Vaccine Target Discovery

Li, Chong; Khan, Mohammad Asif

doi:10.1016/b978-0-12-809633-8.20100-3

Cited by 16 publications

(15 citation statements)

References 130 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This is further exacerbated when the conservation is extended to other family members, a consideration given the possibility of APLs as a result of similar genomic architecture between family members [29, 76]. For example, DENV and HIV-1 had 44 and 78 highly conserved sequences each, respectively, however, only 27 and 74 were conserved across majority of the family members [77]. The remaining were either not present in the family members or were represented with conservation that fluctuated from low to high between the members.…”

Section: Discussionmentioning

confidence: 99%

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

Khan

2019

BMC Genomics

Self Cite

View full text Add to dashboard Cite

BackgroundThe sequence diversity of dengue virus (DENV) is one of the challenges in developing an effective vaccine against the virus. Highly conserved, serotype-specific (HCSS), immune-relevant DENV sequences are attractive candidates for vaccine design, and represent an alternative to the approach of selecting pan-DENV conserved sequences. The former aims to limit the number of possible cross-reactive epitope variants in the population, while the latter aims to limit the cross-reactivity between the serotypes to favour a serotype-specific response. Herein, we performed a large-scale systematic study to map and characterise HCSS sequences in the DENV proteome.MethodsAll reported DENV protein sequence data for each serotype was retrieved from the NCBI Entrez Protein (nr) Database (txid: 12637). The downloaded sequences were then separated according to the individual serotype proteins by use of BLASTp search, and subsequently removed for duplicates and co-aligned across the serotypes. Shannon’s entropy and mutual information (MI) analyses, by use of AVANA, were performed to measure the diversity within and between the serotype proteins to identify HCSS nonamers. The sequences were evaluated for the presence of promiscuous T-cell epitopes by use of NetCTLpan 1.1 and NetMHCIIpan 3.2 server for human leukocyte antigen (HLA) class I and class II supertypes, respectively. The predicted epitopes were matched to reported epitopes in the Immune Epitope Database.ResultsA total of 2321 nonamers met the HCSS selection criteria of entropy < 0.25 and MI > 0.8. Concatenating these resulted in a total of 337 HCSS sequences. DENV4 had the most number of HCSS nonamers; NS5, NS3 and E proteins had among the highest, with none in the C and only one in prM. The HCSS sequences were immune-relevant; 87 HCSS sequences were both reported T-cell epitopes/ligands in human and predicted epitopes, supporting the accuracy of the predictions. A number of the HCSS clustered as immunological hotspots and exhibited putative promiscuity beyond a single HLA supertype. The HCSS sequences represented, on average, ~ 40% of the proteome length for each serotype; more than double of pan-DENV sequences (conserved across the four serotypes), and thus offer a larger choice of sequences for vaccine target selection. HCSS sequences of a given serotype showed significant amino acid difference to all the variants of the other serotypes, supporting the notion of serotype-specificity.ConclusionThis work provides a catalogue of HCSS sequences in the DENV proteome, as candidates for vaccine target selection. The methodology described herein provides a framework for similar application to other pathogens.

show abstract

Section: Discussionmentioning

confidence: 99%

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

Khan

2019

BMC Genomics

Self Cite

View full text Add to dashboard Cite

show abstract

“…Prediction of epitope-based vaccines using computational tools have been successfully reported against the Chikungunya virus, Zika virus, Ebola virus, Herpes simplex virus, Yellow fever virus, etc. [ 43 , 44 , 45 , 46 , 47 ]. The focus of this study was to predict both B-cell and T-cell epitopes using the S protein of SARS-CoV-2 by immunoinformatics method.…”

Section: Discussionmentioning

confidence: 99%

An immunoinformatics study on the spike protein of SARS-CoV-2 revealing potential epitopes as vaccine candidates

Ashik

Hasan

Tasnim

et al. 2020

Heliyon

View full text Add to dashboard Cite

Background The pandemic situation of SARS-CoV-2 infection has sparked global concern due to the disease COVID-19 caused by it. Since the first cluster of confirmed cases in China in December 2019, the infection has been reported across the continents and inflicted upon a substantial number of populations. Method This study is focused on immunoinformatics analyses of the SARS-CoV-2 spike glycoprotein (S protein) which is key for the viral attachment to human host cells. Computational analyses were carried out for the prediction of B-cell and T-cell (MHC class I and II) epitopes of S protein and the analyses were extended further for the prediction of their immunogenic properties. The interaction and binding affinity of T-cell epitopes with HLA-B7 were also investigated by molecular docking. Result Three distinct epitopes for vaccine design were predicted from the sequence of S protein. The potential B-cell epitope was KNHTSPDVDLG possessing the highest antigenicity score of 1.4039 among other B-cell epitopes. T-cell epitope for human MHC class I was VVVLSFELL with an antigenicity score of 1.0909 and binding ability to 29 MHC-I alleles. The predicted T-cell epitope for human MHC class II molecule was VVIGIVNNT with a corresponding 1.3063 antigenicity score, less digesting enzymes, and 7 MHC-II alleles binding ability. All these three peptides were predicted to be highly antigenic, non-allergenic, and non-toxic. Analyses of the physiochemical properties of these predicted epitopes indicate their stable nature for plausible vaccine design. Furthermore, molecular docking investigation between the MHC class-I epitopes and human HLA-B7 reflects the stable interaction with high affinity among them. Conclusion The present study posits three potential epitopes of S protein of SARS-CoV-2 predicted by immunoinformatic methods based on their immunogenic properties and interactions with the host counterpart that can facilitate the development of vaccine against SARS-CoV-2. This study can act as the springboard for the future development of the COVID-19 vaccine.

show abstract

“…Reverse vaccinology has successfully been used for developing vaccines to fight against many viruses i.e., the Zika virus, Chikungunya virus etc. [101] [102].…”

Section: Origin Of Coronavirus Their Morphology Pathology and Othersmentioning

confidence: 99%

The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19

Sarkar

Ullah

Johora

et al. 2020

Preprint

View full text Add to dashboard Cite

Wuhan Novel Coronavirus (2019-nCoV) outbreak has become global pandemic which has raised the concern of scientific community to deign and discover a definitive cure against this deadly virus which has caused deaths of numerous infected people upon infection and spreading. To date, there is no antiviral therapy or vaccine is available which can effectively combat the infection caused by this virus. This study was conducted to design possible epitope-based subunit vaccines against the 2019-nCoV using the approaches of reverse vaccinology and immunoinformatics. Upon continual computational experimentation three possible vaccine constructs were designed and one vaccine construct was selected as the best vaccine based on molecular docking study which is supposed to effectively act against the Wuhan Novel Coronavirus. Later, molecular dynamics simulation and in silico codon adaptation experiments were carried out in order to check biological stability and find effective mass production strategy of the selected vaccine. Hopefully, this study will contribute to uphold the present efforts of the researches to secure a definitive treatment against this nasty virus.

show abstract

Vaccine Target Discovery

Cited by 16 publications

References 130 publications

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

Identification of highly conserved, serotype-specific dengue virus sequences: implications for vaccine design

An immunoinformatics study on the spike protein of SARS-CoV-2 revealing potential epitopes as vaccine candidates

The Essential Facts of Wuhan Novel Coronavirus Outbreak in China and Epitope-based Vaccine Designing against COVID-19

Contact Info

Product

Resources

About