An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus

Evaluation of the Safety and Immunogenicity of a Multiple Epitope Polypeptide from Canine Distemper Virus (CDV) in Mice

BACKGROUND

Morbillivirus canis is the etiological agent of a highly contagious disease that affects diverse domestic and wild animals. Vaccination is considered the most suitable strategy for controlling CDV dissemination, transmission, and distemper disease. However, the emergence of new CDV strains has led to the need to update the current vaccine strategies employed to prevent CDV infection in domestic and wild animals. Currently, there is a lack of effective alternatives for wild animals. Diverse computational tools, especially peptide-based therapies, enable the development of new universal vaccines.

OBJECTIVE

The aim of this study was to evaluate the safety and humoral and cellular immune response of a new generation of vaccines based on CDV peptides as single-peptide mixtures or multiepitope CDV polypeptides in mice.

METHODS

Twenty-four BALB/c mice were subjected to a three-dose regimen for 28 days. Seroconversion was evaluated via ELISA, and cellular immune responses were evaluated via flow cytometry through activation-induced markers (AIMs).

RESULTS

Compared with the placebo, the peptide mixture and multiepitope CDV polypeptide were safe, and seroconversion was statistically significant in the multiepitope CDV polypeptide and commercial vaccine (CV) groups. The numbers of antigen-specific CD4+CD134+ and IFN-γ+ T cells, CD8+ T cells and TNF-α- and IL-6-producing cells were greater in the mice immunized with the multiepitope CDV polypeptide than in the control mice.

CONCLUSION

This combined approach represents a potential step forward in developing new immunization candidates or enhancing current commercial vaccines to control CDV disease in domestic dogs and wild animals.

Universal peptide-based potential vaccine design against canine distemper virus (CDV) using a vaccinomic approach

Canine distemper virus (CDV) affects many domestic and wild animals. Variations among CDV genome linages could lead to vaccination failure. To date, there are several vaccine alternatives, such as a modified live virus and a recombinant vaccine; however, most of these alternatives are based on the ancestral strain Onderstepoort, which has not been circulating for years. Vaccine failures and the need to update vaccines have been widely discussed, and the development of new vaccine candidates is necessary to reduce circulation and mortality. Current vaccination alternatives cannot be used in wildlife animals due to the lack of safety data for most of the species, in addition to the insufficient immune response against circulating strains worldwide in domestic species. Computational tools, including peptide-based therapies, have become essential for developing new-generation vaccines for diverse models. In this work, a peptide-based vaccine candidate with a peptide library derived from CDV H and F protein consensus sequences was constructed employing computational tools. The molecular docking and dynamics of the selected peptides with canine MHC-I and MHC-II and with TLR-2 and TLR-4 were evaluated. In silico safety was assayed through determination of antigenicity, allergenicity, toxicity potential, and homologous canine peptides. Additionally, in vitro safety was also evaluated through cytotoxicity in cell lines and canine peripheral blood mononuclear cells (cPBMCs) and through a hemolysis potential assay using canine red blood cells. A multiepitope CDV polypeptide was constructed, synthetized, and evaluated in silico and in vitro by employing the most promising peptides for comparison with single CDV immunogenic peptides. Our findings suggest that predicting immunogenic CDV peptides derived from most antigenic CDV proteins could aid in the development of new vaccine candidates, such as multiple single CDV peptides and multiepitope CDV polypeptides, that are safe in vitro and optimized in silico. In vivo studies are being conducted to validate potential vaccines that may be effective in preventing CDV infection in domestic and wild animals.

Molecular characterization of canine circovirus based on the Capsid gene in Thailand

BACKGROUND

Canine circovirus (CanineCV) is a single-stranded circular DNA virus that infects domestic and wild canids in many countries. CanineCV is associated with gastroenteritis and diarrhea, respiratory disease, and generalized vasculitis leading to a fatal event. The Capsid protein (Cap) is a structural protein of the virus which has high genetic variability and plays a role in the canine immune response. In this study, we cloned the full-length CanineCV Capsid gene (Cap). In-silico analyses were used to explore the genomic and amino acid variability and natural selection acting on the Cap gene. The immune relevance for T-cell and B-cell epitopes was predicted by the immunoinformatic approach.

RESULTS

According to the Cap gene, our results showed that CanineCV was separated into five phylogenetic groups. The obtained CanineCV strain from this study was grouped with the previously discovered Thai strain (MG737385), as supported by a haplotype network. Entropy analyses revealed high nucleotide and amino acid variability of the Capsid region. Selection pressure analysis revealed four codons at positions 24, 50, 103, and 111 in the Cap protein evolved under diversifying selection. Prediction of B-cell epitopes exhibited four consensus sequences based on physiochemical properties, and eleven peptide sequences were predicted as T-cell epitopes. In addition, the positive selection sites were located within T-cell and B-cell epitopes, suggesting the role of the host immune system as a driving force in virus evolution.

CONCLUSIONS

Our study provides knowledge of CanineCV genetic diversity, virus evolution, and potential epitopes for host cell immune response.

Recombinant expression and characterization of Canine circovirus capsid protein for diagnosis

Canine circovirus (CanineCV) is a contagious virus that causes severe gastroenteritis, diarrhea, respiratory disease, and vasculitis, often resulting in fatality among infected dogs. In this study, a recombinant Capsid protein (rCap) of CanineCV was expressed in the Escherichia coli (E. coli) Rosetta (DE3) pLysS host cell, followed by affinity purification, and then analyzed by SDS-PAGE, revealing a molecular weight of approximately 31 kDa. The antigenicity of the CanineCV rCap protein was confirmed through recognition by a rabbit anti-CanineCV rCap protein polyclonal antibody (PoAb). Additionally, the reactivity and specificity of this PoAb were assessed using indirect enzyme-linked immunosorbent assay (ELISA) and Western blot analysis before applying in an immunohistochemistry (IHC), namely, immunoperoxidase detection. The immunoperoxidase assay using rabbit anti-CanineCV rCap protein PoAb demonstrated that the CanineCV Cap protein was predominantly located in immune cells, especially lymphocytes and macrophages, within the spleen, lung, tracheobronchial lymph nodes, small intestine, and kidney. Similarly, the Cap protein was also found in pneumocytes in the lung and renal tubular epithelial cells in the kidney. These findings reflected the biological activity and cell tropism of the virus. Therefore, the recombinant Cap protein and its PoAb could be used for the development of a valuable diagnostic tool for CanineCV detection.

Immunoinformatics-aided rational design of a multi-epitope vaccine targeting feline infectious peritonitis virus

Feline infectious peritonitis (FIP) is a grave and frequently lethal ailment instigated by feline coronavirus (FCoV) in wild and domestic feline species. The spike (S) protein of FCoV assumes a critical function in viral ingress and infection, thereby presenting a promising avenue for the development of a vaccine. In this investigation, an immunoinformatics approach was employed to ascertain immunogenic epitopes within the S-protein of FIP and formulate an innovative vaccine candidate. By subjecting the amino acid sequence of the FIP S-protein to computational scrutiny, MHC-I binding T-cell epitopes were predicted, which were subsequently evaluated for their antigenicity, toxicity, and allergenicity through in silico tools. Our analyses yielded the identification of 11 potential epitopes capable of provoking a robust immune response against FIPV. Additionally, molecular docking analysis demonstrated the ability of these epitopes to bind with feline MHC class I molecules. Through the utilization of suitable linkers, these epitopes, along with adjuvants, were integrated to design a multi-epitope vaccine candidate. Furthermore, the stability of the interaction between the vaccine candidate and feline Toll-like receptor 4 (TLR4) was established via molecular docking and molecular dynamics simulation analyses. This suggests good prospects for future experimental validation to ascertain the efficacy of our vaccine candidate in inducing a protective immune response against FIP.

Designing a multi-epitope candidate vaccine by employing immunoinformatics approaches to control African swine fever spread

The African swine fever virus has been circulating for decades and is highly infectious, often fatal to farmed and wild pigs. There is currently no approved vaccine or treatment for the disease, making prevention even more difficult. Therefore, vaccine development is necessary and urgent to limit the consequences of ASF and ensure the food chain and sustainability of the swine industry. This research study was conducted to design a multi-epitope vaccine for controlling veterinary diseases caused by the African swine fever virus. We employed the immunoinformatics approaches to reveal 37 epitopes from different viral proteins of ASFV. These epitopes were linked to adjuvants and linkers to form a full-fledged immunogenic vaccine construct. The tertiary structure of the final vaccine was predicted using a deep-learning approach. The molecular docking and molecular dynamics predicted stable interactions between the vaccine and immune receptor TLR5 of Sus scrofa (Pig). The MD simulation studies reflect that the calculated parameters like RMSD, RMSF, number of hydrogen bonds, and finally, the buried interface surface area for the complex remained stable throughout the simulation time. This analysis suggests the stability of interface interactions between the TLR5 and the multi-epitope vaccine construct. Further, the physiochemical analysis demonstrated that our designed vaccine construct was expected to have high stability and prolonged half-life time in mammalian cells. Traditional vaccine design experiments require significant time and financial input from the development stage to the final product. Studies like this can assist in accelerating vaccine development while minimizing the cost.Communicated by Ramaswamy H. Sarma.

Computational analysis of immunogenic epitopes in the p30 and p54 proteins of African swine fever virus

African swine fever (ASF) is a highly infectious viral disease of pigs, which causes acute fatal haemorrhage and is a severe concern to the global pork industry. The present study followed computational approaches to identify B- and T-cell epitopes for the p30 and p54 proteins of the African swine fever virus (ASFV) by interacting with the swine leukocyte antigen (SLA) alleles. The amino acid sequences of p30 and p54 were analysed for variability and relative solvent accessibility, and their three-dimensional structures were predicted and validated. Molecular dynamics simulation was performed to study the structural and dynamic properties of the protein. Six and five linear B-cell epitopes have been predicted for p30 and p54, respectively. Four and three discontinuous B-cell epitopes have been predicted for p30 and p54, respectively. Further, the top five T-cell epitopes for SLA-1, 2, and 3 have been listed for both proteins. These results can help us to understand the immunodominant regions in the p30 and p54 proteins of ASFV and potentially assist in designing peptide-based diagnostics and vaccines. Also, the identified T-cell epitopes may be considered for peptide-based vaccine design against ASFV.Communicated by Ramaswamy H. Sarma.

Immunoinformatics for Novel Multi-Epitope Vaccine Development in Canine Parvovirus Infections

Canine parvovirus (CPV-2) is one of the most important pathogens of dogs of all ages, causing pandemic infections that are characterized by fatal hemorrhagic enteritis. The CPV-2 vaccine is recommended as a core vaccine for pet animals. Despite the intensive practice of active immunization, CPV-2 remains a global threat. In this study, a multi-epitope vaccine against CPV-2 was designed, targeting the highly conserved capsid protein (VP2) via in silico approaches. Several immunoinformatics methods, such as epitope screening, molecular docking, and simulation were used to design a potential vaccine construct. The partial protein sequences of the VP2 gene of CPV-2 and protein sequences retrieved from the NCBI were screened to predict highly antigenic proteins through antigenicity, trans-membrane-topology screening, an allergenicity assessment, and a toxicity analysis. Homologous VP2 protein sequences typically linked to the disease were identified using NCBI BLAST, in which four conserved regions were preferred. Overall, 10 epitopes, DPIGGKTGI, KEFDTDLKP, GTDPDDVQ, GGTNFGYIG, GTFYFDCKP, NRALGLPP, SGTPTN, LGLPPFLNSL, IGGKTG, and VPPVYPN, were selected from the conserved regions to design the vaccine construct. The molecular docking demonstrated the higher binding affinity of these epitopes with dog leukocyte antigen (DLA) molecules. The selected epitopes were linked with Salmonella enterica flagellin FliC adjuvants, along with the PADRE sequence, by GGS linkers to construct a vaccine candidate with 272 nucleotides. The codon adaptation and in silico cloning showed that the generated vaccine can be expressed by the E. coli strain, K12, and the sequence of the vaccine construct showed no similarities with dog protein. Our results suggest that the vaccine construct might be useful in preventing canine parvoviral enteritis (CPE) in dogs. Further in vitro and in vivo experiments are needed for the validation of the vaccine candidate.

MERS virus spike protein HTL-epitopes selection and multi-epitope vaccine design using computational biology

MERS-CoV, a zoonotic virus, poses a serious threat to public health globally. Thus, it is imperative to develop an effective vaccination strategy for protection against MERS-CoV. Immunoinformatics and computational biology tools provide a faster and more cost-effective strategy to design potential vaccine candidates. In this work, the spike proteins from different strains of MERS-CoV were selected to predict HTL-epitopes that show affinity for T-helper MHC-class II HTL allelic determinant (HLA-DRB1:0101). The antigenicity and conservation of these epitopes among the selected spike protein variants in different MERS-CoV strains were analyzed. The analysis identified five epitopes with high antigenicity: QSIFYRLNGVGITQQ, DTIKYYSIIPHSIRS, PEPITSLNTKYVAPQ, INGRLTTLNAFVAQQ and GDMYVYSAGHATGTT. Then, a multi-epitope vaccine candidate was designed using linkers and adjuvant molecules. Finally, the vaccine construct was subjected to molecular docking with TLR5 (Toll-like receptor-5). The proposed vaccine construct had strong binding energy of -32.3 kcal/mol when interacting with TLR5.Molecular dynamics simulation analysis showed that the complex of the vaccine construct and TLR5 is stable. Analysis using in silico immune simulation also showed that the prospective multi-epitope vaccine design had the potential to elicit a response within 70 days, with the immune system producing cytokines and immunoglobulins. Finally, codon adaptation and in silico cloning analysis showed that the candidate vaccine could be expressed in the Escherichia coli K12 strain. Here we also designed support vaccine construct MEV-2 by using B-cell and CD8+ CTL epitopes to generate the complete immunogenic effect. This study opens new avenues for the extension of research on MERS vaccine development.Communicated by Ramaswamy H. Sarma.

An immunoinformatics analysis: design of a multi-epitope vaccine against Cryptosporidium hominis by employing heat shock protein triggers the innate and adaptive immune responses

Cryptosporidium hominis, an anthropologically transferred species in the Cryptosporidium genus, represents many clinical studies in several countries. Its growth in the recent decade is primarily owing to epidemiologic studies. This parasite has complicated life cycles that require differentiation through a variety of phases of development and passage across two or more hosts throughout their lifetimes. As they move from host to host and environment to environment, pathogenic organisms are continually exposed to unexpected changes in the circumstances under which they develop. Heat shock proteins (HSPs) are targets of the host immune response; they are involved in the progression of diseases and play a significant part in this process. It has been discovered that the immunodominant immunogenic antigens in parasite infections HSPs. In this study, we have generated a multi-epitope vaccine against Cryptosporidium hominis (C. hominis) by using heat shock proteins. The epitopes that were selected had a substantial binding affinity for the B- and T-cell reference set of alleles, a high antigenicity score, a nature that was not allergic, a high solubility, non-toxicity and good binders. The epitopes were incorporated into a chimeric vaccine by using appropriate linkers. In order to increase the immunogenicity of the connected epitopes and effectively activate both innate and adaptive immunity, an adjuvant was attached to the epitopes. We have also analyzed the physiochemical characteristics of the vaccine which were satisfactory and then lead to the development of a 3D model. In addition, the binding confirmation of the vaccine to the TLR-4 innate immune receptor was also determined using molecular docking and molecular dynamics (MD) simulation. The results of this simulation show that the vaccine has a strong binding affinity for TLR4, which indicates that the vaccine is highly effective. In general, the vaccine that has been described here has a good potential for inducing protective and targeted immunogenicity, however, this hypothesis is contingent upon more experimental testing.Communicated by Ramaswamy H. Sarma.

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.

Design of a multi-epitope vaccine against the pathogenic fungi Candida tropicalis using an in silico approach

Background

Candida tropicalis causes tropical invasive fungal infections, with a high mortality. This fungus has been found to be resistant to antifungal classes such as azoles, echinocandins, and polyenes in several studies. As a result, it is vital to identify novel approaches to prevent and treat C. tropicalis infections. In this study, an in silico technique was utilized to deduce and evaluate a powerful multivalent epitope-based vaccine against C. tropicalis, which targets the secreted aspartic protease 2 (SAP2) protein. This protein is implicated in virulence and host invasion.

Results

By focusing on the Sap2 protein, 11 highly antigenic, non-allergic, non-toxic, and conserved epitopes were identified. These were subsequently paired with RS09 and flagellin adjuvants, as well as a pan HLA DR-binding epitope (PADRE) sequence to create a vaccine candidate that elicited both cell-mediated and humoral immune responses. It was projected that the vaccine design would be soluble, stable, antigenic, and non-allergic. Ramachandran plot analysis was applied to validate the vaccine construct’s 3-dimensional model. The vaccine construct was tested (at 100 ns) using molecular docking and molecular dynamics simulations, which demonstrated that it can stably connect with MHC-I and Toll-like receptor molecules. Based on in silico studies, we have shown that the vaccine construct can be expressed in E. coli. We surmise that the vaccine design is unrelated to any human proteins, indicating that it is safe to use.

Conclusions

The vaccine design looks to be an effective option for preventing C. tropicalis infections, based on the outcomes of the studies. A fungal vaccine can be proposed as prophylactic medicine and could provide initial protection as sometimes diagnosis of infection could be challenging. However, more in vitro and in vivo research is needed to prove the efficacy and safety of the proposed vaccine design.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00415-3.

Exploratory Algorithm of a Multi-epitope-based Subunit Vaccine Candidate Against Cryptosporidium hominis: Reverse Vaccinology-Based Immunoinformatic Approach

Cryptosporidiosis is the leading protozoan-induced cause of diarrheal illness in children, and it has been linked to childhood mortality, malnutrition, cognitive development, with retardation of growth. Cryptosporidium hominis, the anthroponotically transmitted species within the Cryptosporidium genus, contributes significantly to the global burden of infection, accounting for the majority of clinical cases in numerous nations, as well as its emergence in the last decade is largely due to detections obtained through noteworthy epidemiologic research. Nevertheless, there is no vaccine available, and the only licensed medication, nitazoxanide, has been demonstrated to have efficacy limitations in a number of patient groups recognized to be at high risk of complications. Therefore, current study delineates the computational vaccine design for Cryptosporidium hominis, the notable pathogen for enteric diarrhea. Firstly, a comprehensive literature search was conducted to identify six proteins based on their toxigenicity, allergenicity, antigenicity, and prediction of transmembrane helices to make up a multi-epitope-based subunit vaccine. Following that, antigenic non-toxic HTL epitope, CTL epitope with B cell epitope were predicted from the selected proteins and construct a vaccine candidate with adding an adjuvant and some linkers with immunologically superior epitopes. Afterwards, the constructed vaccine candidates and TLR2 receptor were put into the ClusPro server for molecular dynamic simulation to know the binding stability of the vaccine-TLR2 complex. Following that, Escherichia coli strain K12 was used as a cloning host for the chosen vaccine construct via the JCat server. As a result of the findings, it was resolute that the proposed chimeric peptide vaccine could improve the immune response to Cryptosporidium hominis.

T-cell epitope-based vaccine prediction against Aspergillus fumigatus: a harmful causative agent of aspergillosis

BACKGROUND

Among the most common causes of invasive aspergillosis and acute bronchopulmonary aspergillosis is Aspergillus fumigatus. Transmission with A. fumigatus produces aggressive aspergillosis in allogeneic haematopoietic stem cell transplant recipients, HIV patients, and cancer patients. Asthmatics and cystic fibrosis patients are allergic to A. fumigatus. MHC class-II binding epitopes can initiate immunogenic responses in patients. In this study, we deployed immunoinformatic study to reveal epitopes from fungal proteins.

RESULTS

In modern research, we found multiple epitopes ITLKLLHRYSYKLAG, KLVLRAFPNHFRGDS, RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD from crucial proteins of A. fumigatus 5,8-linoleate diol synthase (ACO55067.2) and ChainB-chitinase A1 (2XVN_B). RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD epitopes interact with HLA-DRB01_0101, while ITLKLLHRYSYKLAG and KLVLRAFPNHFRGDS epitopes interact with HLA-DRB01_1501. Molecular docking analysis reveals atomic contact energy (ACE) value for these five epitopes shown below -5 Kcal/mol in docked state.

CONCLUSIONS

The invasive aspergillosis and acute bronchopulmonary aspergillosis are caused by harmful fungal pathogen Aspergillus fumigatus. Our modern immunoinformatic research shows ITLKLLHRYSYKLAG, KLVLRAFPNHFRGDS, RYSYKLAGVNQVDVV, GKSFELNQAARAVTQ, and LHRYSYKLAGVNQVD epitopes could bind to MHC-II HLA allelic determinants and can initiate immunogenic response in patients affected by Aspergillus fumigatus.

Immunogenic Epitope-Based Vaccine Prediction from Surface Glycoprotein of MERS-CoV by Deploying Immunoinformatics Approach

Middle East respiratory syndrome coronavirus (MERS-CoV) has caused a high mortality rate since its emergence in 2012 in the Middle East. Currently, no effective drug or vaccine is available for MERS-CoV. Supportive care and prevention are the only ways to manage infection. In this study, we identified an epitope-based vaccine that could be an optimal solution for the prevention of MERS-CoV infection. By deploying an immunoinformatics approach, we predicted a subunit vaccine based on the surface glycoprotein (S protein) of MERS-CoV. For this purpose, the proteome of the MERS-CoV spike protein was obtained from the NCBI GenBank database. Then, it was subjected to a check for allergenicity using the Allergen FP v.1.0 tool. The Vaxijen v.2.0 tool was used to conduct antigenicity tests for binding with major histocompatibility complex class I and II molecules. The solidity of the predicted epitope-allele docked complex was evaluated by a molecular dynamics simulation. After docking a total of eight epitopes from the MERS-CoV S protein, further analyses predicted their non-toxicity and therapeutic immunogenic properties. These epitopes have potential utility as vaccine candidates against MERS-CoV, to be validated by wet-lab testing.

Codon usage studies and epitope-based peptide vaccine prediction against Tropheryma whipplei

Background

The Tropheryma whipplei causes acute gastroenteritis to neuronal damages in Homo sapiens. Genomics and codon adaptation studies would be helpful advancements of disease evolution prediction, prevention, and treatment of disease. The codon usage data and codon usage measurement tools were deployed to detect the rare, very rare codons, and also synonymous codons usage. The higher effective number of codon usage values indicates the low codon usage bias in T. whipplei and also in the 23S and 16S ribosomal RNA genes.

Results

In T. whipplei, it was found to hold low codon biasness in genomic sets. The synonymous codons possess the base content in 3rd position that was calculated as A3S% (24.47 and 22.88), C3S% (20.99 and 22.88), T3S% (21.47 and 19.53), and G3S% (33.08 and 34.71) for 23s and 16s rRNA, respectively.

Conclusion

Amino acids like valine, aspartate, leucine, and phenylalanine hold high codon usage frequency and also found to be present in epitopes KPSYLSALSAHLNDK and FKSFNYNVAIGVRQP that were screened from proteins excinuclease ABC subunit UvrC and 3-oxoacyl-ACP reductase FabG, respectively. This method opens novel ways to determine epitope-based peptide vaccines against different pathogenic organisms.

Chikungunya Virus Vaccine Development: Through Computational Proteome Exploration for Finding of HLA and cTAP Binding Novel Epitopes as Vaccine Candidates

Chikungunya virus is a major arbovirus of great public health concern in the whole world, but no vaccine is yet available, still advance therapeutic treatment and effective vaccines are in progress. The present multistep screening and structural binding analysis with CHIKV proteome exploration can be crucial in the development phase of CHIKV epitope based vaccine. The approach employed in two phases (i) Sequence based screening of peptides through propred and IEDB Server (ii) Structure based study through autodocking and NAMD VMD simulation analysis. Among all 29 extracted peptides, only two peptides ²LLANTTFPC¹⁰ of protein E3 and ⁹⁸VNSVAIPLL¹⁰⁶ of protein nsP3 were observed most prominent over all consider parameters such as peptide conserve nature, supertype population coverage, TAP binding, docking and simulation study. During docking interaction study, the best peptide and allele docked complexes such as ²LLANTTFPC¹⁰–B*0702 allele and ⁹⁸VNSVAIPLL¹⁰⁶–A*0301 allele exhibited best binding energy of − 3.13 kcal/mol and − 3.19 kcal/mol, respectively, with stable bonding patterns and their motion during NAMD simulation which confirm conserve peptide and allele stable interaction. The current study also exhibited the good docking interaction of both peptides ²LLANTTFPC¹⁰ and ⁹⁸VNSVAIPLL¹⁰⁶ with c TAP1 protein (1jj7 -PDB ID) cavity which confirm as a channel passageway to peptide transport through the cytoplasm to lumen of ER during antigen processing and presentation. Overall, this multistep screening and crosscheck structural binding analysis with an exploration of the complete proteome of CHIKV can be a novel step in the development of CHIKV epitope based vaccine as well as diagnostic development with aspect of time, cost and side effects.

T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease

Orthohantavirus, a zoonotic virus responsible for causing human cardio-pulmonary disease, is proven to be a fatal disease. Due to the paucity of regimens to cure the disease and efficient management to eradicate this deadly virus, there is a constant need to expand in-silico approaches belonging to immunology domain to formulate best feasible peptide-based vaccine against it. In lieu of that, we have predicted and validated an epitope of nine-residue-long sequence “MIGLLSSRI”. The predicted epitope has shown best interactions with HLA alleles of MHC Class II proteins, namely HLA DRB1_0101, DRB1_0401, DRB1_0405, DRB1_0701, DRB1_0901, DRB1_1302, and DRB1_1501. The structure of the epitope was modeled by deploying PEPFOLD 3.5 and verified by Ramachandran plot analysis. Molecular docking and simulation studies reveal that this epitope has satisfactory binding scores, ACE value and global energies for docked complexes along with selectable range of RMSD and RMSF values. Also, the predicted epitope “MIGLLSSRI” exhibits population coverage of more than 62% in world population and maximum of 70% in the United States of America. In this intensive study, we have used many tools like AllergenFP, NETMHCII 3.2, VaxiJen, ToxinPred, PEPFOLD 3.5, DINC, IEDB-Population coverage, MHCPred and JCat server. Most of these tools are based on modern innovative statistical algorithms like HMM, ANN, ML, etc. that help in better predictions of putative candidates for vaccine crafting. This innovative methodology is facile, cost-effective and time-efficient, which could facilitate designing of a vaccine against this virus.