Immunoinformatics design of multi-epitope peptide-based vaccine against Haemophilus influenzae strain using cell division protein

Abstract

Haemophilus influenzae is a pathogen that causes invasive bacterial infections in humans. The highest prevalence lies in both young children and adults. Generally, there are no vaccines available that target all the strains of Haemophilus influenzae. Hence, the purpose of this research is to employ bioinformatics and immunoinformatics approaches to design a Multi-Epitope Vaccine candidate employing the pathogenic cell division protein FtsN that specifically combat all the Haemophilus influenzae strains. The current research focuses on developing subunit vaccine in contrast to vaccines generated from the entire pathogen. This will be accomplished by combining multiple bioinformatics and immunoinformatics approaches. As a result, prospective T cells (helper T lymphocyte and cytotoxic T lymphocytes) and B cells epitopes were investigated. The human leukocyte antigen allele having strong associations with the antigenic and overlapping epitopes were chosen, with 70% of the total coverage of the world population. To construct a linked vaccine design, multiple linkers were used. To increase the immunogenic profile, an adjuvant was linked using EAAAK linker. The final vaccine construct with 149 amino acids was obtained after adjuvants and linkers were added. The developed Multi-Epitope Vaccine has a high antigenicity as well as viable physiochemical features. The 3D conformation was modeled and undergoes refinement and validation using bioinformatics methods. Furthermore, protein-protein molecular docking analysis was performed to predict the effective binding poses of Multi-Epitope Vaccine with the Toll-like receptor 4 protein. Besides, vaccine underwent the codon translational optimization and computational cloning to verify the reliability and proper Multi-Epitope Vaccine expression. In addition, it is necessary to conduct experiments and research in the laboratory to demonstrate that the vaccine that has been developed is immunogenic and protective.

Keywords: Bioinformatics; Cell division protein; Epitope; Haemophilus influenzae; Linkers.

Fig. 1

Research methodology employed to develop a subunit MEV vaccine against Hi

Fig. 2

SOPMA secondary structure prediction of FtsN protein. Yellow color bars indicate strands, pink bars are representing helices, and grey color lines are coils

Fig. 3

Prediction of FtsN 3D structure and its evaluation: A FtsN refined 3D structure, the cyan color represents the helices in the protein structure and red color represents the beta sheets whereas the pink color represents loops; B identification of favorable amino acid residues in FtsN protein

Fig. 4

HLA alleles population coverage analysis of FtsN epitopes according to regions

Fig. 5

Sequence overview of the MEV construction. It has 149 amino acids, including an adjuvant (shown in purple) connected to the N-terminus of MEV via the EAAAK linker (shown in green). The AAY linker (shown in blue) was utilized to connect the CTL epitopes, whereas the GPGPG linker (in pink) connects the HTL epitopes

Fig. 6

SOPMA secondary structure prediction analysis of the vaccine construct. Yellow colors are indicating strands, helices are shown in pink color, and grey color lines are representing coils

Fig. 7

The 3D structure of the MEV structure prediction and validation: A epitopes are shown in black color in the MEV construct. The adjuvant sequence is shown in green color, EAAAK linker sequence is shown in purple color, the AAY linkers are shown in red color, and the GPGPG linkers are shown in blue colors; B identification of favorable amino acid residues using Ramachandran plot analysis; C MEV refined conformation (alpha-helix are in cyan color, and loops are shown in pink color)

Fig. 8

CABS-flex 2.0 results: A cartoon representation of the top ten models; B residue contact map; C RMSF graph showing simulation-induced MEV residue variations

Fig. 9

Surface representation of the MEV. A Discontinuous B cell epitopes in MEV design are highlighted in red color; B linear B cell epitopes are colored red in MEV

Fig. 10

Molecular docking between the MEV and TLR4: cartoon representation of the docked TLR4–MEV complex. TLR4 is shown in orange–brown color and MEV is shown in cyan color

Fig. 11

A Interacting residues of MEV that interact with TLR4 are shown as a hot-pink color, whereas TLR4 residues that interact with MEV are shown as a green color stick representation. The hydrogen bonds are given as yellow dashed lines; B blue lines represent hydrogen bonds, red lines represent salt bridges, and orange lines represent other interactions. Different colored residues indicate amino acid properties (positive: blue color, negative: red color, aliphatic: grey color, aromatic: pink color, proline and glycine: orange color, and cystine residue: yellow color)

Fig. 12

Simulated immunological responses to MEV: A cytokine, interleukin production; B immunoglobulin synthesis and B cell isotypes after exposure to varied conditions