Virtual screening of rice phytochemical scaffolds targeting peptide deformylase of Xanthomonas Oryzae pv. Oryzae for the control of bacterial leaf blight

Abstract

Bacterial leaf blight (BLB) disease of rice, incited by bacterium Xanthomonas Oryzae pv. Oryzae (Xoo) causes huge loss of rice production. For reviving rice production, various bio-hazardous and eco-unfriendly chemical fertilizers, synthetic pesticides and antibiotics have been employed. Thus, the discovery of safe natural pesticides is an effective approach for managing rice BLB disease. In this study, 235 rice phytochemicals were screened to identify most effective bio-pesticide like molecules against Peptide Deformylase of Xoo (XoPDF), which actively participates in the translation process. Through molecular docking and simulation studies, nine potential lead compounds were screened with reference to Actinonin (a known inhibitor). Structural analysis via molecular dynamics suggests better structural stability and binding affinity of XoPDF with the screened leads in relative to Actinonin. Notably, nine leads exhibit structural backbone similarity with the subclass of anthocyanins (natural antibacterial polyphenols) and flavones viz., pelargonin, isorhamnetin, tricin, peonidin, syringetin, cyanidin, chrysoeriol and isoscoparin. In essence, these lead compounds can serve as potential hits for drug design against BLB disease by targeting XoPDF, thereby limiting Xoo survival and alleviating rice BLB. Since, peptide deformylase (PDF) is found in many other plant pathogens, it can be used as a broad - spectrum disease resistance drug.