Design, Synthesis and SAR Studies of Novel and Potent Dipeptidyl Peptidase 4 Inhibitors

Article abstract of DOI:10.1002/cjoc.202000342

Dipeptidyl peptidase 4 (DPP-4) is a clinically validated target for the treatment of type 2 diabetes mellitus (T2DM). To discover novel and potent DPP-4 inhibitors, three series of compounds were designed and synthesized in this study based on our previou

Full text of DOI:10.1002/cjoc.202000342

Chinese Journal
of Chemistry
CJC
中 国 化 学 - An International Journal
Accepted Article
Title: Design, Synthesis and SAR Studies of Novel and Potent Dipeptidyl Peptidase 4
Inhibitors
Authors: Na Luo, Xiaoyu Fang, Mingbo Su, Xinwen Zhang, Dan Li, Honglin Li ,
Shiliang Li* and Zhenjiang Zhao*
This manuscript has been accepted and appears as an Accepted Article online.
This work may now be cited as: Chin. J. Chem. 2020, 38, 10.1002/cjoc.202000342.
The final Version of Record (VoR) of it with formal page numbers will soon be
published online in Early View: http://dx.doi.org/10.1002/cjoc.202000342.
ISSN 1001-604X • CN 31-1547/O6
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Chinese Journal
of Chemistry
CJC
中 国 化 学 - An International Journal
Accepted Article
Title: Design, Synthesis and SAR Studies of Novel and Potent Dipeptidyl Peptidase 4
Inhibitors
Authors: Na Luo, Xiaoyu Fang, Mingbo Su, Xinwen Zhang, Dan Li, Honglin Li ,
Shiliang Li* and Zhenjiang Zhao*
This manuscript has been accepted and appears as an Accepted Article online.
This work may now be cited as: Chin. J. Chem. 2020, 38, 10.1002/cjoc.202000342.
The final Version of Record (VoR) of it with formal page numbers will soon be
published online in Early View: http://dx.doi.org/10.1002/cjoc.202000342.
ISSN 1001-604X • CN 31-1547/O6
mc.manuscriptcentral.com/cjoc
www.cjc.wiley-vch.de

Chinese Journal
of Chemistry
Type II diabetes; Dipeptidyl peptidase IV; Inhibitors; Molecular docking;
Structure-activity relationship
Report
CJC
中
国 化 学 - An International Journal
Design, Synthesis and SAR Studies of Novel and Potent Dipeptidyl
Peptidase 4 Inhibitors
Na Luo,a Xiaoyu Fang,a Mingbo Su,b Xinwen Zhang, b Dan Li,c Honglin Li a, Shiliang Li*,a and Zhenjiang Zhao *,a
aShanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai
200237, China
b State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences. 555 Zhuchongzhi Raad Shanghai 201203,
China
cShangdong Biopolar Dichang Pharmaceutical Co.,Ltd. RM2306, No.786 Linzi Avenue, Zibo, Shangdong, 255400, China
Cite this paper: Chin. J. Chem. 2019, 37, XXX—XXX. DOI: 10.1002/cjoc.201900XXX
Summary of main observation and conclusion Dipeptidyl Peptidase 4 (DPP-4) is a clinically validated target for the treatment of type 2 diabetes
mellitus (T2DM). To discover novel and potent DPP-4 inhibitors, three series of compounds were designed and synthesized in this study based on our
previously identified novel scaffold of 2-phenyl-3,4-dihydro-2H-benzo[f]chromen-3-amine. Among the designed compounds, 41d-1 was the most potent
one with an IC50 value of 16.00 nM. Besides, 41d-1 (5 mg/kg) displayed a moderate glucose tolerance capability in ICR mice. Structure-activity-relationship
(SAR) studies were discussed in detail, which is constructive for our further optimization.
glucose and benefiting the β cell. Compared to traditional
antihyperglycemic drugs, DPP-4 inhibitors have more advantages,
Background and Originality Content
Diabetes is a severe chronic metabolic disorder. According to
including ease of administration, no weight gain and a low risk of
hypoglycemia in clinical practice.[9-10]
the newest data of IDF, there are about 463 million people in
adults with diabetes around the world. The prevalence of diabetes
is expected to reach 700 million by 2045 and puts a huge burden
on the health-care system. T2DM accounts for around 90% of
cases of diabetes.[1] T2DM could lead to microvascular (stroke,
myocardial infarction) and macrovascular complications
(neuropathy, nephropathy) that cause profound psychological and
physical distress to both patients and carers.[2-3] Traditional oral
antidiabetic agents including biguanides, sulfonylureas,
thiazolidinediones, glinides, α-glucosidase inhibitors helped
patients a lot, but these agents have been associated with
undesirable side effects such as hypoglycemia, weight gain and
gastrointestinal reactions.[4] To explore new, safe and effective
approaches for T2DM therapy, several antidiabetic drugs with new
mechanisms including SGLT-2 inhibitors, GLP-1R agonists and
DPP-4 inhibitors have been developed. DPP-4 inhibitors have been
the most recently developed agents for the treatment of T2DM.[5]
Up to now, 11 DPP-4 inhibitors have been marketed around the
world, and some typical gliptins are shown in Figure 1.
In our previous work, starting with a natural scaffold of
iso-daphnetin (compound 6) and sitagliptin,
2-phenyl-3,4-dihydro-2H-benzo[f]-chromen-3-amine
a
novel lead
(8) was
designed utilizing pharmacophore grafting and scaffold hopping.[11]
Further structural modification guided by fragment molecular
orbital (FMO) method gave a promising candidate (7, Figure 2)
with dramatic improvement in potency (IC50 = 2.10 nM). Further in
vivo evaluation showed that 7 could inhibit >80% of DPP-4 activity
for more than 7 days with a single oral dose of 3 mg/kg in diabetic
mice. The long-term antidiabetic efficacies of 7 (10 mg/kg, qw)
were better than those of the once-weekly omarigliptin (3) and
trelagliptin (4).[12]
In this study, with the expectation of exploring more novel and
active DPP-4 inhibitors, several modification strategies were
conducted based on the dihydrobenzo[f]chromen core of 7. First,
we moved the tail phenyl ring of the naphthalene moiety from the
[f] side to [h] side while kept the orientation of the substituents to
the S2 extensive pocket (Val207, Arg357, Arg358, Ser209), then a
DPP-4 is a ubiquitous serine protease that deactivates a
variety of other bioactive peptides with alanine, proline or serine
at the penultimate position of the N-terminus.[6] Incretins such as
new
family
of
2-(2,4,5-trifluorophenyl)-3,4-dihydro-2H-benzo[h]chromen-3-amin
e derivatives were designed. However, dihydrobenzo[h]chromen
analogs displayed less potent than 8 due to steric clashes. In order
GLP-1 and GIP regulate postprandial blood glucose by
a
glucose-dependent manner and responsible for 50-70% insulin
release.[7] These two incretins stimulate secretory of insulin in
response to food ingestion by recognizing G protein-coupled
receptors on pancreatic β cells [5]. GLP-1 could also decrease islet
glucagon secretion, slow gastric emptying and increase satiety.[6, 8]
However, endogenous GLP-1 has a short half-time of 1-2 minutes
due to being recognized and degraded by DPP-4 enzymes.[8]
Therefore, DPP-4 inhibitors play a vital role in preserving the
function of GLP-1 and GIP, thus controlling the level of blood
to
eliminate
unfavorable
clashes,
a
series
of
2-(2,4,5-trifluorophenyl)-6-phenyl-3,4-dihydro-2H-chroman-3-ami
ne derivatives were designed. Besides, based on the similar
physicochemical properties between atoms O and S, we adopted
bioisosterism
strategy
and
a
series
of
2-(2,4,5-trifluorophenyl)-3,4-dihydro-2H-benzo[f]thiochromen-3-a
mine derivatives were designed. Herein, we reported the synthesis,
SAR studies and biological evaluation of these three series of
derivatives based on the novel skeletons (Figure 3).
This article has been accepted for publication and undergone full peer review but has not been through
the copyediting, typesetting, pagination and proofreading process which may lead to differences between
this version and the Version of Record. Please cite this article as doi: 10.1002/cjoc.202000342
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Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
11g and 11h were afforded by Suzuki-Miyaura coupling of 11a
with respective boric esters. Naphthaldehyde 12a-f could be
prepared by formylation of corresponding starting materials 11a,
11c, 11e-h in the presence of 1,1-dichlorodimethyl ether/TiCl4,
while 12g was obtained by nucleophilic substitution of 12a with
morpholine. Then compounds 12a-g could be converted to
hydroxyl naphthaldehyde 14c-i by demethylation in the presence
of anhydrous AlCl3, while 14a-b were obtained by the same
method as the synthesis of 12a form 13a-b. Intermediates 15a-i
were successfully obtained by Michael addition and aldol
condensation of 14a-i and compound 10. Mixtures of cis/trans
dihydrobenzo[h]chromen derivatives 16a-i were given by
reduction of 15a-i with NaBH4; configuration transformation of the
cis isomers to the trans isomers could occur in one-pot upon
exposure to N,N-Diisopropylethylamine (DIPEA).[13] Subsequently,
16a-i were reduced with Zn powder to yield resulting
dihydrobenzo[h]chromen amine 17a-i via column chromatography
isolation. Compound 17j was produced by ester hydrolysis of 17d.
Starting from 18, compound 19 was given by Vilsmeier-Haack
reaction, and then compound 22 was provided by similar steps
from 19 as preparation of 17a.
F
F
F
F
NH2
F
O
NH2
O
N
N
N
O
OH
N
NH2
N
N
N
N
CN
O
S
CF3
Sitagliptin (1)
Vildagliptin (2)
Omarigliptin (3)
O
F
O
HO
OH
O
O
O
CN
N
N
N
N
N
O
N
N
NH2
N
O
O
O
N
O
N
O
NH2
iso-daphnetin (6)
Trelagliptin (4)
Linagliptin (5)
F
F
NH2
F
O
R1
R2
1
2
=
=
7
R
OMe, R
R2
CN
8 R1
=
=
H
H,
Figure 1 Representative DPP-4 inhibitors.
O
Scheme 1 Synthesis of 2-phenyl-3,4-dihydro-2H-benzo[h]chromen-3-amine
HO
O
OH
O
derivativesa
F
F
O
O
O
F
F
F
Pharmacophore
Grafting
F
NH2
NH2
FMO
F
OH
a)
=
6
14.13 M)
μ
(IC50
F
F
F
F
CHO
O
OMe
CN
a
F
O
R1
R2
Scaffold
Hopping
F
F
NO2
NH2
O
CHO
=
7
2.10 nM)
N
R
(IC50
Once-weekly
13a-b
N
10
N
9
F
N
F
F
b
F
CF3
NO2
OMe
OH
OMe
R
b)
=
6.24 nM)
Sitagliptin (IC50
c
CHO
CHO
b
10
O
d
R
R
j
R
g
Figure 2 Our previous work
11e
11f
14a-i
11g
12a-g
11d
11a
k
h
15a-i
l
11h
11c
12a
12g
i
11b
Y662
F
E206
F
F
F
F
F
F
NH2
F
NH2
D708
H740
F
NH2
OH
E205
O
NO2
OH
OH
NH
F
O
F
O
Structural
Optimization
e
f
O
R4
F
O
N
F
O
f
NH3
F
O
h
R3
Salt bridge
S630
OH
R
R1
S2
extended
R
F
O
Series 1
Series 2
f
OH
F
F
R2
H-bond
Y547
17a-j
h
trans
)
F
R358
trans
(
16a-i
)
m
(
NH2
17d
17j
8 R1
R2
=
=
H
H,
F357
S
R5
R6
F
F
F
F
c)
F
F
F
NH2
NO2
NO2
OH
OH
Series 3
CHO
e
n
10
f
F
O
F
O
O
d
N
N
H
H
18
19
Figure 3 Design and modification strategies of novel DPP-4 inhibitors.
NH
22
NH
NH
20
trans
21
(
)
aReagents and conditions: (a) CH3NO2, NaOH aq, CH3OH, 0-5 °C; ZnCl2 aq,
con. HCl, 5-10 °C, 78% for two steps; (b) 1,1-dichlorodimethyl ether,TiCl4, 0
oC to r.t., 22%-79%; (c) anhydrous AlCl3, DCM, 0 °C to 40 °C, 40%-66%; (d)
L-pipecolinic, Toluene, 120 °C, N2, 10%-42%; (e) 1) NaBH4, THF/CH3OH, r.t.;
2) DIPEA, EtOH, r.t., 40%-55% for two steps; (f) Zn, HCl, EtOH, r.t., 10%-25%;
(g) (3,6-dihydro-2H-pyran-4-yl)-boronic acid pinacol ester, Pd(PPh3)4,
Cs2CO3, DMF/H2O, 90 °C, N2; (2) Pd/C, H2, MeOH, r.t., 73% for two steps; (h)
(3-(methylsulfonyl)phenyl)boronic acid, Pd(PPh3)4, Cs2CO3, DMF/H2O, 95 °C,
N2, 73%; (i) CH3OH, H2SO4, 70 °C, 95%; (j) CH3SO2Cl, pyridine, DCM, 0 °C to
r.t., 45%; (k) Trifluoromethylsulfonic anhydride, Et3N, DCM, -78 °C to r.t.,
68%; (l) morpholine, Pd2(dba)3, BINAP, t-BuOK, Toluene,100 °C, N2, 49%; (m)
Results and Discussion
Synthesis
Scheme 1 mainly describes the general synthesis of 17a-j and
22. Compound 10 was obtained from the condensation of
2,4,5-triflfluorobenzaldehyde 9 and nitromethane. 11c was given
by esterification of reagent 11b with MeOH and H2SO4. Then
starting from 11d, compounds 11e and 11f were prepared by
similar substitution reactions with CH3SO2Cl and Tf2O, respectively.
Chin. J. Chem. 2019, 37, XXX－XXX© 2019 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimwww.cjc.wiley-vch.de
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Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
NaOH, MeOH/H2O, 50 °C, 50%; (n) POCl3, DMF, 0 °C to r.t., 69%.
presence of 10 via Michael addition and aldol condensation.
Dihydrobenzo[f]thiochromen derivatives 40a-f were given by
NaBH4 reduction and configuration transformation form 39a-f.
Dihydrobenzo[f]thiochromen amine derivatives 41a-f were finally
given by reduction of Zn and hydrochloric acid form 40a-f, while
41g was given by hydrolysis from 41d. We also conducted chiral
column chromatography of 41d with high activity to get the single
isomer.
Scheme
2
describes
the general synthesis
of
2-(2,4,5-trifluorophenyl)-6-phenyl-3,4-dihydro-2H-chroman-3-ami
ne derivatives. Salicylaldehyde analogs 28a-j were given by
Suzuki-Miyaura coupling of corresponding starting materials 27a-j
with 5-bromo-2-hydroxybenzaldehyde (23). Next, as described in
Scheme 1, 29a-j were synthesized by Michael addition and aldol
condensation of 28a-j and 10. Subsequently, trans isomers 30a-j
were obtained by reduction of 29a-j with NaBH4 followed by
configuration transformation. Finally, compounds 31a-j were given
by reduction of 30a-j with Zn powder. Starting from 23, compound
26 was given by similar steps like preparation of 31a-j.
Scheme
3
Synthesis
of
2-phenyl-3,4-dihydro-2H-benzo[f]thiochromen-3-amine derivativesa
CHO
Scheme
2
Synthesis
of
R1
R2
OMe
R1
R2
OMe
OH
a
2-phenyl-6-phenyl-3,4-dihydro-2H-chroman-3-amine derivativesa
33a-b
b
32a-b
H
O
H
O
R1
R2
R1
R2
OH
R1
R2
O
N
c
a
d
F
F
F
F
F
F
S
a)
F
F
F
OH
NO2
NH2
34a-d
NO2
36a-f
35a-f
F
F
CHO
c
d
10
F
NO2
H
O
b
H
O
O
O
O
R1
R2
SH
R1
R2
S
N
e
Br
f
g
24
trans
23
trans
25
)
26
S
R1
R2
Br
(
)
Br
Br
(
10
O
F
F
39a-f
38a-f
OH
37a-f
b)
F
CHO
NO2
F
HO
OH
F
F
B
F
F
NH2
23
10
c
NO2
O
R
a
b
R
h
F
S
R1
R2
S
R1
R2
R
29a-j
27a-j
28a-j
trans
41a-g
)
41g
(
trans
40a-f
)
F
(
F
41d
F
F
NH2
NO2
aReagents and conditions: (a) 1,1-dichlorodimethyl ether, TiCl4, DCM,
0 °C-r.t., 17%-46%; (b) anhydrous AlCl3, DCM, 0-40 °C., 47%-93%; (c)
dimethylthiarbamoyl chloride, DABCO, 0-50 °C, 59%; (d) MW, 200-230 °C,
150-200 W, 30%-45%; (e) 3N NaOH, CH3OH, 65 °C; (f)
1,1,3,3-tetramethylguanidine, toluene, 80 °C, 12%-30%; (g) 1) NaBH4,
THF/CH3OH, r.t.; 2) DIPEA, EtOH, r.t., 15%-30% for two steps; (h) Zn, 6N HCl,
EtOH, r.t., 5%; (i) 45% H2SO4 aq., reflux, 20%; (j) chiral separation (Chiralpak
ID 0.46 cm × 15 cm column; mobile phase MeOH/DEA = 100/0.1 (v/v); flow
rate, 1.0 mL/min).
d
F
O
F
O
R
R
trans
30a-j
)
trans
31a-j
)
(
(
aReagents and conditions: (a) Cs2CO3, PdCl2(dppf)2, DMF/H2O, 100 °C, N2,
31-51%; (b) L-pipecolinic, toluene, 120 °C, N2, 23%-50%; (c) 1) NaBH4,
THF/CH3OH, r.t.; 2) DIPEA, EtOH, r.t., 45%-55% for two steps; (d) Zn, HCl,
EtOH, r.t., 20%-69%.
Structure-activity relationship
Scheme
dihydrobenzo[f]thiochromen
3
lists the overall synthesis routine of
amine derivatives. The
Compounds listed in Tables 1-3 were evaluated in vitro for
DPP-4 inhibition.
naphthaldehyde 33a-b were prepared by formylation of starting
materials 32a-b in the presence of 1,1-dichlorodimethyl ether.
Then 33a-b were converted into 35a-b by demethylation in the
presence of AlCl3, while 35c-f were directly afforded by
formylation of 34a-d as the same method of the preparation of
33a-b. Then thiophenol 38a-f were prepared via Newman–Kwart
rearrangement (NKR) from naphthol 35a-f for three steps.[14] First,
compounds 36a-f were obtained by esterification of compounds
35a-f and dimethylthiarbamoyl chloride in the presence of DABCO.
Second, S-arylthioarbamate 37a-f were obtained from
O-arylthiocarbamate 36a-f under microwave irradiation. Finally,
37a-f were converted into 38a-f via ester hydrolysis.
Benzo[f]thiochromen analogs 39a-f were given by 38a-f in the
Table 1 Activities of 2-phenyl-3,4-dihydro-2H-benzo[h]chromen-3-amine
derivatives against the DPP-4 enzyme.
F
F
NH2
F
O
R1
Compounda
R1
IC50 (nM)b
Chin. J. Chem. 2019, 37, XXX－XXX© 2019 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimwww.cjc.wiley-vch.de
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Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
These compounds displayed better potency as expected.
Noticeably, comparing to 17a, large heterocycle substituents like
compounds 17f (IC50 =191.06 nM) and 17g (IC50 =197.75 nM)
displayed around 8-fold boost in potency. The potency
improvement of 17f and 17g suggests that shape matching is an
important factor for improving activities. The predicted binding
mode of 17f showed that hydrogen bond interaction could be
formed between the oxygen atom of the tetrahydropyrane group
and the hydroxyl of Ser209 (Figure 4B). However, bulky groups like
Ph-3-Ms of 17h (IC50 =782.02 nM) offered no advantage over 17f.
We speculated that the binding affinity of 17h might be weakened
by the unfavorable intramolecular tension introduced by the two
H atoms of naphthalene ring and the substituted phenyl group.
Strong polar groups such as –COOH, -NHSO2CF3 displayed a
dramatic reduction of potencies. Moreover, compound 22, an
indole analog, was designed to eliminate the steric clashes
mentioned above in dihydrobenzo[h]chromen amine analogs. As a
result, 22 performed better than 17a as expect.
8
-
110.10 ± 5.67
17a
17b
17c
H
1536.70 ± 30.41
650.71 ± 13.20
5169.64 ± 285.23
OMe
Br
17d
COOMe
288.04 ± 78.89
17e
NHSO2CH3
319.84 ± 34.01
191.06 ± 44.45
197.75 ± 18.97
782.02 ± 12.73
5226.23 ± 207.95
3918.63 ± 149.73
993.71 ± 108.92
2.20 ± 0.66
In a further modification, naphthalene fragment was replaced
by the biphenyl group to eliminate the unfavorable intermolecular
17f
tetrahydropyrane
collision
aforementioned,
then
a
series
of
2-(2,4,5-trifluorophenyl)-6-phenyl-3,4-dihydro-2H-chroman-3-ami
ne derivatives were synthesized and evaluated.
17g
17h
morpholine
Ph-3-Ms
17i
NHSO2CF3
17j
COOH
Figure 4 Predicted binding modes of 17a (A) and 17f (B). The structure of
DPP-4 is shown in a light blue cartoon (PDB id: 4PNZ), the key residues are
displayed as thin yellow sticks, 17a and 17f are shown as thick green sticks,
hydrogen bonds are displayed as orange dashed lines, atom-atom distance
is marked as blue dashed lines.
22
-
-
-
Omarigliptin
Trelagliptin
Compounds based on the biphenyl fragment are shown in
Table 2. First, compound 31a was synthesized and performed
better in potency than 17a. When replacing the phenyl group with
–Br, a slight improvement in potency was observed. In order to
further improve the potency, we decided to introduce some larger
substituents onto the phenyl group of 31a. As displayed in Table 2,
substituents on the 3-position could bring enhanced potency.
Compounds 31b-e with hydrogen-bond receptors were more
potent than 31a, especially compound 31b (IC50 = 112.22 nM),
which is connected with 3-SO2CH3, displayed over 10-fold
improvement in potency. Moreover, given the strong positive
electrostatic potential of the S2 extended pocket, some
electron-withdrawing groups like –CN, -COOH and tetrazole were
introduced. Just as expected, compounds 31f-h were more potent
than 31a. 31g with a tetrazole group displayed the best in vitro
potency (IC50 = 98.74 nM) among the biphenyl-based compounds.
Compounds 31i and 31j with di-substituted groups also performed
better than 31a. 31j (IC50 = 409.26 nM) with 3,4-dimethoxy
substituent was more potent than 31i, which may due to the
strong negative electrostatic potential produced by the
2.58 ± 0.73
aCompounds are trans-racemic structures. bMean values of at least three
independent experiments.
Results of dihydrobenzo[h]chromen amine derivatives were
shown in Table 1. Comparing 17a with compound 8, more than a
10-fold decrease in potency was observed. Considering that the
distance between O atom of naphthalene and C atom of Tyr547
(3.1 Å) is shorter than the sum of van der Waals radius of the two
atoms (3.22 Å), 17a may have steric clashes with Tyr547, which
may contribute to the great loss in potency (Figure 4A). When
small groups like –OMe and –Br were introduced, opposite results
were observed, which suggests that hydrophilic group (-OMe) is
more favorable than the hydrophobic one (-Br) in the solvent area.
Considering that there is a wide entrance of S2 extended pocket,
other larger groups could be introduced to the R1 position to
occupy S2 extended pocket. Therefore, substituents like –COOMe,
–NHSO2CH3, tetrahydropyrane and morpholine were introduced.
Chin. J. Chem. 2019, 37, XXX－XXX© 2019 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimwww.cjc.wiley-vch.de
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Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
co-occurrence of the two methoxy oxygen atoms.[12] The predicted
31g
31h
Ph-3-tetrazole
Ph-3-CN
98.74 ± 22.19
348.06 ± 84.64
binding mode of 31g showed that charge-reinforced hydrogen
bond interaction could be formed between the tetrazole group
and Arg358 (Figure 5). Potency improvement of 31g suggests that
electrostatic complementarity is an important factor for our
further optimization.
746.61
128.01
409.26
206.95
±
±
31i
Ph-2,4-DiF
31j
Ph-3,4-DiOMe
Omariglip
-
2.20 ± 0.66
Figure 5 Predicted binding mode of 31g. The structure of DPP-4 is shown
in a light blue cartoon (PDB id: 4PNZ), the key residues are displayed as
thin yellow sticks, 31g is represented as thick green sticks, hydrogen bonds
are displayed as orange dashed lines.
tin
Trelaglipti
-
2.58 ± 0.73
n
Table 2 2-phenyl-6-phenyl-3,4-dihydro-2H-chroman-3-amine derivatives
against the DPP-4 enzyme.
aCompounds are trans-racemic structures. bMean values of at least three
independent experiments.
F
Results of dihydrobenzo[f]thiochromen analogs were
summarized in Table 3. When replacing the O atom by S atom, the
potency increase in compound 41a was observed, which may
benefit from the favorable van der Waals interactions between
41a and the active site of DPP-4. In order to explore more potent
compounds, different substituents were introduced to R1 and R2
positions of 41a. For the R1 position, both 41c and 41e performed
weaker potency than 41a, suggesting that substituents in the R1
position were unfavorable to potency improvement. While for the
R2 position, polar groups such as –CN (41d) and –COOH (41g)
brought increases in activities comparing with 41b containing a
–Br group. Similarly, incorporating a polar cyano group at the R2
position of 41e, potency improvement was also observed (41f).
Based on the exploration of R2 position, we can conclude that
polar groups are beneficial to improving potency. 41d was the
most active compound and separated as (2R,3S)-isomer (41d-1)
with an IC50 value of 16.00 nM. The binding mode of the 41d-1
suggests that the 2,4,5-trifluorobenzene group penetrates into the
hydrophobic subpocket of DPP-4 formed by residues Val656,
Tyr631, Tyr662, Trp659, Tyr666, and Val711, while the
tetrahydro-2H-thiopyran-3-amine nitrogen atom positions
appropriately to generate salt-bridge and hydrogen bond
interactions with the side chains of Glu205, Glu206, and Tyr662.
The naphthalene fragment forms π-π stacking interactions with
Phe357. Besides, the electron-withdrawing –CN could form a
charge-reinforced hydrogen bond with the flexible Arg358 (Figure
6).
F
NH2
F
O
R1
Compoun
26
R1
Br
Ph
IC50 (nM)b
da
1202.83
±
±
159.65
1360.71
478.49
112.22 ± 12.08
622.34
141.89
274.49 ± 77.84
841.70
202.52
140.51 ± 29.52
31a
31b
31c
31d
31e
31f
Ph-3-Ms
±
Ph-3-COOMe
Ph-3-NHSO2CH3
Ph-3-NHSO2CF3
Ph-3-COOH
±
Chin. J. Chem. 2019, 37, XXX－XXX© 2019 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimwww.cjc.wiley-vch.de
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Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
Table
3
Activities
of
shown in a light blue cartoon (PDB id: 5J3J), the key residues are displayed
as thin yellow sticks, 41d-1 is represented as thick green sticks, hydrogen
bonds are displayed as orange dashed lines.
2-Phenyl-3,4-dihydro-2H-Benzo[f]thiochromen-3-amine
against the DPP-4 enzyme.
Derivatives
F
Oral glucose tolerance test (OGTT) in ICR mice
F
NH2
Considering the good in vitro potency of compound 41d-1
against DPP-4, we further conducted an OGTT to preliminarily
evaluate its ability of improving the glucose clearance capacity in
vivo. The results showed that 41d-1 displayed a moderate blood
glucose reduction efficacy at a low dosage of 5 mg/kg by
decreasing the AUC0−120min of 4.38% (Table S1 and Figure S1 in
supporting information). Higher dosages will be explored in our
future study to comprehensively evaluate the in vivo anti-diabetic
efficacy of 41d-1.
F
S
R1
R2
Compounda
41a
R1
H
R2
H
IC50 (nM)b
33.27 ± 14.15
253.43 ± 6.69
151.04 ± 55.43
21.44 ± 5.23
16.00 ± 2.11
400.99 ± 52.35
125.44 ± 14.25
86.76 ± 33.42
121.62 ±22.52
2.20 ± 0.66
Conclusions
In summary, aiming to discover novel DPP-4 inhibitors with
high potency, structural modifications were conducted based on
the skeleton of our preclinical candidate 7. Three new series of
41b
H
Br
H
41c
Br
H
potent
dihydrobenzo[h]chromen,
DPP-4
inhibitors
with
the
biphenyl
scaffolds
of
and
41d
CN
CN
CN
H
dihydrobenzo[f]thiochromen were synthesized and evaluated.
Their SAR was studied and discussed. Dihydrobenzo[h]chromen
analogs displayed moderate activities that may attribute to the
unfavorable steric clashes between the ligands and protein.
Potency improvement of 31g based on the biphenyl skeleton
suggested that electrostatic complementarity should be taken into
consideration in future structural optimization. Among the
41d-1
41d-2
41e
H
H
derivatives
explored,
41d-1
based
on
OMe
thedihydrobenzo[f]thiochromen core was the most potent one
(IC50 = 16 nM). The in vivo OGTT study showed that 5 mg/kg 41d-1
displayed a moderate efficacy in improving the glucose clearance
capacity (reduction percentage of AUC0−120min: 4.38%) in ICR mice.
The SAR explored will be beneficial for guiding future optimization
of more potent DPP-4 inhibitors based on the three new starting
points.
41f
OMe
CN
COOH
-
41g
H
-
Omarigliptin
Trelagliptin
Experimental
Chemistry
-
-
2.58 ± 0.73
The reagents used in the experiments were all commercially
available, most of which were purchased from Energy Chemical
Company. All the reactions were monitored by TLC. 1H and 13C
spectra were recorded on a Bruker Avance-400 or Ascend 600
spectrometer in CDCl3 or DMSO-d6 with TMS as an internal
standard. High-resolution mass spectra (HRMS) were acquired
with a Xevo G2 TOF MS spectrometer in positive ESI mode or GCT
Premier spectrometer in EI mode. Mass spectra for all
intermediates were recorded on an Agilent Technologies 6100
Series Single Quadrupole LC/MS or Micromass GCT CA 055
instrument. Melting points (m.p.) were measured on a WRS-1B
digital melting point apparatus. The purity of all the tested
compounds was performed on an Agilent 1100 series HPLC using
an Agilent XDB 5 μ C18 column (4.6 mm × 150 mm). Elution was
carried out using water as mobile phase A and acetonitrile as
aThe absolute configuration of 41d-1 is (2R,3S), the absolute configuration
of 41d-2 is (2S,3R). The other compounds are trans-racemic structures.
bMean values of at least three independent experiments.
Figure 6 Predicted binding mode of 41d-1. The structure of DPP-4 is
Chin. J. Chem. 2019, 37, XXX－XXX© 2019 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimwww.cjc.wiley-vch.de
This article is protected by copyright. All rights reserved.

Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
mobile phase B. Elution conditions were at 0 min, phase A 20% +
phase B 80%; at 25 min, phase A 20% + phase B 80%. The flow
rate of the mobile phase was 0.5 mL/min and the injection volume
of the sample was 5 μL. The determined wavelength was 254 nm.
The purity of all compounds was ≥95% as determined by HPLC
analysis. The microwave reactions were executed in a microwave
reactor (CEM, DISCOVERY).
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o
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Acknowledgement (optional)
This work was supported by the National Key Research and
Development Program [2016YFA0502304 to H.L.]; the National
Natural Science Foundation of China (grant 81825020 to H.L.,
81803437 to S.L.); the National Science & Technology Major
Project “Key New Drug Creation and Manufacturing Program”,
China (Number: 2018ZX09711002); the Fundamental Research
Funds for the Central Universities, Special Program for Applied
Research on Super Computation of the NSFC-Guangdong Joint
Fund (the second phase) under Grant No.U1501501. Shiliang Li is
sponsored by Shanghai Sailing Program (No. 18YF1405100).
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This article is protected by copyright. All rights reserved.

Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
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(The following will be filled in by the editorial staff)
Manuscript received: XXXX, 2019
Manuscript revised: XXXX, 2019
Manuscript accepted: XXXX, 2019
Accepted manuscript online: XXXX, 2019
Version of record online: XXXX, 2019
Chin. J. Chem. 2019, 37, XXX－XXX© 2019 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimwww.cjc.wiley-vch.de
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Design, synthesis and SAR studies of novel and potent dipeptidyl peptidase 4 inhibitors
Chin. J. Chem.
Entry for the Table of Contents
xxx
Design, Synthesis and SAR Studies of Novel and
Potent Dipeptidyl Peptidase 4 Inhibitors
A novel DPP-4 inhibitor 41d-1 based on the scaffold of dihydrobenzo[f]thiochromen amine
with an IC50 value of 16.00 nM.
Author, Corresponding Author,* Author
Chin. J. Chem. 2019, 37, XXX－XXX© 2019 SIOC, CAS, Shanghai, & WILEY-VCH Verlag GmbH & Co. KGaA, Weinheimwww.cjc.wiley-vch.de
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