Synthesis and biological activity of thieno[3,2-d]pyrimidines as potent JAK3 inhibitors for the treatment of idiopathic pulmonary fibrosis

Article abstract of DOI:10.1016/j.bmc.2019.115254

Idiopathic pulmonary fibrosis (IPF) is a serious and fatal lung disease, with a median survival of only 3–5 years from diagnosis. Janus kinase 3 (JAK3) has a well-established role in the pathogenesis of various autoimmune diseases, including rheumatoid arthritis (RA) and autoimmune-related pulmonary fibrosis. In this study, through the use of a conformationally-constrained design strategy, a series of thieno[3,2-d]pyrimidines were synthesized as potent JAK3 inhibitors for the treatment of IPF. Among them, the most potent JAK3 inhibitor, namely 8e (IC₅₀ = 1.38 nM), significantly reduced the degree of airsacculitis and fibrosis according to hematoxylin-eosin (HE) staining assay for the lung tissue in the bleomycin (BLM)-induced pulmonary fibrosis mouse model. The clear reduction of the lung collagen deposition by the determination of Masson and hydroxyproline (HYP) content also demonstrated its efficacy in the treatment of fibrosis. In addition, 8e also reduced the expression of the inflammatory markers IL-6, IL-17A, TNF-α and malondialdehyde (MDA) in lung tissue, which indicated its higher anti-inflammatory activity compared with that of the reference agents (nintedanib and gefitinib). Furthermore, it possessed low cytotoxicity against normal human bronchial epithelia (HBE) cells (IC₅₀ > 39.0 μM) and C57BL mice. All these evaluated biological properties suggest that 8e may be a potential JAK3 inhibitor for the treatment of IPF.

Full text of DOI:10.1016/j.bmc.2019.115254

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Synthesis and Biological Activity of Thieno[3,2-d]pyrimidines as Potent
JAK3 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis
Yanming Zhu, Xu Zheng, Changyuan Wang, Xiuli Sun, Huijun Sun, Tengyue
Ma, Yanxia Li, Kexin Liu, Lixue Chen, Xiaodong Ma
PII:
S0968-0896(19)31714-6
https://doi.org/10.1016/j.bmc.2019.115254
BMC 115254
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Reference:
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Bioorganic & Medicinal Chemistry
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6 December 2019
Please cite this article as: Y. Zhu, X. Zheng, C. Wang, X. Sun, H. Sun, T. Ma, Y. Li, K. Liu, L. Chen, X. Ma,
Synthesis and Biological Activity of Thieno[3,2-d]pyrimidines as Potent JAK3 Inhibitors for the Treatment of
Idiopathic Pulmonary Fibrosis, Bioorganic & Medicinal Chemistry (2019), doi: https://doi.org/10.1016/j.bmc.
2019.115254
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Synthesis and Biological Activity of Thieno[3,2-d]pyrimidines
as Potent JAK3 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis
Yanming Zhua,1, Xu Zhenga,1, Changyuan Wanga, Xiuli Sunb, Huijun Suna, Tengyue Mac, Yanxia Lib, Kexin Liua,
Lixue Chena, and Xiaodong Maa,
a College of Pharmacy, College of Basic Medical Science, Dalian Medical University, Dalian 116044, PR China.
b Department of Hematology, Institute of Respiratory Diseases, the First Affiliated Hospital of Dalian Medical
University, Dalian 116011, PR China.
c Dalian Buyun Biological Technology Co., Ltd., 116085, PR China.
1 These authors contributed equally to this work.
E-mail address: chenlx2016@126.com
Abstract
Idiopathic pulmonary fibrosis (IPF) is a serious and fatal lung disease, with a median survival
of only 3 to 5 years from diagnosis. Janus kinase 3 (JAK3) has a well-established role in the
pathogenesis of various autoimmune diseases, including rheumatoid arthritis (RA) and autoimmune-
related pulmonary fibrosis. In this study, through the use of a conformationally-constrained design
strategy, a series of thieno[3,2-d]pyrimidines were synthesized as potent JAK3 inhibitors for the
treatment of IPF. Among them, the most potent JAK3 inhibitor, namely 8e (IC50=1.38 nM),
significantly reduced the degree of airsacculitis and fibrosis according to hematoxylin-eosin (HE)
staining assay for the lung tissue in the bleomycin (BLM)-induced pulmonary fibrosis mouse model.
The clear reduction of the lung collagen deposition by the determination of Masson and
hydroxyproline (HYP) content also demonstrated its efficacy in the treatment of fibrosis. In addition,
8e also reduced the expression of the inflammatory markers IL-6, IL-17A, TNF-α and
malondialdehyde (MDA) in lung tissue, which indicated its higher anti-inflammatory activity
compared with that of the reference agents (nintedanib and gefitinib). Furthermore, it possessed low
cytotoxicity against normal human bronchial epithelia (HBE) cells (IC50>39.0 μM) and C57BL mice.

All these evaluated biological properties suggest that 8e may be a potential JAK3 inhibitor for the
treatment of IPF.
Key words: Idiopathic pulmonary fibrosis; JAK inhibitors; thieno[3,2-d]pyrimidines
1. Introduction
Idiopathic pulmonary fibrosis (IPF) is a fatal lung disease, with a median survival between 3 and
5 years from diagnosis, characterized by alveolar epithelial injury and hyperplasia, inflammatory cell
accumulation, fibroblast proliferation, and deposition of extracellular matrix with fibrotic lesions
[1‒3]. The annual incidence of IPF in the U.S. has been estimated to be between 6.8−8.8 cases per
100,000 population using narrow case definitions and between 16.3−17.4 per 100,000 population
using broad case definitions. Recent analysis of IPF-related mortality data from the U.S. indicates
that the age-adjusted mortality rate has increased to 28.4% in men and 41.3% in women [4]. Even
more serious is that the incidence of IPF continues to increase every year. Accordingly, although IPF
is not cancer, it causes more harm than cancer.
Currently, there are only two drugs approved by the U.S. Food and Drug Administration (FDA)
for the treatment of IPF, namely pirfenidone (1, Esbriet) and nintedanib (2, Ofev). Pirfenidone is an
orally available pyridone derivative that has been approved for the treatment of IPF in various
countries, including Japan, India, China, Europe, Canada, and the United States [5]. Although the
precise mode of action of pirfenidone has not yet been established, its antifibrotic, anti-inflammatory,
and antioxidant properties have been demonstrated [6, 7]. The antifibrotic properties of pirfenidone
are attributed to its ability to reduce the expression of cytokines, such as TGF-β, leading ultimately
to inhibition of fibrosis [8]. Nintedanib [9], formerly known as BIBF1120, is an indolinone derivative

that was identified through a lead compound optimization strategy designed for angiogenesis
inhibitors with anticancer effects. Nintedanib is a potent, orally available, triple tyrosine kinase
inhibitor that targets the PDGF receptors α/β, FGF receptors, and all three vascular endothelial growth
factor (VEGF) receptor subtypes [10, 11]. Pirfenidone and nintedanib significantly reduce the rate of
disease progression. However, these two drugs do not stop or reverse the deterioration of IPF and
thus have shown no benefit in the overall survival of patients with IPF.
F
MeOOC
Me
O
NC
N
NMe
O
S
N
NMe
O
N
N
N
N
N
HN
Et
HN
NMe
N
O
OH
Me
3
(GLPG1690)
ATX inhibitor
1
(Prifenidone)
TGF- inhibitor
2
(Nintedanib)
Multi-PTK inhibitor(PDGF, FGF, VEGF)
N
Cl
Cl
O
N
N
N
NH
Me
F
HN
N
NH
HN
N
N
MeO
HN
Cl
NH
N
O
O
N
NH
O
N
O
NH
N
HN
O
O
OMe
N
N
N
N
Me
O
Me
6
(DPPY)
7
4
(Imatinib)
v-Abl,C-Kit, PDGFR inhibitor
5
(Gefitinib)
EGFR inhibitor
JAK inhibitor
IC50<10 nM, EGFR, BTK, JAK
Fig. 1. Chemical structures of the typical anti-IPF agents and JAK3 inhibitors.
Tyrosine kinases are known to regulate various signaling pathways involved in maintaining
cellular homeostasis, including the pathogenesis of pulmonary fibrosis [12‒14]. For instance, the
novel anti-IPF agent nintedanib blocks VEGFR1, VEGFR2, VEGFR3, FGFR1, FGFR2, FGFR3,
PDGFRα, and PDGFRβ and etc.. The novel autotaxin inhibitor GLPG1690 (3) [15] showed great
efficacy in a bleomycin (BLM)-induced pulmonary fibrosis model in mice and in reducing
extracellular matrix deposition in the lung. GLPG1690 is currently being evaluated in an exploratory

phase III study in patients with idiopathic pulmonary fibrosis (ClinicalTrials.gov; Identifier:
NCT03733444). Imatinib (4) [16] is a multi-target inhibitor of v-Abl, c-Kit and PDGFR, which also
has been shown to have potential efficacy in the treatment of fibrotic lung disease (ClinicalTrials.gov;
Identifier: NCT00131274). Gefitinib (5) [17], a typical EGFR inhibitor that was approved in 2003 by
the U.S. FDA for the treatment of non-small cell lung cancer (NSCLC), has also been found to have
a significant protective effect on BLM-induced lung fibrosis via EGF. (Fig. 1)
S
Cl
N
N
HN
O
N
O
HN
N
NH
Conformationally Constrained
O
Cl
NH
NH
N
NH
N
O
O
O
O
DPPY
Multi-PTK inhibitor
IC50(JAK3, BTK, EGFR)<10 nM
8e (Thi-DPPY)
JAK3 inhibitor(IC50=1.38 nM)
BTK(IC50>62.4 nM)
For treatment of B-cell lymphoma
For treatment of IPF
Fig. 2. Design of conformation-constrained Thi-DPPY derivative as JAK3 inhibtor.
Janus kinases (JAKs) are a family of cytoplasmatic tyrosine kinases which due to their roles in
cytokine signaling processes are attractive targets for the development of anti-inflammatory drugs
[18, 19]. Given that JAK3 functions are restricted to immune cells, an isoform-selective inhibitor for
JAK3 could be particularly useful to achieve more clinically effective and precise effects [20, 21]. In
our previous study, we identified a family of diphenylpyrimidines (DPPYs) as potent JAK3 and BTK
dual inhibitors, and most of them exhibited strong anti-proliferative activity against B-cell lymphoma
cells [22]. However, most of these DPPYs also could blocked BTK activity, and had low selectivity
for JAK3. In this study, a series of thieno[3,2-d] diphenylpyrimidines (Thi-DPPYs) were designed
through a conformationally-constrained design strategy, and many of them not only showed improved
selectivity for JAK3, but also enhanced activity against IPF in vivo (Fig. 2). The synthesis and

evaluation of their biological activity were described in this study.
2. Results and discussion
2.1 Chemistry
NO2
NO2
NH2
S
N
a
b
c
Cl
N
NH
NH2
NH
NH
O
O
NH
11
10
9
12a
O
OH
OH
S
a
N
c
Cl
N
O
NH2
NH
O
NH
13
14
12b
O
S
NO2
NO2
NH2
N
d
b
e
HN
N
X
12a-b
Br
N
N
NH
O
O
N
N
O
O
8a-b
15
16
17a
X=NH, O
S
NO2
NO2
NO2
NH2
g
b
e
f
R1
R1
R1
n
R1
HN
Y
N
O
12b
YH
Y
Y
N
Y
N
R1
n
n
NH
Cl
R1=H, 3'-Cl
Y=O, S
n=2, 3
18a-c
O
n
O
O
N
O
8c-f
19a-d
20a-d
17b-e
Scheme 1. The synthetic route of target compounds 8a-f.
Reagents and conditions: a) Acryloylchloride, NaHCO3, CH3CN, 0 °C, 0.5 h, 81‒92%; b) Fe-aq. NH4Cl,
MeOH‒H2O, 70 °C, 2 h, 71‒85%; c) 2,4-dichlorothiopheno [3,2-d]pyrimidine, DIPEA, 1, 4-dioxane, 80 °C, 5 h,
35‒71%; d) Morpholine, K2CO3, DMF, rt, 5 h, 95%; e) p-Toluenesulfonic acid, n-BuOH, 70 °C, 6 h, 45‒60%; f) 1-
bromo-2-chloroethane/1-bromo-3-chloropropane, K2CO3, CH3CN, 40 °C, 6 h, 77‒82%; g) Morpholine, K2CO3, KI,
CH3CN, 80 °C, 5 h, 81‒88%.
All the Thi-DPPYs were synthesized as illustrated in Scheme 1, according to our previously
reported methods [23]. The commercially available starting material 3-nitroaniline (9) was reacted
with acryloyl chloride to give 10 which was reduced in the presence of Fe-aq. NH4Cl to produce
intermediate 11. Then the substitution of the C-4 chloride atom in 2,4-dichlorothiopheno[3,2-

d]pyrimidine with 11 to produce the key intermediate 12a. 12b was obtained by application of the
similar synthetic route. For the synthesis of 16, bromine atom in 4-nitrobenzyl bromide was
conveniently substituted with morpholine, then reduced the nitro group to an amino group.
Additionally, 18a-c was reacted with 1-bromo-2-chloroethyane or 1-bromo-3-chloropropane to
synthesize 19a-d. Intermediate 19a-d was reacted with morpholine and then 17b-e was prepared via
reduction reaction. The nucleophilic substitution reaction of the helium atom in 12a-b with 17a-e was
carried out under the action of p-toluenesulfonic acid (p-TsOH) to generate the desired 8a-f.
2.2 Biological activity
2.2.1 Enzymatic activity and toxicity in vitro
All the title molecules were evaluated for their activity against BTK and JAK3 kinases using the
ADP-GloTM assay kit (Promega, Madison, WI, USA). The kinase inhibitory activity results, shown
in Table 1, indicated that most of these title compounds strongly inhibited the JAK3 enzymatic
activity at concentrations in the range of 1.38 to 90.8 nM. Among them, compound 8e not only
exhibited the strongest anti-JAK3 activity (IC50=1.38 nM), but also strongly interfered with the
activity of BTK (IC50=62.4 nM). However, the other compounds seem to be less potent against BTK
kinase at concentrations lower than 100 nM. These kinase-based test result revealed that the chloro-
substituent at the C-3 position of the aniline ring is useful to enhance the anti-kinase activity. In
addition, all these compounds were also evaluated for their cytotoxicity against the normal human
bronchial epithelial (HBE) cells. The evaluation results revealed that these compounds have low cell
toxicity (IC50>8.27 μM). Overall, this study identified a potent JAK3 inhibitor, namely 8e, whose
biological activity as potential application for the treatment of IPF warrant further investigation.
Table 1. In vitro enzymatic activity and toxicity to HBE cells of the title compounds 8a-f a.

S
N
HN
N
X
R1
NH
R2
O
Enzymatic activity
(IC50, nM) b
Toxicity to HBE cells
(IC50, μM ) c
Compd.
X
R1
R2
BTK
JAK3
HBE cells
N
N
O
O
8a
NH
O
H
H
>100
>100
>100
>100
62.4
59.39
85.3
90.8
89.2
1.38
46.0
14.6
66.5
16.1
8.27
12.8
8b
8c
O
N
O
H
23.3
O
O
N
8d
O
H
>40.0
39.0
O
O
S
N
N
8e
O
3’-Cl
H
O
O
8f
O
>100
>40.0
HM71224
spebrutinib
ibrutinib
a
b
The data were means of three separate experiments. The enzymatic activity against BTK and JAK3 enzymes
using the ADP-GloTM kinase assay. c The toxicity effects on the proliferation of HBE cells was determined by the
CCK-8 assay.
2.2.2 8e attenuated the pulmonary morphology changes induced by BLM in mouse lung
The therapeutic effect of 8e was investigated in vivo using the BLM-induced pulmonary
inflammation and pulmonary fibrosis model in C57BL mice. For comparison, novel agents for
treatment of IPF, including the multi-protein tyrosine kinase inhibitor nintedanib, the EGFR inhibitor
gefitinib, and pifenidone were evaluated as well. As shown in Fig. 3a and 3b, after administration of
8e at a dose of 30 or 60 mg/kg for 14 days, the structural confusion of the lung tissue and obvious
swelling in the alveolar septum observed by HE staining was clearly improved, achieving similar
therapeutic effects as nintedanib at a dose of 60 mg/kg. Notably, the therapeutic effect of 8e at a

dosage of 60 mg/kg was significantly better than those of the pifenidone (120 mg/kg), gefitinib (60
mg/kg) groups. Additionally, the therapeutic effect of 8e at 60 mg/kg was significantly better than
that at 30 mg/kg, indicating that its effect was dose-dependent. In general, the higher of the lung
coefficient reflected the worse of the therapeutic effect [24]. Evidently, 8e significantly reduced the
lung coefficient in the mice of the BLM-induced pulmonary fibrosis model group (Fig. 3c), revealing
its enhanced anti-IPF efficacy. Taken together, these results indicated that the therapeutic effect of 8e
is similar to that exerted by the same dose of nintedanib, and superior to those of the high dosage
(120 mg/kg) of pifenidone and the dose of gefitinib (60 mg/kg).
a
c
b
Fig. 3. The effects of 8e and the typical anti-IPF agents on the lung morphology and lung coefficient in mouse
model. The groups of C, D, E, F, G, H were given once daily for 14 days after BLM challenge (n = 8 per group).
(A: The control group; B: The BLM model group; C: The BLM model plus nintedanib 30 mg/kg; D: The BLM
model plus nintedanib 60 mg/kg; E: The BLM model plus pirfenidone 120 mg/kg; F: The BLM model plus gefitinib
60 mg/kg; G: The BLM model plus 8e 30 mg/kg; H: The BLM model plus 8e 60 mg/kg). a, The appearance of the
lung; b, Representative histological lung sections stained with HE (200×); c, The lung coefficient of the mice. Data
are reported as means ± SEM. ***p < 0.001 vs. the control group; ##p < 0.01 vs. the BLM group; ###p < 0.001

vs. the BLM group.
2.2.3 8e reduced the collagen disposition induced by BLM in mouse lung
Pulmonary fibrosis is characterized by excessive collagen disposition in the lung, and the content
of hydroxyproline as an important marker is proportional to collagen fibers [25‒27]. Masson staining
results shown that BLM increased the deposition of collagen in lung, while 8e reduced the collagen
disposition induced by BLM in mouse lung (Fig. 4a). Accordingly, in this study, the HYP content in
the mice lung tissue was determined in each mouse model group using HYP content analysis kit. The
results presented in Fig. 4b revealed that the HYP content in the lungs of every drug-treated
experimental group was significantly reduced compared with that of the untreated BLM group. These
results showed that treatment with 8e has similar biological property as nintedanib at a dose of 60
mg/kg.
a
b
Fig. 4. The effects of 8e and the typical anti-IPF agents on the changes of the collagen disposition in mouse model.
The groups of C, D, E, F, G, H were given once daily for 14 days after BLM challenge (n = 8 per group). (A: The
control group; B: The BLM model group; C: The BLM model plus nintedanib 30 mg/kg; D: The BLM model plus
nintedanib 60 mg/kg; E: The BLM model plus pirfenidone 120 mg/kg; F: The BLM model plus gefitinib 60 mg/kg;
G: The BLM model plus 8e 30 mg/kg; H: The BLM model plus 8e 60 mg/kg). a, Histological examination of
Masson’s Trichrome stained sections (200×); b, HYP content in model mice blood. Data are reported as means ±
SEM. **p < 0.01 vs. the control group; ##p < 0.01 vs. the BLM group.
2.2.4 8e attenuated BLM-induced lung inflammatory level in mice
Malondialdehyde (MDA) is one of the most prevalent byproducts of lipid peroxidation

produced during oxidative stress [28]. Thus, we also examined the levels of this indicator. In addition,
we also evaluated the effects of 8e and the reference compounds on the expression of the
inflammatory markers IL-6, IL-17A and TNF-α in the blood of BLM-induced model mice using flow
cytometry analysis. As shown in Fig. 5a‒c, 8e clearly decreased the degree of inflammation with the
increased dosage compared with the untreated control BLM model group. Moreover, treatment with
8e attenuated the oxidant stress in the pulmonary fibrosis mice, as well as level of MDA (Fig. 5d).
The obtained results are clearly consistent with our previous biological data described above. The
levels of MDA in BLM-induced model mice treated with nintedanib or 8e (60 mg/kg) were lower
than those in the groups treated with pirfenidone (120 mg/kg) and gefitinib (60 mg/kg). Additionally,
administration of 8e also exhibited markedly enhanced effects in terms of the above-mentioned three
inflammatory markers compared with the effects of pirfenidone, nintedanib, and gefitinib.

Fig. 5. The effect of 8e and the typical anti-IPF agents on the changes of inflammatory markers in model mice blood
(n = 8 per group). a, IL-6content. b, IL-17A content. c, TNF-α content. d, MDA content. Data are reported as means
± SEM. *p < 0.05 vs. the control group; #p < 0.05 vs. the BLM group; **p < 0.01 vs. the control group; ##p <
0.01 vs. the BLM group.
2.3 Molecular Simulation
Using a molecular docking simulation analysis software, three typical molecules, including the
most potent JAK3 inhibitor 8e, and two less active inhibitors, namely 8b and 8d, were individually
docked into the binding pocket of the JAK3 protein (PDB: 4Z16) [29]. For comparison, the reference
compound spebrutinib was also docked using same procedures. The simulations were performed with
the Auto DOCK software version 4.2 (The Scripps Research Institute, La Jolla, CA, USA) using its
default parameters [30, 31]. Among the obtained simulation conformations, only the minimal energy
conformation is displayed. Additionally, the co-crystal structure of 7 with JAK3 kinase was retained
for comparison.
The results shown in Fig. 6 clearly reveal that the potent inhibitor 8e and 7 can tightly bind with
JAK3 protein in identical manner. Both compounds can form strong covalent bond between
acrylamide group with amino acid Cys909. Although 8d can also form this covalent binding, its
morpholine side chain moves out of the pocket, and thus the binding contacts are reduced. When the
linker between morpholine and aniline is reduced, such as 8b or the morpholine is replaced with a

line 2-methoxyethyl substituent (spebrutinib), the type of binding with JAK3 kinase is quite different
from that of 8e. Importantly, this modification also caused the loss of the strong covalent bond.
Overall, these binding models exactly explained their anti-JAK3 activity data.
Gly829
A)
B)
Gly829
Leu828
Cys909
Leu905
Cys909
Leu905
Leu828
Ala966
Ala966
Met902
Met902
C)
Gly829
Leu828
D)
Gly829
Leu828
Cys909
Leu905
Cys909
Leu905
Ala966
Met902
Ala966
Met902
Gly829
E)
Cys909
Leu905
Leu828
Ala966
Met902
Fig. 6. Proposed binding models of the typical inhibitors with JAK3 (PDB code:4Z16). (A: 7; B: 8b; C: 8d; D: 8e;
E: spebrutinib)
3. Conclusion
Selective JAK3 inhibitors play an important role in the treatment of autoimmune-related
pulmonary fibrosis by regulating abnormal immune inflammatory response. This study involved the
design and synthesis of a series of thieno[3,2-d]diphenylpyrimidines using a conformationally-
constrained design strategy, and identified a potent JAK3 inhibitor, namely 8e, which has an IC50
value of 1.38 nM. In vivo studies in the BLM-induced mouse model, after administration of 8e,

collagen disposition and the expression of the inflammatory factor IL-6, IL-17A, TNF-α and MDA
in lung tissue were reduced significantly, indicating its efficacy for the treatment of fibrosis. Overall,
this work provided a new insight into the treatment of fibrosis by interfering with the JAK3 signaling
pathway.
4. Experimental section
4.1 General methods for chemistry
Unless otherwise indicated, all reagents and solvents were obtained from commercial sources
and used as received. 1H and 13C NMR data were obtained on a Bruker Avance at 400 and 100 MHz,
respectively. Coupling constants (J) were expressed in hertz (Hz). Chemical shifts (δ) of NMR were
reported in parts per million (ppm) units relative to internal control TMS. High-resolution ESI-MS
was performed on an AB Sciex Triple TOF® 4600 LC/MS/MS system. All reactions were monitored
by TLC, using silica gel plates with fluorescence F254 and UV light visualization. Flash
chromatography separations were obtained on Silica Gel (300‒400 mesh) using
dichloromethane/methanol as eluents.
4.2 General procedure for the synthesis of 8a-f
A mixture of 11 (50.0 mmol), 2, 4-dichlorothieno[3,2-d]pyrimidine (50.0 mmol), and DIPEA
(50.0 mmol) in 1,4-dioxane was gradually heated to 80 oC and stirred for 5 h. Then the mixture was
diluted with water and the precipitate was filtrated to obtain crude which was purified by silica-gel
column separation to get the 12a. The similar method was carried out to the preparation of 12b. A
flask was charged with 12a-b (0.10 mmol), 17a-f (0.10 mmol), p-TsOH (0.15 mmol), and n-BuOH
(10 mL). The slurry was heated to 70 °C for 6 h. The reaction mixture was allowed to cool to room

temperature and was neutralized with a saturated aqueous sodium bicarbonate solution. The aqueous
mixture was then extracted with CH2Cl2 (3×20 mL). The crude product was purified using flash
chromatography with dichloromethane/methanol (v/v, 30:1) as eluents.
8a N-(3-((2-((4-(morpholinomethyl)phenyl)amino)thieno[3,2-d]pyrimidin-4-yl)amino)
phenyl)acrylamide
Yield 45.0%. off-white solid. 1H NMR(DMSO-d6): δ 10.16 (s, 1H), 9.57 (s, 1H), 9.05 (s, 1H),
8.07 (d, J = 5.3 Hz, 1H), 8.06 (s, 1H), 7.22 (d, J = 8.2 Hz, 2H), 7.56 (d, J = 7.7 Hz, 1H), 7.45 (d, J =
8.1 Hz, 1H), 7.31 (t, J = 8.0 Hz, 1H), 7.21 (d, J = 5.3 Hz, 1H), 7.10 (d, J = 8.2 Hz, 2H), 6.47 (dd, J =
16.9, 10.0 Hz, 1H), 6.27 (dd, J = 16.9, 1.4 Hz, 1H), 5.77 (dd, J = 10.0, 1.4 Hz, 1H), 3.56 (t, J = 4.3
Hz, 4H), 3.35 (s, 2H), 2.39‒2.22 (m, 4H); 13C NMR (DMSO-d6): 163.6, 162.5, 158.2, 155.9, 140.6,
140.0, 139.6, 134.4, 132.4, 129.9, 129.5 (2C), 129.1, 127.3, 123.8, 118.8 (2C), 118.5, 115.2, 114.3,
108.0, 66.7 (2C), 62.7, 53.6 (2C); δ; HRMS (ESI) for C26H25N5O3S, [M+H]+ calcd: 487.1911, found:
488.1928.
8b N-(3-((2-((4-(morpholinomethyl)phenyl)amino)thieno[3,2-d]pyrimidin-4-yl)oxy)phenyl)
acrylamide
1
Yield 46.8%; off-white solid. H NMR(DMSO-d6): δ 10.37 (s, 1H), 9.50 (s, 1H), 8.31 (d, J =
5.3 Hz, 1H), 7.75 (t, J = 2.2 Hz, 1H), 7.63 (dd, J = 8.1, 2.2 Hz, 1H), 7.54 (d, J = 8.1 Hz, 2H), 7.47 (t,
J = 8.1 Hz, 1H), 7.37 (d, J = 5.3 Hz, 1H), 7.09 (dd, J = 8.1, 2.2 Hz, 1H), 7.04 (d, J = 8.1 Hz, 2H),
6.45 (dd, J = 17.0, 10.1 Hz, 1H), 6.27 (dd, J = 17.0, 2.0 Hz, 1H), 5.79 (dd, J = 10.1, 2.0 Hz, 1H), 3.56
(t, J = 4.6 Hz, 4H), 3.35 (s, 2H), 2.31 (t, J = 4.6 Hz, 4H); 13C NMR (DMSO-d6): δ 165.2, 164.1, 163.8,
158.2, 152.7, 140.8, 139.9, 137.4, 132.1, 130.4 (2C), 129.4 (2C), 127.8, 123.7, 118.9 (2C), 117.5,

117.1, 113.4, 108.0, 66.6 (2C), 62.5, 53.5 (2C); HRMS (ESI) for C26H25N5O3S, [M+H]+ calcd:
488.1751, found: 488.1725.
8c N-(3-((2-((4-(2-morpholinoethoxy)phenyl)amino)thieno[3,2-d]pyrimidin-4-yl)oxy)phenyl)
acrylamide
1
Yield 54.2%; off-white solid. H NMR(DMSO-d6): δ 10.45 (s, 1H), 9.37 (s, 1H), 8.29 (d, J =
5.3 Hz, 1H), 7.73 (t, J = 2.2 Hz, 1H), 7.62 (dd, J = 8.2, 2.2 Hz, 1H), 7.55 (d, J = 8.3 Hz, 2H), 7.47 (t,
J = 8.2 Hz, 1H), 7.34 (d, J = 5.3 Hz, 1H), 7.09 (dd, J = 8.2, 2.2 Hz, 1H), 6.80 (d, J = 8.3 Hz, 2H),
6.45 (dd, J = 17.0, 10.1 Hz, 1H), 6.27 (dd, J = 17.0, 2.0 Hz, 1H), 5.79 (dd, J = 10.1, 2.0 Hz, 1H), 4.25
13
(t, J = 5.0 Hz, 4H), 3.93‒3.69 (m, 4H), 3.35‒2.91 (m, 6H); C NMR (DMSO-d6): δ 165.2, 164.1,
163.9, 158.3, 152.7 (2C), 140.8, 137.3, 135.0, 132.1, 130.4, 127.8, 123.6, 120.7 (2C), 117.5, 117.1,
115.0 (2C), 113.4, 107.8, 64.0 (2C), 63.0, 55.8, 52.3 (2C); HRMS (ESI) for C27H27N5O4S, [M+H]+
calcd: 518.1857, found: 518.1868.
8d N-(3-((2-((4-(3-morpholinopropoxy)phenyl)amino)thieno[3,2-d]pyrimidin-4-yl)oxy)phenyl)
acrylamide
1
Yield 58.3%; off-white solid. H NMR(DMSO-d6): δ 10.38 (s, 1H), 9.31 (s, 1H), 8.28 (d, J =
5.3 Hz, 1H), 7.73 (t, J = 2.2 Hz, 1H), 7.62 (dd, J = 8.2, 2.2 Hz, 1H), 7.48 (d, J = 8.3 Hz, 2H), 7.47 (t,
J = 8.2 Hz, 1H), 7.34 (d, J = 5.3 Hz, 1H), 7.08 (dd, J = 8.2, 2.2 Hz, 1H), 6.70 (d, J = 8.2 Hz, 2H),
6.45 (dd, J = 17.0, 10.1 Hz, 1H), 6.28 (dd, J = 17.0, 2.0 Hz, 1H), 5.79 (dd, J = 10.1, 2.0 Hz, 1H), 3.91
(t, J = 6.3 Hz, 2H), 3.58 (t, J = 4.6 Hz, 4H), 2.40 (t, J = 6.3 Hz, 2H), 2.38‒2.26 (m, 4H), 1.83 (qui, J
= 6.3 Hz, 2H); 13C NMR (DMSO-d6): δ 165.3, 164.1, 163.8, 158.3, 153.7, 152.7, 140.8, 137.3, 134.1,
132.1, 130.4, 127.8, 123.6, 120.7 (2C), 117.5, 117.1, 114.6 (2C), 113.4, 107.6, 66.7 (2C), 66.3, 55.4,

53.8 (2C), 26.4; HRMS (ESI) for C28H29N5O4S, [M+H]+ calcd: 532.2013, found: 532.2019.
8e N-(3-((2-((3-chloro-4-(3-morpholinopropoxy)phenyl)amino)thieno[3,2-d]pyrimidin-4-yl)oxy)
phenyl)acrylamide
1
Yield 57.2%; off-white solid. H NMR(DMSO-d6): δ 10.43 (s, 1H), 9.52 (s, 1H), 8.32 (d, J =
5.4 Hz, 1H), 7.80‒7.62 (m, 2H), 7.61 (d, J = 8.2 Hz, 2H), 7.57‒7.43 (m, 2H), 7.38 (d, J = 5.4 Hz,
1H), 7.09 (d, J = 8.2 Hz, 1H), 6.97 (d, J = 9.0 Hz, 1H), 6.46 (dd, J = 17.0, 10.1 Hz, 1H), 6.27 (dd, J
= 17.0, 2.0 Hz, 1H), 5.78 (dd, J = 10.1, 2.0 Hz, 1H), 4.05 (t, J = 5.9 Hz, 2H), 3.78‒3.48 (m, 4H),
13
3.39‒2.98 m, 6H), 2.14 (qui, J = 5.9 Hz, 2H); C NMR (DMSO-d6): δ 165.0, 164.2, 163.8, 158.0,
152.6, 148.4, 140.9, 137.6, 135.5, 132.1, 130.5, 127.8, 123.6, 121.7, 120.4, 118.8, 117.4, 117.3, 115.0,
113.2, 108.3, 66.9, 64.0 (2C), 54.2, 51.8 (2C), 23.8; HRMS (ESI) for C28H28ClN5O4S, [M+H]+ calcd:
566.1623, found: 566.1620.
8f N-(3-((2-((4-((3-morpholinopropyl)thio)phenyl)amino)thieno[3,2-d]pyrimidin-4-yl)oxy)
phenyl)acrylamide
1
Yield 59.6%; off-white solid. H NMR(DMSO-d6): δ 10.39 (s, 1H), 9.59 (s, 1H), 8.32 (d, J =
5.3 Hz, 1H), 7.76 (t, J = 2.1 Hz, 1H), 7.62 (dd, J = 8.2, 2.2 Hz, 1H), 7.57 (d, J = 8.4 Hz, 2H), 7.48 (t,
J = 8.2 Hz, 1H), 7.38 (d, J = 5.3 Hz, 1H), 7.12 (d, J = 8.4 Hz, 2H), 7.09 (dd, J = 8.2, 2.2 Hz, 1H),
6.45 (dd, J = 17.0, 10.1 Hz, 1H), 6.27 (dd, J = 17.0, 2.0 Hz, 1H), 5.78 (dd, J = 10.1, 2.0 Hz, 1H), 5.45
(t, J = 4.6 Hz, 4H), 2.84 (t, J = 7.1 Hz, 2H), 2.40‒2.21 (m, 6H), 1.64 (qui, J = 7.1 Hz, 2H); 13C NMR
(DMSO-d6): δ 165.1, 164.2, 163.8, 157.9, 152.7, 140.8, 139.7, 137.6, 132.1, 130.8 (2C), 130.5, 127.8,
127.1, 123.7, 119.6 (2C), 117.6, 117.1, 113.4, 108.2, 66.6 (2C), 57.1, 53.7 (2C), 32.2, 26.1; HRMS
(ESI) for C28H29N5O3S2, [M+H]+ calcd: 548.1785, found: 548.1785.

4.3 Bioactivity evaluation
4.3.1 Kinase Enzymatic Assays
The ADP-GloTM kinase assay system (JAK3: Catalog. V3701, Promega Corporation, USA) was
used for the enzymatic biological evaluation. For the tested compounds, concentrations consisting of
0.1, 1, 10, 100, 1000 nM were used. The test was performed in a 384-well plate. All operations are
carried out according to the experimental instructions, which are available at:
https://cn.promega.com/products/cell-signaling/kinase-assays-and-kinase-biology/jak3-kinase-
enzyme-system/?catNum=V3701). The test was performed in a 384-well plate, including the main
steps below: 1) perform a 5 μL kinase reaction using 1 × kinase buffer (e.g., 1 × reaction buffer A),
2) incubate at room temperature for 60 min, 3) add 5 μL of ADP-Glo™ reagent to stop the kinase
reaction and deplete the unconsumed ATP, leaving only ADP and a very low background of ATP, 4)
incubate at room temperature for 40 min, 5) add 10 μL of kinase detection, 6) reagent to convert ADP
to ATP and introduceluciferase and Luciferinto detect ATP, 7) incubate at room temperature for 30
min, 8) plates was measured on TriStar® LB942 Multimode MicroplateReader (BERTHOLD) to
detect the luminescence (Integration time0.5‒1 s). Curve fitting and data presentations were
performed using GraphPad Prism version 5.0.
4.3.2 Animals
The C57BL/6J female mice weighing 20‒25 g in 5‒6 week‒old were provided by the
Laboratory Animal Center of Dalian Medical University, Dalian, China (SCXK: 2013-0003). All
animals were housed in a controlled environment at 20 ± 2 oC under a 12 h dark/light cycle with free
access to food and water. The animal maintenance and experiments were performed in accordance
with the guidelines of the Animal Care and Use Committee.

4.3.3 Experimental Design
Mice were randomized into 8 treatment groups (n=8) were subjected to BLM-induced lung
injury. Intratracheal administration of 33 μg bleomycin (Apollo Scientific) in 50 mL of sterile saline
or saline alone was performed using an insulin syringe on an exposed trachea under isofluorane
anesthesia. Compound 8e was dissolved in 100% DMSO at a concentration of 100 mg/mL and
aliquots stored at ‒20 oC. For each day, 8e for instillation was diluted in sterile saline to give a final
concentration of DMSO in the instillate of 1.4%. Three days after implantation, the mice in CON and
BLM group were received by oral physiological saline (1.4% DMSO), and the mice in other six
groups were oral administrated with drugs by gavage as follows: NIN (30 mg/kg) group was
administrated with Nintedanib 30 mg/kg; NIN (60 mg/kg) group was administrated with Nintedanib
60 mg/kg; PIR (120 mg/kg) group was administrated with Pirfenidone 120 mg/kg; GEF (60 mg/kg)
group was administrated with Gefitinib 60 mg/kg; 8e (30 mg/kg) group was administrated with 8e 30
mg/kg; 8e (60 mg/kg) group was administered with 8e 60 mg/kg. It was administered once a day for
14 days.
4.3.4 Samples
Mice were painlessly sacrificed by CO2 inhalation and a blood sample was taken from the vena
cava. The blood was added appropriate amount of 0.5% heparin sodium, followed by centrifugation
with 3000 rpm for 10 min to obtain plasma. All the plasma was stored at −20 oC before test. The fresh
lung was removed and weighed to calculate the lung index (lung index (%) = lung weight/body weight
× 100). The entire left lobe removed for analysis of total collagen. The lungs were perfused (via the
right ventricle) with 5 mL saline and the lungs lavaged with 3 × 0.8 mL phosphate buffered saline

(PBS) containing 1 mM EDTA. The lungs were removed and the entire left lobe removed for analysis
of collagen. The remaining lung was inflated with 10% formalin and fixed for 24 h before embedding
in paraffin wax for histological examination.
4.3.5 H&E and Massson staining
The tissue samples fixed with 4% formalin for 24 h were processed using graded alcohol, xylene
and paraffin and then blocked in paraffin. The paraffin-embedded sections were sliced into 5 μm
sections and stained using a hematoxylin and eosin (H&E) kit (Biyuntian, Inc., Nantong, China) and
a Masson’s trichrome staining kit (Nanjing Jiancheng Bioengineering Institute, Nanjing, China),
according to the manufacturer’s instructions. The slides with H&E staining and Masson staining were
examined using light microscopy (Eclipse TE2000-S; Nikon Corporation, Tokyo, Japan) and images
were captured to determine the severity of pulmonary fibrosis by a histopathologist who was blinded
to the protocol design.
4.3.6 The detection of IL-6, IL-17A, TNF-α
Plasma levels of IL-6, IL-17A and TNF-α were analysed using the CBA Flex Set system (BD
Biosciences) according to the manufacturer’s protocol. Flow cytometry was conducted using
FACSCalibur (BD Biosciences). Quantitative analysis was performed with FCAP Array v3.0
software (BD Biosciences).
4.3.7 The detection of HYP
The quantity of collagen in the lung tissue was determined by analysis of HYP content according
to the manufacturer’s instructions of the detection kit (Nanjing Jiancheng Bioengineering Institute).
The absorbance was measured at 550 nm and the HYP content was determined using a formula

according to the manufacturer’s instructions.
4.3.8 The detection of MDA
The content of malonaldehyde (MDA), a marker of oxidant stress, in mice plasma was
performed using MDA kits (Biodiagnostic Company) according to the manufacturer’s instructions.
The absorbance was measured at 532 nm and the MDA content was determined using a formula
according to the manufacturer’s instructions.
4.4 Molecular docking study
The AutoDock 4.2 software was used to perform the docking exploration. Detailed tutorials that
guide users through basic AutoDock usage, docking with flexible rings, and virtual screening with
AutoDock may be found at: http://autodock.scripps.edu/faqs-help/tutorial. Generally, the crystal
structure (PDB: 4Z16) of the kinase domain of JAK3 bound to inhibitor 8e was used in the docking
studies. The enzyme preparation and the hydrogen atoms adding was performed in the prepared
process. The whole JAK3 enzyme was defined as a receptor and the site sphere was selected on the
basis of the binding location of 8e. The binding interaction energy was calculated to include Van der
Waals, electrostatic, and torsional energy terms defined in the TRIPOS force field. The structure
optimization was performed using a genetic algorithm, and only the best-scoring ligand protein
complexes were kept for analyses.
Acknowledgments
We are grateful to the “Xing Liao” Talents Project of Liaoning province, China
(XLYC1807011), the Research Fund of Higher Education of Liaoning province (LQ2017008,
LQ2017039), the Natural Science Foundation of Liaoning province (20180530066), the Cultivation

Project of Youth Tech stars, Dalian, China (No. 2016RQ043), and the Foundation of Science and
Technology Innovation of Dalian, China(2019J13SN76) for the financial support of this research.
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Graphical abstract
S
Cl
N
N
HN
O
N
O
HN
N
NH
Conformationally Constrained
O
Cl
NH
NH
N
NH
N
O
O
O
O
DPPY
Multi-PTK inhibitor
IC50(JAK3, BTK, EGFR)<10 nM
For treatment of B-cell lymphoma
8e (Thi-DPPY)
JAK3 inhibitor(IC50=1.38 nM)
BTK(IC50>62.4 nM)
For treatment of IPF