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Ali Z, Cardoza JV, Basak S, Narsaria U, Bhattacharjee S, G UM, Isaac SP, Franca TCC, LaPlante SR, George SS. A Multi-epitope Vaccine Candidate Against Bolivian Hemorrhagic fever Caused by Machupo Virus. Appl Biochem Biotechnol 2024; 196:2137-2160. [PMID: 37479961 DOI: 10.1007/s12010-023-04604-9] [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] [Accepted: 06/19/2023] [Indexed: 07/23/2023]
Abstract
Bolivian hemorrhagic fever (BHF) caused by Machupo virus (MACV) is a New World arenavirus having a reported mortality rate of 25-35%. The BHF starts with fever, followed by headache, and nausea which rapidly progresses to severe hemorrhagic phase within 7 days of disease onset. One of the key promoters for MACV viral entry into the cell followed by viral propagation is performed by the viral glycoprotein (GPC). GPC is post-transcriptionally cleaved into GP1, GP2 and a signal peptide. These proteins all take part in the viral infection in host body. Therefore, GPC protein is an ideal target for developing therapeutics against MACV infection. In this study, GPC protein was considered to design a multi-epitope, multivalent vaccine containing antigenic and immunogenic CTL and HTL epitopes. Different structural validations and physicochemical properties were analysed to validate the vaccine. Docking and molecular dynamics simulations were conducted to understand the interactions of the vaccine with various immune receptors. Finally, the vaccine was codon optimised in silico and along with which immune simulation studies was performed in order to evaluate the vaccine's effectiveness in triggering an efficacious immune response against MACV.
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Affiliation(s)
- Zeeshan Ali
- Krupanidhi College of Physiotherapy, Bangalore, Karnataka, 560035, India
| | | | | | | | | | | | - Samuel Paul Isaac
- Krupanidhi College of Physiotherapy, Bangalore, Karnataka, 560035, India
| | - Tanos C C Franca
- Military Institute of Engineering, Rio de Janerio, Brazil
- INRS - Centre Armand-Frappier Santé Biotechnologie, Université de Québec, Laval, Québec, H7V 1B7, Canada
- University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- INRS - Centre Armand-Frappier Santé Biotechnologie, Université de Québec, Laval, Québec, H7V 1B7, Canada
| | - Sudhan S George
- Krupanidhi College of Physiotherapy, Bangalore, Karnataka, 560035, India.
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52
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Ganji M, Bakhshi S, Ahmadi K, Shoari A, Moeini S, Ghaemi A. Rational design of B-cell and T-cell multi epitope-based vaccine against Zika virus, an in silico study. J Biomol Struct Dyn 2024; 42:3426-3440. [PMID: 37190978 DOI: 10.1080/07391102.2023.2213339] [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: 09/01/2022] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Abstract
The Zika virus (ZKV) is a single-stranded positive-sense, enveloped RNA virus. Zika infection during pregnancy can cause congenital microcephaly, Guillain-Barré syndrome, miscarriage, and other CNS abnormalities. The world needs safe and effective vaccinations to fight against ZIKV infection since vaccination is generally regarded as one of the most effective ways to prevent infectious diseases. In the present work, we used immunoinformatics and docking studies to construct a vaccine containing multi-epitopes using the structural and non-structural proteins of ZKV. The structural models of ZKV proteins (PrE, PrM, NS1, and NS2A) were constructed using Pyre2 and RaptorX servers. The epitopes of B-cell, T-cell (HTL and CTL), and IFN-γ were predicted, and each epitope's immunogenic nature and physiochemical properties were confirmed. As an adjuvant, the CPG-Oligodeoxynucleotide, an agonist of Toll-like receptor 9 (TLR9), is associated to cytotoxic T-lymphocytes (CTL) epitopes via PAPAP linker. To assess the binding affinity and the tendency of the designed vaccine to induce an immune response through TLR9, molecular docking was done. In the next step, molecular dynamics (MD) simulation to 100 nanoseconds (ns) was used to evaluate the stability of the interaction of the designed vaccine with TLR9. The designed vaccine is predicted to be highly antigenic, non-toxic, soluble, and stable with low flexibility in MD simulation. MD studies indicated that the finalized vaccine-TLR9 docked complex was stable during simulation time. The vaccine construct is able to stimulate both humoral and cellular immune responses. We suppose that our constructed model of the vaccine may have the ability to induce the host immune response against ZKV. Further studies, including in vitro and in vivo experimental analyses, are needed to prove the constructed vaccine's efficacy with multi-epitopes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shohreh Bakhshi
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Shoari
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Soheila Moeini
- Department of Surgery, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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53
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Kumar A, Singh N, Anvikar AR, Misra G. Monkeypox virus: insights into pathogenesis and laboratory testing methods. 3 Biotech 2024; 14:67. [PMID: 38357674 PMCID: PMC10861412 DOI: 10.1007/s13205-024-03920-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 01/07/2024] [Indexed: 02/16/2024] Open
Abstract
The monkeypox virus (MPXV) is a zoonotic pathogen that transmits between monkeys and humans, exhibiting clinical similarities with the smallpox virus. Studies on the immunopathogenesis of MPXV revealed that an initial strong innate immune response is elicited on viral infection that subsequently helps in circumventing the host defense. Once the World Health Organization (WHO) declared it a global public health emergency in July 2022, it became essential to clearly demarcate the MPXV-induced symptoms from other viral infections. We have exhaustively searched the various databases involving Google Scholar, PubMed, and Medline to extract the information comprehensively compiled in this review. The primary focus of this review is to describe the diagnostic methods for MPXV such as polymerase chain reaction (PCR), and serological assays, along with developments in viral isolation, imaging techniques, and next-generation sequencing. These innovative technologies have the potential to greatly enhance the accuracy of diagnostic procedures. Significant discoveries involving MPXV immunopathogenesis have also been highlighted. Overall, this will be a knowledge repertoire that will be crucial for the development of efficient monitoring and control strategies in response to the MPXV infection helping clinicians and researchers in formulating healthcare strategies.
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Affiliation(s)
- Anoop Kumar
- National Institute of Biologicals, A-32, Sector-62, Institutional Area, Noida, U.P. 201309 India
| | - Neeraj Singh
- National Institute of Biologicals, A-32, Sector-62, Institutional Area, Noida, U.P. 201309 India
| | - Anupkumar R. Anvikar
- National Institute of Biologicals, A-32, Sector-62, Institutional Area, Noida, U.P. 201309 India
| | - Gauri Misra
- National Institute of Biologicals, A-32, Sector-62, Institutional Area, Noida, U.P. 201309 India
- Head Molecular Diagnostics and COVID-19 Kit Testing Laboratory, National Institute of Biologicals (Ministry of Health and Family Welfare), Noida, U.P. 201309 India
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Lee JJ, Abdullah M, Liu J, Carvalho IA, Junior AS, Moreira MAS, Mohammed H, DeLisa MP, McDonough SP, Chang YF. Proteomic profiling of membrane vesicles from Mycobacterium avium subsp. paratuberculosis: Navigating towards an insilico design of a multi-epitope vaccine targeting membrane vesicle proteins. J Proteomics 2024; 292:105058. [PMID: 38065354 DOI: 10.1016/j.jprot.2023.105058] [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: 04/07/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 01/01/2024]
Abstract
Bacteria typically produce membrane vesicles (MVs) at varying levels depending on the surrounding environments. Gram-negative bacterial outer membrane vesicles (OMVs) have been extensively studied for over 30 years, but MVs from Gram-positive bacteria only recently have been a focus of research. In the present study, we isolated MVs from Mycobacterium avium subsp. paratuberculosis (MAP) and analyzed their protein composition using LC-MS/MS. A total of 316 overlapping proteins from two independent preparations were identified in our study, and topology prediction showed these cargo proteins have different subcellular localization patterns. When MVs were administered to bovine-derived macrophages, significant up-regulation of pro-inflammatory cytokines was observed via qRT-PCR. Proteome functional annotation revealed that many of these proteins are involved in the cellular protein metabolic process, tRNA aminoacylation, and ATP synthesis. Secretory proteins with high antigenicity and adhesion capability were mapped for B-cell and T-cell epitopes. Antigenic, Immunogenic and IFN-γ inducing B-cell, MHC-I, and MHC-II epitopes were stitched together through linkers to form multi-epitope vaccine (MEV) construct against MAP. Strong binding energy was observed during the docking of the 3D structure of the MEV with the bovine TLR2, suggesting that the putative MEV may be a promising vaccine candidate against MAP. However, in vitro and in vivo analysis is required to prove the immunogenic concept of the MEV which we will follow in our future studies. SIGNIFICANCE: Johne's disease is a chronic infection caused by Mycobacterium avium subsp. paratuberculosis that has a potential link to Crohn's disease in humans. The disease is characterized by persistent diarrhea and enteritis, resulting in significant economic losses due to reduced milk yield and premature culling of infected animals. The dairy industry in the United States alone experiences losses of approximately USD 250 million due to Johne's disease. The current vaccine against Johne's disease is limited by several factors, including variable efficacy, limited duration of protection, interference with diagnostic tests, inability to prevent infection, and logistical and cost-related challenges. Nevertheless, a multiepitope vaccine design approach targeting M. avium subsp. paratuberculosis has the potential to overcome these challenges and offer improved protection against Johne's disease.
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Affiliation(s)
- Jen-Jie Lee
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, United States
| | - Mohd Abdullah
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, United States
| | - Jinjing Liu
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, United States
| | - Isabel Azevedo Carvalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, United States
| | - Abelardo Silva Junior
- Laboratory of Research in Virology and Immunology, Institute of Biological Sciences and Health, Federal University of Alagoas, Maceió, AL CEP 57072-900, Brazil
| | | | - Hussni Mohammed
- Departement of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, United States; Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, United States; Cornell Institute of Biotechnology, Cornell University, Ithaca, NY 14853, United States
| | - Sean P McDonough
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, United States
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853, United States.
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Mugunthan SP, Venkatesan D, Govindasamy C, Selvaraj D, Mani Chandra H. A preliminary study of the immunogenic response of plant-derived multi-epitopic peptide vaccine candidate of Mycoplasma gallisepticum in chickens. FRONTIERS IN PLANT SCIENCE 2024; 14:1298880. [PMID: 38322423 PMCID: PMC10846684 DOI: 10.3389/fpls.2023.1298880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/28/2023] [Indexed: 02/08/2024]
Abstract
Mycoplasma gallisepticum (MG) is responsible for chronic respiratory disease in avian species, characterized by symptoms like respiratory rales and coughing. Existing vaccines for MG have limited efficacy and require multiple doses. Certain MG cytoadherence proteins (GapA, CrmA, PlpA, and Hlp3) play a crucial role in the pathogen's respiratory tract colonization and infection. Plant-based proteins and therapeutics have gained attention due to their safety and efficiency. In this study, we designed a 21.4-kDa multi-epitope peptide vaccine (MEPV) using immunogenic segments from cytoadherence proteins. The MEPV's effectiveness was verified through computational simulations. We then cloned the MEPV, introduced it into the plant expression vector pSiM24-eGFP, and expressed it in Nicotiana benthamiana leaves. The plant-produced MEPV proved to be immunogenic when administered intramuscularly to chickens. It significantly boosted the production of immunoglobulin Y (IgY)-neutralizing antibodies against cytoadherence protein epitopes in immunized chickens compared to that in the control group. This preliminary investigation demonstrates that the plant-derived MEPV is effective in triggering an immune response in chickens. To establish an efficient poultry health management system and ensure the sustainability of the poultry industry, further research is needed to develop avian vaccines using plant biotechnology.
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Affiliation(s)
| | | | - Chandramohan Govindasamy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Dhivya Selvaraj
- Artificial Intelligence Laboratory, School of Computer Information and Communication Engineering, Kunsan National University, Gunsan, Republic of Korea
| | - Harish Mani Chandra
- Department of Biotechnology, Thiruvalluvar University, Vellore, Tamil Nadu, India
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56
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Aarthy M, Pandiyan GN, Paramasivan R, Kumar A, Gupta B. Identification and prioritisation of potential vaccine candidates using subtractive proteomics and designing of a multi-epitope vaccine against Wuchereria bancrofti. Sci Rep 2024; 14:1970. [PMID: 38263422 PMCID: PMC10806236 DOI: 10.1038/s41598-024-52457-x] [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: 06/26/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
This study employed subtractive proteomics and immunoinformatics to analyze the Wuchereria bancrofti proteome and identify potential therapeutic targets, with a focus on designing a vaccine against the parasite species. A comprehensive bioinformatics analysis of the parasite's proteome identified 51 probable therapeutic targets, among which "Kunitz/bovine pancreatic trypsin inhibitor domain-containing protein" was identified as the most promising vaccine candidate. The candidate protein was used to design a multi-epitope vaccine, incorporating B-cell and T-cell epitopes identified through various tools. The vaccine construct underwent extensive analysis of its antigenic, physical, and chemical features, including the determination of secondary and tertiary structures. Docking and molecular dynamics simulations were performed with HLA alleles, Toll-like receptor 4 (TLR4), and TLR3 to assess its potential to elicit the human immune response. Immune simulation analysis confirmed the predicted vaccine's strong binding affinity with immunoglobulins, indicating its potential efficacy in generating an immune response. However, experimental validation and testing of this multi-epitope vaccine construct would be needed to assess its potential against W. bancrofti and even for a broader range of lymphatic filarial infections given the similarities between W. bancrofti and Brugia.
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Affiliation(s)
- Murali Aarthy
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - G Navaneetha Pandiyan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - R Paramasivan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre (VCRC), Puducherry, India
- Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Tandhalam, Chennai, Tamil Nadu, 602105, India
| | - Bhavna Gupta
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India.
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57
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Gong S, Qiu J, Thayumanavan S. Self-Assembly of Epitope-Tagged Proteins and Antibodies for Delivering Biologics to Antigen Presenting Cells. J Am Chem Soc 2024; 146:33-38. [PMID: 38147631 PMCID: PMC11131140 DOI: 10.1021/jacs.3c09334] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Inspired by the immune system's own strategy for macrophage activation, we describe here a simple self-assembly strategy for generating artificial immune complexes. The built-in recognition domains in the antibody, viz. the Fab and Fc domains, are judiciously leveraged for cargo conjugation to generate the nanoassembly and macrophage targeting, respectively. A responsive linker is engineered into the nanoassembly for releasing the protein cargo inside the macrophages, while ensuring stability during delivery. The design principles are simple and versatile to be applicable to a range of biologics, from small protein toxins to large enzymes, with high loading capacity. This self-assembly platform has the potential for delivering biologics to immune cells with implications in immunotherapy.
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Affiliation(s)
- Shuai Gong
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Jingyi Qiu
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Biomedical Engineering, University of Massachusetts Amherst, Amherst, MA 01003, USA
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58
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Nguyen TL, Kim H. Designing a Multiepitope Vaccine against Eastern Equine Encephalitis Virus: Immunoinformatics and Computational Approaches. ACS OMEGA 2024; 9:1092-1105. [PMID: 38222668 PMCID: PMC10785064 DOI: 10.1021/acsomega.3c07322] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/21/2023] [Accepted: 11/27/2023] [Indexed: 01/16/2024]
Abstract
Eastern equine encephalitis virus (EEEV) is a significant threat to human and animal populations, causing severe encephalitis, often leading to long-term neurological complications and even mortality. Despite this, no approved antiviral treatments or EEEV human vaccines currently exist. In response, we utilized immunoinformatics and computational approaches to design a multiepitope vaccine candidate for EEEV. By screening the structural polyprotein of EEEV, we predicted both T-cell and linear B-cell epitopes. These epitopes underwent comprehensive evaluations for their antigenicity, toxicity, and allergenicity. From these evaluations, we selected ten epitopes highly suitable for vaccine design, which were connected with adjuvants using a stable linker. The resulting vaccine construct demonstrated exceptional antigenic, nontoxic, nonallergenic, and physicochemical properties. Subsequently, we employed molecular docking and molecular dynamics simulations to reveal a stable interaction pattern between the vaccine candidate and Toll-like receptor 5. Besides, computational immune simulations predicted the vaccine's capability to induce robust immune responses. Our study addresses the urgent need for effective EEEV preventive strategies and offers valuable insights for EEEV vaccine development. As EEEV poses a severe threat with potential spread due to climate change, our research provides a crucial step in enhancing public health defenses against this menacing zoonotic disease.
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Affiliation(s)
- Truc Ly Nguyen
- Department
of Agricultural Biotechnology and Research Institute of Agriculture
and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Heebal Kim
- Department
of Agricultural Biotechnology and Research Institute of Agriculture
and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary
Program in Bioinformatics, Seoul National
University, Seoul 08826, Republic
of Korea
- eGnome,
Inc., Seoul 05836, Republic of Korea
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59
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Janes ME, Gottlieb AP, Park KS, Zhao Z, Mitragotri S. Cancer vaccines in the clinic. Bioeng Transl Med 2024; 9:e10588. [PMID: 38193112 PMCID: PMC10771564 DOI: 10.1002/btm2.10588] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/06/2023] [Accepted: 07/22/2023] [Indexed: 01/10/2024] Open
Abstract
Vaccines are an important tool in the rapidly evolving repertoire of immunotherapies in oncology. Although cancer vaccines have been investigated for over 30 years, very few have achieved meaningful clinical success. However, recent advances in areas such antigen identification, formulation development and manufacturing, combination therapy regimens, and indication and patient selection hold promise to reinvigorate the field. Here, we provide a timely update on the clinical status of cancer vaccines. We identify and critically analyze 360 active trials of cancer vaccines according to delivery vehicle, antigen type, indication, and other metrics, as well as highlight eight globally approved products. Finally, we discuss current limitations and future applications for clinical translation of cancer vaccines.
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Affiliation(s)
- Morgan E. Janes
- John A. Paulson School of Engineering & Applied Sciences, Harvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
- Harvard‐MIT Division of Health Sciences and Technology, Massachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Alexander P. Gottlieb
- John A. Paulson School of Engineering & Applied Sciences, Harvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
| | - Kyung Soo Park
- John A. Paulson School of Engineering & Applied Sciences, Harvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
| | - Zongmin Zhao
- Department of Pharmaceutical SciencesCollege of Pharmacy, University of Illinois ChicagoChicagoIllinoisUSA
- University of Illinois Cancer CenterChicagoIllinoisUSA
| | - Samir Mitragotri
- John A. Paulson School of Engineering & Applied Sciences, Harvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
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60
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Zhang G, Han L, Zhao Y, Li Q, Wang S, Shi H. Development and evaluation of a multi-epitope subunit vaccine against Mycoplasma synoviae infection. Int J Biol Macromol 2023; 253:126685. [PMID: 37666406 DOI: 10.1016/j.ijbiomac.2023.126685] [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] [Received: 07/10/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Mycoplasma synoviae is an extremely significant avian pathogen, causing substantial financial harm to poultry farmers worldwide, and impacting both chicken and turkey production. Multi-epitope vaccines offer higher immunity and lower allergenicity compared to conventional vaccines. In this study, our objective is to develop a multi-epitope vaccine for M. synoviae (MSMV) and to evaluate the immune responses and protective efficacy of MSMV in chickens. We successfully identified a total of 14 B-cell, 5 MHC-I, and 16 MHC-II binding epitopes from the immunodominant proteins RS01790, BMP, GrpE, RS00900, and RS00275. Subsequently, we synthesized the multi-epitope vaccine by connecting all conserved epitopes using appropriate linkers. The resulting MSMV demonstrated notable antigenicity, non-allergenic properties, and stability. Notably, the MSMV effectively stimulated high levels of antibody production in chickens. Furthermore, MSMV the vaccine elicited a robust cellular immune response in chickens, characterized by a well-balanced Th1/Th2-type cytokine profile and enhanced lymphocyte proliferation. In immune protection experiments, the vaccinated chickens exhibited reduced air sac lesion scores and tracheal mucosal thickness compared to their non-vaccinated chickens. Additionally, vaccinated chickens displayed lower M. synoviae loads in throat swabs. These findings collectively suggested that the MSMV holds significant potential as a promising vaccine candidate for managing M. synoviae infections.
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Affiliation(s)
- Guihua Zhang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Lejiabao Han
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yuying Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Quan Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
| | - Shifeng Wang
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611-0880, USA.
| | - Huoying Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, Jiangsu, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University (JIRLAAPS), Yangzhou, China.
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61
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Anwar T, Ismail S, Parvaiz F, Abbasi SW, A. Al-Abbasi F, M. Alghamdi A, Al-Regaiey K, Ul-Haq A, Kaleem I, Bashir S, Waheed Y. Computational design of experimentally validated multi-epitopes vaccine against hepatitis E virus: An immunological approach. PLoS One 2023; 18:e0294663. [PMID: 38096182 PMCID: PMC10721065 DOI: 10.1371/journal.pone.0294663] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Hepatitis E virus (HEV) is one of the leading acute liver infections triggered by viral hepatitis. Patients infected with HEV usually recover and the annual death rate is negligible. Currently, there is no HEV licensed vaccine available globally. This study was carried out to design a multi-epitope HEV peptide-based vaccine by retrieving already experimentally validated epitopes from ViPR database leading to epitope prioritization. Epitopes selected as potential vaccine candidates were non-allergen, immunogenic, soluble, non-toxic and IFN gamma positive. The epitopes were linked together by AAY linkers and the linker EAAAK was used to join adjuvant with epitopes. Toll-like receptor (TLR)-4 agonist was used as an adjuvant to boost efficacy of the vaccine. Furthermore, codon optimization followed by disulfide engineering was performed to analyse the designed vaccine's structural stability. Computational modeling of the immune simulation was done to examine the immune response against the vaccine. The designed vaccine construct was docked with TLR-3 receptor for their interactions and then subjected to molecular dynamic simulations. The vaccine model was examined computationally towards the capability of inducing immune responses which showed the induction of both humoral and cell mediated immunity. Taken together, our study suggests an In-silico designed HEV based multi-epitope peptide-based vaccine (MEPV) that needs to be examined in the wet lab-based data that can help to develop a potential vaccine against HEV.
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Affiliation(s)
- Tasneem Anwar
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Saba Ismail
- Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fahed Parvaiz
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Sumra Wajid Abbasi
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amira M. Alghamdi
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid Al-Regaiey
- Department of Physiology, King Saud University, Riyadh, Saudi Arabia
| | - Asad Ul-Haq
- Division of Rheumatology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Imdad Kaleem
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Shahid Bashir
- Neuroscience Center, King Fahad Specialist Hospital Dammam, Dammam, Saudi Arabia
| | - Yasir Waheed
- Office of Research, Innovation & Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
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62
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Boulton S, Poutou J, Gill R, Alluqmani N, He X, Singaravelu R, Crupi MJ, Petryk J, Austin B, Angka L, Taha Z, Teo I, Singh S, Jamil R, Marius R, Martin N, Jamieson T, Azad T, Diallo JS, Ilkow CS, Bell JC. A T cell-targeted multi-antigen vaccine generates robust cellular and humoral immunity against SARS-CoV-2 infection. Mol Ther Methods Clin Dev 2023; 31:101110. [PMID: 37822719 PMCID: PMC10562195 DOI: 10.1016/j.omtm.2023.101110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
SARS-CoV-2, the etiological agent behind the coronavirus disease 2019 (COVID-19) pandemic, has continued to mutate and create new variants with increased resistance against the WHO-approved spike-based vaccines. With a significant portion of the worldwide population still unvaccinated and with waning immunity against newly emerging variants, there is a pressing need to develop novel vaccines that provide broader and longer-lasting protection. To generate broader protective immunity against COVID-19, we developed our second-generation vaccinia virus-based COVID-19 vaccine, TOH-VAC-2, encoded with modified versions of the spike (S) and nucleocapsid (N) proteins as well as a unique poly-epitope antigen that contains immunodominant T cell epitopes from seven different SARS-CoV-2 proteins. We show that the poly-epitope antigen restimulates T cells from the PBMCs of individuals formerly infected with SARS-CoV-2. In mice, TOH-VAC-2 vaccination produces high titers of S- and N-specific antibodies and generates robust T cell immunity against S, N, and poly-epitope antigens. The immunity generated from TOH-VAC-2 is also capable of protecting mice from heterologous challenge with recombinant VSV viruses that express the same SARS-CoV-2 antigens. Altogether, these findings demonstrate the effectiveness of our versatile vaccine platform as an alternative or complementary approach to current vaccines.
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Affiliation(s)
- Stephen Boulton
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Joanna Poutou
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Rida Gill
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Nouf Alluqmani
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Xiaohong He
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Ragunath Singaravelu
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Mathieu J.F. Crupi
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Julia Petryk
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Bradley Austin
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Leonard Angka
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Zaid Taha
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Iris Teo
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Siddarth Singh
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Rameen Jamil
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Ricardo Marius
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Nikolas Martin
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
| | - Taylor Jamieson
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Taha Azad
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
- Centre de Recherche du CHUS, Sherbrooke, QC J1H 5N4, Canada
| | - Jean-Simon Diallo
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Carolina S. Ilkow
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - John C. Bell
- Ottawa Hospital Research Institute, Ottawa, ON K1H 8L6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Razali SA, Shamsir MS, Ishak NF, Low CF, Azemin WA. Riding the wave of innovation: immunoinformatics in fish disease control. PeerJ 2023; 11:e16419. [PMID: 38089909 PMCID: PMC10712311 DOI: 10.7717/peerj.16419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/17/2023] [Indexed: 12/18/2023] Open
Abstract
The spread of infectious illnesses has been a significant factor restricting aquaculture production. To maximise aquatic animal health, vaccination tactics are very successful and cost-efficient for protecting fish and aquaculture animals against many disease pathogens. However, due to the increasing number of immunological cases and their complexity, it is impossible to manage, analyse, visualise, and interpret such data without the assistance of advanced computational techniques. Hence, the use of immunoinformatics tools is crucial, as they not only facilitate the management of massive amounts of data but also greatly contribute to the creation of fresh hypotheses regarding immune responses. In recent years, advances in biotechnology and immunoinformatics have opened up new research avenues for generating novel vaccines and enhancing existing vaccinations against outbreaks of infectious illnesses, thereby reducing aquaculture losses. This review focuses on understanding in silico epitope-based vaccine design, the creation of multi-epitope vaccines, the molecular interaction of immunogenic vaccines, and the application of immunoinformatics in fish disease based on the frequency of their application and reliable results. It is believed that it can bridge the gap between experimental and computational approaches and reduce the need for experimental research, so that only wet laboratory testing integrated with in silico techniques may yield highly promising results and be useful for the development of vaccines for fish.
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Affiliation(s)
- Siti Aisyah Razali
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
- Biological Security and Sustainability Research Interest Group (BIOSES), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Mohd Shahir Shamsir
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Nur Farahin Ishak
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Chen-Fei Low
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Wan-Atirah Azemin
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
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Ramprasadh SV, Rajakumar S, Srinivasan S, Susha D, Sharma S, Chourasiya R. Computer-Aided Multi-Epitope Based Vaccine Design Against Monkeypox Virus Surface Protein A30L: An Immunoinformatics Approach. Protein J 2023; 42:645-663. [PMID: 37615828 DOI: 10.1007/s10930-023-10150-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
Monkeypox, a viral zoonotic disease resembling smallpox, has emerged as a significant national epidemic primarily in Africa. Nevertheless, the recent global dissemination of this pathogen has engendered apprehension regarding its capacity to metamorphose into a sweeping pandemic. To effectively combat this menace, a multi-epitope vaccine has been meticulously engineered with the specific aim of targeting the cell envelope protein of Monkeypox virus (MPXV), thereby stimulating a potent immunological response while mitigating untoward effects. This new vaccine uses T-cell and B-cell epitopes from a highly antigenic, non-allergenic, non-toxic, conserved, and non-homologous A30L protein to provide protection against the virus. In order to ascertain the vaccine design with the utmost efficacy, protein-protein docking methodologies were employed to anticipate the intricate interactions with Toll-like receptors (TLR) 2, 3, 4, 6, and 8. This meticulous approach led the researchers to discern an optimal vaccine architecture, bolstered by affirmative prognostications derived from both molecular dynamics (MD) simulations and immune simulations. The current research findings indicate that the peptides ATHAAFEYSK, FFIVVATAAV, and MNSLSIFFV exhibited antigenic properties and were determined to be non-allergenic and non-toxic. Through the utilization of codon optimization and in-silico cloning techniques, our investigation revealed that the prospective vaccine exhibited a remarkable expression level within Escherichia coli. Moreover, upon conducting immune simulations, we observed the induction of a robust immune response characterized by elevated levels of both B-cell and T-cell mediated immunity. Moreover, as the initial prediction with in-silico techniques has yielded promising results these epitope-based vaccines can be recommended to in vitro and in silico studies to validate their immunogenic properties.
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Affiliation(s)
- S V Ramprasadh
- Department of Bioinformatics, BioNome, Bangalore, 560043, India
| | | | - S Srinivasan
- Department of Bioinformatics, BioNome, Bangalore, 560043, India
| | - D Susha
- Department of Bioinformatics, BioNome, Bangalore, 560043, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bangalore, 560043, India.
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Bellini C, Vergara E, Bencs F, Fodor K, Bősze S, Krivić D, Bacsa B, Surguta SE, Tóvári J, Reljic R, Horváti K. Design and Characterization of a Multistage Peptide-Based Vaccine Platform to Target Mycobacterium tuberculosis Infection. Bioconjug Chem 2023; 34:1738-1753. [PMID: 37606258 PMCID: PMC10587871 DOI: 10.1021/acs.bioconjchem.3c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/09/2023] [Indexed: 08/23/2023]
Abstract
The complex immunopathology ofMycobacterium tuberculosis(Mtb) is one of the main challenges in developing a novel vaccine against this pathogen, particularly regarding eliciting protection against both active and latent stages. Multistage vaccines, which contain antigens expressed in both phases, represent a promising strategy for addressing this issue, as testified by the tuberculosis vaccine clinical pipeline. Given this approach, we designed and characterized a multistage peptide-based vaccine platform containing CD4+ and CD8+ T cell epitopes previously validated for inducing a relevant T cell response against Mtb. After preliminary screening, CFP10 (32-39), GlfT2 (4-12), HBHA (185-194), and PPE15 (1-15) were selected as promising candidates, and we proved that the PM1 pool of these peptides triggered a T cell response in Mtb-sensitized human peripheral blood mononuclear cells (PBMCs). Taking advantage of the use of thiol-maleimide chemoselective ligation, we synthesized a multiepitope conjugate (Ac-CGHP). Our results showed a structure-activity relationship between the conjugation and a higher tendency to fold and assume an ordered secondary structure. Moreover, the palmitoylated conjugate (Pal-CGHP) comprising the same peptide antigens was associated with an enhanced cellular uptake in human and murine antigen-presenting cells and a better immunogenicity profile. Immunization study, conducted in BALB/c mice, showed that Pal-CGHP induced a significantly higher T cell proliferation and production of IFNγ and TNFα over PM1 formulated in the Sigma Adjuvant System.
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Affiliation(s)
- Chiara Bellini
- MTA-TTK
Lendület “Momentum” Peptide-Based Vaccines Research
Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Budapest 1117, Hungary
- Hevesy
György PhD School of Chemistry, Eötvös
Loránd University, Budapest 1117, Hungary
| | - Emil Vergara
- Institute
for Infection and Immunity, St. George’s,
University of London, London SW17 0RE, U.K.
| | - Fruzsina Bencs
- Hevesy
György PhD School of Chemistry, Eötvös
Loránd University, Budapest 1117, Hungary
- Laboratory
of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Kinga Fodor
- Department
of Laboratory Animal Science and Animal Protection, University of Veterinary Medicine, Budapest 1078, Hungary
| | - Szilvia Bősze
- ELKH-ELTE
Research Group of Peptide Chemistry, Eötvös Loránd
Research Network (ELKH), Eötvös
Loránd University, Budapest 1117, Hungary
| | - Denis Krivić
- Division
of Medical Physics and Biophysics, Gottfried Schatz Research Center, Medical University of Graz, 8010 Graz, Austria
| | - Bernadett Bacsa
- Division
of Medical Physics and Biophysics, Gottfried Schatz Research Center, Medical University of Graz, 8010 Graz, Austria
| | - Sára Eszter Surguta
- Department
of Experimental Pharmacology and National Tumor Biology Laboratory, National Institute of Oncology, Budapest 1122, Hungary
| | - József Tóvári
- Department
of Experimental Pharmacology and National Tumor Biology Laboratory, National Institute of Oncology, Budapest 1122, Hungary
| | - Rajko Reljic
- Institute
for Infection and Immunity, St. George’s,
University of London, London SW17 0RE, U.K.
| | - Kata Horváti
- MTA-TTK
Lendület “Momentum” Peptide-Based Vaccines Research
Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Budapest 1117, Hungary
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66
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Khan S, Aziz S, Waqas M, Kakar MA, Ahmad S. Targeted vaccine development against Bilophila wadsworthia to curb colon diseases: A multiepitope approach based on reverse vaccinology and computational analysis. Int J Biol Macromol 2023; 250:126002. [PMID: 37506789 DOI: 10.1016/j.ijbiomac.2023.126002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
The presence of excessive hydrogen sulfide (H2S)-producing bacteria, particularly Bilophila wadsworthia in appendices, is linked to a weaker colonic mucus barrier, inflammatory bowel disease, and colorectal cancer. Thus, targeting this bacterium could reduce sulfide levels and address associated health concerns. Here, we utilized reverse vaccinology and immunoinformatics to design a chimeric vaccine against B. wadsworthia, focusing on membrane-bound and extracellular proteins. Subtractive proteome analysis identified 18 potential vaccine candidates (PVCs), from which six B-cell, eight CD8+ T cell, and six CD4+ T cell epitopes were predicted. Chosen epitopes were assessed for immunological properties and cross-reactivity with human and mouse proteomes. Subsequently, these epitopes were fused with appropriate linkers, PADRE epitope, TAT peptide, and Cholera Toxin B subunit adjuvant to form a robust multi-epitope vaccine (MEV). The MEV's tertiary structure was modelled and validated for reliable analysis. Molecular docking and dynamics simulations demonstrated stable binding of MEV with Toll-like receptor 4. The MEV showed favorable physicochemical characteristics, high expression potential in Escherichia coli, broad population coverage (∼98 %), and cross-protection against different B. wadsworthia strains. Immune simulation suggested induction of strong B and T cell responses, including primary, secondary, and tertiary immune responses. Further experimental studies are necessary to validate these findings.
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Affiliation(s)
- Sara Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Muhammad Waqas
- Department of Biotechnology and genetic Engineering, Hazara University, Mansehra 21120, Pakistan; Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Oman
| | | | - Sohail Ahmad
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan.
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Hafeez S, Achur R, Kiran SK, Thippeswamy NB. Computational prediction of B and T-cell epitopes of Kyasanur Forest Disease virus marker proteins towards the development of precise diagnosis and potent subunit vaccine. J Biomol Struct Dyn 2023; 41:9157-9176. [PMID: 36336957 DOI: 10.1080/07391102.2022.2141882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Kyasanur Forest Disease (KFD), also known as 'monkey fever', caused by KFD Virus (KFDV), is a highly neglected tropical disease endemic to Western Ghat region of Karnataka, India. Recently, KFD, which is fatal for both monkeys and humans with a mortality rate of 2-10% has been found to spread from its epicenter to neighboring districts and states also. The current ELISA based KFD detection method is very non-specific due to cross-reactivity with other flaviviruses. Further, presently available formalin-inactivated vaccine has been found to be less effective leading to disease susceptibility and severity. To address these, the present study was aimed at predicting the potent specific B and T-cell epitopes of KFDV immunogenic marker proteins using diverse computational tools aiming at developing precise diagnostic method and an effective subunit vaccine. Here, we have chosen E, NS1 and NS5 proteins as markers of KFDV by taking into account of their differential and non-overlapping sequences with selected arboviruses. Based on the linear and nonlinear epitope prediction tools and important biophysical parameters, we identified three potential linear and ten nonlinear B-cell epitopes. We also predicted T-cell epitope peptides which binds to MHC class-I and class-II receptors for the effective T-cell activation. Thus, our molecular docking and molecular dynamics simulation analysis has identified six different TH-cell epitopes based on the distribution frequency of MHC-II haplotypes in the human population and one TC-cell epitope from NS5 protein that has maximum interaction with class-I MHC. Overall, we have successfully identified potential B and T-cell epitope marker peptides present in the envelope and two non-structural proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sayad Hafeez
- Department of PG Studies and Research in Microbiology, Kuvempu University, Shivamogga, India
| | - Rajeshwara Achur
- Department of PG Studies and Research in Biochemistry, Kuvempu University, Shivamogga, India
| | - S K Kiran
- Department of Health and family welfare Government of Karnataka, Virus Diagnostic Laboratory, Shivamogga, India
| | - N B Thippeswamy
- Department of PG Studies and Research in Microbiology, Kuvempu University, Shivamogga, India
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Farzan M, Farzan M, Mirzaei Y, Aiman S, Azadegan-Dehkordi F, Bagheri N. Immunoinformatics-based multi-epitope vaccine design for the re-emerging monkeypox virus. Int Immunopharmacol 2023; 123:110725. [PMID: 37556996 DOI: 10.1016/j.intimp.2023.110725] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND On May 7, 2022, WHO reported a new monkeypox case. By May 2023 over 80,000 cases had been reported worldwide outside previously endemic nations. (This primarily affected the men who have sex with men (MSM) community in rich nations). The present research aims to develop a multi-epitope vaccine for the monkeypox virus (MPXV) using structural and cell surface proteins. METHODS The first part of the research involved retrieving protein sequences. The Immune Epitope Database (IEDB) was then used to analyze the B and T lymphocyte epitopes. After analyzing the sensitizing properties, toxicity, antigenicity, and molecular binding, appropriate linkers were utilizedto connect selected epitopes to adjuvants, and the structure of the vaccine was formulated. Algorithms from the field of immunoinformatics predicted the secondary and tertiary structures of vaccines. The physical, chemical, and structural properties were refined and validated to achieve maximum stability. Molecular docking and molecular dynamic simulations were subsequently employed to assess the vaccine's efficacy. Afterward, the ability of the vaccine to interact with toll-like receptors 3 and 4 (TLR3 and TLR4) was evaluated. Finally, the optimized sequence was then introduced into the Escherichia coli (E. coli) PET30A + vector. RESULTS An immunoinformatics evaluation suggested that such a vaccine might be safe revealed that this vaccine is safe, hydrophilic, temperature- and condition-stable, and can stimulate innate immunity by binding to TLR3 and TLR4. CONCLUSION Our findings suggest that the first step in MPXV pathogenesis is structural and cell surface epitopes. In this study, the most effective and promising epitopes were selected and designed throughprecision servers. Furthermore,through the utilization of multi-epitope structures and a combination of two established adjuvants, this research has the potential to be a landmarkin developing an antiviralvaccine against MPXV. However, additional in vitro and in vivo tests are required to confirm these results.
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Affiliation(s)
- Mahour Farzan
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mahan Farzan
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Yousef Mirzaei
- Department of Medical Biochemical Analysis, Cihan University-Erbil, Kurdistan Region, Iraq
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fatemeh Azadegan-Dehkordi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Nader Bagheri
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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69
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Li X, Wen H, Xiao X, Ren Z, Tan C, Fu C. Design of a novel multi-epitope vaccine candidate against endometrial cancer using immunoinformatics and bioinformatics approaches. J Biomol Struct Dyn 2023; 42:11521-11537. [PMID: 37771176 DOI: 10.1080/07391102.2023.2263213] [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: 04/19/2023] [Accepted: 09/18/2023] [Indexed: 09/30/2023]
Abstract
Endometrial cancer (EC) is one of the most common cancers of the female reproductive system. Multi-epitope vaccine may be a promising and effective strategy against EC. In this study, we designed a novel multi-epitope vaccine based on the antigenic proteins PRAME and TMPRSS4 using immunoinformatics and bioinformatics approaches. After a rigorous selection process, 14 cytotoxic T lymphocyte (CTL) epitopes, 6 helper T lymphocyte (HTL) epitopes, and 8 B cell epitopes (BCEs) were finally selected for vaccine construction. To enhance the immunogenicity of the vaccine candidate, the pan HLA DR-binding epitope was included in the vaccine design as an adjuvant. The final vaccine construct had 455 amino acids and a molecular weight of 49.8 kDa, and was predicted to cover 95.03% of the total world population. Docking analysis showed that there were 10 hydrogen bonds and 19 hydrogen bonds in the vaccine-HLA-A*02:01 and vaccine-HLA-DRB1*01:01 complexes, respectively, indicating that the vaccine has a good affinity to MHC molecules. This was further supported by molecular dynamics (MD) simulation. Immune simulation showed that the designed vaccine was able to induce higher levels of immune cell activity, with the secretion of numerous cytokines. The codon adaptation index (CAI) value and GC content of the optimised codon sequences of the vaccine were 0.986 and 54.43%, respectively, indicating that the vaccine has the potential to be highly expressed. The in silico analysis suggested that the designed vaccine may provide a novel therapeutic option for the individualised treatment of EC patients in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaohan Li
- Department of Obstetrics and Gynecology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haicheng Wen
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, Hunan, China
| | - Xiao Xiao
- Department of Obstetrics and Gynecology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhen Ren
- Department of Obstetrics and Gynecology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Caixia Tan
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chun Fu
- Department of Obstetrics and Gynecology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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Ahmad S, Nazarian S, Alizadeh A, Pashapour Hajialilou M, Tahmasebian S, Alharbi M, Alasmari AF, Shojaeian A, Ghatrehsamani M, Irfan M, Pazoki-Toroudi H, Sanami S. Computational design of a multi-epitope vaccine candidate against Langya henipavirus using surface proteins. J Biomol Struct Dyn 2023; 42:10617-10634. [PMID: 37713338 DOI: 10.1080/07391102.2023.2258403] [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: 05/15/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
In July 2022, Langya henipavirus (LayV) was identified in febrile patients in China. There is currently no approved vaccine against this virus. Therefore, this research aimed to design a multi-epitope vaccine against LayV using reverse vaccinology. The best epitopes were selected from LayV's fusion protein (F) and glycoprotein (G), and a multi-epitope vaccine was designed using these epitopes, adjuvant, and appropriate linkers. The physicochemical properties, antigenicity, allergenicity, toxicity, and solubility of the vaccine were evaluated. The vaccine's secondary and 3D structures were predicted, and molecular docking and molecular dynamics (MD) simulations were used to assess the vaccine's interaction and stability with toll-like receptor 4 (TLR4). Immune simulation, codon optimization, and in silico cloning of the vaccine were also performed. The vaccine candidate showed good physicochemical properties, as well as being antigenic, non-allergenic, and non-toxic, with acceptable solubility. Molecular docking and MD simulation revealed that the vaccine and TLR4 have stable interactions. Furthermore, immunological simulation of the vaccine indicated its ability to elicit immune responses against LayV. The vaccine's increased expression was also ensured using codon optimization. This study's findings were encouraging, but in vitro and in vivo tests are needed to confirm the vaccine's protective effect.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Computer Sciences, Virginia Tech, Blacksburg, VA, USA
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Shahin Nazarian
- Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Akram Alizadeh
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Maryam Pashapour Hajialilou
- School of Metallurgy and Materials Engineering, Iran University of Science and Technology (IUST), Tehran, Iran
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - 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
| | - Ali Shojaeian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mahdi Ghatrehsamani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Samira Sanami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
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Zhao X, Wang X, Yuan M, Zhang X, Yang X, Guan X, Li S, Ma J, Qiu HJ, Li Y. Identification of two novel T cell epitopes on the E2 protein of classical swine fever virus C-strain. Vet Microbiol 2023; 284:109814. [PMID: 37356277 DOI: 10.1016/j.vetmic.2023.109814] [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: 04/25/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/27/2023]
Abstract
C-strain, also known as the HCLV strain, is a well-known live attenuated vaccine against classical swine fever (CSF), a devastating disease caused by classical swine fever virus (CSFV). Vaccination with C-strain induces a rapid onset of protection, which is associated with virus-specific gamma interferon (IFN-γ)-secreting CD8+ T cell responses. The E2 protein of CSFV is a major protective antigen. However, the T cell epitopes on the E2 protein remain largely unknown. In this study, eight overlapping nonapeptides of the E2 protein were predicted and synthesized to screen for potential T cell epitopes on the CSFV C-strain E2 protein. Molecular docking was performed on the candidate epitopes with the swine leukocyte antigen-1*0401. The analysis obtained two highly conserved T cell epitopes, 90STEEMGDDF98 and 331ATDRHSDYF339, which were further identified by enzyme-linked immunospot assay. Interestingly, the mutants deleting or substituting the epitopes are nonviable. Further analysis demonstrated that 90STEEMGDDF98 is crucial for the E2 homodimerization, while CSFV infection is significantly inhibited by the 331ATDRHSDYF339 peptide treatment. The two novel T cell epitopes can be used to design new vaccines that are able to provide rapid-onset protection.
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Affiliation(s)
- Xiaotian Zhao
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China; Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Xiao Wang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Binzhou Medical University, Yantai, China
| | - Mengqi Yuan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xin Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaoke Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiangyu Guan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shuwen Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jifei Ma
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China.
| | - Hua-Ji Qiu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Yongfeng Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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72
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Khan MT, Mahmud A, Islam MM, Sumaia MSN, Rahim Z, Islam K, Iqbal A. Multi-epitope vaccine against drug-resistant strains of Mycobacterium tuberculosis: a proteome-wide subtraction and immunoinformatics approach. Genomics Inform 2023; 21:e42. [PMID: 37813638 PMCID: PMC10584640 DOI: 10.5808/gi.23021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 10/11/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Toll-like receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.
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Affiliation(s)
- Md Tahsin Khan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Araf Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md. Muzahidul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mst. Sayedatun Nessa Sumaia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Zeaur Rahim
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kamrul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Asif Iqbal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
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73
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Rezvanirad A, Habibi M, Farokhi M, Asadi Karam MR. Immunogenic Potential and Therapeutic Efficacy of Multi-Epitope Encapsulated Silk Fibroin Nanoparticles against Pseudomonas aeruginosa-Mediated Urinary Tract Infections. Macromol Biosci 2023; 23:e2300074. [PMID: 37159936 DOI: 10.1002/mabi.202300074] [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: 02/25/2023] [Revised: 05/01/2023] [Indexed: 05/11/2023]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) causing urinary tract infections (UTIs) are a major concern among hospital-acquired infections. The need for an effective vaccine that reduces the infections is imperative. This study aims to evaluate the efficacy of a multi-epitope vaccine encapsulated in silk fibroin nanoparticles (SFNPs) against P. aeruginosa-mediated UTIs. A multi-epitope is constructed from nine proteins of P. aeruginosa using immunoinformatic analysis, expressed, and purified in BL21 (DE3) cells. The encapsulation efficiency of the multi-epitope in SFNPs is 85% with a mean particle size of 130 nm and 24% of the encapsulated antigen is released after 35 days. The vaccine formulations adjuvanted with SFNPs or alum significantly improve systemic and mucosal humoral responses and the cytokine profile (IFN-γ, IL-4, and IL-17) in mice. Additionally, the longevity of the IgG response is maintained for at least 110 days in a steady state. In a bladder challenge, mice treated with the multi-epitope admixed with alum or encapsulated in SFNPs demonstrate significant protection of the bladder and kidneys against P. aeruginosa. This study highlights the promising therapeutic potential of a multi-epitope vaccine encapsulated in SFNPs or adjuvanted with alum against P. aeruginosa infections.
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Affiliation(s)
- Azam Rezvanirad
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Mehri Habibi
- Department of Molecular Biology, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Mehdi Farokhi
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, 1316943551, Iran
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74
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Matos AS, Invenção MDCV, Moura IAD, Freitas ACD, Batista MVDA. Immunoinformatics applications in the development of therapeutic vaccines against human papillomavirus-related infections and cervical cancer. Rev Med Virol 2023; 33:e2463. [PMID: 37291746 DOI: 10.1002/rmv.2463] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/09/2023] [Accepted: 05/27/2023] [Indexed: 06/10/2023]
Abstract
The human papillomavirus (HPV) represents the most prevalent sexually transmitted infectious agent worldwide. HPV penetrates the epithelium through microlesions and establishes an infectious focus that can lead to the development of cervical cancer. Prophylactic HPV vaccines are available, but do not affect already-established infections. Using in silico prediction tools is a promising strategy for identifying and selecting vaccine candidate T cell epitopes. An advantage of this strategy is that epitopes can be selected according to the degree of conservation within a group of antigenic proteins. This makes achieving comprehensive genotypic coverage possible with a small set of epitopes. Therefore, this paper revises the general characteristics of HPV biology and the current knowledge on developing therapeutic peptide vaccines against HPV-related infections and cervical cancer.
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Affiliation(s)
- Alexandre Santos Matos
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, Sao Cristovao, Brazil
| | - Maria da Conceição Viana Invenção
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Ingrid Andrêssa de Moura
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy (LEMTE), Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, Sao Cristovao, Brazil
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75
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Ullah A, Shahid FA, Haq MU, Tahir ul Qamar M, Irfan M, Shaker B, Ahmad S, Alrumaihi F, Allemailem KS, Almatroudi A. An integrative reverse vaccinology, immunoinformatic, docking and simulation approaches towards designing of multi-epitopes based vaccine against monkeypox virus. J Biomol Struct Dyn 2023; 41:7821-7834. [PMID: 36129135 PMCID: PMC9527787 DOI: 10.1080/07391102.2022.2125441] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/11/2022] [Indexed: 12/31/2022]
Abstract
Monkeypox is a viral zoonotic disease that is caused by the monkeypox virus (MPXV) and is mainly transmitted to human through close contact with an infected person, animal, or fomites which is contaminated by the virus. In the present research work, reverse vaccinology and several other bioinformatics and immunoinformatics tools were utilized to design multi-epitopes-based vaccine against MPXV by exploring three probable antigenic extracellular proteins: cupin domain-containing protein, ABC transporter ATP-binding protein and DUF192 domain-containing protein. Both cellular and humoral immunity induction were the main concerning qualities of the vaccine construct, hence from selected proteins both B and T-cells epitopes were predicted. Antigenicity, allergenicity, toxicity, and water solubility of the predicted epitopes were assessed and only probable antigenic, non-allergic, non-toxic and good water-soluble epitopes were used in the multi-epitopes vaccine construct. The developed vaccine was found to be potentially effective against MPXV and to be highly immunogenic, cytokine-producing, antigenic, non-toxic, non-allergenic, and stable. Additionally, to increase stability and expression efficiency in the host E. coli, disulfide engineering, codon adaptation, and in silico cloning were employed. Molecular docking and other biophysical approaches were utilized to evaluate the binding mode and dynamic behavior of the vaccine construct with TLR-2, TLR-4, and TLR-8. The outcomes of the immune simulation demonstrated that both B and T cells responded more strongly to the vaccination component. The detailed in silico analysis concludes that the proposed vaccine will induce a strong immune response against MPXV infection, making it a promising target for additional experimental trials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Farah Ali Shahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mahboob Ul Haq
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - Bilal Shaker
- Department of Biomedical Engineering, Chung-Ang University, Seoul, South Korea
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Faris Alrumaihi
- 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
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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76
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Yin Z, Li M, Niu C, Yu M, Xie X, Haimiti G, Guo W, Shi J, He Y, Ding J, Zhang F. Design of multi-epitope vaccine candidate against Brucella type IV secretion system (T4SS). PLoS One 2023; 18:e0286358. [PMID: 37561685 PMCID: PMC10414599 DOI: 10.1371/journal.pone.0286358] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/22/2023] [Indexed: 08/12/2023] Open
Abstract
Brucellosis is a common zoonosis, which is caused by Brucella infection, and Brucella often infects livestock, leading to abortion and infertility. At present, human brucellosis remains one of the major public health problems in China. According to previous research, most areas in northwest China, including Xinjiang, Tibet, and other regions, are severely affected by Brucella. Although there are vaccines against animal Brucellosis, the effect is often poor. In addition, there is no corresponding vaccine for human Brucellosis infection. Therefore, a new strategy for early prevention and treatment of Brucella is needed. A multi-epitope vaccine should be developed. In this study, we identified the antigenic epitopes of the Brucella type IV secretion system VirB8 and Virb10 using an immunoinformatics approach, and screened out 2 cytotoxic T lymphocyte (CTL) epitopes, 9 helper T lymphocyte (HTL) epitopes, 6 linear B cell epitopes, and 6 conformational B cell epitopes. These advantageous epitopes are spliced together through different linkers to construct a multi-epitope vaccine. The silico tests showed that the multi-epitope vaccine was non-allergenic and had a strong interaction with TLR4 molecular docking. In immune simulation results, the vaccine construct may be useful in helping brucellosis patients to initiate cellular and humoral immunity. Overall, our findings indicated that the multi-epitope vaccine construct has a high-quality structure and suitable characteristics, which may provide a theoretical basis for the development of a Brucella vaccine.
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Affiliation(s)
- Zhengwei Yin
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Min Li
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Ce Niu
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Mingkai Yu
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Xinjiang, China
| | - Xinru Xie
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Gulishati Haimiti
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Wenhong Guo
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Juan Shi
- The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Yueyue He
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Xinjiang, China
| | - Jianbing Ding
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
| | - Fengbo Zhang
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang, China
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77
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Chattopadhyay A, Jailani AAK, Mandal B. Exigency of Plant-Based Vaccine against COVID-19 Emergence as Pandemic Preparedness. Vaccines (Basel) 2023; 11:1347. [PMID: 37631915 PMCID: PMC10458178 DOI: 10.3390/vaccines11081347] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
After two years since the declaration of COVID-19 as a pandemic by the World Health Organization (WHO), more than six million deaths have occurred due to SARS-CoV-2, leading to an unprecedented disruption of the global economy. Fortunately, within a year, a wide range of vaccines, including pathogen-based inactivated and live-attenuated vaccines, replicating and non-replicating vector-based vaccines, nucleic acid (DNA and mRNA)-based vaccines, and protein-based subunit and virus-like particle (VLP)-based vaccines, have been developed to mitigate the severe impacts of the COVID-19 pandemic. These vaccines have proven highly effective in reducing the severity of illness and preventing deaths. However, the availability and supply of COVID-19 vaccines have become an issue due to the prioritization of vaccine distribution in most countries. Additionally, as the virus continues to mutate and spread, questions have arisen regarding the effectiveness of vaccines against new strains of SARS-CoV-2 that can evade host immunity. The urgent need for booster doses to enhance immunity has been recognized. The scarcity of "safe and effective" vaccines has exacerbated global inequalities in terms of vaccine coverage. The development of COVID-19 vaccines has fallen short of the expectations set forth in 2020 and 2021. Furthermore, the equitable distribution of vaccines at the global and national levels remains a challenge, particularly in developing countries. In such circumstances, the exigency of plant virus-based vaccines has become apparent as a means to overcome supply shortages through fast manufacturing processes and to enable quick and convenient distribution to millions of people without the reliance on a cold chain system. Moreover, plant virus-based vaccines have demonstrated both safety and efficacy in eliciting robust cellular immunogenicity against COVID-19 pathogens. This review aims to shed light on the advantages and disadvantages of different types of vaccines developed against SARS-CoV-2 and provide an update on the current status of plant-based vaccines in the fight against the COVID-19 pandemic.
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Affiliation(s)
- Anirudha Chattopadhyay
- Pulses Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar 385506, India;
| | - A. Abdul Kader Jailani
- Department of Plant Pathology, North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
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Jan S, Fratzke AP, Felgner J, Hernandez-Davies JE, Liang L, Nakajima R, Jasinskas A, Supnet M, Jain A, Felgner PL, Davies DH, Gregory AE. Multivalent vaccines demonstrate immunogenicity and protect against Coxiella burnetii aerosol challenge. Front Immunol 2023; 14:1192821. [PMID: 37533862 PMCID: PMC10390735 DOI: 10.3389/fimmu.2023.1192821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Vaccines are among the most cost-effective public health measures for controlling infectious diseases. Coxiella burnetii is the etiological agent of Q fever, a disease with a wide clinical spectrum that ranges from mild symptoms, such as fever and fatigue, to more severe disease, such as pneumonia and endocarditis. The formalin-inactivated whole-cell vaccine Q-VAX® contains hundreds of antigens and confers lifelong protection in humans, but prior sensitization from infection or vaccination can result in deleterious reactogenic responses to vaccination. Consequently, there is great interest in developing non-reactogenic alternatives based on adjuvanted recombinant proteins. In this study, we aimed to develop a multivalent vaccine that conferred protection with reduced reactogenicity. We hypothesized that a multivalent vaccine consisting of multiple antigens would be more immunogenic and protective than a monovalent vaccine owing to the large number of potential protective antigens in the C. burnetii proteome. To address this, we identified immunogenic T and B cell antigens, and selected proteins were purified to evaluate with a combination adjuvant (IVAX-1), with or without C. burnetii lipopolysaccharide (LPS) in immunogenicity studies in vivo in mice and in a Hartley guinea pig intratracheal aerosol challenge model using C. burnetii strain NMI RSA 493. The data showed that multivalent vaccines are more immunogenic than monovalent vaccines and more closely emulate the protection achieved by Q-VAX. Although six antigens were the most immunogenic, we also discovered that multiplexing beyond four antigens introduces detectable reactogenicity, indicating that there is an upper limit to the number of antigens that can be safely included in a multivalent Q-fever vaccine. C. burnetii LPS also demonstrates efficacy as a vaccine antigen in conferring protection in an otherwise monovalent vaccine formulation, suggesting that its addition in multivalent vaccines, as demonstrated by a quadrivalent formulation, would improve protective responses.
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Affiliation(s)
- Sharon Jan
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Alycia P. Fratzke
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, Bryan, TX, United States
- Department of Pathology, Charles River Laboratories, Reno, NV, United States
| | - Jiin Felgner
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Jenny E. Hernandez-Davies
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Li Liang
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Rie Nakajima
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Algimantas Jasinskas
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Medalyn Supnet
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Aarti Jain
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Philip L. Felgner
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - D. Huw Davies
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
| | - Anthony E. Gregory
- Vaccine Research & Development Center, Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA, United States
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79
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Kanse S, Khandelwal M, Pandey RK, Khokhar M, Desai N, Kumbhar BV. Designing a Multi-Epitope Subunit Vaccine against VP1 Major Coat Protein of JC Polyomavirus. Vaccines (Basel) 2023; 11:1182. [PMID: 37514998 PMCID: PMC10386578 DOI: 10.3390/vaccines11071182] [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: 04/19/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The JC polyomavirus virus (JCPyV) affects more than 80% of the human population in their early life stage. It mainly affects immunocompromised individuals where virus replication in oligodendrocytes and astrocytes may lead to fatal progressive multifocal encephalopathy (PML). Virus protein 1 (VP1) is one of the major structural proteins of the viral capsid, responsible for keeping the virus alive in the gastrointestinal and urinary tracts. VP1 is often targeted for antiviral drug and vaccine development. Similarly, this study implied immune-informatics and molecular modeling methods to design a multi-epitope subunit vaccine targeting JCPyV. The VP1 protein epitopic sequences, which are highly conserved, were used to build the vaccine. This designed vaccine includes two adjuvants, five HTL epitopes, five CTL epitopes, and two BCL epitopes to stimulate cellular, humoral, and innate immune responses against the JCPyV. Furthermore, molecular dynamics simulation (100 ns) studies were used to examine the interaction and stability of the vaccine protein with TLR4. Trajectory analysis showed that the vaccine and TLR4 receptor form a stable complex. Overall, this study may contribute to the path of vaccine development against JCPyV.
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Affiliation(s)
- Sukhada Kanse
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Vile Parle (West), Mumbai 400056, Maharashtra, India (N.D.)
| | - Mehak Khandelwal
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Vile Parle (West), Mumbai 400056, Maharashtra, India (N.D.)
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177 Stockholm, Sweden
| | - Manoj Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Jodhpur 342005, Rajasthan, India
| | - Neetin Desai
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Vile Parle (West), Mumbai 400056, Maharashtra, India (N.D.)
| | - Bajarang Vasant Kumbhar
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS (Deemed to be) University, Vile Parle (West), Mumbai 400056, Maharashtra, India (N.D.)
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80
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Moin AT, Ullah MA, Patil RB, Faruqui NA, Araf Y, Das S, Uddin KMK, Hossain MS, Miah MF, Moni MA, Chowdhury DUS, Islam S. A computational approach to design a polyvalent vaccine against human respiratory syncytial virus. Sci Rep 2023; 13:9702. [PMID: 37322049 PMCID: PMC10272159 DOI: 10.1038/s41598-023-35309-y] [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: 11/14/2022] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Human Respiratory Syncytial Virus (RSV) is one of the leading causes of lower respiratory tract infections (LRTI), responsible for infecting people from all age groups-a majority of which comprises infants and children. Primarily, severe RSV infections are accountable for multitudes of deaths worldwide, predominantly of children, every year. Despite several efforts to develop a vaccine against RSV as a potential countermeasure, there has been no approved or licensed vaccine available yet, to control the RSV infection effectively. Therefore, through the utilization of immunoinformatics tools, a computational approach was taken in this study, to design a multi-epitope polyvalent vaccine against two major antigenic subtypes of RSV, RSV-A and RSV-B. Potential predictions of the T-cell and B-cell epitopes were followed by extensive tests of antigenicity, allergenicity, toxicity, conservancy, homology to human proteome, transmembrane topology, and cytokine-inducing ability. The peptide vaccine was modeled, refined, and validated. Molecular docking analysis with specific Toll-like receptors (TLRs) revealed excellent interactions with suitable global binding energies. Additionally, molecular dynamics (MD) simulation ensured the stability of the docking interactions between the vaccine and TLRs. Mechanistic approaches to imitate and predict the potential immune response generated by the administration of vaccines were determined through immune simulations. Subsequent mass production of the vaccine peptide was evaluated; however, there remains a necessity for further in vitro and in vivo experiments to validate its efficacy against RSV infections.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh.
| | - Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Rajesh B Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society's, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Nairita Ahsan Faruqui
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Sowmen Das
- Department of Computer Science and Engineering, School of Physical Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Khaza Md Kapil Uddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Md Shakhawat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Md Faruque Miah
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Mohammad Ali Moni
- Bone Biology Division, The Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, Australia
- Artificial Intelligence and Data Science, Faculty of Health and Behavioural Sciences, School of Health and Rehabilitation Sciences, The University of Queensland, Brisbane, Australia
| | - Dil Umme Salma Chowdhury
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh.
| | - Saiful Islam
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh.
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81
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Ezzemani W, Windisch MP, Altawalah H, Guessous F, Saile R, Benjelloun S, Kettani A, Ezzikouri S. Design of a multi-epitope Zika virus vaccine candidate - an in-silico study. J Biomol Struct Dyn 2023; 41:3762-3771. [PMID: 35318896 DOI: 10.1080/07391102.2022.2055648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/15/2022] [Indexed: 01/12/2023]
Abstract
Zika virus (ZIKV), an RNA virus, rapidly spreads Aedes mosquito-borne sickness. Currently, there are neither effective vaccines nor therapeutics available to prevent or treat ZIKV infection. In this study, to address these unmet medical needs, we aimed to design B- and T-cell candidate multi-epitope-based subunit against ZIKV using an in silico approach. In this study we applied immunoinformatics, molecular docking, and dynamic simulation assessments targeting the most immunogenic proteins; the capsid (C), envelope (E) proteins and the non-stuctural protein (NS1), described in our previous study, and which predicted immunodominant B and T cell epitopes. The final non-allergenic and highly antigenic multi-epitope was constituted of immunogenic screened-epitopes (3 CTL and 3 HTL) and the β-defensin as an adjuvant that have been linked using EAAAK, AAY, and GPGPG linkers, respectively. The final construct containing 143 amino acids was characterized for its allergenicity, antigenicity, and physiochemical properties; and found to be safe and immunogenic with a good prediction of solubility. The existence of IFN-γ epitopes asserts the capacity to trigger strong immune responses. Subsequently, the molecular docking among vaccine and immune receptors (TLR2/TLR4) was revealed with a good binding affinity with and stable molecular interactions. Molecular dynamics simulation confirmed the stability of the complexes. Finally, the construct was subjected to in silico cloning demonstrating the efficiently of its expression in E.coli. However, this study needs the experimental validation to demonstrate vaccine safety and 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
| | - Marc P Windisch
- Applied Molecular Virology Laboratory, Discovery Biology Department, Institut Pasteur Korea, Gyeonggi-do, South Korea
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait
- Virology Unit, Yacoub Behbehani center, Sabah Hospital, Ministry of Health, Kuwait
| | - Fadila Guessous
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Soumaya Benjelloun
- Virology Unit, Viral Hepatitis Laboratory, 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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82
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de Oliveira Matos A, Vilela Rodrigues TC, Tiwari S, Dos Santos Dantas PH, Sartori GR, de Carvalho Azevedo VA, Martins Da Silva JH, de Castro Soares S, Silva-Sales M, Sales-Campos H. Immunoinformatics-guided design of a multi-valent vaccine against Rotavirus and Norovirus (ChRNV22). Comput Biol Med 2023; 159:106941. [PMID: 37105111 DOI: 10.1016/j.compbiomed.2023.106941] [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: 12/02/2022] [Revised: 03/17/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Rotavirus (RV) and Norovirus (NV) are the main viral etiologic agents of acute gastroenteritis (AG), a serious pediatric condition associated with significant death rates and long-term complications. Anti-RV vaccination has been proved efficient in the reduction of severe AG worldwide, however, the available vaccines are all attenuated and have suboptimal efficiencies in developing countries, where AG leads to substantial disease burden. On the other hand, no NV vaccine has been licensed so far. Therefore, we used immunoinformatics tools to develop a multi-epitope vaccine (ChRNV22) to prevent severe AG by RV and NV. Epitopes were predicted against 17 prevalent genotypes of four structural proteins (NV's VP1, RV's VP4, VP6 and VP7), and then assembled in a chimeric protein, with two small adjuvant sequences (tetanus toxin P2 epitope and a conserved sequence of RV's enterotoxin, NSP4). Simulations of the immune response and interactions with immune receptors indicated the immunogenic properties of ChRNV22, including a Th1-biased response. In silico search for putative host-homologous, allergenic and toxic regions also indicated the vaccine safety. In summary, we developed a multi-epitope vaccine against different NV and RV genotypes that seems promising for the prevention of severe AG, which will be further assessed by in vivo tests.
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Affiliation(s)
- Amanda de Oliveira Matos
- Laboratory of Mucosal Immunology and Immunoinformatics (LIM), Institute of Tropical Pathology and Public Health, Federal University of Goiás (UFG), Goiânia, 746050-050, Brazil
| | - Thaís Cristina Vilela Rodrigues
- Laboratory of Cellular and Molecular Genetics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, 31270-901, Brazil
| | - Sandeep Tiwari
- Institute of Biology, Federal University of Bahia (UFBA), Salvador, 40170-115, Brazil; Institute of Health Sciences, Federal University of Bahia (UFBA), Salvador, 40231-300, Brazil
| | - Pedro Henrique Dos Santos Dantas
- Laboratory of Mucosal Immunology and Immunoinformatics (LIM), Institute of Tropical Pathology and Public Health, Federal University of Goiás (UFG), Goiânia, 746050-050, Brazil
| | | | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics (LGCM), Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte, 31270-901, Brazil
| | | | - Siomar de Castro Soares
- Department of Immunology, Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba, 38025-180, Brazil
| | - Marcelle Silva-Sales
- Laboratory of Virology and Cellular Culture (LABVICC), Institute of Tropical Pathology and Public Health, Federal University of Goiás (UFG), Goiânia, 746050-050, Brazil
| | - Helioswilton Sales-Campos
- Laboratory of Mucosal Immunology and Immunoinformatics (LIM), Institute of Tropical Pathology and Public Health, Federal University of Goiás (UFG), Goiânia, 746050-050, Brazil.
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83
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Sanami S, Nazarian S, Ahmad S, Raeisi E, Tahir ul Qamar M, Tahmasebian S, Pazoki-Toroudi H, Fazeli M, Ghatreh Samani M. In silico design and immunoinformatics analysis of a universal multi-epitope vaccine against monkeypox virus. PLoS One 2023; 18:e0286224. [PMID: 37220125 PMCID: PMC10205007 DOI: 10.1371/journal.pone.0286224] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Monkeypox virus (MPXV) outbreaks have been reported in various countries worldwide; however, there is no specific vaccine against MPXV. In this study, therefore, we employed computational approaches to design a multi-epitope vaccine against MPXV. Initially, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), linear B lymphocytes (LBL) epitopes were predicted from the cell surface-binding protein and envelope protein A28 homolog, both of which play essential roles in MPXV pathogenesis. All of the predicted epitopes were evaluated using key parameters. A total of 7 CTL, 4 HTL, and 5 LBL epitopes were chosen and combined with appropriate linkers and adjuvant to construct a multi-epitope vaccine. The CTL and HTL epitopes of the vaccine construct cover 95.57% of the worldwide population. The designed vaccine construct was found to be highly antigenic, non-allergenic, soluble, and to have acceptable physicochemical properties. The 3D structure of the vaccine and its potential interaction with Toll-Like receptor-4 (TLR4) were predicted. Molecular dynamics (MD) simulation confirmed the vaccine's high stability in complex with TLR4. Finally, codon adaptation and in silico cloning confirmed the high expression rate of the vaccine constructs in strain K12 of Escherichia coli (E. coli). These findings are very encouraging; however, in vitro and animal studies are needed to ensure the potency and safety of this vaccine candidate.
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Affiliation(s)
- Samira Sanami
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Shahin Nazarian
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, United States of America
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Elham Raeisi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Muhammad Tahir ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Fazeli
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Mahdi Ghatreh Samani
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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84
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Miles S, Dematteis S, Mourglia-Ettlin G. Experimental cystic echinococcosis as a proof of concept for the development of peptide-based vaccines following a novel rational workflow. Biologicals 2023; 82:101684. [PMID: 37201271 DOI: 10.1016/j.biologicals.2023.101684] [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: 04/19/2022] [Revised: 03/14/2023] [Accepted: 04/24/2023] [Indexed: 05/20/2023] Open
Abstract
Vaccines are among the most important advances in medicine throughout the human history. However, conventional vaccines exhibit several drawbacks in terms of design and production costs. Peptide-based vaccines are attractive alternatives, since they can be designed mainly in silico, can be produced cheaply and safely, and are able to induce immune responses exclusively towards protective epitopes. Yet, a proper peptide design is needed, not only to generate peptide-specific immune responses, but also for them to recognize the native protein in the occurrence of a natural infection. Herein, we propose a rational workflow for developing peptide-based vaccines including novel steps that assure the cross-recognition of native proteins. In this regard, we increased the probability of generating efficient antibodies through the selection of linear B-cell epitopes free of post-translational modifications followed by analyzing the 3D-structure similarity between the peptide in-solution vs. within its parental native protein. As a proof of concept, this workflow was applied to a set of seven previously suggested potential protective antigens against the infection by Echinococcus granulosus sensu lato. Finally, two peptides were obtained showing the capacity to induce specific antibodies able to exert anti-parasite activities in different in vitro settings, as well as to provide significant protection in the murine model of secondary echinococcosis.
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Affiliation(s)
- Sebastian Miles
- Area Inmunología, DEPBIO/IQB, Facultad de Química/Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay; Graduate Program in Chemistry, Facultad de Química, Universidad de la Republica, Uruguay
| | - Sylvia Dematteis
- Area Inmunología, DEPBIO/IQB, Facultad de Química/Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay
| | - Gustavo Mourglia-Ettlin
- Area Inmunología, DEPBIO/IQB, Facultad de Química/Facultad de Ciencias, Universidad de la Republica, Montevideo, Uruguay.
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85
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Loan Young T, Chang Wang K, James Varley A, Li B. Clinical Delivery of Circular RNA: Lessons Learned from RNA Drug Development. Adv Drug Deliv Rev 2023; 197:114826. [PMID: 37088404 DOI: 10.1016/j.addr.2023.114826] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 04/25/2023]
Abstract
Circular RNAs (circRNA) represent a distinct class of covalently closed-loop RNA molecules, which play diverse roles in regulating biological processes and disease states. The enhanced stability of synthetic circRNAs compared to their linear counterparts has recently garnered considerable research interest, paving the way for new therapeutic applications. While clinical circRNA technology is still in its early stages, significant advancements in mRNA technology offer valuable insights into its potential future applications. Two primary obstacles that must be addressed are the development of efficient production methods and the optimization of delivery systems. To expedite progress in this area, this review aims to provide an overview of the current state of knowledge on circRNA structure and function, outline recent techniques for synthesizing circRNAs, highlight key delivery strategies and applications, and discuss the current challenges and future prospects in the field of circRNA-based therapeutics.
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Affiliation(s)
- Tiana Loan Young
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Kevin Chang Wang
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Andrew James Varley
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Bowen Li
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3M2, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada.
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86
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Sukri A, Hanafiah A, Patil S, Lopes BS. The Potential of Alternative Therapies and Vaccine Candidates against Helicobacter pylori. Pharmaceuticals (Basel) 2023; 16:ph16040552. [PMID: 37111309 PMCID: PMC10141204 DOI: 10.3390/ph16040552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Alternative therapies and vaccination are essential to combat the emergence of multidrug-resistant Helicobacter pylori and to prevent the development of gastroduodenal diseases. This review aimed to systematically review recent studies on alternative therapies, i.e., probiotics, nanoparticles, and natural products from plants, as well as recent progress in H. pylori vaccines at the preclinical stage. Articles published from January 2018 to August 2022 were systematically searched using PubMed, Scopus, Web of Science, and Medline. After the screening process, 45 articles were eligible for inclusion in this review. Probiotics (n = 9 studies) and natural products from plants (n = 28 studies) were observed to inhibit the growth of H. pylori, improve immune response, reduce inflammation, and reduce the pathogenic effects of H. pylori virulence factors. Natural products from plants also showed anti-biofilm activity against H. pylori. However, clinical trials of natural products from plants and probiotics are still lacking. A paucity of data assessing the nanoparticle activity of N-acylhomoserine lactonase-stabilized silver against H. pylori was observed. Nonetheless, one nanoparticle study showed anti-biofilm activity against H. pylori. Promising results of H. pylori vaccine candidates (n = 7) were observed at preclinical stage, including elicitation of a humoral and mucosal immune response. Furthermore, the application of new vaccine technology including multi-epitope and vector-based vaccines using bacteria was investigated at the preclinical stage. Taken together, probiotics, natural products from plants, and nanoparticles exhibited antibacterial activity against H. pylori. New vaccine technology shows promising results against H. pylori.
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Affiliation(s)
- Asif Sukri
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Alfizah Hanafiah
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia
| | - Sandip Patil
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Shenzhen 518038, China
| | - Bruno S Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough TS1 3BA, UK
- National Horizons Centre, Teesside University, Darlington DL1 1HG, UK
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87
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Rachman A, Iriani A, Sukrisman L, Rajabto W, Mulansari NA, Lubis AM, Cahyanur R, Prasetyawati F, Priantono D, Rumondor BB, Betsy R, Juanputra S. A comparative study of the COVID-19 vaccine efficacy among cancer patients: mRNA versus non-mRNA. PLoS One 2023; 18:e0281907. [PMID: 36857323 PMCID: PMC9977046 DOI: 10.1371/journal.pone.0281907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/03/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Cancer patients have an increased risk of a severe COVID-19 infection with higher mortality rate. This study aimed to analyze the levels of anti-SARS-CoV-2 S-RBD IgG and NAB among cancer patients who were vaccinated with COVID-19 vaccines, either with BNT162b2, mRNA-1273, AZD1222/ChAdOx1nCoV-19, or Coronavac/BBIBP-CorV vaccines. METHOD A cross-sectional study was conducted among subjects with either solid or hematological cancers who had received two doses of either mRNA or non-mRNA vaccines within 6 months. The levels of anti-SARS-CoV-2 S-RBD IgG and NAb were analyzed using the Mindray Immunoassay Analyzer CL-900i. Statistical analysis was conducted using mean comparison and regression analysis. RESULT The mRNA-1273 vaccine had the highest median levels of S-RBD IgG and NAb, followed by BNT162b, ChAdOx1nCoV-19, and BBIBP-CorV/Coronavac. The levels of S-RBD IgG and NAb in subjects vaccinated with mRNA vaccines were significantly higher than those of non-mRNA vaccines when grouped based on their characteristics, including age, type of cancer, chemotherapy regimen, and comorbidity (p<0.05). Furthermore, the S-RBD IgG and NAb levels between the subjects vaccinated with non-mRNA vaccines and the subjects vaccinated with mRNA vaccines were significantly different (p<0.05). However, there was no significant difference between the same types of vaccines. This study demonstrated a very strong correlation between the level of S-RBD IgG and the level of NAb (R = 0.962; p<0.001). The level of anti-SARS-CoV-2 S-RBD IgG was consistently higher compared to the level of NAb. CONCLUSIONS Generally, mRNA vaccines produced significantly higher anti-SARS-CoV-2 S-RBD IgG and NAb levels than non-mRNA vaccines in cancer subjects.
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Affiliation(s)
- Andhika Rachman
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
- * E-mail:
| | - Anggraini Iriani
- Department of Clinical Pathology, Yarsi University, Jakarta, Indonesia
| | - Lugyanti Sukrisman
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Wulyo Rajabto
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Nadia Ayu Mulansari
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Anna Mira Lubis
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Rahmat Cahyanur
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Findy Prasetyawati
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Dimas Priantono
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Bayu Bijaksana Rumondor
- Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Rachelle Betsy
- Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
| | - Samuel Juanputra
- Department of Internal Medicine, Dr. Cipto Mangunkusumo General Hospital—Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia
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Ullah A, Waqas M, Aziz S, Rahman SU, Khan S, Khalid A, Abdalla AN, Uddin J, Halim SA, Khan A, Al-Harrasi A. Bioinformatics and immunoinformatics approach to develop potent multi-peptide vaccine for coxsackievirus B3 capable of eliciting cellular and humoral immune response. Int J Biol Macromol 2023; 239:124320. [PMID: 37004935 DOI: 10.1016/j.ijbiomac.2023.124320] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
Abstract
Coxsackievirus B3 (CVB3) is a viral pathogen of various human disorders with no effective preventative interventions. Herein, we aimed to design a chimeric vaccine construct for CVB3 using reverse vaccinology and immunoinformatics approaches by screening the whole viral polyprotein sequence. Firstly, screening and mapping of viral polyprotein to predict 21 immunodominant epitopes (B-cell, CD8+ and CD4+ T-cell epitopes), fused with an adjuvant (Resuscitation-promoting factor), appropriate linkers, HIV-TAT peptide, Pan DR epitope, and 6His-tag to assemble a multi-epitope vaccine construct. The chimeric construct is predicted as probable antigen, non-allergen, stable, possess encouraging physicochemical features, and indicates a broader population coverage (98 %). The tertiary structure of the constructed vaccine was predicted and refined, and its interaction with the Toll-like receptor 4 (TLR4) was investigated through molecular docking and dynamics simulation. Computational cloning of the construct was carried out in pET28a (+) plasmid to guarantee the higher expression of the vaccine protein. Lastly, in silico immune simulation foreseen that humoral and cellular immune responses would be elicited in response to the administration of such a potent chimeric construct. Thus, the design constructed could vaccinate against CVB3 infection and various CVB serotypes. However, further in vitro/in vivo research must assess its safety and effectiveness.
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89
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Bayani F, Hashkavaei NS, Arjmand S, Rezaei S, Uskoković V, Alijanianzadeh M, Uversky VN, Ranaei Siadat SO, Mozaffari-Jovin S, Sefidbakht Y. An overview of the vaccine platforms to combat COVID-19 with a focus on the subunit vaccines. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 178:32-49. [PMID: 36801471 PMCID: PMC9938630 DOI: 10.1016/j.pbiomolbio.2023.02.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/21/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that has caused the recent coronavirus disease (COVID-19) global pandemic. The current approved COVID-19 vaccines have shown considerable efficiency against hospitalization and death. However, the continuation of the pandemic for more than two years and the likelihood of new strain emergence despite the global rollout of vaccination highlight the immediate need for the development and improvement of vaccines. mRNA, viral vector, and inactivated virus vaccine platforms were the first members of the worldwide approved vaccine list. Subunit vaccines. which are vaccines based on synthetic peptides or recombinant proteins, have been used in lower numbers and limited countries. The unavoidable advantages of this platform, including safety and precise immune targeting, make it a promising vaccine with wider global use in the near future. This review article summarizes the current knowledge on different vaccine platforms, focusing on the subunit vaccines and their clinical trial advancements against COVID-19.
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Affiliation(s)
- Fatemeh Bayani
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Shokouh Rezaei
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Vuk Uskoković
- Department of Mechanical Engineering, San Diego State University, San Diego, CA, 92182, USA; TardigradeNano LLC, Irvine, CA, 92604, USA
| | - Mahdi Alijanianzadeh
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | | | - Sina Mozaffari-Jovin
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yahya Sefidbakht
- Protein Research Center, Shahid Beheshti University, Tehran, Iran.
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90
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Motamedi H, Ari MM, Shahlaei M, Moradi S, Farhadikia P, Alvandi A, Abiri R. Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach. BMC Bioinformatics 2023; 24:65. [PMID: 36829112 PMCID: PMC9951438 DOI: 10.1186/s12859-023-05197-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/20/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND It seems that several members of intestinal gut microbiota like Streptococcus bovis, Bacteroides fragilis, Helicobacter pylori, Fusobacterium nucleatum, Enterococcus faecalis, Escherichia coli, Peptostreptococcus anaerobius may be considered as the causative agents of Colorectal Cancer (CRC). The present study used bioinformatics and immunoinformatics approaches to design a potential epitope-based multi-epitope vaccine to prevent CRC with optimal population coverage. METHODS In this study, ten amino acid sequences of CRC-related pathogens were retrieved from the NCBI database. Three ABCpred, BCPREDS and LBtope online servers were considered for B cells prediction and the IEDB server for T cells (CD4+ and CD8+) prediction. Then, validation, allergenicity, toxicity and physicochemical analysis of all sequences were performed using web servers. A total of three linkers, AAY, GPGPG, and KK were used to bind CTL, HTL and BCL epitopes, respectively. In addition, the final construct was subjected to disulfide engineering, molecular docking, immune simulation and codon adaptation to design an effective vaccine production strategy. RESULTS A total of 19 sequences of different lengths for linear B-cell epitopes, 19 and 18 sequences were considered as epitopes of CD4+ T and CD8+ cells, respectively. The predicted epitopes were joined by appropriate linkers because they play an important role in producing an extended conformation and protein folding. The final multi-epitope construct and Toll-like receptor 4 (TLR4) were evaluated by molecular docking, which revealed stable and strong binding interactions. Immunity simulation of the vaccine showed significantly high levels of immunoglobulins, helper T cells, cytotoxic T cells and INF-γ. CONCLUSION Finally, the results showed that the designed multi-epitope vaccine could serve as an excellent prophylactic candidate against CRC-associated pathogens, but in vitro and animal studies are needed to justify our findings for its use as a possible preventive measure.
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Affiliation(s)
- Hamid Motamedi
- grid.412112.50000 0001 2012 5829Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran ,grid.412112.50000 0001 2012 5829Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marzie Mahdizade Ari
- grid.411746.10000 0004 4911 7066Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran ,grid.411746.10000 0004 4911 7066Microbial Biotechnology Research Centre, Iran University of Medical Sciences, Tehran, Iran
| | - Mohsen Shahlaei
- grid.412112.50000 0001 2012 5829Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- grid.412112.50000 0001 2012 5829Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Parisa Farhadikia
- grid.412112.50000 0001 2012 5829Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhoushang Alvandi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Medical Technology Research Center, Health Technology Institute,, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ramin Abiri
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran. .,Fertility and Infertility Research Center, Health Technology Institute,, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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91
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Mugunthan SP, Kannan G, Chandra HM, Paital B. Infection, Transmission, Pathogenesis and Vaccine Development against Mycoplasma gallisepticum. Vaccines (Basel) 2023; 11:vaccines11020469. [PMID: 36851345 PMCID: PMC9967393 DOI: 10.3390/vaccines11020469] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Mycoplasma sp. comprises cell wall-less bacteria with reduced genome size and can infect mammals, reptiles, birds, and plants. Avian mycoplasmosis, particularly in chickens, is primarily caused by Mycoplasma gallisepticum (MG) and Mycoplasma synoviae. It causes infection and pathology mainly in the respiratory, reproductive, and musculoskeletal systems. MG is the most widely distributed pathogenic avian mycoplasma with a wide range of host susceptibility and virulence. MG is transmitted both by horizontal and vertical routes. MG infection induces innate, cellular, mucosal, and adaptive immune responses in the host. Macrophages aid in phagocytosis and clearance, and B and T cells play critical roles in the clearance and prevention of MG. The virulent factors of MG are adhesion proteins, lipoproteins, heat shock proteins, and antigenic variation proteins, all of which play pivotal roles in host cell entry and pathogenesis. Prevention of MG relies on farm and flock biosecurity, management strategies, early diagnosis, use of antimicrobials, and vaccination. This review summarizes the vital pathogenic mechanisms underlying MG infection and recapitulates the virulence factors of MG-host cell adhesion, antigenic variation, nutrient transport, and immune evasion. The review also highlights the limitations of current vaccines and the development of innovative future vaccines against MG.
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Affiliation(s)
| | - Ganapathy Kannan
- Institute of Infection, Veterinary & Ecology Sciences (IVES), University of Liverpool, Neston, Cheshire CH64 7TE, UK
| | - Harish Mani Chandra
- Department of Biotechnology, Thiruvalluvar University, Vellore 632115, India
- Correspondence: (H.M.C.); (B.P.)
| | - Biswaranjan Paital
- Redox Regulation Laboratory, Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar 751003, India
- Correspondence: (H.M.C.); (B.P.)
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92
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Umitaibatin R, Harisna AH, Jauhar MM, Syaifie PH, Arda AG, Nugroho DW, Ramadhan D, Mardliyati E, Shalannanda W, Anshori I. Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein. Vaccines (Basel) 2023; 11:vaccines11020399. [PMID: 36851275 PMCID: PMC9964839 DOI: 10.3390/vaccines11020399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.
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Affiliation(s)
- Ramadhita Umitaibatin
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Azza Hanif Harisna
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Putri Hawa Syaifie
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | | | - Dwi Wahyu Nugroho
- Nano Center Indonesia, Jl. Raya Puspiptek, South Tangerang 15314, Indonesia
| | - Donny Ramadhan
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Etik Mardliyati
- Research Center for Vaccine and Drug, National Research and Innovation Agency (BRIN), Cibinong 16911, Indonesia
| | - Wervyan Shalannanda
- Department of Telecommunication Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
| | - Isa Anshori
- Lab-on-Chip Group, Department of Biomedical Engineering, School of Electrical Engineering and Informatics, Bandung Institute of Technology, Bandung 40132, Indonesia
- Correspondence:
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93
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Ali Z, Cardoza JV, Basak S, Narsaria U, Singh VP, Isaac SP, França TCC, LaPlante SR, George SS. Computational design of candidate multi-epitope vaccine against SARS-CoV-2 targeting structural (S and N) and non-structural (NSP3 and NSP12) proteins. J Biomol Struct Dyn 2023; 41:13348-13367. [PMID: 36744449 DOI: 10.1080/07391102.2023.2173297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/20/2023] [Indexed: 02/07/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 virus has created a global damage and has exposed the vulnerable side of scientific research towards novel diseases. The intensity of the pandemic is huge, with mortality rates of more than 6 million people worldwide in a span of 2 years. Considering the gravity of the situation, scientists all across the world are continuously attempting to create successful therapeutic solutions to combat the virus. Various vaccination strategies are being devised to ensure effective immunization against SARS-CoV-2 infection. SARS-CoV-2 spreads very rapidly, and the infection rate is remarkably high than other respiratory tract viruses. The viral entry and recognition of the host cell is facilitated by S protein of the virus. N protein along with NSP3 is majorly responsible for viral genome assembly and NSP12 performs polymerase activity for RNA synthesis. In this study, we have designed a multi-epitope, chimeric vaccine considering the two structural (S and N protein) and two non-structural proteins (NSP3 and NSP12) of SARS-CoV-2 virus. The aim is to induce immune response by generating antibodies against these proteins to target the viral entry and viral replication in the host cell. In this study, computational tools were used, and the reliability of the vaccine was verified using molecular docking, molecular dynamics simulation and immune simulation studies in silico. These studies demonstrate that the vaccine designed shows steady interaction with Toll like receptors with good stability and will be effective in inducing a strong and specific immune response in the body.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zeeshan Ali
- Krupanidhi College of Physiotherapy, Bangalore, India
| | | | | | | | - Vijay Pratap Singh
- Department of Physiotherapy, Kasturba Medical College, Mangalore, Manipal academy of higher education, Mangalore, Manipal, India
| | | | - Tanos C C França
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense, Military Institute of Engineering, Rio de Janeiro, Brazil
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- Université de Québec, INRS - Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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94
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Alam R, Samad A, Ahammad F, Nur SM, Alsaiari AA, Imon RR, Talukder MEK, Nain Z, Rahman MM, Mohammad F, Karpiński TM. In silico formulation of a next-generation multiepitope vaccine for use as a prophylactic candidate against Crimean-Congo hemorrhagic fever. BMC Med 2023; 21:36. [PMID: 36726141 PMCID: PMC9891764 DOI: 10.1186/s12916-023-02750-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Crimean-Congo hemorrhagic fever (CCHF) is a widespread disease transmitted to humans and livestock animals through the bite of infected ticks or close contact with infected persons' blood, organs, or other bodily fluids. The virus is responsible for severe viral hemorrhagic fever outbreaks, with a case fatality rate of up to 40%. Despite having the highest fatality rate of the virus, a suitable treatment option or vaccination has not been developed yet. Therefore, this study aimed to formulate a multiepitope vaccine against CCHF through computational vaccine design approaches. METHODS The glycoprotein, nucleoprotein, and RNA-dependent RNA polymerase of CCHF were utilized to determine immunodominant T- and B-cell epitopes. Subsequently, an integrative computational vaccinology approach was used to formulate a multi-epitopes vaccine candidate against the virus. RESULTS After rigorous assessment, a multiepitope vaccine was constructed, which was antigenic, immunogenic, and non-allergenic with desired physicochemical properties. Molecular dynamics (MD) simulations of the vaccine-receptor complex show strong stability of the vaccine candidates to the targeted immune receptor. Additionally, the immune simulation of the vaccine candidates found that the vaccine could trigger real-life-like immune responses upon administration to humans. CONCLUSIONS Finally, we concluded that the formulated multiepitope vaccine candidates would provide excellent prophylactic properties against CCHF.
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Affiliation(s)
- Rahat Alam
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh
| | - Abdus Samad
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh
| | - Foysal Ahammad
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh
- Division of Biological and Biomedical Sciences (BBS), College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), 34110, Doha, Qatar
| | - Suza Mohammad Nur
- Department of Biochemistry, School of Medicine Case, Western Reserve University, Cleveland, OH, 44106, USA
| | - Ahad Amer Alsaiari
- College of Applied Medical Science, Clinical Laboratories Science Department, Taif University, Taif, 21944, Saudi Arabia
| | - Raihan Rahman Imon
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh
| | - Md Enamul Kabir Talukder
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Laboratory of Computational Biology, Biological Solution Centre (BioSol Centre), Jashore, 7408, Bangladesh
| | - Zulkar Nain
- School of Biomedical Sciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Md Mashiar Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Farhan Mohammad
- Division of Biological and Biomedical Sciences (BBS), College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), 34110, Doha, Qatar.
| | - Tomasz M Karpiński
- Chair and Department of Medical Microbiology, Poznań University of Medical Sciences, Rokietnicka 10, 60-806, Poznań, Poland.
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95
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Moin AT, Singh G, Ahmed N, Saiara SA, Timofeev VI, Ahsan Faruqui N, Sharika Ahsan S, Tabassum A, Nebir SS, Andalib KMS, Araf Y, Ullah MA, Sarkar B, Islam NN, Zohora US. Computational designing of a novel subunit vaccine for human cytomegalovirus by employing the immunoinformatics framework. J Biomol Struct Dyn 2023; 41:833-855. [PMID: 36617426 DOI: 10.1080/07391102.2021.2014969] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Human cytomegalovirus (HCMV) is a widespread virus that can cause serious and irreversible neurological damage in newborns and even death in children who do not have the access to much-needed medications. While some vaccines and drugs are found to be effective against HCMV, their extended use has given rise to dose-limiting toxicities and the development of drug-resistant mutants among patients. Despite half a century's worth of research, the lack of a licensed HCMV vaccine heightens the need to develop newer antiviral therapies and vaccine candidates with improved effectiveness and reduced side effects. In this study, the immunoinformatics approach was utilized to design a potential polyvalent epitope-based vaccine effective against the four virulent strains of HCMV. The vaccine was constructed using seven CD8+ cytotoxic T lymphocytes epitopes, nine CD4+ helper T lymphocyte epitopes, and twelve linear B-cell lymphocyte epitopes that were predicted to be antigenic, non-allergenic, non-toxic, fully conserved, and non-human homologous. Subsequently, molecular docking study, protein-protein interaction analysis, molecular dynamics simulation (including the root mean square fluctuation (RMSF) and root mean square deviation (RMSD)), and immune simulation study rendered promising results assuring the vaccine to be stable, safe, and effective. Finally, in silico cloning was conducted to develop an efficient mass production strategy of the vaccine. However, further in vitro and in vivo research studies on the proposed vaccine are required to confirm its safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Gagandeep Singh
- Section of Microbiology, Central Ayurveda Research Institute, Jhansi, Uttar Pradesh, India.,Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, India
| | - Nafisa Ahmed
- Biotechnology Program, Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | | | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Nairita Ahsan Faruqui
- Biotechnology Program, Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | | | - Afrida Tabassum
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Sadman Sakib Nebir
- Department of Microbiology and Immunology, Bangladesh University of Health Sciences, Dhaka, Bangladesh
| | | | - Yusha Araf
- Community of Biotechnology, Dhaka, Bangladesh.,Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Asad Ullah
- Community of Biotechnology, Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Bishajit Sarkar
- Community of Biotechnology, Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Nafisa Nawal Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Umme Salma Zohora
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
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96
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Malik M, Khan S, Ullah A, Hassan M, Haq MU, Ahmad S, Al-Harbi AI, Sanami S, Abideen SA, Irfan M, Khurram M. Proteome-Wide Screening of Potential Vaccine Targets against Brucella melitensis. Vaccines (Basel) 2023; 11:263. [PMID: 36851141 PMCID: PMC9966016 DOI: 10.3390/vaccines11020263] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023] Open
Abstract
The ongoing antibiotic-resistance crisis is becoming a global problem affecting public health. Urgent efforts are required to design novel therapeutics against pathogenic bacterial species. Brucella melitensis is an etiological agent of brucellosis, which mostly affects sheep and goats but several cases have also been reported in cattle, water buffalo, yaks and dogs. Infected animals also represent the major source of infection for humans. Development of safer and effective vaccines for brucellosis remains a priority to support disease control and eradication in animals and to prevent infection to humans. In this research study, we designed an in-silico multi-epitopes vaccine for B. melitensis using computational approaches. The pathogen core proteome was screened for good vaccine candidates using subtractive proteomics, reverse vaccinology and immunoinformatic tools. In total, 10 proteins: catalase; siderophore ABC transporter substrate-binding protein; pyridoxamine 5'-phosphate oxidase; superoxide dismutase; peptidylprolyl isomerase; superoxide dismutase family protein; septation protein A; hypothetical protein; binding-protein-dependent transport systems inner membrane component; and 4-hydroxy-2-oxoheptanedioate aldolase were selected for epitopes prediction. To induce cellular and antibody base immune responses, the vaccine must comprise both B and T-cells epitopes. The epitopes were next screened for antigenicity, allergic nature and water solubility and the probable antigenic, non-allergic, water-soluble and non-toxic nine epitopes were shortlisted for multi-epitopes vaccine construction. The designed vaccine construct comprises 274 amino acid long sequences having a molecular weight of 28.14 kDa and instability index of 27.62. The vaccine construct was further assessed for binding efficacy with immune cell receptors. Docking results revealed that the designed vaccine had good binding potency with selected immune cell receptors. Furthermore, vaccine-MHC-I, vaccine-MHC-II and vaccine-TLR-4 complexes were opted based on a least-binding energy score of -5.48 kcal/mol, 0.64 kcal/mol and -2.69 kcal/mol. Those selected were then energy refined and subjected to simulation studies to understand dynamic movements of the docked complexes. The docking results were further validated through MMPBSA and MMGBSA analyses. The MMPBSA calculated -235.18 kcal/mol, -206.79 kcal/mol, and -215.73 kcal/mol net binding free energy, while MMGBSA estimated -259.48 kcal/mol, -206.79 kcal/mol and -215.73 kcal/mol for TLR-4, MHC-I and MHC-II complexes, respectively. These findings were validated by water-swap and entropy calculations. Overall, the designed vaccine construct can evoke proper immune responses and the construct could be helpful for experimental researchers in formulation of a protective vaccine against the targeted pathogen for both animal and human use.
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Affiliation(s)
- Mahnoor Malik
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda 24550, Pakistan
| | - Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Muhammad Hassan
- Department of Pharmacy, Bacha Khan University, Charsadda 24461, Pakistan
| | - Mahboob ul Haq
- Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Alhanouf I. Al-Harbi
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu 42353, Saudi Arabia
| | - Samira Sanami
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord 8815713471, Iran
| | - Syed Ainul Abideen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL 32611, USA
| | - Muhammad Khurram
- Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan
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97
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Gul I, Hassan A, Muneeb JM, Akram T, Haq E, Shah RA, Ganai NA, Ahmad SM, Chikan NA, Shabir N. A multiepitope vaccine candidate against infectious bursal disease virus using immunoinformatics-based reverse vaccinology approach. Front Vet Sci 2023; 9:1116400. [PMID: 36713875 PMCID: PMC9880294 DOI: 10.3389/fvets.2022.1116400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Infectious bursal disease virus is the causative agent of infectious bursal disease (Gumboro disease), a highly contagious immunosuppressive disease of chicken with a substantial economic impact on small- and large-scale poultry industries worldwide. Currently, live attenuated vaccines are widely used to control the disease in chickens despite their issues with safety (immunosuppression and bursal atrophy) and efficiency (breaking through the maternally-derived antibody titer). To overcome the drawbacks, the current study has, for the first time, attempted to construct a computational model of a multiepitope based vaccine candidate against infectious bursal disease virus, which has the potential to overcome the safety and protection issues found in the existing live-attenuated vaccines. The current study used a reverse vaccinology based immunoinformatics approach to construct the vaccine candidate using major and minor capsid proteins of the virus, VP2 and VP3, respectively. The vaccine construct was composed of four CD8+ epitopes, seven CD4+ T-cell epitopes, 11 B-cell epitopes and a Cholera Toxin B adjuvant, connected using appropriate flexible peptide linkers. The vaccine construct was evaluated as antigenic with VaxiJen Score of 0.6781, immunogenic with IEDB score of 2.89887 and non-allergenic. The 55.64 kDa construct was further evaluated for its physicochemical characteristics, which revealed that it was stable with an instability index of 16.24, basic with theoretical pI of 9.24, thermostable with aliphatic index of 86.72 and hydrophilic with GRAVY score of -0.256. The docking and molecular dynamics simulation studies of the vaccine construct with Toll-like receptor-3 revealed fair structural interaction (binding affinity of -295.94 kcal/mol) and complex stability. Further, the predicted induction of antibodies and cytokines by the vaccine construct indicated the possible elicitation of the host's immune response against the virus. The work is a significant attempt to develop next-generation vaccines against the infectious bursal disease virus though further experimental studies are required to assess the efficacy and protectivity of the proposed vaccine candidate in vivo.
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Affiliation(s)
- Irfan Gul
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India,Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Amreena Hassan
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India,Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Jan Mohd Muneeb
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Towseef Akram
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Ehtishamul Haq
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Riaz Ahmad Shah
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Nazir Ahmad Ganai
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Syed Mudasir Ahmad
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Naveed Anjum Chikan
- Division of Computational Biology, Daskdan Innovations Pvt. Ltd., Srinagar, India
| | - Nadeem Shabir
- Laboratory of Vaccine Biotechnology, Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India,*Correspondence: Nadeem Shabir ✉
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98
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Rahman MM, Masum MHU, Talukder A, Akter R. An in silico reverse vaccinology approach to design a novel multiepitope peptide vaccine for non-small cell lung cancers. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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99
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Shah SZ, Jabbar B, Mirza MU, Waqas M, Aziz S, Halim SA, Ali A, Rafique S, Idrees M, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean-Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target. Vaccines (Basel) 2022; 11:61. [PMID: 36679906 PMCID: PMC9867508 DOI: 10.3390/vaccines11010061] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Crimean-Congo haemorrhagic fever (CCHF), caused by Crimean-Congo haemorrhagic fever virus (CCHFV), is a disease of worldwide importance (endemic yet not limited to Asia, Middle East, and Africa) and has triggered several outbreaks amounting to a case fatality rate of 10-40% as per the World Health Organization. Genetic diversity and phylogenetic data revealed that the Asia-1 genotype of CCHFV remained dominant in Pakistan, where 688 confirmed cases were reported between the 2012-2022 period. Currently, no approved vaccine is available to tackle the viral infection. Epitope-based vaccine design has gained significant attention in recent years due to its safety, timeliness, and cost efficiency compared to conventional vaccines. In the present study, we employed a robust immunoinformatics-based approach targeting the structural glycoproteins G1 and G2 of CCHFV (Asia-1 genotype) to design a multi-epitope vaccine construct. Five B-cells and six cytotoxic T-lymphocytes (CTL) epitopes were mapped and finalized from G1 and G2 and were fused with suitable linkers (EAAAK, GGGS, AAY, and GPGPG), a PADRE sequence (13 aa), and an adjuvant (50S ribosomal protein L7/L12) to formulate a chimeric vaccine construct. The selected CTL epitopes showed high affinity and stable binding with the binding groove of common human HLA class I molecules (HLA-A*02:01 and HLA-B*44:02) and mouse major histocompatibility complex class I molecules. The chimeric vaccine was predicted to be an antigenic, non-allergenic, and soluble molecule with a suitable physicochemical profile. Molecular docking and molecular dynamics simulation indicated a stable and energetically favourable interaction between the constructed antigen and Toll-like receptors (TLR2, TLR3, and TLR4). Our results demonstrated that innate, adaptive, and humoral immune responses could be elicited upon administration of such a potent muti-epitope vaccine construct. These results could be helpful for an experimental vaccinologist to develop an effective vaccine against the Asia-1 genotype of CCHFV.
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Affiliation(s)
- Syed Zawar Shah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
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100
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Qi W, Qingfeng L, Jing Z, Maolin Z, Zhihui Z, Wangqi D, Shanli Z, Jun C, Pengfei J, Lifang Z. A novel multi-epitope vaccine of HPV16 E5E6E7 oncoprotein delivered by HBc VLPs induced efficient prophylactic and therapeutic antitumor immunity in tumor mice model. Vaccine 2022; 40:7693-7702. [PMID: 36376215 DOI: 10.1016/j.vaccine.2022.10.069] [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: 04/08/2022] [Revised: 09/08/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022]
Abstract
Human papilloma virus type 16 (HPV16) is the most prevalent etiologic agent associated with cervical cancer, and its early proteins E5, E6 and E7 play important roles in cervical epithelium transformation to cervical intraepithelial neoplasia and even cervical cancer. Hence, these oncoproteins are ideal target antigens for developing immunotherapeutic vaccines against HPV-associated infection and cervical cancer. Currently, multi-epitope vaccines have been a promising strategy for immunotherapy for viral infection or cancers. In this study, the E5aa28-46, E6aa37-57 and E7aa26-57 peptides were selected and linked to form a novel multi-epitopes vaccine (E765m), which was inserted into the major immune dominant region (MIR) of hepatitis B virus core antigen (HBc) to construct a HBc-E765m chimeric virus-like particles (cVLPs). The immunogenicity and immunotherapeutic effect of the cVLPs vaccine was evaluated in immunized mice and a tumor-bearing mouse model. The results showed that HBc-E765m cVLPs elicited high E5-, E6- and E7- specific CTL and serum IgG antibody responses, and also relatively high levels of the cytokines IFN-γ, IL-4 and IL-5. More importantly, the cVLPs vaccine significant suppressed tumor growth in mice bearing E5-TC-1 tumors. Our findings provide strong evidence that this novel HBc-E765m cVLPs vaccine could be a candidate vaccine for specific immunotherapy in HPV16-associated cervical intraepithelial neoplasia or cervical cancer.
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Affiliation(s)
- Wang Qi
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Li Qingfeng
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Zhang Jing
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Zheng Maolin
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Zhang Zhihui
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Du Wangqi
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Zhu Shanli
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Chen Jun
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Jiang Pengfei
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China
| | - Zhang Lifang
- Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China; Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical, University, 325035 Zhejiang, Wenzhou, China.
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