Journal of Medicinal Chemistry
Article
2-Ethyl-1-((3-fluorophenyl)sulfonyl)-4-(piperazin-1-yl)-1H-
imidazo[4,5-c]pyridine Acetate (7f). White solid, yield 48%;
UHPLC-UV purity 98% (220 nm); C20H24FN5O4S, MW 449.50.
1H NMR (500 MHz, CD3OD) δ ppm: 1.40 (t, J = 7.3 Hz, 3H), 1.92
UHPLC-UV purity 98% (220 nm); C24H24ClN5O4S, MW 514.00.
1H NMR (500 MHz, CD3OD) δ ppm: 1.92 (s, 3H), 3.19−3.23 (m,
4H), 4.18−4.24 (m, 4H), 7.32−7.36 (m, 1H), 7.44−7.47 (m, 2H),
7.50 (d, J = 4.3 Hz, 4H), 7.59−7.64 (m, 2H), 7.66−7.70 (m, 1H),
8.13 (d, J = 5.7 Hz, 1H). 13C NMR (125 MHz, CD3OD) δ ppm: 23.4,
45.0, 45.6, 103.3, 126.7, 128.4, 129.1, 130.7, 132.2, 132.7, 136.6,
140.4, 142.4, 144.6, 151.9, 152.5; mp 137−140 °C; HRMS (ESI-
TOF) m/z calculated for C22H21ClN5O2S+ [M + H+] 454.1099,
found 454.1098.
1-((3-Fluorophenyl)sulfonyl)-2-phenyl-4-(piperazin-1-yl)-1H-
imidazo[4,5-c]pyridine Acetate (7m). White solid, yield 62%;
UHPLC-UV purity 99% (220 nm); C24H24FN5O4S, MW 497.55.
1H NMR (500 MHz, CD3OD) δ ppm: 1.93 (s, 3H), 3.24−3.27 (m,
4H), 4.21−4.28 (m, 4H), 7.16−7.20 (m, 1H), 7.33−7.38 (m, 1H),
7.43−7.47 (m, 1H), 7.48−7.54 (m, 5H), 7.59−7.64 (m, 2H), 8.14 (d,
J = 6.0 Hz, 1H). 13C NMR (125 MHz, CD3OD) δ ppm: 22.9, 44.8,
45.3, 103.4, 115.7 (2JC−F = 26.4 Hz), 123.7 (2JC−F = 21.6 Hz), 124.5
(4JC−F = 3.6 Hz), 128.4, 129.1, 130.8, 132.2, 133.3 (3JC−F = 8.4 Hz),
142.5, 144.6, 152.1, 152.3, 163.8 (1JC−F = 251.9 Hz), 178.6 (second
3JC−F not detected in the spectrum due to the low concentration of
(s, 3H), 3.14−3.19 (m, 2H), 3.19−3.22 (m, 4H), 4.18−4.25 (m, 4H),
7.43 (d, J = 5.7 Hz, 1H), 7.48−7.55 (m, 1H), 7.67 (td, J = 8.2, 5.2 Hz,
1H), 7.80 (dt, J = 7.9, 2.2 Hz, 1H), 7.85 (dd, J = 8.0, 0.9 Hz, 1H),
8.02 (d, J = 5.7 Hz, 1H). 13C NMR (125 MHz, CD3OD) δ ppm: 12.0,
24.1, 44.9, 45.7, 102.2, 115.3 (2JC−F = 25.2 Hz), 123.6 (2JC−F = 21.6
Hz), 124.3 (4JC−F = 3.6 Hz), 127.7, 133.6 (3JC−F = 8.4 Hz), 143.8,
3
151.9, 154.5 (1JC−F and second JC−F not detected in the spectrum
due to the low concentration of the sample). HRMS (ESI-TOF) m/z
calculated for C18H21FN5O2S+ [M + H+] 390.1395, found 390.1395.
2-Isopropyl-1-(phenylsulfonyl)-4-(piperazin-1-yl)-1H-imidazo-
[4,5-c]pyridine Acetate (7g). White solid, yield 42%; UHPLC-UV
purity 99 + % (220 nm); C21H27N5O4S, MW 445.54. 1H NMR (500
MHz, CD3OD) δ ppm: 1.34 (d, J = 6.6 Hz, 6H), 1.88−1.94 (m, 3H),
3.18−3.26 (m, 4H), 3.77−3.88 (m, 1H), 4.14−4.25 (m, 4H), 7.49 (d,
J = 5.7 Hz, 1H), 7.59−7.67 (m, 2H), 7.70−7.79 (m, 1H), 7.92−8.05
(m, 3H). 13C NMR (125 MHz, CD3OD) δ ppm: 22.8, 23.6, 29.8,
45.0, 45.7, 102.8, 128.2, 131.3, 136.6, 139.6, 141.6, 143.7, 152.0,
159.0; mp 125−130 °C; HRMS (ESI-TOF) m/z calculated for
C19H24N5O2S+ [M + H+] 386.1645, found 386.1648.
1-((3-Chlorophenyl)sulfonyl)-2-isopropyl-4-(piperazin-1-yl)-1H-
imidazo[4,5-c]pyridine Acetate (7h). White solid, yield 43%;
UHPLC-UV purity 99% (220 nm); C21H26ClN5O4S, MW 479.98.
1H NMR (500 MHz, CD3OD) δ ppm: 1.36 (d, J = 6.9 Hz, 6H), 1.92
(s, 3H), 3.18−3.22 (m, 4H), 3.78−3.86 (m, 1H), 4.18−4.25 (m, 4H),
7.46 (d, J = 6.0 Hz, 1H), 7.60−7.64 (m, 1H), 7.76−7.79 (m, 1H),
7.90−7.93 (m, 1H), 8.00 (t, J = 2.0 Hz, 1H), 8.03 (d, J = 5.7 Hz, 1H).
13C NMR (125 MHz, CD3OD) δ ppm: 22.8, 23.7, 30.0, 45.0, 45.9,
the sample); mp 126−128 °C; HRMS (ESI-TOF) m/z calculated for
C22H21FN5O2S+ [M + H+] 438.1395, found 438.1379.
1-((3-Methoxyphenyl)sulfonyl)-2-phenyl-4-(piperazin-1-yl)-1H-
imidazo[4,5-c] pyridine Acetate (7n). White solid, yield 71%;
1
UHPLC-UV purity 99% (220 nm); C25H27N5O5S, MW 509.58. H
NMR (500 MHz, CD3OD) δ ppm: 1.92 (s, 3H), 3.18−3.23 (m, 4H),
3.70 (s, 3H), 4.14−4.25 (m, 4H), 6.86−6.92 (m, 1H), 7.09−7.14 (m,
1H), 7.16−7.22 (m, 1H), 7.33−7.40 (m, 1H), 7.45−7.56 (m, 4H),
7.57−7.64 (m, 2H), 8.04−8.15 (m, 1H). 13C NMR (125 MHz,
CD3OD) δ ppm: 23.6, 45.0, 45.8, 56.4, 103.5, 113.0, 120.3, 122.5,
128.5, 129.0, 131.1, 132.0, 132.1, 132.3, 139.9, 142.5, 144.4, 152.2,
152.5, 161.6; mp 132−135 °C; HRMS (ESI-TOF) m/z calculated for
C23H24N5O3S+ [M + H+] 450.1594, found 450.1565.
In Silico Simulations. pKa Calculation. pKa values calculations
were performed for the lowest energy conformations for each
compound (minimization performed in macroModel)54 in water as
a solvent using Jaguar.55,56 The default settings were used, i.e., the
energy change at level of 5 × 10−05, no SCF level shift, no thermal
smearing, and ultrafine accuracy level.
102.5, 126.6, 127.8, 133.1, 136.7, 137.2, 141.5, 144.0, 152.0, 158.9;
mp 96−101 °C; HRMS (ESI-TOF) m/z calculated for
C19H23ClN5O2S+ [M + H+] 420.1255, found 420.1260.
1-((3-Fluorophenyl)sulfonyl)-2-isopropyl-4-(piperazin-1-yl)-1H-
imidazo[4,5-c]pyridine Acetate (7i). White solid, yield 44%;
UHPLC-UV purity 99+% (220 nm); C21H26FN5O4S, MW 463.53.
1H NMR (500 MHz, CD3OD) δ ppm: 1.36 (d, J = 6.9 Hz, 6H), 1.92
(s, 3H), 3.18−3.23 (m, 4H), 3.78−3.87 (m, 1H), 4.19−4.25 (m, 4H),
7.47 (d, J = 5.7 Hz, 1H), 7.50−7.57 (m, 1H), 7.64−7.70 (m, 1H),
7.77−7.84 (m, 2H), 8.02 (d, J = 5.7 Hz, 1H). 13C NMR (125 MHz,
Molecular Docking. The 5-HT6R homology models built on the β2
receptor template (PDB ID: 4LDE), successfully applied in our earlier
studies of different groups of 5-HT6R ligands, were used in this
study.42,57 In order to tune the conformation of the receptor to the
studied compounds, the induced-fit docking (IFD) procedure from
CD3OD) δ ppm: 22.8, 23.7, 29.9, 45.0, 45.7, 102.6, 115.4 (2JC−F
=
25.2 Hz), 123.8 (2JC−F = 21.6 Hz), 124.3 (4JC−F = 3.6 Hz), 127.9,
133.7 (3JC−F = 7.2 Hz), 141.5, 144.0, 152.0, 158.9 (1JC−F and second
3JC−F not detected in the spectrum due to the low concentration of
̈
the Schrodinger package was used. The three-dimensional structures
of the ligands were obtained using LigPrep v3.6,58 and the appropriate
ionization states at pH = 7.4 1.0 were assigned using Epik v3.4.59
The Protein Preparation Wizard was used to assign the bond orders
and appropriate amino acid ionization states and to check for steric
clashes. The receptor grid was generated (OPLS3 force field)60 by
centering the grid box with a size of 12 Å on the D3.32 side chain.
Automated flexible docking was performed using Glide v6.961 at the
SP level, and 10 poses per ligand were generated.
the sample); mp 97−100 °C; HRMS (ESI-TOF) m/z calculated for
C19H23FN5O2S+ [M + H+] 404.1551, found 404.1552.
2-Isopropyl-1-((3-methoxyphenyl)sulfonyl)-4-(piperazin-1-yl)-
1H-imidazo[4,5-c]pyridine Acetate (7j). White solid, yield 30%;
1
UHPLC-UV purity 99+% (220 nm); C22H29N5O5S, MW 475.56. H
NMR (500 MHz, CD3OD) δ ppm: 1.35 (d, J = 6.9 Hz, 6H), 1.92 (s,
3H), 3.17−3.25 (m, 4H), 3.80−3.88 (m, 4H), 4.17−4.25 (m, 4H),
7.27−7.32 (m, 1H), 7.40−7.44 (m, 1H), 7.48 (d, J = 6.0 Hz, 1H),
7.50−7.56 (m, 2H), 8.0 (d, J = 6.0 Hz, 1H). 13C NMR (125 MHz,
CD3OD) δ ppm: 22.8, 23.6, 29.8, 45.0, 45.8, 56.6, 102.8, 113.1, 119.9,
122.1, 128.0, 132.6, 140.6, 141.6, 143.7, 152.0, 159.0, 162.0; mp 115−
123 °C; HRMS (ESI-TOF) m/z calculated for C20H26N5O3S+ [M +
H+] 416.1751, found 416.1751.
Molecular Dynamics Simulations. A 100 ns-long molecular
dynamics (MD) simulations were performed using Desmond software
̈
from Schrodinger Suite. Each ligand−protein complex was placed in a
two-layer POPC membrane (300 K), in which the position was
calculated using a PPM web server (accessed 26-01-2020). Next, the
system was solvated (the TIP4P potential was used), all atoms were
parametrized (the OPLS3 force field), and the ionic strength was
added (the 0.15 M concentration of NaCl). The MD trajectories were
clustered (the hierarchical clustering method and 10 final clusters)
2-Phenyl-1-(phenylsulfonyl)-4-(piperazin-1-yl)-1H-imidazo[4,5-
c]pyridine Acetate (7k). White solid, yield 56%; UHPLC-UV purity
1
96% (220 nm); C24H25N5O4S, MW 479.56. H NMR (500 MHz,
CD3OD) δ ppm: 1.92 (s, 3H), 3.13−3.25 (m, 4H), 4.11−4.26 (m,
4H), 7.39−7.56 (m, 8H), 7.56−7.61 (m, 1H), 7.62 (d, J = 5.7 Hz,
1H), 7.64−7.69 (m, 1H), 8.11 (d, J = 6.0 Hz, 1H). 13C NMR (125
MHz, CD3OD) δ ppm: 23.6, 45.0, 45.7, 101.5, 103.5, 128.4, 128.5,
129.0, 130.9, 131.1, 132.0, 132.2, 136.5, 139.0, 142.5, 144.4, 152.2,
152.5. HRMS (ESI-TOF) m/z calculated for C22H22N5O2S+ [M +
H+] 420.1489, found 420.1493.
̈
using trajectory analysis tools from Maestro Schrodinger Suite.
Among all clusters, the four top-rated were selected for further
analysis.
Monitoring Changes in Receptor Conformation. In order to
monitor changes occurring in individual fragments of the 5-HT6R
helix during molecular dynamics of receptor-PZ-1444, compound 7e,
and SAM-760 complexes, the spatial coordinates (x,y,z) of atoms
belonging to particular amino acids were converted into single points
1-((3-Chlorophenyl)sulfonyl)-2-phenyl-4-(piperazin-1-yl)-1H-
imidazo[4,5-c]pyridine Acetate (7l). White solid, yield 76%;
1190
J. Med. Chem. 2021, 64, 1180−1196