A Comprehensive Computer Aided Vaccine Design Approach to Propose a Multi-Epitopes Subunit Vaccine against Genus Klebsiella Using Pan-Genomics, Reverse Vaccinology, and Biophysical Techniques

Abstract

Klebsiella is a genus of nosocomial bacterial pathogens and is placed in the most critical list of World Health Organization (WHO) for development of novel therapeutics. The pathogens of the genus are associated with high mortality and morbidity. Owing to their strong resistance profile against different classes of antibiotics and nonavailability of a licensed vaccine, urgent efforts are required to develop a novel vaccine candidate that can tackle all pathogenic species of the Klebsiella genus. The present study aims to design a broad-spectrum vaccine against all species of the Klebsiella genus with objectives to identify the core proteome of pathogen species, prioritize potential core vaccine proteins, analyze immunoinformatics of the vaccine proteins, construct a multi-epitopes vaccine, and provide its biophysical analysis. Herein, we investigated all reference species of the genus to reveal their core proteome. The core proteins were then subjected to multiple reverse vaccinology checks that are mandatory for the prioritization of potential vaccine candidates. Two proteins (TonB-dependent siderophore receptor and siderophore enterobactin receptor FepA) were found to fulfill all vaccine parameters. Both these proteins harbor several potent B-cell-derived T-cell epitopes that are antigenic, nonallergic, nontoxic, virulent, water soluble, IFN-γ producer, and efficient binder of DRB*0101 allele. The selected epitopes were modeled into a multi-epitope peptide comprising linkers and Cholera Toxin B adjuvant. For docking with innate immune and MHC receptors and afterward molecular dynamics simulations and binding free energy analysis, the vaccine structure was modeled for tertiary structure and refined for structural errors. To assess the binding affinity and presentation of the designed vaccine construct, binding mode and interactions analysis were performed using molecular docking and molecular dynamics simulation techniques. These biophysical approaches illustrated the vaccine as a good binder to the immune receptors and revealed robust interactions energies. The vaccine sequence was further translated to nucleotide sequence and cloned into an appropriate vector for expressing it at high rate in Escherichia coli K12 strain. In addition, the vaccine was illustrated to generate a good level of primary, secondary, and tertiary immune responses, proving good immunogenicity of the vaccine. Based on the reported results, the vaccine can be a good candidate to be evaluated for effectiveness in wet laboratory validation studies.

Computational design and characterization of a multiepitope vaccine against carbapenemase-producing Klebsiella pneumoniae strains, derived from antigens identified through reverse vaccinology

“…This approach is based on in silico analysis to screen which proteins within a pathogen’s translated genome have the potential of possessing antigenic properties and be included in vaccination strategies. Reverse vaccinology was a crucial technique employed in the development of the Neisseria meningitidis serogroup B vaccine Bexsero [8] , and is being currently applied to several other pathogens [9] , [10] , [11] , [12] , [13] , [14] , [15] . Consequently, many tools were developed to help characterize antigens identified by reverse vaccinology, either in terms of properties or at structural level [8] , [9] , [14] , [16] .…”

“…Reverse vaccinology was a crucial technique employed in the development of the Neisseria meningitidis serogroup B vaccine Bexsero [8] , and is being currently applied to several other pathogens [9] , [10] , [11] , [12] , [13] , [14] , [15] . Consequently, many tools were developed to help characterize antigens identified by reverse vaccinology, either in terms of properties or at structural level [8] , [9] , [14] , [16] . Although these bioinformatics techniques allow screening of thousands of potential antigens and selection of the few most promising for further costly animal studies, reverse vaccinology and associated tools also have limitations.…”

“…In this work, novel, potential K. pneumoniae antigens with a high predominance in carbapenem-resistant clinical isolates were identified and characterized in silico, using a reverse vaccinology approach. Using several available bioinformatics tools ( Table S1 ) [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , a multiepitope vaccine containing T and B cell epitopes of the antigens was designed and characterized for its antigenic potential. We also assessed the molecular docking between our multiepitope vaccine and TLR-2 and TLR-4, due to their importance in K. pneumoniae infection [2] , [10] , [14] , [18] , [19] .…”

“…Using several available bioinformatics tools ( Table S1 ) [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , a multiepitope vaccine containing T and B cell epitopes of the antigens was designed and characterized for its antigenic potential. We also assessed the molecular docking between our multiepitope vaccine and TLR-2 and TLR-4, due to their importance in K. pneumoniae infection [2] , [10] , [14] , [18] , [19] . A cloning strategy to produce the suggested multiepitope approach is suggested, and an immunization simulation was also performed and analyzed.…”

Designing of a Novel Multi-Antigenic Epitope-Based Vaccine against E. hormaechei: An Intergraded Reverse Vaccinology and Immunoinformatics Approach

“…The net binding free energies for the vaccine and immune receptors were computed through MMPBSA.py module in AMBER20 [ 58 ]. The average values of these net binding free energies were assessed as the overall binding free energy of the systems.…”