The ins and outs of bcr-abl inhibition

Abstract

The development of inhibitors against Abl has changed the landscape for the treatment of chronic myelogenous leukemia (CML) and cancer in general. Beginning with the monumental discovery and approval of imatinib for CML, a second generation of inhibitors, nilotinib and dasatinib, has now gained approval for the treatment of CML. Notably, these second-generation inhibitors are active against many of the mutations in the Abl kinase that confer resistance to imatinib. However, resistance remains a major problem, and new inhibitors such as ponatinib and GNF2/GNF5 have been developed, with activity towards the common gatekeeper T315I mutation. We review here the mechanisms of Abl inhibition with an emphasis on structural elements that are important for the selectivity and design of new molecules. In particular, we focus on how changes in the conformation of the P-loop, the activation loop, the DFG motif, and other structural elements of Abl have been instrumental in developing an understanding of inhibitor binding.

Keywords: BCR-ABL; X-ray crystal structure; dasatinib; imatinib; nilotinib; ponatinib.

Figure 1.

ATP-competitive inhibition. Crystal structures of the Abl kinase domain in complex with ATP competitors: (A) imatinib, (B) nilotinib, and (C) dasatinib. The inhibitors are shown in cyan bound to the cleft between the N- and C-lobes of the kinase domain. The P-loop, activation loop, DFG motif, and helix αC are highlighted in red. Also highlighted in red are key residues, namely Thr315, the gatekeeper residue; Asp381 and Ph382, which comprise the first 2 residues of the DFG motif; and Tyr393 in the activation loop that is phosphorylated to activate the kinase. Note that imatinib and nilotinib bind to the inactive state of the kinase domain with the activation loop in the “closed” conformation and the DFG motif in the “in” conformation. By contrast, dasatinib binds the active state of the kinase with the activation loop in an “open” conformation and the DFG motif in the “out” conformation.

Figure 2.

Chemical structures of the ATP competitors imatinib, nilotinib, dasatinib, and ponatinib, as well as the allosteric inhibitor GNF-2.

Figure 3.

Interactions between the ATP competitors and the active site. The ATP competitors Imatinib (A), Nilotinib (B), Desatinib (C), and Ponatinib (D) are shown in cyan (carbon) and elemental colors (blue for N, red for O, yellow for S, gray for Fl, and green for Cl). The protein residues are shown in gray (carbons) and elemental colors. Hydrogen bonds are depicted in dashed lines. Note that imatinib and nilotinib bind the inactive state of Abl in a similar manner, including a hydrogen bond with the main chain amide of interlobe residue Met318, a hydrogen bond with the gatekeeper residue Thr315, hydrophobic interactions with Phe382 from the DFG motif in the “out” conformation, and hydrophobic interactions with Tyr253 from a kinked or collapsed P-loop, among others. Dasatinib lies more towards the “mouth” of the active site and lacks the pharmacore elements to enter the specificity pocket. As a consequence, the kinase is in the active state with the DFG motif in the “in” conformation. Ponatinib is characterized by a carbon-carbon triple bond (ethynyl linkage) between the methylphenyl and purine groups. There is a hydrogen bond to Thr315, and there is no steric interference when Thr315 is mutated to isoleucine.

Figure 4.

Mapping of residues on the Abl kinase domain that are commonly mutated in imatinib resistance. Most of the residues map close to the imatinib binding site, including Th315, the gatekeeper residue; Leu248, Gly250, Gln252, and Tyr252 that map to the P-loop; Met351, Glu355, and Phe359 that map to the activation loop; and Glu279 that maps to helix αC. Some residues such as Asp276 and Glu459 map further away from the imatinib binding site, and it is not clear how they confer resistance to imatinib.

Figure 5.

Allosteric inhibition. Crystal structure of the Abl kinase domain in complex with imatinib and GNF-2. GNF-2 binds to the myristate site and induces a bend in the C-terminal helix (αI) in the C-lobe of the kinase domain. Although the GNF-2 binding site is far away from the imatinib binding site, the binding of GNF-2 causes a dynamic perturbation of residues near Thr315 that allows imatinib to tolerate isoleucine at this position.