Discovery of potent IDO1 inhibitors derived from tryptophan using scaffold-hopping and structure-based design approaches

Article abstract of DOI:10.1016/j.ejmech.2017.06.039

Indoleamine 2,3-dioxygenase 1 (IDO1) is frequently hijacked by tumors to escape the host immune response, and the enzyme is now firmly established as an attractive target for cancer immunotherapy. To identify novel IDO1 inhibitors suitable for drug development, a scaffold-hopping strategy combined with the average electrostatic potentials calculation was ultilized to design novel benzoxazolinone derivatives. Among these, compounds 7e, 7f and 9c exhibited the inhibitory potency in the low micromolar range and displayed negligible level of cytotoxicity against HeLa cells. Treatment with these three compounds promoted the proliferation of T lymphocyte and led to the dramatic decrease of regulatory T cells in the B16F1 cells and na?ve T cells co-culture system. Subsequent spectroscopic experiments suggested that these benzoxazolinones formed a coordinate bond with the heme iron to stabilize the complex. This study suggested that the benzoxazolinone was an interesting scaffold for discovering novel IDO1 inhibitors, and these compounds are attractive candidates for further development.

Full text of DOI:10.1016/j.ejmech.2017.06.039

Accepted Manuscript
Discovery of potent IDO1 inhibitors derived from tryptophan using scaffold-hopping
and structure-based design approaches
Yi Zou, Yan Wang, Fang Wang, Minghao Luo, Yuezhen Li, Wen Liu, Zhangjian
Huang, Yihua Zhang, Wenjie Guo, Qiang Xu, Yisheng Lai
PII:
S0223-5234(17)30485-3
10.1016/j.ejmech.2017.06.039
EJMECH 9534
DOI:
Reference:
To appear in: European Journal of Medicinal Chemistry
Received Date: 5 March 2017
Revised Date: 7 June 2017
Accepted Date: 22 June 2017
Please cite this article as: Y. Zou, Y. Wang, F. Wang, M. Luo, Y. Li, W. Liu, Z. Huang, Y. Zhang, W.
Guo, Q. Xu, Y. Lai, Discovery of potent IDO1 inhibitors derived from tryptophan using scaffold-hopping
and structure-based design approaches, European Journal of Medicinal Chemistry (2017), doi: 10.1016/
j.ejmech.2017.06.039.
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ACCEPTED MANUSCRIPT
Graphical abstract
Discovery of potent IDO1 inhibitors derived from tryptophan using
scaffold-hopping and structure-based design approaches
Yi Zou a,1, Yan Wang b,1, Fang Wang a,1, Minghao Luo a, Yuezhen Li c, Wen Liu b, Zhangjian
Huang a, Yihua Zhang a, Wenjie Guo b,**, Qiang Xu b,**, Yisheng Lai a,*
aState Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic
Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, PR China
bState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University,
Nanjing 210093, PR China
c Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing
211198, PR China

ACCEPTED MANUSCRIPT
Discovery of potent IDO1 inhibitors derived from tryptophan
using scaffold-hopping and structure-based design approaches
Yi Zou a,1, Yan Wang b,1, Fang Wang a,1, Minghao Luo a, Yuezhen Li c, Wen Liu b,
Zhangjian Huang a, Yihua Zhang a, Wenjie Guo b,**, Qiang Xu b,**, Yisheng Lai a,*
aState Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic
Diseases, Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, PR China
bState Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University,
Nanjing 210093, PR China
c Department of Organic Chemistry, School of Science, China Pharmaceutical University, Nanjing
211198, PR China
Author Contributions
1 Y.Z., Y.W., and F.W. contributed equally to this work.
* Corresponding author. State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of
Drug Discovery for Metabolic Diseases, Center of Drug Discovery, China Pharmaceutical University,
Nanjing 210009, PR China.
** Corresponding author. State Key Laboratory of Pharmaceutical Biotechnology, School of Life
Sciences, Nanjing University, Nanjing 210093, PR China.
E-mail addresses: guowj@nju.edu.cn (W. Guo), molpharm@163.com (Q. Xu), yslai@cpu.edu.cn (Y.
Lai).

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ABSTRACT
Indoleamine 2,3-dioxygenase 1 (IDO1) is frequently hijacked by tumors to escape the host immune
response, and the enzyme is now firmly established as an attractive target for cancer immunotherapy.
To identify novel IDO1 inhibitors suitable for drug development, a scaffold-hopping strategy combined
with the average electrostatic potentials calculation was ultilized to design novel benzoxazolinone
derivatives. Among these, compounds 7e, 7f and 9c exhibited the inhibitory potency in the low
micromolar range and displayed negligible level of cytotoxicity against HeLa cells. Treatment with
these three compounds promoted the proliferation of T lymphocyte and led to the dramatic decrease of
regulatory T cells in the B16F1 cells and naïve T cells co-culture system. Subsequent spectroscopic
experiments suggested that these benzoxazolinones formed a coordinate bond with the heme iron to
stabilize the complex. This study suggested that the benzoxazolinone was an interesting scaffold for
discovering novel IDO1 inhibitors, and these compounds are attractive candidates for further
development.
Keywords:
Indoleamine 2,3-dioxygenase 1; scaffold-hopping; electrostatic potentials calculation; induced fit
docking; QM/MM

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1. Introduction
Although the host immune system is able to recognize and destroy transformed cells, most
malignancies can create an immunosuppressive microenvironment to evade immune destruction [1].
This can be achieved through several molecular mechanisms, including the recruitment of
immunosuppressive cells, activation of immunoinhibitory checkpoint pathways, and exclusion of T
cells [2]. A large body of evidence suggests that indoleamine 2,3-dioxygenase 1 (IDO1) has been
proposed as
a potential contributor to tumor-derived immunosuppression in the tumor
microenvironment both by the depletion of tryptophan and by the accumulation of tryptophan
metabolites [3].
IDO1 is an extrahepatic cytosolic heme-containing dioxygenase that catalyzes the first and
rate-limiting step in the kynurenine pathway, leading to the degradation of the essential amino acid
tryptophan. It is widely expressed at physiological levels in normal human tissues, including spleen,
gut and lung [4]. In human cancer, in addition to being constitutively expressed by a wide variety of
tumor cells via an autocrine AHR-IL-6-STAT3 signaling loop [5], IDO1 can be induced in tumor cells
and the host antigen-representing cells by proinflammatory stimuli such as interferon-γ (IFN-γ) and
transforming growth factor-β (TGF-β) [6,7]. High expression of IDO1 by tumors can lead to the
depletion of tryptophan and the accumulating high levels of kynurenine and its downstream metabolites
in the tumor microenvironment, which trigger downstream signaling through GCN [8], mTOR [9] and
AHR [10,11]. These events can inhibit the proliferation and function of effector T (Teff) cells [7], skew
naïve CD4+ T cells toward differentiation into regulatory T (Treg) cells [9], promote IDO1-expressing
DCs toward an immunosuppressive phenotype [10], and thus enable tumor cells to elude the host
immune response. Indeed, pharmacological inhibition of IDO1 can effectively restore antitumor
immunity and suppress tumor growth in preclinical models [12], and some of IDO1 inhibitors are
currently being tested in clinical trials in patients with various types of malignancies [13].
Not surprisingly, there have been many attempts to discover and develop IDO1 inhibitors in recent
years. Since the design of enzyme inhibitors often begin from its substrate, many IDO1 inhibitors are
tryptophan derivatives such as 1-methyltryptophan (1-MT, Fig. 1) [14]. 1-MT has two stereoisomers
with different biological properties. The L isomer (L-1-MT) was the more potent IDO1 inhibitor (Ki =
30 µM), while the D isomer (D-1-MT, indoximod) showed more anticancer activity in mouse tumor

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models [15]. D-1-MT is recently in phase II clinical trials for the treatment of refractory metastatic
prostate cancer (NCT01560923) and breast cancer (NCT02913430). Subsequently, a more potent
inhibitor MTH-Trp with a methylthiohydantoin ring instead of the amino acidic chain of tryptophan
was discovered through library screening. It was described as a competitive IDO1 inhibitor (Ki = 11.4
µM) and was 20-fold more potent than 1-MT in a cell-based assay [16]. Unfortunately, in addition to
IDO1, MTH-Trp also inhibits receptor-interacting serine/threonine protein kinase 1 (RIPK1), and
therefore the results of the in vitro and in vivo experiments with MTH-Trp must be interpreted with
caution [17,18]. In order to improve the potency of the first chemotype of IDO1 inhibitors, Donovan
and co-workers undertook a screen of commercially available indole-based molecules in 2006, and
found that the natural product brassinin was a moderately potent competitive inhibitor of IDO1 with a
Ki value of 97.7 µM, which bears a methyldithiocarbamate moiety that replaces the α-aminoacetic acid
chain of tryptophan. Structural modifications of brassinin afforded the best inhibitor (1, Ki = 11.5 µM)
that was three-times more potent than 1-MT in vitro through the substitution of the S-methyl group with
a naphthalene ring [19]. Then, Frédérick reported another indole series of competitive IDO1 inhibitors
indol-2-yl ethanones by virtual screening, a notable example being lead compound 2 with micromolar
inhibitory potency (IC50 = 65 µM). It was characterized by an indole ring substituted in the 2-position
by a 2-pyridinyl-ethanone group [20]. Then, structure and activity relationship (SAR) studies on the
indol-2-yl ethanones led to the discovery compound 3 with an IC50 value of 13.1 µM, and showed that
an iron coordinating group on the linker was essential to retain the inhibitory activity [21].
Fig. 1. The representative IDO1 inhibitors possessing an indole scaffold.
In addition to the above IDO1 inhibitors contained an indole fragment, many inhibitors with new
structural scaffolds have been discovered by structure-based design [22], high-throughput screening

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[23], and natural product derivatization [24]. Although significant progress has been made in the
research mentioned above, there are currently only a few drugs in clinical trials testing IDO1 inhibition
as a strategy for the treatment of cancer (e.g. epacadostat and GDC-0919) [25,26]. Thus, it is still an
unmet need to discover novel and structurally diverse IDO1 inhibitors with characterized therapeutic
utility.
In our continuous efforts to identify more potent IDO1 inhibitors, we explored here a series of
novel benzo-fused five-membered heterocycles with two heteroatoms that were designed from IDO1
substrate tryptophan through a scaffold-hopping strategy (Fig. 2). Interestingly, the resulting
compounds 7e, 7f and 9c proved to be potent IDO1 inhibitors with inhibitory potency in the low
micromolar range and displayed negligible level of cytotoxicity against HeLa cells. Subsequent
experiments indicated that these compounds could promote T-cell growth, increase IFN-γ production,
and reduce the conversion of naïve T cells into Treg cells. Furthermore, the binding mode analysis of
them based on induced fit docking (IFD) and quantum mechanics/molecular mechanics (QM/MM)
calculation will give us a direction for further structure optimization.
Fig. 2. Design strategies of the target compounds.
2. Results and discussion
2.1. Design of the target compounds
Despite the lack of IDO1 crystal structure about tryptophan binding, there is a tryptophan
2,3-dioxygenase (TDO, an enzyme functionally related to IDO1)-tryptophan complex (PDB ID: 2NW8)
in protein data bank website that can be a reference for us, because key active site residues of IDO1 and
TDO are conserved [27]. Through superimposing the two crystal structures (PDB ID: 4PK5 and
2NW8), we can obtain the IDO1-tryptophan complex followed by the energy minimization. As can be
seen from Fig. 3, the indole ring of tryptophan is placed in pocket A of the active site, with the amino
acid moiety pointing toward pocket B and positively charged amino group interacting with the heme

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7-propionate group. In consideration of the importance of heme-ligand interaction and other
nonbonding interactions for potent IDO1 inhibitory activity, a scaffold-hopping strategy that was the
replacement of indole ring will be applied here to in-depth modification of tryptophan. First, many
indole bioisosteres were utilized to perform docking experiment and the scaffolds that can directly
interact with the heme iron and have indole-like shape were retained. Then, the average electrostatic
potentials (ESP) calculation was used to evaluate the coordinating capability of the coordinating atom
(see Supplementary data, Page S2-S9). Ultimately, benzoxazolinone whose ESP value of the
coordinating oxygen atom was similar to that of 4-PI (a reported IDO1 inhibitor binding to heme iron)
[28] was chosen as a starting fragment for our discovery study (Fig. 4). In addition, benzimidazolone
and benzoimidazolamine moieties were also investigated for comparison.
Fig. 3. (A) The minimized structure of IDO1-tryptophan complex. (B) Proposed binding mode of
compounds 7f (grey) and 9c (cyan). L-tryptophan (red) was used as a comparison.
Fig. 4. ESP surface of three indole bioisosteres and their corresponding 2D structures. On the right side is
such a plot for ESP, in which blue, white and red correspond to ESP varying from -42 to 50 kcal/mol.

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2.2. Synthesis of the target compounds
Synthetic route for the target compounds 5a-10c was shown in scheme 1. The benzoxazolinone
cores 4 were prepared by cyclization reaction of corresponding substituted 2-aminophenol with
N,N'-carbonyldiimidazole (CDI), followed by substitution with various 2-chloro-1-phenylethan-1-ones,
benzyl chlorides or phenyl ethyl chlorides, acyl chlorides or aromatic amines to yield 5a-5f, 7a-7j,
9a-9c or 10a-10c, respectively. In addition, 5a-5f were reduced by sodium borohydride to give 6a-6f,
while 5-nitrobenzoxazolinone 7i was reduced by zinc powder to yield 5-aminobenzoxazolinone 8.
Scheme 1. Reagents and conditions: (a) CDI, DMF, N2, 80 oC; (b) K2CO3, DMF, 60 oC; (c) NaBH4, THF, 0
oC; (d) K2CO3, DMF, 60 oC; (e) Zn, NH4Cl, ethanol, rt; (f) TEA, THF, 70 oC; (g) Triphosgene, TEA, DCM,
N2, 0 oC.
Preparation of the target compounds 13 and 15 was illustrated in scheme 2. The key intermediate
12 was obtained by acylation of the N-Boc protected substrate 11, followed by cleaving the
Boc-protecting group with HCl in dioxane to give the corresponding benzoimidazolamine 13.
Benzimidazolone 15 was prepared from 1,3-dihydro-2H-benzo[d]imidazol-2-one under similar
conditions as that for preparation of 6.

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o
Scheme 2. Reagents and conditions: (a) Boc2O, THF, TEA, 60 oC; (b) TEA, THF, 70 C; (c) HCl, dioxane,
r.t.; (d) K2CO3, DMF, 60 oC; (e) NaBH4, THF, 0 oC.
2.3. Inhibition of IDO1 activity
In consideration of the rapid, low-cost and valid properties of the cell-based enzymatic assay,
HeLa cell line, expressing native human IDO1 induced with IFN-γ, was used here to evaluate the
inhibitory activity of these compounds against IDO1. This cellular assay, which is informative for drug
development, has been widely used to investigate various IDO1 inhibitors [23c, 24b, 24c, 29], as it
evaluates not only the IDO1 inhibitory effect of the compounds but also their capacity to permeate the
cell and potential cytotoxicity. All synthesized compounds were assayed for their ability to inhibit
tryptophan degradation and kynurenine production in the HeLa kynurenine assay, and both L-1-MT and
GDC-0919 analog (racemic mixture of GDC-0919) were employed as the positive controls. The results
were reported in Table 1.
Table 1. IDO1 inhibitory activity of the target compounds.
IC50
IC50
Compd.
R1
Xa
R2
Compd.
R1
Xa
R2
(µM)b
(µM)b
H
H
p-F
53.13
38.61
Cl
F
p-Cl
m-F
6.08
5a
5b
7f
p-Cl
28.49
7g

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H
Cl
Cl
Cl
H
m-Cl
p-F
49.25
20.68
24.92
76.58
49.34
50.81
80.58
10.20
62.66
60.88
F
NO2
NO2
NH2
H
p-Cl
m-F
80.78
99.83
99.35
> 100
> 100
90.49
6.40
5c
5d
5e
5f
7h
7i
p-Cl
m-Cl
p-F
p-Cl
7j
m-F
8
p-F
6a
6b
6c
6d
6e
6f
9a
9b
9c
O
H
p-Cl
m-Cl
p-F
H
H
H
Cl
p-F
O
O
Cl
Cl
Cl
H
p-OCH3
m-OCH3
p-OCH3
31.82
14.56
> 100
10a
10b
10c
N
H
p-Cl
m-Cl
Cl
N
H
Cl
H
H
H
> 100
30.8
22.73
99.94
7a
7b
13
15
m-F
H
p-Cl
34.96
L-1-MT
77.29
0.41
7c
GDC-0919
analog
Cl
Cl
H
17.91
9.75
7d
7e
m-F
a X represents the linker group connecting the benzoxazolinone core and substituted benzene ring. The left wave line
represents the connection point linking with the benzoxazolinone nitrogen atom, and the right one represents the
connection point linking with substituted benzene ring.
b IC50 values are the mean of at least two independents assays.
The importance of the linker was first investigated. Compared with ketone (5a-5c) and tertiary
alcohol (6a-6c) derivatives, the substitution with aliphatic (7b, 7c) or amide group (10a) gave rise to
the enhancement of activity to a certain extent, whereas the replacement with an ethidene moiety
caused a 3-fold reduction of activity (7a, IC50 > 100 µM). Next, we evaluated the importance of a
single substitution on the phenyl ring (R2 group). The p-chloro analogs 5b and 6b showed improved
potency versus the analogous m-chloro derivatives 5c and 6c, respectively. According to the
comparisons (5a versus 5b, 6a versus 6b), the substitution with fluorine did not produce a remarkable

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effect on IDO1 inhibition. As for the amide 10a, we also found that the phenyl ring substituted with
p-methoxy group did not produce any improvement of the activity (IC50 = 31.82 µM). In addition, we
studied the influence of the substituent groups at the 5-position of benzoxazolinone (R1 group).
Amazingly, most of 5-chloro-substituted analogs displayed increased potency compared with the
corresponding non-substituted counterpart. The two exceptions were 5f and 6e, which displayed
slightly lower potency with an IC50 value of 76.58 and 62.66 µM. Among these compounds, 7f and 9c
exhibited high potency with IC50 values of 6.08 and 6.40 µM, respectively. However, significant
reduction in potency was observed for the 5-F and 5-NO2 substituted analogs (7g-j). Compared to the
5-Cl derivative (7e, IC50 = 9.75 µM), the introduction of an electron-donating amino group at
5-position (8, IC50 > 100 µM) displayed significant reduction in potency, indicating that IDO1
inhibitory activity was sensitive to the electric property of the group at 5-position and 5-Cl substitution
was more favorable in potency in the HeLa kynurenine assay. Finally, two different moieties,
benzimidazolone and benzoimidazolamine, were also investigated through scaffold hopping. It was
found that compound 13 (IC50 = 22.73 µM) exhibited a slightly increased potency compared to 6a
(about 2-fold, IC50 = 49.34 µM), which could be a good start point for future study. Whereas,
benzimidazolone derivative 15 showed poor inhibitory effect against IDO1. These results of the SARs
analysis were summarized in Fig. 5. Since the inhibition of tryptophan degradation could simply be an
effect of cytotoxicity, measurement of cell viability is indispensable when reporting cellular IC50 values.
In this study, for all compounds, cell viability was evaluated at the end of the assay in a classical MTT
assay. The results of this assay indicated that most of the compounds displayed negligible level of
toxicity against HeLa cells under the experimental conditions. The results of cell viability assay of 7e,
7f, 9c, 13 and 15 were shown in Fig. S1.

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Fig. 5. SARs of benzoxazolinone derivatives as IDO1 inhibitors.
To this end, compounds 7e, 7f and 9c were identified as better potent IDO1 inhibitors in a HeLa
cell-based assay measuring IDO1-mediated tryptophan to kynurenine conversion. Further, these three
compounds were turned out to be incapable of suppressing IDO1 expression through Western blot
analysis, suggesting that they inhibited IDO1 enzymatic activity and not its expression in cells (Fig. 6).
Fig. 6. HeLa cells were treated with IFN-γ with or without the inhibitors at their IC50 concentrations for 24
hours, and analyzed by Western blot using an anti-IDO1 antibody. GDC-0919 analog and L-1-MT were used
as references.
2.4. Reversal of IDO1-mediated suppression of T-cell proliferation by 7e, 7f and 9c
It has been known that the resistance of IDO-expressing cells to immune rejection results from an
arrest of T-cell proliferation caused by local tryptophan depletion. A proliferation assay was carried out
to determine if inhibition of IDO1 activity could improve T-cell activity in the presence of cancer cells.
Melanoma is known to be a highly immunogenic tumor and in many types of melanoma cells are
strongly positive for IDO1 [30]. B16F1 cells, which expressed IDO1 in high level (Fig. S2), were thus
used to co-culture with T cells. As shown in Fig. 7A, compounds 7e, 7f, 9c and GDC-0919 analog led
to a significant augmentation of T-cell activity stimulated with B16F1 cells. Especially, compound 7f at
18 µM displayed 52% on the rate of T-cell proliferation. These results were in conformity with the

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increase of IFN-γ levels compared with the T cells and B16F1 cells co-culture system, which can
increase the growth of the neighboring T cells (Fig. 7B). Our finding was that these compounds which
displayed better activity in a HeLa cell-based assay could reverse the suppression of T lymphocyte
caused by IDO1 to a great extent.
Fig. 7. T-cell proliferation (A) and IFN-γ level (B) assays in the B16F1 cells-T cells co-culture system. The
compounds were added to the system at the concentration of their triple IC50 values from the HeLa
cell-based assay ([GDC-0919]: 1.5 µM; [7e]: 30 µM; [7f]: 18 µM; [9c]: 18 µM). Each bar of the graph
indicates the mean of three replicate wells with standard error of the mean.
2.5. Effect of 7e, 7f and 9c on Foxp3+ Tregs in melanoma cells
In addition to the depletion of local tryptophan levels, IDO1 protein expressed by tumor cells
leads to the accumulation of toxic tryptophan metabolites including kynurenine, anthranilic acid,
3-hydroxykynurenine, 3-hydroxyanthranilic acid and quinolinic acid [31]. They can indirectly suppress
Teff cells response by favoring differentiation of Treg cells, promoting immunoescape and thereby
favoring tumor cell growth. As Tregs are a major suppressive factor in the tumor microenvironment, we
were interested to investigate whether our compounds could influence the Tregs conversion. As shown
in Fig. 8, when naïve T cells co-cultured with B16F1 cells, it resulted in an approximately 2-fold
increase in the number of Treg cells. Once the co-culture system treated with compounds 7e, 7f and 9c,
respectively, the number of Treg cells returned to the initial level to some extent. Especially, compound
7e displayed the best effect in this test.

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Fig. 8. Our IDO1 inhibitors decreased differentiation of Treg cells in the B16F1 cells-T cells co-culture
system. (A) A representative plot of FACS analysis is presented. CD4+CD25+FOXP3+ positive cells were
defined as Treg cells. (B) Average values of 3 independent experiments are shown in the graph. Error bars
represent SD. ** p < 0.01 vs T+B16F1.
2.6. UV-visible spectra study
Although the HeLa cell-based assay studies demonstrated the IDO1 inhibition capability of these
compounds, but they failed to provide any direct evidence of ligand binding to the active site of the
enzyme. Since the absorbance spectra of the heme group is highly sensitive to the local surroundings
upon the ligand binding, which changes the spectral properties of the heme, UV absorption spectra of
the characteristic heme peaks have been used to certify a direct binding of compounds to the iron ion in
the IDO1 active site [32,33]. In this paper, we recorded the absorption spectra of ferrous-IDO1 in the
absence and presence of the selected compounds. The results were shown in Fig. 9. In the absence of
the compounds, the absorption spectrum of ferrous-IDO1 exhibited a Soret peak at 424 nm.
Compounds 7e and 7f caused a decrease in the wavelength of the absorbance maxima for ferrous heme,
which shifted the maxima from 424 to 418 nm. This indicated their direct binding to the Fe2+-IDO1
enzyme and the reliability of ESP calculation for predicting coordinating capability.

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Fig. 9. Absorption spectra of ferrous-IDO1 (A), IDO1-compound 7e (B) and IDO1-compound 7f (C).
2.7. Molecular modeling studies
To gain insight into the molecular determinants that modulate the inhibitory activity of our
compounds, molecular modeling studies were performed based on the X-ray cocrystal structure of
IDO1 complex (PDB ID: 4PK5). Since the high flexibility of side chain and backbone of IDO1 protein,
classical semi-flexible docking method often poses a problem for IDO1 docking, whose algorithm
relies on a rigid protein structure. In addition to that, the iron-ligand interaction in the active site of
IDO1 is difficult to reasonably describe by classical molecular force-field parameters [34]. All those
could raise a question about the validity of predicted binding modes [35]. To overcome difficulties
mentioned above, IFD method combined with QM/MM optimization was utilized in this paper. The
first step was to dock the studied compound into the active site of IDO1 by the induced fit docking
protocol in Schrödinger, which could consider the flexibility of hIDO1 protein and ligand, concurrently.
In the second step, QM/MM optimization was performed by using Qsite to further optimize the IFD
docking complex, in which a small region of the system included the full heme ring, the iron, the
coordinating His residue and the inhibitor was chosen to be treated using QM calculation and the
remainder of the system is treated via MM. Finally, we could reliably analyze the binding mode of the
ligand in the QM/MM optimized complex (Fig. S3).
As shown in Fig. 10, the binding modes of compound 7f presented the similar binding
conformation with 9c. The modeling of the ligand to IDO1 assumed that the benzoxazolinone core was
placed deep into hydrophobic pocket A where it is perfectly situated to extend a 5-substituent chlorine
atom into a small hydrophobic channel surrounded by residues Met88, Ile123, Leu124, Val125, Gly126
and Leu234. Too large (5-NO2) or too small (5-F) substituent group was not adapt to this channel and
thus unfavorable for enhancing potency compared with 5-Cl group, which was in good agreement with

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the experimental results. Besides the steric factor, electrical property of 5-position substituted group
also influenced the binding affinity. The oxygen of the carbonyl group was found to coordinate to the
heme iron with a distance of 2.06 Å for 7f-IDO1 binding and 2.14 Å for 9c-IDO1 binding, respectively.
The replacement of 5-position by strong electron-withdrawing group such as fluorine and nitro group
lowered the electron density around the coordinating oxygen atom, leading to the difficulty for the
coordination bond formation. The benzene ring in the benzoxazolinone core was interacted with Tyr126
and Phe163 through π-π interaction, simultaneously. The benzyl group was bent sharply at the
methylene moiety and extended into the hydrophobic cavity of pocket B, interacting with Phe226 and
Arg231 by π-π and π-cation interaction, respectively. In addition to those interactions, the oxygen atom
of the other carbonyl group in 9c formed a hydrogen bond with the main chain NH group of Ala264.
Fig. 10. QM/MM optimized structures. (A) 7f-IDO1 complex. (B) 9c-IDO1complex.
3. Conclusion
IDO1 is a key mediator of immune escape and pathogenic inflammation in cancer and targeting
the IDO1 pathway via inhibition of the IDO1 enzyme is a prime strategy for small-molecule
immunomodulatory drugs in cancer therapy. A scaffold-hopping strategy combined with ESP
calculation were performed in our laboratory to design novel small-molecule IDO1 inhibitors, which
led to the discovery of benzoxazolinone derivatives. Subsequent modification of the linker, R1 and R2
substituent groups directed the identification of the most active compounds 7e, 7f and 9c. Furthermore,
they could promote T-cell proliferation, increase IFN-γ production, and suppress the conversion of
naïve T cells into Foxp3-expressing Treg cells. Spectroscopic experiments suggested that
benzoxazolinones interacted with ferrous-IDO1 enzyme. In attempt to rationalize obtained biological

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results and to improve enzyme inhibition, IFD docking and QM/MM calculation were carried out.
These promising results prompt us for further development of this new class of IDO1 inhibitors.
4. Experimental
4.1. Chemistry
4.1.1. General procedures
Melting points were determined on a RDCSY-I capillary apparatus and were uncorrected. All
materials used were commercially available and used as supplied. HG/T2354-92 silica gel 60 F254
sheets were used for analytical thin-layer chromatography (TLC). Column chromatography was
1
performed on silica gel (200-300 mesh). H NMR spectra were recorded on a Bruker AV-300
spectrometer. Chemical shifts (δ) were given in parts per million (ppm) relative to the solvent peak. J
values are in Hz. Chemical shifts are expressed in ppm downfield from internal standard TMS. MS
analyses were carried out using Shimadzu LCMS-2020 instrument. IR spectra were recorded on
Shimadzu IRTracer-100 in KBr with absorptions in cm-1. All the reagents and solvents were reagent
grade and were used without further purification unless otherwise specified.
4.1.2. General preparation of intermediates 4
The intermediates 4 were prepared as previously described [36] with some modification. Under
the atmosphere of nitrogen, starting material aminophenol (1 equiv.) and N,N'-Carbonyldiimidazole
(CDI) (1.2 equiv.) were mixed in DMF and stirred 80 °C for 5 h .The reaction mixture was allowed to
cool to room temperature and the water was added to quench the reaction. The mixture was and
extracted with ethyl acetate to afford the crude product that was purified by flash column
chromatography on silica gel to yield 4a-d.
4.1.2.1. Benzo[d]oxazol-2(3H)-one (4a)
White solid. Yield 89%. Mp 137-139 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 9.81 (s, 1H),
8.00-6.85 (m, 4H).
4.1.2.2. 5-Chlorobenzo[d]oxazol-2(3H)-one (4b)
White solid. Yield 87%. Mp 189-191 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.87 (s, 1H),
7.28 (d, J = 1.8 Hz, 1H), 7.13 (dp, J = 8.0, 2.1 Hz, 2H).

ACCEPTED MANUSCRIPT
4.1.2.3. 5-Fluorobenzo[d]oxazol-2(3H)-one (4c)
White solid. Yield 90%. Mp 174-176 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 9.60 (s, 1H),
7.13 (dd, J = 8.7, 4.2 Hz, 1H), 6.93-6.68 (m, 2H).
4.1.2.4. 5-Nitrobenzo[d]oxazol-2(3H)-one (4d)
Red solid. Yield 84%. Mp 145-147 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.22 (d, J =
1.5 Hz, 1H), 8.04 (dd, J = 7.4, 1.6 Hz, 1H), 7.33 (d, J = 7.5 Hz, 1H), 6.92 (s, 1H).
4.1.3. General preparation of compounds 5a-f
A mixture of 4a or 4b (1 equiv.) and K2CO3 (3 equiv.) in DMF was stirred at 90 °C for 1 h, then
the solution was allowed to cool to 60 °C and was added different substituted
2-chloro-1-phenylethan-1-one (3 equiv.). The mixture was stirred at 60 °C for another 3 h and allowed
to cool to room temperature. The saturated NH4Cl solution was added to quench the reaction. The
mixture was diluted with water and was extracted with ethyl acetate to afford the crude product that
was purified by flash column chromatography on silica gel to yield the target products.
4.1.3.1. 3-(2-(4-Fluorophenyl)-2-oxoethyl)benzo[d]oxazol-2(3H)-one (5a)
White solid. Yield 85%. Mp 193-195 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.08 (ddd, J
= 9.0, 5.2, 2.1 Hz, 2H), 7.39-6.96 (m, 5H), 6.85 (dq, J = 4.8, 3.3, 2.1 Hz, 1H), 5.22 (d, J = 2.0 Hz, 2H).
MS (EI): m/z 394.1 [M+Na]+. IR (KBr): 3074, 1763, 1694, 1601, 1487, 1232 cm-1.
4.1.3.2. 3-(2-(4-Chlorophenyl)-2-oxoethyl)benzo[d]oxazol-2(3H)-one (5b) [37]
White solid. Yield 83%. Mp 148-150 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.14-7.86
(m, 2H), 7.53 (d, J = 8.0 Hz, 2H), 7.40-7.05 (m, 3H), 6.86 (s, 1H), 5.23 (d, J = 3.1 Hz, 2H). MS (EI):
m/z 288.6 [M+H]+. IR (KBr): 3065, 1763, 1691, 1587, 1487, 1246 cm-1.
4.1.3.3. 3-(2-(3-Chlorophenyl)-2-oxoethyl)benzo[d]oxazol-2(3H)-one (5c)
White solid. Yield 85%. Mp 150-152 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.34-7.84
(m, 2H), 7.83-7.43 (m, 2H), 7.42-7.07 (m, 3H), 7.02-6.76 (m, 1H), 5.23 (qd, J = 8.4, 4.9, 4.3 Hz, 2H).
MS (EI): m/z 288.6 [M+H]+. IR (KBr): 3071, 1722, 1683, 1601, 1512, 1229 cm-1.
4.1.3.4. 5-Chloro-3-(2-(4-fluorophenyl)-2-oxoethyl)benzo[d]oxazol-2(3H)-one (5d)
White solid. Yield 89%. Mp 153-155 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.08 (d, J =

ACCEPTED MANUSCRIPT
7.4 Hz, 2H), 7.20 (dd, J = 30.4, 9.8 Hz, 4H), 6.85 (s, 1H), 5.20 (s, 2H). MS (EI): m/z 306.7 [M+H]+. IR
(KBr): 3076, 1771, 1690, 1599, 1487, 1232 cm-1.
4.1.3.5. 5-Chloro-3-(2-(4-chlorophenyl)-2-oxoethyl)benzo[d]oxazol-2(3H)-one (5e) [38]
White solid. Yield 87%. Mp 167-169 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.05-7.93
(m, 2H), 7.60-7.50 (m, 2H), 7.24-7.12 (m, 2H), 6.85 (d, J = 2.0 Hz, 1H), 5.21 (s, 2H). MS (EI): m/z
323.1 [M+H]+. IR (KBr): 3067, 1772, 1719, 1589, 1485, 1246 cm-1.
4.1.3.6. 5-Chloro-3-(2-(3-chlorophenyl)-2-oxoethyl)benzo[d]oxazol-2(3H)-one (5f)
White solid. Yield 87%. Mp 134-136 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.97 (d, J =
27.1 Hz, 2H), 7.68 (s, 1H), 7.54 (s, 1H), 7.17 (d, J = 10.9 Hz, 2H), 6.84 (s, 1H), 5.22 (s, 2H). MS (EI):
m/z 323.1 [M+H]+. IR (KBr): 3067, 1778, 1703, 1614, 1487, 1223 cm-1.
4.1.4. General preparation of target compounds 6a-f
To a solution one of 5a-5f (1 equiv.) in anhydrous THF was added NaBH4 (3 equiv.) at 0 °C and
the mixture was stirred at that temperature for 1 h. The saturated NH4Cl solution was added to quench
the reaction. The mixture was concentrated in vacuo and the residue was extracted with ethyl acetate to
yield the crude product that was purified by gel chromatography to afford the target products.
4.1.4.1. 3-(2-(4-Fluorophenyl)-2-hydroxyethyl)benzo[d]oxazol-2(3H)-one (6a)
White solid. Yield 99%. Mp 111-113 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.89 (s, 1H),
7.53-7.37 (m, 2H), 7.26-6.86 (m, 5H), 5.79 (t, J = 7.6 Hz, 1H), 4.41 (t, J = 7.1 Hz, 1H), 4.10 (t, J = 5.8
Hz, 1H). MS (EI): m/z 274.3 [M+H]+. IR (KBr): 3645, 3071, 1722, 1601, 1512, 1229, 1103 cm-1.
4.1.4.2. 3-(2-(4-Chlorophenyl)-2-hydroxyethyl)benzo[d]oxazol-2(3H)-one (6b) [38]
White solid. Yield 99%. Mp 140-142 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.36 (q, J =
7.5, 6.4 Hz, 4H), 7.15 (dq, J = 14.1, 6.9 Hz, 3H), 6.99 (d, J = 7.0 Hz, 1H), 5.14 (s, 1H), 3.95 (d, J =
10.8 Hz, 2H), 3.06 (s, 1H). MS (EI): m/z 290.7 [M+H]+. IR (KBr): 3645, 3063, 1748, 1593, 1485, 1240,
1090 cm-1.
4.1.4.3. 3-(2-(3-Chlorophenyl)-2-hydroxyethyl)benzo[d]oxazol-2(3H)-one (6c)
White solid. Yield 99%. Mp 113-115 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.52-7.42
(m, 1H), 7.28 (d, J = 2.2 Hz, 3H), 7.20-7.05 (m, 3H), 7.01 (dd, J = 7.9, 1.7 Hz, 1H), 5.11 (dd, J = 8.2,
4.0 Hz, 1H), 4.13-3.83 (m, 3H), 3.54 (s, 1H). MS (EI): m/z 290.7 [M+H]+. IR (KBr): 3646, 3063, 1759,

ACCEPTED MANUSCRIPT
1599, 1485, 1240, 1103 cm-1.
4.1.4.4. 5-Chloro-3-(2-(4-fluorophenyl)-2-hydroxyethyl)benzo[d]oxazol-2(3H)-one (6d)
White solid. Yield 99%. Mp 142-144 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.42 (dd, J
= 8.4, 5.3 Hz, 2H), 7.18-6.87 (m, 5H), 5.14 (dd, J = 8.4, 3.7 Hz, 1H), 4.17-3.79 (m, 2H), 2.94 (s, 1H).
MS (EI): m/z 308.7 [M+H]+. IR (KBr): 3646, 3089, 1771, 1607, 1485, 1223, 1096 cm-1.
4.1.4.5. 5-Chloro-3-(2-(4-chlorophenyl)-2-hydroxyethyl)benzo[d]oxazol-2(3H)-one (6e) [38]
White solid. Yield 99%. Mp 127-129 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.42-7.32
(m, 4H), 7.09 (d, J = 1.1 Hz, 1H), 7.08 (s, 1H), 7.03 (dd, J = 1.8, 0.8 Hz, 1H), 5.12 (dd, J = 8.3, 3.6 Hz,
1H), 3.99 (dd, J = 14.6, 3.6 Hz, 1H), 3.87 (dd, J = 14.5, 8.3 Hz, 1H), 2.97 (s, 1H). MS (EI): m/z 325.1
[M+H]+. IR (KBr): 3626, 3063, 1767, 1614, 1485, 1252, 1092 cm-1.
4.1.4.6. 5-Chloro-3-(2-(3-chlorophenyl)-2-hydroxyethyl)benzo[d]oxazol-2(3H)-one (6f)
White solid. Yield 99%. Mp 157-159 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.45 (dq, J
= 1.6, 0.9 Hz, 1H), 7.43-7.37 (m, 2H), 7.37-7.31 (m, 1H), 7.16-7.05 (m, 2H), 6.95 (d, J = 8.5 Hz, 1H),
5.74 (t, J = 8.3 Hz, 1H), 4.38 (t, J = 8.9 Hz, 1H), 4.01 (dd, J = 9.1, 7.9 Hz, 1H). MS (EI): m/z 325.1
[M+H]+. IR (KBr): 3647, 3078, 1728, 1599, 1506, 1261, 1099 cm-1.
4.1.5. General preparation of compounds 7a-j
One of 4a-d (1 equiv.) and K2CO3 (3 equiv.) in DMF was stirred at 90 °C for 1 h, then the solution
was allowed to cool to 60 °C and was added different substituted benzyl chlorides or phenyl ethyl
chlorides (3 equiv.). The reaction mixture was stirred at 60 °C for another 7 h and allowed to cool to
room temperature. The saturated NH4Cl solution was added to quench the reaction. The mixture was
diluted with water and extracted with ethyl acetate to afford the crude product that was purified by flash
column chromatography on silica gel to yield the target products.
4.1.5.1. 3-Phenethylbenzo[d]oxazol-2(3H)-one (7a) [39]
White solid. Yield 86%. Mp 116-118 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.29 (d, J =
7.7 Hz, 3H), 7.20 (s, 3H), 7.10 (t, J = 5.9 Hz, 2H), 6.79 (d, J = 7.1 Hz, 1H), 4.06 (t, J = 7.4 Hz, 2H),
3.08 (t, J = 7.2 Hz, 2H). MS (EI): m/z 240.3 [M+H]+. IR (KBr): 3061, 1767, 1614, 1489, 1258 cm-1.
4.1.5.2. 3-(3-Fluorobenzyl)benzo[d]oxazol-2(3H)-one (7b)
White solid. Yield 88%. Mp 119-121 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.48-7.31

ACCEPTED MANUSCRIPT
(m, 2H), 7.30-6.86 (m, 6H), 5.12-4.86 (m, 2H). MS (EI): m/z 244.2 [M+H]+. IR (KBr): 3042, 1757,
1589, 1487, 1252 cm-1.
4.1.5.3. 3-(4-Chlorobenzyl)benzo[d]oxazol-2(3H)-one (7c)
White solid. Yield 87%. Mp 145-147 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.57-7.25
(m, 4H), 7.23 (s, 1H), 7.18-7.01 (m, 2H), 6.95-6.74 (m, 1H), 5.26-4.79 (m, 2H). MS (EI): m/z 260.7
[M+H]+. IR (KBr): 3005, 1771, 1597, 1485, 1275 cm-1.
4.1.5.4. 5-Chloro-3-phenethylbenzo[d]oxazol-2(3H)-one (7d)
White solid. Yield 88%. Mp 102-104 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.36-7.24
(m, 3H), 7.24-7.15 (m, 2H), 7.14-6.99 (m, 2H), 6.67 (d, J = 2.0 Hz, 1H), 4.03 (t, J = 7.3 Hz, 2H), 3.06
(t, J = 7.3 Hz, 2H). MS (EI): m/z 274.7 [M+H]+. IR (KBr): 3057, 1759, 1610, 1485, 1246 cm-1.
4.1.5.5. 5-Chloro-3-(3-fluorobenzyl)benzo[d]oxazol-2(3H)-one (7e)
White solid. Yield 92%. Mp 134-136 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.36 (q, J =
11.9, 9.7 Hz, 1H), 7.22-6.92 (m, 5H), 6.81 (d, J = 14.5 Hz, 1H), 4.96 (d, J = 9.4 Hz, 2H). MS (EI): m/z
278.7 [M+H]+. IR (KBr): 3065, 1772, 1589, 1506, 1256 cm-1.
4.1.5.6. 5-Chloro-3-(4-chlorobenzyl)benzo[d]oxazol-2(3H)-one (7f)
White solid. Yield 91%. Mp 122-124 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.32 (q, J =
8.1 Hz, 4H), 7.23-6.97 (m, 3H), 6.90-6.73 (m, 1H), 4.95 (s, 2H). MS (EI): m/z 295.1 [M+H]+. IR (KBr):
3067, 1767, 1601, 1483, 1252 cm-1.
4.1.5.7. 5-Fluoro-3-(3-fluorobenzyl)benzo[d]oxazol-2(3H)-one (7g)
White solid. Yield 88%. Mp 156-158 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.37 (td, J =
8.3, 5.6 Hz, 1H), 7.23-7.11 (m, 2H), 7.06 (dd, J = 10.2, 4.0 Hz, 2H), 6.83 (td, J = 9.2, 2.6 Hz, 1H), 6.59
(dd, J = 7.7, 2.6 Hz, 1H), 5.00 (s, 2H). MS (EI): m/z 262.1 [M+H]+. IR (KBr): 3063, 1765, 1591, 1487,
1250 cm-1.
4.1.5.8. 3-(4-Chlorobenzyl)-5-fluorobenzo[d]oxazol-2(3H)-one (7h)
White solid. Yield 82%. Mp 103-105 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.46-7.21
(m, 4H), 7.13 (dd, J = 8.8, 4.2 Hz, 1H), 6.79 (td, J = 9.2, 2.6 Hz, 1H), 6.57 (dd, J = 7.6, 2.6 Hz, 1H),
4.94 (s, 2H). MS (EI): m/z 278.2 [M+H]+. IR (KBr): 3061, 1778, 1614, 1489, 1250 cm-1.

ACCEPTED MANUSCRIPT
4.1.5.9. 3-(3-Fluorobenzyl)-5-nitrobenzo[d]oxazol-2(3H)-one (7i)
White solid. Yield 81%. Mp 116-118 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.42 (d, J =
1.8 Hz, 1H), 8.10 (dd, J = 7.5, 2.0 Hz, 1H), 7.40 (d, J = 7.5 Hz, 1H), 7.35-7.25 (m, 2H), 7.19 (dt, J =
8.7, 1.8 Hz, 1H), 6.97 (ddt, J = 8.9, 6.8, 2.3 Hz, 1H), 5.56 (d, J = 1.3 Hz, 2H). MS (EI): m/z 289.1
[M+H]+. IR (KBr): 3065, 1792, 1614, 1506, 1261 cm-1.
4.1.5.10. 3-(4-Chlorobenzyl)-5-nitrobenzo[d]oxazol-2(3H)-one (7j)
White solid. Yield 77%. Mp 165-167 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.14 (dd, J
= 8.8, 2.3 Hz, 1H), 7.76 (d, J = 2.3 Hz, 1H), 7.48-7.29 (m, 5H), 5.05 (s, 2H). MS (EI): m/z 303.1
[M-H]+. IR (KBr): 3080, 1784, 1595, 1522, 1260 cm-1.
4.1.6. General preparation of compounds 9a-c
To a solution of 4a or 4b (1 mol equiv.) in anhydrous THF was added TEA (3 mol equiv.). The
mixture was added drop wise the solution of acyl chlorides (1.1 mol equiv.) in anhydrous THF at 0 °C
and stirred at 70 °C for 6 h. The water was added to quench the reaction. The mitxure was extracted
with ethyl acetate to afford the crude product that was purified by flash column chromatography on
silica gel to yield the target products.
4.1.6.1. 3-(2-(4-Fluorophenyl)acetyl)benzo[d]oxazol-2(3H)-one (9a)
White solid. Yield 86%. Mp 180-182 °C. 1H NMR (300 MHz, DMSO-d6): δ(ppm) 7.98-7.89 (m,
1H), 7.50-7.41 (m, 1H), 7.41-7.28 (m, 4H), 7.24-7.14 (m, 2H), 4.41 (s, 2H). MS (EI): m/z 272.2
[M+H]+. IR (KBr): 3067, 1796, 1721, 1601, 1514, 1248 cm-1.
4.1.6.2. 3-Benzoylbenzo[d]oxazol-2(3H)-one (9b) [40]
1
White solid. Yield 89%. Mp 185-187 °C. H NMR (300 MHz, DMSO-d6): δ(ppm) 7.95-7.85 (m,
2H), 7.84-7.75 (m, 1H), 7.67 (t, J = 7.4 Hz, 1H), 7.53 (t, J = 7.6 Hz, 2H), 7.49-7.42 (m, 1H), 7.40-7.26
(m, 2H). MS (EI): m/z 240.2 [M+H]+. IR (KBr): 3069, 1805, 1697, 1599, 1481, 1250 cm-1.
4.1.6.3. 5-Chloro-3-(2-(4-fluorophenyl)acetyl)benzo[d]oxazol-2(3H)-one (9c)
White solid. Yield 87%. Mp 193-195 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.99 (d, J =
8.2 Hz, 2H), 7.56 (d, J = 8.0 Hz, 2H), 7.35-6.99 (m, 2H), 6.85 (s, 1H), 3.51 (s, 2H). MS (EI): m/z 306.7
[M+H]+. IR (KBr): 3063, 1755, 1715, 1611, 1485, 1246 cm-1.
4.1.7. General preparation of compounds 10a-c

ACCEPTED MANUSCRIPT
To a solution of triphosgene (1 equiv.) in anhydrous dichloromethane was added 4a or 4b (1 equiv.)
and TEA (4 equiv.) in anhydrous dichloromethane at 0 °C. Under the atmosphere of nitrogen, the
mixture was stirred at room temperature for 1 h and added a mixture aromatic amines (1.5 equiv.) and
TEA (1.5 equiv.) in anhydrous dichloromethane at 0 °C. The reaction was allowed to cool to room
temperature and the saturated NH4Cl solution was added to quench the reaction. The mitxure was
diluted with water extracted with dichloromethane to afford the crude product which was purified by
flash column chromatography on silica gel to yield the target products.
4.1.7.1. N-(4-Methoxybenzyl)-2-oxobenzo[d]oxazole-3(2H)-carboxamide (10a)
White solid. Yield 83%. Mp 82-84 °C. 1H NMR (300 MHz, DMSO-d6): δ(ppm) 8.56 (s, 1H), 7.89
(d, J = 8.0 Hz, 1H), 7.43 (s, 1H), 7.41-7.25 (m, 4H), 6.90 (d, J = 7.8 Hz, 2H), 4.45 (d, J = 4.9 Hz, 2H),
3.73 (s, 3H). MS (EI): m/z 299.4 [M+H]+. IR (KBr): 3266, 3009, 2951, 2870, 1761, 1722, 1612, 1514,
1275, 1260, 1034 cm-1.
4.1.7.2. 5-Chloro-N-(3-methoxybenzyl)-2-oxobenzo[d]oxazole-3(2H)-carboxamide (10b)
White solid. Yield 90%. Mp 120-122 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.37 (s, 1H),
8.15 (d, J = 8.2 Hz, 1H), 7.33-7.16 (m, 3H), 6.97-6.84 (m, 3H), 4,60 (d, J = 5.2 Hz, 2H), 3.83 (s, 3H).
MS (EI): m/z 333.7 [M+H]+. IR (KBr): 3354, 3048, 1771, 1724, 1601, 1477, 1265, 1252, 1042 cm-1.
4.1.7.3. 5-Chloro-N-(4-methoxyphenyl)-2-oxobenzo[d]oxazole-3(2H)-carboxamide (10c)
White solid. Yield 86%. Mp 162-164 °C. 1H NMR (300 MHz, DMSO-d6): δ(ppm) 9.85 (s, 1H),
7.89 (d, J = 2.3 Hz, 1H), 7.53 (dd, J = 8.8, 2.4 Hz, 3H), 7.41-7.28 (m, 2H), 7.22-7.07 (m, 2H),
7.03-6.79 (m, 3H), 3.77 (s, 3H), 3.35 (s, 1H). MS (EI): m/z 319.7 [M+H]+. IR (KBr): 3291, 3036, 2957,
2866, 1784, 1734, 1609, 1477, 1246, 1182, 1034 cm-1.
4.1.8. Preparation of 5-amino-3-(3-fluorobenzyl)benzo[d]oxazol-2(3H)-one (8)
A solution of 7i (0.10 g, 0.37 mmol) in ethanol (10 mL) was added NH4Cl (0.19 g, 3.47 mmol) in
water (2 mL) at 0 °C. After that, the mixture was added zinc powder (0.23 g, 3.47 mmol) and stirred at
0 °C for 2 h. The solution was diluted with water and extracted with ethyl acetate to afford the crude
product, which was purified by flash column chromatography on silica gel to yield 8 as a white solid
(0.07 g, 78%). Mp 179-181°C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 7.29 (d, J = 21.3 Hz, 2H),
7.10 (d, J = 7.7 Hz, 1H), 7.03-6.96 (m, 2H), 6.37 (dd, J = 8.5, 2.4 Hz, 1H), 6.15 (d, J = 2.2 Hz, 1H),

ACCEPTED MANUSCRIPT
4.92 (s, 2H), 3.59 (s, 2H). MS (EI): m/z 257.1 [M-H]+. IR (KBr): 3356, 3048, 1746, 1591, 1489, 1254
cm-1.
4.1.9. Preparation of compound 13
4.1.9.1. Tert-butyl (1H-benzo[d]imidazol-2-yl)carbamate (11)
A solution of 1H-benzo[d]imidazol-2-amine (2 g, 15.02 mmol) in THF (30 mL) was added Boc2O
(3.61 g, 16.52 mmol) and TEA (3.04 g, 30.04 mmol) at ambient temperature. Then, the mixture was
o
stirred at 60 C for 3 h. After the completion of the reaction, the mixture was cooled to room
temperature and the solvent was evaporated under reduced pressure. The remained solid was washed
with petroleum ether for 3 times to obtain the crude 13 (3g, 85.62%) as a white solid which will be
used in the following step without any further purification.
4.1.9.2. Tert-butyl (1-(2-(4-fluorophenyl)acetyl)-1H-benzo[d]imidazol-2-yl)carbamate (12)
This compound was prepared as a white solid following a procedure similar to that of preparation
of compounds 9a-c in 53% yield. Mp 310-312 °C. 1H NMR (300 MHz, Chloroform-d): δ(ppm) 8.53 (s,
1H), 7.92-7.80 (m, 1H), 7.76-7.64 (dd, J = 7.7, 1.4 Hz, 1H), 7.41-7.21 (m, 4H), 7.11-6.99 (m, 2H),
4.04-3.88 (t, J = 1.0 Hz, 2H), 1.46 (s, 9H). MS (EI): m/z 370.4 [M+H]+. IR (KBr): 3353, 3038, 1680,
1531, 1423, 1370 cm-1.
4.1.9.3. 1-(2-Amino-1H-benzo[d]imidazol-1-yl)-2-(4-fluorophenyl)ethan-1-one (13)
A solution of 14 (0.5g, 1.35 mmol) in dioxane (5 mL) was added HCl solution (4 M HCl in
dioxane, 6.8 mL) dropwise at 0 oC. After the reaction was stirred at room temperature for 2 h, the white
solid was filtered and washed with dioxane for 3 times to obtain hydrochloride, followed by the
dissociation to give the free amine 15 as a white solid (0.26 g, 71.33%). Mp 237-239 °C. 1H NMR (300
MHz, Chloroform-d): δ(ppm) 7.84-7.69 (m, 2H), 7.36-7.22 (m, 4H), 7.14-7.02 (m, 2H), 6.15-6.08 (d, J
= 5.9 Hz, 1H), 6.06-6.00 (d, J = 5.9 Hz, 1H), 4.03-3.93 (t, J = 1.0 Hz, 2H). MS (EI): m/z 270.2 [M+H]+.
IR (KBr): 3356, 3148, 3048, 1646, 1591, 1419 cm-1.
4.1.10. Preparation of compound 15
4.1.10.1. 1-(2-(4-Fluorophenyl)-2-oxoethyl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (14)
This compound was prepared as a white solid following a procedure similar to that of preparation
1
of compounds 5a-f in 78% yield. Mp 280-282 °C. H NMR (300 MHz, Chloroform-d): δ(ppm)

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8.22-8.03 (m, 2H), 7.43-7.31 (dd, J = 7.9, 1.5 Hz, 1H), 7.26-7.14 (m, 3H), 7.12-7.06 (td, J = 7.6, 1.5 Hz,
1H), 7.05-6.97 (td, J = 7.6, 1.5 Hz, 1H), 5.61 (s, 2H). MS (EI): m/z 273.3 [M+H]+. IR (KBr): 3323,
3018, 1687, 1520, 1439 cm-1.
4.1.10.2. 1-(2-(4-Fluorophenyl)-2-hydroxyethyl)-1,3-dihydro-2H-benzo[d]imidazol-2-one (15)
This compound was prepared as a white solid following a procedure similar to that of preparation
1
of compounds 6a-f in 73% yield. Mp 276-278 °C. H NMR (300 MHz, Chloroform-d): δ(ppm)
7.49-7.43 (m, 2H), 7.39-7.35 (m, 1H), 7.13-7.07 (m, 3H), 7.06-7.01 (td, J = 7.6, 1.5 Hz, 1H), 7.00-6.96
(dd, J = 7.8, 1.5 Hz, 1H), 5.25-5.17 (d, J = 6.4 Hz, 1H), 5.14-5.07 (m, 1H), 4.38-4.27 (d, J = 4.9 Hz,
2H). MS (EI): m/z 273.3 [M+H]+. IR (KBr): 3570, 3343, 3028, 1670, 1521, 1449 cm-1.
4.2. Biology
4.2.1. Hela cell-based enzyme assays
HeLa cells were seeded in 96-well culture plates at a density of 5×103 per well. On the
next day, human IFN-γ (100 ng/mL) and compounds in a total volume of 200 µL culture
medium containing 15 µg/mL of L-tryptophan were added to the cells. After incubation for 24 hours,
140 µL of the supernatant was mixed with 10 µL of 6.1 N trichloroacetic acid and the mixture was
incubated for 30 min at 50 °C. The reaction mixture was then centrifuged for 10 minutes at 4000 rpm
to remove
sediments.
100
µL of the supernatant was mixed with 100 µL of 2%
(w/v) p-dimethylaminobenzaldehyde in acetic acid and measured at 480 nm. The initial wells
containing the cells in the remaining volume of 50 µL were used to estimate cell viability in a classical
MTT assay. To that end, 50 µL of culture medium (Iscove medium with 10% FCS and amino acids)
were added to the wells together with 20 µL 4 mg/mL of MTT. After 4 h of incubation at 37 oC, 200 µL
of DMSO were added to dissolve the crystals of formazan blue and the absorbance at 570 nm was
measured after overnight incubation at 37 oC.
4.2.2. T-cell proliferation assay
T lymphocytes prepared from splenocytes of C57/bl6 mice were resuspended in RPMI 1640
containing 10% FBS, L-glutamate, penicillin, and streptomycin. The B16F1 cells were treated with
mitomycin C at a final concentration of 25 mg/L and then incubated at 37 °C for 30 min. After being

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washed three times, the B16F1 cells were resuspended in RPMI 1640 containing 10% FBS,
L-glutamate, penicillin, and streptomycin. 1×105 T lymphocytes (responder cells) and 2×104 mitomycin
C treated B16F1 cells (stimulator cells) were added to each well of a 96-well plate in RPMI 1640
containing 10% FBS in the presence of ConA (5 µg/mL). Cell proliferation was quantified by MTT
assay. The cells were incubated at 37 °C and 5% CO2 for 48 h; and 10 µL MTT (4 mg/mL) was added
to each well. MTT formazan production was dissolved by DMSO replacing the medium 4 h later. The
absorbance at 570 nm (OD570) was measured by a microplate reader.
4.2.3. Cytokine assays
Supernatant collected from the co-culture system were subjected to ELISA analysis for IFN-γ by
using kits from Dakawe (Beijing, China).
4.2.4. Treg cells experiments
Treg cells were analyzed by using an eBioscience intracellular staining kit according to the
manufacturer’s instructions. After co-cultured with B16F1 cells, T cells were collected. Surface staining
was performed with a CD4-FITC and CD25-PE for 15 min at 4 °C. After this, the cells were fixed and
permeabilized with fixation buffer and permeabilization wash buffer. The intracellular staining was
performed with FOXP3-APC for 20 min. The cells were then analyzed by flow cytometry analysis.
4.2.5. Measurement of IDO1 absorbance spectra
Absorbance spectra (370-700 nm, Safire multifunction microplate reader) were measured
immediately after addition of compounds (2 mM) to rhIDO1 (3 µM) in phosphate buffer (pH 6.5) using
Safire multifunctional microplate reader. Ferrous form of the heme was obtained by adding sodium
dithionite (10 mM) to the solution under N2 atmosphere. Changes in the 424 nm maxima indicated
binding to the ferrous iron of the heme.
4.3. Molecular modeling
4.3.1. Average ESP analysis
Structural optimization of all compounds based on IFD calculation was conducted with the Lee–
Yang–Parr correlation functional (B3LYP)/6-31G** using Gaussian 09 software package [41]. Then,
the wavefunction produced by QM calculation was employed for ESP analysis by Multiwfn [42]. ESP,

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V(r), has been widely used for prediction of nucleophilic and electrophilic sites, as well as molecular
recognition mode for a long time, the theoretical basis is that molecules always tend to approach each
other in a complementary manner of ESP. These analyses of ESP are common performed on molecular
van der Waals (vdW) surface. Through quantitative analysis of molecular surface, the average ESP on
the local surface of the coodinating atom can be calculated to reveal characteristic of atom. It is well
known that electrophiles always prefer to attack the atom which has very low ESP around it, so the
coodinating atom with low ESP value should be an ideal reaction site for coordinate bond formation.
4.3.2 Induced fit docking
In order to consider the flexibility of both ligand and protein, the induced fit docking protocol in
Schrödinger was employed [43]. In IFD calculations, the ligands were first docked into the rigid
receptor using softened energy function in Glide. By default, a maximum 20 poses per ligand were
retained. Then, the protein degrees of freedom for each complex are sampled and the protein-ligand
complexes were minimized. The protein structure in each pose now reflected an induced fit to the
ligand structure and conformation. The best protein-ligand complex was then identified based on the
predicted binding affinities of the docked ligand. Here, the residues within 5 Å of each of the 20 ligand
poses were subjected to a conformational search and energy minimizations, and the residues outside
this range were fixed. Finally, the minimized ligand was rigorously redocked into the induced-fit
protein structure using Glide XP scoring mode, and metal constraints can be applied to both Glide
docking stages in IFD protocol. The choice of the best-docked structure for each ligand was made using
a model energy score that combines the energy grid score, the binding affinity predicted by GlideScore,
and the internal strain energy for the model potential used to direct the conformational-search
algorithm.
4.3.3. QM/MM geometry optimization.
QM/MM calculations were performed via a two-layer Qsite program in Schrödinger [44]. QSite is
a mixed mode QM/MM program used to study geometries and energies of structures not parameterized
for use with molecular mechanics, such as those that contain metal. The reason for this may be
complicated. For example, the partial charge of the metal cation is far from being at least
approximately constant, and its value might be affected by many factors, for instance by switching the

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oxidation state of the metal, the nature of the coordinated ligands, the solvation, and/or other
environmental factors. Nevertheless, the MM simulation can be basically performed with a reasonable
accuracy for a particular coordination sphere when only well-parametrized ligands of the metal interact
with the complex surrounding. This is especially the case of a combined QM/MM method where the
metal and its closest neighborhood are calculated at the QM level. QSite is uniquely equipped to
perform QM/MM calculations because it combines the superior speed and power of Jaguar with the
recognized accuracy of the OPLS force field. Jaguar is used for the quantum mechanical part of the
calculations [45], and Impact provides the molecular mechanics simulation [46]. The QM region is the
full heme ring, the Fe, the coordinating His residue and the inhibitor. This subsystem was optimized by
employing density functional theory (DFT) using Becke's three-parameter hybrid exchange functional
and B3LYP with the lacvp* basis set and the convergence criterion for geometry optimizations
followed the original Qsite defaults [47]. The remaining subsystem was treated with the MM method,
and was geometry-optimized by using OPLS-2005 force field. The geometry optimization convergence
criterion for MM subsystem was set as RMSD of energy gradient 60 kcal mol-1Å-1, and cutoff value
was set to 10 Å for non-bonded interactions during the QM/MM calculations. Throughout the QM/MM
calculation, the cuts between the QM and MM regions were treated as specially parameterized
frozen-orbital boundaries, which was placed between Cα and Cβ of the residue His346.
Acknowledgments
Financial support from the National Natural Science Foundation of China (21472244, 21372261,
21472091 and 81673305) is gratefully acknowledge. This work was also supported by the Jiangsu
Province Funds for Distinguished Young Scientists (BK20160033), the Six Major Talent Peak Project
of Jiangsu Province (2011-YY-004), and the Fundamental Research Funds for the Central Universities
(No. 2015021).
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