Immunoinformatics aided-design of novel multi-epitope based peptide vaccine against Hendra henipavirus through proteome exploration

Hossan, Mohammad Imran; Chowdhury, Afrin Sultana; Hossain, Mohammad Uzzal; Khan, Arif; Mahmood, Tousif Bin; Mizan, Shagufta

doi:10.1016/j.imu.2021.100678

Cited by 17 publications

(7 citation statements)

References 54 publications

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“…B lymphocytes boost humoral immunity by secreting antibodies and cytokines that neutralize foreign antigens [ 38 , 39 ] That's why it is essential to have a sufficient number of B-cell epitopes inside the protein domain. The existence of conformational B-cell epitopes was analyzed using the ElliPro tool of the IEBD server, which found 4 conformational B-cell epitopes of 14–39 residues (Additional file 7 : Table S7) with scores ranging from 0.596–0.809, as shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium

et al. 2022

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Enterococcus faecium is an emerging ESKAPE bacterium that is capable of causing severe public health complications in humans. There are currently no licensed treatments or vaccinations to combat the deadly pathogen. We aimed to design a potent and novel prophylactic chimeric vaccine against E. faecium through an immunoinformatics approach The antigenic Penicillin-binding protein 5 (PBP 5) protein was selected to identify B and T cell epitopes, followed by conservancy analysis, population coverage, physiochemical assessment, secondary and tertiary structural analysis. Using various immunoinformatics methods and tools, two linear B-cell epitopes, five CTL epitopes, and two HTL epitopes were finally selected for vaccine development. The constructed vaccine was determined to be highly immunogenic, cytokine-producing, antigenic, non-toxic, non-allergenic, and stable, as well as potentially effective against E. faecium. In addition, disulfide engineering, codon adaptation, and in silico cloning, were used to improve stability and expression efficiency in the host E. coli. Molecular docking and molecular dynamics simulations indicated that the structure of the vaccine is stable and has a high affinity for the TLR4 receptor. The immune simulation results revealed that both B and T cells had an increased response to the vaccination component. Conclusively, the in-depth in silico analysis suggests, the proposed vaccine to elicit a robust immune response against E. faecium infection and hence a promising target for further experimental trials.

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Section: Resultsmentioning

confidence: 99%

Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium

et al. 2022

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“…The physiochemical characteristics of the selected proteins were analyzed, including instability index, molecular weight, atomic composition, theoretical protein index, aliphatic index, amino acid composition, and the grand average of hydropathicity (GRAVY).ProtParam 29 was used to calculate the physicochemical properties of the proteins. Protein molecular weight was cut-off at 110 KDa and the instability index was < 40 30 . This was used to identify the protein as an appropriate vaccine target.…”

Section: Methodsmentioning

confidence: 99%

Identification and construction of a multi-epitopes vaccine design against Klebsiella aerogenes: molecular modeling study

Alzarea

2022

Sci Rep

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A rapid rise in antibiotic resistance by bacterial pathogens is due to these pathogens adaptation to the changing environmental conditions. Antibiotic resistance infections can be reduced by a number of ways such as development of safe and effective vaccine. Klebsiella aerogene is a gram-negative, rod-shaped bacterium resistant to a variety of antibiotics and no commercial vaccine is available against the pathogen. Identifying antigens that can be easily evaluated experimentally would be crucial to successfully vaccine development. Reverse vaccinology (RV) was used to identify vaccine candidates based on complete pathogen proteomic information. The fully sequenced proteomes include 44,115 total proteins of which 43,316 are redundant and 799 are non-redundant. Subcellular localization showed that only 1 protein in extracellular matrix, 7 were found in outer-membrane proteins, and 27 in the periplasm space. A total of 3 proteins were found virulent. Next in the B-cell-derived T-cell epitopes mapping phase, the 3 proteins (Fe2+− enterobactin, ABC transporter substrate-binding protein, and fimbriae biogenesis outer membrane usher protein) were tested positive for antigenicity, toxicity, and solubility. GPGPG linkers were used to prepare a vaccine construct composed of 7 epitopes and an adjuvant of toxin B subunit (CTBS). Molecular docking of vaccine construct with major histocompatibility-I (MHC-I), major histocompatibility-II (MHC-II), and Toll-like receptor 4 (TLR4) revealed vaccine robust interactions and stable binding pose to the receptors. By using molecular dynamics simulations, the vaccine-receptors complexes unveiled stable dynamics and uniform root mean square deviation (rmsd). Further, binding energies of complex were computed that again depicted strong intermolecular bindings and formation of stable conformation.

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“…Utilizing the constant pressure and Berendsen thermostat, the simulation was conducted for 200 ns and after every 100 ps simulations trajectories were recorded. The recording simulation trajectories after constant intervals were used to measure the hydrogen bond, root mean square deviations, (RMSDs) radius of gyration and solvent accessible surface area 26–31 …”

Section: Methodsmentioning

confidence: 99%

“…The recording simulation trajectories after constant intervals were used to measure the hydrogen bond, root mean square deviations, (RMSDs) radius of gyration and solvent accessible surface area. [26][27][28][29][30][31]…”

Section: Structural Flexibility Analysis By Molecular Dynamics (Md) S...mentioning

confidence: 99%

Missense mutations in spike protein of SARS‐CoV‐2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor

Mahmood

Hossan

Mahmud

et al. 2022

Immunity Inflam & Disease

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Introduction Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID‐19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. Methods In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS‐CoV‐2 delta variant performing different computational analysis. Results From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. Conclusions Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS‐CoV‐2 delta variant.

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Immunoinformatics aided-design of novel multi-epitope based peptide vaccine against Hendra henipavirus through proteome exploration

Cited by 17 publications

References 54 publications

Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium

Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium

Identification and construction of a multi-epitopes vaccine design against Klebsiella aerogenes: molecular modeling study

Missense mutations in spike protein of SARS‐CoV‐2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor

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