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

Abstract

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.

Figure 1

A complete work flow of the study.

Figure 2

Core pan plot of K. aerogenes strains.

Figure 3

K. aerogenes strains phylogenetic tree.

Figure 4

(A) Shows the percentage of the total proteome, core proteome, redundant and non-redundant proteins. (B) Several proteins can be found in the extracellular, periplasmic, and extracellular membranes.

Figure 5

Illustration of the design of the multi-epitope vaccine construct.

Figure 6

A candidate vaccine construct comprises GPGPG linkers in pink color, subunits of cholera toxin B in cyan blue color, and forest green representing EAAAK linkers, as well as vaccine epitopes are represented by purple.

Figure 7

Structures of vaccines that have been mutated. Mutant structures have yellow bands which indicate the introduction of disulfide bonds.

Figure 8

Illustration of interaction with MHC-I (A), MHC-II (B) and TLR-4 (C) with the vaccine.

Figure 9

RMSD graph for analyzing simulations of trajectory.