Screening of Potential Endophytes Against Fungal Pathogens, Curvularia lunata, Bipolaris oryzae and Pyricularia setariae Using In Vitro and Computational Approaches

Curvularia lunata, Bipolaris oryzae and Pyricularia setariae are a group of dematiaceous fungi which pose significant challenges in agriculture. Extensive use of synthetic fungicides to control them has led to cross-kingdom transfer and the development of fungicide resistance. Hence, endophytes and their metabolites can be used as an eco-friendly option to mitigate them. Potential endophytes (Macrophomina phaseolina, Macrophomina pseudophaseolina, Trichoderma asperellum and Polyporales sp.) were tested for their bio-control efficacy through in vitro dual culture and double Petri dish assay. In the dual culture assay, all five endophytes exhibited significantly higher antagonistic activity against C. lunata than other plant pathogens. However, in the double Petri dish assay, which tested the efficacy of volatile organic compounds (VOCs) produced by endophytes for in vitro pathogen control, the growth of P. setariae was notably more inhibited than that of the other pathogens. Further, the individual metabolites produced by the fungal endophytes were characterised by LC–MS/MS and used for in silico docking analysis against specific target proteins: Polyketide synthase (PKS), beta-tubulin and trihydroxynapthalene reductase (THR) of the fungal pathogens. The docking analysis revealed that 3-beta-chloro-Imperialine, quinoline-6,8-disulfonic acid and bucladesine from CSR1 (Macrophomina pseudophaseolina) demonstrated superior binding affinities to β-tubulin of C. lunata, with dock scores of −7.45, −7.3 and −7.24 kcal/mol respectively, outperforming the commercially available fungicide carbendazim (−5.95 kcal/mol). Two metabolites, veratrosine and glimepiride present in Polyporales sp., interacted with THR with binding affinities of −12.4 and −10.76 kcal/mol. In interactions with PKS of B. oryzae, 3-methylcholanthrene and penitrem A from TPS2 (Trichoderma asperellum) showed outstanding dock scores of −11.22 and −10.08 kcal/mol, respectively. These findings highlight the potential of endophyte-derived metabolites as powerful inhibitors of fungal pathogens, offering promising leads for developing novel antifungal treatments.