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Uncoupling of PARP1 trapping and inhibition using selective PARP1 degradation

Nature Chemical Biology volume 15, pages 1223–1231 (2019)Cite this article

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Abstract

PARP1 inhibitors (PARPi) are known to kill tumor cells via two mechanisms (PARP1 catalytic inhibition and PARP1 trapping). The relative contribution of these two pathways in mediating the cytotoxicity of PARPi, however, is not well understood. Here we designed a series of small molecule PARP degraders. Treatment with one such compound iRucaparib-AP6 results in highly efficient and specific PARP1 degradation. iRucaparib-AP6 blocks the enzymatic activity of PARP1 in vitro, and PARP1-mediated poly-ADP-ribosylation signaling in intact cells. This strategy mimics PARP1 genetic depletion, which enables the pharmacological decoupling of PARP1 inhibition from PARP1 trapping. Finally, by depleting PARP1, iRucaparib-AP6 protects muscle cells and primary cardiomyocytes from DNA-damage-induced energy crisis and cell death. In summary, these compounds represent ‘non-trapping’ PARP1 degraders that block both the catalytic activity and scaffolding effects of PARP1, providing an ideal approach for the amelioration of the various pathological conditions caused by PARP1 hyperactivation.

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Fig. 1: Targeted degradation of PARP1.
Fig. 2: iRucaparib-AP6 induces PARP1 degradation.
Fig. 3: iRucaparib-AP6 selectively targets PARP1 for degradation.
Fig. 4: iRucaparib-AP6 inhibits PARylation-mediated signaling events downstream of PARP1.
Fig. 5: iRucaparib-AP6 is a non-trapping PARP1 degrader.
Fig. 6: iRucaparib-AP6 protects cells from genotoxicity-induced cell death.

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Data availability

The MS data have been deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD014838 (Supplementary Dataset 1), PXD014836 and PXD014837 (Supplementary Datasets 2 and 3), PXD014840 (Supplementary Datasets 4 and 5), and PXD014839 (Supplementary Dataset 6). Source data for Figs. 2d, 5d and 6e,f, and Supplementary Fig. 12a–f are available online. Full uncropped blots are shown in Supplementary Fig. 14.

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Acknowledgements

We thank J. A. Hill (UT Southwestern Medical Center) for sharing primary rat neonatal cardiomyocytes and X. Zhong and C. Kim for help with the immunofluorescence microscopy experiments and PARP1 immunoprecipitation experiments, respectively. We thank X. Yu (City of Hope) for providing the GFP-PARP1 construct. We also thank X. D. Wang, L. Yuan and the other members of the Yu laboratory for helpful discussions. This work was supported by grants from the National Institutes of Health (GM122932 to Y.Y. and CA226419 to C.C.) and the Welch foundation (I-1800 to Y.Y.).

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Author notes

  1. These authors contributed equally: Shuai Wang, Lei Han

Authors and Affiliations

  1. Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA

    Shuai Wang, Lei Han, Jungsoo Han, Peng Li, Qing Ding, Chuo Chen & Yonghao Yu

  2. Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA

    Qing-Jun Zhang & Zhi-Ping Liu

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Contributions

Y.Y. conceived the study and designed the overall strategy. L.H., C.C. and Y.Y. designed and synthesized the PARP1 degraders. S.W. and Y.Y. designed all the biochemical and cell biology experiments. S.W., J.H. and P.L. performed biochemical and cell biology experiments. S.W. and Q.D. performed quantitative MS. Q.-J.Z. and Z.-P.L. contributed reagents and technical advice. S.W. and Y.Y. analyzed and interpreted the data. S.W., L.H., C.C. and Y.Y. wrote the manuscript with input from all authors.

Corresponding authors

Correspondence to Chuo Chen or Yonghao Yu.

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Competing interests

Y.Y. receives research support from Pfizer. A provisional patent application on the PARP degraders and technologies described herein has been filed by Y.Y., C.C., S. W. and L. H.

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Supplementary information

Supplementary Information

Supplementary Figures 1–14 and Supplementary Table 1

Reporting Summary

Supplementary Note

Synthetic Procedures

Supplementary Dataset 1

Quantified proteomic data for primary cardiomyocytes treated with DMSO, iRucaparib-AP5 or iRucaparib-AP6 (1 μM) for 24 h.

Supplementary Dataset 2

Quantified proteomic data for HeLa cells treated with DMSO, iRucaparib-TP3 (5 μM) or iRucaparib-TP3 (5 μM) plus Rucaparib (1 μM) for 24 h.

Supplementary Dataset 3

Quantified proteomic data for BT-549 cells treated with DMSO, iRucaparib-TP3 (5 μM) or vRucaparib-TP4 (20 μM) for 24 h.

Supplementary Dataset 4

Quantified PARylated proteomic data for SILAC-labeled HeLa cells treated with DMSO and Rucaparib or DMSO and iRucaparib-AP6 (10 μM).

Supplementary Dataset 5

Quantified PARylated proteomic data for SILAC-labeled HeLa cells treated with DMSO and Rucaparib or DMSO and iRucaparib-TP3 (10 μM).

Supplementary Dataset 6

Quantified chromatin proteomic data for HeLa cells treated with MMS and DMSO, MMS and Rucaparib or MMS and iRucaparib-AP6 for 24 h.

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Wang, S., Han, L., Han, J. et al. Uncoupling of PARP1 trapping and inhibition using selective PARP1 degradation. Nat Chem Biol 15, 1223–1231 (2019). https://doi.org/10.1038/s41589-019-0379-2

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