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Updated: Jun 13, 2026
Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
Published on: December 1, 2020
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
Ekta Khurana1, Russell H Devane, Matteo Dal Peraro
1Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA. ekta.khurana@yale.edu
Abstract:
The M2 protein of influenza A virus performs the crucial function of transporting protons to the interior of virions enclosed in the endosome. Adamantane drugs, amantadine (AMN) and rimantidine (RMN), block the proton conduction in some strains, and have been used for the treatment and prophylaxis of influenza A infections. The structures of the transmembrane (TM) region of M2 that have been solved in micelles using NMR (residues 23-60) (Schnell and Chou, 2008) and by X-ray crystallography (residues 22-46) (Stouffer et al., 2008) suggest different drug binding sites: external and internal for RMN and AMN, respectively. We have used molecular dynamics (MD) simulations to investigate the nature of the binding site and binding mode of adamantane drugs on the membrane-bound tetrameric M2-TM peptide bundles using as initial conformations the low-pH AMN-bound crystal structure, a high-pH model derived from the drug-free crystal structure, and the high-pH NMR structure. The MD simulations indicate that under both low- and high-pH conditions, AMN is stable inside the tetrameric bundle, spanning the region between residues Val27 to Gly34. At low pH the polar group of AMN is oriented toward the His37 gate, while under high-pH conditions its orientation exhibits large fluctuations. The present MD simulations also suggest that AMN and RMN molecules do not show strong affinity to the external binding sites.
Insights
Amantadine (AMN) and rimantidine (RMN) are adamantane drugs used to treat influenza A. Molecular dynamics simulations show AMN remains stable within the M2 protein's transmembrane region, suggesting it acts as an internal gate blocker.
Area of Science:
- Structural biology
- Virology
- Computational biophysics
Background:
- Influenza A virus M2 protein facilitates proton transport, essential for viral replication.
- Adamantane drugs like amantadine (AMN) and rimantadine (RMN) inhibit M2 proton channel function in certain influenza A strains.
- Previous structural studies proposed distinct binding sites for AMN and RMN within the M2 transmembrane domain.
Purpose of the Study:
- To investigate the binding site and mode of adamantane drugs (AMN and RMN) within the membrane-bound M2 protein tetramer.
- To elucidate the behavior of AMN under varying pH conditions within the M2 transmembrane channel.
Main Methods:
- Molecular dynamics (MD) simulations were employed to study drug-protein interactions.
- Simulations utilized initial conformations from low-pH AMN-bound crystal structures, high-pH drug-free crystal structures, and high-pH NMR structures.
- Analysis focused on the stability and orientation of AMN within the tetrameric M2 transmembrane peptide bundle.
Main Results:
- MD simulations confirmed that AMN remains stably bound within the M2 tetramer's transmembrane region (Val27-Gly34) under both low and high pH conditions.
- At low pH, AMN's polar group consistently oriented towards the His37 residue (the gate).
- AMN exhibited significant orientation fluctuations at high pH, and neither AMN nor RMN showed strong affinity for previously proposed external binding sites.
Conclusions:
- Amantadine (AMN) functions as an internal blocker of the M2 proton channel, binding within the transmembrane domain.
- The binding site and stability of AMN are largely independent of pH, although its precise orientation varies.
- Adamantane drugs likely do not bind to external sites on the M2 protein, challenging previous structural interpretations.
