Human indoleamine-2,3-dioxygenase 2 cofactor lability and low substrate affinity explained by homology modeling, molecular dynamics and molecular docking

Abstract

The human indoleamine-2,3-dioxygenase 2 (hIDO2) protein is growing of interest as it is increasingly implicated in multiple diseases (cancer, autoimmune diseases, COVID-19). However, it is only poorly reported in the literature. Its mode of action remains unknown because it does not seem to catalyze the reaction for which it is attributed: the degradation of the L-Tryptophan into N-formyl-kynurenine. This contrasts with its paralog, the human indoleamine-2,3-dioxygenase 1 (hIDO1), which has been extensively studied in the literature and for which several inhibitors are already in clinical trials. Yet, the recent failure of one of the most advanced hIDO1 inhibitors, the Epacadostat, could be caused by a still unknown interaction between hIDO1 and hIDO2. In order to better understand the mechanism of hIDO2, and in the absence of experimental structural data, a computational study mixing homology modeling, Molecular Dynamics, and molecular docking was conducted. The present article highlights an exacerbated lability of the cofactor as well as an inadequate positioning of the substrate in the active site of hIDO2, which might bring part of an answer to its lack of activity.

Communicated by Ramaswamy H. Sarma

Keywords:

• Homology modeling
• molecular dynamic
• molecular docking
• hIDO2
• dioxygenase
• L-Tryptophan

Acknowledgments

The authors thank the CECI staffs for the access to computational facilities and for the precious advices. They also thank the reviewers for their detailed comments. The authors are also grateful to the FRS-FNRS for the financial support as MM is “aspirant FNRS”.

Disclosure statement

The authors declare that they have no conflicts of interest.

Additional information

Funding

This research used resources of the ‘Plateforme Technologique de Calcul Intensif (PTCI)’ (http://www.ptci.unamur.be) located at the University of Namur, Belgium, which is supported by the FNRS-FRFC, the Walloon Region, and the University of Namur (Conventions No. 2.5020.11, GEQ U. G006.15, 1610468 et RW/GEQ2016). The PTCI is member of the ‘Consortium des Equipements de Calcul Intensif (CECI)’ (http://www.ceci-hpc.be), funded by the ‘Fonds de la Recherche Scientifique de Belgique (F.R.S.-FNRS)’ under the Grant No. 2.5020.11 and by the Walloon Region. MM is a research Fellow of the F.R.S.-FNRS.