Computational and experimental studies of targets of protein kinase inhibitors

描述(由申请人提供)：拟议的研究将是一项关于蛋白激酶和小分子抑制剂之间相互作用的实验和计算相结合的研究。蛋白激酶与许多疾病有关，因此是有吸引力的治疗靶点。然而，设计小分子激酶抑制剂的一个主要挑战是如何开发出专门针对目标激酶的抑制剂，同时使体内数百种其他激酶不受影响。为了实现这一目标，需要了解控制抑制剂-激酶相互作用的特异性的因素，而要做到这一点，一种方法是开发能够准确预测抑制剂-激酶复合体的相对亲和力的计算方法。拟议的研究计划旨在通过与一些实验研究相结合来测试、扩展和完善这种计算方法。具体目标包括：(1)将测量商业上可用的小分子抑制剂的抑制常数，其范围约为10个蛋白激酶靶标。这些研究将提供关于抑制剂-激酶相互作用的新的定量数据。(2)用等温滴定量热法测定抑制剂-激酶复合体的结合热力学。结合自由能、结合热焓和结合熵的单独测量将被用来对抑制物-激酶结合作用的能量描述进行参数化。(3)解决了具有不同蛋白激酶靶点的复合体中抑制剂的晶体结构问题。这些研究将提供一个直接和全面的观点，即当一个特定的抑制剂与不同的蛋白激酶复合时，其结合方向发生了多大程度的变化。(4)从AIMS 1-3获得的实验数据将用于开发和测试一种计算方法，用于准确预测一种抑制剂与所有大约500个人蛋白激酶的相对结合亲和力。蛋白激酶与许多不同的癌症类型有关，越来越多地被视为治疗药物的重要靶点。这里提出的这项研究直接解决了对激酶治疗追求的最大挑战：如何设计小分子抑制剂，以特异性地抑制目标激酶。

DESCRIPTION (provided by applicant): The proposed research will be a combined experimental and computational study of the interactions between protein kinases and small molecule inhibitors. Protein kinases are implicated in a number of diseases, and are therefore attractive therapeutic targets. A major challenge however in designing small molecule inhibitors of kinases is how to develop inhibitors that specifically target a kinase of interest while leaving the hundreds of other kinases in the body unaffected. In order to achieve this goal, the factors that control the specificity of inhibitor-kinase interactions need to be understood, and one way to do this is to develop computational methodologies that can accurately predict the relative affinities of inhibitor-kinase complexes. The proposed research plan aims to test, extend and refine such a computational methodology through combination with a number of experimental studies. The specific aims involve: (1) Inhibition constants of commercially available small molecule inhibitors with a range of approximately 10 protein kinase targets will be measured. These studies will provide new quantitative data on inhibitor-kinase interactions. (2) The binding thermodynamics of inhibitor-kinase complexes will be measured with isothermal titration calorimetry. Separate measurements of binding free energies, enthalpies and entropies will be used to parameterize an energetic description of inhibitor-kinase binding interactions. (3) The crystal structures of inhibitors in complex with a range of different protein kinase targets will be solved. These studies will provide a direct and comprehensive view of the extent to which the binding orientations adopted by a given inhibitor change when complexed with different protein kinases. (4) The experimental data obtained from Aims 1-3 will be used to develop and test a computational method for accurately predicting the relative binding affinities of an inhibitor with all approximately 500 human protein kinases. Protein kinases, being implicated in a large number of different cancer types, are increasingly seen as very important targets for therapeutic drugs. The research proposed here directly addresses the single greatest challenge to the therapeutic pursuit of kinases: how to design small molecule inhibitors that can specifically inhibit a kinase of interest.