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to the Lennard-Jones energy (short-range) interaction energies be-
tween 16 (À252 1 kJ/mol) or 19 (À253 1 kJ/mol) and hH1R (Ta-
ble 2). Thus, the dynamic studies support the hypothesis that the
piperazine moiety disturbs the electrostatic interaction between
16 and hH1R. This difference in the short range coulomb interac-
tion is reflected by the experimentally determined pKi values of
16 and 19 at hH1R (Fig. 1A). However, during the molecular dy-
namic simulations, a stable hydrogen bond interaction could be de-
tected between the carbonyl moiety of 16 and Asn2.61 (Fig. 2).
Additionally, an aromatic interaction between the indole moiety
of 16 and Tyr2.64 was observed during the simulation (Fig. 2). In
compound 19, the amino moiety, suggested to interact with
Asp3.32 is flexible, analogous to mepyramine itself and in contrast
to compounds 16–18. Thus, the interaction between the amine
moiety and Asp3.32 can be established well. This is also confirmed
by the stronger electrostatic interaction between hH1R and 19,
compared to 16 (Fig. 2). However, the elongation of mepyramine
by the JNJ7777120 partial structure did not lead to an increased
affinity at hH1R, compared to mepyramine 1. Since there is a signif-
icant difference in affinity of 19 and 20 at hH1R, it may be sug-
gested, that the additional JNJ7777120 partial structure interacts
specifically with the hH1R. A stable hydrogen bond was detected
during the molecular dynamic simulation between the carbonyl
moiety of 19 and Thr182 (E2-loop) (Fig. 2). The exchange of the
piperazine moiety by a more flexible aminopyrrolidine moiety 26
leads only to a slight decrease in affinity at hH1R, compared to
16. The diphenhydramine—JNJ-hybrid compound 21, analogue to
the mepyramine—JNJ-hybrid compound 16, leads to a decrease in
affinity of about 1 log unit at hH1R, compared to diphenhydramine
3. For the analogoue astemizole–JNJ-hybrid compound 45, only a
slight decrease in affinity was observed at hH1R, compared to
astemizole 4. Thus, the introduction of a JNJ partial structure into
mepyramine and diphenhydramine leads to a stronger decrease
in affinity, compared to the corresponding H1 antagonists. In con-
trast, the JNJ–astemizole hybrid shows an affinity in the same
range as found for astemizole (Fig. 3). Compound 38 shows a sig-
nificant decrease in affinity at hH1R, compared to 19. In 38, the
JNJ partial structure is connected to mepyramine via the indole
moiety, whereas in 19, the JNJ partial structure is connected via
the piperazine moiety to mepyramine. Thus, this switch is sug-
gested to be responsible for the observed differences in affinity.
Compound 38 was obtained experimentally as racemate, but in
molecular modelling, both enantiomers were analyzed (Fig. 2).
Molecular dynamic simulations revealed a stable binding mode
for both enantiomers. The mepyramine partial structure (for both
enantiomers) is located in the same part of the binding pocket,
as already described for 16 or 19 and the positively charged amino
moiety of 38 (both enantiomers) interacts electrostatically with
Asp3.32. Molecular dynamic simulations revealed a stable hydrogen
bond interaction between the carbonyl moiety of 38 (R- and S-con-
figuration) and Trp7.40. For 38 (S-configuration), the carbonyl
Scheme 1. Structures of H1 (mepyramine, 1; diphenhydramine, 3; astemizole, 4)
and H4 (JNJ7777120, 2; JNJ-derivative, 5; JNJ-derivative, 6) receptor ligands.
the crystal structure 2RH1,14 analogue, as already described.15
A
comparison of our H1R homology model, refined by molecular dy-
namic simulations, with the recently published hH1R crystal16
showed no significant differences. The compounds 16, 19 and 38
were docked manually into the binding pocket of hH1R using the
software package SYBYL 7.0 (Tripos Inc.). Molecular dynamic sim-
macs.org), were performed, as already described.10 Ligand
parameterization was obtained from the PRODRG server (http://
productive phase in molecular dynamic simulations was per-
formed subsequent to a 1 ns equilibration phase.
The pharmacological and modeling data of reference com-
pounds and the new hybrid compounds are given in Tables 1–4.
For compounds 16 and 19, the experimental pharmacological data
are shown in Figure 1.
Compared to mepyramine, the affinity of compounds 16–18 is
significantly reduced of about 1.5–2 log units at hH1R. The intro-
duction of one chlorine atom in the indole moiety 17 leads to a
slight decrease in affinity to hH1R, compared to 16. The exchange
of the indole moiety 16 into a benzimidazole 18 leads to a decrease
in affinity at hH1R. For compound 19, an affinity comparable to that
of mepyramine 1 at hH1R could be observed. The introduction of
one chlorine atom on the corresponding position in the
JNJ7777120 partial structure 20 leads to a significant decrease in
affinity at hH1R, compared to 19. In compounds 16–18, the basic
nitrogen atom is embedded in a piperazine moiety, which shows
a higher rigidity than an ethylene spacer. This more voluminous
piperazine moiety is suggested to disturb the electrostatic interac-
tion between the positively charged amine and Asp3.32, leading to a
significantly decreased affinity. Based on the molecular dynamic
studies, a mean coulomb energy (short range) between 16 and
hH1R of about À157 1 kJ/mol was detected (Fig. 2). In contrast,
a coulomb energy (short range) of À197 1 kJ/mol was detected
between 19 and hH1R (Fig. 2, Table 2). Both interaction energies
are, according to a t-test, significant different to each other (p
<0.0001). In contrast, there is no significant difference with regard
moiety establishes an additional hydrogen bond to Asn2.61
.
Aromatic interactions between the indole moiety of 38 and the
receptor were not detected. However, both enantiomers showed
slight differences in conformation in its receptor bound state. The-
ses differences are reflected in the interaction energy between 38
and hH1R. Between the R enantiomer of 38 and hH1R, a coulomb
energy (short range) of À166 3 kJ/mol and a Lennard–Jones
energy (short range) of À285 2 kJ/mol was observed. In contrast,
between the S enantiomer of 38 and hH1R, a coulomb energy (short
range) of À241 2 kJ/mol and a Lennard–Jones (short range) of
À284 1 kJ/mol was observed (Table 2).
As shown in Table 2, a comparison of the calculated ligand-
receptor-interaction energies (C+LJ LR, Table 2) does not reflect
the observed pKi values of 16, 19 and 38. However, this observation
can be explained: During molecular dynamic simulations, the