<i>In silico</i>design of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations

Yang, Yi; Sun, Weilai; Guo, Jingjing; Zhao, Guangyu; Sun, Shihui; Yu, Hong; Guo, Yan; Li, Jungfeng; Jin, Xia; Du, Lanying; Jiang, Shibo; Kou, Zheng; Zhou, Yusen

doi:10.1080/21645515.2015.1012017

Cited by 90 publications

(70 citation statements)

References 43 publications

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“…Although not much time has passed since the introduction of the first report about computational vaccine design, in the recent years, a lot of progress has been made in this regard. Subsequently, numerous vaccines were developed based on computational approaches that include efficient vaccine against Toxoplasma gondii [31], Rickettsia prowazekii [32], Streptococcus pneumoniae [33], Leishmania infantum [34], Chlamydia pneumoniae [35], Brucella abortus [36], Staphylococcus aureus [15], Escherichia coli [37], Vibrio cholera [38], Human immunodeficiency virus-1 [39], Hepatitis C virus [40] and many others. In many empirical studies, the efficacy of computationally designed vaccines is approved [34,39,41,42].…”

Section: Introductionmentioning

confidence: 99%

Towards the first multi-epitope recombinant vaccine against Crimean-Congo hemorrhagic fever virus: A computer-aided vaccine design approach

Nosrati

Behbahani

Mohabatkar

2019

Journal of Biomedical Informatics

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A R T I C L E I N F O Keywords:Crimean-Congo hemorrhagic fever Computer-aided vaccine design Multi-epitope vaccine A B S T R A C T Crimean-Congo hemorrhagic fever (CCHF) is considered one of the major public health concerns with case fatality rates of up to 80%. Currently, there is no effective approved vaccine for CCHF. In this study, we used a computer-aided vaccine design approach to develop the first multi-epitope recombinant vaccine for CCHF. For this purpose, linear B-cell and T-cell binding epitopes from two structural glycoproteins of CCHF virus including Gc and Gn were predicted. The epitopes were further studied regarding their antigenicity, allergenicity, hydrophobicity, stability, toxicity and population coverage. A total number of seven epitopes including five T-cell and two B-cell epitopes were screened for the final vaccine construct. Final vaccine construct composed of 382 amino acid residues which were organized in four domains including linear B-cell, T-cell epitopes and cholera toxin B-subunit (CTxB) along with heat labile enterotoxin IIc B subunit (LT-IIc) as adjuvants. All the segments were joined using appropriate linkers. The physicochemical properties as well as the presence of IFN-γ inducing epitopes in the proposed vaccine, was also checked to determining the vaccine stability, solubility and its ability to induce cell-mediated immune responses. The 3D structure of proposed vaccine was subjected to the prediction of computational B-cell epitopes and molecular docking studies with MHC-I and II molecules. Furthermore, molecular dynamics stimulations were performed to study the vaccine-MHCs complexes stability during stimulation time. The results suggest that our proposed vaccine was stable, well soluble in water and potentially antigenic. Results also demonstrated that the vaccine can induce both humoral and cell-mediated immune responses and could serve as a promising anti-CCHF vaccine candidate.

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Section: Introductionmentioning

confidence: 99%

Towards the first multi-epitope recombinant vaccine against Crimean-Congo hemorrhagic fever virus: A computer-aided vaccine design approach

Nosrati

Behbahani

Mohabatkar

2019

Journal of Biomedical Informatics

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“…As PADRE sequence was usually recommended to lessen the polymorphism of HLA molecules in the population (Ghaffari-Nazari et al, 2015), it was also considered to construct the final vaccine molecule. Here, adjuvants would enhance the immunogenicity of the vaccine constructs and appropriate separation of epitopes in the host environment would be ensured by the linker (Yang et al, 2015). Allergenicity, physiochemical properties, antigenicity and three-dimensional structure of vaccine constructs were characterized, and it had been concluded that V3 was superior to V1 and V2 vaccine constr.…”

Section: Discussionmentioning

confidence: 99%

Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine

Akhand

Azim

Hoque

et al. 2020

Preprint

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SARS-CoV-2 is known to infect the neurological, respiratory, enteric, and hepatic systems of human and has already become an unprecedented threat to global healthcare system. COVID-19, the most serious public condition caused by SARS-CoV-2 leads the world to an uncertainty alongside thousands of regular death scenes. Unavailability of specific therapeutics or approved vaccine has made the recovery of COVI-19 more troublesome and challenging. The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein (S), membrane protein (M), envelope protein and nucleocapsid protein (N) were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins (S, E, M and N) reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were generated from the common fragments which were further ranked on the basis of antigenicity, transmembrane topology, conservancy level, toxicity and allergenicity pattern and population coverage analysis.Top putative epitopes were combined with appropriate adjuvants and linkers to construct a novel multiepitope subunit vaccine against COVID-19. The designed constructs were characterized based on physicochemical properties, allergenicity, antigenicity and solubility which revealed the superiority of construct V3 in terms safety and efficacy. Essential molecular dynamics and Normal Mode analysis confirmed minimal deformability of the refined model at molecular level.In addition, disulfide engineering was investigated to accelerate the stability of the protein.Molecular docking study ensured high binding affinity between construct V3 and HLA cells, as well as with different host receptors. Microbial expression and translational efficacy of the constructs were checked using pET28a(+) vector of E. coli strain K12. The development of preventive measures to combat COVID-19 infections might be aided the present study.However, the in vivo and in vitro validation might be ensured with wet lab trials using model animals for the implementation of the presented data.

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“…Linkers in vaccine also enhanced the immunogenicity of the vaccines in previous studies [133,134]. Therefore, we have taken all important factors that can induce the immunogenicity of our vaccine constructs.…”

Section: Discussionmentioning

confidence: 99%

Proteome Exploration of Legionella pneumophila for Identifying Novel Therapeutics: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

Khan

Mahmud

Hasan

et al. 2020

Preprint

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Legionella pneumophila, the causative agent of a serious type of pneumonia (lung infection) called Legionnaires' disease. It is emerging as an antibacterial resistant strain day by day.Hence, identification of novel drug targets and vaccine candidates is essential to fight against this pathogen. Herein attempts were taken through subtractive genomics approach on complete proteome of L. pneumophila to address the challenges of multidrug resistance. A total 2930 proteins from L. pneumophila proteome were investigated through diverse subtractive proteomics approaches, e.g., identification of human non homologous and pathogen specific essential proteins, druggability and 'anti-target' analysis, prediction of subcellular localization, human microbiome non-homology screening, protein-protein interactions studies in order to find out effective drug and vaccine targets. Only 3 were identified that fulfilled all these criteria and proposed as novel drug targets against L. pneumophila. Furthermore, outer membrane protein TolB was identified as potential vaccine target with better antigenicity score and allowed for further in silico analysis to design a unique multiepitope subunit vaccine against it. Antigenicity and transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were adopted to generate the most potent epitopes. The final vaccine was constructed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. The designed vaccine construct showed higher binding interaction with different MHC molecules and human immune TLR2 receptor with minimum deformability at molecular level. The translational potency and microbial expression of the vaccine protein was also analyzed using pET28a(+) vector. The present study aids in the development of novel therapeutics and vaccine candidates for efficient treatment of the infections caused by Legionella pneumophila. However, further wet lab based investigations and in vivo trials are highly recommended to experimentally validate our prediction.

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In silicodesign of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations

Cited by 90 publications

References 43 publications

Towards the first multi-epitope recombinant vaccine against Crimean-Congo hemorrhagic fever virus: A computer-aided vaccine design approach

Towards the first multi-epitope recombinant vaccine against Crimean-Congo hemorrhagic fever virus: A computer-aided vaccine design approach

Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine

Proteome Exploration of Legionella pneumophila for Identifying Novel Therapeutics: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

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