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Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors

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Abstract

The rate-limiting serine biogenesis enzyme PHGDH is overexpressed in cancers. Both serine withdrawal and genetic/pharmacological inhibition of PHGDH have demonstrated promising tumor-suppressing activities. However, the enzyme properties of PHGDH are not well understood and the discovery of PHGDH inhibitors is still in its infancy. Here, oridonin was identified from a natural product library as a new PHGDH inhibitor. The crystal structure of PHGDH in complex with oridonin revealed a new allosteric site. The binding of oridonin to this site reduced the activity of the enzyme by relocating R54, a residue involved in substrate binding. Mutagenesis studies showed that PHGDH activity was very sensitive to cysteine mutations, especially those in the substrate binding domain. Conjugation of oridonin and other reported covalent PHGDH inhibitors to these sites will therefore inhibit PHGDH. In addition to being inhibited enzymatically, PHGDH can also be inhibited by protein aggregation and proteasome-mediated degradation. Several tested PHGDH cancer mutants showed altered enzymatic activity, which can be explained by protein structure and stability. Overall, the above studies present new biophysical and biochemical insights into PHGDH and may facilitate the future design of PHGDH inhibitors.

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Availability of data and material

The resulting model has been deposited in Protein Data Bank with the accession code 7DKM. The MS raw data has been deposited into the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository with a dataset identifier of PXD029445 [49].

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Acknowledgements

We thank the staffs from BL17B1/BL18U1/BL19U1/BL19U2/BL01B beamline of National Facility for Protein Science in Shanghai (NFPS) at Shanghai Synchrotron Radiation Facility, for assistance during data collection [48]. We appreciate Dr. Xiaofei Shen for providing resources and technical assistances.

Funding

YZ is funded by the National S&T Major Project (2018ZX09201018), and LD is funded by the program of National Clinical Research Center for Geriatrics of West China Hospital (No. Z20191001).

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  1. Yuping Tan, Xia Zhou and Yanqiu Gong have contributed equally.

Authors and Affiliations

  1. Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China

    Yuping Tan, Youfu Luo & Qingxiang Sun

  2. State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, 17#, 3rd Section, Ren min South Road, Chengdu, 610041, China

    Xia Zhou, Kun Gou & Yinglan Zhao

  3. National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China

    Yanqiu Gong & Lunzhi Dai

  4. Key Laboratory of Birth Defects and Related Diseases of Women and Children, Division of Neurology, Department of Paediatrics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China

    Da Jia

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  1. Yuping Tan
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Contributions

QS and YT conceived the project and prepared the manuscript. YT, XZ, YG, and KG performed all the experiments. QS, YZ, LD, YL, and DJ supervised the project, and/or provided relevant resources.

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Correspondence to Lunzhi Dai, Yinglan Zhao or Qingxiang Sun.

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Tan, Y., Zhou, X., Gong, Y. et al. Biophysical and biochemical properties of PHGDH revealed by studies on PHGDH inhibitors. Cell. Mol. Life Sci. 79, 27 (2022). https://doi.org/10.1007/s00018-021-04022-2

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