Virtual screening and molecular dynamics simulations for drug repurposing against autophagy to attenuate blast in cereal plants.

Blast disease is a severe fungal infection that primarily impacts cereal crops caused by pathogenic fungus. e.g., Magnaporthe oryzae (M. oryzae) that uses autophagy for its pathogenecity. Experimental studies show the importance of autophagy for programmed cell death of filamentous fungi and the inhibition process of Atg4-mediated Atg8 cleaving by obtaining potential drug molecules to inhibit autophagy process in blast causing fungus. However, the molecular level details of the drug-Atg4 complex remains elusive. In this study, we use virtual screening and Molecular Dynamics (MD) simulations to repurpose drugs which are able to kill the fungus by targeting the Atg4-mediated cleaving of Atg8 in M. oryzae. Of the 3800 FDA-approved drugs, we identify six promising candidates- 31 h-Phthalocyanine, rebastinib, flumatinib, zafirlukast, beigene-283, and radotinib. A total of 18 µs all-atom MD simulations is conducted to further identify the stability of these molecules and their complexes with Atg4 with the help of RMSD, RMSF, Rg, and binding energy. The compound stability is further validated with the number of hydrogen bonds formed between Atg4 and drug molecules during the complete trajectory. Together with binding energy, the stability results indicate distinct ligand binding to Atg4. Our work provides pharmacokinetic properties of the screened compounds, the molecular level details of the key residues involved in Atg4-drug interactions, and dynamic stability of Atg4::drug complexes, establishing a basis for drug repurposing for the inhibition of the Atg4 mediated Atg8 cleavage in M. oryzae.