNPs were predicted for allergic reactions, domain changes, post-translation modification, multiple sequence alignment, secondary structure, molecular dynamic simulation (MDS), and peptide docking influence. Further, the docked complex of three shortlisted deleterious nsSNPs was analyzed using an MDS study, and the highly deleterious shortlisted nsSNP A149T was further analyzed for higher trajectory analysis. MCRT restored the binding tendency influence caused by nsSNPs on the dynamics of stability, functionality, binding affinity, secondary structure, residues connection, motion, and folding of OPRD1 protein.

Identification, inhibition modes, and molecular docking of ACE inhibitory peptides derived from Cheddar cheese

Herein, changes in the angiotensin-converting enzyme (ACE) inhibitory activity in Cheddar cheese during ripening (0–8 months) were studied, and the specific inhibitory types and modes of ACE inhibitory peptides were analyzed. The ACE inhibitory activity of Cheddar cheese was highest after 6 months (68.4%), and the ACE inhibitors of water-soluble extracts at this stage were mainly concentrated below 3 kDa. Six peptides with ACE inhibitory activity were isolated and purified from these peptides, and the inhibition modes of these peptides were studied. The results showed that VRYL and YLGY were competitive inhibitory peptides, RYL was a non-competitive inhibitory peptide, and TTMP was a mixed inhibitory peptide. Through the simulation of molecular docking sites, it was found that VRYL formed nine hydrogen bonds in the docking model and exhibited the highest ACE inhibitory activity. This study provides key insights for the development of functional cheeses and the extraction of ACE inhibitory peptides from Cheddar cheese.

Molecular docking and molecular dynamics simulation of wheat gluten-derived antioxidant peptides acting through the Keap1-Nrf2 pathway.

In our previous study, we successfully identified five peptides from wheat gluten: Ala-Pro-Ser-Tyr (APSY), Leu-Tyr (LY), Pro-Tyr (PY), Arg-Gly-Gly-Tyr (RGGY) and Tyr-Gln (YQ). Molecular docking and molecular dynamics simulation methods were employed to investigate the interaction between these antioxidant peptides and the Kelch-like ECH-associated protein 1 (Keap1 protein), revealing the molecular mechanism of their non-competitive binding. In addition, the total antioxidant capacity of the five peptides was determined using the 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) method. The affinities of APSY, LY, PY, RGGY and YQ were -8.9, -8.3, -8.5, -9.1 and - 7.9 kcal mol-1, respectively. The five peptides effectively bound to Keap1 protein through hydrogen, π-σ, π-alkyl and alkyl interactions. Significant roles were observed for the P1 pocket residue ARG-415 and the P3 pocket residue ALA-556 in the interactions of the Keap1-peptide complexes. Molecular dynamics simulations further elucidated the dynamic process of peptide binding to the Keap1 protein. All five peptides formed stable complexes with Keap1 protein, with van der Waals forces playing crucial roles in these complex systems, indicative of the peptides' strong binding ability to Keap1 protein. The van der Waals forces were -178.74, -123.11, -134.36, -132.59, and -121.44 kJ mol-1 for the Keap1-APSY, Keap1-LY, Keap1-PY, Keap1-RGGY and Keap1-YQ complexes, respectively. These peptides exhibited excellent antioxidant effects. Among them, the YQ peptide exhibited the highest total antioxidant capacity, with an activity value of 1.18 ± 0.06 mmol Trolox equivalent (TE) L-1 at a concentration of 0.10 mg mL-1. The RGGY, PY, LY and APSY peptides followed in descending order, with activity values of 0.91 ± 0.05, 0.72 ± 0.06, 0.62 ± 0.04 and 0.60 ± 0.05 mmol TE L-1, respectively. These results unveiled the molecular mechanism by which the five antioxidant peptides act on active pockets through the Keap1-Nrf2 signaling pathway, providing a theoretical basis for the development of antioxidants. © 2024 Society of Chemical Industry.

Covalent Flexible Peptide Docking in Drug Discovery: Current Challenges and Potential Interventions

Recently, there has been a significant increase in the search for new covalent inhibitors through drug discovery platforms, which has led to the development and implementation of new computational tools, including covalent docking methods to predict the binding mode and affinity of covalent ligands. Since the discovery of insulin nearly a century ago, more than 80 peptide medications have hit the market to treat a wide range of diseases, including diabetes, cancer, osteoporosis, multiple sclerosis, HIV infection, and chronic pain. Electrophilic peptides that form covalent bonds with target proteins have great potential for binding targets that have been previously considered undruggable. Despite the recent advancements in computational performance and docking algorithms, covalent docking still poses a number of challenges. Peptides covalent docking presents additional challenges, the main ones being the choice of the optimal peptide sequence, incorporation of electrophilic warheads, the inherent flexibility of peptide structures, and the fact that, unlike small molecules, peptides do fold. In this review, we present a brief overview of the current state of peptide therapeutics in drug discovery, covalent docking in general, covalent peptide binders, and-with particular emphasis-the difficulties that covalent peptide-protein docking is currently facing and some potential solutions.

Identification and molecular docking of novel antioxidant peptides from Candida utilis

The current trend is the promotion of antioxidants that are beneficial for both health and the environment. Candida utilis have garnered considerable attention due to their commendable attributes such as non-toxicity and the ability to thrive in waste. Therefore, Candida utilis was used as raw material to isolate and identify new antioxidant peptides by employing methods such as ultrafiltration, DEAE Sepharose Fast Flow, and liquid chromatography-tandem mass spectrometry. The antioxidant mechanism of peptides was investigated by molecular docking. The properties of antioxidant peptides were evaluated using a variety of computational tools. This study resulted in the identification of two novel antioxidant peptides. According to the molecular docking results, the antioxidant mechanism of Candida utilis peptides operates by obstructing the entry to the myeloperoxidase activity cavity. The (−) CDOCKER energy of antioxidant peptides was 6.2 and 6.1 kcal/mol, respectively. Additionally, computer predictions indicated that antioxidant peptides exhibited non-toxicity and poor solubility.

Computational analysis of 16D10 effector peptides from root-knot nematodes and their interaction with Mi resistance (R) protein through molecular docking

Plant-parasitic nematodes, especially root-knot nematodes (RKNs), pose significant threats to global agriculture, affecting both the quantity and quality of crop yields. Central to the parasitism strategy of RKNs is the deployment of effector proteins, such as the 16D10 peptide, which interact with host plant resistance mechanisms. This study focuses on the computational analysis and molecular docking of 16D10 effector peptides derived from major RKN species (M. incognita, M. arenaria, M. hapla, M. javanica, and M. chitwoodi) to explore their interaction with the Mi resistance protein in tomatoes. Initial bioinformatics assessments included sequence retrieval, multiple sequence alignment, and phylogenetic analysis, utilizing tools such as CLUSTALW and the MEME Suite. Notably, our phylogenetic analysis revealed a close evolutionary relationship between M. incognita and M. chitwoodi, contrasting with other RKN species based on both DNA and protein data. Subsequent, in silico 3D modeling and docking studies, conducted using Chem-Sketch and MOE software, provided insights into the structural basis of the interaction between 16D10 peptides and the Mi protein. Our findings indicate that these interactions could play a crucial role in the modulation of plant defense mechanisms, potentially leading to effector-triggered susceptibility (ETS). This study not only enhances our understanding of nematode-host interactions but also aids in the development of novel strategies for managing RKN infections in economically important crops.

Determination of HLA class II risk alleles and prediction of self/non-self-epitopes contributing Hashimoto's thyroiditis in a group of Iranian patients.

One of the probable hypotheses for the onset of autoimmunity is molecular mimicry. This study aimed to determine the HLA-II risk alleles for developing Hashimoto's thyroiditis (HT) in order to analyze the molecular homology between candidate pathogen-derived epitopes and potentially self-antigens (thyroid peroxidase, TPO) based on the presence of HLA risk alleles. HLA-DRB1/-DQB1 genotyping was performed in 100 HT patients and 330 ethnically matched healthy controls to determine the predisposing/protective alleles for HT disease. Then, in silico analysis was conducted to examine the sequence homology between epitopes derived from autoantigens and four potentially relevant pathogens and their binding capacities to HLA risk alleles based on peptide docking analysis. We identified HLA-DRB1*03:01, *04:02, *04:05, and *11:04 as predisposing alleles and DRB1*13:01 as a potentially predictive allele for HT disease. Also, DRB1*11:04 ~ DQB1*03:01 (Pc = 0.002; OR, 3.97) and DRB1*03:01 ~ DQB1*02:01 (Pc = 0.004; OR, 2.24) haplotypes conferred a predisposing role for HT. Based on logistic regression analysis, carrying risk alleles increased the risk of HT development 4.5 times in our population (P = 7.09E-10). Also, ROC curve analysis revealed a high predictive power of those risk alleles for discrimination of the susceptible from healthy individuals (AUC, 0.70; P = 6.6E-10). Analysis of peptide sequence homology between epitopes of TPO and epitopes derived from four candidate microorganisms revealed a homology between envelop glycoprotein D of herpes virus and sequence 151-199 of TPO with remarkable binding capacity to HLA-DRB1*03:01 allele. Our findings indicate the increased risk of developing HT in those individuals carrying HLA risk alleles which can also be related to herpes virus infection.

309 Effects of SARS-CoV-2 Variants on CD8+ T cell Epitope Diversity: Estimating Clinical Severity in the United States

OBJECTIVES/GOALS: Our goal was to distinguish SARS-CoV-2 CD8+ T cell epitopes of spike, membrane, and nucleocapsid products in 27 of the most frequent HLA-Aand -B alleles.We hypothesize that differences mediated by variation in SARS-CoV-2 and host HLA genetics affect the differential clinical severity and presentation of acute infection and PASC. METHODS/STUDY POPULATION: Genomic sequences of SARS-CoV-2 variants were blasted against the original Wuhan strain using Ensembl’s SARS-CoV-2 browser. We examined 16 COVID variants: 2 Alpha (B.1 and B.1.1.7), 5 Delta (AY.100, AY.25, AY.3, AY.3.1, and AY.44), and 9 Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, and XBB.1.5), sequenced from the Louisiana patient population. cDNA sequences were translated using the Expasy tool. To predict MHC-I epitope binding, we used the Immune Epitope Database and Analysis Resource, via TepiTool utilizing the IEDB recommended default prediction and the 27 most frequent HLA-A and -B alleles. In silico peptide docking was conducted on FoldX, utilizing HLA-B*15:01 structures (n= 7) from the Protein Data Bank. RESULTS/ANTICIPATED RESULTS: CD8+ epitope conservation was estimated at 87.6-96.5% in S, 92.5-99.6% in M, and 94.6-99% for N. As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1- XBB.1.5 S epitopes experienced decreased predicted binding, as compared to ~ 3% and ~15% in Delta AY.100-AY.44 and Omicron BA.1-BA.5 respectively. Additionally, we identified several novel candidate haplotypes that may be susceptible to severe disease, notably HLA-A*32:01, -A*26:01, -B*58:01, and -B*53:01, and relatively protected from disease, such as -A*01:01, -A*02:01,-A*31:01, -B*15:01, -B*40:01, -B*44:03, and -B*57:01. In silico analysis of COVID peptides and HLA-B*15:01, a common allotype in the United States, largely matched predicted binding patterns. DISCUSSION/SIGNIFICANCE: To elicit long term COVID-19 immunity and prevent PASC, it is important to understand the relationship between T-cells, viral variants, and HLA genetics. This project is one of the first to explore the interaction between CD8+ epitope diversity and viral genetics for the majority of the United States population.

Preparation, identification, and molecular docking of novel angiotensin-converting enzyme inhibitory peptides derived from rice-based distillers' spent cakes.

Rice-based distillers' spent cake (RDSC), a by-product of the Chinese liquor (Baijiu) industry, is a potential source of angiotensin-converting enzyme (ACE) inhibitory peptide. Since ACE plays a crucial role in controlling hypertension, inhibition of ACE has been widely emphasized. The ACE inhibitory active peptide derived from by-products of food has been recognized as a safer and cheaper inhibitor. Aimed to discover ACE-inhibiting active peptides in RDSC. Hydrolysis of RDSC by alcalase for 4 h followed by ultrafiltration yielded low-molecular-weight (< 3 kDa) fractions. Subsequently, a comprehensive method using a combination of liquid chromatography quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) and LC-Q-Exactive-MS to identify the novel short peptides (3-5 amino acids residues; n = 7) and medium-sized peptides (more than 6 amino acids residues; n = 6). In vitro activity assay showed that the peptides KPFFPGL, GFPRPLL, GPPGVF, and VGK exhibited the highest activity with inhibitory concentration of 50% (IC50) of 11.63, 12.34, 19.55, and 33.54 μmol L-1. Molecular docking reveal that the active and inactive sites (Glu123, Asp121, Arg522, and Lys118) play important roles in enhancing the ACE inhibitory activity of peptides. Here we report a comprehensive method that effectively extracted and identified the bioactive peptides from RDSC. Four highly active novel peptides may be the most promising candidates for functional foods against hypertension, provide significant information for enhancing value of rice-based distilled by-products. © 2024 Society of Chemical Industry.