Discovery and characterization of natural products as novel indoleamine 2,3-dioxygenase 1 inhibitors through high-throughput screening.

Indoleamine 2,3-dioxygenase 1 (IDO1) is emerging as a promising therapeutic target for the treatment of malignant tumors characterized by dysregulated tryptophan metabolism. However, the antitumor efficacy of existing small-molecule IDO1 inhibitors is still unsatisfactory, and the underlying mechanism remains largely undefined. To identify novel IDO1 inhibitors, an in-house natural product library of 2000 natural products was screened for inhibitory activity against recombinant human IDO1. High-throughput fluorescence-based screening identified 79 compounds with inhibitory activity > 30% at 20 µM. Nine natural products were further confirmed to inhibit IDO1 activity by > 30% using Ehrlich's reagent reaction. Compounds 2, 7, and 8 were demonstrated to inhibit IDO1 activity in a cellular context. Compounds 2 and 7 were more potent against IDO1 than TDO2 in the enzymatic assay. The kinetic studies showed that compound 2 exhibited noncompetitive inhibition, whereas compounds 7 and 8 were graphically well matched with uncompetitive inhibition. Compounds 7 and 8 were found to bind to the ferric-IDO1 enzyme. Docking stimulations showed that the naphthalene ring of compound 8 formed "T-shaped" π-π interactions with Phe-163 and that the 6-methyl-naphthalene group formed additional hydrophobic interactions with IDO1. Compound 8 was identified as a derivative of tanshinone, and preliminary SAR analysis indicated that tanshinone derivatives may be promising hits for the development of IDO1 inhibitors. This study provides new clues for the discovery of IDO1/TDO2 inhibitors with novel scaffolds.

Tryptophan 2,3-dioxygenase inhibitory activities of tryptanthrin derivatives.

Tryptophan 2,3-dioxygenase (TDO) is becoming a promising therapeutic target due to its involvement in cancer and neurodegenerative diseases. Development of efficient TDO inhibitors is a prime strategy in disease treatment. However, the lack of a TDO inhibitor bioassay system slows the progress of TDO inhibitor research. Herein, an active recombinant human TDO (hTDO) was prepared under optimal expression conditions, an enzymatic assay was optimized, and two cellular assays of TDO activity were developed. Then, the potential TDO inhibitory activities of nine tryptanthrin derivatives (5a-5i) were evaluated, and the inhibitory constants (Ki), enzymatic and cellular half maximal inhibitory concentrations (IC50) were measured, and the type of inhibition was determined. The tryptanthrins had various levels of TDO inhibitory activities; tryptanthrins with a substituent at 8-position had stronger inhibitory activities than the other derivatives. Moreover, most of the compounds, except 5g and 5h, exhibited better inhibitory activities than the previously reported TDO inhibitor LM10. Furthermore, the molecular docking study of compounds 5c and 5d revealed that the O atom of the tryptanthrin ring is directed toward the heme iron (Fe) of hTDO via strong coordination interactions. These findings suggest that tryptanthrin and its derivatives have the potential to be developed as promising molecules for TDO-related target therapy.

Insights into the mechanism of inhibition of tryptophan 2,3-dioxygenase by isatin derivatives.

Tryptophan 2,3-dioxygenase (TDO) is a cytosolic protein with a proven immunomodulatory function that promotes tumoral immune resistance and proliferation. Despite the interest in TDO as a therapeutic target in cancer treatment, the number of biologically useful inhibitors is limited. Herein, we report isatin derivatives as a new class of TDO inhibitors. Through structure-activity relationships and molecular docking studies, we optimized the inhibition potency of isatin derivatives by >130-fold and elucidated the mechanistic details that control their mode of action. Hydrogen bond interactions between the compound and key active site residues of TDO, freedom upon rotation of the C3 chemical moiety and the presence of chlorines in the benzene ring of the compound comprise the properties that an isatin-based inhibitor requires to effectively inhibit the enzymatic activity of TDO.

Characterization and evolution of vertebrate indoleamine 2, 3-dioxygenases IDOs from monotremes and marsupials.

Indoleamine 2,3-dioxygenase (IDO1) and tryptophan 2,3-dioxygenase (TDO) are tryptophan-degrading enzymes that catalyze the first step in tryptophan catabolism via the kynurenine pathway. TDO is widely distributed in both eukaryotes and bacteria. In contrast, IDO has been found only in mammals and yeast. In 2007, a third enzyme, indoleamine 2,3-dioxygenase-2 (IDO2), was discovered. IDO2 is found not only in mammals but also in lower vertebrates. Interestingly, the Km value of IDO2 for L-Trp was 500-1000 fold higher than that of IDO1. In this study, we isolated both IDO1 and IDO2 cDNA from a monotreme, the platypus (Ornithorhynchus anatinus), and a marsupial, the gray short-tailed opossum (Monodelphis domestica). We characterized the recombinant proteins and those of other known IDO1/IDO2 in intact cells and a cell-free system. It was found that methylene blue may not be suitable reductant for IDO2, hence resulting in an underestimation of recombinant IDO2 activity. In intact cells, the Km value of IDO2 for L-Trp was estimated to be much higher than that of IDO1 and this high Km value appears to have been conserved during the evolution of IDO2. The protein encoded by the ancestor gene of IDO1 and IDO2 is likely to have had properties more similar to present day IDO2 than to IDO1.

Purification and biochemical characterization of a recombinant Anopheles gambiae tryptophan 2,3-dioxygenase expressed in Escherichia coli.

In the malaria vector Anopheles gambiae, tryptophan 2,3-dioxygenase (TDO) is the only enzyme able to initiate l-tryptophan degradation through the kynurenine pathway. TDO converts l-tryptophan to N-formylkynurenine by catalyzing the heme-dependent oxidative opening of the substrate indole ring. Despite the central role exerted by kynurenines in the physiology of living organisms, only a few insect TDOs have been subjected to biochemical characterization in vitro. We performed a RT-PCR-based analysis of the tissue distribution of TDO mRNA in A. gambiae that revealed a ubiquitous expression of the gene, thus further underlining the importance of the enzyme in the mosquito biology. We developed an expression/purification procedure yielding pure and active recombinant A. gambiae TDO. Spectral analyses showed that the enzyme was purified in its heme-ferric form that was subsequently used to determining the Michaelis-Menten constants of the TDO catalyzed reaction in the presence of reducing agents. The screening of a number of compounds as potential TDO modulators showed that several kynurenines and other Tryptophan-derived molecules interfere with the enzyme activity in vitro. Our study could contribute to understanding TDO regulation in vivo and to the identification of inhibitors to be used to alter Tryptophan homeostasis in the malaria vector.

Characterization of TioF, a tryptophan 2,3-dioxygenase involved in 3-hydroxyquinaldic acid formation during thiocoraline biosynthesis.

Thiocoraline is a thiodepsipeptide antitumor agent that belongs to the family of bisintercalator natural products that bind duplex DNA through their two planar intercalating moieties. In thiocoraline, the 3-hydroxyquinaldic acid (3HQA) chromophores required for intercalation are derived from L-Trp. We have expressed the Micromonospora sp. ML1 tryptophan 2,3-dioxygenase(TDO) TioF, purified it from E. coli, and confirmed its role in the irreversible oxidation of L-Trp to N-formylkynurenine, the proposed first step during 3HQA biosynthesis. We have established that TioF is a catalyst with broader specificity than other TDOs, but that is less promiscuous than indoleamine 2,3-dioxygenases. TioF was found to display activity with various L-Trp analogs (serotonin, D-Trp, and indole). The TioF reaction products generated during this study will be used as substrates for subsequent analysis of the other enzymes involved in 3HQA biosynthesis.

A kinetic, spectroscopic, and redox study of human tryptophan 2,3-dioxygenase.

The family of heme dioxygenases, as exemplified by indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase, catalyzes the oxidative cleavage of L-tryptophan to N-formylkynurenine. Here, we describe a bacterial expression system for human tryptophan 2,3-dioxygenase (rhTDO) together with spectroscopic, kinetic, and redox analyses. We find unexpected differences between human tryptophan 2,3-dioxygenase and human indoleamine 2,3-dioxygenase [Chauhan et al. (2008) Biochemistry 47, 4761-4769 ]. Thus, in contrast to indoleamine 2,3-dioxygenase, the catalytic ferrous-oxy complex of rhTDO is not observed, nor does the enzyme discriminate against substrate binding to the ferric derivative. In addition, we show that the rhTDO is also catalytically active in the ferric form. These new findings illustrate that significant mechanistic differences exist across the heme dioxygenase family, and the data are discussed within this broader framework.

Production and purification of human indoleamine 2,3-dioxygenase (HuIDO) protein in a baculovirus expression system and production and characterization of egg yolk antibody against the purified HuIDO.

The human indoleamine 2,3-dioxygenase (HuIDO) baculoviral construct, for expression of HuIDO protein with a hexa-histidine and FLAG (DYKDDDDK) tag, was produced using the BacPAK Baculovirus Expression System. HuIDO baculovirus was used to infect Sf21 insect cells to produce functionally active protein in large amounts. Conditions for protein purification by metal affinity chromatography were determined and optimized. Addition of haemin ensured optimal activity of the purified heme-containing oxygenase. The soluble purified protein was used to immunize a chicken to produce large quantities of polyclonal IgY against HuIDO. The anti-HuIDO IgY antibody specifically detected HuIDO produced by a range of cell types including transfectants and native HuIDO expression induced in IFN-gamma-stimulated cells. The antibody detected HuIDO in cell lysates by western blotting and in the cytoplasm of cells by microscopy. The antibody was unable to block the function of the enzyme, indicating that this antibody binds outside the active site of HuIDO.

Tryptophan-derived catabolites are responsible for inhibition of T and natural killer cell proliferation induced by indoleamine 2,3-dioxygenase.

Macrophages exposed to macrophage colony-stimulating factor acquire the capacity to suppress T cell proliferation; this effect is associated with de novo expression of the tryptophan-catabolizing enzyme indoleamine 2,3-dioxygenase (IDO). We have purified IDO and tested its activity in in vitro models of T cell activation. IDO was able to inhibit proliferation of CD4(+) T lymphocytes, CD8(+) T lymphocytes, and natural killer (NK) cells; proliferation of B lymphocytes was not affected. The inhibitory role of tryptophan and of its catabolites was then tested. In the presence of tryptophan, only L-kynurenine and picolinic acid inhibit cell proliferation. In a tryptophan-free medium cell proliferation was not affected. In the absence of tryptophan inhibition induced by L-kynurenine and picolinic acid was observed at concentrations below the lowest concentration that was effective in the presence of tryptophan, and quinolinic acid acquired some inhibitory capacity. Inhibition of cell proliferation induced by the tryptophan catabolites resulting from IDO activity was selective, applying only to cells undergoing activation. Resting cells were not affected and could subsequently activate normally. We suggest that IDO exerts its effect on cell proliferation by (i) starting the cascade of biochemical reactions that produce the three catabolites and by (ii) enhancing their inhibitory potential by depriving the extracellular microenvironment of tryptophan.

Expression and purification of recombinant human indoleamine 2, 3-dioxygenase.

Indoleamine 2,3-dioxygenase, the first and rate-limiting enzyme in human tryptophan metabolism, has been implicated in the pathogenesis of many diseases. The human enzyme was expressed in Escherichia coli EC538 (pREP4) as a fusion protein to a hexahistidyl tag and purified to homogeneity in terms of electrophoretic and mass spectroscopic analysis, by a combination of phosphocellulose and nickel-agarose affinity chromatography. The yield of the fusion protein was 1.4 mg per liter of bacterial culture with an overall recovery of 56% from the crude extract. When the culture medium was supplemented with 7 microM hemin, the purified protein contained 0.8 mol of heme per mole of enzyme and exhibited an absorption spectrum consistent with the ferric form of hemoprotein. The pI value of the recombinant enzyme was 7.09 compared with 6.9 for the native enzyme. This was as expected from the addition of the hexahistidyl tag. Similar to the native enzyme, the recombinant enzyme required methylene blue and ascorbic acid for enzyme activity and oxidized not only l-tryptophan but also d-tryptophan and 5-hydroxy-l-tryptophan. The molecular activities for these substrates and their K(m) values were similar to those of the native enzyme, indicating that the addition of the hexahistidyl tag did not significantly affect catalytic activity. The recombinant protein can therefore be used to investigate properties of the native enzyme. This will aid the development of specific inhibitors of indoleamine 2,3-dioxygenase, which may be effective in halting disease progression.

Tryptophan 2,3-dioxygenase in Saccharomyces cerevisiae.

The tryptophan pyrrole-ring cleavage enzyme (TPCE) was detected in the yeast Saccharomyces cerevisiae. TPCE activity existed constitutively and was markedly induced by culturing the cells in a medium containing 0.1% (w/v) L-tryptophan. We purified partially the enzyme from the L-tryptophan-induced cells by phospho-cellulose column chromatography. The partially purified enzyme was stimulated solely by L-ascorbic acid, a nonspecific reductant, suggesting that the yeast TPCE is not indoleamine 2,3-dioxygenase, but rather tryptophan 2,3-dioxygenase. The enzyme metabolized L-tryptophan preferentially, and D-tryptophan slightly. KCN and NaN3, exogenous ligands of heme, inhibited the enzyme activity drastically, indicating that yeast tryptophan 2,3-dioxygenase contains heme(s) in its active site. The optimal pH of the enzyme was 6.5. Upon two-dimensional polyacrylamide gel electrophoresis, a protein staining spot was identified that was induced by L-tryptophan and whose intensity changed in correlation with the tryptophan 2,3-dioxygenase activity after phospho-cellulose column chromatography. This protein, exhibiting a molecular weight of approximately 38,000 and an isoelectric point of approximately pH 8.0, may be identified as a subunit of yeast tryptophan 2,3-dioxygenase.

Isotope effects and alternative substrate reactivities for tryptophan 2,3-dioxygenase.

Tryptophan 2,3-dioxygenase (EC 1.13.1.12) is a hemoprotein which catalyzes the first step in the oxidative degradation of tryptophan. The reaction is believed to proceed by addition of O2 across the 2,3-bond of the indole ring, followed by decomposition of the resultant dioxetane to give N-formylkynurenine. A primary D2O isotope effect of 4.4 on Vmax/Km was observed at the pH optimum, pH 7.0. This implies that abstraction of the indole proton is at least partially rate-determining. An inverse secondary isotope effect of 0.96 was observed for L-[2-3H]tryptophan at this pH. The secondary isotope effect signals the formation of the C-O bond at C-2. As the rate of proton abstraction increased with increasing pH, the D2O isotope effect decreased to 1.2 at pH 8.5 and the secondary isotope effect increased to 0.92. The rate-determining steps therefore change with increasing pH, and bond formation at C-2 becomes more rate-limiting. The secondary isotope effect did not change significantly with varying O2 concentration so that substrate binding is primarily ordered with O2 binding first. The specificity of the enzyme towards substituted tryptophans shows that substitution of the phenyl ring of the indole is sterically unfavorable. Steric hindrance is highest at the 4- and 7-positions, while the 5- and 6-positions are less sensitive. 6-Fluoro-L-tryptophan was more reactive than tryptophan, and the increased reactivity can be explained by an electronic effect that enhances of the rate of C-O bond formation at C-2.

Purification and characterization of tryptophan dioxygenase from Streptomyces parvulus.

Tryptophan dioxygenase, derived from Streptomyces parvulus, was purified to near homogeneity and shown to have a native Mr of 88,000. Kinetic parameters of the enzyme were determined and evidence suggesting that it is a hemoprotein was obtained. Tryptophan dioxygenase has a high specificity toward L-tryptophan with an apparent Km of 0.3 mM. L-3-Hydroxykynurenine was a competitive inhibitor with respect to L-tryptophan with a Ki of 0.16 mM. In vitro, the enzyme displayed little activity in the absence of a reducing agent; ascorbate, at 50 mM, was the preferred reductant providing almost a 50-fold increase in enzyme activity. The regulation of tryptophan dioxygenase synthesis and activity is described. The expression of the enzyme is correlated with the biosynthesis of actinomycin D in S. parvulus. These results support the hypothesis that tryptophan dioxygenase functions as the first enzyme in the sequence converting L-tryptophan to the chromophore of this antibiotic.

Separation of tryptophan pyrrolooxygenase into three molecular forms. A study of their substrate specificities using tryptophyl-containing peptides and proteins.

Tryptophan pyrrolooxygenase from wheat germ was separated into three molecular forms by microgranular DEAE-cellulose using a stepwise or a linear gradient elution procedure. In the first case molecular forms A and B were eluted with 10 mM Tris/HCl buffer (pH 7.4) and molecular form C was eluted with 50 mM KCl in the same buffer. The same separation could also be achieved with a linear KCl gradient (0-100 mM) in 10 mM Tris/HCl buffer (pH 7.4). The three molecular forms of tryptophan pyrrolooxygenase oxidized L-, D-, DL-Trp as well as many Trp derivatives with formation of N-formylkynurenyl derivatives. They also efficiently oxidized Trp-Phe, Trp-Tyr, Trp-Ala, Ala-Trp, Trp-Gly, Gly-Trp, Trp-Leu, Leu-Trp, Pro-Trp and Val-Trp, although the dipeptides were oxidized at different rates by the three molecular forms. A number of tryptophyl-containing tetra-, penta-, octa-, nona- and decapeptides were also oxidized. The oligopeptides which were known to have a helical conformation were better substrates than the smaller oligopeptides which were devoid of the conformational factor. The three molecular forms of tryptophan pyrrolooxygenase oxidized the tryptophyl residues of lysozyme, pepsin, chymotrypsin, trypsin and bovine serum albumin. It was found that molecular form A oxidized the more exposed (or hydrophilic) Trp residues of the proteins, while molecular form C also oxidized the Trp residues of a more hydrophobic nature. The three molecular forms were inhibited by chelating agents (alpha, alpha'-dipyridyl, EDTA and omicron-phenanthroline), although they differed in their sensitivities to these agents. Their optimum temperatures and inactivation rates at 65 degrees C was also different.

L-tryptophan 2,3-dioxygenase of a moderate thermophile, Bacillus brevis. Purification, properties and a substrate-mediated stabilization of the quaternary structure.

L-Tryptophan 2,3-dioxygenase (L-tryptophan: oxygen 2,3-oxidoreductase ( decycling ), EC 1.13.11.11) from Bacillus brevis, a moderately thermophilic bacteria, was purified to apparent homogeneity. The enzyme had a molecular weight of 110 000 and consisted of four subunits of equal molecular size. The enzyme exhibited the typical absorption spectra of a protohemoprotein . The amino acid composition and catalytic properties of the thermophilic enzyme were almost similar to those of its mesophilic counterpart from Pseudomonas acidovorans. However, the stabilities of the enzyme differed markedly between the two. The thermophilic enzyme was more resistant to heat and several chemical denaturants. The addition of L-tryptophan protected the enzyme from heat- and SDS- denaturations , and the tryptophan-mediated stabilization was more evident for the thermophilic enzyme. The effect of L-tryptophan on the stabilization of the thermophilic enzyme was more effective in preventing the dissociation of the tetrameric form of the enzyme (i.e. stabilizing it) in the case of the native, as compared to the mesophilic enzyme.

Stereospecificity of hepatic L-tryptophan 2,3-dioxygenase.

Tryptophan 2,3-dioxygenase [L-tryptophan--oxygen 2,3-oxidoreductase (decyclizing), EC 1.13.11.11] has been reported to act solely on the L-isomer of tryptophan. However, by using a sensitive assay method with D- and L-[ring-2-14C]tryptophan and improved assay conditions, we were able to demonstrate that both the D- and L-stereoisomers of tryptophan were cleaved by the supernatant fraction (30000 g, 30 min) of liver homogenates of several species of mammals, including rat, mouse, rabbit and human. The ratio of activities toward D- and L-tryptophan was species variable, the highest (0.67) in ox liver and the lowest (0.07) in rat liver, the latter being hitherto exclusively used for the study of hepatic tryptophan 2,3-dioxygenase. In the supernatant fraction from mouse liver, the ratio was 0.23 but the specific activity with D-tryptophan was by far the highest of all the species tested. To identify the D-tryptophan cleaving enzyme activity, the enzyme was purified from mouse liver to apparent homogeneity. The specific activities toward D- and L-tryptophan showed a parallel rise with each purification step. The electrophoretically homogeneous protein had specific activities of 0.55 and 2.13 mumol/min per mg of protein at 25 degrees C toward D- and L-tryptophan, respectively. Additional evidence from heat treatment, inhibition and kinetic studies indicated that the same active site of a single enzyme was responsible for both activities. The molecular weight (150000), subunit structure (alpha 2 beta 2) and haem content (1.95 mol/mol) of the purified enzyme from mouse liver were similar to those of rat liver tryptophan 2,3-dioxygenase. The assay conditions employed in the previous studies on the stereospecificity of hepatic tryptophan 2,3-dioxygenase were apparently inadequate for determination of the D-tryptophan cleaving activity. Under the assay conditions in the present study, the purified enzyme from rat liver also acted on D-tryptophan, whereas the pseudomonad enzyme was strictly specific for the L-isomer.

Negligible amount of copper in hepatic L-tryptophan 2,3-dioxygenase.

During the purification of L-tryptophan 2,3-dioxygenase, a protohemoprotein from rat liver, both copper and heme contents of the preparations were found to be progressively increased as purification proceeded. However, the greater part of copper was removed in the late stages of the purification giving a copper to heme ratio less than 0.4. The small amounts of copper could further be reduced by one-half, by a mild treatment of enzyme with chelators such as ethylenedi aminetetraacetate, without any accompanying decrease in enzymatic activity. Since the turnover number of these enzyme preparations expressed per mol of enzyme-bound heme, 200 to 277 min-1 at 25 degrees, were either comparable to or slightly higher than those reported with homogeneous enzyme preparations, the heme in the preparation was considered to be of fully active L-tryptophan 2,3-dioxygenase and, therefore, such a small ratio of copper to heme, 0.1 to 0.3, indicated that copper is not a constituent of L-tryptophan 2,3-dioxygenase of rat liver. The findings were thus inconsistent with the results of Brady et al. (Brady, F. O., Monaco, M. E. Forman, H. J. Schutz, G., and Feigelson, P. (1972) J. Biol. Chem. 247, 7915-7922), who found that L-tryptophan 2,3-dioxygenase contained 2 g atoms of copper and 2 mol of heme/mol of enzyme. Possible reasons for this discrepancy have been discussed.