Quest for Novel Preventive and Therapeutic Options Against Multidrug-Resistant Pseudomonas aeruginosa

Abstract

Pseudomonas aeruginosa ( P. aeruginosa ) is a critical healthcare challenge due to its ability to cause persistent infections and the acquisition of antibiotic resistance mechanisms. Lack of preventive vaccines and rampant drug resistance phenomenon has rendered patients vulnerable. As new antimicrobials are in the preclinical stages of development, mining for the unexploited drug targets is also crucial. In the present study, we designed a B- and T-cell multi-epitope vaccine against P. aeruginosa using a subtractive proteomics and immunoinformatics approach. A total of five proteins were shortlisted based on essentiality, extracellular localization, virulence, antigenicity, pathway association, hydrophilicity, and low molecular weight. These include two outer membrane porins; OprF (P13794) and OprD (P32722), a protein activator precursor pra (G3XDA9), a probable outer membrane protein precursor PA1288 (Q9I456), and a conserved hypothetical protein PA4874 (Q9HUT9). These shortlisted proteins were further analyzed to identify immunogenic and antigenic B- and T-cell epitopes. The best scoring epitopes were then further subjected to the construction of a polypeptide multi-epitope vaccine and joined with cholera toxin B subunit adjuvant. The final chimeric construct was docked with TLR4 and confirmed by normal mode simulation studies. The designed B- and T-cell multi-epitope vaccine candidate is predicted immunogenic in nature and has shown strong interactions with TLR-4. Immune simulation predicted high-level production of B- and T-cell population and maximal expression was ensured in E. coli strain K12. The identified drug targets qualifying the screening criteria were: UDP-2-acetamido-2-deoxy-d-glucuronic acid 3-dehydrogenase WbpB (G3XD23), aspartate semialdehyde dehydrogenase (Q51344), 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (Q9HV71), 3-deoxy-D-manno-octulosonic-acid transferase (Q9HUH7), glycyl-tRNA synthetase alpha chain (Q9I7B7), riboflavin kinase/FAD synthase (Q9HVM3), aconitate hydratase 2 (Q9I2V5), probable glycosyltransferase WbpH (G3XD85) and UDP-3-O-[3-hydroxylauroyl] glucosamine N-acyltransferase (Q9HXY6). For druggability and pocketome analysis crystal and homology structures of these proteins were retrieved and developed. A sequence-based search was performed in different databases (ChEMBL, Drug Bank, PubChem and Pseudomonas database) for the availability of reported ligands and tested drugs for the screened targets. These predicted targets may provide a basis for the development of reliable antibacterial preventive and therapeutic options against P. aeruginosa . Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10255-3.

Improving Protection to Prevent Bacterial Infections: Preliminary Applications of Reverse Vaccinology against the Main Cystic Fibrosis Pathogens

“…Vaccine efficacy may be enhanced by building chimeric vaccines. Bioinformatic analysis further confirmed that these kinds of vaccines are effective and highly stable [ 67 , 68 , 69 ].…”

“…PA is classified as multi-drug resistant (MDR), characterized by a number of virulence factors and an adaptable genome, which will make the microorganism able to overlap the ongoing treatments. For this reason, the research for new antibiotics and antivirulence compounds is pursued simultaneously with that for vaccines against P. aeruginosa [ 65 , 66 , 67 ]. Vaccine targets include factors that trigger the immune response in the host, characterized by antigenic elements typically found on the bacterial surface, such as lipopolysaccharides (LPS) and outer membrane proteins (OMPs) [ 68 ].…”

“…Vaccine targets include factors that trigger the immune response in the host, characterized by antigenic elements typically found on the bacterial surface, such as lipopolysaccharides (LPS) and outer membrane proteins (OMPs) [ 68 ]. In addition, inner membrane proteins have also been evaluated and further classified by the amount of the most prevalent amino acid and their physical-chemical features [ 67 ]. RV has been largely exploited over the genome of Pseudomonas aeruginosa PAO1 strain, evaluating elements such as lectins and glycan-binding proteins that are involved in adherence to host cells, in order to carry out the bacterial colonization and the formation of the biofilm [ 69 , 70 ].…”

“…Furthermore, by combining the different immunogenic elements found by bioinformatics analysis, many in vivo experiments yielded acceptable outcomes, in particular, merging the protein PA5340, which seems to exist only in P. aeruginosa . Subsequently, a chimeric multi-epitope vaccine has been developed, starting from the different computational analysis, but also using linker and adjuvant to increase the response of the immune system [ 66 , 67 , 68 ]. In bacteria such as P. aeruginosa , the most interesting targets include proteins involved in virulence, which are essential for adhesion, mobility and the penetration in the host cells.…”