Fig. 3: MD simulations models of Protein E (aa 8–65) in complex with amantadine and HMA.
From: Amantadine inhibits known and novel ion channels encoded by SARS-CoV-2 in vitro
a Complex with amantadine, with inset in (b) zooming in at the binding site. c Complex with HMA, with inset in (d) zooming in at the binding site. The models depict an outward orientation of the drugs with Protein E in an open state (ligand carbons and Protein E in gray) from restrained 100 ns-MD simulations with OPLS2005 force field and a force constant of 2 kcal mol Å−2 to the Ca atoms of Protein Ε. Ligand and amino–acid residues (shown in only one of the five α-helices for clarity) are shown as sticks. The PDB ID 5X2916 was used as starting structure (aa 8–65) for the Protein E-amantadine complex.
