Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements.
Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements.
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DOI：
10.1371/journal.pone.0012214
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发表时间：
2010-08-16
期刊：
影响因子：
3.7
通讯作者：
Rognan D
中科院分区：
文献类型：
--
作者：
Defranchi E;Schalon C;Messa M;Onofri F;Benfenati F;Rognan D
在早期药物发现阶段，通过计算方法预测脱靶变得越来越重要。因此，我们提出了一种基于结合位点三维比较的计算方法，该方法促使我们研究蛋白激酶抑制剂与突触蛋白I的交叉反应。突触蛋白I是一种调节突触中神经递质释放的三磷酸腺苷结合蛋白。原癌基因Pim-1激酶的星形孢菌素结合位点与6,412个药物蛋白配体结合位点的系统配对比较表明，突触素I的ATP结合位点可能识别泛激酶抑制剂星形孢子素。这一假说的生化验证是通过星孢菌素与三磷酸腺苷-γ35S与突触素I结合的竞争实验实现的。星孢菌素以及其他三种蛋白激酶抑制剂(CDK2、PIM-1和酪蛋白激酶2)以纳米分子亲和力有效地与突触素I结合，并促进突触素诱导的F-肌动蛋白绑定。选择性的PIM-1激酶抑制剂Quercetagetin被证明是最有效的突触素I结合蛋白(IC50 = 0.15µM)，这与预测的突触素I与各种蛋白激酶的结合位置相似。其他蛋白激酶抑制剂(蛋白激酶A和Chk1抑制剂)、激酶抑制剂(二酰基甘油激酶抑制剂)和各种其他α竞争对手(DNA拓扑异构酶II和热休克蛋白-90 ATP抑制剂)不能与突触素I结合，这是因为它们与突触素I的结合部位与突触素I的相似性较低。目前的数据表明，一些但不是所有蛋白激酶抑制剂对神经递质释放的下调也可能是通过直接与突触素I结合和对突触素I功能的磷酸化非依赖性扰动来实现的。更广泛地说，数据还表明，可以通过系统地对配体注释的结合位点进行成对的相似性测量来检测与各种目标的交叉反应。
Predicting off-targets by computational methods is getting increasing importance in early drug discovery stages. We herewith present a computational method based on binding site three-dimensional comparisons, which prompted us to investigate the cross-reaction of protein kinase inhibitors with synapsin I, an ATP-binding protein regulating neurotransmitter release in the synapse. Systematic pair-wise comparison of the staurosporine-binding site of the proto-oncogene Pim-1 kinase with 6,412 druggable protein-ligand binding sites suggested that the ATP-binding site of synapsin I may recognize the pan-kinase inhibitor staurosporine. Biochemical validation of this hypothesis was realized by competition experiments of staurosporine with ATP-γ35S for binding to synapsin I. Staurosporine, as well as three other inhibitors of protein kinases (cdk2, Pim-1 and casein kinase type 2), effectively bound to synapsin I with nanomolar affinities and promoted synapsin-induced F-actin bundling. The selective Pim-1 kinase inhibitor quercetagetin was shown to be the most potent synapsin I binder (IC50 = 0.15 µM), in agreement with the predicted binding site similarities between synapsin I and various protein kinases. Other protein kinase inhibitors (protein kinase A and chk1 inhibitor), kinase inhibitors (diacylglycerolkinase inhibitor) and various other ATP-competitors (DNA topoisomerase II and HSP-90α inhibitors) did not bind to synapsin I, as predicted from a lower similarity of their respective ATP-binding sites to that of synapsin I. The present data suggest that the observed downregulation of neurotransmitter release by some but not all protein kinase inhibitors may also be contributed by a direct binding to synapsin I and phosphorylation-independent perturbation of synapsin I function. More generally, the data also demonstrate that cross-reactivity with various targets may be detected by systematic pair-wise similarity measurement of ligand-annotated binding sites.
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影响因子：
4.8
作者：
Brautigam, CA;Chelliah, Y;Deisenhofer, J
通讯作者：
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影响因子：
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