Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece.
J Chem Inf Model. 2021 Nov 22;61(11):5550-5568. doi: 10.1021/acs.jcim.1c00264. Epub 2021 Oct 29.
Ion channels located at viral envelopes (viroporins) have a critical function for the replication of infectious viruses and are important drug targets. Over the last decade, the number and duration of molecular dynamics (MD) simulations of the influenza A M2 ion channel owing to the increased computational efficiency. Here, we aimed to define the system setup and simulation conditions for the correct description of the protein-pore and the protein-lipid interactions for influenza A M2 in comparison with experimental data. We performed numerous MD simulations of the influenza A M2 protein in complex with adamantane blockers in standard lipid bilayers using OPLS2005 and CHARMM36 (C36) force fields. We explored the effect of varying the M2 construct (M2(22-46) and M2(22-62)), the lipid buffer size and type (stiffer DMPC or softer POPC with or without 20% cholesterol), the simulation time, the H37 protonation site (N or Ν), the conformational state of the W41 channel gate, and M2's cholesterol binding sites (BSs). We report that the 200 ns MD with M2(22-62) (having N Η37) in the 20 Å lipid buffer with the C36 force field accurately describe: (a) the M2 pore structure and interactions inside the pore, that is, adamantane channel blocker location, water clathrate structure, and water or chloride anion blockage/passage from the M2 pore in the presence of a channel blocker and (b) interactions between M2 and the membrane environment as reflected by the calculation of the M2 bundle tilt, folding of amphipathic helices, and cholesterol BSs. Strikingly, we also observed that the C36 1 μs MD simulations using M2(22-62) embedded in a 20 Å POPC:cholesterol (5:1) scrambled membrane produced frequent interactions with cholesterol, which when combined with computational kinetic analysis, revealed the experimentally observed BSs of cholesterol and suggested three similarly long-interacting positions in the top leaflet that have previously not been observed experimentally. These findings promise to be useful for other viroporin systems.
位于病毒包膜（病毒孔道蛋白）上的离子通道对于传染性病毒的复制具有关键功能，是重要的药物靶点。在过去十年中，由于计算效率的提高，对甲型流感 M2 离子通道的分子动力学（MD）模拟的数量和持续时间都有所增加。在这里，我们旨在确定系统设置和模拟条件，以便正确描述甲型流感 M2 中的蛋白-孔道和蛋白-脂质相互作用，并与实验数据进行比较。我们使用 OPLS2005 和 CHARMM36（C36）力场对甲型流感 M2 蛋白与金刚烷烷抑制剂复合物在标准脂质双层中的进行了大量 MD 模拟。我们探索了改变 M2 结构（M2（22-46）和 M2（22-62））、脂质缓冲大小和类型（较硬的 DMPC 或较软的 POPC 加或不加 20%胆固醇）、模拟时间、H37 质子化位点（N 或 Ν）、W41 通道门的构象状态以及 M2 胆固醇结合位点（BS）对 M2 的影响。我们报告说，200 ns MD 模拟使用 C36 力场的 M2（22-62）（具有 N Η37）和 20 Å 的脂质缓冲液可以准确描述：（a）M2 孔道结构和孔道内的相互作用，即金刚烷烷通道阻滞剂的位置、水笼状结构以及在存在通道阻滞剂时水或氯离子从 M2 孔道的阻断/通过；（b）M2 与膜环境的相互作用，如 M2 束倾斜、两亲性螺旋折叠和胆固醇 BS 的计算所反映的那样。引人注目的是，我们还观察到，使用 M2（22-62）嵌入 20 Å 的 POPC：胆固醇（5:1）混合膜的 C36 1 μs MD 模拟会频繁与胆固醇相互作用，当与计算动力学分析结合使用时，揭示了实验观察到的胆固醇 BS，并提出了三个类似的长相互作用位置，这些位置在顶层中以前没有被实验观察到。这些发现有望对其他病毒孔道蛋白系统有用。
