Small molecule compounds which form colloidal aggregates in solution are problematic in early drug discovery; adsorption of the target protein by these aggregates can lead to false positives in inhibition assays. In this work, we probe the molecular basis of this inhibitory mechanism using molecular dynamics simulations. Specifically, we examine in aqueous solution the adsorption of the enzymes β-lactamase and PTP1B onto aggregates of the drug miconazole. In accordance with experiment, molecular dynamics simulations observe formation of miconazole aggregates as well as subsequent association of these aggregates with β-lactamase and PTP1B. When complexed with aggregate, the proteins do not exhibit significant alteration in protein tertiary structure or dynamics on the microsecond time scale of the simulations, but they do indicate persistent occlusion of the protein active site by miconazole molecules. MD simulations further suggest this occlusion can occur via surficial interactions of protein with miconazole but also potentially by envelopment of the protein by miconazole. The heterogeneous polarity of the miconazole aggregate surface seems to underpin its activity as an invasive and nonspecific inhibitory agent. A deeper understanding of these protein/aggregate systems has implications not only for drug design but also for their exploitation as tools in drug delivery and analytical biochemistry.

中文翻译：

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小分子聚集如何抑制酶活性？分子动力学研究。

在溶液中形成胶体聚集体的小分子化合物在早期药物开发中存在问题；这些聚集体对靶蛋白的吸附会在抑制试验中导致假阳性。在这项工作中，我们使用分子动力学模拟探索了这种抑制机制的分子基础。具体而言，我们在水溶液中检查酶β-内酰胺酶和PTP1B在药物咪康唑聚集体上的吸附。根据实验，分子动力学模拟观察了咪康唑聚集体的形成以及这些聚集体与β-内酰胺酶和PTP1B的随后缔合。当与聚集体复合时，在模拟的微秒级时间范围内，蛋白质的三级结构或动力学不会发生显着变化，但它们确实表明咪康唑分子会持续阻塞蛋白质活性位点。MD模拟进一步表明，这种闭塞可以通过蛋白质与咪康唑的表面相互作用而发生，也可能通过咪康唑对蛋白质的包裹而发生。咪康唑聚集体表面的异质极性似乎巩固了其作为侵入性和非特异性抑制剂的活性。对这些蛋白质/聚集体系统的更深刻理解不仅对药物设计有影响，而且对将其用作药物递送和分析生物化学的工具也有影响。咪康唑聚集体表面的异质极性似乎巩固了其作为侵入性和非特异性抑制剂的活性。对这些蛋白质/聚集体系统的更深刻理解不仅对药物设计有影响，而且对将其用作药物递送和分析生物化学的工具也有影响。咪康唑聚集体表面的异质极性似乎巩固了其作为侵入性和非特异性抑制剂的活性。对这些蛋白质/聚集体系统的更深刻理解不仅对药物设计有影响，而且对将其用作药物递送和分析生物化学的工具也有影响。