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Sarvmeili J, Baghban Kohnehrouz B, Gholizadeh A, Shanehbandi D, Ofoghi H. Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer. Sci Rep 2024; 14:10297. [PMID: 38704475 PMCID: PMC11069592 DOI: 10.1038/s41598-024-61025-2] [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: 11/13/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The ideal vaccines for combating diseases that may emerge in the future require more than simply inactivating a few pathogenic strains. This study aims to provide a peptide-based multi-epitope vaccine effective against various severe acute respiratory syndrome coronavirus 2 strains. To design the vaccine, a library of peptides from the spike, nucleocapsid, membrane, and envelope structural proteins of various strains was prepared. Then, the final vaccine structure was optimized using the fully protected epitopes and the fynomer scaffold. Using bioinformatics tools, the antigenicity, allergenicity, toxicity, physicochemical properties, population coverage, and secondary and three-dimensional structures of the vaccine candidate were evaluated. The bioinformatic analyses confirmed the high quality of the vaccine. According to further investigations, this structure is similar to native protein and there is a stable and strong interaction between vaccine and receptors. Based on molecular dynamics simulation, structural compactness and stability in binding were also observed. In addition, the immune simulation showed that the vaccine can stimulate immune responses similar to real conditions. Finally, codon optimization and in silico cloning confirmed efficient expression in Escherichia coli. In conclusion, the fynomer-based vaccine can be considered as a new style in designing and updating vaccines to protect against coronavirus disease.
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Affiliation(s)
- Javad Sarvmeili
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 51666, Iran
| | | | - Ashraf Gholizadeh
- Department of Animal Biology, University of Tabriz, Tabriz, 51666, Iran
| | - Dariush Shanehbandi
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 51666, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, 33131, Iran
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2
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Poria R, Kala D, Nagraik R, Dhir Y, Dhir S, Singh B, Kaushik NK, Noorani MS, Kaushal A, Gupta S. Vaccine development: Current trends and technologies. Life Sci 2024; 336:122331. [PMID: 38070863 DOI: 10.1016/j.lfs.2023.122331] [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: 09/21/2023] [Revised: 11/24/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023]
Abstract
Despite the effectiveness of vaccination in reducing or eradicating diseases caused by pathogens, there remain certain diseases and emerging infections for which developing effective vaccines is inherently challenging. Additionally, developing vaccines for individuals with compromised immune systems or underlying medical conditions presents significant difficulties. As well as traditional vaccine different methods such as inactivated or live attenuated vaccines, viral vector vaccines, and subunit vaccines, emerging non-viral vaccine technologies, including viral-like particle and nanoparticle vaccines, DNA/RNA vaccines, and rational vaccine design, offer new strategies to address the existing challenges in vaccine development. These advancements have also greatly enhanced our understanding of vaccine immunology, which will guide future vaccine development for a broad range of diseases, including rapidly emerging infectious diseases like COVID-19 and diseases that have historically proven resistant to vaccination. This review provides a comprehensive assessment of emerging non-viral vaccine production methods and their application in addressing the fundamental and current challenges in vaccine development.
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Affiliation(s)
- Renu Poria
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala 134003, India
| | - Deepak Kala
- Centera Laboratories, Institute of High Pressure Physics PAS, 01-142 Warsaw, Poland
| | - Rupak Nagraik
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Yashika Dhir
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala 134003, India
| | - Sunny Dhir
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala 134003, India
| | - Bharat Singh
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala 134003, India
| | - Naveen Kumar Kaushik
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh, India
| | - Md Salik Noorani
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Kaushal
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala 134003, India.
| | - Shagun Gupta
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, Ambala 134003, India.
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3
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Zubair M, Wang J, Yu Y, Rasheed MA, Faisal M, Dawood AS, Ashraf M, Shao G, Feng Z, Xiong Q. Conserved Domains in Variable Surface Lipoproteins A-G of Mycoplasma hyorhinis May Serve as Probable Multi-Epitope Candidate Vaccine: Computational Reverse Vaccinology Approach. Vet Sci 2023; 10:557. [PMID: 37756079 PMCID: PMC10535464 DOI: 10.3390/vetsci10090557] [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: 06/20/2023] [Revised: 08/09/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Mycoplasma hyorhinis (M. hyorhinis) is responsible for infections in the swine population. Such infections are usually cured by using antimicrobials and lead to develop resistance. Until now, there has been no effective vaccine to eradicate the disease. This study used conserved domains found in seven members of the variable lipoprotein (VlpA-G) family in order to design a multi-epitope candidate vaccine (MEV) against M. hyorhinis. The immunoinformatics approach was followed to predict epitopes, and a vaccine construct consisting of an adjuvant, two B cell epitopes, two HTL epitopes, and one CTL epitope was designed. The suitability of the vaccine construct was identified by its non-allergen, non-toxic, and antigenic nature. A molecular dynamic simulation was executed to assess the stability of the TLR2 docked structure. An immune simulation showed a high immune response toward the antigen. The protein sequence was reverse-translated, and codons were optimized to gain a high expression level in E. coli. The proposed vaccine construct may be a candidate for a multi-epitope vaccine. Experimental validation is required in future to test the safety and efficacy of the hypothetical candidate vaccine.
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Affiliation(s)
- Muhammad Zubair
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China; (M.Z.); (J.W.); (Y.Y.); (G.S.); (Z.F.)
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China
| | - Jia Wang
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China; (M.Z.); (J.W.); (Y.Y.); (G.S.); (Z.F.)
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China
| | - Yanfei Yu
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China; (M.Z.); (J.W.); (Y.Y.); (G.S.); (Z.F.)
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Muhammad Asif Rasheed
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus, Islamabad 45550, Pakistan;
| | - Muhammad Faisal
- Division of Hematology, Department of Medicine, The Ohio State University College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA;
| | - Ali Sobhy Dawood
- The State Key Laboratory of Agricultural Microbiology, Department of Preventive Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China;
- Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt
| | - Muhammad Ashraf
- Institute of Microbiology, University of Agriculture Faisalabad, Faisalabad 37000, Pakistan;
| | - Guoqing Shao
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China; (M.Z.); (J.W.); (Y.Y.); (G.S.); (Z.F.)
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhixin Feng
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China; (M.Z.); (J.W.); (Y.Y.); (G.S.); (Z.F.)
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China
| | - Qiyan Xiong
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China; (M.Z.); (J.W.); (Y.Y.); (G.S.); (Z.F.)
- GuoTai (Taizhou) Center of Technology Innovation for Veterinary Biologicals, Taizhou 225300, China
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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4
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Saikat ASM. Computational approaches for molecular characterization and structure-based functional elucidation of a hypothetical protein from Mycobacterium tuberculosis. Genomics Inform 2023; 21:e25. [PMID: 37415455 PMCID: PMC10326535 DOI: 10.5808/gi.23001] [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: 01/04/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 07/08/2023] Open
Abstract
Adaptation of infections and hosts has resulted in several metabolic mechanisms adopted by intracellular pathogens to combat the defense responses and the lack of fuel during infection. Human tuberculosis caused by Mycobacterium tuberculosis (MTB) is the world's first cause of mortality tied to a single disease. This study aims to characterize and anticipate potential antigen characteristics for promising vaccine candidates for the hypothetical protein of MTB through computational strategies. The protein is associated with the catalyzation of dithiol oxidation and/or disulfide reduction because of the protein's anticipated disulfide oxidoreductase properties. This investigation analyzed the protein's physicochemical characteristics, protein-protein interactions, subcellular locations, anticipated active sites, secondary and tertiary structures, allergenicity, antigenicity, and toxicity properties. The protein has significant active amino acid residues with no allergenicity, elevated antigenicity, and no toxicity.
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Affiliation(s)
- Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
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5
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Jahantigh HR, Shahbazi B, Gouklai H, Van der Weken H, Gharibi Z, Rezaei Z, Habibi M, Ahmadi K. Design peptide and multi-epitope protein vaccine candidates against monkeypox virus using reverse vaccinology approach: an in-silico study. J Biomol Struct Dyn 2023; 41:14398-14418. [PMID: 37154825 DOI: 10.1080/07391102.2023.2201850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/11/2023] [Indexed: 05/10/2023]
Abstract
Monkeypox is a zoonotic virus that has recently affected different countries worldwide. On July 23, 2022, the WHO declared the outbreak of monkeypox as a public health emergency of international concern. Surveillance studies conducted in Central Africa in the 1980s and later during outbreaks in the same region showed smallpox vaccines to be clinically somewhat effective against Monkeypox virus. However, there is no specific vaccine against this virus. This research used bioinformatics techniques to establish a novel multi-epitope vaccine candidate against Monkeypox that can induce a strong immune response. Five well-known antigenic proteins (E8L, A30L, A35R, A29L, and B21R) of the virus were picked and assessed as possible immunogenic peptides. Two suitable peptide candidates were selected according to bio-informatics analysis. Based upon in silico evaluation, two multi-epitope vaccine candidates (ALALAR and ALAL) were built with rich-epitope domains consisting of high-ranking T and B-cell epitopes. After predicting and evaluating the 3D structure of the protein candidates, the most efficient 3D models were considered for docking studies with Toll-like receptor 4 (TLR4) and the HLA-A * 11:01, HLA-A*01:01, HLA-A*02:01, HLA-A*03:01, HLA-A*07:02, HLA-A*15:01, HLA-A*30:01 receptors. Subsequently, molecular dynamics (MD) simulation of up to 150 nanoseconds was employed to assess the durability of the interaction of the vaccine candidates with immune receptors. MD studies showed that M5-HLA-A*11:01, ALAL-TLR4, and ALALAR-TLR4 complexes were stable during simulation. Analysis of the in silico outcomes indicates that the M5 peptide and ALAL and ALALAR proteins may be suitable vaccine candidates against the Monkeypox virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamid Reza Jahantigh
- Interdisciplinary Department of Medicine - Section of Occupational Medicine, University of Bari, Bari, Italy
- Animal Health and Zoonosis PhD Course, Department of Veterinary Medicine, University of Bari, Bari, Italy
| | - Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Hamed Gouklai
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hans Van der Weken
- Laboratory of Immunology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Zahra Gharibi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Rezaei
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehri Habibi
- Department of Molecular Biology, Pasteur Institute of Iran, Pasteur Ave., Tehran, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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6
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Castro KM, Scheck A, Xiao S, Correia BE. Computational design of vaccine immunogens. Curr Opin Biotechnol 2022; 78:102821. [PMID: 36279815 DOI: 10.1016/j.copbio.2022.102821] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 12/14/2022]
Abstract
Computational protein engineering has enabled the rational design of customized proteins, which has propelled both sequence-based and structure-based immunogen engineering and delivery. By discerning antigenic determinants of viral pathogens, computational methods have been implemented to successfully engineer representative viral strains able to elicit broadly neutralizing responses or present antigenic sites of viruses for focused immune responses. Combined with improvements in customizable nanoparticle design, immunogens are multivalently displayed to enhance immune responses. These rationally designed immunogens offer unique and powerful approaches to engineer vaccines for pathogens, which have eluded traditional approaches.
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Affiliation(s)
- Karla M Castro
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Andreas Scheck
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Shuhao Xiao
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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7
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Maia MAC, Bettin EB, Barbosa LN, de Oliveira NR, Bunde TT, Pedra ACK, Rosa GA, da Rosa EEB, Seixas Neto ACP, Grassmann AA, McFadden J, Dellagostin OA, McBride AJA. Challenges for the development of a universal vaccine against leptospirosis revealed by the evaluation of 22 vaccine candidates. Front Cell Infect Microbiol 2022; 12:940966. [PMID: 36275031 PMCID: PMC9586249 DOI: 10.3389/fcimb.2022.940966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Leptospirosis is a neglected disease of man and animals that affects nearly half a million people annually and causes considerable economic losses. Current human vaccines are inactivated whole-cell preparations (bacterins) of Leptospira spp. that provide strong homologous protection yet fail to induce a cross-protective immune response. Yearly boosters are required, and serious side-effects are frequently reported so the vaccine is licensed for use in humans in only a handful of countries. Novel universal vaccines require identification of conserved surface-exposed epitopes of leptospiral antigens. Outer membrane β-barrel proteins (βb-OMPs) meet these requirements and have been successfully used as vaccines for other diseases. We report the evaluation of 22 constructs containing protein fragments from 33 leptospiral βb-OMPs, previously identified by reverse and structural vaccinology and cell-surface immunoprecipitation. Three-dimensional structures for each leptospiral βb-OMP were predicted by I-TASSER. The surface-exposed epitopes were predicted using NetMHCII 2.2 and BepiPred 2.0. Recombinant constructs containing regions from one or more βb-OMPs were cloned and expressed in Escherichia coli. IMAC-purified recombinant proteins were adsorbed to an aluminium hydroxide adjuvant to produce the vaccine formulations. Hamsters (4-6 weeks old) were vaccinated with 2 doses containing 50 – 125 μg of recombinant protein, with a 14-day interval between doses. Immunoprotection was evaluated in the hamster model of leptospirosis against a homologous challenge (10 – 20× ED50) with L. interrogans serogroup Icterohaemorrhagiae serovar Copenhageni strain Fiocruz L1-130. Of the vaccine formulations, 20/22 were immunogenic and induced significant humoral immune responses (IgG) prior to challenge. Four constructs induced significant protection (100%, P < 0.001) and sterilizing immunity in two independent experiments, however, this was not reproducible in subsequent evaluations (0 – 33.3% protection, P > 0.05). The lack of reproducibility seen in these challenge experiments and in other reports in the literature, together with the lack of immune correlates and commercially available reagents to characterize the immune response, suggest that the hamster may not be the ideal model for evaluation of leptospirosis vaccines and highlight the need for evaluation of alternative models, such as the mouse.
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Affiliation(s)
- Mara A. C. Maia
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Everton B. Bettin
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Liana N. Barbosa
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Natasha R. de Oliveira
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Tiffany T. Bunde
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Ana Carolina K. Pedra
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Guilherme A. Rosa
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Elias E. B. da Rosa
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Amilton C. P. Seixas Neto
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - André A. Grassmann
- Department of Medicine, University of Connecticut Health, Farmington, CT, United States
| | - Johnjoe McFadden
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Odir A. Dellagostin
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Alan J. A. McBride
- Biotechnology Unit, Technological Development Centre, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- *Correspondence: Alan J. A. McBride,
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Huffman A, Ong E, Hur J, D’Mello A, Tettelin H, He Y. COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Brief Bioinform 2022; 23:bbac190. [PMID: 35649389 PMCID: PMC9294427 DOI: 10.1093/bib/bbac190] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 12/11/2022] Open
Abstract
Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general, computational vaccine design includes three major stages: (i) identification and annotation of experimentally verified gold standard protective antigens through literature mining, (ii) rational vaccine design using reverse vaccinology (RV) and structural vaccinology (SV) and (iii) post-licensure vaccine success and adverse event surveillance and its usage for vaccine design. Protegen is a database of experimentally verified protective antigens, which can be used as gold standard data for rational vaccine design. RV predicts protective antigen targets primarily from genome sequence analysis. SV refines antigens through structural engineering. Recently, RV and SV approaches, with the support of various machine learning methods, have been applied to COVID-19 vaccine design. The analysis of post-licensure vaccine adverse event report data also provides valuable results in terms of vaccine safety and how vaccines should be used or paused. Ontology standardizes and incorporates heterogeneous data and knowledge in a human- and computer-interpretable manner, further supporting machine learning and vaccine design. Future directions on rational vaccine design are discussed.
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Affiliation(s)
- Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Edison Ong
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Junguk Hur
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58202, USA
| | - Adonis D’Mello
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hervé Tettelin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Yongqun He
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Unit for Laboratory Animal Medicine, Department of Microbiology and Immunology, Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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9
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Antibodies to combat viral infections: development strategies and progress. Nat Rev Drug Discov 2022; 21:676-696. [PMID: 35725925 PMCID: PMC9207876 DOI: 10.1038/s41573-022-00495-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/11/2022]
Abstract
Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections owing to characteristics such as their high specificity and their ability to enhance immune responses. Furthermore, antibody engineering can be used to strengthen effector function and prolong mAb half-life, and advances in structural biology have enabled the selection and optimization of potent neutralizing mAbs through identification of vulnerable regions in viral proteins, which can also be relevant for vaccine design. The COVID-19 pandemic has stimulated extensive efforts to develop neutralizing mAbs against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with several mAbs now having received authorization for emergency use, providing not just an important component of strategies to combat COVID-19 but also a boost to efforts to harness mAbs in therapeutic and preventive settings for other infectious diseases. Here, we describe advances in antibody discovery and engineering that have led to the development of mAbs for use against infections caused by viruses including SARS-CoV-2, respiratory syncytial virus (RSV), Ebola virus (EBOV), human cytomegalovirus (HCMV) and influenza. We also discuss the rationale for moving from empirical to structure-guided strategies in vaccine development, based on identifying optimal candidate antigens and vulnerable regions within them that can be targeted by antibodies to result in a strong protective immune response. Monoclonal antibodies (mAbs) are appealing as potential therapeutics and prophylactics for viral infections. This Review describes advances in antibody discovery and engineering that have led to the development of mAbs that target viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), respiratory syncytial virus and Ebola virus, and also considers the implications for vaccine development.
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10
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Vishweshwaraiah YL, Dokholyan NV. Toward rational vaccine engineering. Adv Drug Deliv Rev 2022; 183:114142. [PMID: 35150769 PMCID: PMC8931536 DOI: 10.1016/j.addr.2022.114142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/31/2022] [Accepted: 02/07/2022] [Indexed: 12/29/2022]
Abstract
Technological revolutions in several fields have pushed the boundaries of vaccine design and provided new avenues for vaccine development. Next-generation vaccine platforms have shown promise in targeting challenging antigens, for which traditional approaches have been ineffective. With advances in protein engineering, structural biology, computational biology and immunology, the structural vaccinology approach, which uses protein structure information to develop immunogens, holds promise for future vaccine design. In this review, we highlight various vaccine development strategies, along with their advantages and limitations. We discuss the rational vaccine design approach, which focuses on structure-based vaccine design. Finally, we discuss antigen engineering using the epitope-scaffold approach, gaps in structural vaccinology, and remaining challenges in vaccine design.
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Affiliation(s)
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA; Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, USA.
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11
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Debnath SK, Srivastava R. Potential Application of Bionanoparticles to Treat Severe Acute Respiratory Syndrome Coronavirus-2 Infection. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2021.813847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a contagious virus that spreads exponentially across the world, resulting in serious viral pneumonia. Several companies and researchers have put their tremendous effort into developing novel vaccines or drugs for the complete eradication of COVID-19 caused by SARS-CoV-2. Bionanotechnology plays a vital role in designing functionalized biocompatible nanoparticulate systems with higher antiviral capabilities. Thus, several nanocarriers have been explored in designing and delivering drugs and vaccines. This problem can be overcome with the intervention of biomaterials or bionanoparticles. The present review describes the comparative analysis of SARS infection and its associated etiological agents. This review also highlighted some nanoparticles that have been explored in the treatment of COVID-19. However, these carriers elicit several problems once they come in contact with biological systems. Often, the body’s immune system treats these nanocarriers as foreign particles and antigens. In contrast, some bionanoparticles are highlighted here with their potential application in SARS-CoV-2. However, bionanoparticles have demonstrated some drawbacks discussed here with the possible outcomes. The scope of bioinspired nanoparticles is also discussed in detail to explore the new era of research. It is highly essential for the effective delivery of these nanoparticles to the target site. For effective management of SARS-CoV-2, different delivery patterns are also discussed here.
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Beiranvand S, Doosti A, Mirzaei SA. Putative novel B-cell vaccine candidates identified by reverse vaccinology and genomics approaches to control Acinetobacter baumannii serotypes. INFECTION GENETICS AND EVOLUTION 2021; 96:105138. [PMID: 34793968 DOI: 10.1016/j.meegid.2021.105138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/12/2021] [Accepted: 11/09/2021] [Indexed: 11/26/2022]
Abstract
In the last decade, Multi-drug resistance (MDR)-associated infections of Acinetobacter baumannii have grown worldwide. A cost-effective preventative strategy against this bacterium is vaccination. This study has presented five novel vaccine candidates against A. baumannii produced using the reverse vaccinology method. BLASTn was done to identify the most conserved antigens. PSORTb 3.0.2 was run to predict the subcellular localization of the proteins. The initial screening and antigenicity evaluation were performed using Vaxign. The ccSOL omics was also employed to predict protein solubility. The cross-membrane localization of the protein was predicted using PRED-TMBB. B cell epitope prediction was made for immunogenicity using the IEDB and BepiPred-2.0 database. Eventually, BLASTp was done to verify the extent of similarity to the human proteome to exclude the possibility of autoimmunity. Proteins failing to comply with the set parameters were filtered at each step. In silico, potential vaccines against 21 A. baumannii strains were identified using reverse vaccinology and subtractive genomic techniques. Based on the above criteria, out of the initial 15 A. baumannii proteins selected for screening, nine exposed/secreted/membrane proteins, i.e., Pfsr, LptE, OmpH, CarO, CsuB, CdiB, MlaA, FhuE, and were the most promising candidates. Their solubility and antigenicity were also examined and found to be more than 0.45 and 0.6, respectively. Based on the results, LptE was selected with the highest average antigenic score of 1.043 as the best protein, followed by FimF and Pfsr with scores of 1.022 and 1.014, respectively. In the end, five proteins were verified as promising candidates. Overall, the targets identified herein may be utilized in future strategies to control A. baumannii worldwide.
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Affiliation(s)
- Sheida Beiranvand
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Abbas Doosti
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Seyed Abbas Mirzaei
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran; Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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Ramanto KN, Nurdiansyah R. Structural and immunogenicity analysis of reconstructed ancestral and consensus P48/45 for cross-species anti malaria transmission-blocking vaccine. Comput Biol Chem 2021; 92:107495. [PMID: 33940529 DOI: 10.1016/j.compbiolchem.2021.107495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/21/2021] [Indexed: 11/25/2022]
Abstract
The development of the anti-malaria vaccine holds a promising future in malaria control. One of the anti-malaria vaccine strategies known as the transmission-blocking vaccine (TBV) is to inhibit the parasite transmission between humans and mosquitoes by targeting the parasite gametocyte. Previously, we found that P48/45 included in the 6-Cysteine protein family shared by Plasmodium sp. We also detected vaccine properties possessed by all human-infecting Plasmodium and could be used as a cross-species anti-malaria vaccine. In this study, we investigated the efficacy of P48/45 through the ancestral and consensus reconstruction approach. P48/45 phylogenetic and time tree analysis was done by RAXML and BEAST2. GRASP server and Ugene software were used to reconstruct ancestral and consensus sequences, respectively. The protein structural prediction was made by using a psipred and Rosetta program. Each protein characteristic of P48/45 was analyzed by assessing hydrophobicity and Post-Translational Modification sites. Meanwhile, the Epitope sequence for B-cell, T-cell, and HLA was determined using an immunoinformatics approach. Lastly, molecular docking simulation was done to determine native binding interactions of P48/45-P230. The result showed a distinct protein characteristic of ancestral and consensus sequences. The immunogenicity analysis revealed the number of epitopes in the ancestral sequence is greater than the consensus sequence. The study also found a conserved epitope located in the binding site and consists of specific Post-Translational Modification sites. Hence, our research provides detailed insight into ancestral and consensus P48/45 efficacy for the cross-species anti-malaria vaccine.
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Affiliation(s)
- Kevin Nathanael Ramanto
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Rizky Nurdiansyah
- Department of Bioinformatics, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia.
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Jahantigh HR, Stufano A, Lovreglio P, Rezaee SA, Ahmadi K. In silico identification of epitope-based vaccine candidates against HTLV-1. J Biomol Struct Dyn 2021; 40:6737-6754. [PMID: 33648421 DOI: 10.1080/07391102.2021.1889669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Human T cell leukemia virus type-1 (HTLV-1) is the cause of adult T cell leukemia/lymphoma (ATL), uveitis, and certain pulmonary diseases. In recent decades, many scientists have proposed the development of different treatment and prevention strategies to combat HTLV-1 infection. In this study, we used bioinformatics tools to predict peptide and protein vaccine candidates against HTLV-1 that can potentially induce antibody production and both CD4+ and CD8+ T cell immune responses. Five critical proteins, viz., Hbz, Tax, Pol, Gag, and Env, were analyzed for predicting immunogenic T and B cell epitopes and subsequently evaluated using bioinformatics tools. Based on the predictions, the most antigenic epitopes were selected, and their interaction with immune receptors was investigated. We also designed a protein vaccine candidate with an eight-epitopes-rich domain, including overlapping epitopes detected on both B and T cells. Then, the interaction of the epitope and the designed protein with immune receptors was validated in an in silico docking study. The docking analysis showed that the O2 epitope and D8 protein interact strongly with immune receptors, especially the HLA-A*02:01 receptor. The stability of the interactions was investigated by molecular dynamics (MD) for 100 ns. The root mean square deviation, radius of gyration, hydrogen bonds, and solvent-accessible surface area were calculated for the 100 ns trajectory period. MD studies demonstrated that the O2-HLA-A*02:01 and D8-HLA-A*02:01 complexes were stable during the simulation. Analysis of in silico results showed that the peptide and the designed protein could elicit humoral and cell-mediated immune responses.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hamid Reza Jahantigh
- Interdisciplinary Department of Medicine - Section of Occupational Medicine, University of Bari, Bari, Italy.,Animal Health and Zoonosis PhD Course, Department of Veterinary Medicine, University of Bari, Bari, Italy
| | - Angela Stufano
- Interdisciplinary Department of Medicine - Section of Occupational Medicine, University of Bari, Bari, Italy.,Animal Health and Zoonosis PhD Course, Department of Veterinary Medicine, University of Bari, Bari, Italy
| | - Piero Lovreglio
- Interdisciplinary Department of Medicine - Section of Occupational Medicine, University of Bari, Bari, Italy
| | - Seyed Abdolrahim Rezaee
- Department of Virology, School of Public Health, 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
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Pushparajah D, Jimenez S, Wong S, Alattas H, Nafissi N, Slavcev RA. Advances in gene-based vaccine platforms to address the COVID-19 pandemic. Adv Drug Deliv Rev 2021; 170:113-141. [PMID: 33422546 PMCID: PMC7789827 DOI: 10.1016/j.addr.2021.01.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 01/01/2021] [Indexed: 01/07/2023]
Abstract
The novel betacoronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has spread across the globe at an unprecedented rate since its first emergence in Wuhan City, China in December 2019. Scientific communities around the world have been rigorously working to develop a potent vaccine to combat COVID-19 (coronavirus disease 2019), employing conventional and novel vaccine strategies. Gene-based vaccine platforms based on viral vectors, DNA, and RNA, have shown promising results encompassing both humoral and cell-mediated immune responses in previous studies, supporting their implementation for COVID-19 vaccine development. In fact, the U.S. Food and Drug Administration (FDA) recently authorized the emergency use of two RNA-based COVID-19 vaccines. We review current gene-based vaccine candidates proceeding through clinical trials, including their antigenic targets, delivery vehicles, and route of administration. Important features of previous gene-based vaccine developments against other infectious diseases are discussed in guiding the design and development of effective vaccines against COVID-19 and future derivatives.
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Affiliation(s)
- Deborah Pushparajah
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Salma Jimenez
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada; Theraphage, 151 Charles St W Suite # 199, Kitchener, ON, N2G 1H6, Canada
| | - Shirley Wong
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Hibah Alattas
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Nafiseh Nafissi
- Mediphage Bioceuticals, 661 University Avenue, Suite 1300, Toronto, ON, M5G 0B7, Canada
| | - Roderick A Slavcev
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada; Mediphage Bioceuticals, 661 University Avenue, Suite 1300, Toronto, ON, M5G 0B7, Canada; Theraphage, 151 Charles St W Suite # 199, Kitchener, ON, N2G 1H6, Canada.
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Sun H, Ma L, Wang L, Xiao P, Li H, Zhou M, Song D. Research advances in hydrogen-deuterium exchange mass spectrometry for protein epitope mapping. Anal Bioanal Chem 2021; 413:2345-2359. [PMID: 33404742 DOI: 10.1007/s00216-020-03091-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 12/01/2022]
Abstract
With the development of biomedical technology, epitope mapping of proteins has become critical for developing and evaluating new protein drugs. The application of hydrogen-deuterium exchange for protein epitope mapping holds great potential. Although several reviews addressed the hydrogen-deuterium exchange, to date, only a few systematic reviews have focused on epitope mapping using this technology. Here, we introduce the basic principles, development history, and review research progress in hydrogen-deuterium exchange epitope mapping technology and discuss its advantages. We summarize the main hurdles in applying hydrogen-deuterium exchange epitope mapping technology, combined with relevant examples to provide specific solutions. We describe the epitope mapping of virus assemblies, disease-associated proteins, and polyclonal antibodies as examples of pattern introduction. Finally, we discuss the outlook of hydrogen-deuterium exchange epitope mapping technology. This review will help researchers studying protein epitopes to gain a more comprehensive understanding of this technology.
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Affiliation(s)
- Haofeng Sun
- National Institute of Metrology, Beijing, 100029, China
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lingyun Ma
- National Institute of Metrology, Beijing, 100029, China
| | - Leyu Wang
- College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peng Xiao
- National Institute of Metrology, Beijing, 100029, China
| | - Hongmei Li
- National Institute of Metrology, Beijing, 100029, China
| | - Min Zhou
- School of Chemical and Engineering, Nanjing University of Science and Technology, Jiangsu, 210094, China.
| | - Dewei Song
- National Institute of Metrology, Beijing, 100029, China.
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Changes in Serum Biomarkers of Oxidative Stress in Cattle Vaccinated with Tick Recombinant Antigens: A Pilot Study. Vaccines (Basel) 2020; 9:vaccines9010005. [PMID: 33374141 PMCID: PMC7824418 DOI: 10.3390/vaccines9010005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/17/2020] [Accepted: 12/19/2020] [Indexed: 11/17/2022] Open
Abstract
Tick vaccination is an environmentally friendly alternative for tick control, pathogen infection, and transmission. Tick vaccine protection is sometimes incomplete, which may be due to problems in the stability, conformation, and activity of antibodies. This might be related to oxidative stress, but more studies are needed about the possible relationships between oxidative stress and immune function. The objective of this study was to evaluate and compare various serum biomarkers of antioxidant response and oxidative damage in cattle vaccinated with two recombinant antigens, the chimera of Subolesin- BM95 (homologue antigen of BM86)-MSP1a and BM86, and a control consisting in the adjuvant of the vaccines. Cupric reducing antioxidant capacity (CUPRAC), ferric reducing ability of the plasma (FRAP), trolox equivalent antioxidant capacity (TEAC), total thiol concentrations, and uric acid were evaluated in serum to determine the antioxidant response. To evaluate oxidative status, ferrous oxidation-xylenol orange (FOX), total oxidant status (TOS), advanced oxidation protein products (AOPP) and hydrogen peroxide (H2O2) concentrations in serum were determined. In addition, correlations between biomarkers of oxidative stress and antibody titers were evaluated. A significant decrease in all antioxidant biomarkers, with exception of thiol, and also a decrease in the oxidant markers TOS, AOPP and H2O2 was observed in cattle vaccinated with BM86, that also showed the highest antibody titers response whereas no significant differences in any of the biomarkers were detected in the Subolesin-Bm95-MSP1a and control groups. In addition, the dynamics of Cuprac and H2O2 with time showed significant differences between the groups. Although this is a pilot study and the results should be interpreted with caution and corroborated by studies involving a large number of animals, our results indicate that, in our experimental conditions, those vaccines able to induce a lower oxidative stress produce a higher concentration of antigen-specific antibodies. Overall, the results of the study provided information on the behavior of different biomarkers related to antioxidant defense, and the oxidative damage in cattle in response to vaccination.
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Coimmunization with Two Enterotoxigenic Escherichia coli (ETEC) Fimbrial Multiepitope Fusion Antigens Induces the Production of Neutralizing Antibodies against Five ETEC Fimbriae (F4, F5, F6, F18, and F41). Appl Environ Microbiol 2020; 86:AEM.00217-20. [PMID: 32169934 DOI: 10.1128/aem.00217-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/04/2020] [Indexed: 02/03/2023] Open
Abstract
Fimbriae mediate the initial adherence of enterotoxigenic Escherichia coli (ETEC) to the piglet small intestine and play an important role in development of ETEC-driven postweaning diarrhea (PWD). PWD inflicts huge economic losses on the swine industry each year, making development of alternative treatment and prevention measures for PWD essential. Vaccine candidates that induce antifimbria antibodies that block the initial attachment and colonization of ETEC pathogens with fimbriae are one approach that could help prevent PWD. In this study, we constructed two multiepitope fusion antigens (MEFAs) that carried, expressed, and displayed representative epitopes of F4, F5, F6, F18, and F41 ETEC fimbriae. These MEFAs used either the F4 major subunit FaeG or the F18 adhesive subunit FedF as a backbone. To assess the potential of these MEFAs as antifimbria vaccine candidates that could help prevent PWD, we generated computational models of the MEFAs, constructed them, and then tested their immunogenicity by using them to immunize mice. Computational modeling showed that all relevant epitopes were exposed on the MEFA surface. We found that coadministration of our MEFAs in mice successfully induced five fimbria-specific antibodies in accordance with the epitopes included in the MEFA constructs. Furthermore, the induced antibodies can significantly inhibit the ability of ETEC strains that express F4, F5, F6, F18, and F41 fimbriae to adhere to piglet small intestinal IPEC-1 and IPEC-J2 cells. Our findings indicate that the antifimbria antibodies induced by our FaeG-Fim41a-FanC-FasA and FedF-FasA-Fim41a-FanC fimbria MEFAs blocked adherence of five ETEC fimbriae, suggesting these multivalent fimbria MEFAs may be useful for developing broadly protective antifimbria vaccines against PWD caused by ETEC infections.IMPORTANCE Enterotoxigenic Escherichia coli (ETEC)-associated postweaning diarrhea (PWD) is still a leading disease in recently weaned piglets. Vaccination is considered to be the most ideal and efficacious strategy for preventing PWD. Recently, a commercialized live monovalent F4 oral vaccine and a bivalent F4/F18 oral vaccine have been demonstrated to effectively protect piglets in the F4-positive (F4+) and F18+ ETEC challenge models. However, they will not provide cross-protection against F5+, F6+, or F41+ ETEC-associated PWD cases, as they lack all five fimbria antigens. Thus, a multivalent vaccine containing all five ETEC fimbriae would be more effective in preventing ETEC-driven PWD. In this study, we designed two fimbria-targeted MEFAs using the MEFA technology, and further study demonstrated that these coadministered MEFAs in mice can induce protective antibodies against the five fimbriae expressed by ETEC. These MEFAs could be used as an efficient PWD vaccine candidate; furthermore, MEFA-based structural technology provides an alternative and promising strategy for the development of vaccines against pathogens with heterogeneous virulence factors.
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Forouharmehr A. Engineering an efficient poly-epitope vaccine against Toxoplasma gondii infection: A computational vaccinology study. Microb Pathog 2020; 152:104646. [PMID: 33242641 DOI: 10.1016/j.micpath.2020.104646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
Toxoplasmosis is a zoonotic disease caused by Toxoplasma gondii. Despite the importance of toxoplasmosis, there is no comprehensive strategy to control this disease. Hence, applying the new methods such as the poly-epitope vaccine can be successful. In the current project, to engineer a potent poly-epitope vaccine, 10 antigenic proteins including BiP, GRA1, GRA2, GRA5, MIC8, MIC13, P30, PI1, SOD and Rop2 were selected based on the database. Then, B cell, MHCI and MHCII epitopes of the selected antigenic proteins were isolated by the most accurate servers. The best predicted epitopes along with a molecular adjuvant were employed to engineer a poly-epitope vaccine. After engineering, different physicochemical features, secondary and tertiary structures, molecular docking of the designed vaccine were assessed. The results of this project revealed that the designed vaccine with 730 amino acids in length and molecular weight of 77.67 kDa was a soluble protein which could bind to its receptor with an energy of 6223.43. According to the achievements of this study, it seems the designed vaccine can be an appropriate candidate to apply.
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Affiliation(s)
- Ali Forouharmehr
- Department of Animal Science, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
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Kanoi BN, Nagaoka H, Morita M, Tsuboi T, Takashima E. Leveraging the wheat germ cell-free protein synthesis system to accelerate malaria vaccine development. Parasitol Int 2020; 80:102224. [PMID: 33137499 DOI: 10.1016/j.parint.2020.102224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/04/2020] [Accepted: 09/16/2020] [Indexed: 01/29/2023]
Abstract
Vaccines against infectious diseases have had great successes in the history of public health. Major breakthroughs have occurred in the development of vaccine-based interventions against viral and bacterial pathogens through the application of classical vaccine design strategies. In contrast the development of a malaria vaccine has been slow. Plasmodium falciparum malaria affects millions of people with nearly half of the world population at risk of infection. Decades of dedicated research has taught us that developing an effective vaccine will be time consuming, challenging, and expensive. Nevertheless, recent advancements such as the optimization of robust protein synthesis platforms, high-throughput immunoscreening approaches, reverse vaccinology, structural design of immunogens, lymphocyte repertoire sequencing, and the utilization of artificial intelligence, have renewed the prospects of an accelerated discovery of the key antigens in malaria. A deeper understanding of the major factors underlying the immunological and molecular mechanisms of malaria might provide a comprehensive approach to identifying novel and highly efficacious vaccines. In this review we discuss progress in novel antigen discoveries that leverage on the wheat germ cell-free protein synthesis system (WGCFS) to accelerate malaria vaccine development.
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Affiliation(s)
- Bernard N Kanoi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Hikaru Nagaoka
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Masayuki Morita
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan.
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Brisse M, Vrba SM, Kirk N, Liang Y, Ly H. Emerging Concepts and Technologies in Vaccine Development. Front Immunol 2020; 11:583077. [PMID: 33101309 PMCID: PMC7554600 DOI: 10.3389/fimmu.2020.583077] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Despite the success of vaccination to greatly mitigate or eliminate threat of diseases caused by pathogens, there are still known diseases and emerging pathogens for which the development of successful vaccines against them is inherently difficult. In addition, vaccine development for people with compromised immunity and other pre-existing medical conditions has remained a major challenge. Besides the traditional inactivated or live attenuated, virus-vectored and subunit vaccines, emerging non-viral vaccine technologies, such as viral-like particle and nanoparticle vaccines, DNA/RNA vaccines, and rational vaccine design, offer innovative approaches to address existing challenges of vaccine development. They have also significantly advanced our understanding of vaccine immunology and can guide future vaccine development for many diseases, including rapidly emerging infectious diseases, such as COVID-19, and diseases that have not traditionally been addressed by vaccination, such as cancers and substance abuse. This review provides an integrative discussion of new non-viral vaccine development technologies and their use to address the most fundamental and ongoing challenges of vaccine development.
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Affiliation(s)
- Morgan Brisse
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota Twin Cities, St. Paul, MN, United States
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Sophia M. Vrba
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Natalie Kirk
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
- Comparative Molecular Biosciences Graduate Program, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Yuying Liang
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
| | - Hinh Ly
- Department of Veterinary & Biomedical Sciences, University of Minnesota Twin Cities, St. Paul, MN, United States
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SARS-CoV-2 vaccine research and development: Conventional vaccines and biomimetic nanotechnology strategies. Asian J Pharm Sci 2020; 16:136-146. [PMID: 32905011 PMCID: PMC7462629 DOI: 10.1016/j.ajps.2020.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/16/2020] [Accepted: 08/12/2020] [Indexed: 02/08/2023] Open
Abstract
The development of a massively producible vaccine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, is essential for stopping the current coronavirus disease (COVID-19) pandemic. A vaccine must stimulate effective antibody and T cell responses in vivo to induce long-term protection. Scientific researchers have been developing vaccine candidates for the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) since the outbreaks of these diseases. The prevalence of new biotechnologies such as genetic engineering has shed light on the generation of vaccines against novel viruses. In this review, we present the status of the development of coronavirus vaccines, focusing particularly on the biomimetic nanoparticle technology platform, which is likely to have a major role in future developments of personalized medicine.
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Duan Q, Pang S, Wu W, Jiang B, Zhang W, Liu S, Wang X, Pan Z, Zhu G. A multivalent vaccine candidate targeting enterotoxigenic Escherichia coli fimbriae for broadly protecting against porcine post-weaning diarrhea. Vet Res 2020; 51:93. [PMID: 32703260 PMCID: PMC7376317 DOI: 10.1186/s13567-020-00818-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/11/2020] [Indexed: 11/10/2022] Open
Abstract
Fimbriae-mediated initial adherence is the initial and critical step required for enterotoxigenic Escherichia coli (ETEC) infection. Therefore, vaccine candidates have been developed that target these fimbriae and induce specific anti-fimbriae antibodies to block initial ETEC attachment. While this vaccine effectively protects against ETEC-associated post-weaning diarrhea (PWD), developing a broadly effective vaccine against initial ETEC attachment remains a challenging problem, owing to the immunological heterogeneity among these antigens. Here, we applied multi-epitope fusion antigen (MEFA) technology to construct a FaeG-FedF-FanC-FasA-Fim41a MEFA using the adhesive subunits of predominant fimbriae K88 and F18 as the backbone, which also integrated epitopes from adhesive subunits of the rare fimbriae K99, 987P, and F41; we then generated a MEFA computational model and tested the immunogenicity of this MEFA protein in immunized mice. We next evaluated the potential of the fimbriae-targeted MEFA as a vaccine candidate to effectively prevent PWD using in vitro assessment of its anti-fimbriae, antibody-directed inhibition of bacterial adherence. Computational modeling showed that all relevant epitopes were exposed on the MEFA surface and mice subcutaneously immunized with the MEFA protein developed IgG antibodies to all five fimbriae. Moreover, anti-fimbriae antibodies induced by the MEFA protein significantly inhibited the adhesion of K88+, F18+, K99+, 987P+, and F41+ ETEC strains to piglet small intestinal IPEC-1 and IPEC-J2 cell lines. Taken together, these results indicate that FaeG-FedF-FanC-FasA-Fim41a MEFA protein induced specific anti-fimbriae neutralizing antibodies against the five targeted fimbriae. Critically, these results show the potential of fimbriae-targeted MEFA and indicate their promise as a broad, effective vaccine against PWD.
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Affiliation(s)
- Qiangde Duan
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China
| | - Shengmei Pang
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China
| | - Wenwen Wu
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China
| | - Boyu Jiang
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China
| | - Weiping Zhang
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Siguo Liu
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaojun Wang
- Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhiming Pan
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, China. .,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine (Institute of Comparative Medicine), Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, China. .,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou, China.
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Falahati Z, Mahdavi A, Hassani L. Physicochemical studies on the structural stability of the HIV-1 vaccine candidate recombinant Tat protein. Int J Biol Macromol 2020; 164:403-414. [PMID: 32693138 DOI: 10.1016/j.ijbiomac.2020.07.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022]
Abstract
HIV-1 transactivator of transcription protein is one of the most promising AIDS vaccine candidates and plays central roles in the virus life cycle and pathogenesis. Understanding structural properties of vaccine candidate antigens leads to rational design of vaccines which improves their presentation to immune system and facilitates their manufacturing and storage. This study aims to investigate structural properties and stability of one variant of HIV-1 Tat recombinant protein using different spectroscopic, electrophoretic, and microscopic methods. Therefore, after the gene transformation, protein expression was optimized in E. coli cells and the C-terminal His6-tagged protein was purified using Ni-NTA resin. The structural stability of the pure protein was then investigated under different conditions including pH, Zn2+ ions, thermal and chemical stress. Acidic and alkaline pHs affects spectroscopic properties of the vaccine in different ways. The structure unfolding experiment shows relatively poor stability of the zinc-free protein sample compared to the ion-containing one. According to the quenching experiment and also thermal stability study results, the protein has attained more structural compactness in the presence of Zn2+. Secondary structure of the protein is mainly disordered and didn't significantly affect under various conditions. Finally, different degrees of oligomerization and aggregation were found under physiological conditions.
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Affiliation(s)
- Zahra Falahati
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Gavazang, P.O. Box 451951159, Zanjan, Iran
| | - Atiyeh Mahdavi
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Gavazang, P.O. Box 451951159, Zanjan, Iran.
| | - Leila Hassani
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Gavazang, P.O. Box 451951159, Zanjan, Iran
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25
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Fischinger S, Shin S, Boudreau CM, Ackerman M, Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kim JH, Robb ML, Michael NL, O’Connell RJ, Vasan S, Streeck H, Alter G. Protein-based, but not viral vector alone, HIV vaccine boosting drives an IgG1-biased polyfunctional humoral immune response. JCI Insight 2020; 5:135057. [PMID: 32554928 PMCID: PMC7406243 DOI: 10.1172/jci.insight.135057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 05/07/2020] [Indexed: 12/13/2022] Open
Abstract
The RV144 HIV-1 vaccine trial results showed moderate reduction in viral infections among vaccinees as well as induction of antibody-dependent cellular cytotoxicity and vaccine-specific IgG and IgG3 responses directed at variable loop regions 1 and 2 of the HIV envelope protein. However, with the recent failure of the HVTN 702 clinical trial, comprehensive profiling of humoral immune responses may provide insight for these disappointing results. One of the changes included in the HVTN 702 study was the addition of a late boost, aimed at augmenting peak immunity and durability. The companion vaccine trial RV305 was designed to permit the evaluation of the immunologic impact of late boosting with either the boosting protein antigen alone, the canarypox viral vector ALVAC alone, or a combination of both. Although previous data showed elevated levels of IgG antibodies in both boosting arms, regardless of ALVAC-HIV vector incorporation, the effect on shaping antibody effector function remains unclear. Thus, here we analyzed the antibody and functional profile induced by RV305 boosting regimens and found that although IgG1 levels increased in both arms that included protein boosting, IgG3 levels were reduced compared with the original RV144 vaccine strategy. Most functional responses increased upon protein boosting, regardless of the viral vector-priming agent incorporation. These data suggest that the addition of a late protein boost alone is sufficient to increase functionally potent vaccine-specific antibodies previously associated with reduced risk of infection with HIV.
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Affiliation(s)
- Stephanie Fischinger
- Ragon Institute of MGH, Harvard and MGH, Cambridge, Massachusetts, USA
- Institut für HIV Forschung, Universität Duisburg-Essen, Essen, Germany
| | - Sally Shin
- Ragon Institute of MGH, Harvard and MGH, Cambridge, Massachusetts, USA
| | - Carolyn M. Boudreau
- Ragon Institute of MGH, Harvard and MGH, Cambridge, Massachusetts, USA
- PhD Program in Virology, Harvard University, Boston, Massachusetts, USA
| | - Margaret Ackerman
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | | | - Punnee Pitisuttithum
- Vaccine Trial Centre, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | | | - Merlin L. Robb
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Nelson L. Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Robert J. O’Connell
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Sandhya Vasan
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Hendrik Streeck
- Institut für HIV Forschung, Universität Duisburg-Essen, Essen, Germany
- Institute of Virology, Universitätsklinikum Bonn, Bonn, Germany
| | - Galit Alter
- Ragon Institute of MGH, Harvard and MGH, Cambridge, Massachusetts, USA
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Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria-human protein interactions. Med Microbiol Immunol 2020; 209:265-275. [PMID: 32072248 PMCID: PMC7223518 DOI: 10.1007/s00430-020-00663-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/30/2020] [Indexed: 01/01/2023]
Abstract
A central challenge in infection medicine is to determine the structure and function of host-pathogen protein-protein interactions to understand how these interactions facilitate bacterial adhesion, dissemination and survival. In this review, we focus on proteomics, electron cryo-microscopy and structural modeling to showcase instances where affinity-purification (AP) and cross-linking (XL) mass spectrometry (MS) has advanced our understanding of host-pathogen interactions. We highlight cases where XL-MS in combination with structural modeling has provided insight into the quaternary structure of interspecies protein complexes. We further exemplify how electron cryo-tomography has been used to visualize bacterial-human interactions during attachment and infection. Lastly, we discuss how AP-MS, XL-MS and electron cryo-microscopy and -tomography together with structural modeling approaches can be used in future studies to broaden our knowledge regarding the function, dynamics and evolution of such interactions. This knowledge will be of relevance for future drug and vaccine development programs.
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27
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Diaz-Dinamarca DA, Manzo RA, Soto DA, Avendaño-Valenzuela MJ, Bastias DN, Soto PI, Escobar DF, Vasquez-Saez V, Carrión F, Pizarro-Ortega MS, Wilson CAM, Berrios J, Kalergis AM, Vasquez AE. Surface Immunogenic Protein of Streptococcus Group B is an Agonist of Toll-Like Receptors 2 and 4 and a Potential Immune Adjuvant. Vaccines (Basel) 2020; 8:vaccines8010029. [PMID: 31963234 PMCID: PMC7157747 DOI: 10.3390/vaccines8010029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/20/2019] [Accepted: 01/02/2020] [Indexed: 12/19/2022] Open
Abstract
Vaccine-induced protection against pathogens, especially subunit-based vaccines, are related to antigen properties but mainly in their ability to stimulate the immune system by the use of an adjuvant. Modern vaccines are formulated with a high level of antigen purity, where an efficient adjuvant is necessary. In this context, the use of protein Toll-Like Receptor (TLR) agonists as vaccine adjuvants has been highlighted because of their optimal immunogenicity and minimal toxicity. The Surface Immunogenic Protein (SIP) from Group B Streptococcus (GBS) has gained importance as a new potential protein-based vaccine. Recently, we reported that recombinant SIP (rSIP) expressed by E. coli and purified by High Performance Liquid Chromatography (HPLC) alone induces a protective humoral immune response. In this study, we present the immunomodulatory properties of rSIP as a protein-based adjuvant, as an agonist of TLR. To this end, we showed that C57BL/6 bone marrow-derived dendritic cells pulsed by rSIP resulted in enhanced CD40, CD80, CD86, and Major Histocompatibility Complex (MHC) class II as well as increased secretion proinflammatory cytokines Interleukin (IL)-6, Interferon (IFN)-γ, Tumor Necrosis Factor (TNF)-α, and IL-10. Next, we investigated the in vivo effect of rSIP in the absence or presence of ovalbumin (OVA) on antigen-specific antibody secretion in C57BL/6 mice. Immunization with rSIP plus OVA showed that anti-OVA IgG2a and IgG1a increased significantly compared with OVA alone in C57BL/6 mice. Also, the immunization of rSIP plus OVA generates increased serum cytokines levels characterized by IL-12p70, IL-10, IL-4, and IFN-γ. Interestingly, we observed that rSIP stimulate Toll Like Receptor (TLR)2 and TLR4, individually expressed by Human embryonic kidney (HEK) 293-derived TLR reporter cells. These findings suggest that rSIP is a new potential protein TLR agonist adjuvant and may be employed in the development of new vaccines.
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Affiliation(s)
- Diego A. Diaz-Dinamarca
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (M.S.P.-O.); (A.M.K.)
| | - Ricardo A. Manzo
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
| | - Daniel A. Soto
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
| | - María José Avendaño-Valenzuela
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (M.S.P.-O.); (A.M.K.)
| | - Diego N. Bastias
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (M.S.P.-O.); (A.M.K.)
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Santo Tomas, Santiago 8320000, Chile
| | - Paulina I. Soto
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
| | - Daniel F. Escobar
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
| | - Valeria Vasquez-Saez
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
| | - Flavio Carrión
- Programa de Inmunología Traslacional, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago 8320000, Chile;
| | - Magdalena S. Pizarro-Ortega
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (M.S.P.-O.); (A.M.K.)
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8320000, Chile;
| | - Julio Berrios
- Escuela de Ingeniería en Bioquímica, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile;
| | - Alexis M. Kalergis
- Millenium Institute on Immunology and Immunotherapy, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (M.S.P.-O.); (A.M.K.)
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
| | - Abel E. Vasquez
- Seccion de Biotecnologia, Instituto de Salud Publica de Chile, Santiago 7780050, Chile; (D.A.D.-D.); (R.A.M.); (D.A.S.); (M.J.A.-V.); (D.N.B.); (P.I.S.); (D.F.E.); (V.V.-S.)
- Escuela de Biotecnología, Facultad de Ciencias, Universidad Santo Tomas, Santiago 8320000, Chile
- Facultad de Ciencia, Universidad San Sebastián, Providencia, Santiago 8320000, Chile
- Correspondence: ; Tel.: +56-2-2575-5513
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Zamani-Babgohari M, Hefferon KL, Huang T, AbouHaidar MG. How Computational Epitope Mapping Identifies the Interactions between Nanoparticles Derived from Papaya Mosaic Virus Capsid Proteins and Immune System. Curr Genomics 2020; 20:214-225. [PMID: 31929728 PMCID: PMC6935957 DOI: 10.2174/1389202920666190527080230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 11/22/2022] Open
Abstract
Background Nanoparticles derived from plant viruses possess fascinating structures, versa-tile functions and safe properties, rendering them valuable for a variety of applications. Papaya mosaic Virus-Like Particles (VLPs) are nanoparticles that contain a repetitive number of virus capsid proteins (PMV-CP) and are considered to be promising platforms for vaccine design. Previous studies have re-ported the antigenicity of PMV nanoparticles in mammalian systems. Materials and Methods As experiments that concern vaccine development require careful design and can be time consuming, computational experiments are of particular importance. Therefore, prior to ex-pressing PMV-CP in E. coli and producing nanoparticles, we performed an in silico analysis of the virus particles using software programs based on a series of sophisticated algorithms and modeling networks as useful tools for vaccine design. A computational study of PMV-CP in the context of the immune sys-tem reaction allowed us to clarify particle structure and other unknown features prior to their introduc-tion in vitro. Results The results illustrated that the produced nanoparticles can trigger an immune response in the absence of fusion with any foreign antigen. Conclusion Based on the in silico analyses, the empty capsid protein was determined to be recognised by different B and T cells, as well as cells which carry MHC epitopes.
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Affiliation(s)
| | - Kathleen L Hefferon
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, ON, Canada
| | - Tsu Huang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, ON, Canada
| | - Mounir G AbouHaidar
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, ON, Canada
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Prasasty VD, Grazzolie K, Rosmalena R, Yazid F, Ivan FX, Sinaga E. Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches. Microorganisms 2019; 7:E226. [PMID: 31370224 PMCID: PMC6722788 DOI: 10.3390/microorganisms7080226] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The Zika virus disease, also known as Zika fever is an arboviral disease that became epidemic in the Pacific Islands and had spread to 18 territories of the Americas in 2016. Zika virus disease has been linked to several health problems such as microcephaly and the Guillain-Barré syndrome, but to date, there has been no vaccine available for Zika. Problems related to the development of a vaccine include the vaccination target, which covers pregnant women and children, and the antibody dependent enhancement (ADE), which can be caused by non-neutralizing antibodies. The peptide vaccine was chosen as a focus of this study as a safer platform to develop the Zika vaccine. In this study, a collection of Zika proteomes was used to find the best candidates for T- and B-cell epitopes using the immunoinformatics approach. The most promising T-cell epitopes were mapped using the selected human leukocyte antigen (HLA) alleles, and further molecular docking and dynamics studies showed a good peptide-HLA interaction for the best major histocompatibility complex-II (MHC-II) epitope. The most promising B-cell epitopes include four linear peptides predicted to be cross-reactive with T-cells, and conformational epitopes from two proteins accessible by antibodies in their native biological assembly. It is believed that the use of immunoinformatics methods is a promising strategy against the Zika viral infection in designing an efficacious multiepitope vaccine.
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Affiliation(s)
- Vivitri Dewi Prasasty
- Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia.
| | - Karel Grazzolie
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Rosmalena Rosmalena
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fatmawaty Yazid
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Depok 16424, Indonesia
| | - Fransiskus Xaverius Ivan
- Department of Biology, Faculty of Life Science, Surya University, Tangerang, Banten 15143, Indonesia
| | - Ernawati Sinaga
- Faculty of Biology, Universitas Nasional, Jakarta 12520, Indonesia
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Qiu X, Duvvuri VR, Bahl J. Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines (Basel) 2019; 7:E45. [PMID: 31141933 PMCID: PMC6631137 DOI: 10.3390/vaccines7020045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.
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Affiliation(s)
- Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Venkata R Duvvuri
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30606, USA.
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
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31
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Balke I, Zeltins A. Use of plant viruses and virus-like particles for the creation of novel vaccines. Adv Drug Deliv Rev 2019; 145:119-129. [PMID: 30172923 DOI: 10.1016/j.addr.2018.08.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 07/24/2018] [Accepted: 08/27/2018] [Indexed: 12/15/2022]
Abstract
In recent decades, the development of plant virology and genetic engineering techniques has resulted in the construction of plant virus-based vaccines for protection against different infectious agents, cancers and autoimmune diseases in both humans and animals. Interaction studies between plant viruses and mammalian organisms have suggested that plant viruses and virus-like particles (VLPs) are safe and noninfectious to humans and animals. Plant viruses with introduced antigens are powerful vaccine components due to their strongly organized, repetitive spatial structure; they can elicit strong immune responses similar to those observed with infectious mammalian viruses. The analysis of published data demonstrated that at least 73 experimental vaccines, including 61 prophylactic and 12 therapeutic vaccines, have been constructed using plant viruses as a carrier structure for presentation of different antigens. This information clearly demonstrates that noninfectious viruses are also applicable as vaccine carriers. Moreover, several plant viruses have been used for platform development, and corresponding vaccines are currently being tested in human and veterinary clinical trials. This review therefore discusses the main principles of plant VLP vaccine construction, emphasizing the physical, chemical, genetic and immunological aspects. Results of the latest studies suggest that several plant virus-based vaccines will join the list of approved human and animal vaccines in the near future.
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Affiliation(s)
- Ina Balke
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga LV1067, Latvia
| | - Andris Zeltins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga LV1067, Latvia.
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Abstract
La vaccination représente une des avancées majeures dans le domaine de la santé. Les premiers vaccins ont été produits sur un concept assez empirique reposant sur la stratégie des « 3 i » : isolement, inactivation, injection. Plus récemment sont apparus les vaccins protéiques. Cependant l’émergence de nouveaux pathogènes, l’inefficacité des stratégies vaccinales actuelles pour protéger contre certaines infections, la nécessité de pouvoir développer rapidement et à bas coût de revient des vaccins ont conduit à développer de nouveaux types de vaccins. C’est dans ce contexte que se sont développés des vaccins basés sur l’utilisation des séquences codantes d’acides nucléiques des antigènes d’intérêt (vecteurs viraux, vaccins ADN, vaccins ARN) visant à améliorer l’efficacité des vaccins actuellement disponibles et à proposer des plateformes génériques potentiellement utilisables contre un grand nombre de pathogènes différents. Outre l’utilisation de ces nouveaux vaccins, les recherches vaccinales en cours bénéficient d’évolutions technologiques visant à délivrer de manière optimale les vaccins, en ciblant par exemple les cellules dendritiques, et de mieux caractériser les antigènes d’intérêt via notamment l’utilisation de la vaccinologie inverse.
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Affiliation(s)
- Jean-Daniel Lelièvre
- Vaccine Research Institute, CHU Henri Mondor, 51 avenue Maréchal de Lattre de Tassigny, 94010 Créteil, France
- Service d’immunologie clinique et maladies infectieuses, CHU Henri Mondor, APHP, 51 avenue Maréchal de Lattre de Tassigny, 94010 Créteil, France
- IMRB, équipe 16, CHU Henri Mondor, 51 avenue Maréchal de Lattre de Tassigny, 94010 Créteil, France
- UPEC, 8, rue du Général Sarrail 94010 Créteil Cedex, France
- Auteur correspondant :
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Salvador E, Pires de Souza G, Cotta Malaquias L, Wang T, Leomil Coelho L. Identification of relevant regions on structural and nonstructural proteins of Zika virus for vaccine and diagnostic test development: an in silico approach. New Microbes New Infect 2019; 29:100506. [PMID: 30858979 PMCID: PMC6396434 DOI: 10.1016/j.nmni.2019.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/11/2019] [Accepted: 01/15/2019] [Indexed: 01/07/2023] Open
Abstract
Zika virus (ZIKV) is an arbovirus belonging to the Flaviviridae family and the genus Flavivirus. Infection with ZIKV causes a mild, self-limiting febrile illness called Zika fever. However, ZIKV infection has been recently associated with microcephaly and Guillain-Barré syndrome. Vaccines for the disease are a high priority of World Health Organization. Several studies are currently being conducted to develop a vaccine against ZIKV, but until now there is no licensed ZIKV vaccine. This study used a novel immunoinformatics approach to identify potential T-cell immunogenic epitopes present in the structural and nonstructural proteins of ZIKV. Fourteen T-cell candidate epitopes were identified on ZIKV structural and nonstructural proteins: pr36-50; C61-75; C103-117; E374-382; E477-491; NS2a90-104; NS2a174-188; NS2a179-193; NS2a190-204; NS2a195-209; NS2a200-214; NS3175-189; and NS4a82-96; NS4a99-113. Among these epitopes, only E374-382 is a human leukocyte antigen (HLA) type I restricted epitope. All identified epitopes showed a low similarity with other important flaviviruses but had a high conservation rate among the ZIKV strains and a high population coverage rate. Therefore, these predicted T-cell epitopes are potential candidates targets for development of vaccines to prevent ZIKV infection.
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Affiliation(s)
- E.A. Salvador
- Institute of Biomedical Sciences, Department of Microbiology and Immunology, Federal University of Alfenas, Minas Gerais, Brazil
| | - G.A. Pires de Souza
- Institute of Biomedical Sciences, Department of Microbiology and Immunology, Federal University of Alfenas, Minas Gerais, Brazil
| | - L.C. Cotta Malaquias
- Institute of Biomedical Sciences, Department of Microbiology and Immunology, Federal University of Alfenas, Minas Gerais, Brazil
| | - T. Wang
- Department of Microbiology & Immunology, Department of Pathology, Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - L.F. Leomil Coelho
- Institute of Biomedical Sciences, Department of Microbiology and Immunology, Federal University of Alfenas, Minas Gerais, Brazil
- Corresponding author: L. F. Leomil Coelho, Laboratório de Vacinas, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Rua Gabriel Monteiro, 700 Centro, Alfenasm Minas Gerais, 37130-001, Brazil.
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Virus-Like Particles-Based Mucosal Nanovaccines. NANOVACCINES 2019. [PMCID: PMC7120988 DOI: 10.1007/978-3-030-31668-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Virus-like particles (VLPs) are protein complexes that resemble a virus and constitute highly immunogenic entities as they mimic the pathogen at an important degree. Among nanovaccines, those based on VLPs are the most successful thus far with some formulations already commercialized (e.g., those against hepatitis B and E viruses and human papillomavirus). This chapter highlights the advantages of VLPs-based vaccines, describing approaches for their design and transmittance of the state of the art for mucosal VLPs-based vaccines development. Several candidates have been produced in insect cells, plants, and E. coli and mammalian cells; they have been mainly evaluated in i.n. and oral immunization schemes. i.n. vaccines against the influenza virus and the Norwalk virus are the most advanced applications. For the latter, i.n. formulations are under clinical evaluation. Perspectives for the field comprise the expansion of the use of low-cost platforms such as plants and bacteria, the development of multiepitopic/multivalent vaccines, and computationally designed VLPs. Mucosal VLPs-based vaccines stand as a major promising approach in vaccinology and the initiation of more clinical trials is envisaged in a short time.
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Abstract
With the rise in novel infectious agents and disease pandemics, a new era of vaccine discovery is necessary. To address this, the new field of immunomics is described, which is synergistically powered by integrating bioinformatics methodologies with technological advances in biology and high-throughput instrumentation. By incorporating biological data from immunology and molecular biology with current genomics and proteomics, immunomics is geared to deliver an insight into immune function, optimal stimulation of immune responses and precise mapping and rational selection of immune targets that cover antigenic diversity. These efforts are expected to contribute towards the development of new generation of vaccines, tailored to both the genetic make-up of the human population and of the pathogen. Vaccine technologies are also being explored for prevention or control of non-communicable diseases.
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Charlton Hume HK, Vidigal J, Carrondo MJT, Middelberg APJ, Roldão A, Lua LHL. Synthetic biology for bioengineering virus-like particle vaccines. Biotechnol Bioeng 2018; 116:919-935. [PMID: 30597533 PMCID: PMC7161758 DOI: 10.1002/bit.26890] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/08/2018] [Accepted: 11/29/2018] [Indexed: 12/13/2022]
Abstract
Vaccination is the most effective method of disease prevention and control. Many viruses and bacteria that once caused catastrophic pandemics (e.g., smallpox, poliomyelitis, measles, and diphtheria) are either eradicated or effectively controlled through routine vaccination programs. Nonetheless, vaccine manufacturing remains incredibly challenging. Viruses exhibiting high antigenic diversity and high mutation rates cannot be fairly contested using traditional vaccine production methods and complexities surrounding the manufacturing processes, which impose significant limitations. Virus‐like particles (VLPs) are recombinantly produced viral structures that exhibit immunoprotective traits of native viruses but are noninfectious. Several VLPs that compositionally match a given natural virus have been developed and licensed as vaccines. Expansively, a plethora of studies now confirms that VLPs can be designed to safely present heterologous antigens from a variety of pathogens unrelated to the chosen carrier VLPs. Owing to this design versatility, VLPs offer technological opportunities to modernize vaccine supply and disease response through rational bioengineering. These opportunities are greatly enhanced with the application of synthetic biology, the redesign and construction of novel biological entities. This review outlines how synthetic biology is currently applied to engineer VLP functions and manufacturing process. Current and developing technologies for the identification of novel target‐specific antigens and their usefulness for rational engineering of VLP functions (e.g., presentation of structurally diverse antigens, enhanced antigen immunogenicity, and improved vaccine stability) are described. When applied to manufacturing processes, synthetic biology approaches can also overcome specific challenges in VLP vaccine production. Finally, we address several challenges and benefits associated with the translation of VLP vaccine development into the industry.
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Affiliation(s)
- Hayley K Charlton Hume
- The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, St Lucia, Queensland, Australia
| | - João Vidigal
- Health & Pharma Division, Animal Cell Technology Unit, Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Health & Pharma Division, Animal Cell Technology Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Manuel J T Carrondo
- Health & Pharma Division, Animal Cell Technology Unit, Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | - Anton P J Middelberg
- Faculty of Engineering, Computer and Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - António Roldão
- Health & Pharma Division, Animal Cell Technology Unit, Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Health & Pharma Division, Animal Cell Technology Unit, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, Portugal
| | - Linda H L Lua
- The University of Queensland, St Lucia, Queensland, Australia
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Baarda BI, Martinez FG, Sikora AE. Proteomics, Bioinformatics and Structure-Function Antigen Mining For Gonorrhea Vaccines. Front Immunol 2018; 9:2793. [PMID: 30564232 PMCID: PMC6288298 DOI: 10.3389/fimmu.2018.02793] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
Expanding efforts to develop preventive gonorrhea vaccines is critical because of the serious health consequences combined with the prevalence and the dire possibility of untreatable gonorrhea. Reverse vaccinology, which includes genome and proteome mining, has proven successful in the discovery of vaccine candidates against many pathogenic bacteria. Here, we describe proteomic applications including comprehensive, quantitative proteomic platforms and immunoproteomics coupled with broad-ranging bioinformatics that have been applied for antigen mining to develop gonorrhea vaccine(s). We further focus on outlining the vaccine candidate decision tree, describe the structure-function of novel proteome-derived antigens as well as ways to gain insights into their roles in the cell envelope, and underscore new lessons learned about the fascinating biology of Neisseria gonorrhoeae.
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Affiliation(s)
- Benjamin I. Baarda
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Fabian G. Martinez
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Aleksandra E. Sikora
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, United States
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, OR, United States
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Thu Nguyen TT, Nguyen HT, Vu-Khac H, Wang PC, Chen SC. Identification of protective protein antigens for vaccination against Streptococcus dysgalactiae in cobia (Rachycentron canadum). FISH & SHELLFISH IMMUNOLOGY 2018; 80:88-96. [PMID: 29859310 DOI: 10.1016/j.fsi.2018.05.052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/22/2018] [Accepted: 05/29/2018] [Indexed: 06/08/2023]
Abstract
Streptococcus dysgalactiae is considered a causative agent of severe infection and economic loss for the cobia industry in Taiwan. In this study, protective antigens of this pathogenic bacterium were identified and screened in cobia (Rachycentron canadum). Outer surface proteins (OMPs) of this pathogen were extracted using mutanolysin digestion. Immunogenic targets were detected by western blot and then subjected to peptide sequencing using NanoLC-MS/MS. Two surface proteins, namely phosphoenolpyruvate protein phosphotransferase (PtsA) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), showed strong reactions with cobia antisera against S. dysgalactiae. Recombinant proteins were produced in Escherichia coli cells and their protective efficacies were investigated in cobia. Fish immunised with recombinant proteins, rPtsA + ISA (ISA 763 AVG) and rGAPDH + ISA, elicited higher levels of specific antibody responses against the recombinant proteins and had high levels of lysozyme activity. Notably, vaccinated fish were protected from lethal challenge with relative percentage of survival (RPS) values for rPtsA + ISA and rGAPDH + ISA groups being 91.67% and 83.33%, while 0% RPS value was found in both ISA injected and control groups. The results presented in the study demonstrate that the GAPDH and PtsA are promising vaccine candidates for preventing S. dysgalactiae disease in cobia.
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Affiliation(s)
- Thuy Thi Thu Nguyen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan
| | - Hai Trong Nguyen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan
| | - Hung Vu-Khac
- Institute of Veterinary Research and Development of Central Vietnam, km 4, 2/4 St., Vinh Hoa, Nha Trang, Khanh Hoa, Viet Nam
| | - Pei-Chi Wang
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan; Southern Taiwan Fish Diseases Research Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
| | - Shih-Chu Chen
- Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan; International Degree Program of Ornamental Fish Science and Technology, International College, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan; Southern Taiwan Fish Diseases Research Center, College of Veterinary Medicine, National Pingtung University of Science and Technology, No. 1, Shuefu Road, Neipu, Pingtung, 91201, Taiwan; Research Center for Animal Biologics, National Pingtung University of Science and Technology, No. 1 Shuefu Road, Neipu, Pingtung, 91201, Taiwan.
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39
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Tagliabue A, Rappuoli R. Changing Priorities in Vaccinology: Antibiotic Resistance Moving to the Top. Front Immunol 2018; 9:1068. [PMID: 29910799 PMCID: PMC5992407 DOI: 10.3389/fimmu.2018.01068] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 04/30/2018] [Indexed: 01/08/2023] Open
Abstract
Antimicrobial resistance (AMR) is currently the most alarming issue for human health. AMR already causes 700,000 deaths/year. It is estimated that 10 million deaths due to AMR will occur every year after 2050. This equals the number of people dying of cancer every year in present times. International institutions such as G20, World Bank, World Health Organization (WHO), UN General Assembly, European Union, and the UK and USA governments are calling for new antibiotics. To underline this emergency, a list of antibiotic-resistant "priority pathogens" has been published by WHO. It contains 12 families of bacteria that represent the greatest danger for human health. Resistance to multiple antibiotics is particularly relevant for the Gram-negative bacteria present in the list. The ability of these bacteria to develop mechanisms to resist treatment could be transmitted with genetic material, allowing other bacteria to become drug resistant. Although the search for new antimicrobial drugs remains a top priority, the pipeline for new antibiotics is not promising, and alternative solutions are needed. A possible answer to AMR is vaccination. In fact, while antibiotic resistance emerges rapidly, vaccines can lead to a much longer lasting control of infections. New technologies, such as the high-throughput cloning of human B cells from convalescent or vaccinated people, allow for finding new protective antigens (Ags) that could not be identified with conventional technologies. Antibodies produced by convalescent B cell clones can be screened for their ability to bind, block, and kill bacteria, using novel high-throughput microscopy platforms that rapidly capture digital images, or by conventional technologies such as bactericidal, opsono-phagocytosis and FACS assays. Selected antibodies expressed by recombinant DNA techniques can be used for passive immunization in animal models and tested for protection. Antibodies providing the best protection can be employed to identify new Ags and then used for generating highly specific recombinant Fab fragments. Co-crystallization of Ags bound to Fab fragments will allow us to determine the structure and characteristics of new Ags. This structure-based Ag design will bring to a new generation of vaccines able to target previously elusive infections, thereby offering an effective solution to the problem of AMR.
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Affiliation(s)
- Aldo Tagliabue
- Institute for Genetic and Biomedical Research, CNR, Cagliari, Italy
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40
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Chirani AS, Ghazi M, Goudarzi M, Peerayeh SN, Soleimanjahi H, Dadashi M, Hajikhani B. A survey on chimeric UreB 229-561-HpaA protein targeting Helicobacter pylori: Computational and in vitro urease activity valuation. Comput Biol Chem 2018; 76:42-52. [PMID: 29929167 DOI: 10.1016/j.compbiolchem.2018.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 04/28/2018] [Accepted: 05/01/2018] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori (H. pylori) as microaerophilic, Gram-negative bacterium colonize the human gastric milieu, where it impetuses chronic disorders. Vaccination is a complementary plan, along with antibiotic therapy, for clearance of H. pylori. Today, Computer based tools are essential for the evaluation, design, and experiment for novel chimeric targets for immunological administration. The purpose of this experiment was immunoinformatic analysis of UreB and HpaA molecules in a fusion arrangement and also, construction and expression of recombinant protein containing chimeric sequences. The targets sequences were screened by using of standard in silico tools and immunoinformatic web servers. The high-resolution 3D models of the protein were created and were validated; indeed, the B-and T-cell restricted epitopes were mapped on the chimeric protein. The recombinant protein in frame of the expression vector pET28a were expressed and purified successfully. The urease activity and immunoblotting were performed in vitro condition. This study confirmed that the engineered protein as a highly conserved, hydrophilic, non-allergenic contained remarkable B-cell and T-cell epitopes. It was magnificently attained; chimeric UreB229-561-HpaA could provoke both humoral and cellular immunity. The immunoblotting was shown that the chimeric protein could be detected by serum of immunized animal and H.pylori positive patients. In this study, several antigenic patches from UreB and HpaA were identified that could be an efficient immune system activator. The in vitro analysis of our chimeric molecule confirmed its urease activity. It also confirmed that the chimeric protein could be detected by serum of immunized animal and H.pylori positive patients.
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Affiliation(s)
- Alireza Salimi Chirani
- Department of Medical Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mona Ghazi
- Department of Medical Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Goudarzi
- Department of Medical Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Najar Peerayeh
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hoorieh Soleimanjahi
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Masoud Dadashi
- Department of Medical Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bahareh Hajikhani
- Department of Medical Microbiology, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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41
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New Technologies for Vaccine Development: Harnessing the Power of Human Immunology. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0064-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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42
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Widodo, Veronica Margarecaesha Anyndita N, Dluha N, Rifa'i M, Himmah K, Wahyuningsih MD. Designing and overproducing a tandem epitope of gp350/220 that shows a potential to become an EBV vaccine. Heliyon 2018; 4:e00564. [PMID: 29560474 PMCID: PMC5857718 DOI: 10.1016/j.heliyon.2018.e00564] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/31/2017] [Accepted: 02/28/2018] [Indexed: 11/15/2022] Open
Abstract
Background Epstein-Barr virus (EBV) can cause cancer in people from around the world. There is no EBV vaccine available for use on a global scale. However, emerging evidence suggests that the epitope on the gp350/220 capsid protein may be developed into an EBV vaccine. Nevertheless, the production of small, single epitope is challenging of stability issues and possible alteration of peptide structure. In this study, a tandem epitope was developed consisting of three single epitopes, aimed to improve stability, antigenicity and preserve epitope structure. Materials and methods A tandem epitope was designed using bioinformatics based on the epitope structure of the gp350/220 protein. The tandem epitope structure was analyzed using a protein folding method with Abalone software, which was further refined via YASARA force field and molecular repairing using a FoldX method. Immunogenicity was examined with Epitopia software, whereas allergen properties were tested using AlgPred. The pattern of the tandem epitope binding with anti-gp350/220 antibodies was performed using Z-dock and snugDock. The tandem epitope was then overproduced in E. coli strain BL21 as a host cell. Result Our model demonstrated a successfully designed and overproduced tandem epitope. The tandem epitope demonstrated a similar structure compared with the epitope of whole protein gp350/220. Our epitope also demonstrated non-allergen and antigenicity properties, and possessed antibody binding patterns consistent with whole protein gp350/220. Conclusion and recommendation These data suggest a novel tandem epitope composed of three similar epitopes demonstrates antigenicity, structure, and binding properties consistent with whole protein gp350/220. We also demonstrate successful production of the tandem epitope using E. coli strain BL21 as a host. Future in vivo experimental animal research is necessary to test the ability of this tandem epitope to stimulate antibody production.
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Affiliation(s)
- Widodo
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | | | - Nurul Dluha
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | - Muhaimin Rifa'i
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia.,Pusat Studi Biosistem, LPPM, Brawijaya University, Indonesia
| | - Karimatul Himmah
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
| | - Mulya Dwi Wahyuningsih
- Biology Department, Faculty of Mathematics and Natural Sciences, Brawijaya University, Indonesia
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43
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Mak J, de Marco A. Recent advances in retroviruses via cryo-electron microscopy. Retrovirology 2018; 15:23. [PMID: 29471854 PMCID: PMC5824478 DOI: 10.1186/s12977-018-0405-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 02/14/2018] [Indexed: 12/14/2022] Open
Abstract
Cryo-electron microscopy has undergone a revolution in recent years and it has contributed significantly to a number of different areas in biological research. In this manuscript, we will describe some of the recent advancements in cryo-electron microscopy focussing on the advantages that this technique can bring rather than on the technology. We will then conclude discussing how the field of retrovirology has benefited from cryo-electron microscopy.
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Affiliation(s)
- Johnson Mak
- Institute for Glycomics, Griffith University Gold Coast, Southport, QLD, Australia
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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44
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López-Sagaseta J, Beernink PT, Bianchi F, Santini L, Frigimelica E, Lucas AH, Pizza M, Bottomley MJ. Crystal structure reveals vaccine elicited bactericidal human antibody targeting a conserved epitope on meningococcal fHbp. Nat Commun 2018; 9:528. [PMID: 29410413 PMCID: PMC5802752 DOI: 10.1038/s41467-018-02827-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 01/03/2018] [Indexed: 11/09/2022] Open
Abstract
Data obtained recently in the United Kingdom following a nationwide infant immunization program against serogroup B Neisseria meningitidis (MenB) reported >80% 4CMenB vaccine-mediated protection. Factor H-binding protein (fHbp) is a meningococcal virulence factor and a component of two new MenB vaccines. Here, we investigated the structural bases underlying the fHbp-dependent protective antibody response in humans, which might inform future antigen design efforts. We present the co-crystal structure of a human antibody Fab targeting fHbp. The vaccine-elicited Fab 1A12 is cross-reactive and targets an epitope highly conserved across the repertoire of three naturally occurring fHbp variants. The free Fab structure highlights conformational rearrangements occurring upon antigen binding. Importantly, 1A12 is bactericidal against MenB strains expressing fHbp from all three variants. Our results reveal important immunological features potentially contributing to the broad protection conferred by fHbp vaccination. Our studies fuel the rationale of presenting conserved protein epitopes when developing broadly protective vaccines. Factor H binding protein (fHbp) is a meningococcal virulence factor and a component of vaccines against serogroup B Neisseria meningitidis. Here, the authors characterize the vaccine-elicited human antibody Fab 1A12 and present both the free and the fHbp-bound Fab 1A12 crystal structures.
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Affiliation(s)
| | - Peter T Beernink
- Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA
| | | | - Laura Santini
- GSK Vaccines srl, Via Fiorentina 1, 53100, Siena, Italy
| | | | - Alexander H Lucas
- Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital, 5700 Martin Luther King Jr. Way, Oakland, CA, 94609, USA
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45
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Pfaar O, Bonini S, Cardona V, Demoly P, Jakob T, Jutel M, Kleine-Tebbe J, Klimek L, Klysner S, Kopp MV, Kuna P, Larché M, Muraro A, Schmidt-Weber CB, Shamji MH, Simonsen K, Somoza C, Valovirta E, Zieglmayer P, Zuberbier T, Wahn U. Perspectives in allergen immunotherapy: 2017 and beyond. Allergy 2018; 73 Suppl 104:5-23. [PMID: 29171712 DOI: 10.1111/all.13355] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2017] [Indexed: 01/01/2023]
Abstract
The Future of the Allergists and Specific Immunotherapy (FASIT) workshop provides a regular platform for global experts from academia, allergy clinics, regulatory authorities and industry to review developments in the field of allergen immunotherapy (AIT). The most recent meeting, held in February 2017, had two main themes: advances in AIT and hot topics in AIT from the regulatory point of view. The first theme covered opportunities for personalized AIT, advances in adjuvants and delivery systems, and the development of new molecules and future vaccines for AIT. Key topics in the second part of the meeting were the effects of the enactment of European Directive 2001/83 on the availability of allergens for therapy and diagnosis across the EU, the challenges of conducting Phase 3 studies in the field, the future role of allergen exposure chambers in AIT studies and specific considerations in performing AIT studies in the paediatric population. Finally, the group highlighted the forthcoming EAACI guidelines and their particular importance for the standardization of practice in the treatment of allergies. This review presents a comprehensive insight into those panel discussions and highlights unmet needs and also possible solutions to them for the future.
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Affiliation(s)
- O. Pfaar
- Department of Otorhinolaryngology; Head and Neck Surgery; Universitätsmedizin Mannheim; Medical Faculty Mannheim; Heidelberg University; Mannheim Germany
- Center for Rhinology and Allergology; Wiesbaden Germany
| | - S. Bonini
- Italian National Research Council; Institute of Translational Pharmacology; Rome, and University of Campania ‘Luigi Vanvitelli’; Naples Italy
- Expert-on Secondment at the European Medicines Agency; London UK
| | - V. Cardona
- Hospital Vall D'Hebron, S. Allergologia, S. Medicina Interna; Barcelona Spain
| | - P. Demoly
- Departement de Pneumologie et Addictologie; Hopital Arnaud de Villeneuve; University Hospital of Montpellier; Montpellier France
| | - T. Jakob
- Department of Dermatology and Allergology; University Medical Center Giessen (UKGM); Justus-Liebig-University Giessen; Giessen Germany
- Allergy Research Group; Department of Dermatology; Medical Center - University Freiburg; Freiburg Germany
| | - M. Jutel
- Department of Clinical Immunology; Wroclaw Medical University; Wroclaw Poland
- All-Med Medical Research Institute; Wroclaw Poland
| | - J. Kleine-Tebbe
- Allergy & Asthma Center Westend; Outpatient Clinic and Clinical Research Center; Berlin Germany
| | - L. Klimek
- Center for Rhinology and Allergology; Wiesbaden Germany
| | - S. Klysner
- Expres ion Biotechnologies Aps; Hørsholm Denmark
| | - M. V. Kopp
- Department of Pediatric Allergy and Pulmonology; University of Luebeck; Luebeck Germany
- Airway Research Center North (ARCN); Member of the Deutsches Zentrum für Lungenforschung (DZL); Luebeck Germany
| | - P. Kuna
- Department of Internal Medicine, Asthma and Allergy; Barlicki University Hospital; Medical University of Lodz; Lodz Poland
| | - M. Larché
- Divisions of Clinical Immunology & Allergy, and Respirology; Department of Medicine and Firestone Institute for Respiratory Health; McMaster University; Hamilton ON Canada
| | - A. Muraro
- Food Allergy Referral Centre; Padua University Hospital; Padua Italy
| | - C. B. Schmidt-Weber
- Center of Allergy and Environment (ZAUM); Member of the German Center for Lung Research (DZL); Technical University of Munich and Helmholtz Center Munich; Munich Germany
| | - M. H. Shamji
- Immunomodulation and Tolerance Group; Allergy and Clinical Immunology; Inflammation Repair and Development; National Heart and Lung Institute; Imperial College; London UK
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma; London UK
| | | | - C. Somoza
- Biological Products and Biotechnology Division; Medicines for Human Use Department; Agencia Española de Medicamentos y Productos Sanitarios (AEMPS); Madrid Spain
| | - E. Valovirta
- Department of Lung Disease and Clinical Allergology; University of Turku and Terveystalo Allergy Clinic; Turku Finland
| | - P. Zieglmayer
- Allergy Center Vienna West; Vienna Challenge Chamber; Vienna Austria
| | - T. Zuberbier
- Comprehensive Allergy-Centre-Charité; Department of Dermatology and Allergy; Charité - Universitätsmedizin Berlin; Berlin Germany
- Member of Global Allergy and Asthma European Network (GA LEN); GA LEN coordinating Office; Charité - Universitätsmedizin Berlin; Germany
| | - U. Wahn
- Department for Pediatric Pneumology and Immunology; Charité - Universitätsmedizin Berlin; Berlin Germany
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46
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Abstract
Therapeutic antibodies constitute one of the fastest areas of growth in the field of biologic drugs. A molecular understanding of how antibodies interact with their target antigens is known as epitope mapping. The data provided by epitope mapping is extremely valuable in the process of antibody humanization, as well as in vaccine design. In many cases the epitope recognized by the antibody is a complex, discontinuous 3D conformational epitope. Mapping the interactions of an antibody to a conformational epitope is difficult by many standard approaches. X-ray crystallography is considered to be the gold standard of epitope mapping as it can provide a near atomic resolution model of the antibody-antigen interaction. An X-ray structure allows for inspection of specific antibody-antigen interactions, even in the case of complex conformational epitopes. The method described here can be adapted for structure determination and epitope mapping of any antibody fragment to a simple or complex antigen.
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Affiliation(s)
- Moeko Toride King
- Department of Chemistry, California State University Fresno, 2555 E San Ramon Ave, Fresno, CA, 93740, USA
| | - Cory L Brooks
- Department of Chemistry, California State University Fresno, 2555 E San Ramon Ave, Fresno, CA, 93740, USA.
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Singh SP, Srivastava D, Mishra BN. Genome-wide identification of novel vaccine candidates for Plasmodium falciparum malaria using integrative bioinformatics approaches. 3 Biotech 2017; 7:318. [PMID: 28955615 DOI: 10.1007/s13205-017-0947-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 09/05/2017] [Indexed: 12/12/2022] Open
Abstract
In spite of decades of malaria research and clinical trials, a fully effective and long-lasting preventive vaccine remains elusive. In the present study, 5370 proteins of Plasmodium falciparum genome were screened for the presence of signal peptide/anchor and GPI anchor motifs. Out of 45 screened surface-associated proteins, 22 were consensually predicted as antigens and had no orthologs in human and mouse except circumsporozoite protein (PF3D7_0304600). Among 22 proteins, 19 were identified as new antigens. In the next step, a total of 4944 peptides were predicted as CD8+ T cell epitopes from 22 probable antigens. Of these, the highest scoring 262 epitopes from each antigen were taken for optimization study in the malaria-endemic regions which covered a broad human population (~93.95%). The predicted epitope 13ILFYFFLWV21 of antigen 6-cysteine (PF3D7_1346800) was binding to the HLA-A*0201 allele with the highest fraction (26%) of immunogenicity in the target populations of North-East Asia, South-East Asia, and sub-Saharan Africa. Therefore, these epitopes are proposed to be favored in vaccine designs against malaria.
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Affiliation(s)
- Satarudra Prakash Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh (Lucknow Campus), Lucknow, 226028 India
| | - Deeksha Srivastava
- Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University (Formerly Known as U.P. Technical University), Lucknow, 226021 India
| | - Bhartendu Nath Mishra
- Institute of Engineering and Technology, Dr. A.P.J. Abdul Kalam Technical University (Formerly Known as U.P. Technical University), Lucknow, 226021 India
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48
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Duan Q, Lee KH, Nandre RM, Garcia C, Chen J, Zhang W. MEFA (multiepitope fusion antigen)-Novel Technology for Structural Vaccinology, Proof from Computational and Empirical Immunogenicity Characterization of an Enterotoxigenic Escherichia coli (ETEC) Adhesin MEFA. ACTA ACUST UNITED AC 2017; 8. [PMID: 28944092 PMCID: PMC5606245 DOI: 10.4172/2157-7560.1000367] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Vaccine development often encounters the challenge of virulence heterogeneity. Enterotoxigenic Escherichia coli (ETEC) bacteria producing immunologically heterogeneous virulence factors are a leading cause of children's diarrhea and travelers' diarrhea. Currently, we do not have licensed vaccines against ETEC bacteria. While conventional methods continue to make progress but encounter challenge, new computational and structure-based approaches are explored to accelerate ETEC vaccine development. In this study, we applied a structural vaccinology concept to construct a structure-based multiepitope fusion antigen (MEFA) to carry representing epitopes of the seven most important ETEC adhesins [CFA/I, CFA/II (CS1-CS3), CFA/IV (CS4-CS6)], simulated antigenic structure of the CFA/I/II/IV MEFA with computational atomistic modeling and simulation, characterized immunogenicity in mouse immunization, and examined the potential of structure-informed vaccine design for ETEC vaccine development. A tag-less recombinant MEFA protein (CFA/I/II/IV MEFA) was effectively expressed and extracted. Molecular dynamics simulations indicated that this MEFA immunogen maintained a stable secondary structure and presented epitopes on the protein surface. Empirical data showed that mice immunized with the tagless CFA/I/II/IV MEFA developed strong antigen-specific antibody responses, and mouse serum antibodies significantly inhibited in vitro adherence of bacteria expressing these seven adhesins. These results revealed congruence of antigen immunogenicity between computational simulation and empirical mouse immunization and indicated this tag-less CFA/I/II/IV MEFA potentially an antigen for a broadly protective ETEC vaccine, suggesting a potential application of MEFA-based structural vaccinology for vaccine design against ETEC and likely other pathogens.
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Affiliation(s)
- Qiangde Duan
- Department of Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA
| | - Kuo Hao Lee
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Rahul M Nandre
- Department of Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA
| | - Carolina Garcia
- Department of Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA
| | - Jianhan Chen
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Weiping Zhang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, KS 66506, USA
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49
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Gourlay L, Peri C, Bolognesi M, Colombo G. Structure and Computation in Immunoreagent Design: From Diagnostics to Vaccines. Trends Biotechnol 2017; 35:1208-1220. [PMID: 28739221 DOI: 10.1016/j.tibtech.2017.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022]
Abstract
Novel immunological tools for efficient diagnosis and treatment of emerging infections are urgently required. Advances in the diagnostic and vaccine development fields are continuously progressing, with reverse vaccinology and structural vaccinology (SV) methods for antigen identification and structure-based antigen (re)design playing increasingly relevant roles. SV, in particular, is predicted to be the front-runner in the future development of diagnostics and vaccines targeting challenging diseases such as AIDS and cancer. We review state-of-the-art methodologies for structure-based epitope identification and antigen design, with specific applicative examples. We highlight the implications of such methods for the engineering of biomolecules with improved immunological properties, potential diagnostic and/or therapeutic uses, and discuss the perspectives of structure-based rational design for the production of advanced immunoreagents.
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Affiliation(s)
- Louise Gourlay
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università di Milano, Milan, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy.
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50
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Gori A, Bolognesi M, Colombo G, Gourlay LJ. Structural Vaccinology for Melioidosis Vaccine Design and Immunodiagnostics. CURRENT TROPICAL MEDICINE REPORTS 2017. [DOI: 10.1007/s40475-017-0117-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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