Structure guided discovery of inhibitors of indoleamine 2,3-dioxygenase (IDO1)

Abstract

The enzyme indoleamine 2,3‐dioxygenase‐1 (IDO1) plays a critical role in the regulation of the immune system. IDO1 expression is commonly upregulated in cancer, resulting in a suppressed immune system in patients. Clinical observations that patients with high IDO1‐expressing tumours have a poor prognosis have promoted the discovery of novel inhibitors of IDO1 for development as potential anti‐cancer agents to restore tumour immunity. Work in this thesis used differential scanning fluorimetry and enzyme inhibition assays to screen a fragment library for novel IDO1 inhibitors. Thirty‐five small compounds that interacted with and inhibited the IDO1 enzyme were identified, and included compounds from the chemical classes: benzothiazoles, benzimidazoles, benzoxazoles, indoles, indan‐1‐ones, quinolines, naphthalenes, coumarins, biphenyls, phenols, 4‐phenylimidazole, pyridines, hydroxyamidines and phenylpyruvic acids. Spectroscopic studies show that these compounds interact with the haem complex present in the IDO1 active site. Of these, 4‐phenylimidazole and a hydrazine‐containing benzothiazole compound were found to bind to both the Fe(II) and Fe(III) forms of IDO1. Compounds in the hydrazine sub‐class found within the benzothiazole class of fragments in the library were found to be the most potent inhibitors (phenylhydrazine, IC50:0.3 M). A pharmacophore model was developed based on the predicted binding mode of inhibitory fragments. The use of Goldscore, Chemscore, ChemPLP and Astex Statistical Potential (ASP) scoring functions for sampling and rescoring were assessed to find a docking protocol that enriched for IDO1 inhibitory compounds from a dataset. Goldscore/Chemscore docking achieved a seven‐fold enrichment of IDO1 inhibitors in the top‐scoring 5% of compounds from the dataset. This docking protocol was subsequently applied to a set of over 14, 000 phenylhydrazine‐containing compounds. The selection of compounds based on fitness score and on parameters described in the pharmacophore model identified ten potent IDO1 inhibitors (IC50:0.2‐2.4 M). Crystals of IDO1 were also produced for X‐ray crystallographic analysis of protein‐inhibitor interactions. Although extensive optimisation of conditions for crystal production was undertaken, they failed to produce well‐diffracting crystals. Overall, these studies have identified the hydrazine‐containing compounds as a novel IDO1 inhibitory chemotype that may be a useful scaffold for the further lead development.