Recent crystallography studies have shown that the binding site oxyanion hole plays an important role in inhibitor binding, but can exist in two conformations (active/inactive). We have undertaken molecular dynamics (MD) calculations to better understand oxyanion hole dynamics and thermodynamics. We find that the Zika virus (ZIKV) NS2B/NS3 protease maintains a stable closed conformation over multiple 100-ns conventional MD simulations in both the presence and absence of inhibitors. The S1, S2, and S3 pockets are stable as well. However, in two of eight simulations, the A132-G133 peptide bond in the binding pocket of S1' spontaneously flips to form a 310 -helix that corresponds to the inactive conformation of the oxyanion hole, and then maintains this conformation until the end of the 100-ns conventional MD simulations without inversion of the flip. This conformational change affects the S1' pocket in ZIKV NS2B/NS3 protease active site, which is important for small molecule binding. The simulation results provide evidence at the atomic level that the inactive conformation of the oxyanion hole is more favored energetically when no specific interactions are formed between substrate/inhibitor and oxyanion hole residues. Interestingly, however, transition between the active and inactive conformation of the oxyanion hole can be observed by boosting the valley potential in accelerated MD simulations. This supports a proposed induced-fit mechanism of ZIKV NS2B/NS3 protease from computational methods and provides useful direction to enhance inhibitor binding predictions in structure-based drug design.

中文翻译：

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MD模拟显示Zika病毒NS2B / NS3蛋白酶中氧阴离子孔的替代构象。

最近的晶体学研究表明，结合位点氧阴离子孔在抑制剂结合中起着重要作用，但可以两种构象存在（有活性/无活性）。我们进行了分子动力学（MD）计算，以更好地了解氧阴离子孔动力学和热力学。我们发现在存在和​​不存在抑制剂的情况下，寨卡病毒（ZIKV）NS2B / NS3蛋白酶在多个100 ns常规MD模拟中均保持稳定的闭合构象。S1，S2和S3口袋也很稳定。但是，在八个模拟中的两个模拟中，S1'的结合口袋中的A132-G133肽键自发地翻转形成一个310螺旋，该螺旋对应于氧阴离子孔的非活性构象，然后保持这种构象，直到100 ns传统MD模拟结束，而不会翻转。这种构象变化影响ZIKV NS2B / NS3蛋白酶活性位点的S1'口袋，这对于小分子结合很重要。模拟结果提供了在原子水平上的证据，当在底物/抑制剂与氧阴离子孔残基之间未形成特定的相互作用时，氧阴离子孔的非活性构象在能量上更为有利。然而，有趣的是，可以通过在加速的MD模拟中提高谷底电势来观察氧阴离子孔的活性构象和非活性构象之间的过渡。