Prevalent resistance to inhibitors that target the influenza A M2 proton channel has necessitated a continued drug design effort, supported by a sustained study of the mechanism of channel function and inhibition. Recent high-resolution X-ray crystal structures present the first opportunity to see how the adamantyl amine class of inhibitors bind to M2 and disrupt and interact with the channel’s water network, providing insight into the critical properties that enable their effective inhibition in wild-type M2. In this work, we examine the hypothesis that these drugs act primarily as mechanism-based inhibitors by comparing hydrated excess proton stabilization during proton transport in M2 with the interactions revealed in the crystal structures, using the Multiscale Reactive Molecular Dynamics (MS-RMD) methodology. MS-RMD, unlike classical molecular dynamics, models the hydrated proton (hydronium-like cation) as a dynamic excess charge defect and allows bonds to break and form, capturing the intricate interactions between the hydrated excess proton, protein atoms, and water. Through this, we show that the ammonium group of the inhibitors is effectively positioned to take advantage of the channel’s natural ability to stabilize an excess protonic charge and act as a hydronium mimic. Additionally, we show that the channel is especially stable in the drug binding region, highlighting the importance of this property for binding the adamantane group. Finally, we characterize an additional hinge point near Val27, which dynamically responds to charge and inhibitor binding. Altogether, this work further illuminates a dynamic understanding of the mechanism of drug inhibition in M2, grounded in the fundamental properties that enable the channel to transport and stabilize excess protons, with critical implications for future drug design efforts.

中文翻译：

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通过过量质子稳定和通道动力学机制了解甲型流感 M2 抑制剂结合

对靶向甲型流感 M2 质子通道的抑制剂普遍存在耐药性，因此需要继续进行药物设计工作，并通过对通道功能和抑制机制的持续研究提供支持。最近的高分辨率 X 射线晶体结构提供了第一个机会来了解金刚胺类抑制剂如何与 M2 结合并破坏通道的水网络并与之相互作用，从而深入了解能够有效抑制野生型的关键特性M2。在这项工作中，我们使用多尺度反应分子动力学 (MS-RMD) 方法，通过比较 M2 质子传输过程中水合过量质子的稳定性与晶体结构中揭示的相互作用，检验了这些药物主要作为基于机制的抑制剂的假设. MS-RMD，与经典分子动力学不同，它将水合质子（类水合氢离子）建模为动态过量电荷缺陷，并允许键断裂和形成，捕捉水合过量质子、蛋白质原子和水之间的复杂相互作用。通过这个，我们表明抑制剂的铵基被有效地定位以利用通道的天然能力来稳定过量的质子电荷并充当水合氢模拟物。此外，我们表明该通道在药物结合区域特别稳定，突出了该特性对于结合金刚烷基团的重要性。最后，我们表征了 Val27 附近的一个额外的铰链点，它动态响应电荷和抑制剂的结合。共，