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Heidarnejad F, Namvar A, Sadat SM, Pordanjani PM, Rezaei F, Namdari H, Arjmand S, Bolhassani A. In silico designing of novel epitope-based peptide vaccines against HIV-1. Biotechnol Lett 2024; 46:315-354. [PMID: 38403788 DOI: 10.1007/s10529-023-03464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/16/2023] [Accepted: 12/21/2023] [Indexed: 02/27/2024]
Abstract
The HIV-1 virus has been regarded as a catastrophe for human well-being. The global incidence of HIV-1-infected individuals is increasing. Hence, development of effective immunostimulatory molecules has recently attracted an increasing attention in the field of vaccine design against HIV-1 infection. In this study, we explored the impacts of CD40L and IFN-γ as immunostimulatory adjuvants for our candidate HIV-1 Nef vaccine in human and mouse using immunoinformatics analyses. Overall, 18 IFN-γ-based vaccine constructs (9 constructs in human and 9 constructs in mouse), and 18 CD40L-based vaccine constructs (9 constructs in human and 9 constructs in mouse) were designed. To find immunogenic epitopes, important characteristics of each component (e.g., MHC-I and MHC-II binding, and peptide-MHC-I/MHC-II molecular docking) were determined. Then, the selected epitopes were applied to create multiepitope constructs. Finally, the physicochemical properties, linear and discontinuous B cell epitopes, and molecular interaction between the 3D structure of each construct and CD40, IFN-γ receptor or toll-like receptors (TLRs) were predicted. Our data showed that the full-length CD40L and IFN-γ linked to the N-terminal region of Nef were capable of inducing more effective immune response than multiepitope vaccine constructs. Moreover, molecular docking of the non-allergenic full-length- and epitope-based CD40L and IFN-γ constructs to their cognate receptors, CD40 and IFN-γ receptors, and TLRs 4 and 5 in mouse were more potent than in human. Generally, these findings suggest that the full forms of these adjuvants could be more efficient for improvement of HIV-1 Nef vaccine candidate compared to the designed multiepitope-based constructs.
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Affiliation(s)
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Rezaei
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Haideh Namdari
- Iranian Tissue Bank Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sina Arjmand
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
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2
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Fath T, Bachtiar EW, Alitongbieke G, Pan Y, Hu Y, Widowati R. Immunoinformatic of novel self-amplifying mRNA vaccine lipid nanoparticle against SARS-CoV-2. J Adv Pharm Technol Res 2024; 15:91-98. [PMID: 38903554 PMCID: PMC11186542 DOI: 10.4103/japtr.japtr_424_23] [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: 09/01/2023] [Revised: 01/03/2024] [Accepted: 03/01/2024] [Indexed: 06/22/2024] Open
Abstract
We developed innovative self-amplifying mRNA (sa-mRNA) vaccine based on the derivative of S and Nsp3 proteins, which are considered crucial adhering to human host cells. We performed B-cell, Major histocompatibility complex (MHC) I, and II epitope which were merged with the KK and GPGPG linker. We also incorporated 5' cap sequence, Kozak sequence, replicase sequence, 3'/5' UTR, and poly A tail within the vaccine structure. The vaccine structure was subsequently docked and run the molecular dynamic simulation with TLR7 molecules. As the results of immune response simulation, the immune response was accelerated drastically up to >10-fold for immunoglobulin, interferon-γ, interleukin-2, immunoglobulin M (IgM) + immunoglobulin G (IgG) isotype, IgM isotype, and IgG1 isotype in secondary and tertiary dose, whereas natural killer cells, macrophages, and dendritic cells showed relatively high concentrations after the first dose. As our finding, the IgM + IgG, IgG1 + IgG2, and IgM level (induced by sa-mRNA vaccine) ensued three times with two-fold increase in days 25, and 50, then decreased after days 70-150. However, 150-350 days demonstrated constantly in the range of 20,000-21,000.
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Affiliation(s)
- Turmidzi Fath
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, Fujian 363000, China
- Department of Biology, Faculty of Biology, Universitas Nasional, Jakarta, Indonesia
- Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, Fujian 363000, China
| | - Endang Winiati Bachtiar
- Department of Oral Biology and Oral Science Research Center, Faculty of Dentistry, Universitas Indonesia, Jakarta, Indonesia
| | - Gulimiran Alitongbieke
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, Fujian 363000, China
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, Fujian 363000, China
| | - Yutian Pan
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, Fujian 363000, China
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, Fujian 363000, China
| | - Yuanqing Hu
- Engineering Technological Center of Mushroom Industry, Minnan Normal University, Zhangzhou, Fujian 363000, China
- School of Biological Science and Biotechnology, Minnan Normal University, Zhangzhou, Fujian 363000, China
| | - Retno Widowati
- Department of Biology, Faculty of Biology, Universitas Nasional, Jakarta, Indonesia
- Center for Biotechnology Studies, Universitas Nasional, Jakarta, Indonesia
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3
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Dolley A, Goswami HB, Dowerah D, Dey U, Kumar A, Hmuaka V, Mukhopadhyay R, Kundu D, Varghese GM, Doley R, Chandra Deka R, Namsa ND. Reverse vaccinology and immunoinformatics approach to design a chimeric epitope vaccine against Orientia tsutsugamushi. Heliyon 2024; 10:e23616. [PMID: 38187223 PMCID: PMC10767154 DOI: 10.1016/j.heliyon.2023.e23616] [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: 03/30/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Scrub typhus is a vector-borne infectious disease caused by Orientia tsutsugamushi and it is reportedly associated with up to 20 % of hospitalized cases of febrile illnesses. The major challenge of vaccine development is the lack of identified antigens that can induce both heterotypic and homotypic immunity including the production of antibodies, cytotoxic T lymphocyte, and helper T lymphocytes. We employed a comprehensive immunoinformatic prediction algorithm to identify immunogenic epitopes of the 56-kDa type-specific cell membrane surface antigen and surface cell antigen A of O. tsutsugamushi to select potential candidates for developing vaccines and diagnostic assays. We identified 35 linear and 29 continuous immunogenic B-cell epitopes and 51 and 27 strong-binding T-cell epitopes of major histocompatibility complex class I and class II molecules, respectively, in the conserved and variable regions of the 56-kDa type-specific surface antigen. The predicted B- and T-cell epitopes were used to develop immunogenic multi-epitope candidate vaccines and showed to elicit a broad-range of immune protection. A stable interactions between the multi-epitope vaccines and the host fibronectin protein were observed using docking and simulation methods. Molecular dynamics simulation studies demonstrated that the multi-epitope vaccine constructs and fibronectin docked models were stable during simulation time. Furthermore, the multi-epitope vaccine exhibited properties such as antigenicity, non-allergenicity and ability to induce interferon gamma production and had strong associations with their respective human leukocyte antigen alleles of world-wide population coverage. A correlation of immune simulations and the in-silico predicted immunogenic potential of multi-epitope vaccines implicate for further investigations to accelerate designing of epitope-based vaccine candidates and chimeric antigens for development of serological diagnostic assays for scrub typhus.
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Affiliation(s)
- Anutee Dolley
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Himanshu Ballav Goswami
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Dikshita Dowerah
- Department of Chemical Sciences, Tezpur University, Napaam, 784028, Assam, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Vanlal Hmuaka
- Entomology and Biothreat Management Division, Defence Research Laboratory, Tezpur, 784001, Assam, India
| | - Rupak Mukhopadhyay
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Debasree Kundu
- Department of Infectious Diseases, Christian Medical College, Vellore, 632002, Tamil Nadu, India
| | - George M. Varghese
- Department of Infectious Diseases, Christian Medical College, Vellore, 632002, Tamil Nadu, India
| | - Robin Doley
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
| | - Ramesh Chandra Deka
- Department of Chemical Sciences, Tezpur University, Napaam, 784028, Assam, India
| | - Nima D. Namsa
- Department of Molecular Biology and Biotechnology, Tezpur University, Napaam, 784028, Assam, India
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Jha SK, Imran M, Jha LA, Hasan N, Panthi VK, Paudel KR, Almalki WH, Mohammed Y, Kesharwani P. A Comprehensive review on Pharmacokinetic Studies of Vaccines: Impact of delivery route, carrier-and its modulation on immune response. ENVIRONMENTAL RESEARCH 2023; 236:116823. [PMID: 37543130 DOI: 10.1016/j.envres.2023.116823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
The lack of knowledge about the absorption, distribution, metabolism, and excretion (ADME) of vaccines makes former biopharmaceutical optimization difficult. This was shown during the COVID-19 immunization campaign, where gradual booster doses were introduced.. Thus, understanding vaccine ADME and its effects on immunization effectiveness could result in a more logical vaccine design in terms of formulation, method of administration, and dosing regimens. Herein, we will cover the information available on vaccine pharmacokinetics, impacts of delivery routes and carriers on ADME, utilization and efficiency of nanoparticulate delivery vehicles, impact of dose level and dosing schedule on the therapeutic efficacy of vaccines, intracellular and endosomal trafficking and in vivo fate, perspective on DNA and mRNA vaccines, new generation sequencing and mathematical models to improve cancer vaccination and pharmacology, and the reported toxicological study of COVID-19 vaccines. Altogether, this review will enhance the reader's understanding of the pharmacokinetics of vaccines and methods that can be implied in delivery vehicle design to improve the absorption and distribution of immunizing agents and estimate the appropriate dose to achieve better immunogenic responses and prevent toxicities.
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Affiliation(s)
- Saurav Kumar Jha
- Department of Biomedicine, Health & Life Convergence Sciences, Mokpo National University, Muan-gun, Jeonnam, 58554, Republic of Korea; Department of Biological Sciences and Bioengineering (BSBE), Indian Institute of Technology, Kanpur, 208016, Uttar Pradesh, India.
| | - Mohammad Imran
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, 4102, Australia
| | - Laxmi Akhileshwar Jha
- H. K. College of Pharmacy, Mumbai University, Pratiksha Nagar, Jogeshwari, West Mumbai, 400102, India
| | - Nazeer Hasan
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Vijay Kumar Panthi
- Department of Pharmacy, College of Pharmacy and Natural Medicine Research Institute, Mokpo National University, Jeonnam, 58554, Republic of Korea
| | - Keshav Raj Paudel
- Centre for Inflammation, Faculty of Science, School of Life Science, Centenary Institute and University of Technology Sydney, Sydney, 2007, Australia
| | - Waleed H Almalki
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 24381, Saudi Arabia
| | - Yousuf Mohammed
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, 4102, Australia
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India; Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India.
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5
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Noor F, Nawaz R, Ahad A, Ajmal A, Abrar S, Shahid M, Sarwar A, Naz A, Mehmood U, Idrees M. Structural Analysis and Epitope Prediction of S2 Domain of SARS-CoV-2, Conservation Analysis Among Major Variants. Viral Immunol 2023; 36:110-121. [PMID: 36626119 DOI: 10.1089/vim.2022.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic. There are four structural proteins of the virus: spike, envelope, membrane, and nucleocapsid proteins. Various vaccines were designed and are effectively being used against the spike protein of the virus. However, several vaccine-related complications have been reported worldwide. Assuming that the structural integrity of the whole protein might be contributing to these complications, this study was performed to design epitopes using the S2 domain of the spike protein, which could trigger a strong immune response. We have also predicted antigenic and allergenic properties of the selected epitopes. A total of 49 B cell epitopes passing antigenicity and other assessment filters were found using three methods. Among them, RDLICAQ had the highest antigenicity score (1.1443). However, only one cytotoxic T lymphocyte epitope, RSFIEDLLF, passed the essential filters with an antigenicity score of 0.5782 to show an appropriate immune response for T cells, while among 21 helper T cell lymphocyte epitopes that were filtered, FAMQMAYRFNGIGVT showed the highest (1.3688) antigenicity score. Conservation analysis revealed that the S2 domain is significantly conserved, thus making it an ideal candidate for vaccine development. We have also designed a vaccine construct based on the best suiting components found during the whole study. This construct and S2 domain solely can be future subjects of interest or might be included in a subunit cocktail formulation for attaining unabridged immunogenicity.
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Affiliation(s)
- Faiqa Noor
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Rabia Nawaz
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Ammara Ahad
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Anum Ajmal
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Samyyia Abrar
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Shahid
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aqsa Sarwar
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Aramish Naz
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Uqba Mehmood
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Idrees
- National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Vice Chancellor Office, University of Peshawar, Peshawar, Pakistan
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6
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State of the art in epitope mapping and opportunities in COVID-19. Future Sci OA 2023; 16:FSO832. [PMID: 36897962 PMCID: PMC9987558 DOI: 10.2144/fsoa-2022-0048] [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: 07/29/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
The understanding of any disease calls for studying specific biological structures called epitopes. One important tool recently drawing attention and proving efficiency in both diagnosis and vaccine development is epitope mapping. Several techniques have been developed with the urge to provide precise epitope mapping for use in designing sensitive diagnostic tools and developing rpitope-based vaccines (EBVs) as well as therapeutics. In this review, we will discuss the state of the art in epitope mapping with a special emphasis on accomplishments and opportunities in combating COVID-19. These comprise SARS-CoV-2 variant analysis versus the currently available immune-based diagnostic tools and vaccines, immunological profile-based patient stratification, and finally, exploring novel epitope targets for potential prophylactic, therapeutic or diagnostic agents for COVID-19.
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7
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Rawat SS, Keshri AK, Kaur R, Prasad A. Immunoinformatics Approaches for Vaccine Design: A Fast and Secure Strategy for Successful Vaccine Development. Vaccines (Basel) 2023; 11:vaccines11020221. [PMID: 36851099 PMCID: PMC9959071 DOI: 10.3390/vaccines11020221] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Vaccines are major contributors to the cost-effective interventions in major infectious diseases in the global public health space [...].
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Reducing the Immunogenicity of Pulchellin A-Chain, Ribosome-Inactivating Protein Type 2, by Computational Protein Engineering for Potential New Immunotoxins. J 2023. [DOI: 10.3390/j6010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pulchellin is a plant biotoxin categorized as a type 2 ribosome-inactivating protein (RIPs) which potentially kills cells at very low concentrations. Biotoxins serve as targeting immunotoxins (IT), consisting of antibodies conjugated to toxins. ITs have two independent protein components, a human antibody and a toxin with a bacterial or plant source; therefore, they pose unique setbacks in immunogenicity. To overcome this issue, the engineering of epitopes is one of the beneficial methods to elicit an immunological response. Here, we predicted the tertiary structure of the pulchellin A-chain (PAC) using five common powerful servers and adopted the best model after refining. Then, predicted structure using four distinct computational approaches identified conformational B-cell epitopes. This approach identified some amino acids as a potential for lowering immunogenicity by point mutation. All mutations were then applied to generate a model of pulchellin containing all mutations (so-called PAM). Mutants’ immunogenicity was assessed and compared to the wild type as well as other mutant characteristics, including stability and compactness, were computationally examined in addition to immunogenicity. The findings revealed a reduction in immunogenicity in all mutants and significantly in N146V and R149A. Furthermore, all mutants demonstrated remarkable stability and validity in Molecular Dynamic (MD) simulations. During docking and simulations, the most homologous toxin to pulchellin, Abrin-A was applied as a control. In addition, the toxin candidate containing all mutations (PAM) disclosed a high level of stability, making it a potential model for experimental deployment. In conclusion, by eliminating B-cell epitopes, our computational approach provides a potential less immunogenic IT based on PAC.
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB. A novel vaccine based on SARS-CoV-2 CD4 + and CD8 + T cell conserved epitopes from variants Alpha to Omicron. Sci Rep 2022; 12:16731. [PMID: 36202985 PMCID: PMC9537284 DOI: 10.1038/s41598-022-21207-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/23/2022] [Indexed: 12/03/2022] Open
Abstract
COVID-19 caused, as of September, 1rst, 2022, 599,825,400 confirmed cases, including 6,469,458 deaths. Currently used vaccines reduced severity and mortality but not virus transmission or reinfection by different strains. They are based on the Spike protein of the Wuhan reference virus, which although highly antigenic suffered many mutations in SARS-CoV-2 variants, escaping vaccine-generated immune responses. Multiepitope vaccines based on 100% conserved epitopes of multiple proteins of all SARS-CoV-2 variants, rather than a single highly mutating antigen, could offer more long-lasting protection. In this study, a multiepitope multivariant vaccine was designed using immunoinformatics and in silico approaches. It is composed of highly promiscuous and strong HLA binding CD4+ and CD8+ T cell epitopes of the S, M, N, E, ORF1ab, ORF 6 and ORF8 proteins. Based on the analysis of one genome per WHO clade, the epitopes were 100% conserved among the Wuhan-Hu1, Alpha, Beta, Gamma, Delta, Omicron, Mµ, Zeta, Lambda and R1 variants. An extended epitope-conservancy analysis performed using GISAID metadata of 3,630,666 SARS-CoV-2 genomes of these variants and the additional genomes of the Epsilon, Lota, Theta, Eta, Kappa and GH490 R clades, confirmed the high conservancy of the epitopes. All but one of the CD4 peptides showed a level of conservation greater than 97% among all genomes. All but one of the CD8 epitopes showed a level of conservation greater than 96% among all genomes, with the vast majority greater than 99%. A multiepitope and multivariant recombinant vaccine was designed and it was stable, mildly hydrophobic and non-toxic. The vaccine has good molecular docking with TLR4 and promoted, without adjuvant, strong B and Th1 memory immune responses and secretion of high levels of IL-2, IFN-γ, lower levels of IL-12, TGF-β and IL-10, and no IL-6. Experimental in vivo studies should validate the vaccine's further use as preventive tool with cross-protective properties.
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Affiliation(s)
- Iam Palatnik-de-Sousa
- Department of Electrical Engeneering, Pontifical Catholic University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Stephany Christiny Cavalcante
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Paula Fonseca Ribeiro
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - João Antônio Barbosa Martins Silva
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael Ciro Cavalcante
- Department of Pharmacy, Campus Professor Antônio Garcia Filho, Federal University of Sergipe, Lagarto, Sergipe, Brazil
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pathology, University of California, San Diego, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
- Global Virus Network, Baltimore, MD, USA
| | - Clarisa Beatriz Palatnik-de-Sousa
- Department of General Microbiology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
- Institute for Immunological Investigation (III), INCT, National Council for Scientific and Technological Development (CNPq), São Paulo, Brazil.
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11
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Feng Q, Huang XY, Feng YM, Sun LJ, Sun JY, Li Y, Xie X, Hu J, Guo CY. Identification and analysis of B cell epitopes of hemagglutinin of H1N1 influenza virus. Arch Microbiol 2022; 204:594. [PMID: 36053375 PMCID: PMC9438888 DOI: 10.1007/s00203-022-03133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 11/27/2022]
Abstract
The frequent variation of influenza virus hemagglutinin (HA) antigen is the main cause of influenza pandemic. Therefore, the study of B cell epitopes of HA is of great significance in the prevention and control of influenza virus. In this study, the split vaccine of 2009 H1N1 influenza virus was used as immunogen, and the monoclonal antibodies (mAbs) were prepared by conventional hybridoma fusion and screening techniques. The characteristics of mAbs were identified by ELISA method, Western-blot test and hemagglutination inhibition test (HI). Using the obtained mAbs as a tool, the B cell epitopes of HA were predicted by ELISA blocking test, sandwich ELISA method and computer simulation method. Finally, four mAbs against HA antigen of H1N1 influenza virus were obtained. The results of ELISA and computer prediction showed that there were at least two types of epitopes on HA of influenza virus. The results of this study complemented the existing methods for predicting HA epitopes, and also provided a new method for predicting other pathogenic microorganisms.
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Affiliation(s)
- Qing Feng
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xiao-Yan Huang
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
| | - Yang-Meng Feng
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
| | - Li-Jun Sun
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
| | - Jing-Ying Sun
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yan Li
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xin Xie
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an, China
| | - Jun Hu
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China.
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China.
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China.
| | - Chun-Yan Guo
- Central Laboratory, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China.
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Xi'an, Shaanxi, China.
- Research Center of Cell Immunological Engineering and Technology of Shaanxi Province, Xi'an, Shaanxi, China.
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