N-Myristoylated c-Abl Tyrosine Kinase Localizes to the Endoplasmic Reticulum upon Binding to an Allosteric Inhibitor

Allosteric kinase inhibitors hold promise for revealing unique features of kinases that may not be apparent using conventional ATP-competitive inhibitors. Here we explore the activity of a previously reported allosteric inhibitor of BCR-Abl kinase, GNF-2, against two cellular isoforms of Abl tyrosine kinase: one that carries a myristate in the N terminus and the other that is deficient in N-myristoylation. Our results show that GNF-2 inhibits the kinase activity of non-myristoylated c-Abl more potently than that of myristoylated c-Abl by binding to the myristate-binding pocket in the C-lobe of the kinase domain. Unexpectedly, indirect immunofluorescence reveals a translocation of myristoylated c-Abl to the endoplasmic reticulum in GNF-2-treated cells, whereas GNF-2 has no detectable effect on the localization of non-myristoylated c-Abl. These results indicate that GNF-2 competes with the NH₂-terminal myristate for binding to the c-Abl kinase myristate-binding pocket and that the exposed myristoyl group accounts for the localization to the endoplasmic reticulum. We also demonstrate that GNF-2 can inhibit enzymatic and cellular kinase activity of Arg, a kinase highly homologous to c-Abl, which is also likely to be regulated through intramolecular binding of an NH₂-terminal myristate lipid. These results suggest that non-ATP-competitive inhibitors, such as GNF-2, can serve as chemical tools that can discriminate between c-Abl isoform-specific behaviors.The catalytic activity of a protein kinase can be modulated by binding of a ligand to a site distant from the active site, also referred to as the allosteric site (1). The ligand is referred to as an allosteric kinase inhibitor and induces a protein conformation that is not compatible with kinase activity. Allosteric inhibitors can potentially be exploited to elucidate kinase functions not discovered using ATP-competitive inhibitors, because they can exploit binding sites and regulatory mechanisms that are unique to a particular kinase.The c-Abl and Arg (Abl-related gene) proteins comprise the Abl family of non-receptor tyrosine kinases. Each family member has two isoforms: one that is myristoylated in the N terminus (1b or IV) and the other that is deficient in N-myristoylation due to an alternative splicing of the first exon (1a or I) (Fig. 1A). N-Myristoylation often serves as a mechanism for targeting proteins to cellular membranes. However, Abl family members localize to multiple subcellular compartments; whereas Arg is mostly found in the cytoplasm, c-Abl shuttles between the nucleus and the cytoplasm, where it localizes to the cytosol, endoplasmic reticulum, and mitochondria (2).Open in a separate windowFIGURE 1.A, domain structure of Abl family members (5). The numbers indicate amino acid residues in c-Abl 1b, and the recombinant protein constructs used in this study encompass amino acids 65–534, 83–534, and 248–531. B, ribbon representation of the c-Abl kinase NH₂-terminal half residues, including the SH3, SH2, and kinase domains (Protein Data Bank code 1OPK) (7). The NH₂-terminal cap (amino acids 2–79) is indicated by dotted lines (8). The myristate-binding site and ATP binding pocket are indicated by arrows. C, ribbon representation of an enlarged view of GNF-2 (colored gold) bound to the c-Abl myristate binding site. The location of Ala³⁵⁶ is indicated.The Abl family members share a high degree of sequence identity (∼90%) in the NH₂-terminal half residues, including the SH3,² SH2, and kinase domains (3). The kinase domain is followed by proline-rich motifs that serve as binding sites for SH3 domains. A range of proteins are reported to bind directly or indirectly to the SH3, SH2, and proline-rich domains of c-Abl and are implicated in the proper regulation of the kinase activities of Abl family members in the cytoplasm (4–6). In addition, as revealed by recent crystallographic analyses of inactive and assembled form of recombinant Abl, the kinase activity of c-Abl is modulated by the intrinsic binding of the N-myristoyl residue to a hydrophobic pocket in the C-lobe of the kinase domain, which induces conformational changes in the kinase domain and subsequently allows the SH3 and SH2 domains to pack against the kinase domain (7, 8). Altogether, these observations suggest that the kinase activities of Abl family members in normal cells are tightly regulated by both intra- and intermolecular interactions (2, 9). Disruption of these strong regulatory mechanisms results in deregulated kinase activity, as illustrated by the BCR-Abl and v-Abl oncoproteins.Recent years have seen great advances in pharmacological inhibition of deregulated c-Abl kinase activity. Among the small molecule inhibitors targeting BCR-Abl kinase are imatinib (STI-571; Gleevec), nilotinib (AMN 107), and dasatinib (BMS-354825) (10). These small molecules have been used not only for clinical intervention in patients with leukemia but also as chemical tools to further dissect BCR-Abl kinase-linked signaling pathways in tissue culture cells (11). However, efforts to analyze the effects of monospecific inhibition of BCR-Abl kinase have been complicated by cross-reactivity of ATP-competitive Abl inhibitors with other kinases. For example, in addition to inhibiting c-Abl and BCR-Abl, STI-571 and nilotinib also potently inhibit c-Kit, platelet-derived growth factor receptor, and DDR1, whereas dasatinib potently inhibits all of these kinases as well as the Src family, Tec family, and KDR kinases (12). The multitargeted nature of these ATP-competitive inhibitors makes it difficult to assign a particular biological effect to inhibition of a specific kinase target.We previously reported the discovery of the first non-ATP site-monoselective BCR-Abl inhibitor (GNF-2), which targets not only wild type BCR-Abl but also many clinically relevant STI-571-resistant mutants either alone or in combination with other BCR-Abl inhibitors (13). Molecular modeling, site-directed mutagenesis, competition assays, NMR spectroscopy, and protein crystallography were used to determine that GNF-2 binds to a myristate-binding site in the C-lobe of the c-Abl kinase domain (Fig. 1, B and C) (3). The discovery of GNF-2 was the first demonstration that c-Abl kinase activity could be pharmacologically modulated by an inhibitor that binds outside the ATP or substrate binding sites. Although it remained unclear how GNF-2 is capable of inhibiting c-Abl upon binding to the myristate-binding site, we speculated that GNF-2 probably mimics the function of the N-myristoyl residue in c-Abl. Here, we investigated the effects of GNF-2 on Abl family members with the goals of providing further insights into the mechanism of GNF-2 function and laying the foundation to utilize GNF-2 as a tool to investigate c-Abl- and Arg-linked cellular processes.     

Enhanced SH3/Linker Interaction Overcomes Abl Kinase Activation by Gatekeeper and Myristic Acid Binding Pocket Mutations and Increases Sensitivity to Small Molecule Inhibitors

Multidomain kinases such as c-Src and c-Abl are regulated by complex allosteric interactions involving their noncatalytic SH3 and SH2 domains. Here we show that enhancing natural allosteric control of kinase activity by SH3/linker engagement has long-range suppressive effects on the kinase activity of the c-Abl core. Surprisingly, enhanced SH3/linker interaction also dramatically sensitized the Bcr-Abl tyrosine kinase associated with chronic myelogenous leukemia to small molecule inhibitors that target either the active site or the myristic acid binding pocket in the kinase domain C-lobe. Dynamics analyses using hydrogen exchange mass spectrometry revealed a remarkable allosteric network linking the SH3 domain, the myristic acid binding pocket, and the active site of the c-Abl core, providing a structural basis for the biological observations. These results suggest a rational strategy for enhanced drug targeting of Bcr-Abl and other multidomain kinase systems that use multiple small molecules to exploit natural mechanisms of kinase control.     

Structure and Dynamic Regulation of Abl Kinases

The c-abl proto-oncogene encodes a unique protein-tyrosine kinase (Abl) distinct from c-Src, c-Fes, and other cytoplasmic tyrosine kinases. In normal cells, Abl plays prominent roles in cellular responses to genotoxic stress as well as in the regulation of the actin cytoskeleton. Abl is also well known in the context of Bcr-Abl, the oncogenic fusion protein characteristic of chronic myelogenous leukemia. Selective inhibitors of Bcr-Abl, of which imatinib is the prototype, have had a tremendous impact on clinical outcomes in chronic myelogenous leukemia and revolutionized the field of targeted cancer therapy. In this minireview, we focus on the structural organization and dynamics of Abl kinases and how these features influence inhibitor sensitivity.