Molecular View on the Dissociation Pathways and Transactivation Regulation Mechanism of Nonsteroidal GR Ligands

As a major drug target for anti-inflammatory
therapy, the glucocorticoid
receptor (GR) regulates a wide range of physiological processes through
transactivation (TA) or transrepression. GR TA is involved in many
adverse effects of GR-targeting drugs, and therefore, the discovery
of novel GR ligands with lower TA activity and longer residence time
is quite urgent. Undoubtedly, understanding the ligand dissociation
mechanisms and the structural basis of the TA regulation is crucial
for the development of novel GR-targeting drugs. Here, we used random
accelerated molecular dynamics (RAMD) and funnel metadynamics (FM)
simulations to explore the dissociation mechanisms of 5 classic glucocorticoids
and 6 nonsteroidal GR ligands. Multiple ligand dissociation pathways
were discovered. The classic glucocorticoids exhibit a strong preference
for Path I, and most nonsteroidal ligands tend to dissociate along
mixed pathways. We also find that the distinct unbinding preferences
for AZD2906 and AZD9567, two representative nonsteroidal ligands with
similar scaffolds but different TA activities, are primarily determined
by their different polar interactions with the surrounding residues.
Notably, the binding of AZD9567 poses a substantial impact on the
conformation of the GR homodimer interface, which provides a valuable
clue to understand the mechanisms of the TA-related side effects induced
by the adjustments of the homodimerization process. These findings
are critical for the structure-based rational design of novel GR ligands
with more potent anti-inflammatory potency and reduced side effects.