Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors

Abstract

The haem enzyme indoleamine 2,3-dioxygenase 1 (IDO1) catalyses the rate-limiting step in the kynurenine pathway of tryptophan metabolism and plays an essential role in immunity, neuronal function, and ageing. Expression of IDO1 in cancer cells results in the suppression of an immune response, and therefore IDO1 inhibitors have been developed for use in anti-cancer immunotherapy. Here, we report an extension of our previously described highly efficient haem-binding 1,2,3-triazole and 1,2,4-triazole inhibitor series, the best compound having both enzymatic and cellular IC₅₀ values of 34 nM. We provide enzymatic inhibition data for almost 100 new compounds and X-ray diffraction data for one compound in complex with IDO1. Structural and computational studies explain the dramatic drop in activity upon extension to pocket B, which has been observed in diverse haem-binding inhibitor scaffolds. Our data provides important insights for future IDO1 inhibitor design.

Keywords:

• Cancer immunotherapy
• structure-based drug design
• tryptophan metabolism
• X-ray crystallography

Acknowledgements

We thank Bili Seijo from the Melita Irving and George Coukos laboratory for providing the IDO1 construct and Jean Philippe Gaudry from the Protein Production and Structure Core Facility for rhIDO1 production and purification. We would like to thank Ganesh Kumar Mothukuri for help with the analytical HPLC analysis for purity of the compounds. We acknowledge computational resources from Vital-IT (SIB Swiss Institute of Bioinformatics) and the Scientific Computing and Research Support Unit (University of Lausanne). We thank the local contacts of the Swiss Light Source beamline (SLS-PSI) for their support. We are grateful to Antoine Daina for fruitful discussions. MarvinSketch 21.15, 2021, and InstantJChem 21.2.0, 2020, ChemAxon (http://www.chemaxon.com), were used for displaying and handling chemical structures.

Author contributions

U.F.R. designed the compounds, performed the enzymatic assays and the HPLC analysis of enzymatic and cellular samples, performed docking calculations, determined the X-ray crystallographic protein structures with F.P., analysed and interpreted the data. S.M.R. and P.V. planned, carried out, and documented chemical synthesis and characterisation. A.R. and F.P. performed protein expression and crystallography. N.D., P.R., and K.A. carried out the cellular assays under supervision of M.I. and G.C. O.M. and V.Z. initiated the project, provided critical feedback, and contributed to compound design. U.F.R., S.M.R., P.V., and V.Z. wrote the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Supporting information

X-ray data collection and refinement statistics, previously determined cellular inhibition and toxicity data, binding poses of 5-substituted 4-aryl-1,2,3-triazoles, enzymatic dose-response curves of all compounds, HPLC purity traces, NMR spectra.

Accession codes

Compound MMG-0472, PDB ID 7zv3. Authors will release the atomic coordinates upon article publication.