Computational exploration and molecular dynamics simulations for investigating the potential inhibitory mechanism of amantadine on the ion channel activity of bovine viral diarrhea virus p7.

Bovine viral diarrhea virus (BVDV) p7 functions as a viroporin for the ion balance and membrane permeabilization. Blocking the function of the viroporin is a promising strategy for the treatment of viral infection. Previous studies have demonstrated that the antiviral drug amantadine inhibits BVDV replication by inhibiting BVDV p7 activity. However, the mechanism by which amantadine acts against BVDV p7 remains unclear. In this study, AlphaFold2, molecular docking and molecular dynamics (MD) simulations were employed to investigate the binding sites of amantadine on BVDV p7. Structural analysis by AlphaFold2 and MD simulations showed that BVDV p7 may undergo antiparallel oligomerization, forming a stable hexamer that generates a pore channel. Notably, residues E21, Y25, L28, and R34 within the channel are likely involved in ion transport. Subsequently, the interaction of amantadine with BVDV p7 hexamer was investigated by docking studies and MD simulations analysis, indicating residues Y25 and L28 by van der Waals forces, alkyl and Pi-Alkyl interactions with amantadine. Importantly, the hydrogen bonding was observed between the -NH₃⁺ group of amantadine and residue Y25. By integrating these findings with the potential hexameric assembly of BVDV p7, we further proposed a potential ion channel model in which E21, Y25 and R34 are hypothesized to selectively recruit and dehydrate ions, while residue L28 acts as a hydrophobic restrictor, limiting the free movement of water. The binding of amantadine to residues Y25 and L28 likely disrupts ion transport. Our findings provide possible structural insights into the BVDV p7 ion channel and offer a mechanistic explanation for the inhibitory of amantadine on BVDV p7-mediated ion channel conductance, though experimental validation remains necessary.