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Polymer microarrays rapidly identify competitive adsorbents of virus-like particles. Biointerphases 2020; 15:061005. [PMID: 33203214 DOI: 10.1116/6.0000586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The emergence of SARS-CoV-2 highlights the global need for platform technologies to enable the rapid development of diagnostics, vaccines, treatments, and personal protective equipment (PPE). However, many current technologies require the detailed mechanistic knowledge of specific material-virion interactions before they can be employed, for example, to aid in the purification of vaccine components or in the design of a more effective PPE. Here, we show that an adaption of a polymer microarray method for screening bacterial-surface interactions allows for the screening of polymers for desirable material-virion interactions. Nonpathogenic virus-like particles including fluorophores are exposed to the arrays in an aqueous buffer as a simple model of virions carried to the surface in saliva/sputum. Competitive binding of Lassa and Rubella virus-like particles is measured to probe the relative binding properties of a selection of copolymers. This provides the first step in the development of a method for the discovery of novel materials with promise for viral binding, with the next being development of this method to assess absolute viral adsorption and assessment of the attenuation of the activity of live virus, which we propose would be part of a material scale up step carried out in high containment facilities, alongside the use of more complex media to represent biological fluids.
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Awadelkareem EA, Ali SA. Vaccine design of coronavirus spike (S) glycoprotein in chicken: immunoinformatics and computational approaches. TRANSLATIONAL MEDICINE COMMUNICATIONS 2020; 5:13. [PMID: 32869000 PMCID: PMC7450164 DOI: 10.1186/s41231-020-00063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Infectious bronchitis (IB) is a highly contagious respiratory disease in chickens and produces economic loss within the poultry industry. This disease is caused by a single stranded RNA virus belonging to Cronaviridae family. This study aimed to design a potential multi-epitopes vaccine against infectious bronchitis virus spike protein (S). Protein characterization was also performed for IBV spike protein. METHODS The present study used various tools in Immune Epitope Database (IEDB) to predict conserved B and T cell epitopes against IBV spike (S) protein that may perform a significant role in provoking the resistance response to IBV infection. RESULTS In B cell prediction methods, three epitopes ( 1139 KKSSYY 1144 , 1140 KSSYYT 1145 , 1141 SSYYT 1145 ) were selected as surface, linear and antigenic epitopes.Many MHCI and MHCII epitopes were predicted for IBV S protein. Among them 982YYITARDMY990 and 983 YITARDMYM 991 epitopes displayed high antigenicity, no allergenicity and no toxicity as well as great linkage with MHCI and MHCII alleles. Moreover, docking analysis of MHCI epitopes produced strong binding affinity with BF2 alleles. CONCLUSION Five conserved epitopes were expected from spike glycoprotein of IBV as the best B and T cell epitopes due to high antigenicity, no allergenicity and no toxicity. In addition, MHC epitopes showed great linkage with MHC alleles as well as strong interaction with BF2 alleles. These epitopes should be designed and incorporated and then tested as multi-epitope vaccine against IBV.
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Affiliation(s)
| | - Sumaia A. Ali
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Sudan University of Science and Technology, Khartoum, Sudan
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Identification of Common CD8 + T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone. J Virol 2020; 94:JVI.00153-20. [PMID: 32269122 PMCID: PMC7307091 DOI: 10.1128/jvi.00153-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023] Open
Abstract
The high morbidity and mortality associated with clinical cases of Lassa fever, together with the lack of licensed vaccines and limited and partially effective interventions, make Lassa virus (LASV) an important health concern in its regions of endemicity in West Africa. Previous infection with LASV protects from disease after subsequent exposure, providing a framework for designing vaccines to elicit similar protective immunity. Multiple major lineages of LASV circulate in West Africa, and therefore, ideal vaccine candidates should elicit immunity to all lineages. We therefore sought to identify common T cell epitopes between Lassa fever survivors from Sierra Leone and Nigeria, where distinct lineages circulate. We identified three such epitopes derived from highly conserved regions within LASV proteins. In this process, we also identified nine other T cell epitopes. These data should help in the design of an effective pan-LASV vaccine. Early and robust T cell responses have been associated with survival from Lassa fever (LF), but the Lassa virus-specific memory responses have not been well characterized. Regions within the virus surface glycoprotein (GPC) and nucleoprotein (NP) are the main targets of the Lassa virus-specific T cell responses, but, to date, only a few T cell epitopes within these proteins have been identified. We identified GPC and NP regions containing T cell epitopes and HLA haplotypes from LF survivors and used predictive HLA-binding algorithms to identify putative epitopes, which were then experimentally tested using autologous survivor samples. We identified 12 CD8-positive (CD8+) T cell epitopes, including epitopes common to both Nigerian and Sierra Leonean survivors. These data should be useful for the identification of dominant Lassa virus-specific T cell responses in Lassa fever survivors and vaccinated individuals as well as for designing vaccines that elicit cell-mediated immunity. IMPORTANCE The high morbidity and mortality associated with clinical cases of Lassa fever, together with the lack of licensed vaccines and limited and partially effective interventions, make Lassa virus (LASV) an important health concern in its regions of endemicity in West Africa. Previous infection with LASV protects from disease after subsequent exposure, providing a framework for designing vaccines to elicit similar protective immunity. Multiple major lineages of LASV circulate in West Africa, and therefore, ideal vaccine candidates should elicit immunity to all lineages. We therefore sought to identify common T cell epitopes between Lassa fever survivors from Sierra Leone and Nigeria, where distinct lineages circulate. We identified three such epitopes derived from highly conserved regions within LASV proteins. In this process, we also identified nine other T cell epitopes. These data should help in the design of an effective pan-LASV vaccine.
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In-silico identification of the vaccine candidate epitopes against the Lassa virus hemorrhagic fever. Sci Rep 2020; 10:7667. [PMID: 32376973 PMCID: PMC7203123 DOI: 10.1038/s41598-020-63640-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 03/21/2020] [Indexed: 11/18/2022] Open
Abstract
Lassa virus (LASV), a member of the Arenaviridae, is an ambisense RNA virus that causes severe hemorrhagic fever with a high fatality rate in humans in West and Central Africa. Currently, no FDA approved drugs or vaccines are available for the treatment of LASV fever. The LASV glycoprotein complex (GP) is a promising target for vaccine or drug development. It is situated on the virion envelope and plays key roles in LASV growth, cell tropism, host range, and pathogenicity. In an effort to discover new LASV vaccines, we employ several sequence-based computational prediction tools to identify LASV GP major histocompatibility complex (MHC) class I and II T-cell epitopes. In addition, many sequence- and structure-based computational prediction tools were used to identify LASV GP B-cell epitopes. The predicted T- and B-cell epitopes were further filtered based on the consensus approach that resulted in the identification of thirty new epitopes that have not been previously tested experimentally. Epitope-allele complexes were obtained for selected strongly binding alleles to the MHC-I T-cell epitopes using molecular docking and the complexes were relaxed with molecular dynamics simulations to investigate the interaction and dynamics of the epitope-allele complexes. These predictions provide guidance to the experimental investigations and validation of the epitopes with the potential for stimulating T-cell responses and B-cell antibodies against LASV and allow the design and development of LASV vaccines.
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Ibukun FI. Inter-Lineage Variation of Lassa Virus Glycoprotein Epitopes: A Challenge to Lassa Virus Vaccine Development. Viruses 2020; 12:v12040386. [PMID: 32244402 PMCID: PMC7232328 DOI: 10.3390/v12040386] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/12/2022] Open
Abstract
Lassa virus (LASV), which causes considerable morbidity and mortality annually, has a high genetic diversity across West Africa. LASV glycoprotein (GP) expresses this diversity, but most LASV vaccine candidates utilize only the Lineage IV LASV Josiah strain GP antigen as an immunogen and homologous challenge with Lineage IV LASV. In addition to the sequence variation amongst the LASV lineages, these lineages are also distinguished in their presentations. Inter-lineage variations within previously mapped B-cell and T-cell LASV GP epitopes and the breadth of protection in LASV vaccine/challenge studies were examined critically. Multiple alignments of the GP primary sequence of strains from each LASV lineage showed that LASV GP has diverging degrees of amino acid conservation within known epitopes among LASV lineages. Conformational B-cell epitopes spanning different sites in GP subunits were less impacted by LASV diversity. LASV GP diversity should influence the approach used for LASV vaccine design. Expression of LASV GP on viral vectors, especially in its prefusion configuration, has shown potential for protective LASV vaccines that can overcome LASV diversity. Advanced vaccine candidates should demonstrate efficacy against all LASV lineages for evidence of a pan-LASV vaccine.
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Affiliation(s)
- Francis Ifedayo Ibukun
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, 21201, MD, USA
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6
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Sayed SB, Nain Z, Khan MSA, Abdulla F, Tasmin R, Adhikari UK. Exploring Lassa Virus Proteome to Design a Multi-epitope Vaccine Through Immunoinformatics and Immune Simulation Analyses. Int J Pept Res Ther 2020; 26:2089-2107. [PMID: 32421065 PMCID: PMC7223894 DOI: 10.1007/s10989-019-10003-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Abstract
Lassa virus (LASV) is responsible for a type of acute viral haemorrhagic fever referred to as Lassa fever. Lack of adequate treatment and preventive measures against LASV resulted in a high mortality rate in its endemic regions. In this study, a multi-epitope vaccine was designed using immunoinformatics as a prophylactic agent against the virus. Following a rigorous assessment, the vaccine was built using T-cell (NCTL = 8 and NHTL = 6) and B-cell (NLBL = 4) epitopes from each LASV-derived protein in addition with suitable linkers and adjuvant. The physicochemistry, immunogenic potency and safeness of the designed vaccine (~ 68 kDa) were assessed. In addition, chosen CTL and HTL epitopes of our vaccine showed 97.37% worldwide population coverage. Besides, disulphide engineering also improved the stability of the chimeric vaccine. Molecular docking of our vaccine protein with toll-like receptor 2 (TLR2) showed binding efficiency followed by dynamics simulation for stable interaction. Furthermore, higher levels of cell-mediated immunity and rapid antigen clearance were suggested by immune simulation and repeated-exposure simulation, respectively. Finally, the optimized codons were used in in silico cloning to ensure higher expression within E. coli K12 bacterium. With further assessment both in vitro and in vivo, we believe that our proposed peptide-vaccine would be potential immunogen against Lassa fever.
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Affiliation(s)
- Sifat Bin Sayed
- 1Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Zulkar Nain
- 1Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Md Shakil Ahmed Khan
- 1Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Faruq Abdulla
- 2Department of Statistics, Faculty of Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Rubaia Tasmin
- 3Department of Pharmacy, Faculty of Biological Sciences, Islamic University, Kushtia, 7003 Bangladesh
| | - Utpal Kumar Adhikari
- 4School of Medicine, Western Sydney University, Campbelltown, NSW 2560 Australia
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Raoufi E, Hemmati M, Eftekhari S, Khaksaran K, Mahmodi Z, Farajollahi MM, Mohsenzadegan M. Epitope Prediction by Novel Immunoinformatics Approach: A State-of-the-art Review. Int J Pept Res Ther 2019; 26:1155-1163. [PMID: 32435171 PMCID: PMC7224030 DOI: 10.1007/s10989-019-09918-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 12/21/2022]
Abstract
Immunoinformatics is a science that helps to create significant immunological information using bioinformatics softwares and applications. One of the most important applications of immunoinformatics is the prediction of a variety of specific epitopes for B cell recognition and T cell through MHC class I and II molecules. This method reduces costs and time compared to laboratory tests. In this state-of-the-art review, we review about 50 papers to find the latest and most used immunoinformatic tools as well as their applications for predicting the viral, bacterial and tumoral structural and linear epitopes of B and T cells. In the clinic, the main application of prediction of epitopes is for designing peptide-based vaccines. Peptide-based vaccines are a considerably potential alternative to low-cost vaccines that may reduce the risks related to the production of common vaccines.
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Affiliation(s)
- Ehsan Raoufi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Hemmati
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samane Eftekhari
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Kamal Khaksaran
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Mahmodi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad M. Farajollahi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Monireh Mohsenzadegan
- Department of Medical Laboratory Science, Faculty of Allied Medical Sciences, Iran University of Medical Sciences (IUMS), Hemmat Highway, Tehran, Iran
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The Immunogenicity of OMP31 Peptides and Its Protection Against Brucella melitensis Infection in Mice. Sci Rep 2019; 9:3512. [PMID: 30837598 PMCID: PMC6401381 DOI: 10.1038/s41598-019-40084-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 02/08/2019] [Indexed: 11/08/2022] Open
Abstract
Given brucellosis is a widespread zoonosis in the world, a safe and effective vaccine is urgently needed. Recent trend in vaccine design has shifted to epitope-based vaccines that are safe and specific. In this study, peptide containing both T-cell and B-cell epitopes of OMP31 was synthesized and used to immunize the mice by nasal administration. The protective efficacy was evaluated. Mice immunized with the B epitope or TB epitope peptides of OMP31 had higher levels of IgG1 and IgG2a in the serum. While the BALB/c mice immunized with peptides containing T cell epitope or TB epitope of OMP31 showed high degree of IFN-γ-producing T cells in the lymphocytes from the respiratory draining lymph nodes and spleen. After intranasally challenged with 5 × 105 CFU of Brucella melitensis (strain 16 M), the bacterial loads in lung of the immunized mice were significantly lower than control group. These data demonstrate for the first time that peptides of OMP31 containing T epitope, B epitope or TB epitopes are of high immunogenicity and thus can protect host from Brucella melitensis infection in lung.
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Faisal ARM, Imtiaz SH, Zerin T, Rahman T, Shekhar HU. Computer aided epitope design as a peptide vaccine component against Lassa virus. Bioinformation 2017; 13:417-429. [PMID: 29379262 PMCID: PMC5767920 DOI: 10.6026/97320630013417] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 12/05/2017] [Accepted: 12/05/2017] [Indexed: 12/16/2022] Open
Abstract
Lassa virus (LASV) is an arena virus causing hemorrhagic fever and it is endemic in several regions of West Africa. The disease-causing virus records high mortality rate in endemic regions due to lack of appropriate treatment and prevention strategies. Therefore, it is of interest to design and develop viable vaccine components against the virus. We used the Lassa virus envelope glyco-proteins as a vaccine target to identify linear peptides as potential epitopes with immunogenic properties by computer aided epitope prediction tools. We report a T-cell epitope 'LLGTFTWTL' and a B-cell epitope 'AELKCFGNTAVAKCNE' with predicted potential immunogenicity for further in vivo and in vitro consideration.
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Affiliation(s)
- Ar-Rafi Md. Faisal
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Syed Hassan Imtiaz
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Tasnim Zerin
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Tania Rahman
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000, Bangladesh
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Dash R, Das R, Junaid M, Akash MFC, Islam A, Hosen SZ. In silico-based vaccine design against Ebola virus glycoprotein. Adv Appl Bioinform Chem 2017; 10:11-28. [PMID: 28356762 PMCID: PMC5367765 DOI: 10.2147/aabc.s115859] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Ebola virus (EBOV) is one of the lethal viruses, causing more than 24 epidemic outbreaks to date. Despite having available molecular knowledge of this virus, no definite vaccine or other remedial agents have been developed yet for the management and avoidance of EBOV infections in humans. Disclosing this, the present study described an epitope-based peptide vaccine against EBOV, using a combination of B-cell and T-cell epitope predictions, followed by molecular docking and molecular dynamics simulation approach. Here, protein sequences of all glycoproteins of EBOV were collected and examined via in silico methods to determine the most immunogenic protein. From the identified antigenic protein, the peptide region ranging from 186 to 220 and the sequence HKEGAFFLY from the positions of 154-162 were considered the most potential B-cell and T-cell epitopes, correspondingly. Moreover, this peptide (HKEGAFFLY) interacted with HLA-A*32:15 with the highest binding energy and stability, and also a good conservancy of 83.85% with maximum population coverage. The results imply that the designed epitopes could manifest vigorous enduring defensive immunity against EBOV.
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Affiliation(s)
- Raju Dash
- Molecular Modeling and Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, Bangladesh
| | - Rasel Das
- Nanotechnology and Catalysis Research Center, University of Malaya, Kuala Lumpur, Malaysia
| | - Md Junaid
- Department of Pharmaceutical Sciences, North South University, Dhaka, Bangladesh
| | | | - Ashekul Islam
- Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong, Bangladesh
| | - Sm Zahid Hosen
- Molecular Modeling and Drug Design Laboratory (MMDDL), Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chittagong, Bangladesh
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