Docking and molecular dynamics simulation study of plant origin antifungal peptides with fungal protein of plant pathogen Fusarium oxysporum

Emerging infectious diseases (EID) are serious problems caused by fungi in humans and plants and are considered a threat to world food security. Plant origin antifungal peptides are biologically active peptides. They play a vital role in the primary host defense against microbial invasion. The Fusarium oxysporum species complex includes phytopathogenic & non-pathogenic strains and is usually found in the soil. F. oxysporum has gained significant attention from plant pathologists for more than a century owing to economic losses.

Protein-peptide interactions (PPI) plays important role in living beings and their structural characterization. The current study discusses the molecular interaction study of plant antifungal peptides with the target fungal protein of F. oxysporum. We have already reported 510 plant origin antifungal peptides in the PlantAFP database. Under the current investigation, we have selected 55 amino acids under the criteria of amino acid length size of 4-30 that are strictly natural amino acids. The protein-peptide interaction study yielded peptide models. The top 5 models namely PHYTO5, PHYTO13, PHYTO28, PHYTO1, and PHYTO52 achieved high cluster density with low RMSD values. The peptide docking study was further validated with simulation studies for thermodynamic properties. PHYTO5 provided important H-bond involvement with SER57, GLU59, ARG65, HIS68, GLU74, and GLU 87. This can be used as a probable anti-fungal peptide inhibitor against fungi-based infectious diseases.