Molecule of the Month: c-Abl Protein Kinase and Imatinib

Protein kinases were initially dismissed as targets for cancer chemotherapy. It was well understood that they would make excellent targets since they play significant roles in almost all aspects of cell function, are tightly regulated, and any alterations to their regulation contribute to the development of cancer and other diseases. However, there are many types of kinases in our cells that are all structurally similar and have similar binding sites for ATP. It was long thought that these similarities would inevitably lead to off-target binding and hence side effects for any drugs targeting the active site of these kinases.

Fortunately, structural biology proved these initial reservations to be false. As structures of protein kinases were determined, it was found that their ATP-binding pockets had large enough differences that facilitated the structure-guided discovery and development of selective drugs. The anti-cancer drug imatinib was the breakthrough success. Since then, great strides have been made toward the successful development of selective small-molecule inhibitors for various protein kinases, many being the products of structure-guided drug discovery.

c-Abl, the target of imatinib, is a tyrosine kinase that selectively transfers phosphate groups from ATP to tyrosine. As seen in the computed structure model for the full-length protein (PDB entry AF_AFP00519F1), it is complex with several functional parts. Two regions have stable folded structures and have been studied in detail by x-ray crystallography and NMR spectroscopy: the kinase and regulatory domains (PDB ID 1opl) and the F-actin binding domain (PDB ID 1zzp). They are connected by a long intrinsically disordered segment that ties together these two regions but still allows a lot of flexibility. Finally, there is a short flexible tail at one end, termed the cap region, that is attached to a myristoyl group. The cap region acts as a locking mechanism for the protein, regulating its function. In the inactive state, this myristoyl group binds to a pocket in the kinase domain and induces a conformational change that tightly packs the kinase and regulatory domains together and inhibits catalytic activity. To activate the protein, external cellular signals interact with c-Abl’s regulatory domains and release the myristoyl group from the kinase domain, exposing the active site and allowing phosphorylation of specific substrates.

Genetic abnormalities affecting the c-Abl tyrosine kinase are linked to chronic myelogenous leukemia (CML), a cancer of immature cells in the bone marrow. The cause of CML is a genetic aberration known as the Philadelphia chromosome, formed when a portion of chromosome 9 trades places with a portion of chromosome 22. This balanced translocation of genetic material results in the fusion of the c-abl and bcr genes, which then produces a different protein, called Bcr-Abl. Since it doesn’t include the autoinhibitory cap region and myristoyl group, the mutated tyrosine kinase is constitutively active and does not require activation by the normal cellular signals. Thus, Bcr-Abl allows for continuous cell division. Bcr-Abl also prevents apoptosis, a natural process where a cell induces its own death to prevent accumulation of cancerous cells. The buildup of immature and partially functional blood cells caused by Bcr-Abl have devastating effects on individuals diagnosed with CML, eventually progressing to an acute leukemic condition known as blast phase. Treatment with imatinib or one of the other Bcr-Abl inhibitors approved by the United States Food and Drug Administration has dramatically improved ten-year survival to approximately 85%. Many individuals with CML can now live life-spans nearly as long as those of normal healthy adults.