Elucidating the Role of Binding Kinetics in the Development of Abl Kinase Drug Resistance

项目总结 小分子抑制剂的发展使靶向治疗发生了革命性的变化，特别是在 蛋白激酶。然而，制药发展继续受到两个问题的困扰：(一)设计 具有有限的非靶标毒性的特定药物和(Ii)在抗药性突变中的发生 感兴趣的目标。结合动力学的作用，指的是配体与其靶的缔合和解离速率， 在解决这些问题方面未得到充分开发和利用。在非平衡的环境中 人体、药物开、关率已被证明是候选人的最优优化参数 化合物比传统的IC50和Kd指标更高。此外，减少药物滞留时间的突变， 被定义为一种药物与其靶标结合的时间有多长，可能会对治疗产生抵抗力。 伊马替尼是合理药物设计的开创性成果，它抑制bcr-abl癌蛋白并减少了 慢性粒细胞白血病的死亡率降低了80%。伊马替尼对Abl激酶的特异性是由于其 构象选择性，它的成功引发了人们对发现特定的激酶抑制剂的强烈努力 在癌症和炎症性疾病中调节失调。尽管临床上取得了成功，但由于以下原因，再次使用伊马替尼治疗 耐药突变是常见的，并且对突变与配体的距离有一个基本的理解 结合部位引起的耐药性继续困扰着我们。我们已经初步确定了一系列患者衍生的 抗药性突变矛盾地显示伊马替尼的平衡亲和力没有变化。我们还有 证实Abl N368S突变体通过增加药物解离率而导致伊马替尼耐药。因此， 我建议使用这些abl激酶突变作为一个模型系统来探索结合动力学如何影响配体。 特异度、效力和效力。我的中心假设是改变了抑制剂的结合或解离 动力学可以引起不依赖于抑制剂亲和力的耐药性。我将通过测量来探索这一假设 ABL激酶突变对药物滞留时间和疗效的影响及其构象定义 Abl N368S替换的变化。 通过这些研究，我将确定动力阻力突变的结构机制，这是一种新的类型 我相信这种抗药性延伸到整个基因组。我还将阐明关键的结构性因素 Abl激酶的构象交换和伊马替尼解离过程。此外，我还将提供一些见解 探讨如何通过缓慢的离解速率延长体内药物作用，以开发具有 最小的脱靶毒性。该提案的贡献非常重要，因为它们将验证更改 结合动力学作为高度治疗相关蛋白家族中耐药的新机制 并将其作为提高药物特异性的可行策略。

PROJECT SUMMARY The development of small molecule inhibitors has revolutionized targeted therapeutics, especially in the field of protein kinases. However, pharmaceutical development continues to be plagued by two problems: (i) designing specific drugs with limited off-target toxicity and (ii) combating the occurrence of resistance mutations in the target of interest. The role of binding kinetics, referring to a ligand’s association and dissociation rate to its target, are underexplored and underexploited in addressing these issues. In the non-equilibrium environment of the human body, drug on- and off-rates have proven to be superior optimization parameters for candidate compounds than the traditional IC50 and KD metrics. Furthermore, mutations that reduce drug residence time, defined as how long a drug stays bound to its target, can presumably confer resistance to therapy. Imatinib, the seminal achievement of rational drug design, inhibits the BCR-Abl oncoprotein and has reduced the mortality rate for chronic myelogenous leukemia by 80%. Imatinib’s specificity for Abl kinase is due to its conformational selectivity, and its success has sparked intense efforts to discover specific inhibitors of kinases dysregulated in cancer and inflammatory disease. Despite its clinical success, relapse to imatinib therapy due to resistance mutations is common, and a fundamental understanding of how mutations distant from the ligand binding site cause resistance continues to elude us. We have preliminarily identified a series of patient-derived resistance mutations that paradoxically show no change in equilibrium affinity for imatinib. We have also validated that the Abl N368S mutant causes imatinib resistance by increasing drug dissociation rate. Therefore, I propose using these Abl kinase mutations as a model system to explore how binding kinetics affect ligand specificity, potency, and efficacy. My central hypothesis is that altered inhibitor binding or dissociation kinetics could cause resistance independent of inhibitor affinity. I will explore this hypothesis by measuring the effects of Abl kinase mutations on drug residence time and efficacy and by defining the conformational changes of the Abl N368S substitution. Through these studies, I will determine the structural mechanism of “kinetic resistance” mutations, a novel type of drug resistance which I believe extends throughout the kinome. I will also elucidate key structural factors in the conformational exchange of Abl kinase and the imatinib unbinding process. In addition, I will provide insight into how prolonging in vivo drug action through slow dissociation rates can be applied to develop drugs with minimal off-target toxicity. The contributions from this proposal are significant because they will validate altered binding kinetics as both a novel mechanism of drug resistance in a highly-therapeutically relevant protein family and as a viable strategy to improve drug specificity.