Design of a Multi-epitope Vaccine Against Acinetobacter baumannii Using Immunoinformatics Approach

In silico design of a novel hybrid epitope-based antigen harboring highly exposed immunogenic peptides of BamA, OmpA, and Omp34 against Acinetobacter baumannii

Acinetobacter baumannii, is among the highest priority bacteria according to the WHO categorization which necessitate the exploration of alternative strategies such as vaccination. OmpA, BamA, and Omp34 are assigned as appropriate antigens to serve in vaccine development against this pathogen. Experimentally validated exposed epitopes of OmpA and Omp34 along with selected exposed epitopes predicted by an integrative in silico approach were represented by the barrel domain of BamA as a scaffold. Among the 8 external loops of BamA, 5 loops were replaced with selected loops of OmpA and Omp34. The designed antigen was analyzed regarding the physicochemical properties, antigenicity, epitope retrieval, topology, structure, and safety. BamA is a two-domain OMP with a 16-stranded barrel in which L4, L6, and L7 were the longest loops of BamA in order. The designed antigen consisted of 478 amino acids with antigen probability of 0.7793. The novel antigen was a 16-stranded barrel. No identical 8-meric peptides were found in the human proteome against the designed antigen sequence. The designed construct was safe regarding the allergenicity, toxicity, and human proteome reactivity. The designed antigen could develop higher protection against A. baumannii in comparison to either OmpA, BamA, or Omp34 alone.

Acinetobacter baumannii subunit vaccines: recent progress and challenges

Acinetobacter baumannii is a Gram-negative, opportunistic pathogen that causes nosocomial infection with a high mortality rate in immunocompromised individuals. With the frequent emergence of multidrug-resistant A. baumannii strains that have rapidly gained resistance to most antibiotics, an extensive search for an effective A. baumannii vaccine is ongoing. Over the decade, many subunit vaccine candidates were identified using reverse vaccinology and in vivo animal studies for validation. Nineteen subunit vaccine candidates with a wide range of efficacy, from 14% to 100% preclinical survival rates, were included in this review. This article provides an updated review of several outer membrane proteins (Omp) that emerged as vaccine candidates with great potential, including OmpA, Omp34, Omp22 and BamA, based on their high conservancy, antigenicity, and immune protection against A. baumannii infection. However, there is still no licenced A. baumannii vaccine currently due to several practical issues that have yet to be resolved, such as inconsistencies between validation studies, antigen variability and insolubility. Moving forward, much investigation and innovation are still required to tackle these challenges for the regulatory approval of an A. baumannii subunit vaccine, including standardisation of immunisation study parameters, improving antigen solubility and the incorporation of nucleic acid vaccine technology.

Predictions of Immunodominant Epitope Peptides From the AsaA Type VI Secretion System in Acinetobacter baumannii: A Computational Approach

Introduction Acinetobacter baumannii, designated as a priority pathogen by the World Health Organization (WHO), is responsible for recalcitrant infections in immunocompromised patients. The type VI secretion system (T6SS) is a class of macromolecular secretion machines, contributing to its virulence. The aim of this study is thus to predict the immune-dominant epitope peptides from the Acinetobacter T6SS-associated protein of A. baumannii (AsaA). Methods AsaA protein retrieval from the bacteria was carried out using computational platforms and the evaluation of antigenicity and allergenicity was performed. The T-cell epitopes of major histocompatibility complex class II binders were identified followed by molecular docking of the immune-dominant epitopes with human leukocyte antigen alleles using the ClusterPro server (https://cluspro.org/help.php). Additionally, the B-cell epitopes were predicted. Results Immune-informatic analysis showed immune-dominant peptides in the most favored regions with promising interactions with HLA alleles DP, DQ, DR, and toll-like receptor showing high binding capacity. Conclusion In the present investigation, epitope 1 (LILFLIGNY) was found to be a promising candidate for the synthesis of vaccines. However, it requires further experimentation for its immunological memory and response.

Deciphering the Immunogenicity of Monkeypox Proteins for Designing the Potential mRNA Vaccine

The Monkeypox virus (MPXV), an orthopox virus, is responsible for monkeypox in humans, a zoonotic disease similar to smallpox. This infection first appeared in the 1970s in humans and then in 2003, after which it kept on spreading all around the world. To date, various antivirals have been used to cure this disease, but now, MPXV has developed resistance against these, thus increasing the need for an alternative cure for this deadly disease. In this study, we devised a reverse vaccinology approach against MPXV using a messenger RNA (mRNA) vaccine by pinning down the antigenic proteins of this virus. By using bioinformatic tools, we predicted prospective immunogenic B and T lymphocyte epitopes. Based on cytokine inducibility score, nonallergenicity, nontoxicity, antigenicity, and conservancy, the final epitopes were selected. Our analysis revealed the stable structure of the mRNA vaccine and its efficient expression in host cells. Furthermore, strong interactions were demonstrated with toll-like receptors 2 (TLR2) and 4 (TLR4) according to the molecular dynamic simulation studies. The in silico immune simulation analyses revealed an overall increase in the immune responses following repeated exposure to the designed vaccine. Based on our findings, the vaccine candidate designed in this study has the potential to be tested as a promising novel mRNA therapeutic vaccine against MPXV infection.

A comprehensive immunoinformatic analysis of chitin deacetylase's and MP88 for designing multi-epitope vaccines against Cryptococcus neoformans

Cryptococcus neoformans causes life-threatening pneumonia and meningitis and is regarded as one of the leading killers of immunocompromised individuals. There is currently no vaccine against this pathogen. Recently, WHO placed it at the top among the critical priority groups in the fungal priority pathogens to accelerate the development of effective treatments. Numerous studies suggested the potential of subunit vaccines to overcome the challenges associated with live and inactivated whole-cell vaccines. Therefore, this study exploited integrated reverse vaccinology and immunoinformatic approach to construct and characterize multi-epitope vaccines targeting chitin deacetylases (Cda1, Cda2, Cda3) and MP88 of C. neoformans. 4 CTL, 8 HTL and 6 B cell epitopes were fused with different adjuvants and appropriate linkers to design two multi-epitope vaccines (VC1 and VC2). Both chimeric constructs were predicted to be highly antigenic, non-allergenic, non-toxic, soluble and had satisfactory physicochemical properties. Molecular docking and binding free energy calculation revealed strong binding interactions between vaccine constructs and human TLRs (TLR-2 and TLR-4). Classical MD Simulation and Normal mode analysis verified the stability of the vaccine-TLR complex in the biological environment. Codon adaptation, cloning and in silico expression suggested the efficient expression of recombinant vaccine proteins in E. coli. Both candidates also generated robust immune profiles comprising innate, adaptive and humoral immune responses. Taken together, experimental validations of our findings through extensive in vitro and in vivo testing might provide an effective vaccine for prophylactic control of C. neoformans.Communicated by Ramaswamy H. Sarma.

In silico analysis of the conserved surface-exposed epitopes to design novel multiepitope peptide vaccine for all variants of the SARS-CoV-2

Recently the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pervasive threat to generic health. The SARS-CoV-2 spike (S) glycoprotein plays a fundamental role in binds and fusion to the angiotensin-converting enzyme 2 (ACE2). The multi-epitope peptide vaccines would be able to elicit both long-lasting humoral and cellular immune responses, resulting the eliminating SARS-CoV-2 infections as asymptomatic patients are in large numbers. Recently, the omicron variant of the SARS-CoV-2 became a variant of concern that contained just 15-point mutations in the receptor-binding domain of the spike protein. In order to eliminate new evidence on coronavirus variants of concern detected through epidemic intelligence, the conserved epitopes of the receptor-binding domain (RBD) and spike cleavage site is the most probable target for vaccine development to inducing binds and fusion inhibitors neutralizing antibodies respectively. In this study, we utilized bioinformatics tools for identifying and analyzing the spike (S) glycoprotein sequence, e.g. the prediction of the potential linear B-cell epitopes, B-cell multi‑epitope design, secondary and tertiary structures, physicochemical properties, solubility, antigenicity, allergenicity, the molecular docking and molecular dynamics simulation for the promising vaccine candidate against all variant of concern of SARS-CoV-2. Among the epitopes of the RBD region are surface-exposed epitopes SVYAWNRKRISNCV and ATRFASVYAWNRKR as the conserved sequences in all variants of concern can be a good candidate to induce an immune response.Communicated by Ramaswamy H. Sarma.

Two peptides derivate from Acinetobacter baumannii outer membrane protein K as vaccine candidates: a comprehensive in silico study

BACKGROUND

The lack of appropriate vaccines is an obstacle to the effective management of A. baumannii infections. Peptide vaccines offer an attractive and promising preventive strategy against A. baumannii.

OBJECTIVE

In this study, we identified specific T cell epitopes of A. baumannii outer membrane protein K (OMPK) using comprehensive bioinformatics and detailed molecular docking analysis.

METHODS

Both class-I and class-II T cell epitopes of A. baumannii OMPK were predicted by three tools namely IEDB, SYFPEITHI, and ProPred. The predicted epitopes were shortlisted based on several analyses including prediction scoring, clustering, exclusion of human similarity, considering immunogenicity and cytokine production, and removal of toxic and/or allergen epitopes. The epitopic peptides with high prediction scores and appropriate properties containing both class-I and class-II T cell epitopes were selected. Two of these class I/II epitopic peptides were chosen for molecular docking studies and assessing their physicochemical properties as vaccine candidates.

RESULTS

The results showed many T-cell epitopes of OMPK that could be evaluated for possible immunogenicity. Two of these epitopes (containing both class-I and II epitopes) had high prediction scores, were predicted by several tools, attached to several HLAs, and had the best docking score. They had different physicochemical properties and were conserved among Acinetobacter species.

DISCUSSION

We identified the A. baumannii OMPK high immunogenic class-I and class-II T cell epitopes and introduced two promising high immunogenic peptides as vaccine candidates. It is recommended to perform in vitro/in vivo investigation of these peptides to determine their true efficacy and efficiency.

Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine against Klebsiella pneumoniae and Pseudomonas aeruginosa coinfection

Introduction: Klebsiella pneumoniae (K. pneumoniae) and Pseudomonas aeruginosa (P. aeruginosa) are the most common Gram-negative bacteria associated with pneumonia and coinfecting the same patient. Despite their high virulence, there is no effective vaccine against them. Methods: In the current study, the screening of several proteins from both pathogens highlighted FepA and OmpK35 for K. pneumonia in addition to HasR and OprF from P. aeruginosa as promising candidates for epitope mapping. Those four proteins were linked to form a multitope vaccine, that was formulated with a suitable adjuvant, and PADRE peptides to finalize the multitope vaccine construct. The final vaccine's physicochemical features, antigenicity, toxicity, allergenicity, and solubility were evaluated for use in humans. Results: The output of the computational analysis revealed that the designed multitope construct has passed these assessments with satisfactory scores where, as the last stage, we performed a molecular docking study between the potential vaccine construct and K. pneumonia associated immune receptors, TLR4 and TLR2, showing affinitive to both targets with preferentiality for the TLR4 receptor protein. Validation of the docking studies has proceeded through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for K. pneumoniae and P. aeruginosa coinfection. Here, we describe the approach for the design and assessment of our potential vaccine.

Promising Acinetobacter baumannii Vaccine Candidates and Drug Targets in Recent Years

In parallel to the uncontrolled use of antibiotics, the emergence of multidrug-resistant bacteria, like Acinetobacter baumannii, has posed a severe threat. A. baumannii predominates in the nosocomial setting due to its ability to persist in hospitals and survive antibiotic treatment, thereby eventually leading to an increasing prevalence and mortality due to its infection. With the increasing spectra of drug resistance and the incessant collapse of newly discovered antibiotics, new therapeutic countermeasures have been in high demand. Hence, recent research has shown favouritism towards the long-term solution of designing vaccines. Therefore, being a realistic alternative strategy to combat this pathogen, anti-A. Baumannii vaccines research has continued unearthing various antigens with variable results over the last decade. Again, other approaches, including pan-genomics, subtractive proteomics, and reverse vaccination strategies, have shown promise for identifying promiscuous core vaccine candidates that resulted in chimeric vaccine constructs. In addition, the integration of basic knowledge of the pathobiology of this drug-resistant bacteria has also facilitated the development of effective multiantigen vaccines. As opposed to the conventional trial-and-error approach, incorporating the in silico methods in recent studies, particularly network analysis, has manifested a great promise in unearthing novel vaccine candidates from the A. baumannii proteome. Some studies have used multiple A. baumannii data sources to build the co-functional networks and analyze them by k-shell decomposition. Additionally, Whole Genomic Protein Interactome (GPIN) analysis has utilized a rational approach for identifying essential proteins and presenting them as vaccines effective enough to combat the deadly pathogenic threats posed by A. baumannii. Others have identified multiple immune nodes using network-based centrality measurements for synergistic antigen combinations for different vaccination strategies. Protein-protein interactions have also been inferenced utilizing structural approaches, such as molecular docking and molecular dynamics simulation. Similar workflows and technologies were employed to unveil novel A. baumannii drug targets, with a similar trend in the increasing influx of in silico techniques. This review integrates the latest knowledge on the development of A. baumannii vaccines while highlighting the in silico methods as the future of such exploratory research. In parallel, we also briefly summarize recent advancements in A. baumannii drug target research.