Do mutations in the Anaplastic Lymphoma Kinase affect Crizotinib's Binding Affinity?

Anaplastic lymphoma kinase (ALK) is a tyrosine kinase receptor implicated in cancers like breast cancer, non-small cell lung carcinoma, and neuroblastoma. Crizotinib, an ALK inhibitor, initially succeeded as a treatment for such cancers before mutations caused its failure. We investigated the mechanism of resistance due to mutations like C1156Y, L1196M, G1269A, L1198F, and C1156Y/L1198F through validated computational methods and published experimental data. Our analysis reveals that these mutations do not reduce the binding affinity or alter the binding conformation of crizotinib, consistent with published X-ray crystallographic and biochemical data. This study is the first to show the conformational change in ALK's activation loop (A-loop) due to phosphorylation, as there is no experimental structure for phosphorylated ALK. Principal component analysis confirms that A-loop dynamics is primarily responsible for ALK activation, explaining the changes in catalytic efficiency due to phosphorylation or mutants like C1156Y and L1198F. Our results conclusively demonstrate that mutations like C1156Y influence A-loop dynamics, leading to an ATP-independent activation. Therefore, ATP competitive inhibitors like crizotinib will inevitably lose their therapeutic effectiveness without losing their binding affinity to ALK.