Molecular Docking and Molecular Dynamic Simulation of Squalene Nanoemulsion as an Antiviral Agent Targeting Coat Protein of Papaya Ring Spot Virus—P (PRSV-P) in Papaya

Squalene a terpenoid bioactive compound which has been identified in wild genus of papaya Vasconcellea candamarcensis and Vasconcellea cauliflora were formulated into nanoemulsion using ultra-sonication method with z-average diameter of ≈56.8 nm confirmed by TEM. Antiviral efficacy against PRSV-P was demonstrated using mechanical inoculation with application of squalene nanoemulsion at 160 ppm concentration, and viral detection was validated by RT-PCR. Molecular docking interactions using AutoDock and PyRx demonstrated binding affinity (–8.4 kcal/mol) between squalene and coat protein of PRSV-P indicating effective inhibition of viral replication and molecular dynamics simulations over 50 ns confirmed the stability of these complexes, with minimal fluctuations in RMSD values. These findings highlight the potential of squalene compound as lead candidates in the development of plant-derived antiviral strategies against PRSV-P in papaya.