Hypoxia-inducible factor-2 (HIF-2) is a heterodimeric transcription factor formed through dimerization between an oxygen-sensitive HIF-2α subunit and its obligate partner subunit ARNT. Enhanced HIF-2 activity drives some cancers, whereas reduced activity causes anemia in chronic kidney disease. Therefore, modulation of HIF-2 activity via direct-binding ligands could provide many new therapeutic benefits. Here, we explored HIF-2α chemical ligands using combined crystallographic, biophysical, and cell-based functional studies. We found chemically unrelated antagonists to employ the same mechanism of action. Their binding displaced residue M252 from inside the HIF-2α PAS-B pocket toward the ARNT subunit to weaken heterodimerization. We also identified first-in-class HIF-2α agonists and found that they significantly displaced pocket residue Y281. Its dramatic side chain movement increases heterodimerization stability and transcriptional activity. Our findings show that despite binding to the same HIF-2α PAS-B pocket, ligands can manifest as inhibitors versus activators by mobilizing different pocket residues to allosterically alter HIF-2α–ARNT heterodimerization.
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We thank members of the Structural Biology Center at Argonne National Laboratory for their help with data collection at the 19-ID beamline, D. Liu and I. Pass at Sanford Burnham Prebys for kindly providing materials, and G.N. Murshudov at University of Cambridge for the help with ligand building at the 2016 CCP4/APS summer school. This work was supported by the Wellcome Trust and by grants from the National Institutes of Health (R01GM117013, R01DK118297) and US ARMY Medical Research (W81XWH-16-1-0322) to F.R., as well as grants from Shandong University (Qilu Young Scholar 86963072), National Natural Science Foundation of China (31700114), Natural Science Foundation of Jiangsu Province (BK20170399), and the 111 Project (B16030) to D.W.
The authors declare no competing interests.
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Wu, D., Su, X., Lu, J. et al. Bidirectional modulation of HIF-2 activity through chemical ligands. Nat Chem Biol 15, 367–376 (2019). https://doi.org/10.1038/s41589-019-0234-5
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