Inhibition Mechanisms of Human Indoleamine 2,3 Dioxygenase 1

Abstract

Human indoleamine 2,3-dioxygenase 1 (hIDO1) and tryptophan dioxygenase (hTDO) catalyze the same dioxygenation reaction of Trp to generate N-formyl kynurenine (NFK). They share high structural similarity, especially in the active site. However, hIDO1 possesses a unique inhibitory substrate binding site (Si) that is absent in hTDO. In addition, in hIDO1, the indoleamine group of the substrate Trp is H-bonded to S167 through a bridging water, while that in hTDO is directly H-bonded to H76. Here we show that Trp binding to the Si site or the mutation of S167 to histidine in hIDO1 retards its turnover activity and that the inhibited activity can be rescued by an effector, 3-indole ethanol (IDE). Kinetic studies reveal that the inhibited activity introduced by Trp binding to the Si site is a result of retarded recombination of the ferryl moiety with Trp epoxide to form NFK and that IDE reverses the effect by preventing Trp from binding to the Si site. In contrast, the abolished activity induced by the S167H mutation is primarily a result of ∼5000-fold reduction in the O binding rate constant, possibly due to the blockage of a ligand delivery tunnel, and that IDE binding to the Si site reverses the effect by reopening the tunnel. The data offer new insights into structure-based design of hIDO1-selective inhibitors.

Tracking Hidden Binding Pockets Along the Molecular Recognition Path of l‐Trp to Indoleamine 2,3‐Dioxygenase 1

“…Results have allowed disclosing for the first time high and low dissociation constants (K d ) of l ‐Trp to IDO1, as well as the presence of a metastable interaction site located close to the C‐terminal part of the JK‐loop and defined by Lys238. Furthermore, results provide an additional support to the reported key role of the C‐terminal part of the JK‐loop in regulating the catalytic activity of the enzyme …”

“…Of note, the importance of such loop in controlling the catalytic activity of IDO1 was independently reported in literature by distinct research groups . In particular, other studies used different molecular dynamic approaches in combination with mutagenesis experiments (Thr379Ala) to show that the conserved “GTGG” motif of JK‐loop C affects the binding of substrate to IDO1, adopting closed and open conformational states .…”

“…Of note, the importance of such loop in controlling the catalytic activity of IDO1 was independently reported in literature by distinct research groups. [25][26][27][28][29] In particular, other studies used different molecular dynamic approaches in combination with mutagenesis experiments (Thr379Ala) to show that the conserved "GTGG" motif of JK-loop C affects the binding of substrate to IDO1, adopting closed and open conformational states. [26] Consistent with these previous findings, our suMD and new mutagenesis results support a role for the "GTGG" motif of JK-loop C in the molecular recognition path of substrate, suggesting that conformational movements of the JK-loop C can facilitate entering of l-Trp into the catalytic cleft of IDO1.…”

“…Furthermore, results provide an additional support to the reported key role of the C-terminal part of the JK-loop in regulating the catalytic activity of the enzyme. [25][26][27][28][29]…”

New Insights from Crystallographic Data: Diversity of Structural Motifs and Molecular Recognition Properties between Groups of IDO1 Structures

“…Since the disclosure of the first crystal structure in 2006, applications of SBDD approaches to IDO1 have been fostered by the ever increasing number of entries in the PDB database (Figure ; Table S1 in the Supporting Information) . However, only few of these entries have hitherto been used for SBDD screening campaigns (33 %, Figure ) …”