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Noble JE, Vila-Gómez P, Rey S, Dondi C, Briones A, Aggarwal P, Hoose A, Baran M, Ryadnov MG. Folding-Mediated DNA Delivery by α-Helical Amphipathic Peptides. ACS Biomater Sci Eng 2023; 9:2584-2595. [PMID: 37014978 DOI: 10.1021/acsbiomaterials.3c00221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The renaissance gene therapy experiences these days requires specialist biomaterials and a systemic understanding of major factors influencing their ability to deliver genetic material. Peptide transfection systems represent a major class of such biomaterials. Several peptidic reagents have been commercialized to date. However, a comparative assessment of peptide sequences alone without auxiliary support or excipients against a common determinant for their ability to complex and deliver DNA has been lacking. This study cross-compares commercial and experimental transfection reagents from the same family of helical amphiphiles. Factors defining the efficacy of DNA delivery including cell uptake and gene expression are assessed along with cytotoxicity and DNA complexation. The results show that despite differences in sequence composition, length, and origin, peptide reagents of the same structural family exhibit similar characteristics and limitations with common variability trends. The cross-comparison revealed that functional DNA delivery is independent of the peptide sequence used but is mediated by the ability of the reagents to co-fold with DNA. Peptide folding proved to be the common determinant for DNA complexation and delivery by peptidic transfection reagents.
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Affiliation(s)
- James E Noble
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Paula Vila-Gómez
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Brain Sciences, Imperial College London, London W12 0TR, U.K
| | - Stephanie Rey
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Camilla Dondi
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Andrea Briones
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Purnank Aggarwal
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Alex Hoose
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maryana Baran
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Maxim G Ryadnov
- National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Physics, King's College London, London WC2R 2LS, U.K
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De Oliveira DH, Biler M, Mim C, Enstedt L, Kvick M, Norman P, Linares M, Hedhammar M. Silk Assembly against Hydrophobic Surfaces─Modeling and Imaging of Formation of Nanofibrils. ACS APPLIED BIO MATERIALS 2023; 6:1011-1018. [PMID: 36791416 PMCID: PMC10031558 DOI: 10.1021/acsabm.2c00878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, β-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of ∼7 nm and a width of ∼11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.
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Affiliation(s)
- Danilo Hirabae De Oliveira
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Michal Biler
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Carsten Mim
- Department of Biomedical Engineering and Health Systems, Royal Technical Institute (KTH), Hälsovägen 11C, SE-141 27 Huddinge, Sweden
| | - Linnea Enstedt
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | | | - Patrick Norman
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
| | - Mathieu Linares
- Laboratory of Organic Electronics and Scientific Visualization Group, ITN, Linköping University, SE-581 83 Linköping, Sweden
| | - My Hedhammar
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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53
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Exploring the Potential of Black Soldier Fly Larval Proteins as Bioactive Peptide Sources through in Silico Gastrointestinal Proteolysis: A Cheminformatic Investigation. Catalysts 2023. [DOI: 10.3390/catal13030605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Despite their potential as a protein source for human consumption, the health benefits of black soldier fly larvae (BSFL) proteins following human gastrointestinal (GI) digestion are poorly understood. This computational study explored the potential of BSFL proteins to release health-promoting peptides after human GI digestion. Twenty-six proteins were virtually proteolyzed with GI proteases. The resultant peptides were screened for high GI absorption and non-toxicity. Shortlisted peptides were searched against the BIOPEP-UWM and Scopus databases to identify their bioactivities. The potential of the peptides as inhibitors of myeloperoxidase (MPO), NADPH oxidase (NOX), and xanthine oxidase (XO), as well as a disruptor of Keap1–Nrf2 protein–protein interaction, were predicted using molecular docking and dynamics simulation. Our results revealed that about 95% of the 5218 fragments generated from the proteolysis of BSFL proteins came from muscle proteins. Dipeptides comprised the largest group (about 25%) of fragments arising from each muscular protein. Screening of 1994 di- and tripeptides using SwissADME and STopTox tools revealed 65 unique sequences with high GI absorption and non-toxicity. A search of the databases identified 16 antioxidant peptides, 14 anti-angiotensin-converting enzyme peptides, and 17 anti-dipeptidyl peptidase IV peptides among these sequences. Results from molecular docking and dynamic simulation suggest that the dipeptide DF has the potential to inhibit Keap1–Nrf2 interaction and interact with MPO within a short time frame, whereas the dipeptide TF shows promise as an XO inhibitor. BSFL peptides were likely weak NOX inhibitors. Our in silico results suggest that upon GI digestion, BSFL proteins may yield high-GI-absorbed and non-toxic peptides with potential health benefits. This study is the first to investigate the bioactivity of peptides liberated from BSFL proteins following human GI digestion. Our findings provide a basis for further investigations into the potential use of BSFL proteins as a functional food ingredient with significant health benefits.
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Ranjbarian P, Goudarzi F, Akya A, Heidarinia H, Farasat A, Rostamian M. Finding epitopes of Klebsiella pneumoniae outer membrane protein-K17 (OMPK17) and introducing a 25-mer peptide of it as a vaccine candidate. Biologia (Bratisl) 2023; 78:1-11. [PMID: 37363641 PMCID: PMC10012306 DOI: 10.1007/s11756-023-01371-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 02/23/2023] [Indexed: 03/15/2023]
Abstract
No approved vaccine exists for Klebsiella pneumoniae yet. Outer membrane protein-K17 (OMPK17) is involved in K. pneumoniae pathogenesis. No information has been found about OMPK17 dominant epitopes in the literature. Therefore, this study aimed to predict both T cell and B cell epitopes of K. pneumoniae OMPK17 via immunoinformatics approaches. Both T cell (class-I and II) and B cell (linear and discontinuous) epitopes of OMPK17 were predicted. Several screening analyses were performed including clustering, immunogenicity, human similarity, toxicity, allergenicity, conservancy, docking, and structural/physicochemical suitability. The results showed that some regions of OMPK17 have more potential as epitopes. The most possible epitopes were found via several analyses including the selection of higher-scoring epitopes, the epitopes predicted with more tools, more immunogenic epitopes, the epitopes capable of producing interferon-gamma, the epitopes with more dissimilarity to human peptides, and non-toxic and non-allergenic epitopes. By comparing the best T cell and B cell epitopes, we reached a 25-mer peptide containing both T cell (class-I and class-II) and B cell (linear) epitopes and comprising appropriate physicochemical characteristics that are required for K. pneumoniae vaccine development. The in vitro/in vivo study of this peptide is recommended to clarify its actual efficiency and efficacy. Supplementary information The online version contains supplementary material available at 10.1007/s11756-023-01371-0.
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Affiliation(s)
- Parivash Ranjbarian
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Farjam Goudarzi
- Regenerative Medicine Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Alisha Akya
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Parastar Blvd, Imam Reza Hospital, Kermanshah, 6714415333 Iran
| | - Hana Heidarinia
- Department of Microbiology, Faculty of Basic Sciences, Shahrekord Branch of Islamic Azad University, Shahrekord, Iran
| | - Alireza Farasat
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Parastar Blvd, Imam Reza Hospital, Kermanshah, 6714415333 Iran
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Wiman E, Zattarin E, Aili D, Bengtsson T, Selegård R, Khalaf H. Development of novel broad-spectrum antimicrobial lipopeptides derived from plantaricin NC8 β. Sci Rep 2023; 13:4104. [PMID: 36914718 PMCID: PMC10011573 DOI: 10.1038/s41598-023-31185-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Bacterial resistance towards antibiotics is a major global health issue. Very few novel antimicrobial agents and therapies have been made available for clinical use during the past decades, despite an increasing need. Antimicrobial peptides have been intensely studied, many of which have shown great promise in vitro. We have previously demonstrated that the bacteriocin Plantaricin NC8 αβ (PLNC8 αβ) from Lactobacillus plantarum effectively inhibits Staphylococcus spp., and shows little to no cytotoxicity towards human keratinocytes. However, due to its limitations in inhibiting gram-negative species, the aim of the present study was to identify novel antimicrobial peptidomimetic compounds with an enhanced spectrum of activity, derived from the β peptide of PLNC8 αβ. We have rationally designed and synthesized a small library of lipopeptides with significantly improved antimicrobial activity towards both gram-positive and gram-negative bacteria, including the ESKAPE pathogens. The lipopeptides consist of 16 amino acids with a terminal fatty acid chain and assemble into micelles that effectively inhibit and kill bacteria by permeabilizing their cell membranes. They demonstrate low hemolytic activity and liposome model systems further confirm selectivity for bacterial lipid membranes. The combination of lipopeptides with different antibiotics enhanced the effects in a synergistic or additive manner. Our data suggest that the novel lipopeptides are promising as future antimicrobial agents, however additional experiments using relevant animal models are necessary to further validate their in vivo efficacy.
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Affiliation(s)
- Emanuel Wiman
- School of Medical Sciences, Faculty of Medicine and Health, Department of Microbiology, Immunology and Reproductive Science, Örebro University, Örebro, Sweden
| | - Elisa Zattarin
- Laboratory of Molecular Materials, Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Daniel Aili
- Laboratory of Molecular Materials, Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden
| | - Torbjörn Bengtsson
- School of Medical Sciences, Faculty of Medicine and Health, Department of Microbiology, Immunology and Reproductive Science, Örebro University, Örebro, Sweden
| | - Robert Selegård
- Laboratory of Molecular Materials, Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology, Linköping University, 581 83, Linköping, Sweden.
| | - Hazem Khalaf
- School of Medical Sciences, Faculty of Medicine and Health, Department of Microbiology, Immunology and Reproductive Science, Örebro University, Örebro, Sweden.
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56
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Calderón-Rivera N, Múnera-Jaramillo J, Jaramillo-Berrio S, Suesca E, Manrique-Moreno M, Leidy C. Cardiolipin Strongly Inhibits the Leakage Activity of the Short Antimicrobial Peptide ATRA-1 in Comparison to LL-37, in Model Membranes Mimicking the Lipid Composition of Staphylococcus aureus. MEMBRANES 2023; 13:304. [PMID: 36984691 PMCID: PMC10051595 DOI: 10.3390/membranes13030304] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Cardiolipin is one of the main phospholipid components of Staphylococcus aureus membranes. This lipid is found at varying concentrations in the bilayer, depending on the growth stage of the bacteria, and as a response to environmental stress. Cardiolipin is an anionic phospholipid with four acyl chains, which modulates the bending properties of the membrane due to its inverted conical shape. It has been shown to inhibit the pore forming activity of several antimicrobial peptides, in general doubling the peptide concentration needed to induce leakage. Here we find that the short snake-derived antimicrobial peptide ATRA-1 is inhibited by several orders of magnitude in the presence of cardiolipin in saturated membranes (DMPG) compared to the human cathelicidin LL-37, which is only inhibited two-fold in its leakage-inducing concentration. The ATRA-1 is too short to span the membrane and its leakage activity is likely related to detergent-like alterations of bilayer structure. Fluorescence spectroscopy shows only a minor effect on ATRA-1 binding to DMPG membranes due to the presence of cardiolipin. However, FTIR spectroscopy shows that the acyl chain structure of DMPG membranes, containing cardiolipin, become more organized in the presence of ATRA-1, as reflected by an increase in the gel to liquid-crystalline phase transition temperature. Instead, a depression in the melting temperature is induced by ATRA-1 in DMPG in the absence of cardiolipin. In comparison, LL-37 induces a depression of the main phase transition of DMPG even in the presence of cardiolipin. These data suggest that cardiolipin inhibits the penetration of ATRA-1 into the membrane core, impeding its capacity to disrupt lipid packing.
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Affiliation(s)
- Nathalia Calderón-Rivera
- Biophysics Group, Physics Department, Universidad de los Andes, Bogotá 111711, Cundinamarca, Colombia
| | - Jessica Múnera-Jaramillo
- Faculty of Natural of Exact Sciences, Chemistry Institute, University of Antioquia, A.A. 1226, Medellin 050010, Antioquia, Colombia
| | - Sara Jaramillo-Berrio
- Biophysics Group, Physics Department, Universidad de los Andes, Bogotá 111711, Cundinamarca, Colombia
| | - Elizabeth Suesca
- Biophysics Group, Physics Department, Universidad de los Andes, Bogotá 111711, Cundinamarca, Colombia
| | - Marcela Manrique-Moreno
- Faculty of Natural of Exact Sciences, Chemistry Institute, University of Antioquia, A.A. 1226, Medellin 050010, Antioquia, Colombia
| | - Chad Leidy
- Biophysics Group, Physics Department, Universidad de los Andes, Bogotá 111711, Cundinamarca, Colombia
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57
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A Novel Peptide-Based Detection of SARS-CoV-2 Antibodies. Biomimetics (Basel) 2023; 8:biomimetics8010089. [PMID: 36975319 PMCID: PMC10046560 DOI: 10.3390/biomimetics8010089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
The need for rapidly developed diagnostic tests has gained significant attention after the recent pandemic. Production of neutralizing antibodies for vaccine development or antibodies to be used in diagnostic tests usually require the usage of recombinant proteins representing the infectious agent. However, peptides that can mimic these recombinant proteins may be rapidly utilized, especially in emergencies such as the recent outbreak. Here, we report two peptides that mimic the receptor binding domain of the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and investigate their binding behavior against the corresponding human immunoglobulin G and immunoglobulin M (IgG and IgM) antibodies in a clinical sample using a quartz crystal microbalance (QCM) sensor. These peptides were immobilized on a QCM sensor surface, and their binding behavior was studied against a clinical serum sample that was previously determined to be IgG and IgM-positive. It was determined that designed peptides bind to SARS-CoV-2 antibodies in a clinical sample. These peptides might be useful for the detection of SARS-CoV-2 antibodies using different methods such as enzyme-linked immunosorbent assay (ELISA) or lateral flow assays. A similar platform might prove to be useful for the detection and development of antibodies in other infections.
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58
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Mirnejad R, Fasihi-Ramandi M, Behmard E, Najafi A, Moosazadeh Moghaddam M. Interaction of antibacterial CM11 peptide with the gram-positive and gram-negative bacterial membrane models: a molecular dynamics simulations study. CHEMICAL PAPERS 2023. [DOI: 10.1007/s11696-023-02735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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59
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Bai B, Zhang G, Pei B, Song Q, Hao X, Zhao L, Wu Y. The function of the phytoplasma effector SWP12 depends on the properties of two key amino acids. J Biol Chem 2023; 299:103052. [PMID: 36813236 PMCID: PMC10040895 DOI: 10.1016/j.jbc.2023.103052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/23/2023] Open
Abstract
Phytoplasmas are insect-borne bacterial pathogens capable of secreting effectors into host cells and interfering with host plant defense response processes. Previous studies have found that the Candidatus Phytoplasma tritici effector SWP12 binds to and destabilizes the wheat transcription factor TaWRKY74, increasing wheat susceptibility to phytoplasmas. Here, we used a Nicotiana benthamiana transient expression system to identify two key functional sites of SWP12 and screened a series of truncated mutants and amino acid substitution mutants to determine whether they inhibit Bax-induced cell death. Using a subcellular localization assay and online structure analysis websites, we found that structure rather than intracellular localization probably affects the function of SWP12. D33A and P85H are two inactive substitution mutants, neither of which interacts with TaWRKY74, and P85H does not inhibit Bax-induced cell death, suppress flg22-triggered reactive oxygen species (ROS) bursts, degrade TaWRKY74, or promote phytoplasma accumulation. D33A can weakly suppress Bax-induced cell death and flg22-triggered ROS bursts and degrade a portion of TaWRKY74 and weakly promote phytoplasma accumulation. S53L, CPP, and EPWB are three SWP12 homolog proteins from other phytoplasmas. Sequence analysis revealed that D33 was conserved in these proteins, and they exhibited the same polarity at P85. Transient expression in N. benthamiana showed that these proteins could inhibit Bax-induced cell death and suppress ROS bursts. Our findings clarified that P85 and D33 of SWP12 play critical and minor roles, respectively, in suppressing the plant defense response and that they play a preliminary role in determining the functions of homologous proteins.
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Affiliation(s)
- Bixin Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Guoding Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Baoyan Pei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingting Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Xing'an Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Lei Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.
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60
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Liao F, Chen Y, Shu A, Chen X, Wang T, Jiang Y, Ma C, Zhou M, Chen T, Shaw C, Wang L. A Novel Strategy for the Design of Aurein 1.2 Analogs with Enhanced Bioactivities by Conjunction of Cell-Penetrating Regions. Antibiotics (Basel) 2023; 12:antibiotics12020412. [PMID: 36830322 PMCID: PMC9952496 DOI: 10.3390/antibiotics12020412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The rational design modification of membrane-active peptide structures by introducing additional membrane-penetrating regions has become a good strategy for the improvement of action and potency. Aurein 1.2 (GLFDIIKKIAESF-NH2) is a multifunctional antimicrobial peptide isolated from the green and golden bell frog, Litoria aurea, and the southern bell frog Litoria raniformis skin secretions. Its bio-functionality has been widely investigated. However, its lack of a potent action failed to provide aurein 1.2 with a competitive edge for further development as a therapeutic agent for clinical use. Herein, aurein 1.2 was chosen as a template for rational modification to achieve a more potent bio-functionality. KLA-2 (GLFDIIKKLAKLAESF-NH2), which a double KLA region inserted into the sequence, presented a 2-16-fold enhancement of antimicrobial activity, a 2-8-fold greater anti-biofilm activity (including biofilm prevention and eradication), and a 7-fold more potent anti-proliferation activity and hence was regarded as the most broad-spectrum active peptide. Additionally, with respect to antimicrobial activity, the IIKK-modified analog, IK-3 (GLFDIIKKIIKKIIKKI-NH2), also demonstrated a potent enhancement of activity against various pathogens, exhibiting a 2-8-fold enhanced activity compared to the parent peptide. Moreover, the selectivities of KLA-1 and KLA-2 were enhanced significantly. In conclusion, peptide modification, through the introduction of additional membrane penetrating regions, can increase both the potency and activity spectra of natural template peptides, making them suitable candidates for new drug development.
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Affiliation(s)
- Fengting Liao
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Yuping Chen
- Department of Basic Medical Science, Jiangsu Vocational College of Medicine, Yancheng 224005, China
| | - Anmei Shu
- Department of Basic Medical Science, Jiangsu Vocational College of Medicine, Yancheng 224005, China
| | - Xiaoling Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
- Correspondence: (X.C.); (L.W.)
| | - Tao Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Yangyang Jiang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Chengbang Ma
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Chris Shaw
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Queen’s University Belfast, Belfast BT9 7BL, Northern Ireland, UK
- Correspondence: (X.C.); (L.W.)
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61
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You Y, Liu H, Zhu Y, Zheng H. Rational design of stapled antimicrobial peptides. Amino Acids 2023; 55:421-442. [PMID: 36781451 DOI: 10.1007/s00726-023-03245-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/30/2023] [Indexed: 02/15/2023]
Abstract
The global increase in antimicrobial drug resistance has dramatically reduced the effectiveness of traditional antibiotics. Structurally diverse antibiotics are urgently needed to combat multiple-resistant bacterial infections. As part of innate immunity, antimicrobial peptides have been recognized as the most promising candidates because they comprise diverse sequences and mechanisms of action and have a relatively low induction rate of resistance. However, because of their low chemical stability, susceptibility to proteases, and high hemolytic effect, their usage is subject to many restrictions. Chemical modifications such as D-amino acid substitution, cyclization, and unnatural amino acid modification have been used to improve the stability of antimicrobial peptides for decades. Among them, a side-chain covalent bridge modification, the so-called stapled peptide, has attracted much attention. The stapled side-chain bridge stabilizes the secondary structure, induces protease resistance, and increases cell penetration and biological activity. Recent progress in computer-aided drug design and artificial intelligence methods has also been used in the design of stapled antimicrobial peptides and has led to the successful discovery of many prospective peptides. This article reviews the possible structure-activity relationships of stapled antimicrobial peptides, the physicochemical properties that influence their activity (such as net charge, hydrophobicity, helicity, and dipole moment), and computer-aided methods of stapled peptide design. Antimicrobial peptides under clinical trial: Pexiganan (NCT01594762, 2012-05-07). Omiganan (NCT02576847, 2015-10-13).
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Affiliation(s)
- YuHao You
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - HongYu Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - YouZhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
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62
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Stopar A, Nicholson AW. Multivalent forms of the ribonuclease H1 hybrid binding domain are high-affinity binders of RNA-DNA hybrids. FEBS Lett 2023; 597:472-482. [PMID: 36443824 DOI: 10.1002/1873-3468.14541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/30/2022]
Abstract
The hybrid binding domain (HBD) is a conserved fold present in ribonucleases H1 that selectively recognizes RNA-DNA hybrids, which are structures present in cellular R-loops and participate in diverse biological processes. We engineered multivalent HBD proteins to create high-affinity hybrid binders. Using EMSA- and SPR-based analyses, we showed that the triple-HBD protein exhibits a ~ 22 000-fold increase in hybrid affinity (KD 370 pm) relative to the single HBD (KD 8.29 μm), with the length and sequence of the linkers enabling optimal function. These findings provide a framework for testing models that correlate multivalency and affinity to understand how multivalent proteins function and also can serve to guide applications that exploit multivalency as a strategy to enhance binding affinity.
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Affiliation(s)
- Alex Stopar
- Department of Biology, Temple University, Philadelphia, PA, USA
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63
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Tufféry P, Derreumaux P. A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. FRONTIERS IN BIOINFORMATICS 2023; 3:1113928. [PMID: 36727106 PMCID: PMC9885153 DOI: 10.3389/fbinf.2023.1113928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/06/2023] [Indexed: 01/17/2023] Open
Abstract
Introduction: Peptides carry out diverse biological functions and the knowledge of the conformational ensemble of polypeptides in various experimental conditions is important for biological applications. All fast dedicated softwares perform well in aqueous solution at neutral pH. Methods: In this study, we go one step beyond by combining the Debye-Hückel formalism for charged-charged amino acid interactions and a coarse-grained potential of the amino acids to treat pH and salt variations. Results: Using the PEP-FOLD framework, we show that our approach performs as well as the machine-leaning AlphaFold2 and TrRosetta methods for 15 well-structured sequences, but shows significant improvement in structure prediction of six poly-charged amino acids and two sequences that have no homologous in the Protein Data Bank, expanding the range of possibilities for the understanding of peptide biological roles and the design of candidate therapeutic peptides.
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Affiliation(s)
- Pierre Tufféry
- Université Paris Cité, CNRS UMR 8251, INSERM U1133, Paris, France,*Correspondence: Pierre Tufféry,
| | - Philippe Derreumaux
- Université Paris Cité, CNRSUPR9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France,Institut Universitaire de France (IUF), Paris, France
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64
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Jade D, Gupta S, Mohan S, Ponnambalam S, Harrison M, Bhatnagar R. Homology modelling and molecular simulation approach to prediction of B-cell and T-cell epitopes in an OMP25 peptide vaccine against Brucella abortus. MOLECULAR SIMULATION 2023. [DOI: 10.1080/08927022.2023.2165126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Dhananjay Jade
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, JNU, New Delhi India
- School of Biomedical Sciences, University of Leeds School of Molecular and Cellular Biology, Leeds, UK
- School of Molecular & Cellular Biology, University of Leeds, Leeds, UK
| | - Sonal Gupta
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, JNU, New Delhi India
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA
| | - Surender Mohan
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, JNU, New Delhi India
| | | | - Michael Harrison
- School of Biomedical Sciences, University of Leeds School of Molecular and Cellular Biology, Leeds, UK
| | - Rakesh Bhatnagar
- Laboratory of Molecular Biology and Genetic Engineering, School of Biotechnology, JNU, New Delhi India
- Banaras Hindu University, Banaras, India
- Amity University Jaipur, Jaipur, India
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65
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Marzella DF, Crocioni G, Parizi FM, Xue LC. The PANDORA Software for Anchor-Restrained Peptide:MHC Modeling. Methods Mol Biol 2023; 2673:251-271. [PMID: 37258920 DOI: 10.1007/978-1-0716-3239-0_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Major histocompatibility complexes (MHC) play a key role in the immune surveillance system in all jawed vertebrates. MHC class I molecules randomly sample cytosolic peptides from inside the cell, while MHC class II sample exogenous peptides. Both types of peptide:MHC complex are then presented on the cell surface for recognition by αβ T cells (CD8+ and CD4+, respectively). The three-dimensional structure of such complexes can give crucial insights in the presentation and recognition mechanisms. For this reason, softwares like PANDORA have been developed to rapidly and accurately generate peptide:MHC (pMHC) 3D structures. In this chapter, we describe the protocol of PANDORA. PANDORA exploits the structural knowledge on anchor pockets that MHC molecules use to dock peptides. PANDORA provides anchor positions as restraints to guide the modeling process. This allows PANDORA to generate twenty 3D models in just about 5 min. PANDORA is highly customizable, easy to install, supports parallel processing, and is suitable to provide large datasets for deep learning algorithms.
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Affiliation(s)
- Dario F Marzella
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | | | - Farzaneh M Parizi
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - Li C Xue
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands.
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Klaiss-Luna MC, Jemioła-Rzemińska M, Strzałka K, Manrique-Moreno M. Understanding the Biophysical Interaction of LTX-315 with Tumoral Model Membranes. Int J Mol Sci 2022; 24:ijms24010581. [PMID: 36614022 PMCID: PMC9820754 DOI: 10.3390/ijms24010581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Host defense peptides are found primarily as natural antimicrobial agents among all lifeforms. These peptides and their synthetic derivatives have been extensively studied for their potential use as therapeutic agents. The most accepted mechanism of action of these peptides is related to a nonspecific mechanism associated with their interaction with the negatively charged groups present in membranes, inducing bilayer destabilization and cell death through several routes. Among the most recently reported peptides, LTX-315 has emerged as an important oncolytic peptide that is currently in several clinical trials against different cancer types. However, there is a lack of biophysical studies regarding LTX-315 and its interaction with membranes. This research focuses primarily on the understanding of the molecular bases of LTX-315's interaction with eukaryotic lipids, based on two artificial systems representative of non-tumoral and tumoral membranes. Additionally, the interaction with individual lipids was studied by differential scanning calorimetry and Fourier-transformed infrared spectroscopy. The results showed a strong interaction of LTX-315 with the negatively charged phosphatidylserine. The results are important for understanding and facilitating the design and development of improved peptides with anticancer activity.
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Affiliation(s)
- Maria C. Klaiss-Luna
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A 1226, Medellin 050010, Colombia
| | - Małgorzata Jemioła-Rzemińska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-392 Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Kazimierz Strzałka
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-392 Krakow, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
- Correspondence: (K.S.); (M.M.-M.); Tel.: +48-(12)-664-65-09 (K.S.); +57-300-7078-928 (M.M.-M.)
| | - Marcela Manrique-Moreno
- Chemistry Institute, Faculty of Exact and Natural Sciences, University of Antioquia, A.A 1226, Medellin 050010, Colombia
- Correspondence: (K.S.); (M.M.-M.); Tel.: +48-(12)-664-65-09 (K.S.); +57-300-7078-928 (M.M.-M.)
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Mohammadi Y, Nezafat N, Negahdaripour M, Eskandari S, Zamani M. In silico design and evaluation of a novel mRNA vaccine against BK virus: a reverse vaccinology approach. Immunol Res 2022; 71:422-441. [PMID: 36580228 PMCID: PMC9797904 DOI: 10.1007/s12026-022-09351-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 12/02/2022] [Indexed: 12/30/2022]
Abstract
Human polyomavirus type 1, or BK virus (BKV), is a ubiquitous pathogen belonging to the polyomaviridae family mostly known for causing BKV-associated nephropathy (BKVN) and allograft rejection in kidney transplant recipients (KTRs) following the immunosuppression regimens recommended in these patients. Reduction of the immunosuppression level and anti-viral agents are the usual approaches for BKV clearance, which have not met a desired outcome yet. There are also debating matters such as the effect of this pathogen on emerging various comorbidities and the related malignancies in the human population. In this study, a reverse vaccinology approach was implemented to design a mRNA vaccine against BKV by identifying the most antigenic proteins of this pathogen. Potential immunogenic T and B lymphocyte epitopes were predicted through various immunoinformatic tools. The final epitopes were selected according to antigenicity, toxicity, allergenicity, and cytokine inducibility scores. According to the obtained results, the designed vaccine was antigenic, neutral at the physiological pH, non-toxic, and non-allergenic with a world population coverage of 93.77%. Since the mRNA codon optimization ensures the efficient expression of the vaccine in a host cell, evaluation of different parameters showed our designed mRNA vaccine has a stable structure. Moreover, it had strong interactions with toll-like receptor 4 (TLR4) according to the molecular dynamic simulation studies. The in silico immune simulation analyses revealed an overall increase in the immune responses following repeated exposure to the designed vaccine. Based on our findings, the vaccine candidate is ready to be tested as a promising novel mRNA therapeutic vaccine against BKV.
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Affiliation(s)
- Yasaman Mohammadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Navid Nezafat
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran.
| | - Manica Negahdaripour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran.
| | - Sedigheh Eskandari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Science, Shiraz, Iran
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Benslama Y, Dennouni-Medjati N, Dali-Sahi M, Meziane FZ, Harek Y. Childhood type 1 diabetes mellitus and risk factor of interactions between dietary cow's milk intake and HLA-DR3/DR4 genotype. J Biomol Struct Dyn 2022; 40:10931-10939. [PMID: 34282715 DOI: 10.1080/07391102.2021.1953599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Short-term breastfeeding and early exposure to dairy products into infant diets, may be critical factors for development of type 1 diabetes. In this study, we investigate whether cow's milk proteins are risk factors for type 1 diabetes in genetically susceptible individuals (HLA DR3/DR4) by using statistical analysis and in silico approach. In order to verify the potential risk of the early introduction of cow's milk, we conducted this study to validate the veracity of this hypothesis in our population. We included 121 subjects, 55 type 1 diabetics and 74 controls from the region of Tlemcen (Algeria). Thus, the in silico approach was performed to determine the molecular mimicry region between Bovine serum albumin and beta-lactoglobulin with self-Islet antigen 2 and glutamate decarboxylase 65 by determining their sequences and their 3D structures. The risk factors associated with type 1 diabetes in a genetically predisposed individual (HLA DR3/DR4) retained by the logistic model are: type 1 and type 2 diabetes inheritance, the early introduction of cow's milk before 6 months and breastfeeding less than 9 months. Besides, the epitopes of cow's milk proteins have the capacity to bind to predisposing HLA class II molecules (HLA DR3/DR4) and induce an immune reaction by the secretion of Interleukin 4 (Th2) and Interferon (Th1) which lead to the destruction of pancreatic beta cells. The early introduction of cow's milk proteins in susceptible individuals is considered as risk factors for the pathogenesis of T1DM. The in silico approach confirm that BSA and BLG share sequence and structure homology with IA2 and GAD65.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yasmine Benslama
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Nouria Dennouni-Medjati
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Majda Dali-Sahi
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Fatima Zahra Meziane
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
| | - Yahia Harek
- Laboratory of Analytical Chemistry and Electrochemistry, Abou Bekr Belkaid University of Tlemcen, Tlemcen, Algeria
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69
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Serrano-Quintero A, Sequeda-Juárez A, Pérez-Hernández CA, Sosa-Delgado SM, Mendez-Tenorio A, Ramón-Gallegos E. Immunogenic analysis of epitope-based vaccine candidate induced by photodynamic therapy in MDA-MB-231 triple-negative breast cancer cells. Photodiagnosis Photodyn Ther 2022; 40:103174. [PMID: 36602069 DOI: 10.1016/j.pdpdt.2022.103174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/20/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Photodynamic therapy (PDT) is used to treat tumors through selective cytotoxic effects. PDT induces damage-associated molecular patterns (DAMPs) expression, which can cause an immunogenic death cell (IDC). In this study we identified potential immunogenic epitopes generated by PDT on triple-negative breast cancer cell line (MDA-MB-231). METHODS MDA-MB-231 cells were exposed to PDT using ALA (160 µg/mL)/630 nm at 8 J/cm2. Membrane proteins were extracted and separated by 2D PAGE. Proteins overexpressed were identified by LC-MS/MS and analyzed in silico through a peptide-HLA docking in order to identify the epitopes with more immunogenicity and antigenicity properties, as well as lower allergenicity and toxicity activity. The selected peptides were evaluated in response to macrophage activation and cytokine release by flow cytometry. RESULTS Differential proteins were overexpressed in the cells treated with PDT. A group of 16 peptides were identified from them, established in a rigorous selection by measuring antigenicity, immunogenicity, allergenicity, and toxicity in silico. The final selection was based on molecular dynamics, where 2 peptides showed the highest stability regarding to the RMSD value. These peptides were obtained from the proteins calreticulin and HSP90. The cytokine analysis evidenced macrophage activation by the releasing of TNF. CONCLUSION Two peptides were identified from calreticulin and HSP90; proteins induced by PDT in MDA-MB-231 cells. Both epitopes showed immunogenic potential as a peptide-based vaccine for triple-negative breast cancer.
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Affiliation(s)
- Alina Serrano-Quintero
- Laboratorio de Citopatología Ambiental, ENCB, Instituto Politécnico Nacional (IPN), Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda. Manuel Stampa, Col. Zacatenco. Alcaldia Gustavo A. Madero, Mexico City C.P. 07738, Mexico
| | - Alfonso Sequeda-Juárez
- Laboratorio de Citopatología Ambiental, ENCB, Instituto Politécnico Nacional (IPN), Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda. Manuel Stampa, Col. Zacatenco. Alcaldia Gustavo A. Madero, Mexico City C.P. 07738, Mexico
| | - C Angélica Pérez-Hernández
- Laboratorio de Citopatología Ambiental, ENCB, Instituto Politécnico Nacional (IPN), Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda. Manuel Stampa, Col. Zacatenco. Alcaldia Gustavo A. Madero, Mexico City C.P. 07738, Mexico
| | - Sara M Sosa-Delgado
- Laboratorio de Citopatología Ambiental, ENCB, Instituto Politécnico Nacional (IPN), Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda. Manuel Stampa, Col. Zacatenco. Alcaldia Gustavo A. Madero, Mexico City C.P. 07738, Mexico
| | - Alfonso Mendez-Tenorio
- Laboratorio de Bioinformática y Biotecnología Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Eva Ramón-Gallegos
- Laboratorio de Citopatología Ambiental, ENCB, Instituto Politécnico Nacional (IPN), Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda. Manuel Stampa, Col. Zacatenco. Alcaldia Gustavo A. Madero, Mexico City C.P. 07738, Mexico.
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70
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Sarkar B, Ullah MA, Araf Y, Islam NN, Zohora US. Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV). Expert Rev Vaccines 2022; 21:1851-1871. [PMID: 33435759 PMCID: PMC7989953 DOI: 10.1080/14760584.2021.1874925] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 01/08/2021] [Indexed: 01/12/2023]
Abstract
OBJECTIVES The group of human coronaviruses (HCoVs) consists of some highly pathogenic viruses that have caused several outbreaks in the past. The newly emerged strain of HCoV, the SARS-CoV-2 is responsible for the recent global pandemic that has already caused the death of hundreds of thousands of people due to the lack of effective therapeutic options. METHODS In this study, immunoinformatics methods were used to design epitope-based polyvalent vaccines which are expected to be effective against four different pathogenic strains of HCoV i.e., HCoV-OC43, HCoV-SARS, HCoV-MERS, and SARS-CoV-2. RESULTS The constructed vaccines consist of highly antigenic, non-allergenic, nontoxic, conserved, and non-homologous T-cell and B-cell epitopes from all the four viral strains. Therefore, they should be able to provide strong protection against all these strains. Protein-protein docking was performed to predict the best vaccine construct. Later, the MD simulation and immune simulation of the best vaccine construct also predicted satisfactory results. Finally, in silico cloning was performed to develop a mass production strategy of the vaccine. CONCLUSION If satisfactory results are achieved in further in vivo and in vitro studies, then the vaccines designed in this study might be effective as preventative measures against the selected HCoV strains.
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Affiliation(s)
- Bishajit Sarkar
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md. Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nafisa Nawal Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Umme Salma Zohora
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
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71
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Kar PP, Araveti PB, Kuriakose A, Srivastava A. Design of a multi-epitope protein as a subunit vaccine against lumpy skin disease using an immunoinformatics approach. Sci Rep 2022; 12:19411. [PMID: 36371522 PMCID: PMC9653426 DOI: 10.1038/s41598-022-23272-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Lumpy skin disease (LSD) is a transboundary viral disease of cattle that causes substantial economic loss globally. There is no specific treatment and subunit vaccine for this disease to date. Reports of the global spread of this disease are worrisome. We designed a multi-epitope protein using an immunoinformatics approach in this study. We analyzed the proteome of LSDV and found 32 structural/surface proteins. Four of these 32 proteins were predicted as antigenic and non-homologous to bovine and highly conserved in 26 LSDV isolates. The predicted B-cell epitopes and CTL epitopes were stitched together with the help of an AAY linker leading to the formation of a multi-epitope protein. The in silico study revealed that the modeled subunit vaccine candidate and TLR4 receptor interact with high affinity. This interaction was also found to be stable using a molecular dynamics simulation study. Our study demonstrates a leap towards developing a subunit vaccine against LSD.
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Affiliation(s)
- Prajna Parimita Kar
- grid.508105.90000 0004 1798 2821National Institute of Animal Biotechnology (NIAB), Gachibowli, Gopanpalli, Hyderabad, 500 032 Telangana India ,grid.502122.60000 0004 1774 5631Regional Centre for Biotechnology (RCB), Faridabad, 121 001 Haryana India
| | - Prasanna Babu Araveti
- grid.508105.90000 0004 1798 2821National Institute of Animal Biotechnology (NIAB), Gachibowli, Gopanpalli, Hyderabad, 500 032 Telangana India ,grid.502122.60000 0004 1774 5631Regional Centre for Biotechnology (RCB), Faridabad, 121 001 Haryana India
| | - Akshay Kuriakose
- grid.508105.90000 0004 1798 2821National Institute of Animal Biotechnology (NIAB), Gachibowli, Gopanpalli, Hyderabad, 500 032 Telangana India
| | - Anand Srivastava
- grid.508105.90000 0004 1798 2821National Institute of Animal Biotechnology (NIAB), Gachibowli, Gopanpalli, Hyderabad, 500 032 Telangana India ,grid.502122.60000 0004 1774 5631Regional Centre for Biotechnology (RCB), Faridabad, 121 001 Haryana India
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Characterization of the Interaction of Polymeric Micelles with siRNA: A Combined Experimental and Molecular Dynamics Study. Polymers (Basel) 2022; 14:polym14204409. [PMID: 36297986 PMCID: PMC9611052 DOI: 10.3390/polym14204409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
The simulation of large molecular systems remains a daunting challenge, which justifies the exploration of novel methodologies to keep computers as an ideal companion tool for everyday laboratory work. Whole micelles, bigger than 20 nm in size, formed by the self-assembly of hundreds of copolymers containing more than 50 repeating units, have until now rarely been simulated, due to a lack of computational power. Therefore, a flexible amphiphilic triblock copolymer (mPEG45-α-PLL10-PLA25) containing a total of 80 repeating units, has been emulated and synthesized to embody compactified nanoconstructs of over 900 assembled copolymers, sized between 80 and 100 nm, for siRNA complexing purposes. In this study, the tailored triblock copolymers containing a controlled number of amino groups, were used as a support model to address the binding behavior of STAT3-siRNA, in the formation of micelleplexes. Since increasingly complex drug delivery systems require an ever more optimized physicochemical characterization, a converging description has been implemented by a combination of experimentation and computational simulations. The computational data were advantageous in allowing for the assumption of an optimal N/P ratio favoring both conformational rigidifications of STAT3-siRNA with low competitive phenomena at the binding sites of the micellar carriers. These calculations were consistent with the experimental data showing that an N/P ratio of 1.5 resulted in a sufficient amount of complexed STAT3-siRNA with an electrical potential at the slipping plane of the nanopharmaceuticals, close to the charge neutralization.
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Cruz MR, Cristy S, Guha S, De Cesare GB, Evdokimova E, Sanchez H, Borek D, Miramón P, Yano J, Fidel PL, Savchenko A, Andes DR, Stogios PJ, Lorenz MC, Garsin DA. Structural and functional analysis of EntV reveals a 12 amino acid fragment protective against fungal infections. Nat Commun 2022; 13:6047. [PMID: 36229448 PMCID: PMC9562342 DOI: 10.1038/s41467-022-33613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/23/2022] [Indexed: 01/25/2023] Open
Abstract
Fungal pathogens are a continuing challenge due to few effective antifungals and a rise in resistance. In previous work, we described the inhibition of Candida albicans virulence following exposure to the 68 amino acid bacteriocin, EntV, secreted by Enterococcus faecalis. Here, to optimize EntV as a potential therapeutic and better understand its antifungal features, an X-ray structure is obtained. The structure consists of six alpha helices enclosing a seventh 16 amino acid helix (α7). The individual helices are tested for antifungal activity using in vitro and nematode infection assays. Interestingly, α7 retains antifungal, but not antibacterial activity and is also effective against Candida auris and Cryptococcus neoformans. Further reduction of α7 to 12 amino acids retains full antifungal activity, and excellent efficacy is observed in rodent models of C. albicans oropharyngeal, systemic, and venous catheter infections. Together, these results showcase EntV-derived peptides as promising candidates for antifungal therapeutic development.
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Affiliation(s)
- Melissa R. Cruz
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Shane Cristy
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Shantanu Guha
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Giuseppe Buda De Cesare
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Elena Evdokimova
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada
| | - Hiram Sanchez
- grid.28803.310000 0001 0701 8607Department of Medicine, University of Wisconsin, Madison, WI 53705 USA ,grid.28803.310000 0001 0701 8607Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53705 USA
| | - Dominika Borek
- grid.267313.20000 0000 9482 7121Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390 USA ,grid.267313.20000 0000 9482 7121Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390 USA
| | - Pedro Miramón
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Junko Yano
- grid.279863.10000 0000 8954 1233Department of Oral and Craniofacial Biology, Louisiana State University Health School of Dentistry, New Orleans, LA 70119 USA
| | - Paul L. Fidel
- grid.279863.10000 0000 8954 1233Department of Oral and Craniofacial Biology, Louisiana State University Health School of Dentistry, New Orleans, LA 70119 USA
| | - Alexei Savchenko
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada ,grid.22072.350000 0004 1936 7697Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB T2N 4N1 Canada ,Center for Structural Genomics of Infectious Diseases (CSGID), Chicago, IL USA
| | - David R. Andes
- grid.28803.310000 0001 0701 8607Department of Medicine, University of Wisconsin, Madison, WI 53705 USA ,grid.28803.310000 0001 0701 8607Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53705 USA
| | - Peter J. Stogios
- grid.17063.330000 0001 2157 2938BioZone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5 Canada
| | - Michael C. Lorenz
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Danielle A. Garsin
- grid.267308.80000 0000 9206 2401Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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74
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Fehér B, Gascoigne L, Giezen SN, Voets IK. Impact of arginine modified SNARE peptides on interactions with phospholipid bilayers and coiled-coil formation: A molecular dynamics study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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75
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Pirmoradi S. In-silico Designing of Immunogenic Construct Based on Peptide Epitopes Using Immuno-informatics Tools Against Tuberculosis. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2022. [DOI: 10.30699/ijmm.16.6.506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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76
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Fogarty CE, Suwansa-ard S, Phan P, McManus DP, Duke MG, Wyeth RC, Cummins SF, Wang T. Identification of Putative Neuropeptides That Alter the Behaviour of Schistosoma mansoni Cercariae. BIOLOGY 2022; 11:biology11091344. [PMID: 36138823 PMCID: PMC9495596 DOI: 10.3390/biology11091344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/31/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022]
Abstract
Elucidating the infectivity of Schistosoma mansoni, one of the main etiological agents of human schistosomiasis, requires an improved understanding of the behavioural mechanisms of cercariae, the non-feeding mammalian infective stage. This study investigated the presence and effect of cercariae-derived putative neuropeptides on cercarial behaviour when applied externally. Cercariae were peptidomically analysed and 11 neuropeptide precursor proteins, all of which were specific to the Schistosoma genus and most of which highly expressed in the cercarial stage, were identified in cercariae for the first time. Protein–protein interaction analysis predicted the interaction of various neuropeptide precursors (e.g., Sm-npp-30, Sm-npp-33, Sm-npp-35) with cercarial structural proteins (e.g., myosin heavy chain and titin). In total, nine putative neuropeptides, selected based on their high hydrophobicity and small size (~1 kilodalton), were tested on cercariae (3 mg/mL) in acute exposure (1 min) and prolonged exposure (360 min) behavioural bioassays. The peptides AAYMDLPW-NH2, NRKIDQSFYSYY-NH2, FLLALPSP-OH, and NYLWDTRL-NH2 stimulated acute increases in cercarial spinning, stopping, and directional change during active states. However, only NRKIDQSFYSYY-NH2 caused the same behavioural changes at a lower concentration (0.1 mg/mL). After prolonged exposure, AAYMDLPW-NH2 and NYLWDTRL-NH2 caused increasing passive behaviour and NRKIDQSFYSYY-NH2 caused increasing body-first and head-pulling movements. These findings characterise behaviour-altering novel putative neuropeptides, which may inform future biocontrol innovations to prevent human schistosomiasis.
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Affiliation(s)
- Conor E. Fogarty
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Saowaros Suwansa-ard
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Phong Phan
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Donald P. McManus
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Mary G. Duke
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Russell C. Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS B2G 2W5, Canada
| | - Scott F. Cummins
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
| | - Tianfang Wang
- Centre for Bioinnovation, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556, Australia
- Correspondence:
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Kang YJ, Yang WG, Chae WS, Kim DW, Kim SG, Rotaru H. Administration of 4‑hexylresorcinol increases p53‑mediated transcriptional activity in oral cancer cells with the p53 mutation. Oncol Rep 2022; 48:160. [PMID: 35856441 PMCID: PMC9350967 DOI: 10.3892/or.2022.8375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/30/2022] [Indexed: 11/30/2022] Open
Abstract
The p53 mutation is inherent in over 50% of human cancers. In head and neck squamous cell carcinoma, the p53 mutation is associated with a poor prognosis. 4-Hexylresorcinol (4HR) is a pharmacologic chaperone. The present study aimed to investigate the effect of 4HR on p53 transcriptional activity in oral carcinoma cells with p53 mutations. To identify conformational changes induced by 4HR administration, peptides including the DNA-binding domain from mutant and wild-type p53 were synthesized, and Fourier transform infrared spectroscopy was performed. To determine the effect of 4HR on p53 mutant carcinoma cells, western blot analysis, p53 transcriptional activity analysis, MTT assay and apoptosis immunocytochemistry were performed. The YD-15 cell line has a mutation in the DNA binding domain of p53 (Glu258Ala). When p53 Ala-258 was coupled by 4HR, the p53 Ala-258 structure lost its original conformation and approached a conformation similar to that of p53 Glu-258. In the cell experiments, 4HR administration to p53 mutant cells increased p53 transcriptional activity and the expression levels of apoptosis-associated proteins such as B-cell lymphoma 2 (BCL2), BCL2-associated X (BAX) and BCL2-associated agonist of cell death (BAD). Accordingly, 4HR administration on YD-15 cells decreased cell viability and increased apoptosis. In conclusion, 4HR is a potential substance for use in the recovery of loss-of-function in mutant p53 as a pharmacologic chaperone.
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Affiliation(s)
- Yei-Jin Kang
- Department of Oral and Maxillofacial Surgery, Gangneung‑Wonju National University, Gangneung, Gangwon-do 25457, Republic of Korea
| | - Won-Geun Yang
- Daegu Center, Korea Basic Science Institute, Daegu 41566, Republic of Korea
| | - Weon-Sik Chae
- Daegu Center, Korea Basic Science Institute, Daegu 41566, Republic of Korea
| | - Dae-Won Kim
- Department of Oral Biochemistry, College of Dentistry, Gangneung‑Wonju National University, Gangneung, Gangwon-do 25457, Republic of Korea
| | - Seong-Gon Kim
- Department of Oral and Maxillofacial Surgery, Gangneung‑Wonju National University, Gangneung, Gangwon-do 25457, Republic of Korea
| | - Horatiu Rotaru
- Department of Cranio‑Maxillofacial Surgery, 'Iuliu Hatieganu' University of Medicine and Pharmacy, Cluj‑Napoca 400000, Romania
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78
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Zhou H, Safdar B, Li H, Yang L, Ying Z, Liu X. Identification of a novel α-amylase inhibitory activity peptide from quinoa protein hydrolysate. Food Chem 2022; 403:134434. [DOI: 10.1016/j.foodchem.2022.134434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 10/14/2022]
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Moten D, Teneva I, Apostolova D, Batsalova T, Dzhambazov B. Molecular Mimicry of the Rheumatoid Arthritis-Related Immunodominant T-Cell Epitope within Type II Collagen (CII260-270) by the Bacterial L-Asparaginase. Int J Mol Sci 2022; 23:ijms23169149. [PMID: 36012429 PMCID: PMC9408948 DOI: 10.3390/ijms23169149] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 12/01/2022] Open
Abstract
The etiology of most autoimmune diseases, including rheumatoid arthritis (RA), remains unclear. Both genetic and environmental factors are believed to be involved in pathogenesis. Molecular mimicry is considered one of the mechanisms for the occurrence of autoimmune diseases. The aim of the study was to determine whether the bacterial peptide L-ASNase67-81, which mimics the immunodominant T-cell epitope CII259-273, can induce T-cell reactivity in blood samples from RA patients and healthy subjects through molecular mimicry. Using bioinformatic molecular modeling methods, we first determined whether the L-ASNase67-81 peptide binds to the HLA-DRB1*04:01 molecule and whether the formed MHCII–peptide complex interacts with the corresponding T-cell receptor. To validate the obtained results, leukocytes isolated from early RA patients and healthy individuals were stimulated in vitro with L-ASNase67-81 and CII259-273 peptides as well as with bacterial L-asparaginase or human type II collagen (huCII). The activated T cells (CD4+CD154+) were analyzed by flow cytometry (FACS), and the levels of cytokines produced (IL-2, IL-17A/F, and IFN-γ) were measured by ELISA. Our in silico analyses showed that the bacterial peptide L-ASNase67-81 binds better to HLA-DRB1*04:01 compared to the immunodominant T-cell epitope CII259-273, mimicking its structure and localization in the binding groove of MHCII. Six contact points were involved in the molecular interaction of the peptide with the TCR. FACS data showed that after in vitro stimulation with the L-ASNase67-81 peptide, the percentage of activated T cells (CD154+CD4+) was significantly increased in both cell cultures isolated from ERA patients and those isolated from healthy individuals, as higher values were observed for the ERA group (9.92 ± 0.23 vs. 4.82 ± 0.22). Furthermore, the ELISA assays revealed that after stimulation with L-ASNase67-81, a significant increase in the production of the cytokines IL-2, IL-17A/F, and IFN-γ was detected in the group of ERA patients. Our data showed that the bacterial L-ASNase67-81 peptide can mimic the immunodominant T-cell epitope CII259-273 and activate HLA-DRB1*04:01-restricted T cells as well as induce cytokine production in cells isolated from ERA patients. These results are the first to demonstrate that a specific bacterial antigen could play a role in the pathogenesis of RA, mimicking the immunodominant T-cell epitope from type II collagen.
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80
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Ramirez-Acosta K, Rosales-Fuerte IA, Perez-Sanchez JE, Nuñez-Rivera A, Juarez J, Cadena-Nava RD. Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2022; 13:699-711. [PMID: 35957673 PMCID: PMC9344557 DOI: 10.3762/bjnano.13.62] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/12/2022] [Indexed: 05/05/2023]
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently one of the most contagious viruses in existence and the cause of the worst pandemic in this century, COVID-19. SARS-CoV-2 infection begins with the recognition of the cellular receptor angiotensin converting enzyme-2 by its spike glycoprotein receptor-binding domain (RBD). Thus, the use of small peptides to neutralize the infective mechanism of SARS-CoV-2 through the RBD is an interesting strategy. The binding ability of 104 peptides (University of Nebraska Medical Center's Antimicrobial Peptide Database) to the RBD was assessed using molecular docking. Based on the molecular docking results, peptides with great affinity to the RBD were selected. The most common amino acids involved in the recognition of the RBD were identified to design novel peptides based on the number of hydrogen bonds that were formed. At physiological pH, these peptides are almost neutral and soluble in aqueous media. Interestingly, several peptides showed the capability to bind to the active surface area of the RBD of the Wuhan strain, as well as to the RBD of the Delta variant and other SARS-Cov-2 variants. Therefore, these peptides have promising potential in the treatment of the COVID-19 disease caused by different variants of SARS-CoV-2. This research work will be focused on the molecular docking of peptides by molecular dynamics, in addition to an analysis of the possible interaction of these peptides with physiological proteins. This methodology could be extended to design peptides that are active against other viruses.
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Affiliation(s)
- Kendra Ramirez-Acosta
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - Ivan A Rosales-Fuerte
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - J Eduardo Perez-Sanchez
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - Alfredo Nuñez-Rivera
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - Josue Juarez
- Departamento de Física, Universidad de Sonora, Blvd. Luis Encinas y Rosales, Hermosillo, Sonora, México
| | - Ruben D Cadena-Nava
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
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Soltan MA, Abdulsahib WK, Amer M, Refaat AM, Bagalagel AA, Diri RM, Albogami S, Fayad E, Eid RA, Sharaf SMA, Elhady SS, Darwish KM, Eldeen MA. Mining of Marburg Virus Proteome for Designing an Epitope-Based Vaccine. Front Immunol 2022; 13:907481. [PMID: 35911751 PMCID: PMC9334820 DOI: 10.3389/fimmu.2022.907481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/16/2022] [Indexed: 12/11/2022] Open
Abstract
Marburg virus (MARV) is one of the most harmful zoonotic viruses with deadly effects on both humans and nonhuman primates. Because of its severe outbreaks with a high rate of fatality, the world health organization put it as a risk group 4 pathogen and focused on the urgent need for the development of effective solutions against that virus. However, up to date, there is no effective vaccine against MARV in the market. In the current study, the complete proteome of MARV (seven proteins) was analyzed for the antigenicity score and the virulence or physiological role of each protein where we nominated envelope glycoprotein (Gp), Transcriptional activator (VP30), and membrane-associated protein (VP24) as the candidates for epitope prediction. Following that, a vaccine construct was designed based on CTL, HTL, and BCL epitopes of the selected protein candidates and to finalize the vaccine construct, several amino acid linkers, β-defensin adjuvant, and PADRE peptides were incorporated. The generated potential vaccine was assessed computationally for several properties such as antigenicity, allergenicity, stability, and other structural features where the outcomes of these assessments nominated this potential vaccine to be validated for its binding affinity with two molecular targets TLR-8 and TLR-4. The binding score and the stability of the vaccine-receptor complex, which was deeply studied through molecular docking-coupled dynamics simulation, supported the selection of our designed vaccine as a putative solution for MARV that should be validated through future wet-lab experiments. Here, we describe the computational approach for designing and analysis of this potential vaccine.
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Affiliation(s)
- Mohamed A. Soltan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismailia, Egypt
- *Correspondence: Mohamed A. Soltan, ; Muhammad Alaa Eldeen,
| | - Waleed K. Abdulsahib
- Department of pharmacology and Toxicology, College of Pharmacy, Al- Farahidi University, Baghdad, Iraq
| | - Mahmoud Amer
- Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmed M. Refaat
- Zoology Department, Faculty of Science, Minia University, El-Minia, Egypt
| | - Alaa A. Bagalagel
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem M. Diri
- Department of Pharmacy Practice, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Eman Fayad
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Refaat A. Eid
- Department of Pathology, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | | | - Sameh S. Elhady
- Department of Natural Products, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Muhammad Alaa Eldeen
- Cell Biology, Histology and Genetics Division, Zoology Department, Faculty of Science, Zagazig University, Zagazig, Egypt
- *Correspondence: Mohamed A. Soltan, ; Muhammad Alaa Eldeen,
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Jakhmola S, Sk MF, Chatterjee A, Jain K, Kar P, Jha HC. A plausible contributor to multiple sclerosis; presentation of antigenic myelin protein epitopes by major histocompatibility complexes. Comput Biol Med 2022; 148:105856. [PMID: 35863244 DOI: 10.1016/j.compbiomed.2022.105856] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/17/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) can be induced upon successful presentation of myelin antigens by MHC I/II. Antigenic similarity between the myelin and viral proteins may worsen the immunological responses. METHODOLOGY Antigenic regions within myelin proteins; PLP1, MBP, MOG, and MAG were analyzed using SVMTrip and EMBOSS. Homology search identified sequence similarity between the predicted host epitopes and viral proteins. NetMHCpan predicted MHC I/II binding followed by peptide-protein docking through the HPEPDOCK server. Thereafter we analyzed conformational flexibility and stability of 15 protein-peptide complexes based on high docking scores. The binding free energy was calculated using conventional (MD) and Gaussian accelerated molecular dynamics simulation. RESULTS PLP1, MBP, MAG and MOG contained numerous antigenic epitopes. MBP and MOG epitopes had sequence similarity to HHV-6 BALF5; EBNA1 and CMV glycoprotein M (gM), and EBV LMP2B, gp350/220; HHV-8 ORFs respectively. Many herpes virus proteins like tegument, envelope glycoproteins, and ORFs of EBV, CMV, HHV-6, and HHV-8 demonstrated sequence similarity with MAG and PLP1. Some antigenic peptides were also linear B-cell epitopes and influenced cytokine production by T-cell. MHC I allele HLA-B*57:01 bound to PLP1 peptide and HLA-A*68:02 bound to a MAG peptide strongly. MHC II alleles HLA-DRB1*04:05 and HLA-DR1*01:01 associated with MAG- and MOG-derived peptides, respectively, demonstrating high HPEPDOCK scores. MD simulations established stable binding of certain peptides with the MHC namely HLA-B*51:01-MBP(DYKSAHKGFKGVDAQGTLSKIFKL), HLA-B*57:01-PLP1(PDKFVGITYALTVVWLLVFACSAVPVYIYF), HLA-DR1*01:01-MOG(VEDPFYWVSPGVLVLLAVLPVLLLQITVGLVFLCLQYR) and HLA-DRB1*04:05-MAG(TWVQVSLLHFVPTREA). CONCLUSIONS Cross-reactivity between self-antigens and pathogen derived immunodominant epitopes may induce MS. Our study supported the role of specific MHC alleles as a contributing MS risk factor.
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Affiliation(s)
- Shweta Jakhmola
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India.
| | - Md Fulbabu Sk
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Akash Chatterjee
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Khushboo Jain
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India
| | - Parimal Kar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India.
| | - Hem Chandra Jha
- Infection Bioengineering Group, Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, India.
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83
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Lau CYJ, Benne N, Lou B, Zharkova O, Ting HJ, Ter Braake D, van Kronenburg N, Fens MH, Broere F, Hennink WE, Wang JW, Mastrobattista E. Modulating albumin-mediated transport of peptide-drug conjugates for antigen-specific Treg induction. J Control Release 2022; 348:938-950. [PMID: 35732251 DOI: 10.1016/j.jconrel.2022.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/22/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
The therapeutic potential of antigen-specific regulatory T cells (Treg) has been extensively explored, leading to the development of several tolerogenic vaccines. Dexamethasone-antigen conjugates represent a prominent class of tolerogenic vaccines that enable coordinated delivery of antigen and dexamethasone to target immune cells. The importance of nonspecific albumin association towards the biodistribution of antigen-adjuvant conjugates has gained increasing attention, by which hydrophobic and electrostatic interactions govern the association capacity. Using an ensemble of computational and experimental techniques, we evaluate the impact of charged residues adjacent to the drug conjugation site in dexamethasone-antigen conjugates (Dex-K/E4-OVA323, K: lysine, E: glutamate) towards their albumin association capacity and induction of antigen-specific Treg. We find that Dex-K4-OVA323 possesses a higher albumin association capacity than Dex-E4-OVA323, leading to enhanced liver distribution and antigen-presenting cell uptake. Furthermore, using an OVA323-specific adoptive-transfer mouse model, we show that Dex-K4-OVA323 selectively upregulated OVA323-specific Treg cells, whereas Dex-E4-OVA323 exerted no significant effect on Treg cells. Our findings serve as a guide to optimize the functionality of dexamethasone-antigen conjugate amid switching vaccine epitope sequences. Moreover, our study demonstrates that moderating the residues adjacent to the conjugation sites can serve as an engineering approach for future peptide-drug conjugate development.
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Affiliation(s)
- Chun Yin Jerry Lau
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Naomi Benne
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Bo Lou
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, 119228 Singapore, Singapore
| | - Olga Zharkova
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, 119228 Singapore, Singapore; Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Hui Jun Ting
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, 119228 Singapore, Singapore; Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore
| | - Daniëlle Ter Braake
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Nicky van Kronenburg
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Marcel H Fens
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Femke Broere
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, the Netherlands
| | - Wim E Hennink
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands
| | - Jiong-Wei Wang
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, 119228 Singapore, Singapore; Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599, Singapore; Department of Physiology, National University of Singapore, 2 Medical Drive, 117593 Singapore, Singapore; Nanomedicine Translational Research Programme, Centre for NanoMedicine, Yong Loo Lin School of Medicine, National University of Singapore, 30 Medical Drive, 117609 Singapore, Singapore.
| | - Enrico Mastrobattista
- Utrecht Institute for Pharmaceutical Sciences, Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands.
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84
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Efficient transdermal delivery of functional protein cargoes by a hydrophobic peptide MTD 1067. Sci Rep 2022; 12:10853. [PMID: 35760980 PMCID: PMC9237094 DOI: 10.1038/s41598-022-14463-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
The skin has a protective barrier against the external environment, making the transdermal delivery of active macromolecules very difficult. Cell-penetrating peptides (CPPs) have been accepted as useful delivery tools owing to their high transduction efficiency and low cytotoxicity. In this study, we evaluated the hydrophobic peptide, macromolecule transduction domain 1067 (MTD 1067) as a CPP for the transdermal delivery of protein cargoes of various sizes, including growth hormone-releasing hexapeptide-6 (GHRP-6), a truncated form of insulin-like growth factor-I (des(1-3)IGF-I), and platelet-derived growth factor BB (PDGF-BB). The MTD 1067-conjugated GHRP-6 (MTD-GHRP-6) was chemically synthesized, whereas the MTD 1067-conjugated des(1-3)IGF-I and PDGF-BB proteins (MTD-des(1-3)IGF-I and MTD-PDGF-BB) were generated as recombinant proteins. All the MTD 1067-conjugated cargoes exhibited biological activities identical or improved when compared to those of the original cargoes. The analysis of confocal microscopy images showed that MTD-GHRP-6, MTD-des(1-3)IGF-I, and MTD-PDGF-BB were detected at 4.4-, 18.8-, and 32.9-times higher levels in the dermis, respectively, compared to the control group without MTD. Furthermore, the MTD 1067-conjugated cargoes did not show cytotoxicity. Altogether, our data demonstrate the potential of MTD 1067 conjugation in developing functional macromolecules for cosmetics and drugs with enhanced transdermal permeability.
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85
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Imran MA, Islam MR, Saha A, Ferdousee S, Mishu MA, Ghosh A. Development of Multi-epitope Based Subunit Vaccine Against Crimean-Congo Hemorrhagic Fever Virus Using Reverse Vaccinology Approach. Int J Pept Res Ther 2022; 28:124. [PMID: 35789799 PMCID: PMC9244561 DOI: 10.1007/s10989-022-10430-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Md. Ashik Imran
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Md. Rubiath Islam
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Akash Saha
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Shahida Ferdousee
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Moshiul Alam Mishu
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
| | - Ajit Ghosh
- Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114 Bangladesh
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86
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Khandibharad S, Singh S. Artificial intelligence channelizing protein-peptide interactions pipeline for host-parasite paradigm in IL-10 and IL-12 reciprocity by SHP-1. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166466. [PMID: 35750267 DOI: 10.1016/j.bbadis.2022.166466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/12/2022]
Abstract
Identification of molecular targets in any cellular phenomena is a challenge and a path that one endeavors upon independently. We have identified a phosphatase SHP-1 as a point of intervention of IL-10 and IL-12 reciprocity in leishmaniasis. The therapeutic model that we have developed uniquely targets this protein but the pipeline in general can be used by the researchers for their unique targets. Naturally occurring peptides are well known for their biochemical participation in cellular functions hence we were motivated to use this uniqueness of physico-chemical properties of peptides conferred by amino acids through machine learning to channelize a mode of therapeutic exploration in infectious disease. Using computational approaches, we identified high order sequence conservation and similarity in SHP-1 sequence which was also evolutionarily conserved, complete structure of Mouse SHP-1 was predicted and validated, a unique motif of the same was identified against which library of synthetic peptides were designed and validated followed by screening the library by docking them with MuSHP-1 protein structure. Our findings showed 3 peptides had high binding affinity and in future can be validated using cell based and in vivo assays.
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Affiliation(s)
- Shweta Khandibharad
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, INDIA
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, INDIA.
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87
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Wang J, Sakai K, Kiwa T. Rational Design of Peptides Derived from Odorant-Binding Proteins for SARS-CoV-2-Related Volatile Organic Compounds Recognition. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123917. [PMID: 35745038 PMCID: PMC9229983 DOI: 10.3390/molecules27123917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Peptides are promising molecular-binding elements and have attracted great interest in novel biosensor development. In this study, a series of peptides derived from odorant-binding proteins (OBPs) were rationally designed for recognition of SARS-CoV-2-related volatile organic compounds (VOCs). Ethanol, nonanal, benzaldehyde, acetic acid, and acetone were selected as representative VOCs in the exhaled breath during the COVID-19 infection. Computational docking and prediction tools were utilized for OBPs peptide characterization and analysis. Multiple parameters, including the docking model, binding affinity, sequence specification, and structural folding, were investigated. The results demonstrated a rational, rapid, and efficient approach for designing breath-borne VOC-recognition peptides, which could further improve the biosensor performance for pioneering COVID-19 screening and many other applications.
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Affiliation(s)
- Jin Wang
- Correspondence: ; Tel.: +81-86-251-8129
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88
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Sohn YS, Losub-Amir A, Cardenas AE, Karmi O, Yahana MD, Gruman T, Rowland L, Marjault HB, Webb LJ, Mittler R, Elber R, Friedler A, Nechushtai R. A peptide-derived strategy for specifically targeting the mitochondria and ER of cancer cells: a new approach in fighting cancer. Chem Sci 2022; 13:6929-6941. [PMID: 35774163 PMCID: PMC9200128 DOI: 10.1039/d2sc01934e] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/18/2022] [Indexed: 12/13/2022] Open
Abstract
An effective anti-cancer therapy should exclusively target cancer cells and trigger in them a broad spectrum of cell death pathways that will prevent avoidance. Here, we present a new approach in cancer therapy that specifically targets the mitochondria and ER of cancer cells. We developed a peptide derived from the flexible and transmembrane domains of the human protein NAF-1/CISD2. This peptide (NAF-144-67) specifically permeates through the plasma membranes of human epithelial breast cancer cells, abolishes their mitochondria and ER, and triggers cell death with characteristics of apoptosis, ferroptosis and necroptosis. In vivo analysis revealed that the peptide significantly decreases tumor growth in mice carrying xenograft human tumors. Computational simulations of cancer vs. normal cell membranes reveal that the specificity of the peptide to cancer cells is due to its selective recognition of their membrane composition. NAF-144-67 represents a promising anti-cancer lead compound that acts via a unique mechanism.
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Affiliation(s)
- Yang Sung Sohn
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
| | - Anat Losub-Amir
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
| | - Alfredo E Cardenas
- Institute for Computational Engineering and Science and Department of Chemistry, University of Texas at Austin Austin Texas 78712 USA
| | - Ola Karmi
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center University of Missouri. 1201 Rollins St Columbia MO 65201 USA
| | - Merav Darash Yahana
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
| | - Tal Gruman
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
| | - Linda Rowland
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center University of Missouri. 1201 Rollins St Columbia MO 65201 USA
| | - Henri-Baptiste Marjault
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
| | - Lauren J Webb
- Department of Chemistry, The University of Texas at Austin 2506 Speedway STOP A5300 Austin TX 78712 USA
| | - Ron Mittler
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center University of Missouri. 1201 Rollins St Columbia MO 65201 USA
| | - Ron Elber
- Institute for Computational Engineering and Science and Department of Chemistry, University of Texas at Austin Austin Texas 78712 USA
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram Jerusalem 9190401 Israel
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89
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Identification and Characterization of a Potential Antimicrobial Peptide Isolated from Soil Brevibacillus sp. WUL10 and Its Activity against MRSA Pathogens. Trop Med Infect Dis 2022; 7:tropicalmed7060093. [PMID: 35736972 PMCID: PMC9228811 DOI: 10.3390/tropicalmed7060093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 11/17/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a severe threat to public health globally. The development of novel agents has encountered the repeated mechanism of drug resistance. This study aimed to investigate an anti-MRSA substance isolated from a promising soil bacterium. The result showed that an isolate (WUL10) was in the Brevibacillus genus. The minimum inhibitory concentration (MIC) of the purified substance was 1 µg/mL against S. aureus TISTR 517 and MRSA strains. This substance showed the bactericidal effect at the concentration of 1–2 µg/mL against these bacterial indicators. The activity of the substance retained more than 95% when encountering high temperatures and a wide range of pH, but it was sensitive to proteolytic enzymes and SDS. It was identified as a novel antimicrobial peptide (KVLVKYLGGLLKLAALMV-COOH) with the predicted structure of α-helix. The substance could rupture the cell wall of the tested pathogen. MIC and MBC of the synthesized peptide were 16 and 64 µg/mL, respectively. The difference in the activity between the isolated and synthetic peptides might be from the synergistic effects of other AMPs in the purified substance. This novel AMP would provide an advantage for further development of anti-MRSA substances to manage the situation of antibiotic resistance.
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90
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Anti-tumor and anti-metastatic activity of the FGF2 118-126 fragment dependent on the loop structure. Biochem J 2022; 479:1285-1302. [PMID: 35638868 DOI: 10.1042/bcj20210830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 11/17/2022]
Abstract
Fibroblast Growth Factor /FGF Receptor 1 (FGF2/FGFR1) system regulates the growth and metastasis of different cancers. Inhibition of this signaling pathway is an attractive target for cancer therapy. Here, we aimed to reproduce the 118-126 fragment of FGF2 to interfere with the FGF2-FGFR1 interaction. To determine whether the loop structure affects the function of this fragment, we compared cyclic (disulfide-bonded) and linear peptide variants. The cyclic peptide (referred to as BGF1) effectively inhibited the FGF2-induced proliferation of HUVECs, 4T1 mammary carcinoma, U87 glioblastoma, and SKOV3 ovarian carcinoma cells. It led to apoptosis induction in HUVECs, whereas the linear peptide (referred to as BGF2) was ineffective. In a murine 4T1 tumor model, BGF1 inhibited tumor growth more effectively than Avastin and increased animals' survival without causing weight loss, but the linear peptide BGF2 had no significant anti-tumor effects. According to immunohistochemical studies, the anti-tumor properties of BGF1 were associated with suppression of tumor cell proliferation (Ki-67 expression), angiogenesis (CD31 expression), and apoptosis induction (as was shown by increased p53 expression and TUNEL staining and decreased Bcl-2 expression). The potential of BGF1 to suppress tumor invasion was indicated by quantitative analysis of the metastasis-related proteins, including FGFR1, pFGFR1, NF-κB, p-NF-κB, MMP-9, E-cadherin, N-cadherin, and Vimentin, and supported by small animal positron emission tomography (PET) used 18Fluorodeoxyglucose (18F-FDG). These results demonstrate that the functional properties of the 118-126 region of FGF2 depend on the loop structure and the peptide derived from this fragment encourages further preclinical investigations.
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91
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Parra ALC, Bezerra LP, Shawar DE, Neto NAS, Mesquita FP, da Silva GO, Souza PFN. Synthetic antiviral peptides: a new way to develop targeted antiviral drugs. Future Virol 2022. [DOI: 10.2217/fvl-2021-0308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The global concern over emerging and re-emerging viral infections has spurred the search for novel antiviral agents. Peptides with antiviral activity stand out, by overcoming limitations of the current drugs utilized, due to their biocompatibility, specificity and effectiveness. Synthetic peptides have been shown to be viable alternatives to natural peptides due to several difficulties of using of the latter in clinical trials. Various platforms have been utilized by researchers to predict the most effective peptide sequences against HIV, influenza, dengue, MERS and SARS. Synthetic peptides are already employed in the treatment of HIV infection. The novelty of this study is to discuss, for the first time, the potential of synthetic peptides as antiviral molecules. We conclude that synthetic peptides can act as new weapons against viral threats to humans.
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Affiliation(s)
- Aura LC Parra
- Department of Biochemistry & Molecular Biology, Federal University of Ceara, Fortaleza, Ceara, 60440-554, Brazil
| | - Leandro P Bezerra
- Department of Biochemistry & Molecular Biology, Federal University of Ceara, Fortaleza, Ceara, 60440-554, Brazil
| | - Dur E Shawar
- Department of Biochemistry & Molecular Biology, Federal University of Ceara, Fortaleza, Ceara, 60440-554, Brazil
| | - Nilton AS Neto
- Department of Biochemistry & Molecular Biology, Federal University of Ceara, Fortaleza, Ceara, 60440-554, Brazil
| | - Felipe P Mesquita
- Drug Research & Development Center (NPDM), Federal University of Ceará, Cel. Nunes de Melo, Rodolfo Teófilo, 1000, Fortaleza, Brazil
| | - Gabrielly O da Silva
- Department of Biochemistry & Molecular Biology, Federal University of Ceara, Fortaleza, Ceara, 60440-554, Brazil
| | - Pedro FN Souza
- Department of Biochemistry & Molecular Biology, Federal University of Ceara, Fortaleza, Ceara, 60440-554, Brazil
- Drug Research & Development Center (NPDM), Federal University of Ceará, Cel. Nunes de Melo, Rodolfo Teófilo, 1000, Fortaleza, Brazil
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92
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Hong FU, Castro M, Linse K. Tumor specifically internalizing peptide ‘HN-1’: Targeting the putative receptor retinoblastoma-regulated discoidin domain receptor 1 involved in metastasis. World J Clin Oncol 2022; 13:323-338. [PMID: 35662982 PMCID: PMC9153073 DOI: 10.5306/wjco.v13.i5.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/06/2021] [Accepted: 04/22/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Less than 0.5% of intravenously injected drugs reach tumors, contributing to side effects. To limit damage to healthy cells, various delivery vectors have been formulated; yet, previously developed vectors suffer from poor penetration into solid tumors. This issue was resolved by the discovery of HN-1 peptide isolated via biopanning a phage-display library. HN-1 targets human head and neck squamous cell carcinoma (HNSCC) (breast, thyroid; potentially lung, cervix, uterine, colon cancer), translocates across the cell membrane, and efficiently infiltrates solid tumors. HN-1 peptide has been conjugated to various anticancer drugs and imaging agents though the identity of its receptor remained enigmatic.
AIM To decipher the clues that pointed to retinoblastoma (Rb)-regulated discoidin-domain receptor 1 as the putative receptor for HN-1 is described.
METHODS HN-1 peptide was synthesized and purified using reverse-phase high-performance liquid chromatography and gel electrophoresis. The predicted mass was confirmed by mass spectroscopy. To image the 3-dimensional structure of HN-1 peptide, PyMOL was used. Molecular modeling was also performed with PEP-FOLD3 software via RPBS bioinformatics web portal (INSERM, France). The immunohistochemistry results of discoidin domain receptor 1 (DDR1) protein were obtained from the publicly accessible database in the Human Protein Atlas portal, which contained the images of immunohistochemically labeled human cancers and the corresponding normal tissues.
RESULTS The clues that led to DDR1 involved in metastasis as the putative receptor mediating HN-1 endocytosis are the following: (1) HN-1 is internalized in phosphate-buffered saline and its uptake is competitively inhibited; (2) HN-1 (TSPLNIHNGQKL) exhibits similarity with a stretch of amino acids in alpha5 beta3 integrin (KLLITIHDRKEF). Aside from two identical residues (Ile-His) in the middle, the overall distribution of polar and nonpolar residues throughout the sequences is nearly identical. As HN-1 sequence lacks the Arg-Gly-Asp motif recognized by integrins, HN-1 may interact with an "integrin-like" molecule. The tertiary structure of both peptides showed similarity at the 3-dimensional level; (3) HN-1 is internalized by attached cells but not by suspended cells. As culture plates are typically coated with collagen, collagen-binding receptor (expressed by adherent but not suspended cells) may represent the receptor for HN-1; (4) DDR1 is highly expressed in head and neck cancer (or breast cancer) targeted by HN-1; (5) Upon activation by collagen, DDR1 becomes internalized and compartmentalized in endosomes consistent with the determination of ’energy-dependent clathrin-mediated endocytosis’ as the HN-1 entry route and the identification of HN-1 entrapped vesicles as endosomes; and (6) DDR1 is essential for the development of mammary glands consistent with the common embryonic lineage rationale used to identify breast cancer as an additional target of HN-1. In summary, collagen-activated tyrosine kinase receptor DDR1 overexpressed in HNSCC assumes a critical role in metastasis. Further studies are warranted to assess HN-1 peptide’s interaction with DDR1 and the therapeutic potential of treating metastatic cancer. Additionally, advances in delivery (conformation, endocytic mechanism, repertoire of targeted cancers of HN-1 peptide), tracking (HN-1 conjugated imaging agents), and activity (HN-1 conjugated therapeutic agents) are described.
CONCLUSION The discovery of DDR1 as HN-1 peptide’s putative receptor represents a significant advance as it enables identification of metastatic cancers or clinical application of previously developed therapeutics to block metastasis.
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Affiliation(s)
- Frank-Un Hong
- Research & Development, Bio-Synthesis, Inc., Lewisville, TX 75057, United States
| | - Miguel Castro
- Research & Development, Bio-Synthesis, Inc., Lewisville, TX 75057, United States
| | - Klaus Linse
- Research & Development, Bio-Synthesis, Inc., Lewisville, TX 75057, United States
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93
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Toldrá F, Mora L. Peptidomics as a useful tool in the follow-up of food bioactive peptides. ADVANCES IN FOOD AND NUTRITION RESEARCH 2022; 100:1-47. [PMID: 35659349 DOI: 10.1016/bs.afnr.2022.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
There is an intense research activity on bioactive peptides derived from food proteins in view of their health benefits for consumers. However, their identification is quite challenging as a consequence of their small size and low abundance in complex matrices such as foods or hydrolyzates. Recent advances in peptidomics and bioinformatics are getting improved sensitivity and accuracy and therefore such tools are contributing to the development of sophisticated methodologies for the identification and quantification of peptides. These developments are very useful for the follow-up of peptides released through proteolysis either in the food itself through the action of endogenous peptidases during processing stages like fermentation, drying or ripening, or from food proteins hydrolyzed by commercial peptidases or microorganisms with proteolytic activity. This chapter is presenting the latest advances in peptidomics and its use for the identification and quantification of peptides, and as a useful tool for controlling the proteolysis phenomena in foods and protein hydrolyzates.
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Affiliation(s)
- Fidel Toldrá
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Paterna, Spain.
| | - Leticia Mora
- Instituto de Agroquímica y Tecnología de Alimentos (CSIC), Paterna, Spain
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94
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Marzella DF, Parizi FM, van Tilborg D, Renaud N, Sybrandi D, Buzatu R, Rademaker DT, ‘t Hoen PAC, Xue LC. PANDORA: A Fast, Anchor-Restrained Modelling Protocol for Peptide: MHC Complexes. Front Immunol 2022; 13:878762. [PMID: 35619705 PMCID: PMC9127323 DOI: 10.3389/fimmu.2022.878762] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 11/21/2022] Open
Abstract
Deeper understanding of T-cell-mediated adaptive immune responses is important for the design of cancer immunotherapies and antiviral vaccines against pandemic outbreaks. T-cells are activated when they recognize foreign peptides that are presented on the cell surface by Major Histocompatibility Complexes (MHC), forming peptide:MHC (pMHC) complexes. 3D structures of pMHC complexes provide fundamental insight into T-cell recognition mechanism and aids immunotherapy design. High MHC and peptide diversities necessitate efficient computational modelling to enable whole proteome structural analysis. We developed PANDORA, a generic modelling pipeline for pMHC class I and II (pMHC-I and pMHC-II), and present its performance on pMHC-I here. Given a query, PANDORA searches for structural templates in its extensive database and then applies anchor restraints to the modelling process. This restrained energy minimization ensures one of the fastest pMHC modelling pipelines so far. On a set of 835 pMHC-I complexes over 78 MHC types, PANDORA generated models with a median RMSD of 0.70 Å and achieved a 93% success rate in top 10 models. PANDORA performs competitively with three pMHC-I modelling state-of-the-art approaches and outperforms AlphaFold2 in terms of accuracy while being superior to it in speed. PANDORA is a modularized and user-configurable python package with easy installation. We envision PANDORA to fuel deep learning algorithms with large-scale high-quality 3D models to tackle long-standing immunology challenges.
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Affiliation(s)
- Dario F. Marzella
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Farzaneh M. Parizi
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Derek van Tilborg
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
- Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nicolas Renaud
- Natural Sciences and Engineering section, Netherlands eScience Center, Amsterdam, Netherlands
| | - Daan Sybrandi
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, Netherlands
| | - Rafaella Buzatu
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Daniel T. Rademaker
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Peter A. C. ‘t Hoen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
| | - Li C. Xue
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, Netherlands
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95
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Laustsen A, Gless BH, Jenkins TP, Meyhoff-Madsen M, Bjärtun J, Munk AS, Oscoz S, Fernández J, Gutiérrez JM, Lomonte B, Lohse B. In Vivo Neutralization of Myotoxin II, a Phospholipase A 2 Homologue from Bothrops asper Venom, Using Peptides Discovered via Phage Display Technology. ACS OMEGA 2022; 7:15561-15569. [PMID: 35571794 PMCID: PMC9096979 DOI: 10.1021/acsomega.2c00280] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
Many snake venom toxins cause local tissue damage in prey and victims, which constitutes an important pathology that is challenging to treat with existing antivenoms. One of the notorious toxins that causes such effects is myotoxin II present in the venom of the Central and Northern South American viper, Bothrops asper. This Lys49 PLA2 homologue is devoid of enzymatic activity and causes myotoxicity by disrupting the cell membranes of muscle tissue. To improve envenoming therapy, novel approaches are needed, warranting the discovery and development of inhibitors that target key toxins that are currently difficult to neutralize. Here, we report the identification of a new peptide (JB006), discovered using phage display technology, that is capable of binding to and neutralizing the toxic effects of myotoxin II in vitro and in vivo. Through computational modeling, we further identify hypothetical binding interactions between the toxin and the peptide to enable further development of inhibitors that can neutralize myotoxin II.
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Affiliation(s)
- Andreas
H. Laustsen
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Lyngby DK-2800, Denmark
| | - Bengt H. Gless
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Copenhagen DK-2100, Denmark
| | - Timothy P. Jenkins
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Lyngby DK-2800, Denmark
| | - Maria Meyhoff-Madsen
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Copenhagen DK-2100, Denmark
| | - Johanna Bjärtun
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Copenhagen DK-2100, Denmark
| | - Andreas S. Munk
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Lyngby DK-2800, Denmark
| | - Saioa Oscoz
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, Lyngby DK-2800, Denmark
| | - Julián Fernández
- Instituto
Clodomiro Picado, Faculty of Microbiology, University of Costa Rica, San
José 11501-2060, Costa Rica
| | - José María Gutiérrez
- Instituto
Clodomiro Picado, Faculty of Microbiology, University of Costa Rica, San
José 11501-2060, Costa Rica
| | - Bruno Lomonte
- Instituto
Clodomiro Picado, Faculty of Microbiology, University of Costa Rica, San
José 11501-2060, Costa Rica
| | - Brian Lohse
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Copenhagen DK-2100, Denmark
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Kaushal N, Jain S, Baranwal M. Computational design of immunogenic peptide constructs comprising multiple HLA restricted Dengue virus envelope epitopes. J Mol Recognit 2022; 35:e2961. [PMID: 35514257 DOI: 10.1002/jmr.2961] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/01/2022] [Accepted: 05/02/2022] [Indexed: 11/09/2022]
Abstract
Dengue virus (DENV) is endemic in 100 countries with ability to impact nearly 50% of world population. DENV envelope (E) protein is responsible for viral attachment to host cells and has been target of various countermeasure development efforts. The current study focuses on a consensus computational approach to identify cross-reactive, immunogenic DENV-2 E peptides displaying promiscuity with a wide array of HLA molecules. Four conserved peptides (FP-1, FP-2, FP-3 and FP-4) containing multiple CD8+ and CD4+ T cell epitopes were identified by employment of various immunoinformatics tools. FP-1, FP-2, FP-3 and FP-4 were estimated to bind with 227, 1787, 1008 and 834 HLA alleles respectively. RMSD values obtained by Molecular docking (CABS-Dock) with 20 HLA alleles (10 each of HLA class I and II) resulted into comparable RMSD values of identified epitopes with native peptides which represents the natural presentation of epitopes to HLA molecules. These peptides were also found to be part of previous experimentally validated immunogenic peptides. Further, a dengue immunogenic peptide construct was generated by linking the four peptides, an adjuvant and a 6x histidine tag. The construct showed strong binding and stability with Toll-like receptor (TLR4). Collectively, these results provide strong evidence in the support of the immunogenic potential of the dengue immunogenic peptide construct. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Neha Kaushal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Sahil Jain
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India.,University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
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97
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Efficient 3D conformer generation of cyclic peptides formed by a disulfide bond. J Cheminform 2022; 14:26. [PMID: 35505401 PMCID: PMC9066754 DOI: 10.1186/s13321-022-00605-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 04/03/2022] [Indexed: 02/07/2023] Open
Abstract
Cyclic peptides formed by disulfide bonds have been one large group of common drug candidates in drug development. Structural information of a peptide is essential to understand its interaction with its target. However, due to the high flexibility of peptides, it is difficult to sample the near-native conformations of a peptide. Here, we have developed an extended version of our MODPEP approach, named MODPEP2.0, to fast generate the conformations of cyclic peptides formed by a disulfide bond. MODPEP2.0 builds the three-dimensional (3D) structures of a cyclic peptide from scratch by assembling amino acids one by one onto the cyclic fragment based on the constructed rotamer and cyclic backbone libraries. Being tested on a data set of 193 diverse cyclic peptides, MODPEP2.0 obtained a considerable advantage in both accuracy and computational efficiency, compared with other sampling algorithms including PEP-FOLD, ETKDG, and modified ETKDG (mETKDG). MODPEP2.0 achieved a high sampling accuracy with an average C\documentclass[12pt]{minimal}
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\begin{document}$$\alpha$$\end{document}α RMSD of 2.20 Å and 1.66 Å when 10 and 100 conformations were considered, respectively, compared with 3.41 Å and 2.62 Å for PEP-FOLD, 3.44 Å and 3.16 Å for ETKDG, 3.09 Å and 2.72 Å for mETKDG. MODPEP2.0 also reproduced experimental peptide structures for 81.35% of the test cases when an ensemble of 100 conformations were considered, compared with 54.95%, 37.50% and 50.00% for PEP-FOLD, ETKDG, and mETKDG. MODPEP2.0 is computationally efficient and can generate 100 peptide conformations in one second. MODPEP2.0 will be useful in sampling cyclic peptide structures and modeling related protein-peptide interactions, facilitating the development of cyclic peptide drugs.
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98
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Houston S, Schovanek E, Conway KME, Mustafa S, Gomez A, Ramaswamy R, Haimour A, Boulanger MJ, Reynolds LA, Cameron CE. Identification and Functional Characterization of Peptides With Antimicrobial Activity From the Syphilis Spirochete, Treponema pallidum. Front Microbiol 2022; 13:888525. [PMID: 35722306 PMCID: PMC9200625 DOI: 10.3389/fmicb.2022.888525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/08/2022] [Indexed: 12/02/2022] Open
Abstract
The etiological agent of syphilis, Treponema pallidum ssp. pallidum, is a highly invasive “stealth” pathogen that can evade the host immune response and persist within the host for decades. This obligate human pathogen is adept at establishing infection and surviving at sites within the host that have a multitude of competing microbes, sometimes including pathogens. One survival strategy employed by bacteria found at polymicrobial sites is elimination of competing microorganisms by production of antimicrobial peptides (AMPs). Antimicrobial peptides are low molecular weight proteins (miniproteins) that function directly via inhibition and killing of microbes and/or indirectly via modulation of the host immune response, which can facilitate immune evasion. In the current study, we used bioinformatics to show that approximately 7% of the T. pallidum proteome is comprised of miniproteins of 150 amino acids or less with unknown functions. To investigate the possibility that AMP production is an unrecognized defense strategy used by T. pallidum during infection, we developed a bioinformatics pipeline to analyze the complement of T. pallidum miniproteins of unknown function for the identification of potential AMPs. This analysis identified 45 T. pallidum AMP candidates; of these, Tp0451a and Tp0749 were subjected to further bioinformatic analyses to identify AMP critical core regions (AMPCCRs). Four potential AMPCCRs from the two predicted AMPs were identified and peptides corresponding to these AMPCCRs were experimentally confirmed to exhibit bacteriostatic and bactericidal activity against a panel of biologically relevant Gram-positive and Gram-negative bacteria. Immunomodulation assays performed under inflammatory conditions demonstrated that one of the AMPCCRs was also capable of differentially regulating expression of two pro-inflammatory chemokines [monocyte chemoattractant protein-1 (MCP-1) and interleukin-8 (IL-8)]. These findings demonstrate proof-of-concept for our developed AMP identification pipeline and are consistent with the novel concept that T. pallidum expresses AMPs to defend against competing microbes and modulate the host immune response.
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Affiliation(s)
- Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Ethan Schovanek
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Kate M. E. Conway
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Sarah Mustafa
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Alloysius Gomez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Raghavendran Ramaswamy
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Ayman Haimour
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Martin J. Boulanger
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Lisa A. Reynolds
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Caroline E. Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States
- *Correspondence: Caroline E. Cameron,
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99
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Mastouri M, Baachaoui S, Mosbah A, Raouafi N. In silico screening for oligopeptides useful as capture and reporting probes for interleukin-6 biosensing. RSC Adv 2022; 12:13003-13013. [PMID: 35497015 PMCID: PMC9049833 DOI: 10.1039/d2ra01496c] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/24/2022] [Indexed: 11/21/2022] Open
Abstract
IL-6 is an important interleukin associated with inflammation and several diseases such as cancer. Evaluation of its levels in human blood sera is a critical step for an accurate diagnosis of the diseases. Our goal is to design peptides that can selectively bind in different poses with good affinities to IL-6. For this purpose, we started from the crystal structures of different IL-6/protein complexes available in the Protein Data Bank (PDB) to select short peptides in the interaction zones, in which we intentionally introduced point mutations to increase their stability and affinity. To examine their usefulness as capture and reporting probes for the IL-6 biosensing, the five peptides and their interaction with IL-6 were studied in saline aqueous solution. Molecular docking, MD, and MM-PBSA were used to investigate the affinity and stability of these complexes. The conformational changes, the distance between the mass centers, the gyration radii, and the numbers of hydrogen bonds were analyzed to select the most suitable candidates. Three peptides, namely CTE17, CAY15 and CSE25, have the highest affinities presenting significant numbers of residues that have contact frequencies greater than 50% of simulation run time and are the most promising candidates. CTE17 and CSE25 showed they can form a stable sandwich with the target protein. For sake of comparison, we examined the previously known peptides (FND20, INL19 and CEK17) having affinity to IL-6 and the affinity of the lead i.e. CSE25 to two other interleukin family members (IL-4 and to IL-10).
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Affiliation(s)
- Mohamed Mastouri
- Sensors and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Sabrine Baachaoui
- Sensors and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
| | - Amor Mosbah
- BVBGR Laboratory (LR11ES31), ISBST, Biotechnopole Sidi Thabet, University of Manouba Ariana 2020 Tunisia
| | - Noureddine Raouafi
- Sensors and Biosensors Group, Laboratory of Analytical Chemistry & Electrochemistry (LR99ES15), Faculty of Science, University of Tunis El Manar 2092 Tunis El Manar Tunisia
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Gupta E, Mishra RK, Kumar Niraj RR. Identification of Potential Vaccine Candidates Against SARS-CoV-2 to Fight COVID-19: Reverse Vaccinology Approach. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022; 3:e32401. [PMID: 35506029 PMCID: PMC9048139 DOI: 10.2196/32401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/02/2021] [Accepted: 12/27/2021] [Indexed: 01/23/2023]
Abstract
Background The recent emergence of COVID-19 has caused an immense global public health crisis. The etiological agent of COVID-19 is the novel coronavirus SARS-CoV-2. More research in the field of developing effective vaccines against this emergent viral disease is indeed a need of the hour. Objective The aim of this study was to identify effective vaccine candidates that can offer a new milestone in the battle against COVID-19. Methods We used a reverse vaccinology approach to explore the SARS-CoV-2 genome among strains prominent in India. Epitopes were predicted and then molecular docking and simulation were used to verify the molecular interaction of the candidate antigenic peptide with corresponding amino acid residues of the host protein. Results A promising antigenic peptide, GVYFASTEK, from the surface glycoprotein of SARS-CoV-2 (protein accession number QIA98583.1) was predicted to interact with the human major histocompatibility complex (MHC) class I human leukocyte antigen (HLA)-A*11-01 allele, showing up to 90% conservancy and a high antigenicity value. After vigorous analysis, this peptide was predicted to be a suitable epitope capable of inducing a strong cell-mediated immune response against SARS-CoV-2. Conclusions These results could facilitate selecting SARS-CoV-2 epitopes for vaccine production pipelines in the immediate future. This novel research will certainly pave the way for a fast, reliable, and effective platform to provide a timely countermeasure against this dangerous virus responsible for the COVID-19 pandemic.
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Affiliation(s)
- Ekta Gupta
- Dr. B. Lal Institute of Biotechnology Jaipur India
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