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Ritaparna P, Ray M, Dhal AK, Mahapatra RK. An immunoinformatics approach for design and validation of multi-subunit vaccine against Plasmodium falciparum from essential hypothetical proteins. J Parasit Dis 2024; 48:593-609. [PMID: 39145352 PMCID: PMC11319695 DOI: 10.1007/s12639-024-01696-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/11/2024] [Indexed: 08/16/2024] Open
Abstract
Malaria, caused by Plasmodium falciparum, remains a pressing global health concern. Advancements in combating this parasite involve the development of a protein vaccine. This study employs immunoinformatics to identify potential vaccine candidates within the repertoire of 218 P. falciparum exported essential proteins identified through saturaturation mutagenesis study. Our screening approach narrows down to 65 Plasmodium-exported proteins with uncharacterized functions while exhibiting non-mutability in CDS (coding sequences). The transmembrane helix, antigenicity, allergenicity of the shortlisted proteins was assessed through diverse prediction algorithm, culminating in the identification of five promising vaccination contenders, based on probability scores. We discerned B-cell, helper T-lymphocyte, and cytotoxic T-lymphocyte epitopes. Two proteins with the most favorable epitope were harnessed to construct a multi-subunit vaccine, through judicious linker integration. Employing the I-TASSER software, three-dimensional models of the constituent proteins was obtained and was validated using diverse tools like ProSA, VERIFY3D, and ERRAT. The modelled proteins underwent Molecular Dynamics (MD) simulation in a solvent environment to evaluate the stability of the multi-subunit vaccine. Furthermore, we conducted molecular docking through the ClusPro web server to elucidate potential interactions with Toll-like receptors (TLR2 and TLR4). Docking scores revealed a pronounced affinity of the multi-subunit vaccine for TLR2. Significantly, 100 ns MD simulation of the protein-receptor complex unveiled a persistent hydrogen bond linkage between the ARG63 residue of the sub-unit vaccine and the GLU32 residue of the TLR2 receptor. These findings collectively advocate the potential efficacy of the first multi-subunit vaccine from the potential hypothetical proteins of P. falciparum. Supplementary Information The online version contains supplementary material available at 10.1007/s12639-024-01696-w.
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Affiliation(s)
- Prajna Ritaparna
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha 751024 India
- National Innovation Foundation, India, KIIT-TBI, Bhubaneswar, Odisha 751024 India
| | - Muskan Ray
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha 751024 India
| | - Ajit Kumar Dhal
- School of Biotechnology, KIIT Deemed to Be University, Bhubaneswar, Odisha 751024 India
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2
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Chavda VP, Ghali ENHK, Balar PC, Chauhan SC, Tiwari N, Shukla S, Athalye M, Patravale V, Apostolopoulos V, Yallapu MM. Protein subunit vaccines: Promising frontiers against COVID-19. J Control Release 2024; 366:761-782. [PMID: 38219913 DOI: 10.1016/j.jconrel.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/16/2024]
Abstract
The emergence of COVID-19 has posed an unprecedented global health crisis, challenging the healthcare systems worldwide. Amidst the rapid development of several vaccine formulations, protein subunit vaccines have emerged as a promising approach. This article provides an in-depth evaluation of the role of protein subunit vaccines in the management of COVID-19. Leveraging viral protein fragments, particularly the spike protein from SARS-CoV-2, these vaccines elicit a targeted immune response without the risk of inducing disease. Notably, the robust safety profile of protein subunit vaccines makes them a compelling candidate in the management of COVID-19. Various innovative approaches, including reverse vaccinology, virus like particles, and recombinant modifications are incorporated to develop protein subunit vaccines. In addition, the utilization of advanced manufacturing techniques facilitates large-scale production, ensuring widespread distribution. Despite these advancements, challenges persist, such as the requirement for cold-chain storage and the necessity for booster doses. This article evaluates the formulation and applications of protein subunit vaccines, providing a comprehensive overview of their clinical development and approvals in the context of COVID-19. By addressing the current status and challenges, this review aims to contribute to the ongoing discourse on optimizing protein subunit vaccines for effective pandemic control.
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Affiliation(s)
- Vivek P Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India.
| | - Eswara Naga Hanuma Kumar Ghali
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.
| | - Pankti C Balar
- Pharmacy Section, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Subhash C Chauhan
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.
| | - Nikita Tiwari
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India
| | - Somanshi Shukla
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India
| | - Mansi Athalye
- Department of Pharmaceutics and Pharmaceutical Technology, L. M. College of Pharmacy, Ahmedabad 380009, Gujarat, India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India
| | - Vasso Apostolopoulos
- Institute for Health and Sport, Immunology and Translational Research, Victoria University, Melbourne, VIC 3030, Australia; Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC 3021, Australia.
| | - Murali M Yallapu
- Department of Immunology and Microbiology, School of Medicine, The University of Texas Rio Grande Valley, McAllen, TX 78504, USA; South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA.
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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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Arwansyah A, Arif AR, Kade A, Taiyeb M, Ramli I, Santoso T, Ningsih P, Natsir H, Tahril T, Uday Kumar K. Molecular modelling on multiepitope-based vaccine against SARS-CoV-2 using immunoinformatics, molecular docking, and molecular dynamics simulation. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:649-675. [PMID: 36083166 DOI: 10.1080/1062936x.2022.2117846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
The pandemic of COVID-19 caused by SARS-CoV-2 has made a worldwide health emergency. Despite the fact that current vaccines are readily available, several SARSCoV-2 variants affecting the existing vaccine are to be less effective due to the mutations in the structural proteins. Furthermore, the appearance of the new variants cannot be easily predicted in the future. Therefore, the attempts to construct new vaccines or to modify the current vaccines are still pivotal works for preventing the spread of the virus. In the present investigation, the computational analysis through immunoinformatics, molecular docking, and molecular dynamics (MD) simulation is employed to construct an effective vaccine against SARS-CoV2. The structural proteins of SARS-CoV2 are utilized to create a multiepitope-based vaccine (MEV). According to our findings presented by systematic procedures in the current investigation, the MEV construct may be able to trigger a strong immunological response against the virus. Therefore, the designed MEV could be a potential vaccine candidate against SARS-CoV-2, and also it is expected to be effective for other variants.
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Affiliation(s)
- A Arwansyah
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - A R Arif
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - A Kade
- Department of Physics Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - M Taiyeb
- Department of Biology, Faculty of Mathematics and Natural Sciences, Makassar State University, Makassar, Indonesia
| | - I Ramli
- Department of Physics, Faculty of Science, Universitas Cokroaminoto Palopo, Palopo, Indonesia
| | - T Santoso
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - P Ningsih
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - H Natsir
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - T Tahril
- Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
| | - K Uday Kumar
- Department of Radiology, Toxicology and Population Protection, Faculty of Health and Social Studies, University of South Bohemia Cesk´e Budˇejovice, Czech Republic
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Chen J, Deng Y, Huang B, Han D, Wang W, Huang M, Zhai C, Zhao Z, Yang R, Zhao Y, Wang W, Zhai D, Tan W. DNA Vaccines Expressing the Envelope and Membrane Proteins Provide Partial Protection Against SARS-CoV-2 in Mice. Front Immunol 2022; 13:827605. [PMID: 35281016 PMCID: PMC8907653 DOI: 10.3389/fimmu.2022.827605] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/07/2022] [Indexed: 12/11/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a public health emergency of international concern, and an effective vaccine is urgently needed to control the pandemic. Envelope (E) and membrane (M) proteins are highly conserved structural proteins among SARS-CoV-2 and SARS-CoV and have been proposed as potential targets for the development of cross-protective vaccines. Here, synthetic DNA vaccines encoding SARS-CoV-2 E/M proteins (called p-SARS-CoV-2-E/M) were developed, and mice were immunised with three doses via intramuscular injection and electroporation. Significant cellular immune responses were elicited, whereas no robust humoral immunity was detected. In addition, novel H-2d-restricted T-cell epitopes were identified. Notably, although no drop in lung tissue virus titre was detected in DNA-vaccinated mice post-challenge with SARS-CoV-2, immunisation with either p-SARS-CoV-2-E or p-SARS-CoV-2-M provided minor protection and co-immunisation with p-SARS-CoV-2-E+M increased protection. Therefore, E/M proteins should be considered as vaccine candidates as they may be valuable in the optimisation of vaccination strategies against COVID-19.
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Affiliation(s)
- Jinni Chen
- School of Public Health, Xinxiang Medical University, Xinxiang, China.,National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yao Deng
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Baoying Huang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Di Han
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.,Basic Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Wen Wang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Mengjing Huang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.,Basic Medical College, Inner Mongolia Medical University, Hohhot, China
| | - Chengcheng Zhai
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.,School of Public Health, Baotou Medical College, Baotou, China
| | - Zhimin Zhao
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Ren Yang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Ying Zhao
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Wenling Wang
- National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Desheng Zhai
- School of Public Health, Xinxiang Medical University, Xinxiang, China
| | - Wenjie Tan
- School of Public Health, Xinxiang Medical University, Xinxiang, China.,National Health Commission (NHC) Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
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