Prediction of MAYV peptide antigens for immunodiagnostic tests by immunoinformatics and molecular dynamics simulations

Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review

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.

Predicting Antigenic Peptides from Rocio Virus NS1 Protein for Immunodiagnostic Testing Using Immunoinformatics and Molecular Dynamics Simulation

The mosquito-borne disease caused by the Rocio virus is a neglected threat, and new immune inputs for serological testing are urgently required for diagnosis in low-resource settings and epidemiological surveillance. We used in silico approaches to identify a specific antigenic peptide (p_ROCV2) in the NS1 protein of the Rocio virus that was theoretically predicted to be stable and exposed on its surface, where it demonstrated key properties allowing it to interact with antibodies. These findings related to the molecular dynamics of this peptide provide important insights for advancing diagnostic platforms and investigating therapeutic alternatives.

Expression, Purification, and Refolding of Chikungunya Virus Full-Length Envelope E2 Protein along with B-Cell and T-Cell Epitope Analyses Using Immuno-Informatics Approaches

Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus, which causes severe illness in humans and is responsible for epidemic outbreaks in Africa, Asia, North and South America, and Europe. Despite its increased global prevalence, no licensed vaccines are available to date for treating or preventing CHIKV infection. The envelope E2 protein is one of the promising subunit vaccine candidates against CHIKV. In this study, we describe successful cloning, expression, and purification of CHIKV E2 full-length (E2-FL) and truncated (E2-ΔC and E2-ΔNC) proteins in the Escherichia coli expression system. The recombinant E2 proteins were purified from inclusion bodies using Ni-NTA chromatography. Further, we describe a detailed refolding procedure for obtaining the CHIKV E2-FL protein in native conformation, which was confirmed using circular dichroism and Fourier transform infrared spectroscopy. BALB/c mice immunized with the three different E2 proteins exhibited increased E2-specific antibody titers compared to sham-immunized controls, suggesting induction of strong humoral immune response. On analyzing the E2-specific antibody response generated in immunized mice, the CHIKV E2-FL protein was observed to be the most immunogenic among the three different CHIKV E2 antigens used in the study. Our B-cell and T-cell epitope mapping results indicate that the presence of specific immunogenic peptides located in the N-terminal and C-terminal regions of the CHIKV E2-FL protein may contribute to its increased immunogenicity, compared to truncated CHIKV E2 proteins. In summary, our study provides a detailed protocol for expressing, purifying, and refolding of the CHIKV E2-FL protein and provides an understanding of its immunogenic epitopes, which can be exploited for the development of novel multiepitope-based anti-CHIKV vaccine strategies.

Identification of promiscuous T cell epitopes on Mayaro virus structural proteins using immunoinformatics, molecular modeling, and QM:MM approaches

The Mayaro virus (MAYV) belongs to genus Alphavirus (family Togaviridae) and has been reported in several countries, especially in tropical regions of America. Due to its outbreaks and potential lack of medication, an effective vaccine formulation is strongly required. This study aimed to predict promiscuous T cell epitopes from structural polyproteins of MAYV using an immunoinformatics approach. For this purpose, consensus sequences were used to identify short protein sequences capable of binding to MHC class I and class II alleles. Our analysis pointed out 4 MHC-I/TCD8+ and 21 MHC-II/TCD4+ epitopes on capside (1;3), E1 (2;5), E2 (1;10), E3 (0;2), and 6 K (0;1) proteins. These predicted epitopes were characterized by high antigenicity, immunogenicity, conservancy, non-allergenic, non-toxic, and good population coverage rate values for North and South American geographical areas. Afterwards, we used the crystal structure of human toll-like receptor 3 (TLR3) ectodomain as a template to predict, through docking essays, the placement of a vaccine prototype at the TLR3 receptor binding site. Finally, classical and quantum mechanics/molecular mechanics (QM:MM) computations were employed to improve the quality of docking calculations, with the QM part of the simulations being accomplished by using the density functional theory (DFT) formalism. These results provide important insights into the advancement of diagnostic platforms, the development of vaccines, and immunotherapeutic interventions.

Scouting the receptor-binding domain of SARS coronavirus 2: a comprehensive immunoinformatics inquisition

Aim: December 2019 witnessed the emergence of a worldwide outbreak of a novel strain of coronavirus (CoV) termed SARS-CoV-2. Several preventive strategies are being developed, such as vaccines, to stop the spread of infection. Materials & methods: A comprehensive immunoinformatics approach was used to map conserved peptide sequences on the receptor binding domain of SARS-CoV-2 for their B-cell, T-helper & T-cytotoxic cell epitope profiles. Results & conclusion: The antigenic B-cell epitopes were LFRKSN and SYGFQPT. Among T-cell epitopes, CVADYSVLY and FTNVYADSF exhibited affinity for MHC class I, while YRLFRKSNL and VYAWNRKRI exhibited affinity for of MHC class II alleles. The overlapping epitope between B- and T-cells was YRLFRKSNL. The deployment of these epitopes in potential vaccine development against COVID-19 may help in slowing down the SARS-CoV-2 spread.