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

Hypoxia-inducible factors (HIFs) are heterodimeric transcription factors that are critical for cellular adaptation to low oxygen conditions. Both enhancement and inhibition of HIF-2 activity have 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 an 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 the stability. We report a ligand-dependent effect on the DNA-binding bHLH domain's structure and dynamics, impacting the hypoxia response element (HRE) binding. To understand the pathway of allosteric signal propagation, we employed a network-based analysis of residue correlations, revealing a structurally embedded and evolutionarily conserved communication network that mediates long-range signaling between the ligand-binding and DNA-binding domains. 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.