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

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.