ATP Site Ligands Determine the Assembly State of the Abelson Kinase Regulatory Core via the Activation Loop Conformation

Abstract

The constituent SH3, SH2, and kinase domains of the Abl kinase regulatory core can adopt an assembled (inactive) or a disassembled (active) conformation. We show that this assembly state strictly correlates with the conformation of the kinase activation loop induced by a total of 14 ATP site ligands, comprising all FDA-approved Bcr-Abl inhibiting drugs. The disassembly of the core by certain (type II) ligands can be explained by an induced push on the kinase N-lobe via A- and P-loop toward the SH3 domain. A similar sized P-loop motion is expected during nucleotide binding and release, which would be impeded in the assembled state, in agreement with its strongly reduced kinase activity.

How ATP-Competitive Inhibitors Allosterically Modulate Tyrosine Kinases That Contain a Src-like Regulatory Architecture

“…Conversely, the SH3 domain of Abl-1 V256C/2a complex was efficiently enriched by the immobilized SH3 ligand, consistent with DFG-out stabilizing inhibitor 2a promoting an open, intramolecularly disengaged Abl-1 SH3-SH2-CD module, like its underivatized counterpart. Thus, consistent with previous observations, 25,29 an inhibitor that stabilizes the DFG-out inactive ATP-binding site conformation significantly promotes a regulatory domain-disengaged conformation of Abl-1's SH3-SH2-CD module. Inhibitors that stabilize the helix aC-out inactive ATP-binding site conformation promote a closed Abl-1's SH3-SH2-CD module, which further highlights the Src-like allosteric communication between Abl-1's regulatory domains and its ATP-binding site.…”

“…Recent studies have shown that the ability of inhibitors to flip the DFG-motif of Abl-1's activation loop highly correlates with their promotion of an open global conformation of Abl-1's SH3-SH2-CD module. 29 Our observations in Src made us interested in revisiting the molecular binding features of 14 ligands that have previously been reported to promote an open global conformation of Abl-1, which was determined by characteristic NMR 1 H-15 N backbone chemical shifts within the SH3 and SH2 domains ( Figure S4). 29 We found that all inhibitors-including imatinib, nilotinib, ponatinib, rebastinib, and bafetinib-that promote an open global conformation of Abl-1's SH3-SH2-CD module also form a H-bonding interaction with the side-chain of Abl-1's Glu286 that stabilize its helix aC in the active conformation ( Figure S5).…”

“…29 Our observations in Src made us interested in revisiting the molecular binding features of 14 ligands that have previously been reported to promote an open global conformation of Abl-1, which was determined by characteristic NMR 1 H-15 N backbone chemical shifts within the SH3 and SH2 domains ( Figure S4). 29 We found that all inhibitors-including imatinib, nilotinib, ponatinib, rebastinib, and bafetinib-that promote an open global conformation of Abl-1's SH3-SH2-CD module also form a H-bonding interaction with the side-chain of Abl-1's Glu286 that stabilize its helix aC in the active conformation ( Figure S5). In contrast, inhibitors that lack the ability to form a H-bonding interaction with Glu286 do not promote an open global conformation of Abl-1 ( Figure S4B).…”

“…[25][26][27][28] Specifically, the ability of inhibitors to flip the DFG-motif in the activation loop correlates with their abilities to promote an open global conformation of Abl-1's SH3-SH2-CD module. 29 Beyond the SFKs and Abl-1/Arg, there are at least 10 additional tyrosine kinases that contain an SH3-SH2-CD module ( Figure S1). 30 It is currently unknown whether inhibitors that stabilize the DFG-out and helix aC-out inactive ATP-binding site conformations can also allosterically modulate the global conformation of SH3-SH2-CD modules of tyrosine kinases beyond the SFKs.…”

Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants

“…Less of an issue perhaps since Class-5 and Class-6 conformations that were obtained from the released ligand-bound structures (Figure 1b), as well as taking conformational flexibility into account, suggests that the EGFR kinase-ligand binding would induce a specific binding mode and EGFR kinase conformation change. Recently, Sonti et al 38 reported a similar ligand-induced binding mechanism for Abelson tyrosine kinase (Abl). Abl belongs to the TK group, like the EGFR kinase, and has 60% sequence similarity 48 .…”