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双效激酶抑制剂影响p38α丝裂原活化蛋白激酶的去磷酸化。

Dual-action kinase inhibitors influence p38α MAP kinase dephosphorylation.

作者信息

Stadnicki Emily J, Ludewig Hannes, Kumar Ramasamy P, Wang Xicong, Qiao Youwei, Kern Dorothee, Bradshaw Niels

机构信息

Department of Biochemistry, Brandeis University, Waltham, MA 02454.

HHMI, Brandeis University, Waltham, MA 02454.

出版信息

Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2415150122. doi: 10.1073/pnas.2415150122. Epub 2024 Dec 31.


DOI:10.1073/pnas.2415150122
PMID:39739785
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11725910/
Abstract

Reversible protein phosphorylation directs essential cellular processes including cell division, cell growth, cell death, inflammation, and differentiation. Because protein phosphorylation drives diverse diseases, kinases and phosphatases have been targets for drug discovery, with some achieving remarkable clinical success. Most protein kinases are activated by phosphorylation of their activation loops, which shifts the conformational equilibrium of the kinase toward the active state. To turn off the kinase, protein phosphatases dephosphorylate these sites, but how the conformation of the dynamic activation loop contributes to dephosphorylation was not known. To answer this, we modulated the activation loop conformational equilibrium of human p38α ΜΑP kinase with existing kinase inhibitors that bind and stabilize specific inactive activation loop conformations. From this, we identified three inhibitors that increase the rate of dephosphorylation of the activation loop phospho-threonine by the PPM serine/threonine phosphatase WIP1. Hence, these compounds are "dual-action" inhibitors that simultaneously block the active site and promote p38α dephosphorylation. Our X-ray crystal structures of phosphorylated p38α bound to the dual-action inhibitors reveal a shared flipped conformation of the activation loop with a fully accessible phospho-threonine. In contrast, our X-ray crystal structure of phosphorylated apo human p38α reveals a different activation loop conformation with an inaccessible phospho-threonine, thereby explaining the increased rate of dephosphorylation upon inhibitor binding. These findings reveal a conformational preference of phosphatases for their targets and suggest a unique approach to achieving improved potency and specificity for therapeutic kinase inhibitors.

摘要

可逆性蛋白质磷酸化指导着包括细胞分裂、细胞生长、细胞死亡、炎症和分化在内的重要细胞过程。由于蛋白质磷酸化引发多种疾病,激酶和磷酸酶已成为药物研发的靶点,其中一些已取得显著的临床成功。大多数蛋白激酶通过其激活环的磷酸化而被激活,这会使激酶的构象平衡向活性状态转变。为了关闭激酶,蛋白磷酸酶会使这些位点去磷酸化,但动态激活环的构象如何促进去磷酸化尚不清楚。为了回答这个问题,我们用现有的激酶抑制剂调节人p38α丝裂原活化蛋白激酶的激活环构象平衡,这些抑制剂能结合并稳定特定的无活性激活环构象。由此,我们鉴定出三种抑制剂,它们能提高PPM丝氨酸/苏氨酸磷酸酶WIP1对激活环磷酸苏氨酸的去磷酸化速率。因此,这些化合物是“双作用”抑制剂,它们能同时阻断活性位点并促进p38α去磷酸化。我们的磷酸化p38α与双作用抑制剂结合的X射线晶体结构显示,激活环具有共同的翻转构象,磷酸苏氨酸完全可及。相比之下,我们的磷酸化人p38α无配体X射线晶体结构显示出不同的激活环构象,磷酸苏氨酸不可及,从而解释了抑制剂结合后去磷酸化速率增加的原因。这些发现揭示了磷酸酶对其靶点的构象偏好,并提出了一种独特的方法来提高治疗性激酶抑制剂的效力和特异性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/ad4cb5853d2c/pnas.2415150122fig05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/1752eafc6eb4/pnas.2415150122fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/eb035ef5c129/pnas.2415150122fig02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/e188afab8c5b/pnas.2415150122fig03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/03edce34bda1/pnas.2415150122fig04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/ad4cb5853d2c/pnas.2415150122fig05.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/1752eafc6eb4/pnas.2415150122fig01.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/eb035ef5c129/pnas.2415150122fig02.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/e188afab8c5b/pnas.2415150122fig03.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/03edce34bda1/pnas.2415150122fig04.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3fd6/11725910/ad4cb5853d2c/pnas.2415150122fig05.jpg

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本文引用的文献

[1]
Crystal structure and mechanistic studies of the PPM1D serine/threonine phosphatase catalytic domain.

J Biol Chem. 2024-8

[2]
EGFR targeting PhosTACs as a dual inhibitory approach reveals differential downstream signaling.

Sci Adv. 2024-3-29

[3]
Structural basis of a redox-dependent conformational switch that regulates the stress kinase p38α.

Nat Commun. 2023-12-1

[4]
Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation.

Science. 2023-9-15

[5]
Lewy Body Dementia: An Overview of Promising Therapeutics.

Curr Neurol Neurosci Rep. 2023-10

[6]
Inhibition of discoidin domain receptor (DDR)-1 with nilotinib alters CSF miRNAs and is associated with reduced inflammation and vascular fibrosis in Alzheimer's disease.

J Neuroinflammation. 2023-5-16

[7]
An affinity-directed phosphatase, AdPhosphatase, system for targeted protein dephosphorylation.

Cell Chem Biol. 2023-2-16

[8]
Nilotinib modulates LPS-induced cognitive impairment and neuroinflammatory responses by regulating P38/STAT3 signaling.

J Neuroinflammation. 2022-7-15

[9]
Allosteric inhibition of PPM1D serine/threonine phosphatase via an altered conformational state.

Nat Commun. 2022-6-30

[10]
MAPK-Activated Protein Kinases: Servant or Partner?

Annu Rev Biochem. 2022-6-21

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