IN SILICO INVESTIGATION OF NATURAL LIGANDS AGAINST BACTERIAL NITRITE REDUCTASE FOR BIOLOGICAL NITROGEN REMOVAL IN AQUACULTURE WASTE WATER

Abstract

Aquaculture wastewater contains nitrogenous compounds such as ammonia, nitrite, nitrate, and dissolved organic nitrogen, which can affect aquatic animal health, microbial stability, and the ecological quality of receiving water bodies. Biological nitrogen removal is largely mediated by bacterial enzymes involved in nitrification and denitrification pathways. Since these enzymes regulate the transformation of toxic nitrogen compounds into less harmful forms, their molecular-level interaction with bioactive compounds can provide useful preliminary insight for environmental biotechnology and aquaculture wastewater management. The present study aimed to perform an in silico molecular docking analysis of selected natural compounds against cd1 nitrite reductase NirS, a bacterial enzyme associated with nitrogen removal from aquaculture wastewater. The target nitrite reductase enzyme was prepared as the receptor for docking and docked with five selected natural ligands: apigenin, catechin, naringenin, quercetin, and kaempferol. Molecular docking was performed using PyRx with the Auto Dock Vina algorithm, and the resulting docked complexes were analysed on the basis of binding affinity, binding pose, and protein–ligand interaction patterns. The docking results showed that all selected ligands interacted with the target enzyme with measurable binding affinity. Among the screened compounds, apigenin showed the strongest predicted binding affinity with a docking score of −9.2 kcal/mol, followed by catechin at −8.6 kcal/mol, naringenin at −8.4 kcal/mol, quercetin at −8.3 kcal/mol, and kaempferol at −7.1 kcal/mol. The findings indicate that apigenin demonstrated the most favourable binding compatibility with the selected cd1 nitrite reductase NirS under the applied docking conditions. Catechin, naringenin, and quercetin also showed comparatively strong interactions, suggesting their potential relevance for further computational and experimental investigation. The study supports the use of molecular docking as a preliminary screening method for exploring enzyme–ligand interactions related to nitrogen-removal processes in aquaculture wastewater. However, the docking findings are predictive and require further validation through molecular dynamics simulation, enzyme assays, microbial studies, and wastewater-scale experiments.