Targeting transient protein states for the design of chemical probes of Cyclophilins function

该项目的主要目标是利用化学、结构和计算生物学的一系列最先进的方法，为开发亲环素功能的新型化学探针做出贡献。抑制不同的亲环素亚型可以为免疫抑制、神经保护和病毒疾病等不同领域的新治疗方法铺平道路。然而，由于选择性地抑制给定的亲环素亚型的挑战，药物开发努力在历史上一直受到限制。我们的实验室长期以来一直对使用生物物理和计算方法来发现新型亲环素配体1感兴趣。在这个博士项目中，您将在我们以前和当前工作的基础上，通过利用蛋白质动力学来揭示在结构中不容易通过X射线结晶学实验解决的瞬时蛋白质状态，从而实现亲环素抑制的挑战。我们开发了一种方法，通过一种综合的结构生物学方法来检测这种瞬时蛋白质状态，该方法将X射线结晶学和蛋白质核磁共振测量与分子动力学模拟相结合，以提供亲环素的动力学模型。模型分析为合理设计小分子提供了信息，以选择性地结合和稳定这些暂态。这样的小分子是从现有的文库中挑选出来的，或者是合成的，并使用核磁共振和等温滴定量热法实验来分析结合和功能行为。通过瞄准特定亲环素异构体特有的瞬时蛋白质状态，您将识别具有高亚型选择性的小分子。

The main objective of this project is to contribute to the development of novel chemical probes of Cyclophilins function using a range of state-of the art methodologies from chemical, structural and computational biology. Inhibition of diverse Cyclophilin isoforms could pave the way for novel therapeutic treatments in diverse areas of immunosuppression, neuroprotection, and viral diseases. Yet drug development efforts have been limited historically due to the challenge of selectively inhibiting a given Cyclophilin isoform. Our laboratories have a long-standing interest in the use of biophysical and computational methods to discover novel Cyclophilin ligands.1. In this PhD project you will build on our previous and current body of work and pursue the challenge of Cyclophilin inhibition by exploiting protein dynamics to reveal transient protein states that are not apparent in structures readily solved by X-ray crystallography experiments.2. We have developed a methodology to detect such transient protein states via an integrative structural biology approach that combines X-ray crystallography and protein NMR measurements with molecular dynamics simulations to deliver dynamical models of Cyclophilins. Model analysis informs the rational design of small molecules to selectively bind and stabilize such transient states. Such small molecules are selected from existing libraries, or synthesized and assayed for binding and functional behaviour using NMR and isothermal titration calorimetry experiments. Through targeting a transient protein state that is unique to a given Cyclophilin isoform, you will identify small molecules with high sub-type selectivity.