A comprehensive analysis of predicted HLA binding peptides of JE viral proteins specific to north Indian isolates

Towards the First Multiepitope Vaccine Candidate against Neospora caninum in Mouse Model: Immunoinformatic Standpoint

Neospora caninum is an economically significant parasite among livestock, particularly in dairy cattle herds, causing storm abortions. Vaccination seems necessary to limit the infection and its harsh consequences. This is the first steps towards developing a multiepitope vaccine candidate against N. caninum using in silico approaches. High-ranked mouse MHC-binding and shared linear B-cell epitopes from six proteins (SRS2, MIC3, MIC6, GRA1, IMP-1, and profilin) as well as IFN-γ-inducing epitopes (from SAG1) were predicted, screened, and connected together through appropriate linkers. Finally, RS-09 protein (TLR4 agonist) and histidine tag were added to N- and C-terminal of the vaccine sequence, yielding 486 residues in length. Physicochemical properties showed a stable (instability index: 27.23), highly soluble, antigenic (VaxiJen score: 0.9554), and nonallergenic candidate. Secondary structure of the multiepitope protein included 58.85% random coil, 20.99% extended strand, and 20.16% alpha helix. Also, the tertiary structure was predicted, and further analyses validated a stable interaction between the vaccine model and mouse TLR4 (binding score: -1261.6). Virtual simulation of immune profile demonstrated potently stimulated humoral (IgG+IgM) and cell-mediated (IFN-γ) responses upon multiepitope vaccine injection. Altogether, a potentially immunogenic vaccine candidate was developed using several N. caninum proteins, with the capability to elicit IFN-γ upsurge and other components of cellular immunity, and can be used in prophylactic purposes against neosporosis.

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.

Top Down Computational Approach: A Vaccine Development Step to Find Novel Superantigenic HLA Binding Epitopes from Dengue Virus Proteome

Dengue virus (DENV) is a major mosquito vector based human pathogenic flavivirus which is causing major threat worldwide, yet the availability of therapeutic treatment and several vaccines, still called for advance treatment and vaccine development. The present top down computational approach is a vaccine development step to find novel super antigenic HLA binding epitopes from DENV proteome. The approach used sequence based screening to find complete conserve and high population coverage, common epitopes among all DENV serotype. Propred and Immune Epitope Data Base were used for sequence based screening with recommended parameters. Among top 29 identified epitopes, five structural protein epitopes viz. ³³LQGRGPLKL⁴¹, ²⁴⁹VVVLGSQEG²⁵⁷, ¹⁷²LVGIVTLYL¹⁸⁰, ¹⁴⁶MKILIGVVI¹⁵⁴, ⁷²YIIVGVEPG⁸⁰ and one nonstructural protein epitope ¹⁸LKNDIPMTG²⁶ were showed high conserve nature and high population coverage from complete DENV proteome. Further structure based study involving docking and molecular dynamic simulation to confirm stable behavior of HLA allele–peptide complex to give potent cell mediated immune response. Docking of epitope ⁷²YIIVGVEPG⁸⁰–DRB1 0401 allele and epitope ³³LQGRGPLKL⁴¹–B*5101 allele complexes showed the best binding energy of − 7.71 and − 7.20 kcal/mol, respectively and stable binding pattern over the time window during molecular dynamic simulation. This computational approach resulted novel epitopes which can be used in the design and development of short epitope based vaccines as well as diagnosis tools for dengue infection.

Review of Emerging Japanese Encephalitis Virus: New Aspects and Concepts about Entry into the Brain and Inter-Cellular Spreading

Japanese encephalitis virus (JEV) is an emerging flavivirus of the Asia-Pacific region. More than two billion people live in endemic or epidemic areas and are at risk of infection. Recently, the first autochthonous human case was recorded in Africa, and infected birds have been found in Europe. JEV may spread even further to other continents. The first section of this review covers established and new information about the epidemiology of JEV. The subsequent sections focus on the impact of JEV on humans, including the natural course and immunity. Furthermore, new concepts are discussed about JEV’s entry into the brain. Finally, interactions of JEV and host cells are covered, as well as how JEV may spread in the body through latently infected immune cells and cell-to-cell transmission of virions or via other infectious material, including JEV genomic RNA.