Docking and Molecular Dynamics (MD) Simulations in Potential Drugs Discovery: An Application to Influenza Virus M2 Protein

• Published in: American journal of biochemistry and biotechnology Vol. 10; no. 3; pp. 180 - 188
• Main Authors: Bozdaganyan, Marine E., Orekhov, Philipp S., Bragazzi, Nicola L., Panatto, Donatella, Amicizia, Daniela, Pechkova, Eugenia, Nicolini, Claudio, Gasparini, Roberto
• Format: Journal Article
• Language: English
• Published: 11-11-2014
• Subjects: Influenza virus
• ISSN: 1553-3468; 1558-6332
• DOI: 10.3844/ajbbsp.2014.180.188

Molecular docking is a common method for searching new potential drugs. Improvement of the results of docking can be achieved by different ways-one of them is molecular dynamics simulations of protein-ligand complexes. As a model for this research, the authors have chose M2 membrane protein from influenza virus. M2 protein is a high selective tetrameric pH-gated proton channel. It was previously shown that Omeprazole Family Compounds (OFC) block the "proton pump", though they hypothesized further that they could interfere with the mechanism of fusion of the virus envelope and endosomal membrane, thereby hindering the M2 proton pump mechanism of influenza viruses. They carried out a Molecular Dynamics simulation in order to predict constant of binding for OFC. They simulated M2 Protein in complex with its ligands: Amantadine, rimantadine as positive controls and omeprazole as putative ligand. They demonstrate that the thermodynamic integration method predicts free energies of ligand binding better than molecular docking while embedding of M2 protein in a membrane further improves the calculated free energy values.