Molecular Dynamics Simulation of SARS-CoV-2 E Ion Channel: The Study of Lone Protein and its Conformational Changes in Complex with Potential Cage Inhibitors.

This study presents a computational approach that can be used to design ligands for E ion channels and identify potential inhibitors, providing valuable insights into the development of new antiviral therapies. The behavior of the E protein pentamer of SARS-CoV-2 in its native environment was investigated using Molecular Dynamics (MD), resulting in an equilibrated structure that could be used to develop new inhibitors through molecular docking. Simulation of the MD of E-channel complexes with amantadine analogues allowed for the identification of the main types of ligand-protein interactions that are responsible for the good binding of ligands within the channel's inner chamber.