Development of a submit candidate vaccine for the prevention of Dengue fever using immunoinformaics methods

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Abstract

The prediction of epitopes was carried out. The structural stability of the candidate vaccine was studied by the molecular dynamics method using the Gromacs-2023 software package. The results showed the preservation of the structural stability of all the studied subdomains. The final stage was the simulation of the cellular immune response using the C-IMMSIMM program. The results predict the ability of candidate vaccines to elicit both a vibrant primary and persistent secondary immune response.

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About the authors

A. A. Tulenev

National Research Center “Kurchatov Institute”

Author for correspondence.
Email: tiulenev.aa@phystech.edu
Russian Federation, Moscow

V. I. Timofeev

National Research Center “Kurchatov Institute”

Email: tiulenev.aa@phystech.edu
Russian Federation, Moscow

A. A. Cherniavsky

National Research Center “Kurchatov Institute”

Email: tiulenev.aa@phystech.edu
Russian Federation, Moscow

A. S. Ivanovsky

National Research Center “Kurchatov Institute”

Email: tiulenev.aa@phystech.edu
Russian Federation, Moscow

Y. V. Kordonskaya

National Research Center “Kurchatov Institute”

Email: tiulenev.aa@phystech.edu
Russian Federation, Moscow

Y. V. Pisarevsky

National Research Center “Kurchatov Institute”

Email: tiulenev.aa@phystech.edu
Russian Federation, Moscow

Y. A. Dyakova

National Research Center “Kurchatov Institute”

Email: tiulenev.aa@phystech.edu
Russian Federation, Moscow

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Supplementary files

Supplementary Files
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1. JATS XML
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2. Fig. 1. The location of the protein relative to the cell membrane; the numbers 1, 2 and 3 indicate the studied supramembrane domains.

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3. Fig. 2. Spatial structure of the first studied domain of the A0A6B7HXR6 protein (T-cell epitopes are highlighted in dark gray, B-cell epitopes are highlighted in light gray, the subdomain richest in epitopes is highlighted in black circle).

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4. Fig. 3. Spatial structure of the second studied domain of the A0A6B7HXR6 protein (T-cell epitopes are highlighted in dark gray, B-cell epitopes are highlighted in light gray, the subdomain richest in epitopes is highlighted in black circle).

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5. Fig. 4. Spatial structure of the third studied domain of the A0A6B7HXR6 protein (T-cell epitopes are highlighted in dark gray, B-cell epitopes are highlighted in light gray, the subdomain richest in epitopes is highlighted in black circle).

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6. Fig. 5. Spatial structure of the candidate vaccine (dark parts are epitopes, light parts are non-epitopes).

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7. Fig. 6. Standard deviation of candidate vaccine atoms during molecular dynamics simulation.

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8. Fig. 7. Root-mean-square fluctuation of amino acid residues of the vaccine candidate during molecular dynamics simulation.

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9. Fig. 8. Radius of gyration of the vaccine candidate during molecular dynamics simulation.

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10. Fig. 9.

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11. Fig. 9.

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12. Fig. 9. Immune response to a vaccine. Antibodies are classified by isotype (a). Concentration of cytokines and interleukins (b). D in the inset is a cytokine storm danger signal. Total number of B lymphocytes, memory cells and their division into isotypes (c). Number of B lymphocytes in blood plasma, divided into isotypes (d). Total number of T helper lymphocytes and memory cells (e). Total number of T regulatory lymphocytes, active cells and memory cells (e). Total number of macrophages, internalized, representing the major histocompatibility complex class II, active and resting macrophages (g).

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13. Supplement
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