Subtractive Proteomics and Reverse Vaccinology Strategies for Designing a Multiepitope Vaccine Targeting Membrane Proteins of Klebsiella pneumoniae

Exploring the journey: A comprehensive review of vaccine development against Klebsiella pneumoniae

Klebsiella pneumoniae, a prominent nosocomial pathogen, poses a critical global health threat due to its multidrug-resistant (MDR) and hypervirulent strains. This comprehensive review focuses into the complex approaches undertaken in the development of vaccines against K. pneumoniae. Traditional methods, such as whole-cell and ribosomal-based vaccines, are compared with modern strategies, including DNA and mRNA vaccines, and extracellular vesicles (EVs), among others. Each method presents unique advantages and challenges, emphasising the complexity of developing an effective vaccine against this pathogen. Significant advancements in computational tools and artificial intelligence (AI) have revolutionised antigen identification and vaccine design, enhancing the precision and efficiency of developing multiepitope-based vaccines. The review also highlights the potential of glycomics and immunoinformatics in identifying key antigenic components and elucidating immune evasion mechanisms employed by K. pneumoniae. Despite progress, challenges remain in ensuring the safety, efficacy, and manufacturability of these vaccines. Notably, EVs demonstrate promise due to their intrinsic adjuvant properties and ability to elicit robust immune responses, although concerns regarding inflammation and antigen variability persist. This review provides a critical overview of the current landscape of K. pneumoniae vaccine development, stressing the need for continued innovation and interdisciplinary collaboration to address this pressing public health issue. The integration of advanced computational methods and AI holds the potential to accelerate the development of effective immunotherapies, paving the way for novel vaccines against MDR K. pneumoniae.

Computational strategies in Klebsiella pneumoniae vaccine design: navigating the landscape of in silico insights

The emergence of multidrug-resistant Klebsiella pneumoniae poses a grave threat to global public health, necessitating urgent strategies for vaccine development. In this context, computational tools have emerged as indispensable assets, offering unprecedented insights into klebsiellal biology and facilitating the design of effective vaccines. Here, a review of the application of computational methods in the development of K. pneumoniae vaccines is presented, elucidating the transformative impact of in silico approaches. Through a systematic exploration of bioinformatics, structural biology, and immunoinformatics techniques, the complex landscape of K. pneumoniae pathogenesis and antigenicity was unravelled. Key insights into virulence factors, antigen discovery, and immune response mechanisms are discussed, highlighting the pivotal role of computational tools in accelerating vaccine development efforts. Advancements in epitope prediction, antigen selection, and vaccine design optimisation are examined, highlighting the potential of in silico approaches to update vaccine development pipelines. Furthermore, challenges and future directions in leveraging computational tools to combat K. pneumoniae are discussed, emphasizing the importance of multidisciplinary collaboration and data integration. This review provides a comprehensive overview of the current state of computational contributions to K. pneumoniae vaccine development, offering insights into innovative strategies for addressing this urgent global health challenge.

Investigation of Peptidoglycan-Associated Lipoprotein of Acinetobacter baumannii and Its Interaction with Fibronectin To Find Its Therapeutic Potential

Acinetobacter baumannii causes hospital-acquired infections and is responsible for high mortality and morbidity. The interaction of this bacterium with the host is critical in bacterial pathogenesis and infection. Here, we report the interaction of peptidoglycan-associated lipoprotein (PAL) of A. baumannii with host fibronectin (FN) to find its therapeutic potential. The proteome of A. baumannii was explored in the host-pathogen interaction database to filter out the PAL of the bacterial outer membrane that interacts with the host's FN protein. This interaction was confirmed experimentally using purified recombinant PAL and pure FN protein. To investigate the pleiotropic role of PAL protein, different biochemical assays using wild-type PAL and PAL mutants were performed. The result showed that PAL mediates bacterial pathogenesis, adherence, and invasion in host pulmonary epithelial cells and has a role in the biofilm formation, bacterial motility, and membrane integrity of bacteria. All of the results suggest that PAL's interaction with FN plays a vital role in host-cell interaction. In addition, the PAL protein also interacts with Toll-like receptor 2 and MARCO receptor, which suggests the role of PAL protein in innate immune responses. We have also investigated the therapeutic potential of this protein for vaccine and therapeutic design. Using reverse vaccinology, PAL's potential epitopes were filtered out that exhibit binding potential with host major histocompatibility complex class I (MHC-I), MHC-II, and B cells, suggesting that PAL protein is a potential vaccine target. The immune simulation showed that PAL protein could elevate innate and adaptive immune response with the generation of memory cells and would have subsequent potential to eliminate bacterial infection. Therefore, the present study highlights the interaction ability of a novel host-pathogen interacting partner (PAL-FN) and uncovers its therapeutic potential to combat infection caused by A. baumannii.

Reverse vaccinology approach to design a vaccine targeting membrane lipoproteins of Salmonella typhi

Typhoid fever caused by Salmonella is one of the major health issues worldwide, resulting in millions of cases and has very high rates of morbidities. The therapeutic approaches need to be updated for the effective elimination of the bacterial pathogen. The designing of the multiepitope vaccine against Salmonella using comparative proteomics and reverse vaccinology has covered up all the epitopes that induce sufficient immune responses in the host body. Out of the 4293 proteins, 15 outer membrane proteins have been selected based on their antigenicity, low transmembrane helix (<1), and virulence-associated factors. With the help of the reverse vaccinology approach, the epitopes of MHC Class I, Class II, and B-cell with antigenic, low toxicity, and that have the potential to generate immunogenic response have been identified. Based on the comparative analysis of all the epitopes, a multiepitope-based construct has been designed. Based on physicochemical properties and docking scores for HLA and TLR4, the VC5 construct has been selected, and the molecular dynamic simulation studies have confirmed their interaction. The dissociation constant of the VC5 and TLR4 was found to be 3.1 x 10^-9. Different immune cell activation has been analyzed, representing the potentiality of the VC5 construct as an effective vaccine target. In silico cloning of VC5 in pET28a has also been performed, which requires experimental validation. Therefore, the present study designs a multi-epitope vaccine VC5 targeted to the membrane lipoproteins of Salmonella typhi.Communicated by Ramaswamy H. Sarma.

Reverse vaccinology approach for multi-epitope centered vaccine design against delta variant of the SARS-CoV-2

The ongoing COVID-19 outbreak, initially identified in Wuhan, China, has impacted people all over the globe and new variants of concern continue to threaten hundreds of thousands of people. The delta variant (first reported in India) is currently classified as one of the most contagious variants of SARS-CoV-2. It is estimated that the transmission rate of delta variant is 225% times faster than the alpha variant, and it is causing havoc worldwide (especially in the USA, UK, and South Asia). The mutations found in the spike protein of delta variant make it more infective than other variants in addition to ruining the global efficacy of available vaccines. In the current study, an in silico reverse vaccinology approach was applied for multi-epitope vaccine construction against the spike protein of delta variant, which could induce an immune response against COVID-19 infection. Non-toxic, highly conserved, non-allergenic and highly antigenic B-cell, HTL, and CTL epitopes were identified to minimize adverse effects and maximize the efficacy of chimeric vaccines that could be developed from these epitopes. Finally, V1 vaccine construct model was shortlisted and 3D modeling was performed by refinement, docking against HLAs and TLR4 protein, simulation and in silico expression. In silico evaluation showed that the designed chimeric vaccine could elicit an immune response (i.e., cell-mediated and humoral) identified through immune simulation. This study could add to the efforts of overcoming global burden of COVID-19 particularly the variants of concern.

Modern vaccine development via reverse vaccinology to combat antimicrobial resistance

With the continuous evolution of bacteria, the global antimicrobial resistance health threat is causing millions of deaths yearly. While depending on antibiotics as a primary treatment has its merits, there are no effective alternatives thus far in the pharmaceutical market against some drug-resistant bacteria. In recent years, vaccinology has become a key topic in scientific research. Combining with the growth of technology, vaccine research is seeing a new light where the process is made faster and more efficient. Although less discussed, bacterial vaccine is a feasible strategy to combat antimicrobial resistance. Some vaccines have shown promising results with good efficacy against numerous multidrug-resistant strains of bacteria. In this review, we aim to discuss the findings from studies utilizing reverse vaccinology for vaccine development against some multidrug-resistant bacteria, as well as provide a summary of multi-year bacterial vaccine studies in clinical trials. The advantages of reverse vaccinology in the generation of new bacterial vaccines are also highlighted. Meanwhile, the limitations and future prospects of bacterial vaccine concludes this review.

Immunoinformatic approach for the construction of multi-epitopes vaccine against omicron COVID-19 variant

The newly discovered SARS-CoV-2 Omicron variant B.1.1.529 is a Variant of Concern (VOC) announced by the World Health Organization (WHO). It's becoming increasingly difficult to keep these variants from spreading over the planet. The fifth wave has begun in several countries because of Omicron variant, and it is posing a threat to human civilization. As a result, we need effective vaccination that can tackle Omicron SARS-CoV-2 variants that are bound to emerge. Therefore, the current study is an initiative to design a peptide-based chimeric vaccine that may potentially battle SARS-CoV-2 Omicron variant. As a result, the most relevant epitopes present in the mutagenic areas of Omicron spike protein were identified using a set of computational tools and immunoinformatic techniques to uncover common MHC-1, MHC-II, and B cell epitopes that may have the ability to influence the host immune mechanism. A final of three epitopes from CD8+ T-cell, CD4+ T-cell epitopes, and B-cell were shortlisted from spike protein, and that are highly antigenic, IFN-γ inducer, as well as overlapping for the construction of twelve vaccine models. As a result, the antigenic epitopes were coupled with a flexible and stable peptide linker, and the adjuvant was added at the N-terminal end to create a unique vaccine candidate. The structure of a 3D vaccine candidate was refined, and its quality was assessed by using web servers. However, the applied immunoinformatic study along with the molecular docking and simulation of 12 modeled vaccines constructs against six distinct HLAs, and TLRs (TLR2, and TLR4) complexes revealed that the V1 construct was non-allergenic, non-toxic, highly immunogenic, antigenic, and most stable. The vaccine candidate's stability was confirmed by molecular dynamics investigations. Finally, we studied the expression of the suggested vaccination using codon optimization and in-silico cloning. The current study proposed V1 Multi-Epitope Vaccine (MEV) as a significant vaccine candidate that may help the scientific community to treat SARS-CoV-2 infections.

A Novel Multi-Epitope Edible Vaccine Candidate for Newcastle Disease Virus: In Silico Approach

Background

Newcastle disease, is one of the most important illnesses in the aviculture industry which shows a constant threat. In this case, the vaccine could be considered an important solution to prevent and control this disease. So, the development of a new and more effective vaccine against Newcastle disease is an urgent need. Immune informatics is an important field that provides insight into the experimental procedure and could facilitate the analysis of large amounts of immunological data generated by experimental research and help to design a new vaccine candidate.

Objectives

This study is aimed at bioinformatics to investigate and select the most immunogenic and conserved epitopes derived from F and HN glycoproteins, which play a key role in pathogenesis and immunity. This strategy could cover a wide range of Newcastle disease viruses.

Materials and Method

For expression in both E. coli (as an injectable recombinant vaccine candidate) and maize plant (as an edible vaccine candidate) host, two constructs were designed and analyzed separately. Furthermore, the role of LTB as an effective bio-adjuvant for general eliciting of the immune system and simultaneous expressions with those two antigens was evaluated. Hence, here a multimeric recombinant protein with the abbreviation LHN2F from the highly immunogenic part of HN, F and LTB proteins were designed. The synthetic construct was analyzed based on different bioinformatics tools.

Results

The proper immunogenicity and stability of this multimeric fusion protein have been shown by immunoinformatic methods from various servers. To confirm the function of the designed protein, the final molecule was docked to chicken MHC class I using the Pyrex-python 0.8 program. the results of Immune Epitope analysis were confirmed by the docking results between protein and receptor.

Conclusions

‎The results of structural and immunological computational studies proposed that the protein deduced from this novel construct could act as a vaccine candidate for Newcastle disease virus‎ control and prophylactic.

An integrated in silico based subtractive genomics and reverse vaccinology approach for the identification of novel vaccine candidate and chimeric vaccine against XDR Salmonella typhi H58

Salmonella typhi is notorious for causing enteric fever which is also known as typhoid fever. It emerged as an extreme drug resistant strain that requires urgent attention to prevent its global spread. Statistically, about 11-17 million typhoid illnesses are reported worldwide annually. The only alternative approach for the control of this illness is proper vaccination. However, available typhoid vaccine has certain limitations such as poor long-term efficacy, and non-recommendation for below 6 years children, which opens the avenues for designing new vaccines to overcome such limitations. Computational-based reverse vaccinology along with subtractive genomics analysis is one of the robust approaches used for the prioritization of vaccine candidates through direct screening of genome sequence assemblies. In the current study, we have successfully designed a peptide-based novel antigen chimeric vaccine candidate against the XDR strain of S. typhi H58. The pipeline revealed four peptides from WP_001176621.1 i.e., peptidoglycan-associated lipoprotein Pal and two peptides from WP_000747548.1 i.e., OmpA family lipoprotein as promising target for the induction of immune response against S. typhi. The six epitopes from both proteins were found as immunogenic, antigenic, virulent, highly conserved, nontoxic, and non-allergenic among whole Salmonella H58 proteome. Furthermore, the binding interaction between a chimeric vaccine and human population alleles was unveiled through structure-based studies. So far, these proteins have never been characterized as vaccine targets against S. typhi. The current study proposed that construct V2 could be a significant vaccine candidate against S. typhi H58. However, to ascertain this, future experimental holistic studies are recommended as follow-up.

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

Klebsiella pneumoniae is a Gram-negative pathogen of clinical relevance, which can provoke serious urinary and blood infections and pneumonia. This bacterium is a major public health threat due to its resistance to several antibiotic classes. Using a reverse vaccinology approach, 7 potential antigens were identified, of which 4 were present in most of the sequences of Italian carbapenem-resistant K. pneumoniae clinical isolates. Bioinformatics tools demonstrated the antigenic potential of these bacterial proteins and allowed for the identification of T and B cell epitopes. This led to a rational design and in silico characterization of a multiepitope vaccine against carbapenem-resistant K. pneumoniae strains. As adjuvant, the mycobacterial heparin-binding hemagglutinin adhesin (HBHA), which is a Toll-like receptor 4 (TLR-4) agonist, was included, to increase the immunogenicity of the construct. The multiepitope vaccine candidate was analyzed by bioinformatics tools to assess its antigenicity, solubility, allergenicity, toxicity, physical and chemical parameters, and secondary and tertiary structures. Molecular docking binding energies to TLR-2 and TLR-4, two important innate immunity receptors involved in the immune response against K. pneumoniae infections, and molecular dynamics simulations of such complexes supported active interactions. A codon optimized multiepitope sequence cloning strategy is proposed, for production of recombinant vaccine in classical bacterial vectors. Finally, a 3 dose-immunization simulation with the multiepitope construct induced both cellular and humoral immune responses. These results suggest that this multiepitope construct has potential as a vaccination strategy against carbapenem-resistant K. pneumoniae and deserves further validation.

Subtractive Proteomics and Immuno-informatics Approaches for Multi-peptide Vaccine Prediction Against Klebsiella oxytoca and Validation Through In Silico Expression

Klebsiella oxytoca is a gram-negative bacterium. It is opportunistic in nature and causes hospital acquired infections. Subtractive proteomics and reverse vaccinology approaches were employed to screen out the best proteins for vaccine designing. Whole proteome of K. oxytoca strain ATCC 8724, consisting of 5483 proteins, was used for designing the vaccine. Total 1670 cytotoxic T lymphocyte (CTL) epitope were predicted through NetCTL while 1270 helper T lymphocyte (HTL) epitopes were predicted through IEDB server. The epitopes were screened for non-toxicity, allergenicity, antigenicity and water solubility. After epitope screening 300 CTL and 250 HTL epitopes were submitted to IFN-γ epitope server to predict their Interferon-γ induction response. The selected IFN-γ positive epitopes were tested for their binding affinity with MHCI-DRB1 by MHCPred. The 15 CTL and 13 HTL epitopes were joined by linkers AAY and GPGPG respectively in vaccine construct. Chain C of Pam3CSK4 (PDB ID; 2Z7X) was linked to the vaccine construct as an adjuvant. A 450aa long vaccine construct was submitted to I-TASSER server for 3D structure prediction. Thirteen Linear B cells were predicted by ABCPred server and 10 sets of discontinues epitopes for 3D vaccine structure were predicted by DiscoTope server. The modeled 3D vaccine construct was docked with human Toll-like receptor 2 (PDB ID: 6NIG) by PatchDock. The docked complexes were refined by FireDock. The selected docked complex showed five hydrogen bonds and one salt bridge. The vaccine sequence was reverse transcribed to get nucleotide sequence for In silico cloning. The reverse transcribed sequence strand was cloned in pET28a(+) expression vector. A clone containing 6586 bp was constructed including the 450 bp of query gene sequence.

Prioritization of potential vaccine candidates and designing a multiepitope-based subunit vaccine against multidrug-resistant Salmonella Typhi str. CT18: A subtractive proteomics and immunoinformatics approach

Salmonella enterica serovar Typhi (S. Typhi), a causative agent of typhoid fever, is a Gram-negative, human-restricted pathogen that causes significant morbidity and mortality, particularly in developing countries. The currently available typhoid vaccines are not recommended to children below six years of age and have poor long-term efficacy. Due to these limitations and the emerging threat of multidrug-resistance (MDR) strains, the development of a new vaccine is urgently needed. The present study aims to design a multiepitope-based subunit vaccine (MESV) against MDR S. Typhi str. CT18 using a computational-based approach comprising subtractive proteomics and immunoinformatics. Firstly, we investigated the proteome of S. Typhi str. CT18 using subtractive proteomics and identified twelve essential, virulent, host non-homologous, and antigenic outer membrane proteins (OMPs) as potential vaccine candidates with low transmembrane helices (≤1) and molecular weight (≤110 kDa). The OMPs were mapped for cytotoxic T lymphocyte(CTL) epitopes, helper T lymphocyte (HTL) epitopes, and linear B lymphocyte (LBL) epitopes using various immunoinformatics tools and servers. A total of 6, 12, and 11 CTL, HTL, and LBL epitopes were shortlisted, respectively, based on their immunogenicity, antigenicity, allergenicity, toxicity, and hydropathicity potential. Four MESV constructs (MESVCs), MESVC-1, MESVC-2, MESVC-3, and MESVC-4, were designed by linking the CTL, HTL, and LBL epitopes with immune-modulating adjuvants, linkers, and PADRE (Pan HLA DR-binding epitope) sequences. The MESVCs were evaluated for their physicochemical properties, allergenicity, antigenicity, toxicity, and solubility potential to ensure their safety and immunogenic behavior. Secondary and tertiary structures of shortlisted MESVCs (MESVC-1, MESVC-3, and MESVC-4) were predicted, modeled, refined, validated, and then docked with various MHC I, MHC II, and TLR4/MD2 complex. Molecular dynamics (MD) simulation of the final selected MESVC-4 with TLR4/MD2 complex confirms its binding affinity and stability. Codon optimization and in silico cloning verified the translation efficiency and successful expression of MESVC-4 in E. coli str. K12. Finally, the efficiency of MESVC-4 to trigger an effective immune response was assessed by an in silico immune simulation. In conclusion, our findings show that the designed MESVC-4 can elicit humoral and cellular immune responses, implying that it may be used for prophylactic or therapeutic purposes. Therefore, it should be subjected to further experimental validations.