Structure Based Drug Design of Crizotinib (PF-02341066), a Potent and Selective Dual Inhibitor of Mesenchymal–Epithelial Transition Factor (c-MET) Kinase and Anaplastic Lymphoma Kinase (ALK)

Abstract

Because of the critical roles of aberrant signaling in cancer, both c-MET and ALK receptor tyrosine kinases are attractive oncology targets for therapeutic intervention. The cocrystal structure of 3 (PHA-665752), bound to c-MET kinase domain, revealed a novel ATP site environment, which served as the target to guide parallel, multiattribute drug design. A novel 2-amino-5-aryl-3-benzyloxypyridine series was created to more effectively make the key interactions achieved with 3. In the novel series, the 2-aminopyridine core allowed a 3-benzyloxy group to reach into the same pocket as the 2,6-dichlorophenyl group of 3 via a more direct vector and thus with a better ligand efficiency (LE). Further optimization of the lead series generated the clinical candidate crizotinib (PF-02341066), which demonstrated potent in vitro and in vivo c-MET kinase and ALK inhibition, effective tumor growth inhibition, and good pharmaceutical properties.

The R1275Q Neuroblastoma Mutant and Certain ATP-competitive Inhibitors Stabilize Alternative Activation Loop Conformations of Anaplastic Lymphoma Kinase

“…The most notable is Gleevec (imatinib), which is a type II kinase inhibitor targeting the DFG-out conformation of its targets c-Abl and c-kit (64). Crizotinib itself does this in its complex with c-Met, the kinase toward which it was initially targeted, by interacting with Tyr 1230 on a unique, inactive conformation of the A-loop (19). Perturbations to the wild-type, inactive ALK kinase domain structure do occur and alternative conformations can be trapped by small molecule inhibitors as we have shown.…”

“…During the course of these investigations, we sought to understand the structural basis for activation of ALK by the two most common neuroblastoma mutants, F1174L and R1275Q. We report here crystal structures of both mutants and we use the published structure of the ALK-crizotinib complex to show that these mutants produce no steric impediment to crizotinib binding (19). In addition, during the course of our medicinal chemistry efforts two other classes of ALK inhibitors were identified that stabilized the ALK A-loop in previously unobserved conformations.…”

“…All of the structures described in this work use ALK(1084 -1410) C1097S. By way of comparison, ALK kinase domain structures have also been determined using constructs with the boundaries 1072-1410, 1094 -1407, 1093-1411, and 1069 -1411 (19,38,39,52).…”

“…Model generation of crizotinib binding to the F1174L and R1275Q neuroblastoma mutants used the published co-crystal structure of crizotinib in complex with wild-type ALK (19) and took advantage of the similarities between the mutant and wildtype structures. Both secondary structure matching and simple least squares matching algorithms gave excellent superposition of the F1174L-ALK and R1275Q-ALK structures onto the wildtype ALK-crizotinib structure (PDB ID 2XP2).…”

Advances in ALK Targeted Therapy for Neuroblastoma

“…It is an oral small-molecule tyrosine kinase inhibitor, originally developed as a c-MET inhibitor and later found an inhibitor for ALK phosphorylation [30,31]. In vitro studies demonstrated that crizotinib is potent in neuroblastoma cell lines with ALK amplification or the R1275Q mutation, one of the most common ALK variants in neuroblastoma [32].…”