Molecular Interaction Study to Explore the Nigella sativa Bioactive Components as an Inhibitor of Peptide Deformylase to Inhibit the Xanthomonas oryzae pv. oryzae via Applying Computational Approach

Bacterial leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most damaging diseases to rice across the world. Various chemicals have been employed so far for the management of bacterial leaf blight. On the other hand, these compounds are damaging to the ecosystem and have an impact on non-target species such as humans and animals. As a result, there is a need to create a new natural inhibitor for BLB management. Deformylase (PDF) enzyme is present in all eubacteria and its necessity in bacterial protein synthesis reveals it as an attractive target for drug development. In this study, the active components of Nigella sativa have been selected based on their previously reported antimicrobial activity and screened on the active site of bacterial PDF by the in silico art of techniques. Among these compounds, dithymoquinone and p-cymene strongly bind with the PDF enzyme with binding energy values of 7.77 kcal/mol and 7.26 kcal/mol, respectively, which is comparatively higher than the control compound (−6.73 kcal/mol). Hence, the “dithymoquinone-PDF” and “p-cymene-PDF” complexes were selected for further study, and their stability was assessed by molecular dynamic (MD) simulation. In MD simulation, both selected compounds exhibited steady-state interaction with PDF for 20 ns. It has been hypothesized that p-cymene and dithymoquinone inhibit peptide deformylase and could be used as antibacterials or pesticides against Xoo against the BLB disease.