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Malaina I, Martinez L, Salcines-Cuevas D, Teran-Navarro H, Ocejo-Vinyals JG, Gonzalez-Lopez E, Soriano V, Ubeda M, Perez Pinilla MB, Martinez de la Fuente I, Alvarez-Dominguez C. Testing a vaccine candidate against Hepatitis C virus designed by combinatorial optimization. Sci Rep 2023; 13:21746. [PMID: 38066027 PMCID: PMC10709393 DOI: 10.1038/s41598-023-48458-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
This paper presents a new procedure for vaccine design against highly variable viruses such as Hepatitis C. The procedure uses an optimization algorithm to design vaccines that maximize the coverage of epitopes across different virus variants. Weighted epitopes based on the success ratio of immunological assays are used to prioritize the selection of epitopes for vaccine design. The procedure was successfully applied to design DC vaccines loaded with two HCV peptides, STG and DYP, which were shown to be safe, immunogenic, and able to induce significant levels of anti-viral cytokines, peptide-specific cellular immune responses and IgG antibodies. The procedure could potentially be applied to other highly variable viruses that currently lack effective vaccines.
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Affiliation(s)
- Iker Malaina
- Department of Mathematics, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain.
- Biocruces Health Research Institute, Bilbao, Spain.
| | - Luis Martinez
- Department of Mathematics, University of the Basque Country (UPV/EHU), 48080, Bilbao, Spain
- Biocruces Health Research Institute, Bilbao, Spain
- Basque Center of Applied Mathematics (BCAM), 48009, Bilbao, Spain
| | - David Salcines-Cuevas
- Facultad de Ciencias de La Salud, Universidad Internacional de La Rioja (UNIR), MEDONLINE Group, Avda. de La Paz, 137, 26006, Logroño, La Rioja, Spain
| | - Hector Teran-Navarro
- Facultad de Ciencias de La Salud, Universidad Internacional de La Rioja (UNIR), MEDONLINE Group, Avda. de La Paz, 137, 26006, Logroño, La Rioja, Spain
| | - J Gonzalo Ocejo-Vinyals
- Servicio de Inmunología, Cantabria and Instituto de Investigación Marqués de Valdecilla (IDIVAL), Hospital Universitario Marqués de Valdecilla, Avda. de Valdecilla S/N, 39008, Santander, Spain
| | - Elena Gonzalez-Lopez
- Servicio de Inmunología, Cantabria and Instituto de Investigación Marqués de Valdecilla (IDIVAL), Hospital Universitario Marqués de Valdecilla, Avda. de Valdecilla S/N, 39008, Santander, Spain
| | - Vicente Soriano
- Facultad de Ciencias de La Salud, Universidad Internacional de La Rioja (UNIR), MEDONLINE Group, Avda. de La Paz, 137, 26006, Logroño, La Rioja, Spain
| | - María Ubeda
- Facultad de Ciencias de La Salud, Universidad Internacional de La Rioja (UNIR), MEDONLINE Group, Avda. de La Paz, 137, 26006, Logroño, La Rioja, Spain
| | | | | | - Carmen Alvarez-Dominguez
- Facultad de Ciencias de La Salud, Universidad Internacional de La Rioja (UNIR), MEDONLINE Group, Avda. de La Paz, 137, 26006, Logroño, La Rioja, Spain.
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Gupta Y, Baranwal M, Chudasama B. Immunoinformatics-Based Identification of the Conserved Immunogenic Peptides Targeting of Zika Virus Precursor Membrane Protein. Viral Immunol 2023; 36:503-519. [PMID: 37486711 DOI: 10.1089/vim.2023.0015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
Zika virus infections lead to neurological complications such as congenital Zika syndrome and Guillain-Barré syndrome. Rising Zika infections in newborns and adults have triggered the need for vaccine development. In the current study, the precursor membrane (prM) protein of the Zika virus is explored for its functional importance and design of epitopes enriched conserved peptides with the usage of different immunoinformatics approach. Phylogenetic and mutational analyses inferred that the prM protein is highly conserved. Three conserved peptides containing multiple T and B cell epitopes were designed by employing different epitope prediction algorithms. IEDB population coverage analysis of selected peptides in six different continents has shown the population coverage of 60-99.8% (class I HLA) and 80-100% (class II HLA). Molecular docking of selected peptides/epitopes was carried out with each of class I and II HLA alleles using HADDOCK. A majority of peptide-HLA complex (pHLA) have HADDOCK scores found to be comparable and more than native-HLA complex representing the good binding interaction of peptides to HLA. Molecular dynamics simulation with best docked pHLA complexes revealed that pHLA complexes are stable with RMSD <5.5Å. Current work highlights the importance of prM as a strong antigenic protein and selected peptides have the potential to elicit humoral and cell-mediated immune responses.
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Affiliation(s)
- Yogita Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Bhupendra Chudasama
- School of Physics & Materials Science, Thapar Institute of Engineering and Technology, Patiala, India
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Kalita P, Tripathi T, Padhi AK. Computational Protein Design for COVID-19 Research and Emerging Therapeutics. ACS CENTRAL SCIENCE 2023; 9:602-613. [PMID: 37122454 PMCID: PMC10042144 DOI: 10.1021/acscentsci.2c01513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 05/03/2023]
Abstract
As the world struggles with the ongoing COVID-19 pandemic, unprecedented obstacles have continuously been traversed as new SARS-CoV-2 variants continually emerge. Infectious disease outbreaks are unavoidable, but the knowledge gained from the successes and failures will help create a robust health management system to deal with such pandemics. Previously, scientists required years to develop diagnostics, therapeutics, or vaccines; however, we have seen that, with the rapid deployment of high-throughput technologies and unprecedented scientific collaboration worldwide, breakthrough discoveries can be accelerated and insights broadened. Computational protein design (CPD) is a game-changing new technology that has provided alternative therapeutic strategies for pandemic management. In addition to the development of peptide-based inhibitors, miniprotein binders, decoys, biosensors, nanobodies, and monoclonal antibodies, CPD has also been used to redesign native SARS-CoV-2 proteins and human ACE2 receptors. We discuss how novel CPD strategies have been exploited to develop rationally designed and robust COVID-19 treatment strategies.
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Affiliation(s)
- Parismita Kalita
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
| | - Timir Tripathi
- Molecular
and Structural Biophysics Laboratory, Department of Biochemistry, North-Eastern Hill University, Shillong 793022, India
- Regional
Director’s Office, Indira Gandhi
National Open University, Regional Centre Kohima, Kenuozou, Kohima 797001, India
| | - Aditya K. Padhi
- Laboratory
for Computational Biology & Biomolecular Design, School of Biochemical
Engineering, Indian Institute of Technology
(BHU), Varanasi 221005, Uttar Pradesh, India
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García-Machorro J, Ramírez-Salinas GL, Martinez-Archundia M, Correa-Basurto J. The Advantage of Using Immunoinformatic Tools on Vaccine Design and Development for Coronavirus. Vaccines (Basel) 2022; 10:1844. [PMID: 36366353 PMCID: PMC9693616 DOI: 10.3390/vaccines10111844] [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: 06/09/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 10/28/2023] Open
Abstract
After the outbreak of SARS-CoV-2 by the end of 2019, the vaccine development strategies became a worldwide priority. Furthermore, the appearances of novel SARS-CoV-2 variants challenge researchers to develop new pharmacological or preventive strategies. However, vaccines still represent an efficient way to control the SARS-CoV-2 pandemic worldwide. This review describes the importance of bioinformatic and immunoinformatic tools (in silico) for guide vaccine design. In silico strategies permit the identification of epitopes (immunogenic peptides) which could be used as potential vaccines, as well as nonacarriers such as: vector viral based vaccines, RNA-based vaccines and dendrimers through immunoinformatics. Currently, nucleic acid and protein sequential as well structural analyses through bioinformatic tools allow us to get immunogenic epitopes which can induce immune response alone or in complex with nanocarriers. One of the advantages of in silico techniques is that they facilitate the identification of epitopes, while accelerating the process and helping to economize some stages of the development of safe vaccines.
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Affiliation(s)
- Jazmín García-Machorro
- Laboratorio de Medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Gema Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - Marlet Martinez-Archundia
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City 11340, Mexico
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Jonny J, Putranto TA, Sitepu EC, Irfon R. Dendritic cell vaccine as a potential strategy to end the COVID-19 pandemic. Why should it be Ex Vivo? Expert Rev Vaccines 2022; 21:1111-1120. [PMID: 35593184 DOI: 10.1080/14760584.2022.2080658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Developing a safe and efficacious vaccine that can induce broad and long-term immunity for SARS-CoV-2 infection is the most critical research to date. As the most potent APCs, dendritic cells (DCs) can induce a robust T cell immunity. In addition, DCs also play an essential role in COVID-19 pathogenesis, making them a potential vaccination target. However, the DCs-based vaccine with ex vivo loading has not yet been explored for COVID-19. AREAS COVERED This review aims to provide the rationale for developing a DCs-based vaccine with ex vivo loading of SARS-CoV-2 antigen. Here, we discuss the role of DCs in immunity and the effect of SARS-CoV-2 infection on DCs. Then, we propose the mechanism of the DCs-based vaccine in inducing immunity and highlight the benefits of ex vivo loading of antigen. EXPERT OPINION We make the case that an ex vivo loaded DC-based vaccination is appropriate for COVID-19 prevention.
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Affiliation(s)
- Jonny Jonny
- Cellcure Center, Gatot Soebroto Central Army Hospital, Jakarta, Indonesia
| | | | | | - Raoulian Irfon
- Cellcure Center, Gatot Soebroto Central Army Hospital, Jakarta, Indonesia
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