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D. Zampieri et al. / Bioorg. Med. Chem. Lett. 24 (2014) 1021–1025
All new arylcarboxamide derivatives 2a–p have been synthe-
R1
sized starting from the commercially available 4-aminomethylpi-
peridine and acetaldehyde according to the pathway illustrated
in Scheme 1. A typical Shiff reaction led to the imine derivatives
3 which were further alkylated to the piperidine nitrogen atom
with benzyl chloride or 4-chlorobenzyl chloride to obtain interme-
diates 4 and 5, respectively. Subsequently, the Shiff bases were re-
duced with NaBH4 and the corresponding derivatives (6, 7)
acylated on the nitrogen atom of the secondary amine to afford
the final arylcarboxamide compounds 2a–p. All the derivatives
were obtained as hydrochlorides.
N
N
O
CH3
R2
R1= H, Cl
R2= H, Cl, CH3
1
The acetamide derivatives 1 were characterized by the presence
of chemical features matching the requirement of a 1 receptor 3D
Intriguingly, the presence of a furyl group and an unsubstituted
benzene (or an aromatic group bearing a small substituent as chlo-
rine atom) produced compounds 2m and 2p, gifted with the higher
r
pharmacophore model recently developed by our group.26 Briefly,
the two benzene rings map two hydrophobic aromatic pharmaco-
phore features, the piperidine basic nitrogen fits the positive ioniz-
able model site, the carbonyl oxygen of the acetamide group
overlaps the hydrogen bond acceptor feature and, lastly, the small
substituents at the para position of the benzyl moiety linked to the
basic nitrogen atom (e.g., –Cl, –CH3, or –H) match the last hydro-
phobic feature of the pharmacophore model. Accordingly, a 3D
pharmacophore model mapping of compound 1 (R1 = Cl, R2 = H) re-
r
1-R affinity (Ki(r1) = 21.2 and 13.6 nM) and the best selectivity
(Ki( 2)/Ki( 1) >140 and >40, respectively) of the series.
r
r
In general, all compounds showed very low r2 affinities, with
values ranging from 270 up to 3000 nM (Table 2).
The decrease in r1 receptor affinity of the new arylcarboxa-
mides 2a–p with respect to the acetamide derivatives 1 was ratio-
nalized via a well-validated computational approach based on the
3D-pharmacophore model26 and the 3D homology model25 for r1
receptor recently developed by our group. Although compounds
2a–p possess the typical chemical functions required for binding
sulted in predicted affinity for the
agreement with the corresponding experimental value (Ki(-
1) = 1.87 nM).26 Based on this encouraging result, a number of
r1-R of 1.04 nM, in excellent
r
the
r1 protein, the introduction of a bulkier substituent at the car-
other variously substituted derivatives 1 were synthesized, some
of which were indeed found endowed with high r1 affinity.
On the spur of this favorable result, and with the twofold aim of
(i) designing a second generation of stronger r1 binders and (ii)
understanding the effect of the aromatic portions of the original
molecular scaffold (compound 1) on r1 affinity, we went further
and replaced the substituted benzyl moiety linked to the acetam-
ide group by a small ethyl chain while the acetyl residue was con-
verted into a number of aroyl moieties, ultimately yielding the new
derivatives 2a–p (Table 1).
boxamide moiety results in a suboptimal mapping of the pharma-
cophore features onto the 3D pharmacophore model in comparison
with the lead compounds 1, as showed in Figure 1.
We see that, while all chemical groups of 1 (R1 = Cl, R2 = H) per-
fectly overlay the corresponding features of our 3D pharmacophore
model, the different orientation assumed by the oxygen atom of
derivatives 2f and 2p results in an imperfect fit of the H-bond
acceptor feature which, in turn, negatively influences the mapping
of the hydrophobic features by their proximal aromatic portion. On
the other hand, the original N-benzylpiperidine scaffold still as-
sumes the conformation required for an apt positioning of the
remaining chemical groups onto the corresponding pharmaco-
phoric features (Fig. 1). Taking again compounds 2f and 2p as a
proof-of-concept, further details of the interactions of compounds
N
R
N
Ary
O
2a–p with the
r1 receptor were gathered from extensive MM/PBSA
molecular dynamics (MD) simulations25,27 performed on the corre-
sponding compound/protein complexes, as shown in Table 3.
According to our predictions the two molecules show quite dif-
2a-p
R= H, 4-Cl
Ary= Ph, 4-ClPh, 4-CH3Ph, 4-OCH3Ph,
1-Naphtyl, 2-Naphtyl, 2-Furyl
ferent affinities towards the receptor, as
mol for 2f and
Gbind = À10.95 0.31 kcal/mol for 2p, respectively.
Importantly, the corresponding 1Ki,calc values nicely compare
with the affinity values experimentally tested toward the 1 recep-
D
Gbind = À9.09 0.29 kcal/
D
r
r
tor (220 nM vs 155 nM for 2f, and 9.4 vs 13.6 nM for 2p). The
deconvolution of the total free energy of binding into its different
Table 1
contributions (Table 3) reveals that the solvation (
DGSOL) and the
Compds
R
Ary
Yield (%)
mp (°C)
C H N
entropic (ÀT
D
Sbind) terms for these two compounds are similarly
unfavorable, a result somewhat expected since 2f and 2p are very
similar from a structural viewpoint. The difference in r1 affinity
between the two compounds hence stems mainly from the more
favorable enthalpic contribution exhibited by the furyl-substituted
2a
2b
2c
2d
2e
2f
2g
2h
2i
2j
2k
2l
2m
2n
2o
2p
H
H
H
H
–Ph
4-Cl-Ph
4-CH3-Ph
1-Naphtyl
2-Naphtyl
–Ph
77
73
85
89
96
74
47
70
61
87
76
92
64
86
74
59
80–84
76–80
108–112
94–98
90–94
126–130
140–144
120–124
75–78
110–114
104–108
94–97
C
C
22H29ClN2O
22H28Cl2N2O
C23H31ClN2O
C
C
C
C
26H31ClN2O
26H31ClN2O
22H28Cl2N2O
22H27Cl3N2O
H
2p (
tive 2f (
This difference in the enthalpically-driven affinity of 2f and 2p
for the 1-R was further investigated by performing a per residue
D
Hbind = À36.06 kcal/mol) with respect to the phenyl deriva-
4-Cl
4-Cl
4-Cl
4-Cl
4-Cl
4-Cl
H
H
H
4-Cl
4-Cl
D
Hbind = À34.04 kcal/mol).
4-Cl-Ph
4-CH3-Ph
4-OCH3-Ph
1-Naphtyl
2-Naphtyl
–Ph-4-Ph
2-Furyl
4-OCH3-Ph
–Ph-4-Ph
2-Furyl
C23H30Cl2N2O
C23H30Cl2N2O2
C26H30Cl2N2O
r
binding free energy decomposition, as detailed in Figure 2.
As well illustrated in Figure 2A, both molecules assume a simi-
lar binding pose within the receptor binding site. Similarly to the
previously reported acetamide derivatives 1, the N-chlorobenzylpi-
peridine moiety satisfies two important pharmacophore require-
ment: (1) a polar interaction via a salt bridge between the
piperidine –NH+ atom and the side chain of Asp126 (Fig. 2B),
C
C
C
26H30Cl2N2O
28H33ClN2O
20H27ClN2O2
86–90
88–92
106–110
82–85
C23H31ClN2O2
C28H32Cl2N2O
C
20H26Cl2N2O2
Characterization of derivatives 2a–p.