Exploring T &amp; B-cell epitopes and designing multi-epitope subunit vaccine targeting integration step of HIV-1 lifecycle using immunoinformatics approach

Abdulla, Faruq; Adhikari, Utpal; Uddin, M. Kamal

doi:10.1016/j.micpath.2019.103791

Cited by 39 publications

(36 citation statements)

References 82 publications

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“…By proposing this vaccine polypeptide, this study also hopes to encourage a rapid design and screening strategy to find one formulation with the highest immunogenicity and biosafety. to predict the CD8 + T-cell epitopes borne in S, E, M and N proteins 12,40,41 . In this step, the ANN 4.0 method was set as the prediction method.…”

Section: Resultsmentioning

confidence: 99%

“…IL10pred server tools, respectively [53][54][55] . The IL4pred and IL10pred operations were carried out based on SVM method and hybrid method respectively, with other parameters kept as default 12,13 .…”

Section: Resultsmentioning

confidence: 99%

“…To construct the vaccine polypeptide, the selected CTL, HTL and LBL epitopes were fused together using appropriate linkers 56,57 . An adjuvant was also considered to increase the immunogenic capacity of the multiepitope vaccine 12,46 . Accordingly, a 45-amino acid sequence prepared from β-defensin-2 protein was added to the N terminus of the vaccine sequence using the EAAAK linker 57 .…”

Section: Resultsmentioning

confidence: 99%

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Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2

Behmard

Soleymani

Najafi

et al. 2020

Preprint

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Coronavirus disease-19 (COVID-19) is an acute resolved disease, with estimated 3.4% case fatality rate. Due to insufficient data and short onset time of the disease, researchers have to change the strategy against its associated virus, SARS-CoV-2. One of these strategies is the use of computational methods in the field of drug and vaccine design, which can greatly reduce the time and cost of the therapeutic or immunogenic development projects. In this study, we employed various immunoinformatics tools to design a multi-epitope vaccine polypeptide with the highest potential for activating the human immune system against SARS-CoV-2. The initial epitope set was extracted from the whole set of viral structural proteins. Their potential non-toxic and non-allergenic T-cell and B-cell binding and cytokine inducing epitopes were then identified through a priori immunoinformatic prediction. Selected epitopes were bonded to each other with appropriate links. A suitable adjuvant was added to the N-terminus of the vaccine polypeptide sequence to increase its immunogenicity. Molecular modelling of the 3D structure of the vaccine polypeptide, docking, molecular dynamics simulations and free energy calculations confirmed that the designed vaccine had high affinity for Toll-like receptor 3 binding, and that the vaccine-receptor complex was highly stable. Therefore, the designed polypeptide is promising for antigenicity and inducing an effective and safe immune response against SARS-CoV-2 inside the human body.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2

Behmard

Soleymani

Najafi

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…The study identi ed a total number of 24 highly immunogenic B-Cell epitopes from COVID-19 proteins (17 epitopes of S; 1 epitopes of M; 1 epitopes of E; 5 epitopes of N). Conservancy analysis (Table 3) demonstrated that selected epitopes were highly conserved in of other homologous strains of COVID-19 which suggested the possibility of peptide based vaccine development from S, M, N or E proteins [35][36][37]. Moreover, potential B-Cell epitopes were also identi ed from HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26 proteins (Supplementary Table 1).…”

Section: Discussionmentioning

confidence: 99%

Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective

Uddin

Hasan

Harun-Al-Rashid

et al. 2020

Preprint

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Recently a new coronavirus strain, COVID-19 has emerged in Wuhan City, China which cause disease and in many cases deaths to humans. Considering its severity a number of works are working on it and full genomic sequences has already released in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Based on currently available genomic information a phylogenetic tree was constructed from four types of representative viral proteins (Spike, Membrane, Envelope and Nucleoproetin) of COVID-19, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26 clearly demonstrated that the ancestral origin and distant evolutionary relation of newly epidemic novel coronavirus (COVID-19). It had been found that COVID-19 was evolutionary related to SARS-CoV. It was also found that COVID-19 proteins were almost more than ninety (90%) similar and identical with SARS-CoV proteins. The cross-checked conservancy analysis of COVID-19 antigenic epitopes showed significant conservancy with SARS-CoV proteins. VaxiJen server reveal almost 100% immunogenic potential of four viral proteins with COVID-19. In this article, we present an effort on molecular evolutionary analysis, temperature comparison and compile and analyze epidemiological outbreak information on the 2019 novel coronavirus based on the several open datasets on COVID-19 (SARS-COV-2) and possible threat to Bangladesh.Authors Md Bashir Uddin and Mahmudul Hasan contributed equally to this work

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“…Recently, the multi-epitope vaccine is an ideal approach for the prevention and treatment of tumors or viral infections [40][41][42][43][44] . There are many multi-epitope vaccine design studies involving various viruses like HIV 45 , Dengue virus 46 , Hepatitis B virus 47 , Hepatitis C virus 48,49 , Ebola virus 50 , Chikungunya virus 51 , Avian influenza A (H7N9) virus 52 , Zika virus 53 , Classical swine fever virus 54 , Nipah virus 55 , and Norovirus 56 . An ideal multi-epitope vaccine should be designed to include a series of or overlapping epitopes so that its every basic unit called antigenic peptide fragment can elicit either a cellular or a humoral immune response against the targeted tumor or virus 39 .…”

mentioning

confidence: 99%

Computational Approach for Screening the Whole Proteome of Hantavirus and Designing a Multi-Epitope Subunit Vaccine

Abdulla

Nain

et al. 2019

Preprint

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Hantaviruses are a newly zoonotic emerging group of rodent-borne viruses that have a significant impact on global public health by increasing amplitude and magnitude of outbreaks. As no permanent cure yet, it is now growing and challenging interest to develop a vaccine against Hantavirus. This study endeavored to design a robust subunit vaccine using a novel immunoinformatics approach. After meticulous evaluation, top ones from predicted CTL, HTL, and B-cell epitopes were considered as potential vaccine candidates. Among generated four vaccine models with different adjuvant, the model with TLR-4 agonist adjuvant was selected for its high antigenicity, non-allergenicity, and structural quality. The conformational B-cell epitope prediction assured its humoral response inducing ability. Thereafter, the molecular docking and dynamics simulation confirmed a good binding affinity with immune receptor TLR-4 and stability of the vaccine-receptor complex. In immune simulation, significantly high levels of IgM and IgG1 immunoglobulins, TC and TH-cell populations, and various cytokines (i.e. IFN-γ, IL-2 etc.) are coherence with actual immune response and also showed faster antigen clearance for repeated exposures. Finally, disulfide engineering enhanced vaccine stability and in silico cloning confirmed the better expression in E. coli K12. Nonetheless, experimental validation can proof the proposed vaccine's safety and ability to control Hantavirus infection.

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Exploring T & B-cell epitopes and designing multi-epitope subunit vaccine targeting integration step of HIV-1 lifecycle using immunoinformatics approach

Cited by 39 publications

References 82 publications

Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2

Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2

Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective

Computational Approach for Screening the Whole Proteome of Hantavirus and Designing a Multi-Epitope Subunit Vaccine

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