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癌突变导致 p53 失活的结构基础及其对突变型 p53 复活剂开发的启示。

Structural basis of p53 inactivation by cavity-creating cancer mutations and its implications for the development of mutant p53 reactivators.

机构信息

Institute of Pharmaceutical Chemistry, Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.

Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany.

出版信息

Cell Death Dis. 2024 Jun 11;15(6):408. doi: 10.1038/s41419-024-06739-x.


DOI:10.1038/s41419-024-06739-x
PMID:38862470
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11166945/
Abstract

The cavity-creating p53 cancer mutation Y220C is an ideal paradigm for developing small-molecule drugs based on protein stabilization. Here, we have systematically analyzed the structural and stability effects of all oncogenic Tyr-to-Cys mutations (Y126C, Y163C, Y205C, Y220C, Y234C, and Y236C) in the p53 DNA-binding domain (DBD). They were all highly destabilizing, drastically lowering the melting temperature of the protein by 8-17 °C. In contrast, two non-cancerous mutations, Y103C and Y107C, had only a moderate effect on protein stability. Differential stabilization of the mutants upon treatment with the anticancer agent arsenic trioxide and stibogluconate revealed an interesting proximity effect. Crystallographic studies complemented by MD simulations showed that two of the mutations, Y234C and Y236C, create internal cavities of different size and shape, whereas the others induce unique surface lesions. The mutation-induced pockets in the Y126C and Y205C mutant were, however, relatively small compared with that of the already druggable Y220C mutant. Intriguingly, our structural studies suggest a pronounced plasticity of the mutation-induced pocket in the frequently occurring Y163C mutant, which may be exploited for the development of small-molecule stabilizers. We point out general principles for reactivating thermolabile cancer mutants and highlight special cases where mutant-specific drugs are needed for the pharmacological rescue of p53 function in tumors.

摘要

致癌突变 p53 Y220C 能形成空洞,为基于蛋白质稳定化的小分子药物研发提供了理想模型。在此,我们系统分析了 p53 DNA 结合域(DBD)中所有致癌性 Tyr-to-Cys 突变(Y126C、Y163C、Y205C、Y220C、Y234C 和 Y236C)的结构和稳定性影响。这些突变均显著降低了蛋白质的稳定性,使蛋白的熔点降低了 8-17°C。相比之下,两种非癌性突变 Y103C 和 Y107C 对蛋白质稳定性的影响则较为温和。用抗癌药物三氧化二砷和葡萄糖酸锑钠处理突变体后,发现它们具有有趣的临近效应,进一步证明了这一点。晶体学研究与 MD 模拟相辅相成,表明其中两个突变(Y234C 和 Y236C)会产生不同大小和形状的内部空洞,而其他突变则会导致独特的表面损伤。然而,与已可成药的 Y220C 突变相比,Y126C 和 Y205C 突变诱导的口袋相对较小。有趣的是,我们的结构研究表明,在常见的 Y163C 突变中,突变诱导的口袋具有明显的可塑性,这可能为开发小分子稳定剂提供契机。我们指出了使不稳定的癌症突变体重新激活的一般原则,并强调了在药理学上恢复肿瘤中 p53 功能时需要特定于突变体的药物的特殊情况。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/57b7ecb65421/41419_2024_6739_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/45cd556c435a/41419_2024_6739_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/04b79ce587d7/41419_2024_6739_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/33344cc602ee/41419_2024_6739_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/bfc350a903f5/41419_2024_6739_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/57b7ecb65421/41419_2024_6739_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/45cd556c435a/41419_2024_6739_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/04b79ce587d7/41419_2024_6739_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/33344cc602ee/41419_2024_6739_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/bfc350a903f5/41419_2024_6739_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c64b/11166945/57b7ecb65421/41419_2024_6739_Fig5_HTML.jpg

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[3]
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[5]
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[6]
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本文引用的文献

[1]
Diverse rescue potencies of p53 mutations to ATO are predetermined by intrinsic mutational properties.

Sci Transl Med. 2023-4-5

[2]
Common activities and predictive gene signature identified for genetic hypomorphs of .

Proc Natl Acad Sci U S A. 2023-2-14

[3]
Discovery of Nanomolar-Affinity Pharmacological Chaperones Stabilizing the Oncogenic p53 Mutant Y220C.

ACS Pharmacol Transl Sci. 2022-10-11

[4]
Drugging p53 in cancer: one protein, many targets.

Nat Rev Drug Discov. 2023-2

[5]
A Small Molecule Reacts with the p53 Somatic Mutant Y220C to Rescue Wild-type Thermal Stability.

Cancer Discov. 2023-1-9

[6]
Discovery of compounds that reactivate p53 mutants in vitro and in vivo.

Cell Chem Biol. 2022-9-15

[7]
p53 and Zinc: A Malleable Relationship.

Front Mol Biosci. 2022-4-13

[8]
Repurposing antiparasitic antimonials to noncovalently rescue temperature-sensitive p53 mutations.

Cell Rep. 2022-4-12

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The TP53 Database: transition from the International Agency for Research on Cancer to the US National Cancer Institute.

Cell Death Differ. 2022-5

[10]
Evolutionary history of the p53 family DNA-binding domain: insights from an Alvinella pompejana homolog.

Cell Death Dis. 2022-3-7

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