Studies of antibacterial activity and molecular docking of potential bioactive compounds of plant extracts against KdgR protein of Dickeya dadantii

Dickeya dadantii, the causal organism of bacterial stalk rot of sorghum, is India’s widely spread and destructive disease. To explore sources of natural bactericides as alternative approaches in an integrated disease management strategy against D. dadantii, methanolic and aqueous extracts of twenty different plants were evaluated. In vitro antibacterial activity assays demonstrated that Eucalyptus globulus and Aegle marmelos produced compounds that exhibited the highest zone of inhibition against D. dadantii, (i.e., 1.67-2.00 cm) at 20% concentration. Pot assays conducted in the greenhouse and the field showed that these extracts could decrease the disease incidence in sorghum seedlings and also seemed to have some plant-growth-promoting factors. Hence, extracts of E. globulus and A. marmelos were further analyzed by GC-MS to identify the bioactive compounds present that could bind KdgR, a repressor protein involved in the pectin degradation pathway of D. dadantii. Ten of the 155 compounds identified showed a high-binging affinity (i.e., -7.5 to -8.6 Kcal/mol) with KdgR, the target pectin degradation repressor protein of D. dadantii. In addition, SEM analysis showed that the plant extracts caused morphological changes in the cell wall of the D. dadantii. Our results suggest that E. globulus and A. marmelos produce compounds that could be used as natural bactericides against D. dadantii and perhaps other plant pathogenic bacteria.