Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses

Immunoinformatics Approach to Design a Multi-Epitope Vaccine against Cutaneous Leishmaniasis

Cutaneous Leishmaniasis (CL), a neglected vector-borne disease caused by protozoan parasite Leishmania major (L. major), is a major public health concern, and the development of new strategies to reduce the disease incidence has become a top priority. Advances in immunoinformatics and in-silico epitope prediction could be a promising approach to designing a finest vaccine candidate. In this study, we aimed to design a peptide-based vaccine against CL using computational tools and identified ten B-cell-derived T-cell epitopes from the glycoprotein gp63 of L. major. All of the potential immunodominant epitopes were used to design a vaccine construct along with a linker and an adjuvant at the N-terminal for enhancing its immunogenicity. Additionally, many characteristics of the proposed vaccine were examined, and it was confirmed to be non-allergenic, non-toxic, and thermally stable. To assess the vaccine interaction with the innate immune toll-like receptor-4 (TLR-4), a 3D structure of the vaccine construct was developed. Molecular docking and molecular dynamic simulation were used to confirm the binding and to assess the stability of the vaccine-TLR4 complex and interactions, respectively. In conclusion, our multi-epitope vaccine will provide a gateway to analyze the protein function of a potential vaccine candidate against CL.

In silico design and validation of a novel multi-epitope vaccine candidate against structural proteins of Chikungunya virus using comprehensive immunoinformatics analyses

Chikungunya virus (CHIKV) is an emerging viral infectious agent with the potential of causing pandemic. There is neither a protective vaccine nor an approved drug against the virus. The aim of this study was design of a novel multi-epitope vaccine (MEV) candidate against the CHIKV structural proteins using comprehensive immunoinformatics and immune simulation analyses. In this study, using comprehensive immunoinformatics approaches, we developed a novel MEV candidate using the CHIKV structural proteins (E1, E2, 6 K, and E3). The polyprotein sequence was obtained from the UniProt Knowledgebase and saved in FASTA format. The helper and cytotoxic T lymphocytes (HTLs and CTLs respectively) and B cell epitopes were predicted. The toll-like receptor 4 (TLR4) agonist RS09 and PADRE epitope were employed as promising immunostimulatory adjuvant proteins. All vaccine components were fused using proper linkers. The MEV construct was checked in terms of antigenicity, allergenicity, immunogenicity, and physicochemical features. The docking of the MEV construct and the TLR4 and molecular dynamics (MD) simulation were also performed to assess the binding stability. The designed construct was non-allergen and was immunogen which efficiently stimulated immune responses using the proper synthetic adjuvant. The MEV candidate exhibited acceptable physicochemical features. Immune provocation included prediction of HTL, B cell, and CTL epitopes. The docking and MD simulation confirmed the stability of the docked TLR4-MEV complex. The high-level protein expression in the Escherichia coli (E. coli) host was observed through in silico cloning. The in vitro, in vivo, and clinical trial investigations are required to verify the findings of the current study.

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.

A Review of Omics Studies on Arboviruses: Alphavirus, Orthobunyavirus and Phlebovirus

Since the intricate and complex steps in pathogenesis and host-viral interactions of arthropod-borne viruses or arboviruses are not completely understood, the multi-omics approaches, which encompass proteomics, transcriptomics, genomics and metabolomics network analysis, are of great importance. We have reviewed the omics studies on mosquito-borne viruses of the Togaviridae, Peribuyaviridae and Phenuiviridae families, specifically for Chikungunya, Mayaro, Oropouche and Rift Valley Fever viruses. Omics studies can potentially provide a new perspective on the pathophysiology of arboviruses, contributing to a better comprehension of these diseases and their effects and, hence, provide novel insights for the development of new antiviral drugs or therapies.

mRNA Vaccine Designing Using Chikungunya Virus E Glycoprotein through Immunoinformatics-Guided Approaches

Chikungunya virus is an alphavirus transmitted by mosquitos that develops into chikungunya fever and joint pain in humans. This virus’ name originated from a Makonde term used to describe an illness that changes the joints and refers to the posture of afflicted patients who are affected by excruciating joint pain. There is currently no commercially available drug or vaccine for chikungunya virus infection and the treatment is performed by symptom reduction. Herein, we have developed a computationally constructed mRNA vaccine construct featuring envelope glycoprotein as the target molecule to aid in the treatment process. We have utilized the reverse vaccinology approach to determine epitopes that would generate adaptive immune reactions. The resulting T and B lymphocytes epitopes were screened by various immunoinformatic tools and a peptide vaccine construct was designed. It was validated by proceeding to docking and MD simulation studies. The following design was then back-translated in nucleotide sequence and codons were optimized according to the expression host system (H. sapiens). Various sequences, including 3′ and 5′ UTR regions, Kozak sequence, poly (A) tail, etc., were introduced into the sequence for the construction of the final mRNA vaccine construct. The secondary structure was generated for validation of the mRNA vaccine construct sequence. Additionally, in silico cloning was also performed to design a vector for proceeding towards in vitro experimentation. The proposed designed vaccine construct may proceed with experimental testing for further efficacy verification and the final development of a vaccine against chikungunya virus infection.

Not all T cell epitopes are equally desired: a review of in silico tools for the prediction of cytokine-inducing potential of T-cell epitopes

Assessment of protective or harmful T cell response induced by any antigenic epitope is important in designing any immunotherapeutic molecule. The understanding of cytokine induction potential also helps us to monitor antigen-specific cellular immune responses and rational vaccine design. The classical immunoinformatics tools served well for prediction of B cell and T cell epitopes. However, in the last decade, the prediction algorithms for T cell epitope inducing specific cytokines have also been developed and appreciated in the scientific community. This review summarizes the current status of such tools, their applications, background algorithms, their use in experimental setup and functionalities available in the tools/web servers.

Refining the DC-targeting vaccination for preventing emerging infectious diseases

The development of safe, long-term, effective vaccines is still a challenge for many infectious diseases. Thus, the search of new vaccine strategies and production platforms that allow rapidly and effectively responding against emerging or reemerging pathogens has become a priority in the last years. Targeting the antigens directly to dendritic cells (DCs) has emerged as a new approach to enhance the immune response after vaccination. This strategy is based on the fusion of the antigens of choice to monoclonal antibodies directed against specific DC surface receptors such as CD40. Since time is essential, in silico approaches are of high interest to select the most immunogenic and conserved epitopes to improve the T- and B-cells responses. The purpose of this review is to present the advances in DC vaccination, with special focus on DC targeting vaccines and epitope mapping strategies and provide a new framework for improving vaccine responses against infectious diseases.

Implementation of immuno-chemoinformatics approaches to construct multi-epitope for vaccine development against Omicron and Delta SARS-CoV-2 variants

Background

The new coronavirus is still a life-threatening menace, because of its changing nature and capacity to produce many mutations to bypass the immune system. The vaccination is the first effective weapon against COVID-19.

Aim

The study's goal was to design a multi-epitope peptide vaccine (MEPV) for a mix of Omicron and Delta Coronavirus strains using immuno-chemoinformatics tools.

Methods

To create the vaccine epitopes, seven proteins from the Omicron and Delta coronavirus strains were selected (ORF1a, ORF3a, surface protein, membrane protein, ORF7a, ORF8, and nucleocapsid protein). Antigenicity, toxicity, and allergenicity of the epitopes were evaluated.

Results

The designed vaccine is made up of 534 amino acids that are homogeneous, antigenic, and non-toxic. Sticky restriction enzymes (XhoI and XbaI) were used to incorporate the MEPV into the pmirGLO luciferase vector. SnapGene server was used to create primers for PCR testing. Developing the MEPV is a terrific cost-effective strategy. The created MEPV's physiochemical properties have been determined to be basic, hydrophobic, and stableImmunogenicity and immune response profiles of the developed vaccine candidate were better assessed using in silico immunological simulations.

Conclusions

We advocate moving the built vaccine to the biological validation step, where it may test our findings using appropriate model organisms.

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.

Implementation of immuno-chemoinformatics approaches to construct multi-epitope for vaccine development against Omicron and Delta SARS-CoV-2 variants

Background

The new coronavirus is still a life-threatening menace, because of its changing nature and capacity to produce many mutations to bypass the immune system. The vaccination is the first effective weapon against COVID-19.

Aim

The study's goal was to design a multi-epitope peptide vaccine (MEPV) for a mix of Omicron and Delta Coronavirus strains using immuno-chemoinformatics tools.

Methods

To create the vaccine epitopes, seven proteins from the Omicron and Delta coronavirus strains were selected (ORF1a, ORF3a, surface protein, membrane protein, ORF7a, ORF8, and nucleocapsid protein). Antigenicity, toxicity, and allergenicity of the epitopes were evaluated.

Results

The designed vaccine is made up of 534 amino acids that are homogeneous, antigenic, and non-toxic. Sticky restriction enzymes (XhoI and XbaI) were used to incorporate the MEPV into the pmirGLO luciferase vector. SnapGene server was used to create primers for PCR testing. Developing the MEPV is a terrific cost-effective strategy. The created MEPV's physiochemical properties have been determined to be basic, hydrophobic, and stableImmunogenicity and immune response profiles of the developed vaccine candidate were better assessed using in silico immunological simulations.

Conclusions

We advocate moving the built vaccine to the biological validation step, where it may test our findings using appropriate model organisms.

Mayaro Virus Non-Structural Protein 2 Circumvents the Induction of Interferon in Part by Depleting Host Transcription Initiation Factor IIE Subunit 2

Mayaro virus (MAYV) is an emerging mosquito-transmitted virus that belongs to the genus Alphavirus within the family Togaviridae. Humans infected with MAYV often develop chronic and debilitating arthralgia and myalgia. The virus is primarily maintained via a sylvatic cycle, but it has the potential to adapt to urban settings, which could lead to large outbreaks. The interferon (IFN) system is a critical antiviral response that limits replication and pathogenesis of many different RNA viruses, including alphaviruses. Here, we investigated how MAYV infection affects the induction phase of the IFN response. Production of type I and III IFNs was efficiently suppressed during MAYV infection, and mapping revealed that expression of the viral non-structural protein 2 (nsP2) was sufficient for this process. Interactome analysis showed that nsP2 interacts with DNA-directed RNA polymerase II subunit A (Rpb1) and transcription initiation factor IIE subunit 2 (TFIIE2), which are host proteins required for RNA polymerase II-mediated transcription. Levels of these host proteins were reduced by nsP2 expression and during infection by MAYV and related alphaviruses, suggesting that nsP2-mediated inhibition of host cell transcription is an important aspect of how some alphaviruses block IFN induction. The findings from this study may prove useful in design of vaccines and antivirals, which are currently not available for protection against MAYV and infection by other alphaviruses.

Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

Cycline-dependent kinase 4 (CDK4), an enzyme of the cycline dependent or Ser/Thr protein kinase family, plays a role in cell cycle progression (G1 phase) by phosphorylating a tumor suppressor protein called pRB. Alteration of this enzyme due to missense mutation/ nonsynonymous single nucleotide polymorphisms (nsSNPs) are responsible for various types of cancer progression, e.g. melanoma, lung cancer, and breast cancer. Hence, this study is designed to identify the malignant missense mutation of CDK4 from the single nucleotide polymorphism database (dbSNP) by incorporating computational algorithms. Out of 239 nsSNPs; G15S, D140Y and D140H were predicted to be highly malignant variants which may have a devastating impact on protein structure or function. We also found defective binding motif of these three mutants with the CDK4 inhibitor ribociclib and ATP. However, by incorporating molecular dynamic simulation, our study concludes that the superiority of G15S than the other two mutants (D140Y and D140H) in destabilizing proteins nature.

Immunoinformatics and molecular dynamics approaches: Next generation vaccine design against West Nile virus

West Nile Virus (WNV) is a life threatening flavivirus that causes significant morbidity and mortality worldwide. No preventive therapeutics including vaccines against WNV are available for human use. In this study, immunoinformatics approach was performed to design a multi epitope-based subunit vaccine against this deadly pathogen. Human (HLA) and Mice (H-2) allele specific potential T-cell and B-cell epitopes were shortlisted through a stringent procedure. Molecular docking showed selected epitopes that have stronger binding affinity with human TLR-4. Molecular dynamics simulation confirmed the stable nature of the docked complex. Furthermore, in silico cloning analysis ensures efficient expression of desired gene in the microbial system. Interestingly, previous studies showed that two of our selected epitopes have strong immune response against WNV. Therefore, selected epitopes could be strong vaccine candidates to prevent WNV infections in human. However, further in vitro and in vivo investigations could be strengthening the validation of the vaccine candidate against WNV.