Secondary metabolites protect against metal and metalloid stress in rice: an in silico investigation using dehydroascorbate reductase

Abstract

Plant metabolites including ascorbic acid (AA), reduced glutathione (GSH), serotonin, jasmonic acid (JA) and salicylic acid (SA) alleviate metal/metalloid-induced stress in plants, mainly by regulating the redox homeostasis. This possibly improves stress tolerance and augments productivity. The present computational modeling analysis was performed to understand the potential of these five metabolites in ameliorating metal/metalloid stress in rice, using dehydroascorbate reductase (DHAR) as a model. Six metal/metalloid ions (As3+, As5+, Cd2+, Cu2+, Pb2+, Zn2+) were used in the study, and the relative affinity, binding geometry and electrostatic surfaces of secondary metabolites and ions with the active site of DHAR were predicted. The results revealed that all the metabolites and ions may potentially interact with the active catalytic site of DHAR. However, the free energies of binding (docking score) of the metabolites (ranging from − 50.64 to − 81.56 kcal/mol) were many-folds higher than those of the ions (ranging from − 16.21 to − 16.23 kcal/mol). On comparison, the docking score of As3+ was found to be 28.29% of that of AA. Further, compared to AA, SA had lower score, and GSH, JA and serotonin showed 1.42-, 1.30- and 1.18-fold higher score than AA. Further analysis revealed that the electrostatic surfaces of the metabolites and ions overlap with one another. Statistical analysis was performed to determine the properties of the ligands which are crucial in facilitating interaction of the ligands. Based on the findings, it is argued that the secondary metabolites may interfere with the binding of the ions with DHAR, and when present in higher quantities, these metabolites may ameliorate metal/metalloid-induced stress responses.