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Ezzemani W, Ouladlahsen A, Altawalah H, Saile R, Sarih M, Kettani A, Ezzikouri S. Identification of novel T-cell epitopes on monkeypox virus and development of multi-epitopes vaccine using immunoinformatics approaches. J Biomol Struct Dyn 2024; 42:5349-5364. [PMID: 37354141 DOI: 10.1080/07391102.2023.2226733] [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: 10/25/2022] [Accepted: 06/10/2023] [Indexed: 06/26/2023]
Abstract
Monkeypox virus (MPV) is closely related to the smallpox virus, and previous data from Africa suggest that the smallpox vaccine (VARV) is at least 85% effective in preventing MPV. No multi-epitope vaccine has yet been developed to prevent MPV infection. In this work, we used in silico structural biology and advanced immunoinformatic strategies to design a multi-epitope subunit vaccine against MPV infection. The designed vaccine sequence is adjuvanted with CpG-ODN and includes HTL/CTL epitopes for similar proteins between vaccinia virus (VACV) that induced T-cell production in vaccinated volunteers and the first draft sequence of the MPV genome associated with the suspected outbreak in several countries, May 2022. In addition, the specific binding of the modified vaccine and the immune Toll-like receptor 9 (TLR9) was estimated by molecular interaction studies. Strong interaction in the binding groove as well as good docking scores confirmed the stringency of the modified vaccine. The stability of the interaction was confirmed by a classical molecular dynamics simulation and normal mode analysis. Then, the immune simulation also indicated the ability of this vaccine to induce an effective immune response against MPV. Codon optimization and in silico cloning of the vaccine into the pET-28a (+) vector also showed its expression potential in the E. coli K12 system. The promising data obtained from the various in silico studies indicate that this vaccine is effective against MPV. However, additional in vitro and in vivo studies are still needed to confirm its efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ahd Ouladlahsen
- Faculté de médecine et de pharmacie, Université Hassan II, Casablanca, Morocco
- Service des maladies infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - M'hammed Sarih
- Service de Parasitologie et des Maladies Vectorielles, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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Ullah A, Ul Haq M, Iqbal M, Irfan M, Khan S, Muhammad R, Ullah A, Khurram M, Alharbi M, Alasmari AF, Ahmad S. A computational quest for identifying potential vaccine candidates against Moraxella lacunata: a multi-pronged approach. J Biomol Struct Dyn 2024; 42:2976-2989. [PMID: 37177816 DOI: 10.1080/07391102.2023.2212793] [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: 12/12/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Moraxella lacunata is an emerging gram-negative bacterium that is responsible for multiple nosocomial infections. The bacterium is evolving resistance to several antibiotics, and currently, no effective licensed vaccines are available, which warrants the search for new therapeutics. A multi-epitope-based vaccine has been designed for M. lacunata. The complete proteome of M. lacunata contains 10,110 core proteins. Subcellular localization analysis revealed the presence of five proteins in the extracellular matrix, while 19 proteins were predicted to be located in the outer membrane, and 21 proteins were predicted to be located in the periplasmic region. Only two proteins, the type VI secretion system tube protein (Hcp) and the transporter substrate-binding domain-containing protein, were selected for epitope prediction as they fulfilled all the criteria for being potential vaccine candidates. Shortlisted epitopes from the selected proteins were fused together using "GPGPG" linkers to overcome the limitations of single-epitope vaccines. Next, the cholera toxin-B adjuvant was attached to the peptide epitope using an EAAAK linker. Docking analysis was performed to examine the interaction between the vaccine and immune cell receptors, revealing robust intermolecular interactions and a stable binding conformation. Molecular dynamics simulation findings revealed no drastic changes in the binding conformation of complexes during the simulation period. The net binding free energy of vaccine-receptor complexes was estimated using the molecular mechanics energies combined with the Poisson-Boltzmann and surface area continuum solvation (MM-PBSA) method. The reported values were -586.38 kcal/mol, -283.74 kcal/mol, and -296.88 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. Furthermore, the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) analysis predicted binding free energies of -596.69 kcal/mol, -287.39 kcal/mol, and -298.28 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. The theoretical vaccine design proposed in the study could potentially serve as a powerful therapeutic against targeted pathogens, subject to validation through experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Madiha Iqbal
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Irfan
- College of Dentistry, Department of Oral Biology, University of Florida, Gainesville, FL, USA
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Amin Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
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3
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Koçkaya ES, Can H, Yaman Y, Ün C. In silico discovery of epitopes of gag and env proteins for the development of a multi-epitope vaccine candidate against Maedi Visna Virus using reverse vaccinology approach. Biologicals 2023; 84:101715. [PMID: 37793308 DOI: 10.1016/j.biologicals.2023.101715] [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: 04/23/2023] [Revised: 08/28/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Maedi Visna Virus (MVV) causes a chronic viral disease in sheep. Since there is no specific therapeutic drug that targets MVV, development of a vaccine against the MVV is inevitable. This study aimed to analyze the gag and env proteins as vaccine candidate proteins and to identify epitopes in these proteins. In addition, it was aimed to construct a multi-epitope vaccine candidate. According to the obtained results, the gag protein was detected to be more conserved and had a higher antigenicity value. Also, the number of alpha helix in the secondary structure was higher and transmembrane helices were not detected. Although many B cell and MHC-I/II epitopes were predicted, only 19 of them were detected to have the properties of antigenic, non-allergenic, non-toxic, soluble, and non-hemolytic. Of these epitopes, five were remarkable due to having the highest antigenicity value. However, the final multi-epitope vaccine was constructed with 19 epitopes. A strong affinity was shown between the final multi-epitope vaccine and TLR-2/4. In conclusion, the gag protein was a better antigen. However, both proteins had epitopes with high antigenicity value. Also, the final multi-epitope vaccine construct had a potential to be used as a peptide vaccine due to its immuno-informatics results.
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Affiliation(s)
- Ecem Su Koçkaya
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye
| | - Hüseyin Can
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye
| | - Yalçın Yaman
- Siirt University Faculty of Veterinary Medicine, Department of Genetics, Siirt, Türkiye
| | - Cemal Ün
- Ege University Faculty of Science Department of Biology Molecular Biology Section, İzmir, Türkiye.
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Ullah A, Ullah Khan S, Haq MU, Ahmad S, Irfan M, Asif M, Muhseen ZT, Alkeraidees MS, Allemailem KS, Alrumaihi F, Almatroudi A. Computational study to investigate Proteus mirabilis proteomes for multi-epitope vaccine construct design. J Biomol Struct Dyn 2023; 41:10190-10201. [PMID: 36476074 DOI: 10.1080/07391102.2022.2153920] [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: 07/18/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022]
Abstract
Proteus mirabilis is a gram-negative bacterium particularly known for its unique swarming ability. The swarming gives the bacteria ability to enhance adherence to the catheter surface and epithelium cells of the urethra to cause catheter associated urinary tract infections. P. mirabilis has evolved resistant to antibiotics. Additionally, there is an approved vaccine against P. mirabilis, thus demanding for identification of new vaccine targets. This gram-negative bacterium consists of 19,502 core proteins, out of which 19,063 are redundant proteins and remaining 439 are non-redundant proteins. The non-redundant proteins have 21 proteins present on the cell surface out of which 11 proteins are virulent. Antigenicity analysis predicted only 2 proteins as antigenic (fimbrial biogenesis outer membrane usher protein and ligand-gated channel protein). Four and seven B-cells epitopes were predicted from the former and later proteins, respectively. The predicted B-cells epitopes were used for T- cells epitopes prediction. The predicted epitopes were linked to each other through GPGPG linkers and joined with cholera toxin beta subunit adjuvant. A multi-epitopes vaccine construct consisting of 226 residues was docked with MHC-I, MHC-II and TLR-4. The best docked complex in each case has binding energy of -714.6, -744.6 and -829.5 kcal/mol, respectively. Moreover, the docking results were validated through molecular dynamics simulation and binding free energies estimation. The net energy of -137.2 kcal/mol was calculated for vaccine-MHC-I complex, -133.39 kcal/mol for vaccine-MHC-II and -158.68 kcal/mol for vaccine-TLR-4 complex. The designed vaccine construct could provoke immune responses against targeted pathogen and may be used in experimental testing.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Saif Ullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Muhammad Asif
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Ziyad Tariq Muhseen
- Department of Pharmacy, Al-Mustaqbal University College, Hillah, Babylon, Iraq
| | - Monerh Saleh Alkeraidees
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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Ferrara G, Colitti B, Flores-Ramirez G, Pagnini U, Iovane G, Rosati S, Montagnaro S. Detection of Coxiella antibodies in ruminants using a SucB recombinant antigen. J Vet Diagn Invest 2023; 35:721-726. [PMID: 37705242 PMCID: PMC10621550 DOI: 10.1177/10406387231199964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
The detection of Coxiella burnetii in ruminants remains challenging despite the use of new technology and the accumulation of novel knowledge. Serology tools, the primary methods of infection surveillance in veterinary medicine, have limitations. We used recombinant antigen production to develop an ELISA based on the SucB protein, one of the major immunodominant antigens described in humans and laboratory animals. We produced the antigen successfully in an Escherichia coli heterologous system, confirmed by sequencing and mass spectrometry, and seen as a band of ~50 kDa in SDS-PAGE and on western blot analysis. We compared the performance of the recombinant ELISA with a commercial ELISA. We observed agreement of 83.5% and a substantial Cohen κ value of 0.67 in our pilot study.
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Affiliation(s)
- Gianmarco Ferrara
- Department of Veterinary Medicine and Animal Productions, University of Naples, “Federico II”, Naples, Italy
| | - Barbara Colitti
- Department of Veterinary Science, University of Turin, Grugliasco, TO, Italy
| | | | - Ugo Pagnini
- Department of Veterinary Medicine and Animal Productions, University of Naples, “Federico II”, Naples, Italy
| | - Giuseppe Iovane
- Department of Veterinary Medicine and Animal Productions, University of Naples, “Federico II”, Naples, Italy
| | - Sergio Rosati
- Department of Veterinary Science, University of Turin, Grugliasco, TO, Italy
| | - Serena Montagnaro
- Department of Veterinary Medicine and Animal Productions, University of Naples, “Federico II”, Naples, Italy
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6
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Bach E, Fitzgerald SF, Williams-MacDonald SE, Mitchell M, Golde WT, Longbottom D, Nisbet AJ, Dinkla A, Sullivan E, Pinapati RS, Tan JC, Joosten LAB, Roest HJ, Østerbye T, Koets AP, Buus S, McNeilly TN. Genome-wide epitope mapping across multiple host species reveals significant diversity in antibody responses to Coxiella burnetii vaccination and infection. Front Immunol 2023; 14:1257722. [PMID: 37954609 PMCID: PMC10637584 DOI: 10.3389/fimmu.2023.1257722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/19/2023] [Indexed: 11/14/2023] Open
Abstract
Coxiella burnetii is an important zoonotic bacterial pathogen of global importance, causing the disease Q fever in a wide range of animal hosts. Ruminant livestock, in particular sheep and goats, are considered the main reservoir of human infection. Vaccination is a key control measure, and two commercial vaccines based on formalin-inactivated C. burnetii bacterins are currently available for use in livestock and humans. However, their deployment is limited due to significant reactogenicity in individuals previously sensitized to C. burnetii antigens. Furthermore, these vaccines interfere with available serodiagnostic tests which are also based on C. burnetii bacterin antigens. Defined subunit antigen vaccines offer significant advantages, as they can be engineered to reduce reactogenicity and co-designed with serodiagnostic tests to allow discrimination between vaccinated and infected individuals. This study aimed to investigate the diversity of antibody responses to C. burnetii vaccination and/or infection in cattle, goats, humans, and sheep through genome-wide linear epitope mapping to identify candidate vaccine and diagnostic antigens within the predicted bacterial proteome. Using high-density peptide microarrays, we analyzed the seroreactivity in 156 serum samples from vaccinated and infected individuals to peptides derived from 2,092 open-reading frames in the C. burnetii genome. We found significant diversity in the antibody responses within and between species and across different types of C. burnetii exposure. Through the implementation of three different vaccine candidate selection methods, we identified 493 candidate protein antigens for protein subunit vaccine design or serodiagnostic evaluation, of which 65 have been previously described. This is the first study to investigate multi-species seroreactivity against the entire C. burnetii proteome presented as overlapping linear peptides and provides the basis for the selection of antigen targets for next-generation Q fever vaccines and diagnostic tests.
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Affiliation(s)
- Emil Bach
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Annemieke Dinkla
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Eric Sullivan
- Nimble Therapeutics, Inc., Madison, WI, United States
| | | | - John C. Tan
- Nimble Therapeutics, Inc., Madison, WI, United States
| | - Leo A. B. Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hendrik-Jan Roest
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
- Ministry of Agriculture, Nature and Food Quality, Den Haag, Netherlands
- Department of Infection and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thomas Østerbye
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ad P. Koets
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Søren Buus
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
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Vivekanandam R, Rajagopalan K, Jeevanandam M, Ganesan H, Jagannathan V, Selvan Christyraj JD, Kalimuthu K, Selvan Christyraj JRS, Mohan M. Designing of cytotoxic T lymphocyte-based multi-epitope vaccine against SARS-CoV2: a reverse vaccinology approach. J Biomol Struct Dyn 2022; 40:13711-13726. [PMID: 34696708 DOI: 10.1080/07391102.2021.1993338] [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: 12/29/2022]
Abstract
SARS-CoV2 is a single-stranded RNA virus, gaining much attention after it out broke in China in December 2019. The virus rapidly spread to several countries around the world and caused severe respiratory illness to humans. Since the outbreak, researchers around the world have devoted maximum resources and effort to develop a potent vaccine that would offer protection to uninfected individuals against SARS-CoV2. Reverse vaccinology is a relatively new approach that thrives faster in vaccine research. In this study, we constructed Cytotoxic T Lymphocytes (CTL)-based multi-epitope vaccine using hybrid epitope prediction methods. A total of 121 immunogenic CTL epitopes were screened by various sequence-based prediction methods and docked with their respective HLA alleles using the AutoDock Vina v1.1.2. In all, 17 epitopes were selected based on their binding affinity, followed by the construction of multi-epitope vaccine by placing the appropriate linkers between the epitopes and tuberculosis heparin-binding hemagglutinin (HBHA) adjuvant. The final vaccine construct was modeled by the I-TASSER server and the best model was further validated by ERRAT, ProSA, and PROCHECK servers. Furthermore, the molecular interaction of the constructed vaccine with TLR4 was assessed by ClusPro 2.0 and PROtein binDIng enerGY prediction (PRODIGY) server. The immune simulation analysis confirms that the constructed vaccine was capable of inducing long-lasting memory T helper (Th) and CTL responses. Finally, the nucleotide sequence was codon-optimized by the JCAT tool and cloned into the pET21a (+) vector. The current results reveal that the candidate vaccine is capable of provoking robust CTL response against the SARS-CoV2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Reethu Vivekanandam
- Department of Biotechnology, Bharathiyar University, Coimbatore, Tamilnadu, India
| | - Kamarajan Rajagopalan
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Madesh Jeevanandam
- Department of Biochemistry, PSG college of Arts and Science, Coimbatore, Tamilnadu, India
| | - Harsha Ganesan
- Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai, Tamilnadu, India
| | - Vaishnavi Jagannathan
- Institute of Forest Genetics and Tree Breeding (IFGTB), Coimbatore, Tamilnadu, India
| | - Jackson Durairaj Selvan Christyraj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Kalishwaralal Kalimuthu
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Johnson Retnaraj Samuel Selvan Christyraj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, India
| | - Manikandan Mohan
- Vaxigen International Research Center Private Limited, Coimbatore, Tamilnadu, India.,Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
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Irfan M, Khan S, Hameed AR, Al-Harbi AI, Abideen SA, Ismail S, Ullah A, Abbasi SW, Ahmad S. Computational Based Designing of a Multi-Epitopes Vaccine against Burkholderia mallei. Vaccines (Basel) 2022; 10:vaccines10101580. [PMID: 36298444 PMCID: PMC9607922 DOI: 10.3390/vaccines10101580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The emergence of antibiotic resistance in bacterial species is a major threat to public health and has resulted in high mortality as well as high health care costs. Burkholderia mallei is one of the etiological agents of health care-associated infections. As no licensed vaccine is available against the pathogen herein, using reverse vaccinology, bioinformatics, and immunoinformatics approaches, a multi-epitope-based vaccine against B. mallei was designed. In completely sequenced proteomes of B. mallei, 18,405 core, 3671 non-redundant, and 14,734 redundant proteins were predicted. Among the 3671 non-redundant proteins, 3 proteins were predicted in the extracellular matrix, 11 were predicted as outer membrane proteins, and 11 proteins were predicted in the periplasmic membrane. Only two proteins, type VI secretion system tube protein (Hcp) and type IV pilus secretin proteins, were selected for epitope prediction. Six epitopes, EAMPERMPAA, RSSPPAAGA, DNRPISINL, RQRFDAHAR, AERERQRFDA, and HARAAQLEPL, were shortlisted for multi-epitopes vaccine design. The predicted epitopes were linked to each other via a specific GPGPG linker and the epitopes peptide was then linked to an adjuvant molecule through an EAAAK linker to make the designed vaccine more immunologically potent. The designed vaccine was also found to have favorable physicochemical properties with a low molecular weight and fewer transmembrane helices. Molecular docking studies revealed vaccine construct stable binding with MHC-I, MHC-II, and TLR-4 with energy scores of −944.1 kcal/mol, −975.5 kcal/mol, and −1067.3 kcal/mol, respectively. Molecular dynamic simulation assay noticed stable dynamics of the docked vaccine-receptors complexes and no drastic changes were observed. Binding free energies estimation revealed a net value of −283.74 kcal/mol for the vaccine-MHC-I complex, −296.88 kcal/mol for the vaccine-MHC-II complex, and −586.38 kcal/mol for the vaccine-TLR-4 complex. These findings validate that the designed vaccine construct showed promising ability in terms of binding to immune receptors and may be capable of eliciting strong immune responses once administered to the host. Further evidence from experimentations in mice models is required to validate real immune protection of the designed vaccine construct against B. mallei.
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Affiliation(s)
- Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32611, USA
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda 24461, Pakistan
| | - Alaa R. Hameed
- Department of Medical Laboratory Techniques, School of Life Sciences, Dijlah University College, Baghdad 00964, Iraq
| | - Alhanouf I. Al-Harbi
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu 41477, Saudi Arabia
| | - Syed Ainul Abideen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200000, China
| | - Saba Ismail
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
- Correspondence: (S.I.); (S.A.)
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
- Correspondence: (S.I.); (S.A.)
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9
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Hasan M, Mia M. Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach. Int J Pept Res Ther 2022; 28:134. [PMID: 35911179 PMCID: PMC9315849 DOI: 10.1007/s10989-022-10438-6] [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] [Accepted: 06/26/2022] [Indexed: 12/03/2022]
Abstract
Cryptosporidiosis is the leading protozoan-induced cause of diarrheal illness in children, and it has been linked to childhood mortality, malnutrition, cognitive development, with retardation of growth. Cryptosporidium hominis, the anthroponotically transmitted species within the Cryptosporidium genus, contributes significantly to the global burden of infection, accounting for the majority of clinical cases in numerous nations, as well as its emergence in the last decade is largely due to detections obtained through noteworthy epidemiologic research. Nevertheless, there is no vaccine available, and the only licensed medication, nitazoxanide, has been demonstrated to have efficacy limitations in a number of patient groups recognized to be at high risk of complications. Therefore, current study delineates the computational vaccine design for Cryptosporidium hominis, the notable pathogen for enteric diarrhea. Firstly, a comprehensive literature search was conducted to identify six proteins based on their toxigenicity, allergenicity, antigenicity, and prediction of transmembrane helices to make up a multi-epitope-based subunit vaccine. Following that, antigenic non-toxic HTL epitope, CTL epitope with B cell epitope were predicted from the selected proteins and construct a vaccine candidate with adding an adjuvant and some linkers with immunologically superior epitopes. Afterwards, the constructed vaccine candidates and TLR2 receptor were put into the ClusPro server for molecular dynamic simulation to know the binding stability of the vaccine-TLR2 complex. Following that, Escherichia coli strain K12 was used as a cloning host for the chosen vaccine construct via the JCat server. As a result of the findings, it was resolute that the proposed chimeric peptide vaccine could improve the immune response to Cryptosporidium hominis.
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Affiliation(s)
- Mahamudul Hasan
- Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, 3100 Bangladesh
| | - Mukthar Mia
- Department of Poultry Science, Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, 3100 Bangladesh.,Faculty of Veterinary, Animal and Biomedical Sciences, Sylhet Agricultural University, Sylhet, 3100 Bangladesh
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Forouharmehr A, Nazifi N, Mousavi SM, Jaydari A. Designing an Efficient Epitope-based Vaccine Conjugated with a Molecular Adjuvant against Bovine Babesiosis: A Computational Study. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Vaccinomics to Design a Multi-Epitopes Vaccine for Acinetobacter baumannii. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095568. [PMID: 35564967 PMCID: PMC9104312 DOI: 10.3390/ijerph19095568] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance (AR) is the result of microbes’ natural evolution to withstand the action of antibiotics used against them. AR is rising to a high level across the globe, and novel resistant strains are emerging and spreading very fast. Acinetobacter baumannii is a multidrug resistant Gram-negative bacteria, responsible for causing severe nosocomial infections that are treated with several broad spectrum antibiotics: carbapenems, β-lactam, aminoglycosides, tetracycline, gentamicin, impanel, piperacillin, and amikacin. The A. baumannii genome is superplastic to acquire new resistant mechanisms and, as there is no vaccine in the development process for this pathogen, the situation is more worrisome. This study was conducted to identify protective antigens from the core genome of the pathogen. Genomic data of fully sequenced strains of A. baumannii were retrieved from the national center for biotechnological information (NCBI) database and subjected to various genomics, immunoinformatics, proteomics, and biophysical analyses to identify potential vaccine antigens against A. baumannii. By doing so, four outer membrane proteins were prioritized: TonB-dependent siderphore receptor, OmpA family protein, type IV pilus biogenesis stability protein, and OprD family outer membrane porin. Immuoinformatics predicted B-cell and T-cell epitopes from all four proteins. The antigenic epitopes were linked to design a multi-epitopes vaccine construct using GPGPG linkers and adjuvant cholera toxin B subunit to boost the immune responses. A 3D model of the vaccine construct was built, loop refined, and considered for extensive error examination. Disulfide engineering was performed for the stability of the vaccine construct. Blind docking of the vaccine was conducted with host MHC-I, MHC-II, and toll-like receptors 4 (TLR-4) molecules. Molecular dynamic simulation was carried out to understand the vaccine-receptors dynamics and binding stability, as well as to evaluate the presentation of epitopes to the host immune system. Binding energies estimation was achieved to understand intermolecular interaction energies and validate docking and simulation studies. The results suggested that the designed vaccine construct has high potential to induce protective host immune responses and can be a good vaccine candidate for experimental in vivo and in vitro studies.
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Forouharmehr A, Banan A, Mousavi SM, Jaydari A. Development of a Novel Multi-Epitope Vaccine Candidate against Streptococcus Iniae Infection in Fish: An Immunoinformatics Study. ARCHIVES OF RAZI INSTITUTE 2022; 77:45-56. [PMID: 35891737 DOI: 10.22092/ari.2021.353377.1601] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/03/2021] [Indexed: 12/26/2022]
Abstract
Streptococcus Iniae infection is recognized as a disease with substantial economic losses, infecting a wide range of fish species. The limitations of current vaccines and strategies have led to the identification of new methods to control this disease. Multi-epitope vaccines which employ various immunogenic proteins can be promising. The current research project aimed to design an efficient multi-epitope vaccine against Streptococcus Iniae infection in fish. To this end, six immunogenic proteins of Streptococcus Iniae, including FBA, ENO, Sip11, GAPDH, MtsB, and SCPI proteins, were applied for epitope prediction. The best B cell, T cell, and IFNγ epitopes of the immunogenic proteins, as well as interleukin-8, were used to construct a multi-epitope vaccine. Thereafter, different parameters of the designed vaccine, including physicochemical features, antigenicity, secondary structure, and tertiary structure, were evaluated. Moreover, the interaction of the interleukin-8 domain of the designed vaccine and its receptor was investigated by molecular docking strategy. Finally, nucleotide sequence of the vaccine was adapted to express in Escherichia coli. The results of the present study pointed out that the designed vaccine was a stable vaccine with molecular weight and antigenicity score of 45 kDa and 0.936, respectively. Furthermore, the structure analysis results revealed that the designed vaccine contained 23.49% alpha helix, with 90.5% residues in favored region. Finally, it was demonstrated that the interleukin-8 domain of the designed vaccine could be successfully docked to its receptor with the lowest energy of -1020.9. Based on the obtained results, it seems that the designed vaccine can be an efficient candidate to prevent Streptococcus Iniae infection in fish.
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Affiliation(s)
- A Forouharmehr
- Department of Animal Science, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - A Banan
- Department of Marine Science, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - S M Mousavi
- Department of Animal Science, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - A Jaydari
- Department of Pathobiology, Faculty of Veterinary Medicine, Lorestan University, Khorramabad, Iran
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Sireci G, Badami GD, Di Liberto D, Blanda V, Grippi F, Di Paola L, Guercio A, de la Fuente J, Torina A. Recent Advances on the Innate Immune Response to Coxiella burnetii. Front Cell Infect Microbiol 2021; 11:754455. [PMID: 34796128 PMCID: PMC8593175 DOI: 10.3389/fcimb.2021.754455] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
Coxiella burnetii is an obligate intracellular Gram-negative bacterium and the causative agent of a worldwide zoonosis known as Q fever. The pathogen invades monocytes and macrophages, replicating within acidic phagolysosomes and evading host defenses through different immune evasion strategies that are mainly associated with the structure of its lipopolysaccharide. The main transmission routes are aerosols and ingestion of fomites from infected animals. The innate immune system provides the first host defense against the microorganism, and it is crucial to direct the infection towards a self-limiting respiratory disease or the chronic form. This review reports the advances in understanding the mechanisms of innate immunity acting during C. burnetii infection and the strategies that pathogen put in place to infect the host cells and to modify the expression of specific host cell genes in order to subvert cellular processes. The mechanisms through which different cell types with different genetic backgrounds are differently susceptible to C. burnetii intracellular growth are discussed. The subsets of cytokines induced following C. burnetii infection as well as the pathogen influence on an inflammasome-mediated response are also described. Finally, we discuss the use of animal experimental systems for studying the innate immune response against C. burnetii and discovering novel methods for prevention and treatment of disease in humans and livestock.
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Affiliation(s)
- Guido Sireci
- Central Laboratory of Advanced Diagnostic and Biological Research (CLADIBIOR), Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University Hospital "Paolo Giaccone", Università degli studi di Palermo, Palermo, Italy
| | - Giusto Davide Badami
- Central Laboratory of Advanced Diagnostic and Biological Research (CLADIBIOR), Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University Hospital "Paolo Giaccone", Università degli studi di Palermo, Palermo, Italy
| | - Diana Di Liberto
- Central Laboratory of Advanced Diagnostic and Biological Research (CLADIBIOR), Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), University Hospital "Paolo Giaccone", Università degli studi di Palermo, Palermo, Italy
| | - Valeria Blanda
- Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
| | - Francesca Grippi
- Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
| | - Laura Di Paola
- Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
| | - Annalisa Guercio
- Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
| | - José de la Fuente
- SaBio Health and Biotechnology, Instituto de Investigación en Recursos Cinegéticos, IREC -Spanish National Research Council CSIC - University of Castilla-La Mancha UCLM - Regional Government of Castilla-La Mancha JCCM, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
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Akıl M, Aykur M, Karakavuk M, Can H, Döşkaya M. Construction of a multiepitope vaccine candidate against Fasciola hepatica: an in silico design using various immunogenic excretory/secretory antigens. Expert Rev Vaccines 2021; 21:993-1006. [PMID: 34666598 DOI: 10.1080/14760584.2022.1996233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Fasciola hepatica is an important pathogen that causes liver fluke disease in definitive hosts such as livestock animals and humans. Various excretory/secretory products have been used in serological diagnosis and vaccination studies targeting fasciolosis. There are no commercial vaccines against fasciolosis yet. Bioinformatic analysis based on computational methods have lower cost and provide faster output compared to conventional vaccine antigen discovery techniques. The aim of this study was to predict B- and T-cell specific epitopes of four excretory/secretory antigens (Kunitz-type serine protease inhibitor, cathepsin L1, helminth defense molecule, and glutathione S-transferase) of Fasciola hepatica and to construct a multiepitope vaccine candidate against fasciolosis. METHODS AND RESULTS Initially, nonallergic and the highest antigenic B- and T- cell epitopes were selected and then, physico-chemical parameters, secondary and tertiary structures of designed multiepitope vaccine candidate were predicted. Tertiary structure was refined and validated using online bioinformatic tools. Linear and discontinuous B-cell epitopes and disulfide bonds were determined. Finally, molecular docking analysis for MHC-I and MHC-II receptors was performed. CONCLUSION This multi-epitope vaccine candidate antigen, with high immunological properties, can be considered as a promising vaccine candidate for animal experiments and wet lab studies.
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Affiliation(s)
- Mesut Akıl
- Faculty of Medicine, Department of Parasitology, Istanbul Medeniyet University, Istanbul, TURKEY
| | - Mehmet Aykur
- Faculty of Medicine, Department of Parasitology, Tokat Gaziosmanpasa University, Tokat, TURKEY
| | - Muhammet Karakavuk
- Odemis Vocational School, Ege University, Izmir, TURKEY.,Faculty of Medicine, Department of Parasitology, Ege University, Izmir, TURKEY
| | - Hüseyin Can
- Faculty of Science, Department of Biology, Molecular Biology Section, Ege University, Izmir, TURKEY
| | - Mert Döşkaya
- Faculty of Medicine, Department of Parasitology, Ege University, Izmir, TURKEY
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Li Y, Zhu Y, Sha T, Chen Z, Yu M, Zhang F, Ding J. A Multi-Epitope Chitosan Nanoparticles Vaccine of Canine Against Echinococcus granulosus. J Biomed Nanotechnol 2021; 17:910-920. [PMID: 34082876 DOI: 10.1166/jbn.2021.3065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cystic Echinococcosis (CE) is caused by Echinococcus granulosus (Eg), which endangers the health of the intermediate host. Therefore, effective canid vaccines against Eg infection are urgently needed to reduce the incidence of this disease. In the present work, the aim was to predict epitopes in four vaccine candidate antigens (VCAs) in Eg as a basis to design a multi-epitope canine-directed vaccine. This vaccine is based on chitosan nanoparticles (CS-NPs) and is directed against Eg infection in the definitive host. The canine-directed vaccine was designed based on Eg antigens EgM9, Eg_10196, EgA31 and EgG1Y162. Several tools in online servers were used to predict VCAs information, which was combined with B cell, CTL and Th epitopes. Considering that acquiring experimental information in canids is difficult, and that it may be possible to perform future experiments in mice, we predicted both canine and murine T cell epitopes. The multi-epitope vaccine was synthetically prepared by ionic crosslinking method, and CS-NPs was used as adjuvant. The mice were immunized by oral gavage and laser scanning confocal microscopy was used to localize the fluorescein- labeled multi-epitope peptide in the intestinal tract. The final multi-epitope vaccine was construct consist of Co1 targeting peptide, four B-cell epitopes, four canine-directed CTL epitopes and four murine-directed Th epitopes. It has been proven experimentally by this research that multi-epitope antigen concentration merged with microfold cells was high in the CS-NPs vaccine group. The present bioinformatics study is a first step towards the construction of a canine-specific multiepitope vaccine against Eg with twelve predicted epitopes. CS-NPs is a potential adjuvant with relatively safe penetration enhancement delivery and a potent immunostimulant.
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Affiliation(s)
- Yujiao Li
- School of Public Health, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Yuejie Zhu
- Department of Blood Transfusion, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830011, PR China
| | - Tong Sha
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Zhiqiang Chen
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Mingkai Yu
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
| | - Fengbo Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang 830011, PR China
| | - Jianbing Ding
- Department of Immunology, College of Basic Medicine, Xinjiang Medical University, Xinjiang 830011, PR China
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Forouharmehr A. Engineering an efficient poly-epitope vaccine against Toxoplasma gondii infection: A computational vaccinology study. Microb Pathog 2020; 152:104646. [PMID: 33242641 DOI: 10.1016/j.micpath.2020.104646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
Toxoplasmosis is a zoonotic disease caused by Toxoplasma gondii. Despite the importance of toxoplasmosis, there is no comprehensive strategy to control this disease. Hence, applying the new methods such as the poly-epitope vaccine can be successful. In the current project, to engineer a potent poly-epitope vaccine, 10 antigenic proteins including BiP, GRA1, GRA2, GRA5, MIC8, MIC13, P30, PI1, SOD and Rop2 were selected based on the database. Then, B cell, MHCI and MHCII epitopes of the selected antigenic proteins were isolated by the most accurate servers. The best predicted epitopes along with a molecular adjuvant were employed to engineer a poly-epitope vaccine. After engineering, different physicochemical features, secondary and tertiary structures, molecular docking of the designed vaccine were assessed. The results of this project revealed that the designed vaccine with 730 amino acids in length and molecular weight of 77.67 kDa was a soluble protein which could bind to its receptor with an energy of 6223.43. According to the achievements of this study, it seems the designed vaccine can be an appropriate candidate to apply.
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Affiliation(s)
- Ali Forouharmehr
- Department of Animal Science, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
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