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Identification of indoles as potential endogenous ligands of ERRγ and their modulation on drug binding

Acta Pharmacologica Sinica volume 46, pages 2574–2582 (2025)Cite this article

Abstract

Estrogen-related receptor γ (ERRγ) is an orphan nuclear receptor in the ERR subfamily that plays a crucial role in regulating energy metabolism. To date, no endogenous ligand has been identified for ERRγ, posing a challenge for developing targeted therapeutics. Here, we identified that indole and skatole produced by the gut microbiota are potential endogenous ligands of ERRγ using biochemical, cellular, structural, and computational approaches. Indole and skatole increased ERRγ thermostability and directly bound to the ligand-binding domain (LBD) with a Kd of approximately 1–2 μM but had no significant effect or weak inhibitory activity on the transcriptional efficiency. However, RNA sequencing revealed that ERRγ could coregulate several lipid metabolism- and immune-related genes with indole, suggesting a role for ERRγ in the indole pathway. Interestingly, indole and skatole differentially attenuated the activities of ERRγ ligands: they both neutralized the agonistic activity of GSK4716, while indole reduced the antagonistic activity of 4-hydroxytamoxifen (4OHT) and GSK5182, and skatole affected the agonistic activity of endocrine disruptor bisphenol A (BPA). We further screened additional indole metabolites and analogs, resolved the complex structures of ERRγ-LBD with these compounds, and conducted molecular dynamics simulations to determine their binding site and elucidate their binding mechanisms. This study identified potential endogenous ligands of ERRγ, suggesting a novel link between the energy metabolism regulation and the indole pathway. Our findings highlight the need to consider endogenous ligands when designing and optimizing ERRγ-targeted drugs.

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Fig. 1: Functional characterization of compounds with indole rings.
Fig. 2: ERRγ cellular activity with or without compound treatment evaluated via the luciferase reporter-based transcription assay.
Fig. 3: The interferences of indole and skatole on drug binding as determined with luciferase assays with the ERRE.
Fig. 4: Compounds bind to ERRγ-LBD but have a limited structural impact on its constitutively active conformation.

Data availability

Coordinates and structure factors for ERRγ in complex with indole, 6NI, 5NI, 4028691, and 4034496 have been deposited in the RCSB protein data bank with ID 9KND, 9KNC, 9KNE, 9KNF, and 9KNG, respectively. Raw diffraction data are available on the Guangzhou Institutes of Biomedicine and Health Supercomputing Center server.

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Acknowledgements

The authors thank Dr Lin-bing Qu and Dr San-ling Liu for providing the gene template and the staff members of beamline 17U1 and 19U1 at the National Center for Protein Science Shanghai and the Shanghai Synchrotron Radiation Facility, the People’s Republic of China, for assistance with diffraction data collection. We would also like to thank the support from the Guangzhou Branch of the Supercomputing Center of CAS.

Funding

This work was supported by Guangdong Basic and Applied Basic Research Foundation (2023A1515030039, 2021A1515220013), Queensland-Chinese Academy of Sciences Collaborative Science Fund (188GJHZ2023069MI), Guangzhou Basic and Applied Basic Research Foundation (2025A04J5436, 202201010711), State Key Laboratory of Respiratory Disease (SKLRD-Z-202519), the Youth Innovation Promotion Association of CAS (2021357), and Guangdong Provincial Key Laboratory of Biocomputing Grant (2016B030301007).

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Author notes

  1. These authors contributed equally: Yuan-yuan Shuai, Hong-yang Zhang, Rui Chen.

Authors and Affiliations

  1. Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China

    Yuan-yuan Shuai & Jin-song Liu

  2. State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China

    Yuan-yuan Shuai, Rui Chen, Bai-ling Wang, Ping Ding, Yan Dong, Ming-ze Sun, Xi-shan Wu, Yong Xu, Yan Zhang, Jin-song Liu, Na Wang & Ting-ting Xu

  3. School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 117004, China

    Hong-yang Zhang

  4. Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China

    Hong-yang Zhang, Jin-song Liu, Na Wang & Ting-ting Xu

  5. Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China

    Bai-ling Wang

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Contributions

TTX and NW designed the experiments. YYS, HYZ, RC, NW, PD, BLW, YD, and MZS performed the experiments. YYS, HYZ, TTX, JSL, XSW, YX, and YZ performed the analyses. JSL, TTX edited the manuscript. NW and TTX wrote the manuscript.

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Correspondence to Jin-song Liu, Na Wang or Ting-ting Xu.

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Shuai, Yy., Zhang, Hy., Chen, R. et al. Identification of indoles as potential endogenous ligands of ERRγ and their modulation on drug binding. Acta Pharmacol Sin 46, 2574–2582 (2025). https://doi.org/10.1038/s41401-025-01550-6

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