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bioRxiv · 10.1101/2025.04.23.650354

Structural, Thermodynamic, and Dynamic Descriptors for Differential Mechanism of HIF-2 Activity Modulators

Punia, R.·Goel, G.
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Abstract

Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors critical for cellular adaptation to low oxygen conditions. Both enhancement and inhibition of HIF-2 activity has been shown to have a significant therapeutic relevance. We used all atom molecular dynamics (MD) simulations to elucidate the molecular mechanism for the differential effects of HIF-2 ligands on its complex with aryl hydrocarbon receptor nuclear translocator (ARNT). We find that agonists and antagonists differentially alter the binding site conformation, enthalpically strengthening or weakening the heterodimerization, respectively. These local changes were linked to conformational fluctuations of the HIF-2/ARNT complex, adding an entropic component to the effect of ligand binding on stability. Finally, we report a ligand-dependent effect on the DNA-binding bHLH domains structure and dynamics, impacting the hypoxia response element (HRE) binding. Based on these findings, we present a multiscale approach to enable high-throughput virtual screening of ligands for differential modulation of the structure, dynamics, and transcriptional activity of the HIF-2/ARNT complex. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/650354v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@10d5f96org.highwire.dtl.DTLVardef@fe9c79org.highwire.dtl.DTLVardef@1d2fdaeorg.highwire.dtl.DTLVardef@10ce1cf_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Punia, R., Goel, G.. 2025-04-26. Structural, Thermodynamic, and Dynamic Descriptors for Differential Mechanism of HIF-2 Activity Modulators. https://doi.org/10.1101/2025.04.23.650354

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