Vibrio harveyi belongs to the Vibrio genus that causes vibriosis in marine and aquatic fish species through double-stranded DNA virus replication. In humans, around 12 Vibrio species can cause gastroenteritis (gastrointestinal illness). A large amount of virus particles can be found in the cytoplasm of infected cells, which may cause death. Despite these devastating complications, there is still no cure or vaccine for the virus. As a result, we used an immunoinformatics approach to develop a multi-epitope vaccine against most pathogenic hemolysin gene of V. harveyi. The immunodominant T- and B-cell epitopes were identified using the hemolysin protein. We developed a vaccine employing three possible epitopes: cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocyte epitopes, after thorough testing. The vaccine was developed to be antigenic, immunogenic, and non-allergenic, as well as having a better solubility. Molecular dynamics simulation revealed significant structural stiffness and binding stability. In addition, the immunological simulation generated by computer revealed that the vaccination might elicit immune reactions in the actual life after injection. Finally, using Escherichia coli K12 as a model, codon optimization yielded ideal GC content and a higher codon adaptation index value, which was then included in the cloning vector pET2+ (a). Altogether, our experiment implies that the proposed peptide vaccine might be a good option for vibriosis prophylaxis.

Nervous necrosis virus (NNV) is a devastating infectious pathogen for fish species with 100% mortality. To date, no specific drugs or vaccines have been developed that can prevent infections in aquaculture caused by NNV. It has been found that the NNV utilizes capsid protein to enter into the host cell in Asian sea bass and cause disease. In this study, we evaluated the inhibitory potential of Allium sativum compounds that have been reported to show antiviral activity against various pathogens. The capsid protein was modeled and the binding affinity of all the compounds was calculated with the docking approach and top 2 (PubChem CID: 122130381 and CID 12303662) inhibitory compounds were selected for further ADMET properties and DFT analysis. Both the geometry optimization and redocking of the two inhibitory compounds (PubChem CID: 122130381 and CID 12303662) showed a strong binding affinity of -8.2 and -8.0 kcal/mol, respectively with the capsid protein. The molecular dynamic simulation approach further validated the capsid protein – CID: 122130381 and capsid protein- CID 12303662 complex stability. In conclusion, this study deduces that these Allium sativum phytochemicals might act as significant inhibitors of the NNV in sea bass, which can be further validated experimentally.

Nervous necrosis virus (NNV) is a deadly infectious disease that affects several fish species. It has been found that the NNV utilizes grouper heat shock cognate protein 70 (GHSC70) to enter the host cell. Thus, blocking the virus entry by targeting the responsible protein can protect the fishes from disease. The main objective of the study was to evaluate the inhibitory potentiality of 70 compounds of Azadirachta indica (Neem plant) which has been reported to show potential antiviral activity against various pathogens, but activity against the NNV has not yet been reported. The binding affinity of 70 compounds was calculated against the GHSC70 with the docking and molecular dynamics (MD) simulation approaches. Both the docking and MD methods predict 4 (PubChem CID: 14492795, 10134, 5280863, and 11119228) inhibitory compounds that bind strongly with the GHSC70 protein with a binding affinity of –9.7, –9.5, –9.1, and –9.0 kcal/mol, respectively. Also, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties of the compounds confirmed the drug-likeness properties. As a result of the investigation, it may be inferred that Neem plant compounds may act as significant inhibitors of viral entry into the host cell. More in-vitro testing is needed to establish their effectiveness.

A wide variety of Pseudoalteromonas spp. found in Kappaphycus alvarezii (marine seaweed) causing deadliest Ice-ice disease and in Laminaria japonica (brown seaweed) found to cause red spots disease. However, very little is known about this pathogen and its genome characteristics. Furthermore, several proteins in its genome are classified as hypothetical proteins (HPs). As a result, the current work sought to elucidate the roles of an HP found in the genome of Pseudoalteromonas spp. To determine the structure and function of this protein, many bioinformatics methods were used. The active site and interacting proteins were examined using CASTp and the STRING server. An important biological activity of the HP is that it contains single functional domains that may be responsible for exopolysaccharide biosynthesis and can be a potential biomarker. Further, protein-protein interactions within selected HP revealed several functional partners that are essential for bacterial survival. In addition, molecular docking and simulation results showed stable bonding between HP and HSP90. Finally, the current work shows that the annotated HP is associated with possible protein sorting signals in the environment as well as having a stable binding with the HSP90, which might be of significant relevance to future bacterial genetics research.

This study used a comprehensive bioinformatic application to discover the functions of the HP33 protein, which is responsible for the scale drop and muscle necrosis disease (SDMND) in fish. The main objective of the study was to the characterization of the HP33 protein and predict the homo-oligomer models to understand the physical effect of the protein for further research. At first, multiple sequence alignment and sub-cellular localization of the HP33 were predicted by the in-silico approach. The result suggests that this putative protein clustered with another hypothetical protein, Vibrio harveyi, and is an unstable, nonpolar, and outer membrane protein. Functional analysis of the protein by Pfam, InterProScan, and SMART tools predicts that the HP has a single functional domain that may signify a cluster of biosynthetic genes. The prediction of the active site, as well as the protein-protein interaction, were also predicted in this study. Furthermore, a protein-ligand docking investigation revealed two potential therapeutic compounds (Ferroheme C, Valine) that can be effective against HP33 pathogenesis. In conclusion, the homo-oligomers model's predictions and the ab-initio docking findings will offer important information for an additional immunological investigation, which may be beneficial in a future study on SDMND prophylaxis.