The accurate experimental estimation of protein–ligand systems’ residence time (τ) has become very relevant in drug design projects due to its importance in the last stages of refinement of the drug’s pharmacodynamics and pharmacokinetics. It is now well-known that it is not sufficient to estimate the affinity of a protein-drug complex in the thermodynamic equilibrium process in in vitro experiments (closed systems), where the concentrations of the drug and protein remain constant. On the contrary, it is mandatory to consider the conformational dynamics of the system in terms of the binding and unbinding processes between protein and drugs in in vivo experiments (open systems), where their concentrations are in constant flux. This last model has been proven to dictate much of several drugs’ pharmacological activities in vivo. At the atomistic level, molecular dynamics simulations can explain why some drugs are more effective than others or unveil the molecular aspects that make some drugs work better in one molecular target. Here, the protein kinases Aurora A/B, complexed with its inhibitor Danusertib, were studied using conventional and enhanced molecular dynamics (MD) simulations to estimate the dissociation paths and, therefore, the computational τ values and their comparison with experimental ones. Using classical molecular dynamics (cMD), three differential residues within the Aurora A/B active site, which seems to play an essential role in the observed experimental Danusertib’s residence time against these kinases, were characterized. Then, using WT-MetaD, the relative Danusertib‘s residence times against Aurora A/B kinases were measured in a nanosecond time scale and were compared to those τ values observed experimentally. In addition, the potential dissociation paths of Danusertib in Aurora A and B were characterized, and differences that might be explained by the differential residues in the enzyme’s active sites were found. In perspective, it is expected that this computational protocol can be applied to other protein–ligand complexes to understand, at the molecular level, the differences in residence times and amino acids that may contribute to it.

中文翻译：

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了解 Danusertib 在 Aurora 激酶 A/B 中的停留时间的差异：使用传统和增强型分子动力学模拟识别的解离路径和关键残留物


蛋白质-配体系统停留时间 (τ) 的准确实验估计在药物设计项目中变得非常重要，因为它在药物药效学和药代动力学细化的最后阶段非常重要。现在众所周知，在体外实验（封闭系统）中，药物和蛋白质的浓度保持恒定，在热力学平衡过程中估计蛋白质-药物复合物的亲和力是不够的。相反，必须根据体内实验（开放系统）中蛋白质和药物之间的结合和解离过程来考虑系统的构象动力学，其中它们的浓度处于恒定变化。最后一个模型已被证明可以决定多种药物的体内药理活性。在原子水平上，分子动力学模拟可以解释为什么某些药物比其他药物更有效，或者揭示使某些药物在一个分子靶点上发挥更好作用的分子方面。在这里，使用传统和增强的分子动力学 (MD) 模拟来研究蛋白激酶 Aurora A/B 及其抑制剂 Danusertib 的复合物，以估计解离路径，从而估计计算的 τ 值及其与实验值的比较。使用经典分子动力学 (cMD)，对 Aurora A/B 活性位点内的三个差异残基进行了表征，这似乎在观察到的实验 Danusertib 针对这些激酶的停留时间中发挥着重要作用。然后，使用 WT-MetaD，以纳秒时间尺度测量 Danusertib 针对 Aurora A/B 激酶的相对停留时间，并与实验观察到的 τ 值进行比较。 此外，还对 Aurora A 和 B 中 Danusertib 的潜在解离路径进行了表征，并发现了可能由酶活性位点中的差异残基解释的差异。从角度来看，预计该计算协议可以应用于其他蛋白质-配体复合物，以在分子水平上了解可能有助于其的停留时间和氨基酸的差异。