BacScan: a novel genome-wide strategy for uncovering broadly immunogenic proteins in bacteria.

In response to the global threat posed by bacterial pathogens, which are the second leading cause of death worldwide, vaccine development is challenged by the diversity of bacterial serotypes and the lack of immunoprotection across serotypes. To address this, we introduce BacScan, a novel genome-wide technology for the rapid discovery of conserved highly immunogenic proteins (HIPs) across serotypes. Using bacterial-specific serum, BacScan combines phage display, immunoprecipitation, and next-generation sequencing to comprehensively identify all the HIPs in a single assay, thereby paving the way for the development of universally protective vaccines. Our validation of this technique with Streptococcus suis, a major pathogenic threat, led to the identification of 19 HIPs, eight of which conferred 20-100% protection against S. suis challenge in animal models. Remarkably, HIP 8455 induced complete immunity, making it an exemplary vaccine target. BacScan's adaptability to any bacterial pathogen positions it as a revolutionary tool that can expedite the development of vaccines with broad efficacy, thus playing a critical role in curbing bacterial transmission and slowing the march of antimicrobial resistance.

Targeting Plasmodium Life Cycle with Novel Parasite Ligands as Vaccine Antigens.

The WHO reported an estimated 249 million malaria cases and 608,000 malaria deaths in 85 countries in 2022. A total of 94% of malaria deaths occurred in Africa, 80% of which were children under 5. In other words, one child dies every minute from malaria. The RTS,S/AS01 malaria vaccine, which uses the Plasmodium falciparum circumsporozoite protein (CSP) to target sporozoite infection of the liver, achieved modest efficacy. The Malaria Vaccine Implementation Program (MVIP), coordinated by the WHO and completed at the end of 2023, found that immunization reduced mortality by only 13%. To further reduce malaria death, the development of a more effective malaria vaccine is a high priority. Three malaria vaccine targets being considered are the sporozoite liver infection (pre-erythrocytic stage), the merozoite red blood cell infection (asexual erythrocytic stage), and the gamete/zygote mosquito infection (sexual/transmission stage). These targets involve specific ligand-receptor interactions. However, most current malaria vaccine candidates that target two major parasite population bottlenecks, liver infection, and mosquito midgut infection, do not focus on such parasite ligands. Here, we evaluate the potential of newly identified parasite ligands with a phage peptide-display technique as novel malaria vaccine antigens.

The potential role of protein disulfide isomerases (PDIs) during parasitic infections: a focus on Leishmania spp.

Leishmaniasis is a group of vector-borne diseases caused by intracellular protozoan parasites belonging to the genus Leishmania. Leishmania parasites can employ different and numerous sophisticated strategies, including modulating host proteins, cell signaling, and cell responses by parasite proteins, to change the infected host conditions to favor the parasite persistence and induce pathogenesis. In this sense, protein disulfide isomerases (PDIs) have been described as crucial proteins that can be modulated during leishmaniasis and affect the pathogenesis process. The effect of modulated PDIs can be investigated in both aspects, parasite PDIs and infected host cell PDIs, during infection. The information concerning PDIs is not sufficient in parasitology; however, this study aimed to provide data regarding the biological functions of such crucial proteins in parasites with a focus on Leishmania spp. and their relevant effects on the pathogenesis process. Although there are no clinical trial vaccines and therapeutic approaches, highlighting this information might be fruitful for the development of novel strategies based on PDIs for the management of parasitic diseases, especially leishmaniasis.

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.

Recent trends in next generation immunoinformatics harnessed for universal coronavirus vaccine design.

The ongoing pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally devastated public health, the economies of many countries and quality of life universally. The recent emergence of immune-escaped variants and scenario of vaccinated individuals being infected has raised the global concerns about the effectiveness of the current available vaccines in transmission control and disease prevention. Given the high rate mutation of SARS-CoV-2, an efficacious vaccine targeting against multiple variants that contains virus-specific epitopes is desperately needed. An immunoinformatics approach is gaining traction in vaccine design and development due to the significant reduction in time and cost of immunogenicity studies and increasing reliability of the generated results. It can underpin the development of novel therapeutic methods and accelerate the design and production of peptide vaccines for infectious diseases. Structural proteins, particularly spike protein (S), along with other proteins have been studied intensively as promising coronavirus vaccine targets. Numbers of promising online immunological databases, tools and web servers have widely been employed for the design and development of next generation COVID-19 vaccines. This review highlights the role of immunoinformatics in identifying immunogenic peptides as potential vaccine targets, involving databases, and prediction and characterization of epitopes which can be harnessed for designing future coronavirus vaccines.

Immunoinformatic-guided designing of multi-epitope vaccine construct against Brucella Suis 1300.

Brucella suis mediates the transmission of brucellosis in humans and animals and a significant facultative zoonotic pathogen found in livestock. It has the capacity to survive and multiply in a phagocytic environment and to acquire resistance under hostile conditions thus becoming a threat globally. Antibiotic resistance is posing a substantial public health threat, hence there is an unmet and urgent clinical need for immune-based non-antibiotic methods to treat brucellosis. Hence, we aimed to explore the whole proteome of Brucella suis to predict antigenic proteins as a vaccine target and designed a novel chimeric vaccine (multi-epitope vaccine) through subtractive genomics-based reverse vaccinology approaches. The applied subsequent hierarchical shortlisting resulted in the identification of Multidrug efflux Resistance-nodulation-division (RND) transporter outer membrane subunit (gene BepC) that may act as a potential vaccine target. T-cell and B-cell epitopes have been predicted from target proteins using a number of immunoinformatic methods. Six MHC I, ten MHC II, and four B-cell epitopes were used to create a 324-amino-acid MEV construct, which was coupled with appropriate linkers and adjuvant. To boost the immunological response to the vaccine, the vaccine was combined with the TLR4 agonist HBHA protein. The MEV structure predicted was found to be highly antigenic, non-toxic, non-allergenic, flexible, stable, and soluble. To confirm the interactions with the receptors, a molecular docking simulation of the MEV was done using the human TLR4 (toll-like receptor 4) and HLAs. The stability and binding of the MEV-docked complexes with TLR4 were assessed using molecular dynamics (MD) simulation. Finally, MEV was reverse translated, its cDNA structure was evaluated, and then, in silico cloning into an E. coli expression host was conducted to promote maximum vaccine protein production with appropriate post-translational modifications. These comprehensive computer calculations backed up the efficacy of the suggested MEV in protecting against B. suis infections. However, more experimental validations are needed to adequately assess the vaccine candidate's potential. HIGHLIGHTS: • Subtractive genomic analysis and reverse vaccinology for the prioritization of novel vaccine target • Examination of chimeric vaccine in terms of allergenicity, antigenicity, MHC I, II binding efficacy, and structural-based studies • Molecular docking simulation method to rank based vaccine candidate and understand their binding modes.

Human Pulmonary Tuberculosis: Understanding the Immune Response in the Bronchoalveolar System.

Mycobacterium tuberculosis, the causal agent of one of the most devastating infectious diseases worldwide, can evade or modulate the host immune response and remain dormant for many years. In this review, we focus on identifying the local immune response induced in vivo by M. tuberculosis in the lungs of patients with active tuberculosis by analyzing data from untouched cells from bronchoalveolar lavage fluid (BALF) or exhaled breath condensate (EBC) samples. The most abundant resident cells in patients with active tuberculosis are macrophages and lymphocytes, which facilitate the recruitment of neutrophils. The cellular response is characterized by an inflammatory state and oxidative stress produced mainly by macrophages and T lymphocytes. In the alveolar microenvironment, the levels of cytokines such as interleukins (IL), chemokines, and matrix metalloproteinases (MMP) are increased compared with healthy patients. The production of cytokines such as interferon (IFN)-γ and IL-17 and specific immunoglobulin (Ig) A and G against M. tuberculosis indicate that the adaptive immune response is induced despite the presence of a chronic infection. The role of epithelial cells, the processing and presentation of antigens by macrophages and dendritic cells, as well as the role of tissue-resident memory T cells (Trm) for in situ vaccination remains to be understood.

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.

Evidence of episodic positive selection in Corynebacterium diphtheriae complex of species and its implementations in identification of drug and vaccine targets.

BACKGROUND: Within the pathogenic bacterial species Corynebacterium genus, six species that can produce diphtheria toxin (C. belfantii, C. diphtheriae, C. pseudotuberculosis, C. rouxii, C. silvaticum and C. ulcerans) form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets. METHODS: Forty genomes were sampled to represent species, subspecies or biovars of Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets. RESULTS: Nineteen genes were detected in the species C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.

Prevalence and conservation of ebp genes in Enterococcus faecalis originated from animals.

AIMS: The study aimed to investigate the prevalence and conservation of endocarditis and biofilm-associated pili (ebp) genes in Enterococcus faecalis originated from animals and the potential of developing Ebp into serological diagnostic and vaccine targets. METHODS AND RESULTS: In this work, we investigated the prevalence and conservation of ebp genes in 116 strains of E. faecalis originated from animals by using PCR and sequencing methods. The results demonstrated the presence of ebp genes (ebpA, ebpB and ebpC) in all 116 strains of E. faecalis, and their amino acid homology ranges from 96.6% to 100.0%. Moreover, the phylogenetic analysis of ebp genes in all 164 E. faecalis strains (including 48 reference strains) revealed that ebp genes show no significant correlation with species origins and regions of E. faecalis, indicating that ebp genes are conserved features in E. faecalis, even though it evolved under environmental pressures from various regions and origins. Given that EbpA1 as a part of the adhesion protein EbpA has immunogenicity, we further determined whether amino acid mutations have effects on the function and 3D structure of EbpA1. The results showed that two of the 26 mutations, at amino acids positions 178 and 387, had deleterious effects on the biological function of EbpA1 protein, while all mutations had no effect on the 3D structure or binding pockets of EbpA1 protein. CONCLUSIONS: This study suggests that ebp genes are prevalent and conserved in E. faecalis originated from diverse animal origins and regions. EbpA1 could be a potential target for serological diagnosis and vaccine development to prevent E. faecalis infection. SIGNIFICANCE AND IMPACT OF STUDY: The current study provides data to support further research on Ebp as a serological diagnostic and vaccine target against E. faecalis infection.

Reverse vaccinology approach for the identifications of potential vaccine candidates against Salmonella.

Salmonella is a leading cause of foodborne pathogen which causes intestinal and systemic diseases across the world. Vaccination is the most effective protection against Salmonella, but the identification and design of an effective broad-spectrum vaccine is still a great challenge, because of the multi-serotypes of Salmonella. Reverse vaccinology is a new tool to discovery and design vaccine antigens combining human immunology, structural biology and computational biology with microbial genomics. In this study, reverse vaccinology, an in-silico approach was established to screen appropriate immunogen targets by calculating the immunogenicity score of 583 non-redundant outer membrane and secreted proteins of Salmonella. Herein among 100 proteins identified with top-ranked scores, 15 representative antigens were selected randomly. Applying the sequence conservation test, four proteins (FliK, BcsZ, FhuA and FepA) remained as potential vaccine candidates for in vivo evaluation of immunogenicity and immunoprotection. All four candidates were capable to trigger the immune response and stimulate the production of antiserum in mice. Furthermore, top-ranked proteins including FliK and BcsZ provided wide antigenic coverage among the multi-serotype of Salmonella. The S. Typhimurium LT2 challenge model used in mice immunized with FliK and BcsZ showed a high relative percentage survival (RPS) of 52.74 % and 64.71 % respectively. In conclusion, this study constructed an in-silico pipeline able to successfully pre-screen the vaccine targets characterized by high immunogenicity and protective immunity. We show that reverse vaccinology allowed screening of appropriate broad-spectrum vaccines for Salmonella.

Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2).

BACKGROUND: The present pandemic COVID-19 is caused by SARS-CoV-2, a single-stranded positive-sense RNA virus from the Coronaviridae family. Due to a lack of antiviral drugs, vaccines against the virus are urgently required. METHODS: In this study, validated computational approaches were used to identify peptide-based epitopes from six structural proteins having antigenic properties. The Net-CTL 1.2 tool was used for the prediction of CD8+ T-cell epitopes, while the robust tools Bepi-Pred 2 and LBtope was employed for the identification of linear B-cell epitopes. Docking studies of the identified epitopes were performed using HADDOCK 2.4 and the structures were visualized by Discovery Studio and LigPlot+. Antigenicity, immunogenicity, conservancy, population coverage and allergenicity of the predicted epitopes were determined by the bioinformatics tools like VaxiJen v2.0 server, the Immune Epitope Database tools and AllerTOP v.2.0, AllergenFP 1.0 and ElliPro. RESULTS: The predicted T cell and linear B-cell epitopes were considered as prime vaccine targets in case they passed the requisite parameters like antigenicity, immunogenicity, conservancy, non-allergenicity and broad range of population coverage. Among the predicted CD8+ T cell epitopes, potential vaccine targets from surface glycoprotein were; YQPYRVVVL, PYRVVVLSF, GVYFASTEK, QLTPTWRVY, and those from ORF3a protein were LKKRWQLAL, HVTFFIYNK. Similarly, RFLYIIKLI, LTWICLLQF from membrane protein and three epitopes viz; SPRWYFYYL, TWLTYTGAI, KTFPPTEPK from nucleocapsid phosphoprotein were the superior vaccine targets observed in our study. The negative values of HADDOCK and Z scores obtained for the best cluster indicated the potential of the epitopes as suitable vaccine candidates. Analysis of the 3D and 2D interaction diagrams of best cluster produced by HADDOCK 2.4 displayed the binding interaction of leading T cell epitopes within the MHC-1 peptide binding clefts. On the other hand, among linear B cell epitopes the majority of potential vaccine targets were from nucleocapsid protein, viz; 59-HGKEDLKFPRGQGVPINTNSSPDDQIGYYRRATRRIRGGDGKMKDLS-105, 227-LNQLE SKMSGKGQQQQGQTVTKKSAAEASKKPRQKRTATK-266, 3-DNGPQNQRNAPRITFGGP-20, 29-GERSGARSKQRRPQGL-45. Two other prime vaccine targets, 370-NSASFSTFKCYGVSPTKLNDLCFTNV-395 and 260-AGAAAYYVGYLQPRT-274 were identified in the spike protein. The potential B-cell conformational epitopes were predicted on the basis of a higher protrusion index indicating greater solvent accessibility. These conformational epitopes were of various lengths and belonged to spike, ORF3a, membrane and nucleocapsid proteins. CONCLUSIONS: Taken together, eleven T cell epitopes, seven B cell linear epitopes and ten B cell conformational epitopes were identified from five structural proteins of SARS-CoV-2 using advanced computational tools. These potential vaccine candidates may provide important timely directives for an effective vaccine against SARS-CoV-2.

A Decade in Review: A Systematic Review of Universal Influenza Vaccines in Clinical Trials during the 2010 Decade.

On average, there are 3-5 million severe cases of influenza virus infections globally each year. Seasonal influenza vaccines provide limited protection against divergent influenza strains. Therefore, the development of a universal influenza vaccine is a top priority for the NIH. Here, we report a comprehensive summary of all universal influenza vaccines that were tested in clinical trials during the 2010-2019 decade. Of the 1597 studies found, 69 eligible clinical trials, which investigated 27 vaccines, were included in this review. Information from each trial was compiled for vaccine target, vaccine platform, adjuvant inclusion, clinical trial phase, and results. As we look forward, there are currently three vaccines in phase III clinical trials which could provide significant improvement over seasonal influenza vaccines. This systematic review of universal influenza vaccine clinical trials during the 2010-2019 decade provides an update on the progress towards an improved influenza vaccine.

Seasonal influenza vaccination in Kenya: an economic evaluation using dynamic transmission modelling.

BACKGROUND: There is substantial burden of seasonal influenza in Kenya, which led the government to consider introducing a national influenza vaccination programme. Given the cost implications of a nationwide programme, local economic evaluation data are needed to inform policy on the design and benefits of influenza vaccination. We set out to estimate the cost-effectiveness of seasonal influenza vaccination in Kenya. METHODS: We fitted an age-stratified dynamic transmission model to active surveillance data from patients with influenza from 2010 to 2018. Using a societal perspective, we developed a decision tree cost-effectiveness model and estimated the incremental cost-effectiveness ratio (ICER) per disability-adjusted life year (DALY) averted for three vaccine target groups: children 6-23 months (strategy I), 2-5 years (strategy II) and 6-14 years (strategy III) with either the Southern Hemisphere influenza vaccine (Strategy A) or Northern Hemisphere vaccine (Strategy B) or both (Strategy C: twice yearly vaccination campaigns, or Strategy D: year-round vaccination campaigns). We assessed cost-effectiveness by calculating incremental net monetary benefits (INMB) using a willingness-to-pay (WTP) threshold of 1-51% of the annual gross domestic product per capita ($17-$872). RESULTS: The mean number of infections across all ages was 2-15 million per year. When vaccination was well timed to influenza activity, the annual mean ICER per DALY averted for vaccinating children 6-23 months ranged between $749 and $1385 for strategy IA, $442 and $1877 for strategy IB, $678 and $4106 for strategy IC and $1147 and $7933 for strategy ID. For children 2-5 years, it ranged between $945 and $1573 for strategy IIA, $563 and $1869 for strategy IIB, $662 and $4085 for strategy IIC, and $1169 and $7897 for strategy IID. For children 6-14 years, it ranged between $923 and $3116 for strategy IIIA, $1005 and $2223 for strategy IIIB, $883 and $4727 for strategy IIIC and $1467 and $6813 for strategy IIID. Overall, no vaccination strategy was cost-effective at the minimum ($17) and median ($445) WTP thresholds. Vaccinating children 6-23 months once a year had the highest mean INMB value at $872 (WTP threshold upper limit); however, this strategy had very low probability of the highest net benefit. CONCLUSION: Vaccinating children 6-23 months once a year was the most favourable vaccination option; however, the strategy is unlikely to be cost-effective given the current WTP thresholds.

The use of proteomics for the identification of promising vaccine and diagnostic biomarkers in Plasmodium falciparum.

Plasmodium falciparum is the main cause of severe malaria in humans that can lead to death. There is growing evidence of drug-resistance in P. falciparum treatment, and the design of effective vaccines remains an ongoing strategy to control the disease. On the other hand, the recognition of specific diagnostic markers for P. falciparum can accelerate the diagnosis of this parasite in the early stages of infection. Therefore, the identification of novel antigenic proteins especially by proteomic tools is urgent for vaccination and diagnosis of P. falciparum. The proteome diversity of the life cycle stages of P. falciparum, the altered proteome of P. falciparum-infected human sera and altered proteins in P. falciparum-infected erythrocytes could be proposed as appropriate proteins for the aforementioned aims. Accordingly, this review highlights and proposes different proteins identified using proteomic approaches as promising markers in the diagnosis and vaccination of P. falciparum. It seems that most of the candidates identified in this study were able to elicit immune responses in the P. falciparum-infected hosts and they also played major roles in the life cycle, pathogenicity and key pathways of this parasite.

Immunoinformatics and Structural Analysis for Identification of Immunodominant Epitopes in SARS-CoV-2 as Potential Vaccine Targets.

A new coronavirus infection, COVID-19, has recently emerged, and has caused a global pandemic along with an international public health emergency. Currently, no licensed vaccines are available for COVID-19. The identification of immunodominant epitopes for both B- and T-cells that induce protective responses in the host is crucial for effective vaccine design. Computational prediction of potential epitopes might significantly reduce the time required to screen peptide libraries as part of emergent vaccine design. In our present study, we used an extensive immunoinformatics-based approach to predict conserved immunodominant epitopes from the proteome of SARS-CoV-2. Regions from SARS-CoV-2 protein sequences were defined as immunodominant, based on the following three criteria regarding B- and T-cell epitopes: (i) they were both mapped, (ii) they predicted protective antigens, and (iii) they were completely identical to experimentally validated epitopes of SARS-CoV. Further, structural and molecular docking analyses were performed in order to understand the binding interactions of the identified immunodominant epitopes with human major histocompatibility complexes (MHC). Our study provides a set of potential immunodominant epitopes that could enable the generation of both antibody- and cell-mediated immunity. This could contribute to developing peptide vaccine-based adaptive immunotherapy against SARS-CoV-2 infections and prevent future pandemic outbreaks.

Novel Target Exploration from Hypothetical Proteins of Klebsiella pneumoniae MGH 78578 Reveals a Protein Involved in Host-Pathogen Interaction.

The opportunistic pathogen Klebsiella pneumoniae is a causative agent of several hospital-acquired infections. It has become resistant to a wide range of currently available antibiotics, leading to high mortality rates among patients; this has further led to a demand for novel therapeutic intervention to treat such infections. Using a series of in silico analyses, the present study aims to explore novel drug/vaccine candidates from the hypothetical proteins of K. pneumoniae. A total of 540 proteins were found to be hypothetical in this organism. Analysis of these 540 hypothetical proteins revealed 30 pathogen-specific proteins essential for pathogen survival. A motifs/domain family analysis, similarity search against known proteins, gene ontology, and protein-protein interaction analysis of the shortlisted 30 proteins led to functional assignment for 17 proteins. They were mainly cataloged as enzymes, lipoproteins, stress-induced proteins, transporters, and other proteins (viz., two-component proteins, skeletal proteins and toxins). Among the annotated proteins, 16 proteins, located in the cytoplasm, periplasm, and inner membrane, were considered as potential drug targets, and one extracellular protein was considered as a vaccine candidate. A druggability analysis indicated that the identified 17 drug/vaccine candidates were "novel". Furthermore, a host-pathogen interaction analysis of these identified target candidates revealed a betaine/carnitine/choline transporters (BCCT) family protein showing interactions with five host proteins. Structure prediction and validation were carried out for this protein, which could aid in structure-based inhibitor design.

Identification of potential drug targets and vaccine candidates in Clostridium botulinum using subtractive genomics approach.

A subtractive genomic approach has been utilized for the identification of potential drug targets and vaccine candidates in Clostridium botulinum, the causative agent of flaccid paralysis in humans. The emergence of drug-resistant pathogenic strains has become a significant global public health threat. Treatment with antitoxin can target the neurotoxin at the extracellular level, however, can't converse the paralysis caused by botulism. Therefore, identification of drug targets and vaccine candidates in C. botulinum would be crucial to overcome drug resistance to existing antibiotic therapy. A total of 1729 crucial proteins, including chokepoint, virulence, plasmid and resistance proteins were mined and used for subtractive channel of analysis. This analysis disclosed 15 potential targets, which were non-similar to human, gut micro flora, and anti-targets in the host. The cellular localization of 6 targets was observed in the cytoplasm and might be used as a drug target, whereas 9 targets were localized in extracellular and membrane bound proteins and can be used as vaccine candidates. Furthermore, 4 targets were observed to be homologous to more than 75 pathogens and hence are considered as broad-spectrum antibiotic targets. The identified drug and vaccine targets in this study would be useful in the design and discovery of novel therapeutic compounds against botulism.

Immunogenic reactivity of recombinant PKF and AbOmpA proteins as serum resistance factors against sepsis of Acinetobacter baumannii.

Acinetobacter baumannii is considered as a major cause of nosocomial infection worldwide. Various vaccine formulations have been mostly studied based on secreted or surface-exposed proteins of A. baumannii in murine models. Serum resistance proteins are critical virulence factors in bloodstream infections. AbOmpA and PKF are two major factors involved in serum resistance and could be considered as promising vaccine targets. In this study IgG1, IgG2c, Total-IgG concentrations, survival rates and spleen bacterial loads were studied in C57/BL mice model according to PKF, AbOmpA and AbOmpA + PKF vaccine formulations. The findings showed significant raises of IgG2c and Total-IgG in all three vaccinated groups in comparison with the control group. Whereas, there were low concentrations of IgG1 in all immunization plans. Colony counts of mice spleen showed the bacterial load of PKF plan had the most decrease of bacterial load (DBL = 5 log10 CFU/g). Taken together, this evaluation indicated that PKF vaccination plan induced a polarized Th1 response and rendered an effective protection against bloodstream infection caused by A. baumannii.