An In-silico Approach for Identifying Phytochemical Inhibitors Against Nervous Necrosis Virus (NNV) in Asian Sea Bass by Targeting Capsid Protein

Abstract

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.

High-throughput virtual screening of marine algae metabolites as high-affinity inhibitors of ISKNV major capsid protein: An analysis of in-silico models and DFT calculation to find novel drug molecules for fighting infectious spleen and kidney necrosis virus (ISKNV)

“…To compute DFT, Becke's three parameters (B3LYP) and Lee-Yang-Parr functionals (B3LYP-D3) were combined with the dispersion correction energy term D3. The typical arrangement of capabilities B3LYP-D3 was selected for this study and 6-31G(d,p) was chosen to characterize the electronic wave function of the molecule [ 15 , 38 , 39 ]. Conventional B3LYP method have shown remarkable accuracy but one of the major limitations is its failure to accurately represent London Dispersion Interactions.…”

An In-silico approaches for identification of potential natural antiviral drug candidates against Erythrocytic necrosis virus (Iridovirus) by targeting Major capsid protein: A Quantum mechanics calculations approach

“…The 3D structure of the protein was modeled and developed using the following criteria: water, metal ions, and cofactors were removed, polar hydrogen atoms were introduced, nonpolar hydrogen was combined, and gasteiger charges were calculated using AutoDockTools [32,33].…”

“…As a result, the ProTox-II (http://tox. charite.de/protox II) website was used to assess the early-stage toxicity of the chosen medication candidates [11]. With ProTox-II, you can identify compounds that are acutely toxic, hepatotoxic, cytotoxic, carcinogenic, mutagenic, and immunotoxic [49].…”

“…Garlic is one of the world's oldest cultivated plants [11,12]. For over 4000 years, it has been used as a spice, food, and traditional medicine, and it is the most extensively investigated medicinal plant.…”

Homo-oligomer models prediction, functional characterization, and Ab initio docking analysis of hypothetical protein HP33 from Vibrio harveyi strain

“…The most probable protein-ligand binding poses and templates model for another protein-ligand complex were given in Figure 4. Ligand-binding residues depend on the de nition of residue-ligand contact (Islam, Mou, et al, 2022b). If the distance between an amino acid residue and a ligand atom is less than the sum of van der Waals radii of the two atoms + 0.5 A, the residue is considered as a binding site residue (Chen et The interface area (Ǻ 2 ) between one chain and the other chains is calculated using the Naccess program by the Galaxy server (Baek et al, 2017).…”