Discovery and Characterisation of Dual Inhibitors of Tryptophan 2,3-Dioxygenase (TDO2) and Indoleamine 2,3-Dioxygenase 1 (IDO1) Using Virtual Screening

Abstract

Cancers express tryptophan catabolising enzymes indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO2) to produce immunosuppressive tryptophan metabolites that undermine patients’ immune systems, leading to poor disease outcomes. Both enzymes are validated targets for cancer immunotherapy but there is a paucity of potent TDO2 and dual IDO1/TDO2 inhibitors. To identify novel dual IDO1/TDO2 scaffolds, 3D shape similarity and pharmacophore in silico screening was conducted using TDO2 as a model for both systems. The obtained hits were tested in cancer cell lines expressing mainly IDO1 (SKOV3—ovarian), predominantly TDO2 (A172—brain), and both IDO1 and TDO2 (BT549—breast). Three virtual screening hits were confirmed as inhibitors (TD12, TD18 and TD34). Dose response experiments showed that TD34 is the most potent inhibitor capable of blocking both IDO1 and TDO2 activity, with the IC50 value for BT549 at 3.42 µM. This work identified new scaffolds able to inhibit both IDO1 and TDO2, thus enriching the collection of dual IDO1/TDO2 inhibitors and providing chemical matter for potential development into future anticancer drugs.

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

“…Figure shows the extent of coverage of the molecular recognition space by IDO1 structures that have been used in SBDD campaigns as reported in literature . The inspection of the plot reveals that all these IDO1 structures are located at values of PC1 B <2, whereas chain structures occupying values of PC1 B >6 form an uncharted cluster of structures with different steric and hydrophilic features of ligand binding pocket.…”

“…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 ) …”

Different effects of tryptophan 2,3-dioxygenase inhibition on SK-Mel-28 and HCT-8 cancer cell lines

“…The latest phase III trial ECHO-301 have reported that the combination of epacadostat (IDO1 selective inhibitor) and PD-1 inhibitor pembrolizumab did not provide any additional survival benefit compared to pembrolizumab alone in advanced melanoma patients (Long et al 2019 ). These findings indicate that IDO1-specific inhibitors cannot completely block the production of immunosuppressive trp catabolites involved in the immune escape, suggesting that TDO comes into play (Muller et al 2019 ; Sari et al 2019 ).…”

Advances in Anticancer Drug Discovery

“…The biological mechanism of action was further elucidated for known and new bioactive compounds; 10-gingerol was shown to target lipid rafts in triple negative breast cancer cells [ 5 ], a new barbituric acid derivative has antiproliferative and antimigratory effects in hepatocellular carcinoma [ 6 ], pyrimethamine, an established antiparasitic drug, was identified in a screen of known drugs against exon 2-depleted splice variant of aminoacyl-tRNA synthetase-interacting multifunctional protein 2, and was effective in mouse xenografts, making it a promising repositioned drug [ 7 ], the flavonoid quercetin was tested with docetaxel as a potential adjuvant therapy for breast cancer [ 8 ], the immunomodulating drugs thalidomide, lenalidomide, and pomalidomide were tested on cultured normal monocytes, cancer-supporting stromal cells, altering their metabolism and cell–cell communication [ 9 ], another flavonoid kushenol Z, isolated from the roots of Sophora flavescens used in Traditional Chinese Medicine (TCM), inhibited proliferation and induced apoptosis in non-small-cell lung cancer cells [ 10 ], and finally, three new dual inhibitors of tryptophan catabolizing enzymes indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO2), valid cancer immunotherapy targets, were established using virtual screening of natural products [ 11 ].…”

“…The biological mechanism of action was further elucidated for known and new bioactive compounds; 10-gingerol was shown to target lipid rafts in triple negative breast cancer cells [5], a new barbituric acid derivative has antiproliferative and antimigratory effects in hepatocellular carcinoma [6], pyrimethamine, an established antiparasitic drug, was identified in a screen of known drugs against exon 2-depleted splice variant of aminoacyl-tRNA synthetase-interacting multifunctional protein 2, and was effective in mouse xenografts, making it a promising repositioned drug [7], the flavonoid quercetin was tested with docetaxel as a potential adjuvant therapy for breast cancer [8], the immunomodulating drugs thalidomide, lenalidomide, and pomalidomide were tested on cultured normal monocytes, cancer-supporting stromal cells, altering their metabolism and cellcell communication [9], another flavonoid kushenol Z, isolated from the roots of Sophora flavescens used in Traditional Chinese Medicine (TCM), inhibited proliferation and induced apoptosis in non-small-cell lung cancer cells [10], and finally, three new dual inhibitors of tryptophan catabolizing enzymes indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO2), valid cancer immunotherapy targets, were established using virtual screening of natural products [11]. The biological mechanism of action was further elucidated for known and new bioactive compounds; 10-gingerol was shown to target lipid rafts in triple negative breast cancer cells [5], a new barbituric acid derivative has antiproliferative and antimigratory effects in hepatocellular carcinoma [6], pyrimethamine, an established antiparasitic drug, was identified in a screen of known drugs against exon 2-depleted splice variant of aminoacyl-tRNA synthetase-interacting multifunctional protein 2, and was effective in mouse xenografts, making it a promising repositioned drug [7], the flavonoid quercetin was tested with docetaxel as a potential adjuvant therapy for breast cancer [8], the immunomodulating drugs thalidomide, lenalidomide, and pomalidomide were tested on cultured normal monocytes, cancer-supporting stromal cells, altering their metabolism and cell-cell communication [9], another flavonoid kushenol Z, isolated from the roots of Sophora flavescens used in Traditional Chinese Medicine (TCM), inhibited proliferation and induced apoptosis in non-small-cell lung cancer cells [10], and finally, three new dual inhibitors of tryptophan catabolizing enzymes indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO2), valid cancer immunotherapy targets, were established using virtual screening of natural products [11]. The review articles were just as varied as the research papers regarding their topics; tannic acid was reviewed for its anticancer activity and its capacity as a drug delivery vehicle [12], the effect of the integrin peptide TNIIIA2 acting as a pro-cancer factor and peptide FNIII14 acting as an anticancer agent was reviewed based on the regulation on β1-integrin activation, which are matricellu...…”