Designing and Modeling of Complex DNA Vaccine Based on Tropomyosin Protein of Boophilus Genus Tick

Abstract

Boophilus tick is a bloodsucking ectoparasite that transfers some pathogens, reducing production and thus leading to economical losses in the cattle industry. Tropomyosin (TPM) protein is a salivary protein, has actin regulator activity, and plays an important role in immune reactions against parasites. In the current study, besides developing a safe, effective, and broad spectrum protective measure against Boophilus genus tick based on TPM protein, we attempted to minimize possible problems occurring in the design of polytopic vaccines. Briefly, the steps that were followed in the present study were as follows: retrieving sequences and finding the mutational/conservative regions, selecting consensus and high immunogenic epitopes of B and CD4(+) T cells by different approaches, three-dimensional structure (3D structure) prediction and representation of epitopes and highly variable/conserve regions, designing vaccinal construct by fusion of B and T cell epitopes by special patterns and improving immunogenicity, evaluation of the constructs' primary structure and posttranslational modification, calculation of hydrophobic regions, reverse translation, codon optimization, open reading frame checking, insertion of start/end codon, Kozak sequence, and finally constructing the DNA vaccine. Variation plot showed some shared epitopes among the ticks' and mites' species that some might be effective only in some species. Finally, by following the steps mentioned above, two constructs for B and T cells were achieved. Checking constructs revealed their reliability and efficacy for in vitro production and utilization. Successful in silico modeling is an essential step of designing vigorous vaccines. We developed a novel protective and therapeutic vaccine against Boophilus genus (based on TPM protein). At the next step, constructed DNA vaccine would be produced in vitro and administrated to cattle, and its potency to induction of immune response and protection against Boophilus genus as well as other ticks and mites will be evaluated.

Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information

“…We have previously developed and used different strategies to increase the ability of computer-aided vaccine designing approaches to identify vaccine candidates such as (1) epitope selection from conserved regions ( 74 ), (2) profile similarity method to analyze biased-ness of predicted epitopes toward profiles of experimentally validated epitopes ( 74 ), (3) introducing cleavage sites for targeted cleavage of multi-epitopic vaccine ( 56 , 75 ), (4) B-cell epitope prediction by docking ( 74 ), (5) structure-based epitope identification ( 57 ), (6) CpG optimization ( 76 ), (7) sequence homology search against host ( 77 ), (8) adding adjuvant such as IL-12 ( 78 ), and (9) population coverage analysis ( 58 , 77 ). In this study, we integrated the evolutionary analysis with our reverse vaccinology, i.e., bioinformatical genome and epitope search pipeline ( 74 , 77 ) to identify vaccine candidates.…”

Sequence-based approach for rapid identification of cross-clade CD8+ T-cell vaccine candidates from all high-risk HPV strains

“…Moreover, the immunoinformatics techniques applied to T-cells have advanced to a greater degree than those dealing with B-cells. Indeed, it is now a common practice to identify the vaccine candidates using in silico approaches before being subjected to in vitro confirmatory studies (Gupta et al 2009 ; Ranjbar et al 2015 ). The major objective of our study was to identify an immunogenic peptide pool containing epitopes that can be effective against all the high-risk HPV strains circulating globally.…”

In Silico Vaccine Design: Targeting Highly Epitopic Regions ofClostridium perfringensType D Epsilon Toxin andClostridium novyiType B Alpha Toxin for Optimal Immunogenicity

“…These linkers, acting as spacers, aid in the proper folding of the conformational epitopes in the chimeric proteins. To connect the MHC-II binding epitopes, the NH2- GPGPG-COOH linker was utilized, and for the B-cell epitopic fragments, the NH2-GGSSGG-COOH sequence was employed (Negahdaripour et al, 2017; Nezafat et al, 2017; Ranjbar et al, 2015).…”