In-silico analysis of recombinant protein vaccines based on the spike protein of Indonesian SARS-CoV-2 through a reverse vaccinology approach

Febrianti, Riska Ayu; Narulita, Erlia

doi:10.1016/j.jtumed.2022.02.007

Cited by 3 publications

(1 citation statement)

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“…They were validated using the physicochemical structure and analyzed further through cross-reactivity, molecular docking, and immune simulation. Meanwhile, Febrianti and Narulita (2022) [ 17 ] designed a multiepitope COVID-19 vaccine using spike glycoprotein and validated its sequence using physicochemical structure, which also continued to the design of a plasmid vector. Regarding these studies, our research started by constructing a phylogenetic tree from the evolution of the target sequence in Indonesia, searching the epitope of T and B cells, constructing and validating the vaccines and their 3D structure, docking them with TLR-3 or TLR-4, performing a molecular dynamics study, in silico immune simulations, and constructing a plasmid vector.…”

Section: Introductionmentioning

confidence: 99%

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

et al. 2023

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The coronavirus disease 2019 outbreak has become a huge challenge in the human sector for the past two years. The coronavirus is capable of mutating at a higher rate than other viruses. Thus, an approach for creating an effective vaccine is still needed to induce antibodies against multiple variants with lower side effects. Currently, there is a lack of research on designing a multiepitope of the COVID-19 spike protein for the Indonesian population with comprehensive immunoinformatic analysis. Therefore, this study aimed to design a multiepitope-based vaccine for the Indonesian population using an immunoinformatic approach. This study was conducted using the SARS-CoV-2 spike glycoprotein sequences from Indonesia that were retrieved from the GISAID database. Three SARS-CoV-2 sequences, with IDs of EIJK-61453, UGM0002, and B.1.1.7 were selected. The CD8+ cytotoxic T-cell lymphocyte (CTL) epitope, CD4+ helper T lymphocyte (HTL) epitope, B-cell epitope, and IFN-γ production were predicted. After modeling the vaccines, molecular docking, molecular dynamics, in silico immune simulations, and plasmid vector design were performed. The designed vaccine is antigenic, non-allergenic, non-toxic, capable of inducing IFN-γ with a population reach of 86.29% in Indonesia, and has good stability during molecular dynamics and immune simulation. Hence, this vaccine model is recommended to be investigated for further study.

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Section: Introductionmentioning

confidence: 99%

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

et al. 2023

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Immunology to Immunotherapeutics of SARS-CoV-2: Identification of Immunogenic Epitopes for Vaccine Development

2022

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The emergence of COVID19 pandemic caused by SARS-CoV-2 virus has created a global public health and socio-economic crisis. Immunoinformatics-based approaches to investigate the potential antigens is the fastest way to move towards a multiepitope-based vaccine development. This review encompasses the underlying mechanisms of pathogenesis, innate and adaptive immune signaling along with evasion pathways of SARS-CoV-2. Furthermore, it compiles the promiscuous peptides from in silico studies which are subjected to prediction of cytokine milieu using web-based servers. Out of the 434 peptides retrieved from all studies, we have identified 33 most promising T cell vaccine candidates. This review presents a list of the most potential epitopes from several proteins of the virus based on their immunogenicity, homology, conservancy and population coverage studies. These epitopes can form a basis of second generation of vaccine development as the first generation vaccines in various stages of trials mostly focus only on Spike protein. We therefore, propose them as most potential candidates which can be taken up immediately for confirmation by experimental studies. Supplementary Information The online version contains supplementary material available at 10.1007/s00284-022-03003-3.

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Computational design and evaluation of mRNA- and protein-based conjugate vaccines for influenza A and SARS-CoV-2 viruses

Elalouf,

Kedarya,

Elalouf

et al. 2023

Journal of Genetic Engineering and Biotechnology

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Background Israel confirmed the first case of “flurona”—a co-infection of seasonal flu (IAV) and SARS-CoV-2 in an unvaccinated pregnant woman. This twindemic has been confirmed in multiple countries and underscores the importance of managing respiratory viral illnesses. Results The novel conjugate vaccine was designed by joining four hemagglutinin, three neuraminidase, and four S protein of B-cell epitopes, two hemagglutinin, three neuraminidase, and four S proteins of MHC-I epitopes, and three hemagglutinin, nine neuraminidase, and five S proteins of MHC-II epitopes with linkers and adjuvants. The constructed conjugate vaccine was found stable, non-toxic, non-allergic, and antigenic with 0.6466 scores. The vaccine contained 14.87% alpha helix, 29.85% extended strand, 9.64% beta-turn, and 45.64% random coil, which was modeled to a 3D structure with 94.7% residues in the most favored region of the Ramachandran plot and Z-score of −3.33. The molecular docking of the vaccine with TLR3 represented −1513.9 kcal/mol of binding energy with 39 hydrogen bonds and 514 non-bonded contacts, and 1.582925e-07 of eigenvalue complex. Immune stimulation prediction showed the conjugate vaccine could activate T and B lymphocytes to produce high levels of Th1 cytokines and antibodies. Conclusion The in silico-designed vaccine against IAV and SARS-CoV-2 showed good population coverage and immune response with predicted T- and B-cell epitopes, favorable molecular docking, Ramachandran plot results, and good protein expression. It fulfilled safety criteria, indicating potential for preclinical studies and experimental clinical trials.

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In-silico analysis of recombinant protein vaccines based on the spike protein of Indonesian SARS-CoV-2 through a reverse vaccinology approach

Cited by 3 publications

References 29 publications

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

Immunoinformatics Study: Multi-Epitope Based Vaccine Design from SARS-CoV-2 Spike Glycoprotein

Immunology to Immunotherapeutics of SARS-CoV-2: Identification of Immunogenic Epitopes for Vaccine Development

Computational design and evaluation of mRNA- and protein-based conjugate vaccines for influenza A and SARS-CoV-2 viruses

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