Targeting the Major Capsid Protein of Rock Bream Iridovirus by Trapa Natans Phytochemical Compounds; a Molecular Docking Approach

Abstract

Asian rock bream aquaculture is challenged by iridovirus, a pathogen with no effective vaccines or antiviral agents. The present study aimed to identify natural antiviral compounds from Trapa natans, an aquatic plant, with potential to target the activities of major capsid protein in rock bream iridovirus (RBIVmcp). The investigation commenced by constructing a novel 3D homology structure for RBIVmcp using I-TASSER server, followed by refinement and validation through galaxy refiner, ModRefiner, PDBSum, ProSA, and ERRAT servers. Active binding regions of refined protein structures were employed for molecular docking simulations using PyRx and AutoDock Vina tools. Leveraging IMPPAT and PubChem servers, a total of 13 phytochemical compounds from Trapa natans were identified in silico and subjected to docking analysis against RBIVmcp. Among them, Ellagic acid, Galactoarabinan, and Thiamine exhibited the most favorable docking scores of -5.1 kcal/mol, -6.4 kcal/mol, and -5.9 kcal/mol, respectively. Assessment of compounds' toxicity and ADME properties by Swiss-ADME and ProTox-II servers indicated their non-hepatotoxic, non-carcinogenic, non-immunotoxic, and non-mutagenic nature within environments. These findings suggest aforementioned compounds might act as promising antiviral agents against RBIV by interacting with its major capsid protein. However, in vitro and in vivo studies are essential to validate their efficacy.