Evolutionary Analysis and Prediction of Peptide Vaccine Candidates for Foot-and-Mouth-Disease Virus Types A and O in Bangladesh

Momtaz, Samina; Rahman, Arafat; Sultana, Munawar; Hossain, Md. Anwar

doi:10.4137/ebo.s17027

Cited by 14 publications

(12 citation statements)

References 53 publications

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“…13 bovine leukocyte antigen class I (BolA-I) were described (Bamford et al 1995;De Groot et al 2003;Gaddum et al 1996a;Gaddum et al 1996b;MacHugh et al 2011;Momtaz et al 2014. MHC-II binding predictions are not as well developed as MHC-I binding predictions, yet they are still developing at a fast rate (Tong and Ren 2009;Momtaz et al 2014;Al Asari et al 2017). In this study, we weren't able to predict MHC-II epitopes in the virus protein due to a lack of alleles in the software special for bovine that would bind with the viruses that affected cattle.…”

Section: Discussionmentioning

confidence: 99%

Epitopes- Based Vaccine Design Against Foot and Mouth DiseaseSAT2Serotype from Sudanese Isolate by Using Immunoinformatic Approaches

Habiballa

Raouf

Alhaj

et al. 2022

Preprint

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Foot and mouth disease (FMD) has been endemic in Sudan for decades and causes continuous outbreaks that have a direct negative impact on the animal population and prevent the exportation of animals from the country. The high diversity of FMD serotypes, especially SAT2 and A serotypes, hinders the development of effective vaccines since the most important component of vaccination is the degree of cross-protection provided by the vaccine against currently circulating field viruses. An immunoinformatic approach was utilized to predict a multi-epitope peptide vaccine design against the SAT2 serotype from a Sudanese isolate targeting virus capsid region P1. The virus capsid region P1 comprises the major immunogenic epitopes that confer protection against the FMD virus. Two predicted T-cell epitopes were identified that showed high binding affinity with MHC1 alleles (VQRSRQSTL and YHAEWDTGL) and high conservation with SAT2 African serotypes and were located within the VP1 and VP3 proteins, respectively. Only one epitope was predicted for B cells (LPATPEDAAH), which scored above the threshold in Bepipred linear epitope, Emini surface accessibility, and Kolaskar and Tongaonkar antigenicity and is located in VP3 protein. Molecular docking of the peptides (VQRSRQSTL and YHAEWDTGL) with the MHC1 allele showed satisfactory interaction with the binding sites of BoLA-HD6 using UCSF chimera 1.13.1 software. The peptide VQRSRQSTL showed remarkable hydrophobic interaction with the BoLA-HD6 allele, which was superior to the other peptides. This study is the first to propose a peptide vaccine against FMD SAT2 serotypes from a Sudanese isolate.

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Section: Discussionmentioning

confidence: 99%

Epitopes- Based Vaccine Design Against Foot and Mouth DiseaseSAT2Serotype from Sudanese Isolate by Using Immunoinformatic Approaches

Habiballa

Raouf

Alhaj

et al. 2022

Preprint

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“…The antigenicity value calculation determined four sites to have a higher antigenicity value than the preset threshold. The sites are DKKTEETTLLEDRI (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14), STTQSSVGVTYGY (24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36), TSGLETRV (48-55), and NQFNGGCLLVA (114-124) ( Table 2). The sites were found to have surface exposure and a functionally active structural configuration (Figure 2A), indicating their possible interaction with the immune cells.…”

Section: Discussionmentioning

confidence: 99%

“…Among the four structural proteins of FMDV, VP4 is completely internalized ( 31 ) and thus cannot be used for the development of any diagnostic approach. Although VP1-based diagnostic methods are widely used ( 32 – 35 ), serotypic structural diversity due to VP1 sequence variation can be responsible for the false-negative identification of anti-viral antibody and limiting serotype-independent detection of FMD.…”

Section: Discussionmentioning

confidence: 99%

In silico Evolutionary Divergence Analysis Suggests the Potentiality of Capsid Protein VP2 in Serotype-Independent Foot-and-Mouth Disease Virus Detection

Mishu

Akter

Alam³

et al. 2020

Front. Vet. Sci.

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Foot-and-mouth disease (FMD) is an economically devastating disease of the livestock worldwide and caused by the FMD virus (FMDV), which has seven immunologically distinct serotypes (O, A, Asia1, C, and SAT1-SAT3). Studies suggest that VP2 is relatively conserved among three surface-exposed capsid proteins (VP1-VP3) of FMDV, but the level of conservation has not yet been reported. Here we analyzed the comparative evolutionary divergence of VP2 and VP1 to determine the level of conservation in VP2 at different hierarchical levels of three FMDV serotypes (O, A, and Asia1) currently circulating in Asia through an in-depth computational analysis of 14 compiled datasets and designed a consensus VP2 protein that can be used for the development of a serotype-independent FMDV detection tool. The phylogenetic analysis clearly represented a significant level of conservation in VP2 over VP1 at each subgroup level. The protein variability analysis and mutational study showed the presence of 67.4% invariant amino acids in VP2, with the N-terminal end being highly conserved. Nine inter-serotypically conserved fragments located on VP2 have been identified, among which four sites showed promising antigenicity value and surface exposure. The designed 130 amino acid long consensus VP2 protein possessed six surface-exposed B cell epitopes, which suggests the possible potentiality of the protein for the development of a serotype-independent FMDV detection tool in Asia. Conclusively, this is the first study to report the comparative evolutionary divergence between VP2 and VP1, along with proposing the possible potentiality of a designed protein candidate in serotype-independent FMDV detection.

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“…Lower the percentile rank the higher the interaction shown between the peptide and MHC molecules. IC 50 values divided in three different categories: high binding affinity, IC 50 value < 50 nM; intermediate binding affinity, IC 50 value < 500 nM; and low binding affinity, IC 50 value < 5000 nM 36 .…”

Section: Methodsmentioning

confidence: 99%

Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii

Solanki

Tiwari

2018

Sci Rep

223

158

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The emergence of drug-resistant Acinetobacter baumannii is the global health problem associated with high mortality and morbidity. Therefore it is high time to find a suitable therapeutics for this pathogen. In the present study, subtractive proteomics along with reverse vaccinology approaches were used to predict suitable therapeutics against A. baumannii. Using subtractive proteomics, we have identified promiscuous antigenic membrane proteins that contain the virulence factors, resistance factors and essentiality factor for this pathogenic bacteria. Selected promiscuous targeted membrane proteins were used for the design of chimeric-subunit vaccine with the help of reverse vaccinology. Available best tools and servers were used for the identification of MHC class I, II and B cell epitopes. All selected epitopes were further shortlisted computationally to know their immunogenicity, antigenicity, allergenicity, conservancy and toxicity potentials. Immunogenic predicted promiscuous peptides used for the development of chimeric subunit vaccine with immune-modulating adjuvants, linkers, and PADRE (Pan HLA-DR epitopes) amino acid sequence. Designed vaccine construct V4 also interact with the MHC, and TLR4/MD2 complex as confirm by docking and molecular dynamics simulation studies. Therefore designed vaccine construct V4 can be developed to control the host-pathogen interaction or infection caused by A. baumannii.

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Evolutionary Analysis and Prediction of Peptide Vaccine Candidates for Foot-and-Mouth-Disease Virus Types A and O in Bangladesh

Cited by 14 publications

References 53 publications

Epitopes- Based Vaccine Design Against Foot and Mouth DiseaseSAT2Serotype from Sudanese Isolate by Using Immunoinformatic Approaches

Epitopes- Based Vaccine Design Against Foot and Mouth DiseaseSAT2Serotype from Sudanese Isolate by Using Immunoinformatic Approaches

In silico Evolutionary Divergence Analysis Suggests the Potentiality of Capsid Protein VP2 in Serotype-Independent Foot-and-Mouth Disease Virus Detection

Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii

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