X‐Ray Crystal Structure of Bone Marrow Kinase in the X Chromosome: A Tec Family Kinase

Abstract

Bone marrow kinase in the X chromosome, a member of the Tec family of tyrosine kinases, plays a role in both monocyte ⁄ macrophage trafficking as well as cytokine secretion. Although the structures of Tec family kinases Bruton's tyrosine kinase and IL-2-inducible T-cell kinase are known, the crystal structures of other Tec family kinases have remained elusive. We report the X-ray crystal structures of bone marrow kinase in the X chromosome in complex with dasatinib at 2.4 Å resolution and PP2 at 1.9 Å resolution. The bone marrow kinase in the X chromosome structures reveal a typical kinase protein fold; with well-ordered protein conformation that includes an open ⁄ extended activation loop and a stabilized DFG-motif rendering the kinase in an inactive conformation. Dasatinib and PP2 bind to bone marrow kinase in the X chromosome in the ATP binding pocket and display similar binding modes to that observed in other Tec and Src protein kinases. The bone marrow kinase in the X chromosome structures identify conformational elements of the DFG-motif that could potentially be utilized to design potent and ⁄ or selective bone marrow kinase in the X chromosome inhibitors.

Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

“…We also simulated conformational dynamics of Dasatinib binding using crystal structures of Dasatinib complexes with ABL [23], SRC [40], LYN [41], EPHA4 [42], BMX [43], and BTK [44], and P38 kinases. The projection of MD trajectories onto the essential space of low frequency modes revealed characteristic similarities in the distribution of structurally rigid and conformationally flexible regions of the kinase core (S1 Fig).…”

“…Large-scale profiling studies have revealed a significant promiscuity of Dasatinib that can target over 30 different tyrosine and Ser/Thr kinases [35–39]. Crystal structures of Dasatinib complexes with ABL [23], SRC [40], LYN [41], EPHA4 [42], BMX [43], and BTK kinases [44] have supported the notion that functional promiscuity of this inhibitor may be associated with conformational tolerance to multiple kinase forms. Structural plasticity of protein kinase conformations in complexes with Dasatinib ranged from fully active DFG-in states (in ABL, SRC, LYN, EPHA4, and BTK kinases) to an inactive DFG-out conformation of BMX [43], and an intermediate DFG-out form of BTK kinase [44].…”

“…Crystal structures of Dasatinib complexes with ABL [23], SRC [40], LYN [41], EPHA4 [42], BMX [43], and BTK kinases [44] have supported the notion that functional promiscuity of this inhibitor may be associated with conformational tolerance to multiple kinase forms. Structural plasticity of protein kinase conformations in complexes with Dasatinib ranged from fully active DFG-in states (in ABL, SRC, LYN, EPHA4, and BTK kinases) to an inactive DFG-out conformation of BMX [43], and an intermediate DFG-out form of BTK kinase [44]. NMR studies of Dasatinib binding with ABL kinase [45] have reassured structural preferences of the inhibitor to bind an active DFG-in form, but this conformational state may not be mandatory for a productive inhibitor binding.…”

Design, Synthesis, and Evaluation of Dasatinib–Amino Acid and Dasatinib–Fatty Acid Conjugates as Protein Tyrosine Kinase Inhibitors

“…The Boc protecting group from the coupled amino acid derivatives was removed in the presence of para-toluenesulfonic acid (pTsOH) in acetonitrile. The crude products were purified by flash silica gel columnc hromatography.A ll synthesized compounds were characterized by 1 Ha nd 13 CNMR spectroscopy and high-resolution time-of-flight electrospray mass spectrometry.T he purity of final products (! 95 %) was confirmed by reversed-phasea nalytical HPLC.…”

“…[5] It has also been crystallized as ab ound ligand to Abl, BMX, BTK, EphA4,L yn, p38a,p 38MAP,a nd Src kinases. [7][8][9][10][11][12][13][14] The common manner by which it binds to each of thesek inases suggestsi t should be similar for many other kinases as well. This may,i n part, explain the sidee ffects of the compound at clinical dosage.…”