7W80

Crystal Structure of the Heterodimeric HIF-2 in Complex with Antagonist Belzutifan

PDB DOI: 10.2210/pdb7W80/pdb

Classification: TRANSCRIPTION
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-07 Released: 2022-09-21
Deposition Author(s): Ren, X., Diao, X., Zhuang, J., Wu, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.274
R-Value Work: 0.216
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for the allosteric inhibition of hypoxia-inducible factor (HIF)-2 by belzutifan.

Ren, X., Diao, X., Zhuang, J., Wu, D.

(2022) Mol Pharmacol

PubMed: 36167425 Search on PubMed
DOI: 10.1124/molpharm.122.000525
Primary Citation of Related Structures:
7W80

PubMed Abstract:

Hypoxia-inducible factor (HIF)-2α and its obligate heterodimerization partner aryl hydrocarbon receptor nuclear translocator (ARNT), are both members of the basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factor family. Previous studies have identified HIF-2α as a key oncogenic driver in clear cell renal cell carcinoma (ccRCC), rendering it a promising drug target for this type of kidney cancer. Belzutifan is the first HIF-2α inhibitor approved for treating ccRCC and other cancers associated with the von Hippel-Lindau (VHL) disease. However, the detailed inhibitory mechanism of belzutifan at molecular level is still unclear. Here we obtained the crystal structure of HIF-2α-ARNT heterodimer in complex with belzutifan at 2.75 Å resolution. The complex structure shows that belzutifan binds into the PAS-B pocket of HIF-2α, and it destabilizes the dimerization of HIF-2α and ARNT through allosteric effects mainly mediated by the key residue M252 of HIF-2α near the dimer interface. We further explored the inhibitory effects of belzutifan using biochemical and functional assays. The time-resolved fluorescence energy transfer (TR-FRET)-based binding assay showed that belzutifan disrupts the dimerization of HIF-2α and ARNT with a K _i value of 20 nM. The luciferase reporter assay indicated that belzutifan can efficiently inhibit the transcriptional activity of HIF-2α with an IC ₅₀ value of 17 nM. Besides, the real-time PCR assay illustrated that belzutifan can reduce the expression of HIF-2α downstream genes in 786-O kidney cancer cells in a dose-dependent manner. Our work reveals the molecular mechanism by which belzutifan allosterically inhibits HIF-2α and provides valuable information for the subsequent drug development targeting HIF-2α. Significance Statement The bHLH-PAS family of transcription factors are an emerging group of small-molecule drug targets. Belzutifan, originally developed by Peloton Therapeutics, is the first FDA-approved drug directly binding to a bHLH-PAS protein, the hypoxia-inducible factor (HIF)-2α. Based on the protein-drug complex structure, biochemical binding assays, and functional profiling of downstream gene expression, this study reveals the regulatory mechanism of how belzutifan allosterically destabilizes HIF-2α's heterodimerization with its obligate partner protein, thus reducing their transcriptional activity that links to tumor progression.

Organizational Affiliation:

State Key Laboratory of Microbial Technology, Shandong University, China dlwu@sdu.edu.cn.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aryl hydrocarbon receptor nuclear translocator	A	384	Mus musculus	Mutation(s): 0 Gene Names: Arnt
UniProt & NIH Common Fund Data Resources
Find proteins for P53762 (Mus musculus) Explore P53762 Go to UniProtKB: P53762
IMPC: MGI:88071
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53762
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothelial PAS domain-containing protein 1	B	360	Mus musculus	Mutation(s): 0 Gene Names: Epas1, Hif2a
UniProt & NIH Common Fund Data Resources
Find proteins for P97481 (Mus musculus) Explore P97481 Go to UniProtKB: P97481
IMPC: MGI:109169
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P97481
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
72Q (Subject of Investigation/LOI) Query on 72Q Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	3-{[(1S,2S,3R)-2,3-difluoro-1-hydroxy-7-(methylsulfonyl)-2,3-dihydro-1H-inden-4-yl]oxy}-5-fluorobenzonitrile C₁₇ H₁₂ F₃ N O₄ S LOMMPXLFBTZENJ-ZACQAIPSSA-N		Ligand Interaction