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Awad N, Mohamed RH, Ghoneim NI, Elmehrath AO, El-Badri N. Immunoinformatics approach of epitope prediction for SARS-CoV-2. J Genet Eng Biotechnol 2022; 20:60. [PMID: 35441904 PMCID: PMC9019534 DOI: 10.1186/s43141-022-00344-1] [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: 08/10/2021] [Accepted: 03/30/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND The novel coronavirus (SARS-CoV-2) caused lethal infections worldwide during an unprecedented pandemic. Identification of the candidate viral epitopes is the first step in the design of vaccines against the viral infection. Several immunoinformatic approaches were employed to identify the SARS-CoV-2 epitopes that bind specifically with the major histocompatibility molecules class I (MHC-I). We utilized immunoinformatic tools to analyze the whole viral protein sequences, to identify the SARS-CoV-2 epitopes responsible for binding to the most frequent human leukocyte antigen (HLA) alleles in the Egyptian population. These alleles were also found with high frequency in other populations worldwide. RESULTS Molecular docking approach showed that using the co-crystallized MHC-I and T cell receptor (TCR) instead of using MHC-I structure only, significantly enhanced docking scores and stabilized the conformation, as well as the binding affinity of the identified SARS-CoV-2 epitopes. Our approach directly predicts 7 potential vaccine subunits from the available SARS-CoV-2 spike and ORF1ab protein sequence. This prediction has been confirmed by published experimentally validated and in silico predicted spike epitope. On the other hand, we predicted novel epitopes (RDLPQGFSA and FCLEASFNY) showing high docking scores and antigenicity response with both MHC-I and TCR. Moreover, antigenicity, allergenicity, toxicity, and physicochemical properties of the predicted SARS-CoV-2 epitopes were evaluated via state-of-the-art bioinformatic approaches, showing high efficacy of the proposed epitopes as a vaccine candidate. CONCLUSION Our predicted SARS-CoV-2 epitopes can facilitate vaccine development to enhance the immunogenicity against SARS-CoV-2 and provide supportive data for further experimental validation. Our proposed molecular docking approach of exploiting both MHC and TCR structures can be used to identify potential epitopes for most microbial pathogens, provided the crystal structure of MHC co-crystallized with TCR.
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Affiliation(s)
- Nourelislam Awad
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.,Center of Informatics Sciences, Nile University, Giza, Egypt
| | - Rania Hassan Mohamed
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.,Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Nehal I Ghoneim
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt
| | - Ahmed O Elmehrath
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.,Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nagwa El-Badri
- Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City of Science and Technology, Giza, Egypt.
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2
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Fu S, Liu H, Huang Y, Wang J, Qian K, Ding M, Ye J. Molecular cloning, characterization and expression analysis of major histocompatibility complex class I alpha gene of pufferfish (Takifugu obscurus). JOURNAL OF FISH DISEASES 2021; 44:613-625. [PMID: 33220160 DOI: 10.1111/jfd.13307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 06/11/2023]
Abstract
The major histocompatibility complex (MHC) genes play a key role in immune response in vertebrates. In this study, an MHC I alpha homolog gene (PfMHC Ⅰα) from pufferfish (Takifugu obscurus) was identified and its subcellular localization and expression patterns of PfMHC Ⅰα after challenge in vivo and in vitro were analysed. The open reading frame of PfMHC Ⅰα was 1,089 bp in length, encoding 362 aa. The immunofluorescence result revealed that PfMHC Ⅰα was presented on the membrane of lymphocytes. qRT-PCR analysis indicated that PfMHC Ⅰα was expressed in all examined tissues, with the highest expression in skin, followed by the expression in gills and whole blood. After challenge of Aeromonas hydrophila or polyinosinic: polycytidylic acid (Poly I:C) in vitro, the expression levels of PfMHC Ⅰα on pufferfish kidney lymphocytes were significantly up-regulated, with the highest expression level at 48 hr post-challenge. After infection with A. hydrophila or Poly I:C in vivo, the expression levels of PfMHC Ⅰα in the skin, whole blood and kidneys were significantly up-regulated. Taken together, it is speculated that PfMHC Ⅰα associates with resistance to both intracellular and extracellular antigens and plays an important role in the host response against pathogen infection in pufferfish.
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Affiliation(s)
- Shengli Fu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, China
- Institute of Modern Aquaculture Science and Engineering, South China Normal University, Guangzhou, China
| | - Haisu Liu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
- Institute of Modern Aquaculture Science and Engineering, South China Normal University, Guangzhou, China
| | - Yu Huang
- Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Guangdong Ocean University, Zhanjiang, China
| | - Junru Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
- Institute of Modern Aquaculture Science and Engineering, South China Normal University, Guangzhou, China
| | - Kun Qian
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Mingmei Ding
- School of medicine, Sun Yat-Sen University, Guangzhou, China
| | - Jianmin Ye
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, China
- Institute of Modern Aquaculture Science and Engineering, South China Normal University, Guangzhou, China
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3
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Rojas-Ocáriz V, Compañón I, Aydillo C, Castro-Loṕez J, Jiménez-Barbero J, Hurtado-Guerrero R, Avenoza A, Zurbano MM, Peregrina JM, Busto JH, Corzana F. Design of α-S-Neoglycopeptides Derived from MUC1 with a Flexible and Solvent-Exposed Sugar Moiety. J Org Chem 2016; 81:5929-41. [PMID: 27305427 DOI: 10.1021/acs.joc.6b00833] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The use of vaccines based on MUC1 glycopeptides is a promising approach to treat cancer. We present herein several sulfa-Tn antigens incorporated in MUC1 sequences that possess a variable linker between the carbohydrate (GalNAc) and the peptide backbone. The main conformations of these molecules in solution have been evaluated by combining NMR experiments and molecular dynamics simulations. The linker plays a key role in the modulation of the conformation of these compounds at different levels, blocking a direct contact between the sugar moiety and the backbone, promoting a helix-like conformation for the glycosylated residue and favoring the proper presentation of the sugar unit for molecular recognition events. The feasibility of these novel compounds as mimics of MUC1 antigens has been validated by the X-ray diffraction structure of one of these unnatural derivatives complexed to an anti-MUC1 monoclonal antibody. These features, together with potential lack of immune suppression, render these unnatural glycopeptides promising candidates for designing alternative therapeutic vaccines against cancer.
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Affiliation(s)
- Víctor Rojas-Ocáriz
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
| | - Ismael Compañón
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
| | - Carlos Aydillo
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
| | - Jorge Castro-Loṕez
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit , Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Jesús Jiménez-Barbero
- Structural Biology Unit, CIC bioGUNE , Parque Tecnológico de Bizkaia Building 801 A, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science , 48011 Bilbao, Spain.,Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas , CSIC Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ramón Hurtado-Guerrero
- BIFI, University of Zaragoza, BIFI-IQFR (CSIC) Joint Unit , Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain.,Fundación ARAID , 50018 Zaragoza, Spain
| | - Alberto Avenoza
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
| | - María M Zurbano
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
| | - Jesús M Peregrina
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
| | - Jesús H Busto
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja , Madre de Dios 53, 26006 Logroño, Spain
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Alvarado R, O'Brien B, Tanaka A, Dalton JP, Donnelly S. A parasitic helminth-derived peptide that targets the macrophage lysosome is a novel therapeutic option for autoimmune disease. Immunobiology 2014; 220:262-9. [PMID: 25466586 DOI: 10.1016/j.imbio.2014.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 11/06/2014] [Accepted: 11/07/2014] [Indexed: 12/24/2022]
Abstract
Parasitic worms (helminths) reside in their mammalian hosts for many years. This is attributable, in part, to their ability to skew the host's immune system away from pro-inflammatory responses and towards anti-inflammatory or regulatory responses. This immune modulatory ability ensures helminth longevity within the host, while simultaneously minimises tissue destruction for the host. The molecules that the parasite releases clearly exert potent immune-modulatory actions, which could be exploited clinically, for example in the prophylactic and therapeutic treatment of pro-inflammatory and autoimmune diseases. We have identified a novel family of immune-modulatory proteins, termed helminth defence molecules (HDMs), which are secreted by several medically important helminth parasites. These HDMs share biochemical and structural characteristics with mammalian cathelicidin-like host defence peptides (HDPs), which are significant components of the innate immune system. Like their mammalian counterparts, parasite HDMs block the activation of macrophages via toll like receptor (TLR) 4 signalling, however HDMs are significantly less cytotoxic than HDPs. HDMs can traverse the cell membrane of macrophages and enter the endolysosomal system where they reduce the acidification of lysosomal compartments by inhibiting vacuolar (v)-ATPase activity. In doing this, HDMs can modulate critical cellular functions, such as cytokine secretion and antigen processing/presentation. Here, we review the role of macrophages, specifically their lysosomal mediated activities, in the initiation and perpetuation of pro-inflammatory immune responses. We also discuss the potential of helminth defence molecules (HDMs) as therapeutics to counteract the pro-inflammatory responses underlying autoimmune disease. Given the current lack of effective, non-cytotoxic treatment options to limit the progression of autoimmune pathologies, HDMs open novel treatment avenues.
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Affiliation(s)
- Raquel Alvarado
- School of Medical and Molecular Biosciences, University of Technology, Sydney, Sydney, NSW, Australia
| | - Bronwyn O'Brien
- School of Medical and Molecular Biosciences, University of Technology, Sydney, Sydney, NSW, Australia
| | - Akane Tanaka
- School of Medical and Molecular Biosciences, University of Technology, Sydney, Sydney, NSW, Australia
| | - John P Dalton
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast, Belfast, Northern Ireland, UK
| | - Sheila Donnelly
- School of Medical and Molecular Biosciences, University of Technology, Sydney, Sydney, NSW, Australia; The i3 Institute, University of Technology, Sydney, Sydney, NSW, Australia.
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Wines BD, Trist HM, Farrugia W, Ngo C, Trowsdale J, Areschoug T, Lindahl G, Fraser JD, Ramsland PA. A conserved host and pathogen recognition site on immunoglobulins: structural and functional aspects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 946:87-112. [PMID: 21948364 DOI: 10.1007/978-1-4614-0106-3_6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A common site in the constant region (Fc) of immunoglobulins is recognized by host receptors and is a frequent target of proteins expressed by pathogens. This site is located at the junction of two constant domains in the antibody heavy chains and produces a large shallow cavity formed by loops of the CH2 and CH3 domains in IgG and IgA (CH3 and CH4 domains in IgM). Crystal structures have been determined for complexes of IgG-Fc and IgA-Fc with a structurally diverse set of host, pathogen and in vitro selected ligands. While pathogen proteins may directly block interactions with the immunoglobulins thereby evading host immunity, it is likely that the same pathogen molecules also interact with other host factors to carry out their primary biological function. Herein we review the structural and functional aspects of host and pathogen molecular recognition of the common site on the Fc of immunoglobulins. We also propose that some pathogen proteins may promote virulence by affecting the bridging between innate and adaptive immunity.
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Affiliation(s)
- Bruce D Wines
- Centre for Immunology, Burnet Institute, Melbourne, VIC 3004, Australia.
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Katsara M, Minigo G, Plebanski M, Apostolopoulos V. The good, the bad and the ugly: how altered peptide ligands modulate immunity. Expert Opin Biol Ther 2009; 8:1873-84. [PMID: 18990075 DOI: 10.1517/14712590802494501] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The basis of T cell immune responses is the specific recognition of an immunogenic peptide epitope by a T cell receptor. Peptide alterations of such T cell epitopes with single or few amino acid variations can have drastic effects on the outcome of this recognition. These altered peptide ligands can act as modulators of immune responses as they are capable of downregulating or upregulating responses. OBJECTIVE/METHODS We review how altered peptide ligands can have 'good' 'bad' and 'ugly' outcomes in treating diseases. RESULTS/CONCLUSION Altered peptide ligands have been used as immunotherapeutics in autoimmune (and allergic) diseases, infectious diseases and cancer. In the next five years we anticipate seeing a number of altered peptide ligands in clinical trials, progressing from contradictory classifications of good, bad or ugly, to the exciting outcome of 'useful'.
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Affiliation(s)
- Maria Katsara
- Immunology and Vaccine Laboratory, The Macfarlane Burnet Institute incorporating The Austin Research Institute, Studley Road, Heidelberg, VIC 3084, Australia
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