Prediction and Conservancy Analysis of Multiepitope Based Peptide Vaccine Against Merkel Cell Polyomavirus: An Immunoinformatics Approach

Awad-Elkareem, Mawadda A; Osman, Soada Ahmed; Mohamed, Hanaa; Hassan, Hadeel Abdelrahman; Abu-haraz, Ahmed Hamdi; Abd-elrahman, Khoubieb Ali; Salih, Mohamed Ahmed

doi:10.4172/1745-7580.1000134

Cited by 8 publications

(9 citation statements)

References 53 publications

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“…Except for the Ile115Phe substitution, all the variations detected in this study are involved in epitopes recognized by B cells. None of these mutations are involved in epitopes recognized by T cells [51]. Regarding the protein stability, in order to predict the effect of single point mutations on VP1, structure-based analysis was performed by PROVEAN and DynaMut servers.…”

Section: Discussionmentioning

confidence: 99%

Structural Analysis of Merkel Cell Polyomavirus (MCPyV) Viral Capsid Protein 1 (VP1) in HIV-1 Infected Individuals

Prezioso

Bianchi

Obregón

et al. 2020

IJMS

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Merkel cell polyomavirus (MCPyV) viral protein 1 (VP1) is the capsid protein that mediates virus attachment to host cell receptors and is the major immune target. Given the limited data on MCPyV VP1 mutations, the VP1 genetic variability was examined in 100 plasma and 100 urine samples from 100 HIV+ individuals. Sequencing of VP1 DNA in 17 urine and 17 plasma specimens, simultaneously MCPyV DNA positive, revealed that 27 samples displayed sequences identical to VP1 of MCC350 strain. VP1 from two urine specimens had either Thr47Ser or Ile115Phe substitution, whereas VP1 of one plasma contained Asp69Val and Ser251Phe substitutions plus deletion (∆) of Tyr79. VP1 DNA in the remaining samples had mutations encoding truncated protein. Three-dimensional prediction models revealed that Asp69Val, Ser251Phe, and Ile115Phe caused neutral effects while Thr47Ser and Tyr79∆ produced a deleterious effect reducing VP1 stability. A549 cells infected with urine or plasma samples containing full-length VP1 variants with substitutions, sustained viral DNA replication and VP1 expression. Moreover, medium harvested from these cells was able to infect new A549 cells. In cells infected by samples with truncated VP1, MCPyV replication was hampered. In conclusion, MCPyV strains with unique mutations in the VP1 gene are circulating in HIV+ patients. These strains display altered replication efficiency compared to the MCC350 prototype strain in A549 cells.

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Section: Discussionmentioning

confidence: 99%

Structural Analysis of Merkel Cell Polyomavirus (MCPyV) Viral Capsid Protein 1 (VP1) in HIV-1 Infected Individuals

Prezioso

Bianchi

Obregón

et al. 2020

IJMS

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“…We used Immuno informatics tools to identify epitopes for multiple peptide vaccine, these tools was recently used to design vaccines for many viruses such as Ebola [42], Zika virus [43], merkel cell polyomavirus [44] and human papillomavirus [45]. Rubella virus contains two projections that are mainly protein in nature, E1 and E2, which anchored to the outer layer of the membrane and many forms of nucleocapsid envelope protein.…”

Section: Discussionmentioning

confidence: 99%

Prediction of Multiple Peptide Based Vaccine from E1, E2 and Capsid Proteins of Rubella Virus: An In-Silico Approach

Elgenaid¹,

Al-Hajj²,

Ibrahim³

et al. 2018

Immunome Res

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Rubella is a single strand RNA virus in structure that belongs to Togaviridae family. It causes rubella by respiratory droplet transmission and congenital rubella syndrome if infection to the mother occurs during pregnancy. The current life attenuated vaccine is given as part of MMR vaccine. It has many side effects and contraindicated in pregnancy and immunosuppressed persons. The aim of this study is to determine antigenic peptides from E1, E2, and Capsid proteins that can be used for multiple peptide vaccine design using In-Silico study. A total of 189 sequences of three proteins were obtained from NCBI and subjected to multiple sequence alignments using CLUSTALW tool to determine conserved regions.

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“…So firstly we must be achieve the FASTA format of "Glycoprotein E" with identified number "NP_040190.1" from NCBI data base followed by the initial antibody epitope prediction of B cell examination by Bepipred linear Epitope predication method to predict the location of B-cell using a combination of a hidden Markov model and propensity scale method. The result with scores above threshold "0.210" was considered to be part of an epitope [36][37][38][39][40].…”

Section: Discussionmentioning

confidence: 99%

Immunoinformatics Approach-Multiple Peptides Vaccine Design from Glycoprotein E of Herpes Simplex Virus-3

Albagi¹,

Ahmed²,

Mohamme³

et al. 2018

Immunome Res

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Background: Herpes simplex virus (HSV) is a common human pathogen, causing infections of orofacial mucosal surfaces (HSV-1) and genital mucosal surfaces (HSV-2). Productive infection results in the formation of vesicular lesions in the mucosal epithelia, followed by spread of the virus to sensory neurons and establishment of a latent infection that may remain for the life of the host. Material and method: All sequences of glycoprotein E [Human herpes virus 3] were obtained from NCBI and these sequences were subjected to IEDB predicted tools, including B cell and T cell examination, with B cell having multiple tests such as epitopes prediction, surface accessibility and antigenicity prediction; T cell included MHC I and MHC II predicted tools. Finally we used population coverage to select a highest percent of peptides related with different alleles. Result: We obtained some candidate peptides as vaccine derived peptides from B cell test which had a highest score in Emini surface accessibility ("DEDKLDTNSVYEPYYHSDHAESSWVNRGESSRKAYDHNSPYIWPRNDYDGF") of 21.807, and "LKFVDTPESL" with score 1.061 for Kolaskar and Tongaonkar antigenicity test, in another hand we got a highest affinity of peptides that interacted with major coverage of different alleles in MHC I ("KAYDHNSPY") and in MHC II ("MWNYHSHVF"). Conclusion: The efficiency and safety degree in predicted candidate epitopes by computational examination methods are required to be estimated through studies of animal model, to check whether they are able to induce a good defending immune response or not with previous mentioned properties, and we considered this study as first promising peptide based vaccine of [Human herpes virus 3] glycoprotein E in comparison to the previous studies.

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Prediction and Conservancy Analysis of Multiepitope Based Peptide Vaccine Against Merkel Cell Polyomavirus: An Immunoinformatics Approach

Cited by 8 publications

References 53 publications

Structural Analysis of Merkel Cell Polyomavirus (MCPyV) Viral Capsid Protein 1 (VP1) in HIV-1 Infected Individuals

Structural Analysis of Merkel Cell Polyomavirus (MCPyV) Viral Capsid Protein 1 (VP1) in HIV-1 Infected Individuals

Prediction of Multiple Peptide Based Vaccine from E1, E2 and Capsid Proteins of Rubella Virus: An In-Silico Approach

Immunoinformatics Approach-Multiple Peptides Vaccine Design from Glycoprotein E of Herpes Simplex Virus-3

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