Structural States of RORγt: X‐ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds

Abstract

The T-cell-specific retinoic acid receptor (RAR)-related orphan receptor-γ (RORγt) is a key transcription factor for the production of pro-inflammatory Th17 cytokines, which are implicated in the pathogenesis of autoimmune diseases. Over the years, several structurally diverse RORγt inverse agonists have been reported, but combining high potency and good physicochemical properties has remained a challenging task. We recently reported a new series of inverse agonists based on an imidazopyridine core with good physicochemical properties and excellent selectivity. Herein we report eight new X-ray crystal structures for different classes of natural and synthetic compounds, including examples selected from the patent literature. Analysis of their respective binding modes revealed insight into the molecular mechanisms that lead to agonism, antagonism, or inverse agonism. We report new molecular mechanisms for RORγt agonism and propose a separation of the inverse agonists into two classes: those that act via steric clash and those that act via other mechanisms (for the latter, co-crystallization with a co-activator peptide and helix 12 in the agonist position is still possible). For the non-steric clash inverse agonists, we propose a new mechanism ("water trapping") which can be combined with other mechanisms (e.g., close contacts with H479). In addition, we compare the interactions made for selected compounds in the "back pocket" near S404 and in the "sulfate pocket" near R364 and R367. Taken together, these new mechanistic insights should prove useful for the design and optimization of further RORγt modulators.

Computational insights into the interaction mechanisms of estrogen‐related receptor alpha with endogenous ligand cholesterol

“…Based on the analysis of hydrogen‐bonding and hydrophobic interactions, it was inferred that IFD_GLU might be the most reasonable CLR‐ERRα complex. Meanwhile, IFD_GLU was consistent with the crystal structures of CLR complexed with NRs (Kallen et al., , ) and the docking poses from Wei et al. ().…”

“…Based on the analysis of hydrogen-bonding and hydrophobic interactions, it was inferred that IFD_GLU might be the most reasonable CLR-ERRα complex. Meanwhile, IFD_GLU was consistent with the crystal structures of CLR complexed with NRs (Kallen et al, 2002(Kallen et al, , 2017 and the docking poses from Wei et al (2016). Therefore, IFD_GLU should be the most reasonable conformation of ERRα-cholesterol complex, while the four Phe residues and Glu235 of ERRα play important roles in CLR binding.…”

Pharmacological inhibition of RORγt suppresses the Th17 pathway and alleviates arthritis in vivo

“…In this article, we report a detailed in vitro characterization of an imidazopyridine RORγt inverse agonist recently identified from an extensive chemical optimization campaign [ 21 ]. Cpd 1 binds in the ligand binding pocket of the RORγt ligand binding domain as we have recently shown by X-ray crystallography in [ 29 ] (where cpd 1 is designated “4”; the coordinates are deposited in the PDB databank (PDB access code = 5M96)). We could show that cpd 1 sterically displaces helix 12 from the agonist position, which leads to decreased interaction between the receptor and the RIP140 co-activator peptide.…”

Natural products as modulators of retinoic acid receptor-related orphan receptors (RORs)

“…If the His-Tyr lock is broken, the aromatic interactions are also terminated and helix 12 is destabilized as a consequence. [8][9][10] Inverse agonistic ligands are characterized by their ability to repress the transcriptional activity of its nuclear receptor below basal level via recruitment of additional co-repressors and have been shown to disrupt the active conformation of helix 12. Co-repressors contain a different interaction motif than co-activators with a similar amphipathic core (4XX44; 4 is a hydrophobic amino acid) but additional anking sequences and increased length (reviewed in ref .…”