close
Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022;11(1):2.
doi: 10.1007/s13721-021-00339-x. Epub 2021 Dec 7.

T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease

Affiliations

T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease

Amit Joshi et al. Netw Model Anal Health Inform Bioinform. 2022.

Abstract

Orthohantavirus, a zoonotic virus responsible for causing human cardio-pulmonary disease, is proven to be a fatal disease. Due to the paucity of regimens to cure the disease and efficient management to eradicate this deadly virus, there is a constant need to expand in-silico approaches belonging to immunology domain to formulate best feasible peptide-based vaccine against it. In lieu of that, we have predicted and validated an epitope of nine-residue-long sequence "MIGLLSSRI". The predicted epitope has shown best interactions with HLA alleles of MHC Class II proteins, namely HLA DRB1_0101, DRB1_0401, DRB1_0405, DRB1_0701, DRB1_0901, DRB1_1302, and DRB1_1501. The structure of the epitope was modeled by deploying PEPFOLD 3.5 and verified by Ramachandran plot analysis. Molecular docking and simulation studies reveal that this epitope has satisfactory binding scores, ACE value and global energies for docked complexes along with selectable range of RMSD and RMSF values. Also, the predicted epitope "MIGLLSSRI" exhibits population coverage of more than 62% in world population and maximum of 70% in the United States of America. In this intensive study, we have used many tools like AllergenFP, NETMHCII 3.2, VaxiJen, ToxinPred, PEPFOLD 3.5, DINC, IEDB-Population coverage, MHCPred and JCat server. Most of these tools are based on modern innovative statistical algorithms like HMM, ANN, ML, etc. that help in better predictions of putative candidates for vaccine crafting. This innovative methodology is facile, cost-effective and time-efficient, which could facilitate designing of a vaccine against this virus.

Keywords: Docking; Epitope; Peptide; Simulation; Surface glycoprotein; Vaccine.

PubMed Disclaimer

Conflict of interest statement

Conflict of interestThe authors hereby declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Relative synonymous codon usage (RSCU) for coding sequence of surface glycoprotein of Orthohantavirus
Fig. 2
Fig. 2
1-log50k values plotted against epitope MIGLLSSRI and HLA alleles
Fig. 3
Fig. 3
Structural prediction-related aspects of Epitope obtained from surface glycoprotein of Hantavirus by deploying Pepfold-3.5 A MIGLLSSRI epitope structure view in PyMOL. B Probability plot obtained during structural prediction
Fig. 4
Fig. 4
Ramachandran plot analysis for screened Epitope MIGLLSSRI using MolProbity web server
Fig. 5
Fig. 5
Interaction analysis based on docking studies: graphical representation of Binding score, ACE value, and global energy for docked complexes
Fig. 6
Fig. 6
Best docking result for 1FV1-MIGLLSSRI obtained by DINC web server. A Ligand in binding pocket (Far view). B Ligand in binding pocket (zoom view). C Docked epitope or ligand on binding pocket visualized in PyMOL
Fig. 7
Fig. 7
Simulation results for docked complex 1FV1-MIGLLSSRI. A RMSD value for docked complex at 10 ns. B RMSF plot for all amino acid side chains
Fig. 8
Fig. 8
IEDB-population conservancy analysis of the selected epitope “MIGLLSSRI”

References

    1. Abdulla F, Nain Z, Hossain MM, Syed SB, Khan MSA, Adhikari UK. A comprehensive screening of the whole proteome of hantavirus and designing a multi-epitope subunit vaccine for cross-protection against hantavirus: structural vaccinology and immunoinformatics study. Microb Pathog. 2021;150:104705. doi: 10.1016/j.micpath.2020.104705. - DOI - PubMed
    1. Akhtar N, Joshi A, Singh B, Kaushik V. Immuno-Informatics quest against COVID-19/SARS-COV-2: determining putative T-cell epitopes for vaccine prediction. Infect Disord Drug Targets. 2020 doi: 10.2174/1871526520666200921154149. - DOI - PubMed
    1. Akhtar N, Joshi A, Kaushik V, Kumar M, Mannan MAU. In-silico design of a multivalent epitope-based vaccine against Candida auris. Microb Pathog. 2021;155:104879. doi: 10.1016/j.micpath.2021.104879. - DOI - PubMed
    1. Akhtar N, Joshi A, Singh J, Kaushik V. Design of a novel and potent multivalent epitope based human cytomegalovirus peptide vaccine: an immunoinformatics approach. J Mol Liq. 2021 doi: 10.1016/j.molliq.2021.116586. - DOI
    1. Ali M, Pandey RK, Khatoon N, Narula A, Mishra A, Prajapati VK. Exploring dengue genome to construct a multi-epitope-based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Sci Rep. 2017;7(1):1–13. doi: 10.1038/s41598-017-09199-w. - DOI - PMC - PubMed

LinkOut - more resources