Delineating blueprint of an epitope-based peptide vaccine against the multiple serovars of dengue virus: A hierarchical reverse vaccinology approach

Islam, Rahatul; Parvez, Sorwer Alam; Anwar, Saeed

doi:10.1016/j.imu.2020.100430

Cited by 13 publications

(8 citation statements)

References 60 publications

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“…Molecular docking analysis was conducted to further emphasize the supposition as to which mutants have more negative impact on the protein. Molecular docking is a popular In silico method which is particularly used in drug designing and vaccine designing approaches to resolve the binding status between a drug/vaccine with its corresponding macromolecules [ 63 , 64 ]. Ribociclib is such kind of drug (act as CDK4/6 inhibitor) used for treatment of HR+, HER2– advanced or metastatic breast cancer.…”

Section: Discussionmentioning

confidence: 99%

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Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

et al. 2021

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Cycline-dependent kinase 4 (CDK4), an enzyme of the cycline dependent or Ser/Thr protein kinase family, plays a role in cell cycle progression (G1 phase) by phosphorylating a tumor suppressor protein called pRB. Alteration of this enzyme due to missense mutation/ nonsynonymous single nucleotide polymorphisms (nsSNPs) are responsible for various types of cancer progression, e.g. melanoma, lung cancer, and breast cancer. Hence, this study is designed to identify the malignant missense mutation of CDK4 from the single nucleotide polymorphism database (dbSNP) by incorporating computational algorithms. Out of 239 nsSNPs; G15S, D140Y and D140H were predicted to be highly malignant variants which may have a devastating impact on protein structure or function. We also found defective binding motif of these three mutants with the CDK4 inhibitor ribociclib and ATP. However, by incorporating molecular dynamic simulation, our study concludes that the superiority of G15S than the other two mutants (D140Y and D140H) in destabilizing proteins nature.

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Section: Discussionmentioning

confidence: 99%

“…silico method which is particularly used in drug designing and vaccine designing approaches to resolve the binding status between a drug/vaccine with its corresponding macromolecules [63,64]. Ribociclib is such kind of drug (act as CDK4/6 inhibitor) used for treatment of HR+, HER2-advanced or metastatic breast cancer.…”

Section: Plos Onementioning

confidence: 99%

Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

et al. 2021

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“…Besides, the recent advancement in the in silco peptide vaccine designing with reverse vaccinology approach is getting popular day by day because of its low threats of re-activation as like as live attenuated vaccine. The first epitope based vaccine was designed against N. meningitides using bioinformatics and after that many of the vaccines are designed for different infections including Dengue virus [ 45 ], Nipah virus [ 46 ], Ebola virus [ 47 ], Herpes simplex virus [ 48 ], human norovirus [ 49 ] and so on.…”

Section: Discussionmentioning

confidence: 99%

Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses

Hoque

Islam

Ghosh

et al. 2021

Heliyon

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Being a Positive sense RNA virus the recent reemergence of Chikungunya and Mayaro virus has taken the concern of the leading scientific communities of the world. Though the outbreak of Mayaro virus is limited to Neotropical region only, Chikungunya is already identified in over 60 countries around the world. Besides, the lack of a strong protective treatment, misdiagnosis issue and co-circulation of both the viruses calls for a new strategy which could potentially prevent these infections from spreading. In this study, we therefore, identified the peptide based vaccine candidates e.g. epitopes for B cell and T cell from Chikungunya virus which also showed to be homologous to the Mayaro virus through immuno-informatics and computational approaches. Final epitopes identified from the most antigenic structural polyprotein of both the viruses were 5 for CD8+ T cell Epitopes ( 209 KPGDSGRPI 217 , 219 TGTMGHFIL 227 , 239 ALSVVTWNK 247 , 98 KPGRRERMC 106 and 100 GRRERMCMK 108 ), 2 epitopes for CD4+ T cell ( 105 MCMKIENDCIFEVKH 119 and 502 DRTLLSQQSGNVKIT 516 ) and a single epitope for B cell ( 504 GGRFTIPTGAGKPGDSGRPI 518 ). Analysis of our predicted epitopes for population coverage showed prominent population coverage (92.43%) around the world. Finally, molecular docking simulation of the foreseen T cell epitopes with respondent HLA alleles secured good HLA-epitope interaction. This study was directed towards the discovery of potential antigenic epitopes which can open up a new skyline to design novel vaccines for combating both of the diseases at the same time.

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“…These PVCs are poise to induce both B-cell and T-cells responses. Reverse vaccinology approaches have been applied in several infectious diseases such as malaria (Tuju et al 2017), multiple sclerosis (Islam et.al 2020) and Plasmodium falciparum (Pritam et al 2019). Even though there have been several endevours to develop vaccines pertaining to specific diseases, the attempts were unfruitful.…”

Section: Discussionmentioning

confidence: 99%

Designing of multiepitope-based vaccine against Leptospirosis using Immuno-Informatics approaches

Abdullah

Kadivella

Sharma

et al. 2021

Preprint

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Leptospira is a zoonotic pathogen causing significant morbidity and mortality both in animals and humans. Although several surface proteins have been identified as vaccine candidate, they failed to induce sterilizing immunity and cross protection against different serovars. Thus, identification of highly immunogenic antigens that are conserved among pathogenic serovars would be first step towards development of universal vaccine for Leptospirosis. Here we used reverse vaccinology pipeline to screen core genome of pathogenic Leptospira spp.in order to identify suitable vaccine candidates. Based on properties like sub cellular localization, adhesin, homology to human proteins, antigenicity and allergenicity, 18 antigenic proteins were identified through this pipeline and were further investigated for immunological properties. Based on immunogenicity, Protegenicity, Antigenicity, B-cell and promiscuous T-cell epitopes, 6 Potential Vaccine Candidates (PVCs) were finally selected which covered most of the affected world population. For designing a Multi-Epitope Vaccine (MEV), 6 B-cell and 6 promiscuous MHC-I and MHC-II epitopes from each candidate were clustered with linkers in between and stitched along with a TLR4 adjuvant (APPHALS) at the N-terminal forming a construct of 361 amino acids. The physiochemical properties, secondary and tertiary structure analysis revealed that MEV was highly stable. Molecular docking analysis revealed the deep binding interactions of the MEV construct within the grooves of human TLR4 (4G8A). In-silico codon optimization and cloning of the vaccine construct assured good expression. Further, immune simulations have shown that MEV could induce strong and diverse B-cell and T-cell responses. Taken together our results indicate that the designed MEV could be a promising subunit vaccine candidate against Leptospirosis, however it requires experimental validation.

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Delineating blueprint of an epitope-based peptide vaccine against the multiple serovars of dengue virus: A hierarchical reverse vaccinology approach

Cited by 13 publications

References 60 publications

Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

Computational and structural based approach to identify malignant nonsynonymous single nucleotide polymorphisms associated with CDK4 gene

Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses

Designing of multiepitope-based vaccine against Leptospirosis using Immuno-Informatics approaches

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