Inhibitor Scaffolds as New Allele Specific Kinase Substrates
摘要:
The elucidation of protein kinase signaling networks is challenging due to the large size of the protein kinase superfamily (> 500 human kinases). Here we describe a new class of orthogonal triphosphate substrate analogues for the direct labeling of analogue-specific kinase protein targets. These analogues were constructed as derivatives of the Src family kinase inhibitor PP1 and were designed based on the crystal structures of PP1 bound to HCK and N-6-(benzyl)-ADP bound to c-Src (T338G). 3-Benzylpyrazolopyrimidine triphosphate (3-benzyl-PPTP) proved to be a substrate for a mutant of the MAP kinase p38 (p38-T106G/A157L/L167A). 3-Benzyl-PPTP was preferred by v-Src (T338G) (k(cat)/K-M = 3.2 x 10(6) min(-1) M-1) over ATP or the previously described ATP analogue, N-6 (benzyl) ATP. For the kinase CDK2 (F80G)/cyclin E, 3-benzyl-PPTP demonstrated catalytic efficiency (k(cat)/K-M = 2.6 x 10(4) min(-1) M-1) comparable to ATP (k(cat)/K-M = 5.0 x 10(4) min(-1) M-1) largely due to a significantly better K-M (6.4 muM vs 530 muM). In kinase protein substrate labeling experiments both 3-benzyl-PPTP and 3-phenyl-PPTP prove to be over 4 times more orthogonal than N-6-(benzyl)-ATP with respect to the wild-type kinases found in murine spleenocyte cell lysates. These experiments also demonstrate that [gamma-P-32]-3-benzyl-PPTP is an excellent phosphodonor for labeling the direct protein substrates of CDK2 (F80G)/E in murine spleenocyte cell lysates, even while competing with cellular levels (4 mM) of unlabeled ATP. The fact that this new more highly orthogonal nucleotide is accepted by three widely divergent kinases studied here suggests that it is likely to be generalizable across the entire kinase superfamily.
在本研究中,我们着手基于吡唑并[3,4- d ]嘧啶支架合理优化PKD抑制剂。本研究的先导化合物是 1-NM-PP1,我们和其他人之前发现它可以抑制 PKD。在我们的筛选中,我们鉴定出一种化合物 (3-IN-PP1),其效力比 1-NM-PP1 提高 10 倍,为对吡唑并显示敏感性的激酶的特定蛋白激酶抑制剂开辟了新的可能性[3,4- d ]嘧啶衍生的化合物。有趣的是,观察到的 SAR 与通常观察到的结合模式并不完全一致,其中吡唑并[3,4- d ]嘧啶化合物以与 PKD 天然配体 ATP 类似的方式结合。因此,我们建议采用另一种结合模式,其中化合物翻转 180 度。这种基于吡唑并[3,4- d ]嘧啶的化合物的可能的替代结合模式可以为用于对吡唑并[3,4- d ]嘧啶敏感的激酶的新型特异性蛋白激酶抑制剂铺平道路。