Computational Design and Analysis of a Poly-Epitope Fusion Protein: A New Vaccine Candidate for Hepatitis and Poliovirus

Bahrami, Armina Alagheband; Bandehpour, Mojgan; Khalesi, Bahman; Kazemi, Bahram

doi:10.1007/s10989-019-09845-z

Cited by 7 publications

(11 citation statements)

References 71 publications

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“…The binding affinity of the HLA haplotype to individual epitopes is the major factor related to the immune-dominance of CTL (Cytotoxic T lymphocyte) epitopes. According to allele frequency of different Iranian populations and among all HLA alleles, HLA-A*0201 is the most available ones in the world (Creary et al 2019 ; Bahrami et al 2020 ); Therefore, epitopes prediction was performed for this allele. The MHC I (HLA-A*0201)-restricted T cell epitopes were predicted by SYFPEITHI at ( http://www.syfpe ithi.de/) (Rashidian et al 2020 ) and Bioinformatics and Molecular Analysis Section (BIMAS) at ( https://www-bimas.cit.nih.gov/molbio/hla_bind/ ) (Pan et al 2017 ); Furthermore, MHCpred at ( http://www.ddg-pharm fac.net/mhcpred/MHCPred/) (Li et al 2010 ).…”

Section: Methodsmentioning

confidence: 99%

“…The quality of the 3D models was measured using the QMEAN and PROSA software at ( https://swissmodel.expasy.org/qmean/ ) (Pereira et al 2019 ) and ( https://prosa.services.came.sbg.ac.at/prosa.php ) (Basak et al 2020 ), respectively. The quality of the predicted structures was assessed by Rampage software at ( http://mordred.bioc.cam.ac.uk/~rapper/rampage.php ) (Bahrami et al 2020 ). Finally, the 3D models were visually analyzed by the PyMOL software (Pymol molecular graphics systemV.…”

Section: Methodsmentioning

confidence: 99%

“…Finally, the 3D models were visually analyzed by the PyMOL software (Pymol molecular graphics systemV. 1) (Bahrami et al 2020 ; Gainza et al 2020 ).…”

Section: Methodsmentioning

confidence: 99%

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Computational Design and Analysis of a Multi-epitope Against Influenza A virus

Rostaminia

Aghaei

Farahmand

et al. 2021

Int J Pept Res Ther

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Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. For this reason, to combat this disease, we have designed a novel multi-epitope vaccine candidate based on the several conserved and potential linear B-cell and T-cell binding epitopes by using the in silico approach. This vaccine consists of an ER signal conserved sequence, the PADRE conserved epitope and two conserved epitopes of Influenza matrix protein 2. T-cell binding epitopes from Matrix protein 2 were predicted by in silico tools of epitope prediction. The selected epitopes were joined by flexible linkers and physicochemical properties, toxicity, and allergenecity were investigated. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. The final multi-epitope construct was modeled, confirmed by different programs and the molecular interactions with immune receptors were considered. The molecular docking assay indicated the interactions with immune-stimulatory toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHCI). The HADDOCK and H DOCK servers were used to make docking analysis, respectively. The docking analysis indicated a strong and stable binding interaction between the vaccine construct with major histocompatibility complex (MHC) class I and toll-like receptor 3. Overall, the findings suggest that the current vaccine may be a promising vaccine to prevent Influenza infection.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Computational Design and Analysis of a Multi-epitope Against Influenza A virus

Rostaminia

Aghaei

Farahmand

et al. 2021

Int J Pept Res Ther

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“…These information have high importance in prediction of the tertiary protein structure. 41 The tertiary structure was predicted by RaptorX server which computes the solvent accessibility, disordered regions, and binding sites of the PKS protein. 44 The quality of the selected model is indicated on the basis of p-value, GDT (global distance test), and uGDT (un-normalized GDT).…”

Section: Transmission Electron Microscopymentioning

confidence: 99%

“…41 The secondary structure of PKS sequence was predicted by Self-Optimized Prediction Method with Alignment (SOPMA) server. 41 The tertiary structure of PKS protein was predicted using RaptorX server which predicts the protein structure and function. 44 The best template having maximum identity with the target and modeling structure was then evaluated using PROCHECK.…”

Section: Procurement Of Fungal Strains and The Naturalmentioning

confidence: 99%

cis-9-Hexadecenal, a Natural Compound Targeting Cell Wall Organization, Critical Growth Factor, and Virulence of Aspergillus fumigatus

et al. 2020

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Aspergillus fumigatus causes several nosocomial pulmonary infections and accounts for high morbidity and mortality rate globally. Among various virulence factors, 1,8-dihydroxynaphthalene-melanin plays an important role in the survival during unfavorable conditions both in vivo and in vitro, masks various molecular patterns associated with A. fumigatus, and protects it from the host immune system. In the present study, we aim to understand the potential of cis-9-hexadecenal as an antimelanogenic compound and its role in modulating other associated virulence factors in A. fumigatus. cis-9-Hexadecenal is a bioactive compound that belongs to C 16 mono-unsaturated fatty-aldehyde groups. Minimum effective concentration of cis-9-hexadecenal affecting A. fumigatus melanin biosynthesis was determined using broth microdilution method. The spectrophotometric analysis revealed reduced melanin content (91%) and hydrophobicity (59%) at 0.293 mM of cis-9-hexadecenal. Cell surface organizational changes using electron microscopy showed altered demelanized smooth A. fumigatus conidial surface without any protrusions after cis-9-hexadecenal treatment. The transcript analysis of polyketide synthase (PKS) pksP/alb1 gene was quantified through qRT-PCR which revealed an upregulated expression. Total proteome profiling conducted through LC-MS-MS showed upregulated PKS enzyme but other downstream proteins involved in the 1,8-dihydroxynaphthalene-melanin biosynthesis pathway were absent. The homology modeling of PKS using Expasy's web server predicted that PKS is stable at varied conditions and is hydrophilic in nature. The Ramachandran plot by PROCHECK confirmed the 3-D structure of PKS to be reliable. Docking analysis using AutoDock-4.2.6 predicted the binding of cis-9-hexadecenal and PKS at Thr-264 and Ser-171 residue via hydrogen bonding at a low binding energy of −4.95 kcal/mol.

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