Application of pan genomics towards the druggability of Clostridium botulinum

Designing a multi-epitope vaccine against Shigella dysenteriae using immuno-informatics approach

Shigella dysenteriae has been recognized as the second most prevalent pathogen associated with diarrhea that contains blood, contributing to 12.9% of reported cases, and it is additionally responsible for approximately 200,000 deaths each year. Currently, there is no S. dysenteriae licensed vaccine. Multidrug resistance in all Shigella spp. is a growing concern. Current vaccines, such as O-polysaccharide (OPS) conjugates, are in clinical trials but are ineffective in children but protective in adults. Thus, innovative treatments and vaccines are needed to combat antibiotic resistance. In this study, we used immuno-informatics to design a new multiepitope vaccine and identified S. dysenteriae strain SD197's membrane protein targets using in-silico methods. The target protein was prioritized using membrane protein topology analysis to find membrane proteins. B and T-cell epitopes were predicted for vaccine formulation. The epitopes were shortlisted based on an IC50 value <50, antigenicity, allergenicity, and a toxicity analysis. In the final vaccine construct, a total of 8 B-cell epitopes, 12 MHC Class I epitopes, and 7 MHC Class II epitopes were identified for the Lipopolysaccharide export system permease protein LptF. Additionally, 17 MHC Class I epitopes and 14 MHC Class II epitopes were predicted for the Lipoprotein-releasing ABC transporter permease subunit LolE. These epitopes were selected and linked via KK, AAY, and GGGS linkers, respectively. To enhance the immunogenic response, RGD (arginine-glycine-aspartate) adjuvant was incorporated into the final vaccine construct. The refined vaccine structure exhibits a Ramachandran score of 91.5% and demonstrates stable interaction with TLR4. Normal Mode Analysis (NMA) reveals low eigenvalues (3.925996e-07), indicating steady and flexible molecular mobility of docked complexes. Codon optimization was carried out in an effective microbial expression system of the Escherichia coli K12 strain using the recombinant plasmid pET-28a (+). Finally, the entire in-silico analysis suggests that the suggested vaccine may induce a significant immune response against S. dysenteriae, making it a promising option for additional experimental trials.

Antibacterial and Antibiofilm Activity of Juglone Derivatives against Enterococcus faecalis: An In Silico and In Vitro Approach

Enterococcus faecalis is a Gram-positive bacterium that is normally found in the gastrointestinal tract of humans and animals. E. faecalis is an opportunistic pathogen that causes a number of invasive and noninvasive infections. The emergence of multidrug resistance and biofilm formation by the bacterium have rendered the treatment of E. faecalis infections very difficult. Due its high rate of resistance and biofilm formation, there are very few options of treatment. Therefore, the current study was designed to evaluate the antibacterial and biofilm activities of juglone derivatives such as 2-methoxy-6-acetyl-7-methyljuglone and 2-ethoxy-6-acetyl-7-methyljuglone against multidrug-resistant (MDR) and biofilm-producing strains of E. faecalis. Agar well diffusion and broth microdilution methods were used to determine the antibacterial activities. Biofilm attachment and preformed biofilm inhibition were determined using crystal violet staining assay. Both juglone derivatives displayed promising antibacterial and antibiofilm activities against E. faecalis. Among these compounds, 2-ethoxy-6-acetyl-7-methyljuglone possessed better inhibitory activity with minimum inhibitory concentration (MIC) of $9.7\pm 3\mu \text{M}$ as compared to 2-methoxy-6-acetyl-7-methyljuglone (MIC, $19.5\pm 2\mu \text{M}$ ). Additionally, 2-ethoxy-6-acetyl-7-methyljuglone also showed stronger antibiofilm activity than 2-methoxy-6-acetyl-7-methyljuglone. Furthermore, both the ligand molecules were docked into the binding site of the enterococcal surface protein, and the results revealed that both the molecules are actively binding in the target site. Based on these findings, juglone derivatives may be considered useful for the treatment of E. faecalis infections; however, further studies are required to elucidate the mechanism of action.