Ligand Binding and Functional Selectivity of l-Tryptophan Metabolites at the Mouse Aryl Hydrocarbon Receptor (mAhR)

Abstract

The aryl hydrocarbon receptor (AhR) is a nuclear receptor regulating a wide range of biological and toxicological effects. Metabolites of L-tryptophan are able to bind and activate AhR, providing a link between tryptophan catabolism and a novel mechanism of protective tolerance, referred to as "disease tolerance". The notion that pharmacologic modulation of genes associated with endotoxin tolerance would be beneficial in clinical settings dominated by acute hyperinflammatory responses to infection thrusts AhR into the limelight as an interesting druggable target. Combining homology modeling, docking studies, and molecular dynamic simulations with mutagenesis experiments and gene profiling, in this work we report that 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and two different L-tryptophan metabolites, namely L-Kynurenine and FICZ (6-formylindolo[3,2-b]carbazole), are able to bind to mAhR, exploiting different key interactions with distinct set of fingerprint residues. As a result, they stabilize different conformations of mAhR that, in turn, selectively regulate downstream signaling and transcription of specific target genes. Collectively, these results open new avenues for the design and development of selective AhR modulators that, by targeting specific receptor conformations associated with specific AhR functions, may offer novel therapeutic opportunities in infectious diseases and other morbidity that may be associated with the receptor.

Binding Mode and Structure–Activity Relationships of ITE as an Aryl Hydrocarbon Receptor (AhR) Agonist

“…On the basis of the results of docking study and MD simulations of ITE ( 7 ), two mutant AhR receptors were engineered carrying His285Ala (H285A) and Tyr316Ala (Y316A) mutations. It is worth noting that residue Gln 377 was formerly identified as important in mediating a key hydrogen bond interaction with l ‐Kyn ( 3 ) but not involved in interactions with TCDD ( 1 ) and FICZ ( 5 ) . Residue Gln 377 did not fall within 3 Å of an ITE docked pose and showed only a weak hydrogen bond interaction with the ligand in one simulation (fourth MD simulation, average occupancy value=0.19±0.20).…”

“…MD simulations were performed using Desmond 4.0 (Schrödinger LLC, New York, NY, 2014) and the OPLS‐2005 force field. The simulation protocol included starting relaxation steps and a final production phase of 50 ns, as previously reported . The occupancy of intermolecular hydrogen bonds, aromatic interactions, and hydrophobic contacts was calculated along the last 48 ns of the production phase of each MD simulation, using a cut‐off value of 30 % and the Simulation Interaction Diagram tools implemented in Maestro 10.0 (Schrödinger Release 2014‐4: Maestro, Schrödinger LLC, New York, NY, 2014).…”

“…[18,19] More recently,w eh ave shown that TCDD (1)a nd two other different l-Trp metabolites, namely l-Kyn (3)a nd FICZ (5), bind to PAS-B of AhR, exploitingd ifferent key interactions with distinct sets of fingerprint residues. [20] The outcomei st he stabilization of different conformations of the receptor associated with the transcription of specific target genes.…”

Kynurenine pathway metabolism and the microbiota-gut-brain axis

“…Activation of aryl hydrocarbon receptor facilitates host-microbe homeostasis and indole produced from tryptophan by microbes is an important ligand for this transcription factor (Hubbard et al, 2015). Although kynurenine has been regarded as an inert precursor to downstream neuroactive agents, it also activates the aryl hydrocarbon receptor (Julliard et al, 2014;Kawasaki et al, 2014;Nuti et al, 2014;Opitz et al, 2011). Meanwhile, aryl hydrocarbon receptor itself plays a role in the regulation of IDO and TDO expression (Bessede et al, 2014;Jaronen and Quintana, 2014).…”

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms

“…adopted an ensemble-docking protocol in which the different protein conformations were obtained by mono- and multi-template homology models of the mAhR based on different apo and holo HIF-2α structures [68]. Docking of TCDD, FICZ, and the endogenous ligand L-kynurenine, followed by a MD simulation step, led to predict that diverse ligands fit different AhR LBD conformations and show specific interaction patterns with the binding site residues [68]. The obtained L-kynurenine binding mode was experimentally confirmed and it contributed to an in-depth study on the role of AhR in the induction of endotoxin tolerance [69].…”