The reversible inhibitor SR-4835 binds Cdk12/cyclin K in a noncanonical G-loop conformation.
The reversible inhibitor SR-4835 binds Cdk12/cyclin K in a noncanonical G-loop conformation.
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DOI：
10.1016/j.jbc.2023.105501
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发表时间：
2024-01
影响因子：
4.8
通讯作者：
Geyer, Matthias
中科院分区：
文献类型：
--
作者：
Schmitz, Maximilian;Kaltheuner, Ines H;Anand, Kanchan;Duster, Robert;Moecking, Jonas;Monastyrskyi, Andrii;Duckett, Derek R;Roush, William R;Geyer, Matthias
细胞周期蛋白依赖性激酶（CDK）的抑制已经发展成为一种新兴的抗癌策略。除了细胞周期调节激酶外，转录激酶Cdk12和Cdk13已成为人们关注的焦点，因为它们介导多种功能，包括从转录起始到延伸和终止的转变、前体mRNA剪接和内含子聚腺苷酸化。在这里，我们确定的小分子抑制剂SR-4835结合的Cdk12/细胞周期蛋白K复合物的晶体结构在2.68 μ m分辨率。该化合物的苯并咪唑部分嵌入由激酶铰链区介导的独特氢键网络中，Y815和D819侧链的侧接羟基基团。而SR-4835头基靶向腺嘌呤结合口袋，激酶的富含甘氨酸的环向下移动到激活环。此外，α C-螺旋采用向内构象，磷酸化的T环苏氨酸与所有三种典型的丝氨酸相互作用，这是CDK激活的标志，在Cdk12和Cdk13中发生改变。重组CMGC激酶的剂量反应抑制测量结果表明，SR-4835对Cdk12和Cdk13具有高度特异性，对Cdk10的效价低10倍。而其他CDK靶向化合物表现出更紧密的结合亲和力和更高的激酶抑制效力，SR-4835可以被认为是一种选择性转录延伸拮抗剂。我们的研究结果为SR-4835对Cdk12的抑制作用的合理改善和对其他转录调节CDKs的选择性增益提供了基础。
Inhibition of cyclin-dependent kinases (CDKs) has evolved as an emerging anticancer strategy. In addition to the cell cycle-regulating CDKs, the transcriptional kinases Cdk12 and Cdk13 have become the focus of interest as they mediate a variety of functions, including the transition from transcription initiation to elongation and termination, precursor mRNA splicing, and intronic polyadenylation. Here, we determine the crystal structure of the small molecular inhibitor SR-4835 bound to the Cdk12/cyclin K complex at 2.68 Å resolution. The compound’s benzimidazole moiety is embedded in a unique hydrogen bond network mediated by the kinase hinge region with flanking hydroxy groups of the Y815 and D819 side chains. Whereas the SR-4835 head group targets the adenine-binding pocket, the kinase’s glycine-rich loop is shifted down toward the activation loop. Additionally, the αC-helix adopts an inward conformation, and the phosphorylated T-loop threonine interacts with all three canonical arginines, a hallmark of CDK activation that is altered in Cdk12 and Cdk13. Dose-response inhibition measurements with recombinant CMGC kinases show that SR-4835 is highly specific for Cdk12 and Cdk13 following a 10-fold lower potency for Cdk10. Whereas other CDK-targeting compounds exhibit tighter binding affinities and higher potencies for kinase inhibition, SR-4835 can be considered a selective transcription elongation antagonist. Our results provide the basis for a rational improvement of SR-4835 toward Cdk12 inhibition and a gain in selectivity over other transcription regulating CDKs.