2-(Halogenated Phenyl) acetamides and propanamides as potent TRPV1 antagonists

Article abstract of DOI:10.1016/j.bmcl.2021.128266

A series consisting of 117 2-(halogenated phenyl) acetamide and propanamide analogs were investigated as TRPV1 antagonists. The structure–activity analysis targeting their three pharmacophoric regions indicated that halogenated phenyl A-region analogs exhibited a broad functional profile ranging from agonism to antagonism. Among the compounds, antagonists 28 and 92 exhibited potent antagonism toward capsaicin for hTRPV1 with K_i[CAP] = 2.6 and 6.9 nM, respectively. Further, antagonist 92 displayed promising analgesic activity in vivo in both phases of the formalin mouse pain model. A molecular modeling study of 92 indicated that the two fluoro groups in the A-region made hydrophobic interactions with the receptor.

Full text of DOI:10.1016/j.bmcl.2021.128266

Bioorg. Med. Chem. Lett. 48 (2021) 128266
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
2-(Halogenated Phenyl) acetamides and propanamides as potent
TRPV1 antagonists
Jin Mi Kanga, Sun Ok Kwona, Jihyae Anna, Sunho Leea, Changhoon Kima, Nayeon Doa,
Jin Ju Jeonga, Peter M. Blumberga, Heejin Hab, Thi Ngoc Lan Vuc, Sanghee Yoonc, Sun Choic,
Robert Frank-Foltynd, Bernhard Leschd, Gregor Bahrenbergd, Hannelore Stockhausend,
,
*
Thomas Christophd, Jeewoo Leea
a Laboratory of Medicinal Chemistry, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
b Medifron DBT, Seoul 08502, Republic of Korea
c Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
d Grünenthal Innovation, Grünenthal GmbH, D-52078 Aachen, Germany
A R T I C L E I N F O
A B S T R A C T
Keywords:
A series consisting of 117 2-(halogenated phenyl) acetamide and propanamide analogs were investigated as
TRPV1 antagonists. The structure–activity analysis targeting their three pharmacophoric regions indicated that
halogenated phenyl A-region analogs exhibited a broad functional profile ranging from agonism to antagonism.
Among the compounds, antagonists 28 and 92 exhibited potent antagonism toward capsaicin for hTRPV1 with Ki
[CAP] = 2.6 and 6.9 nM, respectively. Further, antagonist 92 displayed promising analgesic activity in vivo in both
phases of the formalin mouse pain model. A molecular modeling study of 92 indicated that the two fluoro groups
in the A-region made hydrophobic interactions with the receptor.
Vanilloid Receptor 1
TRPV1 Antagonist
Analgesic
The transient receptor potential vanilloid 1 (TRPV1) is a molecular
integrator of nociceptive stimuli expressed in primary sensory neuro-
ns.1–6 Functionally, it is a nonselective cation channel and is activated by
vanilloids such as capsaicin and resiniferatoxin and by noxious stimuli
including heat, low pH or inflammatory mediators.7–10 Blockade of
TRPV1 activation is considered a promising therapeutic target for the
treatment of neuropathic pain.
selective TRPV1 antagonist that potently blocked channel activation
by capsaicin, but did not block activation by protons, did not cause
hyperthermia.13 The goal of the present study is to further explore
structure–activity relationships for TRPV1 antagonists. The longer term
objective will be to integrate these insights to identify activator-selective
TRPV1 antagonists to yield novel analgesics with reduced side effects as
second-generation antagonists.14,15
However, despite of the extensive efforts made for the development
of clinical TRPV1 antagonists as novel non-opioid analgesics,11 almost
all of the antagonists to date have failed in the clinical stage mostly due
to mechanism-associated side effects such as hyperthermia or loss of
sensitivity to thermal pain. The current understanding is that the side
effects are linked to antagonists that block all activation modes of
TRPV1, and in particular that hyperthermia is associated with the in-
hibition of the proton activation mode of TRPV1 channel.12,13 Since the
different modes of TRPV1 activation are differentially associated with
the pattern of response at the whole animal level, antagonists with
selectivity among the activation modes of TRPV1 would be of particular
interest for avoidance of such side effects.
Previously, we have investigated a series of 2-(3-fluoro-4-methyl-
sulfonamidophenyl)propanamides as hTRPV1 antagonists. Among
them, compounds 1–3 displayed exceptionally potent antagonism to
capsaicin (Ki[CAP] = 0.2 nM for 1, Ki[CAP] = 0.1 nM for 2 and 3) and
blocked the hypothermic effect of capsaicin in vivo, consistent with their
in vitro mechanism (Fig. 1).16,17 Their activity was stereospecific for the
S-configuration. Whereas antagonists 1 and 2 showed full antagonism to
all activators, antagonist 3 exhibited antagonism selective for capsaicin
and N-arachidonoyl dopamine (NADA) but not for low pH or heat
(45 ◦C). The pharmacophoric region of the antagonistic scaffold can be
divided into so-called A- (red), B- (black) and C-regions (blue), previ-
ously designated for capsaicin (Fig. 1).
In support of this concept, it was recently reported that a mode-
The basis for the high potencies of the antagonists was revealed by
* Corresponding author.
E-mail address: jeewoo@snu.ac.kr (J. Lee).
https://doi.org/10.1016/j.bmcl.2021.128266
Received 14 June 2021; Received in revised form 1 July 2021; Accepted 11 July 2021
Available online 14 July 2021
0960-894X/© 2021 Elsevier Ltd. All rights reserved.

J.M. Kang et al.
Bioorganic & Medicinal Chemistry Letters 48 (2021) 128266
Scheme 3. Synthesis of the 3-trifluoromethylpyrazole C-region. Reagents and
conditions: (a) LiAlH4, Et2O, ꢀ 78 ◦C, 2 h; (b) (3-Cl)Ph-NHNH2, EtOH, reflux, 5
h; (c) NCS, DMF, r.t.; (d) 2-chloroacrylonitrile, TEA, toluene, 80 ◦C, 20 h; (e)
LiAlH4, THF, 0 ◦C to r.t., 3 h.
Fig. 1. Prototype TRPV1 antagonists.
Scheme 4. Synthesis of the 3-t-butylpyrazole C-region. Reagents and condi-
tions: (a) (3-Cl)Ph-NHNH2, EtOH:H2O (1:1), reflux, overnight; (b) t-BuONO,
CuI, CH3CN, 0 ◦C to 65 ◦C; (c) Zn(CN)2, Pd(PPh3)4, DMF, reflux, overnight; (d)
LiAlH4, THF, 0 ◦C to r.t., 1 h.
Scheme 1. Synthesis of the halogenated phenyl A-region Reagents and condi-
tions: (a) EtOH, H2SO4, reflux, 2 h; (b) MeI, NaH, DMF, 0 ◦C, 2 h; (c) LiOH, r.t.,
THF-H2O (1:1), overnight.
Scheme 5. Synthesis of final amide compounds. Reagents and conditions: (a) 1-
(3-dimethylaminopropyl)-3-ethyl-carbodiimide hydrochloride, 1-hydroxyben-
zotriazole, DMF, r.t., overnight.
Scheme 2. Synthesis of the 6-trifluoromethylpyridine C-region. Reagents and
conditions: (a) (CF3CO2)2O, pyridine; (b) NCCH2CONH2, K2CO3, toluene; (c)
POCl3; (d) 4-methylpiperidine; (e) BH3-SMe2 in THF.
region were employed for the synthesis of the final compounds. For the
synthesis of 2-(halogenated phenyl) propionic acid as an A-region
(Scheme 1), the corresponding acetic acids (4) were converted to ethyl
esters, which were α-alkylated with methyl iodide and then hydrolyzed
molecular docking studies using our established hTRPV1 homology
model, demonstrating that the two hydrophobic interactions in the C-
region were critical for potent antagonism. For instance, the 2-substitu-
ent and the 6-CF3 group in the pyridine for 1 and the 1-substituent and
the 3-CF3/t-butyl in pyrazole for 2 and 3 made hydrophobic interactions
with pockets composed of Met514/Leu515 and Leu547/Thr550 regions,
respectively, or vice versa. Therefore, the pyridine and pyrazole C-re-
gion of 1–3 have been employed as prototype C-region for the respective
optimization of the A- and B-regions.16,17 For the discovery of a clinical
candidate for neuropathic pain, we have extensively modified the three
pharmacophoric regions of our template. Much of our effort has been
directed at the structure activity relationship (SAR) of the C-region18
under basic conditions to provide propionic acids (5), respectively.
For the synthesis of (2-(4-methylpiperidin-1-yl)-6-(trifluoromethyl)
pyridin-3-yl)methanamine (6) as
a C-region (Scheme 2), tri-
fluoromethylacetylation of ethylvinyl ether followed by condensation
with cyanoacetamide provided the pyridone intermediate, which was
readily converted to 2-chloropyridine by POCl3 and then its nitrile group
was reduced to yield the 6-trifluoromethylpyridine C-region amine.
For the synthesis of (1-(3-chlorophenyl)-3-trifluoromethyl-1H-pyr-
azol-5-yl)methylamine (7) as a C-region (Scheme 3), ethyl tri-
fluoroacetate as a starting material was reduced to the corresponding
aldehyde and then was condensed with 3-chlorophenyl hydrazine to
afford the phenyl hydrazone. The chlorination of hydrazone followed by
the reaction with 2-chloroacrylonitrile provided 4-cyanopyrazole which
was reduced to afford the 3-trifluoromethylpyrazole C-region amine (7).
For the synthesis of (1-(3-chlorophenyl)-3-t-butyl-1H-pyrazol-5-yl)
methylamine (8) as a C-region (Scheme 4), 4,4-Dimethyl-3-oxopentane-
nitrile was condensed with 3-chlorophenyl hydrazine to provide 1-(3-
chlorophenyl) 3-t-butyl-5-aminopyrazole whose amine was converted to
the corresponding nitrile group and then reduced to afford the 3-t-
butylpyrazole C-region amine (8).
and the A-region19–21
.
Here, as part of our continuing efforts to optimize the A-region of our
TRPV1 antagonistic template, we have investigated 2-(halogenated
phenyl) acetamides and propanamides fixed with the prototype C-re-
gions of 1–3. In this study, we describe the syntheses of a series of
halogenated phenyl A-region derivatives and characterize their antag-
onism toward activation of hTRPV1 by capsaicin. With a selected potent
antagonist in the series, we further characterize its analgesic effect in a
pain model and performed a molecular modeling study to elucidate the
key binding interactions.
The prepared 2-(halogenated phenyl) acetic (4) and propionic (5)
acids (A-region) were coupled with 6-trifluoromethylpyridine (6), 3-
Commercially available 2-(halogenated phenyl) acetic acids as an A-
2

J.M. Kang et al.
Bioorganic & Medicinal Chemistry Letters 48 (2021) 128266
Table 1
Table 2
In vitro hTRPV1 functional activities for 2-(halogenated phenyl) acetamides and
propanamides with a 6-trifluoromethylpyridine C-region.
In vitro hTRPV1 functional activities for 2-(halogenated phenyl) acetamides and
propanamides with a 3-trifluoromethylpyrazole C-region.
X
R
Ki[CAP] (nM)a
X
R
Ki[CAP] (nM)a
2 (rac)
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
CH3
H
3-F, 4-NHMs
2-F
0.3
1 (rac)
9
CH3
H
3-F, 4-NHMs
2-F
0.3
80.7
51.8
pAG
26.2
6.2
9.9
H
3-F
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
H
3-F
34
H
4-F
H
4-F
AG
H
2-Cl
H
2-Cl
9.1
H
3-Cl
H
3-Cl
6.1
H
4-Cl
6.3
H
4-Cl
AG
H
2,3-F2
2,4-F2
2,5-F2
2,6-F2
3,4-F2
3,5-F2
2,3-Cl2
2,4-Cl2
2,6-Cl2
3,4-Cl2
3-F, 4-Cl
3-Cl, 4-F
3-CF3, 4-F
2-F, 6-Cl
2-Cl, 4-F
2-F
11.5
43.3
58.9
WE
H
2,3-F2
2,4-F2
2,5-F2
2,6-F2
3,4-F2
3,5-F2
2,3-Cl2
2,4-Cl2
2,6-Cl2
3,4-Cl2
3-F, 4-Cl
3-Cl, 4-F
3-CF3, 4-F
2-F, 6-Cl
2-Cl, 4-F
2-F
9.4
H
H
AG
H
H
30
H
H
38
H
pAG
13.7
22.6
NE
H
pAG
10.3
4.9
H
H
H
H
H
H
46
H
WE
H
39.7
6.7
H
3.8
H
H
20.9
26.9
11.9
35.7
38.8
NT
H
pAG
12.9
9.8
H
H
H
H
H
H
2.6
H
H
14.2
60.4
AG
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
3-F
pAG
pAG
41.9
pAG
pAG
18.4
pAG
56.7
33.6
pAG
pAG
13.2
NE
3-F
4-F
4-F
AG
2-Cl
2-Cl
72.8
13.8
pAG
31.4
pAG
59.6
110
AG
3-Cl
3-Cl
4-Cl
4-Cl
2,3-F2
2,4-F2
2,5-F2
2,6-F2
3,4-F2
3,5-F2
2,3-Cl2
2,4-Cl2
3,4-Cl2
3-F, 4-Cl
2,3-F2
2,4-F2
2,5-F2
2,6-F2
3,4-F2
3,5-F2
2,3-Cl2
2,4-Cl2
3,4-Cl2
3-F, 4-Cl
3-Cl, 4-F
3-CF3, 4-F
2-Cl, 4-F
24.7
75.3
NE
7.6
pAG
pAG
17.7
10.8
AG
9.5
a
Values from triplicate experiments (AG: agonist, pAG: partial agonist, NE:
not effective).
a
Values from triplicate experiments (AG: agonist, pAG: partial agonist, NE:
the other hand, whereas the 2-chloro and 3-chloro isomers exhibited
potent antagonism, the 4-chloro isomer was an agonist like the 4-fluoro
isomer. In the analogs of dihalophenyl acetamide, most isomers
exhibited antagonism, but some showed different functional profiles.
The 2,4-difluoro isomer (16) displayed agonism, and the 3,4-difluoro
(19) and the 3-fluoro-4-chloro isomers (25) showed partial agonism.
Among the antagonists, 2-fluoro-6-chloro isomer (28) displayed the
most potent antagonism with Ki[CAP] = 2.6 nM. In the analogs of mon-
ohalophenyl propanamide, most compounds showed less potent antag-
onism compared to the corresponding acetamide surrogate. Among
them, the 3-fluoro and 4-fluoro isomers were agonists. In the analogs of
dihalophenyl propanamide, the compounds showed a similar pattern to
that of monohalophenyl propanamide. Among them, the 3,4-difluoro
isomer and the 2-chloro-4-fluoro isomer were found to be agonists.
In conclusion, the SAR analysis of pyridine C-region analogs indi-
cated that (1) acetamide B-region analogs were more potent than the
corresponding propanamide B-region surrogates. (2) The order of
antagonism in positional isomers of the acetamide analogs was 2-isomer
> 3-isomer > 4-isomer and the 4-halo substituent shifted functional
activity to agonism for both acetamide and propanamide.
not effective).
trifluoromethylpyrazole (7) or 3-t-butylpyrazole (8) amines (C-region)
to provide the final amide compounds (9–125), respectively, whose
structures were confirmed by spectroscopic analysis (Scheme 5).22
The in vitro assay for TRPV1 antagonism was performed using a
fluorometric imaging plate reader (FLIPR) with hTRPV1 heterologously
expressed in Chinese hamster ovary (CHO) cells.16 The activity of the
synthesized compounds was measured by inhibition of TRPV1 activa-
tion by capsaicin (100 nM) and expressed as the inhibition constant (Ki
[CAP]). The results are summarized in Tables 1–3.
For the SAR study of the halogenated phenyl A-region, mono-
fluorophenyl, monochlorophenyl, difluorophenyl, dichlorophenyl, and
mixed dihalophenyl analogs were examined.
First, we investigated the functional activities of the 2-(halogenated
phenyl) acetamides (9–29) and propanamides (30–48) with the 6-tri-
fluoromethylpyridine C-region (Table 1).
In the analogs of monohalophenyl acetamide, the 2-fluoro isomer (9)
showed potent antagonism, but the 3-fluoro (10) and 4-fluoro (11)
isomers exhibited moderate antagonism and agonism, respectively. In
3

J.M. Kang et al.
Bioorganic & Medicinal Chemistry Letters 48 (2021) 128266
Table 3
1st phase
2nd phase
150
100
50
In vitro hTRPV1 functional activities for 2-(halogenated phenyl) acetamides and
propanamides with a 3-t-butylpyrazole C-region.
**
*
**
**
X
R
Ki[CAP] (nM)a
**
3 (rac)
86
CH3
H
3-F, 4-NHMs
2-F
0.3
0
pAG
AG
Veh 10 30 50 100
Veh 10 30 50 100
87
H
3-F
88
H
4-F
AG
92 [mg/kg]
89
H
2-Cl
7.7
90
H
3-Cl
AG
91
H
4-Cl
AG
Fig. 2. Analgesic activity of 92 in the formalin pain model by i.p. injection.
92
H
2,3-F2
2,4-F2
2,5-F2
2,6-F2
3,4-F2
3,5-F2
2,3-Cl2
2,4-Cl2
2,6-Cl2
3,4-Cl2
3-F, 4-Cl
3-Cl, 4-F
3-CF3, 4-F
2-F, 6-Cl
2-Cl, 4-F
2-F
6.9
93
H
pAG
pAG
49.6
AG
showed potent antagonism and the additive 3,4-dichloro isomer pro-
vided high potency.
94
H
95
H
96
H
Thirdly, we investigated the functional activities of the 2-(haloge-
nated phenyl) acetamides (86–106) and propanamides (107–125) with
a 3-t-butylpyrazole C-region (Table 3).
97
H
pAG
4.0
98
H
99
H
16.7
NE
In the series of TRPV1 ligands, the 3-t-butylpyrazole C-region
generally shifted the functional activity to agonism compared to the
pyridine and 3-trifluoromethyl pyrazole C-regions as examined previ-
ously17. In the analogs of monohalophenyl acetamide, most compounds
were agonists or partial agonists except for the 2-chloro isomer. In the
analogs of dihalophenyl acetamide, the compounds also showed partial
agonism or agonism due to the C-region. In the analogs of mono-
halophenyl and dihalophenyl propanamide, most compounds proved to
be agonists or partial agonists.
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
H
H
pAG
pAG
AG
H
H
H
8.8
H
19
H
19.9
AG
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
CH3
3-F
AG
4-F
AG
2-Cl
pAG
AG
The SAR analysis of 3-t-butylpyrazole C-region analogs indicated
that (1) similar to the SAR for the other C-regions, acetamide B-region
analogs were more potent than the corresponding propanamide B-re-
gion surrogates. (2) The C-region shifted the activity to agonism,
rendering most compounds partial agonists or agonists.
3-Cl
4-Cl
AG
2,3-F2
2,4-F2
2,5-F2
2,6-F2
3,4-F2
3,5-F2
2,3-Cl2
2,4-Cl2
3,4-Cl2
3-F, 4-Cl
3-Cl, 4-F
3-CF3, 4-F
2-Cl, 4-F
pAG
AG
pAG
pAG
AG
Lipophilicity of TRPV1 ligands is one of important factors deter-
mining the agonism/antagonism potency because the binding site for
the ligand is located by the inner surface of the cell membrane. As the
lipophilicity of the ligand increases, its potency is usually enhanced.
However, excessive lipophilicity causes low solubility, which will affect
bioavailability. In fact, a number of clinical antagonists have suffered
from this solubility issue. Since dichlorophenyl analogs have very high
lipophilicity (ex. 64: cLogP = 5.85), they are thus less appealing can-
didates for further study in terms of drug development.
AG
pAG
AG
AG
AG
AG
59
26
a
Values from triplicate experiments (AG: agonist, pAG: partial agonist, NE:
not effective).
To evaluate the in vivo activity of selected potent antagonists, two
antagonists 28 (Ki[CAP] = 2.6 nM) and 92 (Ki[CAP] = 6.9 nM) were
examined for their antinociceptive activity after administration by
intraperitoneal injection (i.p.) in the formalin mouse model.23
Whereas compound 28 exhibited weak analgesic activity, compound
92 demonstrated reasonable analgesic activity in both the 1st and 2nd
phase in a dose-dependent manner, providing an ED50 of 50.5 mg/kg in
the 1st phase and 29.5 mg/kg in the 2nd phase, respectively (Fig. 2). The
weak in vivo activity of 28 was not further explored, but could reflect,
among other explanations, either a problem of bioavailability due to its
high lipophilicity or a species difference between mouse and human
TRPV1. In additiom, to examine the effect of antagonist 92 on ther-
moregulation, the body temperature was measured after i.p. adminis-
tration of 10 mg/kg of the compound in mice. It did not cause any
hyperthermia at given dose.
Secondly, we investigated the functional activities of the 2-(haloge-
nated phenyl) acetamides (49–69) and propanamide (70–85) with a 3-
trifluoromethylpyrazole C-region (Table 2).
In the analogs of monohalophenyl acetamide, the chloro isomers
showed higher antagonism than the corresponding fluoro isomers.
Among the compounds, the 3-chloro and 4-chloro isomers displayed
potent antagonism. In the analogs of dihalophenyl acetamide, most
compounds exhibited moderate to weak antagonism except for the 3,4-
dichloro isomer, probably due to their high lipophilicity. In the analogs
of monohalophenyl and dihalophenyl propanamide, similar to the SAR
for the pyridine C-region, propanamide analogs were found to be less
potent than the corresponding acetamide surrogates, showing weak
antagonism or partial agonism.
The SAR analysis of 3-trifluoromethylpyrazole C-region analogs
indicated that (1) acetamide B-region analogs were more potent than the
corresponding propanamide B-region surrogates. (2) In positional iso-
mers of the acetamide analogs, the 3-chloro and 4-chloro isomers
Binding modes of compound 92 were investigated with our recently
published homology models of hTRPV1,21 which were constructed
based on the cryo-EM structure of rTRPV1 complexed with the antago-
nist, capsazepine. In order to consider the flexibility of hTRPV1, we
4

J.M. Kang et al.
Bioorganic & Medicinal Chemistry Letters 48 (2021) 128266
(A)
(B)
(C)
Leu663
Ala546
Ala546, Leu547
Thr550, Phe591
Leu663, Ala666
Phe591
Leu547
Ala666
Thr550
Leu518
Tyr511
Met514
Tyr511
Leu515
Leu518
Leu547
Tyr511
Leu553
Ala566
Ile569
F
Leu515
Met514
Cl
Thr550
Tyr511
Leu553
Ile569
Tyr511
F
Leu515
Leu553, Ala566
Ala566
Fig. 3. Binding mode of 92 in the hTRPV1 homology model. (A) Binding mode of 92 represented in ball-and-sticks with the atoms colored as: C in magenta, F in
green–blue, N in blue, O in red, Cl in green, H in white. The interacting residues are depicted in sticks with their carbon atoms in grey. The secondary structure of the
hTRPV1 model is displayed in ribbon. This representation is generated with PyMOL Molecular Graphics System version 1.8.6.2 (Schrodinger, LLC, NY, USA). (B) The
Fast Connolly surface presented with the lipophilic potential property of hTRPV1 and the van der Waals surface of 92, created by MOLCAD program implemented in
SYBYL-X 2.1.1 (Tripos Int., St. Louis, MO, USA). For clarity, the surface of hTRPV1 is Z-clipped and that of the ligand is colored by magenta. (C) 2-D representation of
the binding interactions between 92 and hTRPV1. Hydrophobic interactions are displayed with bronze curved patches. Hydrogen bonds are marked in black-dashed
lines, and nonpolar hydrogen atoms are undisplayed for clarity.
applied the ensemble docking and induced fit docking using the six
discrete conformations of the homology models derived from the clus-
tering after the molecular dynamics simulations.24
examined.
Declaration of Competing Interest
As shown in Fig. 3, the A-region of 92 occupies the bottom of the
vanilloid pocket with the phenyl ring making hydrophobic interactions
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
with Tyr511, Leu553, Ala566 and Ile569, along with the π–π stacking
with Tyr511. Moreover, both of the two fluoro groups in the phenyl ring
form hydrophobic interactions: the 2-fluoro group with Tyr511, Leu515
and Leu553; and the 3-fluoro group with Tyr511, Leu553 and Ala566.
The amide group in the B-region participates in two hydrogen bonds
with Tyr511 and Thr550, which were observed in other amide-
containing TRPV1 ligands in previous studies.17,21,25 These in-
teractions allow the C-region of the ligand to hold the position where the
t-butyl-pyrazole group occupies the shallow upper niche, resulting in
hydrophobic interactions with Ala546, Leu547, Thr550, Phe591,
Leu663, and Ala666. In addition, the chlorophenyl group settles down in
the middle open region and makes hydrophobic interactions with
Tyr511, Met514, Leu515, Leu518 and Leu547.
Acknowledgments
This work was supported by the Midcareer Researcher Program
(NRF-2019R1A2C2006837 and NRF-2020R1A2C2101636) funded by
the National Research Foundation of Korea (NRF).
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Å, 14 Å, 19 Å. The scaling of ligand van der Waals radii for nonpolar atoms was set at
0.8, partial charge cutoff value at 0.15, and number of poses to generate at 30. Then,
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keeping the other settings as default. For the analysis of the docking results,
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computational studies were undertaken on an Intel® Xeon® Gold 6254 CPU 3.10
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