Why Amantadine Loses Its Function in Influenza M2 Mutants: MD Simulations

Molecular dynamics simulations of the drug-resistant M2 mutants, A30T, S31N, and L26I, were carried out to investigate the inhibition of M2 activity using amantadine (AMT). The closed and open channel conformations were examined via non- and triply protonated H37. For the nonprotonated state, these mutants exhibited zero water density in the conducting region, and AMT was still bound to the channel pore. Thus, water transport is totally suppressed, similar to the wild-type channel. In contrast, the triply protonated states of the mutants exhibited a different water density and AMT position. A30T and L26I both have a greater water density compared to the wild-type M2, while for the A30T system, AMT is no longer inside the pore. Hydrogen bonding between AMT and H37 crucial for the bioactivity is entirely lost in the open conformation. The elimination of this important interaction of these mutations is responsible for the lost of AMT's function in influenza A M2. This is different for the S31N mutant in which AMT was observed to locate at the pore opening region and bond with V27 instead of S31.

[1]  K. Choi,et al.  Epidemiology of H 5 N 1 avian influenza , 2005 .

[2]  I. Arkin,et al.  A novel method of resistance for influenza against a channel‐blocking antiviral drug , 2004, Proteins.

[3]  H. Berendsen,et al.  A consistent empirical potential for water–protein interactions , 1984 .

[4]  Gabriele Neumann,et al.  Human infection with highly pathogenic H5N1 influenza virus , 2008, The Lancet.

[5]  D. M. F. Aalten,et al.  PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules , 1996, J. Comput. Aided Mol. Des..

[6]  M S Sansom,et al.  An alamethicin channel in a lipid bilayer: molecular dynamics simulations. , 1999, Biophysical journal.

[7]  I. Barr,et al.  Increased adamantane resistance in influenza A(H3) viruses in Australia and neighbouring countries in 2005. , 2007, Antiviral research.

[8]  R. Lamb,et al.  Controlling influenza virus replication by inhibiting its proton channel. , 2007, Molecular bioSystems.

[9]  H. Steinhoff,et al.  Effects of solubilization on the structure and function of the sensory rhodopsin II/transducer complex. , 2006, Journal of molecular biology.

[10]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[11]  Xiyan Xu,et al.  Incidence of adamantane resistance among influenza A (H3N2) viruses isolated worldwide from 1994 to 2005: a cause for concern , 2005, The Lancet.

[12]  Huan‐Xiang Zhou,et al.  Histidines, heart of the hydrogen ion channel from influenza A virus: toward an understanding of conductance and proton selectivity. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[13]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[14]  Gregory A Voth,et al.  Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. , 2007, Biophysical journal.

[15]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[16]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..

[17]  Comparison of three structures of the multidrug transporter EmrE. , 2006, Current opinion in structural biology.

[18]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[19]  R. Lamb,et al.  Chemical Rescue of Histidine Selectivity Filter Mutants of the M2 Ion Channel of Influenza A Virus* , 2005, Journal of Biological Chemistry.

[20]  Gavin J. D. Smith,et al.  Distribution of amantadine-resistant H5N1 avian influenza variants in Asia. , 2006, The Journal of infectious diseases.

[21]  R. Webster,et al.  Detection of amantadine-resistant variants among avian influenza viruses isolated in North America and Asia. , 2005, Virology.

[22]  A. Sali,et al.  Alignment of protein sequences by their profiles , 2004, Protein science : a publication of the Protein Society.

[23]  Thanyada Rungrotmongkol,et al.  How amantadine and rimantadine inhibit proton transport in the M2 protein channel. , 2008, Journal of molecular graphics & modelling.

[24]  J. Bradshaw,et al.  Neutron diffraction reveals the site of amantadine blockade in the influenza A M2 ion channel. , 1994, Virology.

[25]  Lawrence H. Pinto,et al.  Influenza virus M2 protein has ion channel activity , 1992, Cell.

[26]  Sanguk Kim,et al.  The closed state of a H+ channel helical bundle combining precise orientational and distance restraints from solid state NMR. , 2002, Biochemistry.

[27]  G. T. Marks,et al.  Short, strong hydrogen bonds on enzymes: NMR and mechanistic studies , 2002 .

[28]  F. Bezanilla.  The voltage-sensor structure in a voltage-gated channel. , 2005, Trends in biochemical sciences.

[29]  Narayanan Eswar,et al.  Protein structure modeling with MODELLER. , 2008, Methods in molecular biology.

[30]  G. Boivin,et al.  Generation and Characterization of Recombinant Influenza A (H1N1) Viruses Harboring Amantadine Resistance Mutations , 2005, Antimicrobial Agents and Chemotherapy.

[31]  Q Zhong,et al.  Two possible conducting states of the influenza A virus M2 ion channel , 2000, FEBS letters.

[32]  H. Takeuchi,et al.  Protonation of histidine and histidine-tryptophan interaction in the activation of the M2 ion channel from influenza a virus. , 2001, Biochemistry.

[33]  R. Lamb,et al.  Ion channel activity of influenza A virus M2 protein: characterization of the amantadine block , 1993, Journal of virology.

[34]  I. Barr,et al.  Susceptibility of highly pathogenic A(H5N1) avian influenza viruses to the neuraminidase inhibitors and adamantanes. , 2007, Antiviral research.

[35]  A. Hay,et al.  Selective proton permeability and pH regulation of the influenza virus M2 channel expressed in mouse erythroleukaemia cells. , 1996, The Journal of physiology.

[36]  Riqiang Fu,et al.  The chemical and dynamical influence of the anti-viral drug amantadine on the M2 proton channel transmembrane domain. , 2007, Biophysical journal.

[37]  R. Lamb,et al.  Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue. , 1995, Biophysical journal.

[38]  R. Lamb,et al.  The M2 Proton Channels of Influenza A and B Viruses* , 2006, Journal of Biological Chemistry.

[39]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[40]  R. Lamb,et al.  Cu(II) Inhibition of the Proton Translocation Machinery of the Influenza A Virus M2 Protein* , 1999, The Journal of Biological Chemistry.

[41]  I. Arkin,et al.  How pH opens a H+ channel: the gating mechanism of influenza A M2. , 2005, Structure.

[42]  D. Kern,et al.  The role of dynamics in allosteric regulation. , 2003, Current opinion in structural biology.

[43]  Michael Levitt,et al.  Detailed Hydration Maps of Benzene and Cyclohexane Reveal Distinct Water Structures , 2004 .