Azadirachtin A as a Candidate for Postharvest Control of Potato Soft Rot Caused by <i>Pectobacterium atrosepticum</i> : Promising Pathogenicity Effects and Mechanistic Insights From Molecular Docking and <scp>DFT</scp> Studies

Abstract

ABSTRACT Azadirachtin A was assessed in vitro against Pectobacterium atrosepticum with no observed inhibitory effect; its effect on pathogenicity was tested as a pretreatment on potato tuber slices. A significant reduction in the weight of rotting of potato slices was observed. Docking simulations were conducted against two potential molecular targets: the Svx protein, responsible for activation of the invasion pathway, and pectate lyase (Pel3) from Pectobacterium carotovorum , involved in the breakdown of the plant extracellular matrix. These simulations aimed to validate the potential inhibition of the two major virulence pathways involved in P. atrosepticum infection. Prior to this, the reactivity descriptors of azadirachtin A were calculated using density functional theory (DFT) at the B3LYP functional with several basis sets in gas phase: 6‐31 G (d,p), 6‐31++ G (d,p), 6‐311 G (d,p), 6‐311++ G (d,p) and 6‐311++ G (2d,2p), along with the molecular electrostatic surface potential (MEP), in order to identify the active site of the compound. Azadirachtin A exhibited good binding into a hydrophobic pocket of Svx, near the active site, with a docking energy of −7.7 kcal/mol and metal–acceptor interaction with Zn 2+ atom, blocking the metal ions necessary for the optimal functioning of the metalloprotein. The predicted molecular interactions of azadirachtin A with the binding site of Pel3 showed good interactions, including common hydrogen bonds with two active site residues and a binding energy of −7.6 kcal/mol. These findings highlight the potential of azadirachtin A as an ecofriendly solution for managing soft rot disease in potato tubers.