<i>De Novo</i>Structural Modeling and Conserved Epitopes Prediction of Zika Virus Envelop Protein for Vaccine Development

Ashfaq, Usman Ali; Ahmed, Bilal

doi:10.1089/vim.2016.0033

Cited by 33 publications

(25 citation statements)

References 20 publications

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“…Especially cost-effective and fast methods such as immunoinformatics tools have been quickly harnessed by researchers in different countries to, for example, predict possible antigenic epitopes from ZIKV proteins (especially the E protein) for peptide vaccine development (see for example these very recent studies in refs 40, 41, 42, 43, 44, 45, 46, 47). In general, such in silico approaches help reduce the number of in vitro experimental assays and provide an essential tool in vaccine design272829.…”

Section: Discussionmentioning

confidence: 99%

Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

Mirza

Rafique

Ali

et al. 2016

Sci Rep

101

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The recent outbreak of Zika virus (ZIKV) infection in Brazil has developed to a global health concern due to its likely association with birth defects (primary microcephaly) and neurological complications. Consequently, there is an urgent need to develop a vaccine to prevent or a medicine to treat the infection. In this study, immunoinformatics approach was employed to predict antigenic epitopes of Zika viral proteins to aid in development of a peptide vaccine against ZIKV. Both linear and conformational B-cell epitopes as well as cytotoxic T-lymphocyte (CTL) epitopes were predicted for ZIKV Envelope (E), NS3 and NS5 proteins. We further investigated the binding interactions of altogether 15 antigenic CTL epitopes with three class I major histocompatibility complex (MHC I) proteins after docking the peptides to the binding groove of the MHC I proteins. The stability of the resulting peptide-MHC I complexes was further studied by molecular dynamics simulations. The simulation results highlight the limits of rigid-body docking methods. Some of the antigenic epitopes predicted and analyzed in this work might present a preliminary set of peptides for future vaccine development against ZIKV.

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Section: Discussionmentioning

confidence: 99%

Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

Mirza

Rafique

Ali

et al. 2016

Sci Rep

101

View full text Add to dashboard Cite

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“…Some authors have published ZKV MHC class II epitope prediction based on MHC binding search engines alone (35, 56, 57). In order to generate a realistic list of MHC-1 binding peptides on ZKV E and M proteins, not only did we use a binding prediction tool, but we also performed matching known DNV class I epitopes to peptides on ZKV.…”

Section: Specific Potential Advantages Of Ctl Versus Antibody Vaccinementioning

confidence: 99%

An Approach for a Synthetic CTL Vaccine Design against Zika Flavivirus Using Class I and Class II Epitopes Identified by Computer Modeling

et al. 2017

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The threat posed by severe congenital abnormalities related to Zika virus (ZKV) infection during pregnancy has turned development of a ZKV vaccine into an emergency. Recent work suggests that the cytotoxic T lymphocyte (CTL) response to infection is an important defense mechanism in response to ZKV. Here, we develop the rationale and strategy for a new approach to developing cytotoxic T lymphocyte (CTL) vaccines for ZKV flavivirus infection. The proposed approach is based on recent studies using a protein structure computer model for HIV epitope selection designed to select epitopes for CTL attack optimized for viruses that exhibit antigenic drift. Because naturally processed and presented human ZKV T cell epitopes have not yet been described, we identified predicted class I peptide sequences on ZKV matching previously identified DNV (Dengue) class I epitopes and by using a Major Histocompatibility Complex (MHC) binding prediction tool. A subset of those met the criteria for optimal CD8+ attack based on physical chemistry parameters determined by analysis of the ZKV protein structure encoded in open source Protein Data File (PDB) format files. We also identified candidate ZKV epitopes predicted to bind promiscuously to multiple HLA class II molecules that could provide help to the CTL responses. This work suggests that a CTL vaccine for ZKV may be possible even if ZKV exhibits significant antigenic drift. We have previously described a microsphere-based CTL vaccine platform capable of eliciting an immune response for class I epitopes in mice and are currently working toward in vivo testing of class I and class II epitope delivery directed against ZKV epitopes using the same microsphere-based vaccine.

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“…Ashfaq and Ahmed are other researchers who used ProPred1 and ProPred, but focused in the envelope protein, inding two highly antigenic candidates among T-cell epitopes. They also performed a molecular docking to study the interactions of B-cell epitopes with HLA-B7 [68].…”

Section: Zika Virus Diseasementioning

confidence: 99%

The Impact of Bioinformatics on Vaccine Design and Development

María¹,

Arturo²,

Alicia³

et al. 2017

Vaccines

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Vaccines are the pharmaceutical products that ofer the best cost-beneit ratio in the prevention or treatment of diseases. In that a vaccine is a pharmaceutical product, vaccine development and production are costly and it takes years for this to be accomplished. Several approaches have been applied to reduce the times and costs of vaccine development, mainly focusing on the selection of appropriate antigens or antigenic structures, carriers, and adjuvants. One of these approaches is the incorporation of bioinformatics methods and analyses into vaccine development. This chapter provides an overview of the application of bioinformatics strategies in vaccine design and development, supplying some successful examples of vaccines in which bioinformatics has furnished a cuting edge in their development. Reverse vaccinology, immunoinformatics, and structural vaccinology are described and addressed in the design and development of speciic vaccines against infectious diseases caused by bacteria, viruses, and parasites. These include some emerging or re-emerging infectious diseases, as well as therapeutic vaccines to ight cancer, allergies, and substance abuse, which have been facilitated and improved by using bioinformatics tools or which are under development based on bioinformatics strategies.

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De NovoStructural Modeling and Conserved Epitopes Prediction of Zika Virus Envelop Protein for Vaccine Development

Cited by 33 publications

References 20 publications

Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins

An Approach for a Synthetic CTL Vaccine Design against Zika Flavivirus Using Class I and Class II Epitopes Identified by Computer Modeling

The Impact of Bioinformatics on Vaccine Design and Development

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