How amantadine and rimantadine inhibit proton transport in the M2 protein channel

Evaluating how rimantadines control the proton gating of the influenza A M2-proton port via allosteric binding outside of the M2-channel: MD simulations

“…This observation is in good agreement with a previous electrophysiological study where the binding of RMT outside of the M2 channel was found to not be the primary site for pharmacological inhibition or proton transport [30]. In contrast, water penetration was completely prevented in the 3H state when RMT was bound inside the M2 pore [28]. A clear picture of water passing through the pH sensor His37 and proton gate Trp41 residues in the 3H state can be ascribed as follows.…”

“…Therefore, the interhelical salt bridge between the Asp44 and Arg45 was well formed [8]. Regarding drug interactions, the relatively high pK a values of 10.4 [33] made the side chain of the RMT have a protonated form (R-NH 3 + ) [28] and consequently this -NH 3 + group was in contact with the -COO − group of Asp44 at the allosteric binding region [8]. Each system was separately built according to the designed protonation state of the His37 tetrad with the RMT inhibitor bound and then inserted into a pre-equilibrated lipid bilayer, initially made up of 77 molecules of 1-palmitoyl-2 -oleoyl-sn-glycerol-3-phosphatidylcholine (POPC) lipid [34] embedded in 3760 molecules of FLEXSPC water [35].…”

“…The inhibitor's topology file was taken from our previous studies [28,38]. The whole structure was optimised by the steepest descent minimisations.…”

“…Although the model structures of M2-TM are experimentally [12][13][14][15][16][17] and computationally available [18][19][20][21][22][23][24][25][26][27][28][29], high resolution structures have only recently been determined [7,8]. X-ray diffraction analysis has been used to solve the M2-TM structures under neutral and low pH conditions.…”

“…X-ray diffraction analysis has been used to solve the M2-TM structures under neutral and low pH conditions. The crystal structure revealed that a single AMT molecule in the pore of the channel was surrounded by Val27, Ala30, Ser31 and Gly34 [27,28]. In contrast, Schnell and Chou reported an NMR structure for the peptide spanning residues 18-60 in detergent micelles at high pH [8], where four RMT molecules were bound outside of the protein helix, facing the lipid bilayer and located in the membrane environment at the end of the helix towards the cytoplasmic face of the channel (Figure 1).…”