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Aktaş E, Özdemir Özgentürk N. A comprehensive examination of ACE2 receptor and prediction of spike glycoprotein and ACE2 interaction based on in silico analysis of ACE2 receptor. J Biomol Struct Dyn 2024; 42:4412-4428. [PMID: 37349943 DOI: 10.1080/07391102.2023.2220814] [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] [Received: 02/12/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
The ACE2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in various other diseases, including cardiovascular diseases and ARDS. While studies have explored the interactions between ACE2 and SARS-CoV proteins, comprehensive research utilizing bioinformatic tools on the ACE2 protein has been lacking. The one aim of present study was to extensively analyze the regions of the ACE2 protein. After utilizing all bioinformatics tools especially G104 and L108 regions on ACE2 were come forward. The results of our analysis revealed that possible mutations or deletions in the G104 and L108 regions play a critical role in both the biological functioning and the determination of the chemical-physical properties of ACE2. Additionally, these regions were found to be more susceptible to mutations or deletions compared to other regions of the ACE2 protein. Notably, the randomly selected peptide, LQQNGSSVLS (100-109), which includes G104 and L108, exhibited a crucial role in binding the RBD of the spike protein, as supported by docking scores. Furthermore, both MDs and iMODs results provided evidence that G104 and L108 influence the dynamics of ACE2-spike complexes. This study is expected to offer a new perspective on the ACE2-SARS-CoV interaction and other research areas where ACE2 plays a significant role, such as biotechnology (protein engineering, enzyme optimization), medicine (RAS, pulmonary and cardiac diseases), and basic research (structural motifs, stabilizing protein folds, or facilitating important inter molecular contacts, protein's proper structure and function).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Emre Aktaş
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Nehir Özdemir Özgentürk
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
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2
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Köseoğlu AE, Özgül F, Işıksal EN, Şeflekçi Y, Tülümen D, Özgültekin B, Deniz Köseoğlu G, Özyiğit S, Ihlamur M, Ekenoğlu Merdan Y. In silico discovery of diagnostic/vaccine candidate antigenic epitopes and a multi-epitope peptide vaccine (NaeVac) design for the brain-eating amoeba Naegleria fowleri causing human meningitis. Gene 2024; 902:148192. [PMID: 38253295 DOI: 10.1016/j.gene.2024.148192] [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] [Received: 09/05/2023] [Revised: 12/14/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024]
Abstract
Naegleria fowleri, the brain-eating amoeba, is a free-living amoeboflagellate with three different life cycles (trophozoite, flagellated, and cyst) that lives in a variety of habitats around the world including warm freshwater and soil. It causes a disease called naegleriasis leading meningitis and primary amoebic meningoencephalitis (PAM) in humans. N. fowleri is transmitted through contaminated water sources such as insufficiently chlorinated swimming pool water or contaminated tap water, and swimmers are at risk. N. fowleri is found all over the world, and most infections were reported in both developed and developing countries with high mortality rates and serious clinical findings. Until now, there is no FDA approved vaccine and early diagnosis is urgent against this pathogen. In this study, by analyzing the N. fowleri vaccine candidate proteins (Mp2CL5, Nfa1, Nf314, proNP-A and proNP-B), it was aimed to discover diagnostic/vaccine candidate epitopes and to design a multi-epitope peptide vaccine against this pathogen. After the in silico evaluation, three prominent diagnostic/vaccine candidate epitopes (EAKDSK, LLPHIRILVY, and FYAKLLPHIRILVYS) with the highest antigenicities were discovered and a potentially highly immunogenic/antigenic multi-epitope peptide vaccine (NaeVac) was designed against the brain-eating amoeba N. fowleri causing human meningitis.
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Affiliation(s)
- Ahmet Efe Köseoğlu
- Duisburg-Essen University, Faculty of Chemistry, Department of Environmental Microbiology and Biotechnology, Essen, Germany.
| | - Filiz Özgül
- Biruni University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Elif Naz Işıksal
- Biruni University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, Istanbul, Turkey; Biruni University, Faculty of Pharmacy, Department of Pharmacy, Istanbul, Turkey
| | - Yusuf Şeflekçi
- Biruni University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Deniz Tülümen
- Biruni University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | - Buminhan Özgültekin
- Bogaziçi University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, Istanbul, Turkey
| | | | - Sena Özyiğit
- Biruni University, Faculty of Engineering and Natural Sciences, Department of Biomedical Engineering, Istanbul, Turkey
| | - Murat Ihlamur
- Biruni University, Vocational School, Department of Electronics and Automation, Istanbul, Turkey; Yıldız Technical University, Graduate School of Science and Engineering, Department of Bioengineering, Istanbul, Turkey
| | - Yağmur Ekenoğlu Merdan
- Biruni University, Faculty of Medicine, Department of Medical Microbiology, Istanbul, Turkey
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3
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Köseoğlu AE, Can H, Güvendi M, Erkunt Alak S, Değirmenci Döşkaya A, Karakavuk M, Döşkaya M, Ün C. Molecular characterization of Anaplasma ovis Msp4 protein in strains isolated from ticks in Turkey: A multi-epitope synthetic vaccine antigen design against Anaplasma ovis using immunoinformatic tools. Biologicals 2024; 85:101749. [PMID: 38325003 DOI: 10.1016/j.biologicals.2024.101749] [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] [Received: 07/24/2023] [Revised: 01/07/2024] [Accepted: 01/29/2024] [Indexed: 02/09/2024] Open
Abstract
Tick-borne pathogens increasingly threaten animal and human health as well as cause great economic loss in the livestock industry. Among these pathogens, Anaplasma ovis causing a decrease in meat and milk yield is frequently detected in sheep in many countries including Turkey. This study aimed to reveal potential vaccine candidate epitopes in Msp4 protein using sequence data from Anaplasma ovis isolates and then to design a multi-epitope protein to be used in vaccine formulations against Anaplasma ovis. For this purpose, Msp4 gene was sequenced from Anaplasma ovis isolates (n:6) detected in ticks collected from sheep in Turkey and the sequence data was compared with previous sequences from different countries in order to detect the variations of Msp4 gene/protein. Potential vaccine candidate and diagnostic epitopes were predicted using various immunoinformatics tools. Among the discovered vaccine candidate epitopes, antigenic and conserved were selected, and then a multi-epitope protein was designed. The designed vaccine protein was tested for the assessment of TLR-2, IgG, and IFN-g responses by molecular docking and immune simulation analyses. Among the discovered epitopes, EVASEGSGVM and YQFTPEISLV epitopes with properties of high antigenicity, non-allergenicity, and non-toxicity were proposed to be used for Anaplasma ovis in further serodiagnostic and vaccine studies.
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Affiliation(s)
- Ahmet Efe Köseoğlu
- Duisburg-Essen University, Faculty of Chemistry, Department of Environmental Microbiology and Biotechnology, Essen, Germany
| | - Hüseyin Can
- Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, İzmir, Turkiye; Ege University, Vaccine Development Application and Research Center, İzmir, Turkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Turkiye
| | - Mervenur Güvendi
- Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, İzmir, Turkiye
| | - Sedef Erkunt Alak
- Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, İzmir, Turkiye; Ege University, Vaccine Development Application and Research Center, İzmir, Turkiye
| | - Aysu Değirmenci Döşkaya
- Ege University, Vaccine Development Application and Research Center, İzmir, Turkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Turkiye; Ege University, Faculty of Medicine, Department of Parasitology, İzmir, Turkiye
| | - Muhammet Karakavuk
- Ege University, Vaccine Development Application and Research Center, İzmir, Turkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Turkiye; Ege University, Odemis Vocational School, İzmir, Turkiye
| | - Mert Döşkaya
- Ege University, Vaccine Development Application and Research Center, İzmir, Turkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Turkiye; Ege University, Faculty of Medicine, Department of Parasitology, İzmir, Turkiye
| | - Cemal Ün
- Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, İzmir, Turkiye; Ege University, Vaccine Development Application and Research Center, İzmir, Turkiye; Ege University, Institute of Health Sciences, Department of Vaccine Studies, İzmir, Turkiye.
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Marques PH, Rodrigues TCV, Santos EH, Bleicher L, Aburjaile FF, Martins FS, Oliveira CJF, Azevedo V, Tiwari S, Soares S. Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches. J Biomol Struct Dyn 2023:1-16. [PMID: 38112302 DOI: 10.1080/07391102.2023.2293256] [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: 02/08/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pedro Henrique Marques
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Thais Cristina Vilela Rodrigues
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eduardo Horta Santos
- Institute of Biological Sciences, Post-graduate Interunits Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flavia Figueira Aburjaile
- Department of Preventive Veterinary Medicine, School of Veterinary Medicine, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Flaviano S Martins
- Department of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlo Jose Freire Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Institute of Biology, Federal University of Bahia, Salvador, BA, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA, Brazil
| | - Siomar Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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Damas MSF, Mazur FG, Freire CCDM, da Cunha AF, Pranchevicius MCDS. A Systematic Immuno-Informatic Approach to Design a Multiepitope-Based Vaccine Against Emerging Multiple Drug Resistant Serratia marcescens. Front Immunol 2022; 13:768569. [PMID: 35371033 PMCID: PMC8967166 DOI: 10.3389/fimmu.2022.768569] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/14/2022] [Indexed: 11/24/2022] Open
Abstract
Serratia marcescens is now an important opportunistic pathogen that can cause serious infections in hospitalized or immunocompromised patients. Here, we used extensive bioinformatic analyses based on reverse vaccinology and subtractive proteomics-based approach to predict potential vaccine candidates against S. marcescens. We analyzed the complete proteome sequence of 49 isolate of Serratia marcescens and identified 5 that were conserved proteins, non-homologous from human and gut flora, extracellular or exported to the outer membrane, and antigenic. The identified proteins were used to select 5 CTL, 12 HTL, and 12 BCL epitopes antigenic, non-allergenic, conserved, hydrophilic, and non-toxic. In addition, HTL epitopes were able to induce interferon-gamma immune response. The selected peptides were used to design 4 multi-epitope vaccines constructs (SMV1, SMV2, SMV3 and SMV4) with immune-modulating adjuvants, PADRE sequence, and linkers. Peptide cleavage analysis showed that antigen vaccines are processed and presented via of MHC class molecule. Several physiochemical and immunological analyses revealed that all multiepitope vaccines were non-allergenic, stable, hydrophilic, and soluble and induced the immunity with high antigenicity. The secondary structure analysis revealed the designed vaccines contain mainly coil structure and alpha helix structures. 3D analyses showed high-quality structure. Molecular docking analyses revealed SMV4 as the best vaccine construct among the four constructed vaccines, demonstrating high affinity with the immune receptor. Molecular dynamics simulation confirmed the low deformability and stability of the vaccine candidate. Discontinuous epitope residues analyses of SMV4 revealed that they are flexible and can interact with antibodies. In silico immune simulation indicated that the designed SMV4 vaccine triggers an effective immune response. In silico codon optimization and cloning in expression vector indicate that SMV4 vaccine can be efficiently expressed in E. coli system. Overall, we showed that SMV4 multi-epitope vaccine successfully elicited antigen-specific humoral and cellular immune responses and may be a potential vaccine candidate against S. marcescens. Further experimental validations could confirm its exact efficacy, the safety and immunogenicity profile. Our findings bring a valuable addition to the development of new strategies to prevent and control the spread of multidrug-resistant Gram-negative bacteria with high clinical relevance.
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Affiliation(s)
| | - Fernando Gabriel Mazur
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | | | | | - Maria-Cristina da Silva Pranchevicius
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Centro de Ciências Biológicas e da Saúde, Biodiversidade Tropical – BIOTROP, Universidade Federal de São Carlos, São Carlos, Brazil
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Shan X, Fu J, Li X, Peng X, Chen L. Comparative proteomics and secretomics revealed virulence, and coresistance-related factors in non O1/O139 Vibrio cholerae recovered from 16 species of consumable aquatic animals. J Proteomics 2022; 251:104408. [PMID: 34737110 DOI: 10.1016/j.jprot.2021.104408] [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: 03/29/2021] [Revised: 09/12/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023]
Abstract
Vibrio cholerae can cause pandemic cholera in humans. The bacterium resides in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. In this study, we determined virulence-associated genes, cross-resistance between antibiotics and heavy metals, and genome fingerprinting profiles of non O1/O139 V. cholerae isolates (n = 20) recovered from 16 species of consumable aquatic animals. Secretomes and proteomes of V. cholerae with distinct genotypes and phenotypes were obtained by using two-dimensional gel electrophoresis (2D-GE) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques. Comparative secretomic analysis revealed 4 common and 45 differential extracellular proteins among 20 V. cholerae strains, including 13 virulence- and 8 resistance-associated proteins. A total of 21,972 intracellular proteins were identified, and comparative proteomic analysis revealed 215 common and 913 differential intracellular proteins, including 22 virulence- and 8 resistance-associated proteins. Additionally, different secretomes and proteomes were observed between V. cholerae isolates of fish and shellfish origins. A number of novel proteins with unknown function and strain-specific proteins were also discovered in the V. cholerae isolates. SIGNIFICANCE: V. cholerae can cause pandemic cholera in humans. The bacterium is distributed in aquatic environments worldwide. Identification of risk factors of V. cholerae in aquatic products is imperative for assuming food safety. Non-O1/O139 V. cholerae has been reported to cause sporadic cholera-like diarrhea and bacteremia diseases, which indicates virulence factors rather than the major cholera toxin (CT) exist. This study for the first time investigated proteomes and secretomes of non-O1/O139 V. cholerae originating from aquatic animals. This resulted in the identification of a number of virulence and coresistance-related factors, as well as novel proteins and strain-specific proteins in V. cholerae isolates recovered from 16 species of consumable aquatic animals. These results fill gaps for better understanding of pathogenesis and resistance of V. cholerae, and also support the increasing need for novel diagnosis and vaccine targets against the leading waterborne pathogen worldwide.
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Affiliation(s)
- Xinying Shan
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Junfeng Fu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaohui Li
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China.
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Akter Z, Haque A, Hossain MS, Ahmed F, Islam MA. Aggregation Prone Regions in Antibody Sequences Raised Against Vibrio cholerae: A Bioinformatic Approach. Curr Bioinform 2021. [DOI: 10.2174/1574893615666200106120504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Background:
Cholera, a diarrheal illness, causes millions of deaths worldwide due to
large outbreaks. The monoclonal antibody used as therapeutic purposes of cholera is prone to be
unstable due to various factors including self-aggregation.
Objectives:
In this bioinformatic analysis, we identified the aggregation prone regions (APRs) of
antibody sequences of different immunogens (i.e., CTB, ZnM-CTB, ZnP-CTB, TcpA-CT-CTB,
ZnM-TcpA-CT-CTB, ZnP-TcpA-CT-CTB, ZnM-TcpA, ZnP-TcpA, TcpA-CT-TcpA, ZnM-TcpACT-
TcpA, ZnP-TcpA-CT-TcpA, Ogawa, Inaba and ZnM-Inaba) raised against Vibrio cholerae.
Methods:
To determine APRs in antibody sequences that were generated after immunizing Vibrio
cholerae immunogens on Mus musculus, a total of 94 sequences were downloaded as FASTA
format from a protein database and the algorithms such as Tango, Waltz, PASTA 2.0, and
AGGRESCAN were followed to analyze probable APRs in all of the sequences.
Results:
A remarkably high number of regions in the monoclonal antibodies were identified to be
APRs which could explain a cause of instability/short term protection of the anticholera vaccine.
Conclusion:
To increase the stability, it would be interesting to eliminate the APR residues from
the therapeutic antibodies in such a way that the antigen-binding sites or the complementarity
determining region loops involved in antigen recognition are not disrupted.
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Affiliation(s)
- Zakia Akter
- Department of Biochemistry and Molecular Biology, Gono Bishwabidyalay, Savar, Dhaka 1344, Bangladesh
| | - Anamul Haque
- Biomedical Data Science and Informatics Program, School of Computing, Clemson University, Clemson, SC, United States
| | - Md. Sabir Hossain
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka 1342, Bangladesh
| | - Firoz Ahmed
- Molecular and Serodiagnostic Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Md Asiful Islam
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
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Can H, Köseoğlu AE, Erkunt Alak S, Güvendi M, Döşkaya M, Karakavuk M, Gürüz AY, Ün C. In silico discovery of antigenic proteins and epitopes of SARS-CoV-2 for the development of a vaccine or a diagnostic approach for COVID-19. Sci Rep 2020; 10:22387. [PMID: 33372181 PMCID: PMC7769971 DOI: 10.1038/s41598-020-79645-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
In the genome of SARS-CoV-2, the 5′-terminus encodes a polyprotein, which is further cleaved into 15 non-structural proteins whereas the 3′ terminus encodes four structural proteins and eight accessory proteins. Among these 27 proteins, the present study aimed to discover likely antigenic proteins and epitopes to be used for the development of a vaccine or serodiagnostic assay using an in silico approach. For this purpose, after the full genome analysis of SARS-CoV-2 Wuhan isolate and variant proteins that are detected frequently, surface proteins including spike, envelope, and membrane proteins as well as proteins with signal peptide were determined as probable vaccine candidates whereas the remaining were considered as possible antigens to be used during the development of serodiagnostic assays. According to results obtained, among 27 proteins, 26 of them were predicted as probable antigen. In 26 proteins, spike protein was selected as the best vaccine candidate because of having a signal peptide, negative GRAVY value, one transmembrane helix, moderate aliphatic index, a big molecular weight, a long-estimated half-life, beta wrap motifs as well as having stable, soluble and non-allergic features. In addition, orf7a, orf8, and nsp-10 proteins with signal peptide were considered as potential vaccine candidates. Nucleocapsid protein and a highly antigenic GGDGKMKD epitope were identified as ideal antigens to be used in the development of serodiagnostic assays. Moreover, considering MHC-I alleles, highly antigenic KLNDLCFTNV and ITLCFTLKRK epitopes can be used to develop an epitope-based peptide vaccine.
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Affiliation(s)
- Hüseyin Can
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, Bornova, İzmir, Turkey
| | - Ahmet Efe Köseoğlu
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, Bornova, İzmir, Turkey
| | - Sedef Erkunt Alak
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, Bornova, İzmir, Turkey
| | - Mervenur Güvendi
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, Bornova, İzmir, Turkey
| | - Mert Döşkaya
- Department of Parasitology, Faculty of Medicine, Ege University, Bornova, İzmir, Turkey
| | | | - Adnan Yüksel Gürüz
- Department of Parasitology, Faculty of Medicine, Ege University, Bornova, İzmir, Turkey
| | - Cemal Ün
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, Bornova, İzmir, Turkey.
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