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Allosteric inhibition of hypoxia inducible factor-2 with small molecules


Hypoxia inducible factors (HIFs) are heterodimeric transcription factors induced in many cancers where they frequently promote the expression of protumorigenic pathways. Though transcription factors are typically considered 'undruggable', the PAS-B domain of the HIF-2α subunit contains a large cavity within its hydrophobic core that offers a unique foothold for small-molecule regulation. Here we identify artificial ligands that bind within this pocket and characterize the resulting structural and functional changes caused by binding. Notably, these ligands antagonize HIF-2 heterodimerization and DNA-binding activity in vitro and in cultured cells, reducing HIF-2 target gene expression. Despite the high sequence identity between HIF-2α and HIF-1α, these ligands are highly selective and do not affect HIF-1 function. These chemical tools establish the molecular basis for selective regulation of HIF-2, providing potential therapeutic opportunities to intervene in HIF-2–driven tumors, such as renal cell carcinomas.

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Figure 1: Biophysical characterization of the HIF-2α PAS-B–2 complex.
Figure 2: Binding of 2 into HIF-2α PAS-B affects the heterodimeric β-sheet interface between HIF PAS-B domains.
Figure 3: 2 disrupts HIF-2 heterodimerization in vitro.
Figure 4: 2 binds selectively to HIF-2α over HIF-1α PAS-B.
Figure 5: 2 selectively antagonizes HIF-2 activity in cultured cells.

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The authors thank S. Wang and members of the University of Texas Southwestern High-Throughput Screening Core Facility, D. Tomchick, C. Brautigam, J. MacMillan, N. Williams and members of our laboratories for their help. This work was funded by grants from the US National Institutes of Health (P01 CA095471, P30 CA142543) and the Cancer Prevention Research Institute of Texas (RP-100846). R.K.B. is the Michael L. Rosenberg Scholar in Medical Research and was supported by a Career Award in the Biomedical Sciences from the Burroughs Wellcome Fund; K.H.G. is the Virginia Lazenby O'Hara Chair in Biochemistry and W.W. Caruth Scholar in Biomedical Research; and U.K.T. is a W.W. Caruth Jr. Scholar in Biomedical Research. J.A.G. was supported by funds provided by the Department of Veterans Affairs. Results shown in this report are derived from work performed at Argonne National Laboratory, Structural Biology Center at the Advanced Photon Source. Argonne National Laboratory is operated by UChicago Argonne, LLC, for the US Department of Energy, Office of Biological and Environmental Research under contract DE-AC02-06CH11357. This investigation was conducted in a facility constructed with support from the Research Facilities Improvement Program (grant no. C06 RR 15437-01) from the National Center for Research Resources, US National Institutes of Health.

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R.K.B. and K.H.G. conceived and designed the experiments. T.H.S., Q.L., H.-W.M., L.Z., R.C., J.N. and J.L. performed the experiments. R.K.B., K.H.G., T.H.S., J.K., J.A.G., D.E.F. and U.K.T. analyzed the data. R.K.B., K.H.G. and T.H.S. wrote the paper.

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Correspondence to Kevin H Gardner or Richard K Bruick.

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Declaration: R.K.B., D.E.F., K.H.G., T.H.S. and U.K.T. have filed US Patent Application no. 61/583,662 covering the method described in the paper. R.K.B., K.H.G., T.H.S., J.K. and U.K.T. have received stock options and other financial compensation from Peloton Therapeutics, Inc.

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Scheuermann, T., Li, Q., Ma, HW. et al. Allosteric inhibition of hypoxia inducible factor-2 with small molecules. Nat Chem Biol 9, 271–276 (2013).

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