Antifungal plant flavonoids identified in silico with potential to control rice blast disease caused by Magnaporthe oryzae

Abstract

Rice blast disease, caused by the fungus Magnaporthe oryzae, poses a severe threat to rice production, particularly in Asia where rice is a staple food. Concerns over fungicide resistance and environmental impact have sparked interest in exploring natural fungicides as potential alternatives. This study aimed to identify highly potent natural fungicides against M. oryzae to combat rice blast disease, using advanced molecular dynamics techniques. Four key proteins (CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PRE-MRNA-SPLICING FACTOR CEF1) involved in M. oryzae's infection process were identified. A list of 30 plant metabolites with documented antifungal properties was compiled for evaluation as potential fungicides. Molecular docking studies revealed that 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin exhibited superior binding affinities compared to reference fungicides (Azoxystrobin and Tricyclazole). High throughput molecular dynamics simulations were performed, analyzing parameters like RMSD, RMSF, Rg, SASA, hydrogen bonds, contact analysis, Gibbs free energy, and cluster analysis. The results revealed stable interactions between the selected metabolites and the target proteins, involving important hydrogen bonds and contacts. The SwissADME server analysis indicated that the metabolites possess fungicide properties, making them effective and safe fungicides with low toxicity to the environment and living beings. Additionally, bioactivity assays confirmed their biological activity as nuclear receptor ligands and enzyme inhibitors. Overall, this study offers valuable insights into potential natural fungicides for combating rice blast disease, with 2-Coumaroylquinic acid, Myricetin, Rosmarinic Acid, and Quercetin standing out as promising and environmentally friendly alternatives to conventional fungicides. These findings have significant implications for developing crop protection strategies and enhancing global food security, particularly in rice-dependent regions.

Fig 1. Schematic representation of the methods followed in the whole study.

Fig 2

Interaction of polar binding site residues in CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PMSF proteins with various compounds: A) 2-Coumaroylquinic acid, B) Myricetin, C) Quercetin, and D) Rosmarinic Acid for CATALASE PEROXIDASES 2; E) 2-Coumaroylquinic acid, F) Myricetin, G) Quercetin, and H) Rosmarinic Acid for HYBRID PKS-NRPS SYNTHETASE TAS1; I) 2-Coumaroylquinic acid, J) Myricetin, K) Quercetin, and L) Rosmarinic Acid for MANGANESE LIPOXYGENASE; and M) 2-Coumaroylquinic acid, N) Myricetin, O) Quercetin, and P) Rosmarinic Acid for PMSF.

Fig 3

RMSD analysis of backbone atoms in CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PMSF proteins (A), and RMSD analysis of azoxystrobin, 2-coumaroylquinic acid, and rosmarinic acid in respective complexes (B).

Fig 4

(A) RMSF in side chain atoms of residues in CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PMSF proteins, and (B) Radius of gyration for corresponding systems of CATALASE PEROXIDASES 2, HYBRID PKS-NRPS SYNTHETASE TAS1, MANGANESE LIPOXYGENASE, and PMSF.

Fig 5

(A) Solvent accessible surface area analysis, and (B) Hydrogen bond analysis.

Fig 6

Hydrogen bonds between CATALASE PEROXIDASES 2 and (A) Azoxystrobin and (B) 2-Coumaroylquinic acid.

Fig 7

Hydrogen bonds between HYBRID PKS-NRPS SYNTHETASE TAS1 and (A) Azoxystrobin and (B) Rosmarinic acid.

Fig 8

Hydrogen bonds between MANGANESE LIPOXYGENASE and (A) Azoxystrobin and (B) Rosmarinic acid.

Fig 9

Hydrogen bonds between PMSF and (A) Azoxystrobin and (B) Rosmarinic acid.

Fig 10

Gibbs’ free energy landscape: (A) Apo CATALASE PEROXIDASES 2 and respective CATALASE PEROXIDASES 2 complexes, (B) Apo HYBRID PKS-NRPS SYNTHETASE TAS1 and respective HYBRID PKS-NRPS SYNTHETASE TAS1 complexes, (C) Apo MANGANESE LIPOXYGENASE and respective MANGANESE LIPOXYGENASE complexes, and (D) Apo PMSF and respective PMSF complexes.

Fig 11

Cluster analysis for CATALASE PEROXIDASES 2 complexes: (A) CATALASE PEROXIDASES 2-azoxystrobin complex and (B) CATALASE PEROXIDASES 2-2-coumaroylquinic acid complex. Cluster analysis for HYBRID PKS-NRPS SYNTHETASE TAS1 complexes: (C) HYBRID PKS-NRPS SYNTHETASE TAS1-azoxystrobin complex and (D) HYBRID PKS-NRPS SYNTHETASE TAS1-rosmarinic acid complex.

Fig 12

Cluster analysis for MANGANESE LIPOXYGENASE complexes: (A) MANGANESE LIPOXYGENASE-azoxystrobin complex and (B) MANGANESE LIPOXYGENASE-rosmarinic acid complex. Cluster analysis for PMSF complexes: (C) PMSF-azoxystrobin complex and (D) PMSF-myricetin complex.