Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

Abstract

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination of an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.

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 .…”

“…According to crystallographic studies, the inhibitory substrate pocket is located below the plane of the heme group and defined by residues Phe270, Asp274 and Arg343 . The authors generated the Phe270Gly IDO1 mutant for increasing the plasticity of the site and thus allowing the capture of one molecule of l ‐Trp into the inhibitory substrate pocket.…”

“…Only productive steps were saved to generate suMD trajectories that were then analyzed. RMSD values (Å) of ligand along trajectories of models A–C were calculated from the atomic coordinates of l ‐Trp heavy atoms as obtained in the substrate co‐crystal structure of IDO1 (pdb code: 5WMU) . Ligand‐protein interaction energy was calculated using NAMD Energy extension available in VMD .…”

“…Moreover, disappointing results have been very recently reported for the most advanced IDO1 inhibitor, i. e. epacadostat ( 4 ), and compound 6 and 7 have also been withdrawn from the clinic . Additional studies have sought to better understand the complex biology of the enzyme and aid the design and development of next‐generation IDO1 inhibitors . In the current report, we investigated the molecular recognition path of l ‐Trp ( 1 ) to human IDO1 through a synergic approach based on microscale thermophoresis, supervised molecular dynamics (SuMD) and mutagenesis experiments.…”