Refinement of histamine H3 ligands pharmacophore model leads to a new class of potent and selective naphthalene inverse agonists

Article abstract of DOI:10.1016/j.bmcl.2008.06.062

The refinement of our original five point pharmacophore model for the H₃ receptor with the addition of a new acceptor feature is presented. The importance of this new acceptor feature for the binding and the selectivity against H₁, H₂ and H₄ has been validated using a newly synthesized naphthalene series. With the SAR deduced from several hundred naphthalene derivatives in various sub-classes the specific role of each pharmacophoric feature, by varying the geometry, size and charge of the molecules, was elucidated. This led to the discovery of a highly potent and selective new compounds series.

Full text of DOI:10.1016/j.bmcl.2008.06.062

Bioorganic & Medicinal Chemistry Letters 18 (2008) 4377–4379
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Refinement of histamine H3 ligands pharmacophore model leads to a new
class of potent and selective naphthalene inverse agonists
*
Olivier Roche, Matthias Nettekoven , Walter Vifian, Rosa Maria Rodriguez Sarmiento
F. Hoffmann-La Roche Ltd., Pharmaceutical Research Basel, Discovery Chemistry, CH-4070 Basel, Switzerland
a r t i c l e i n f o
a b s t r a c t
Article history:
The refinement of our original five point pharmacophore model for the H3 receptor with the addition of a
new acceptor feature is presented. The importance of this new acceptor feature for the binding and the
selectivity against H1, H2 and H4 has been validated using a newly synthesized naphthalene series. With
the SAR deduced from several hundred naphthalene derivatives in various sub-classes the specific role of
each pharmacophoric feature, by varying the geometry, size and charge of the molecules, was elucidated.
This led to the discovery of a highly potent and selective new compounds series.
Received 3 June 2008
Revised 17 June 2008
Accepted 18 June 2008
Available online 21 June 2008
Keywords:
Histamine H3 receptor
SAR
Ó 2008 Elsevier Ltd. All rights reserved.
Pharmacophore model
Naphthalene
GPCR
To date four distinct histamine receptors are known.1 They be-
long to the family A of G-protein coupled receptors and are in-
volved in the regulation of various pharmacological processes.
The H1 and H2 receptors are clinically validated targets. H1 receptor
antagonists are used for the treatment of allergies and sleep disor-
ders,2 whereas H2 receptor antagonists serve as agents for the
treatment of the peptic ulcer disease.3 More recently, H3 ligands
have advanced to clinical phase trials for the treatment of CNS dis-
orders like migraine, narcolepsy, attention-deficit hyperactivity
disorder and Alzheimer’s dementia.4 However, H3 ligands might
also be useful to control food-intake and obesity.5 H4 receptor ago-
nists and antagonists are less well studied. Nevertheless, due to
their preferred expression in T-cells, dendritic cells, monocytes
and mast cells, it is likely that H4 receptors are involved in the reg-
ulation of the immune responses.6
Many of the first generation H3 receptor antagonists contained
an imidazole moiety which is structurally close to the natural li-
gand histamine but carry a potential liability towards cyto-
chrome-P450 interaction.7 The second generation H3 receptor
antagonists are devoid of an imidazole moiety, but contain one
or even two basic nitrogens, and several compounds of this class
are currently being developed and recently entered human clinical
trials.4
novo initiative described previously.8 At the time, the model con-
sisted of two aromatics, two positively charged features and one
central electron rich features (Fig. 1a). The observation that many
ligands (Fig. 2) displayed an acceptor functionality in close vicinity
to the largest aromatic feature led to the refinement of our existing
model (Fig. 1b).
In parallel to this ligand-based approach, a homology model
has been built based on the bovine rhodopsin template using
the software MOE in order to discover the potential amino acids
interacting with our features (data not shown).11 From the spa-
tial distribution of our pharmacophore, we identified the same
residues than the ones described in the work of B. Schlegel. et
al., meaning an interaction between the distal basic nitrogen
and the conserved aspartate in helix 3 (ASP3.32),12 but more
interestingly, we also identified an interaction between the
new acceptor position and the Threonine 6.52, which is specific
to H3.13
This newly in-house established pharmacophore model served
for the prioritization of all proposals for new chemical series. From
the many ideas filtered by the pharmacophore model, naphthalene
derivatives were investigated first. Isomeric naphthalenes with an
oxygen-atom linker 3 and 4 were pursued. The pharmacophore
model predicted a much better fit for the 2-naphthoic amide deriv-
atives 3 than the respective 1-naphthoic amide derivatives 4. To
verify this hypothesis both compound series were synthesized.
Also, naphthalene derivatives with a nitrogen linker-atom 7 (of
which only the 4-amino-piperidine derivatives are shown as exam-
ple) have been synthesized to support the pharmacophore model
validation. For each naphthalene derivative 3, 4 and 7, a straight-
As part of our strategy to develop new and potent H3 receptor
inverse agonists, we refine and apply the five features pharmaco-
phore model that has been validated with the results of the de
* Corresponding author. Tel.: +41 61 6886227; fax: +41 61 6886459.
E-mail address: matthias.nettekoven@roche.com (M. Nettekoven).
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.06.062

4378
O. Roche et al. / Bioorg. Med. Chem. Lett. 18 (2008) 4377–4379
Electron rich/Acceptor
Aromatic/lipophilic
New acceptor
Positively charged
Figure 1. (a) Pharmacophore model used with the de novo approach (b) New pharmacophore model used in this study with FUB 836 fitted.9
O
N
N
O
H
R
N
O
O
N
N
ABT-239
hH3R Ki: 4 nM
A-349821
hH3R Ki: 12 nM
FUB 836
hH3R Ki: 0.5 nM
O
N
NC
Figure 2. Representative set of potent H3 receptor antagonists displaying the new acceptor feature (red circle).10
forward two-step chemistry route was devised giving access to a
variety of compounds (Scheme 1).
nano-molar range, whereas in comparison the respective isomers
4a–4c were in general markedly less active. This was in agreement
with the prediction from the pharmacophore model and validated
our ligand-based approach. Also in comparison to compounds 3a–
3c, nitrogen-atom linked naphthalenes 7a–7c were generally
found to be only active in the micro-molar range. We could observe
here an important shift in activity between the oxygen-atom
linked naphthalene 3b and the nitrogen-atom linked naphthalene
7a. These two types of linkers have a small influence on the confor-
mation of the molecule and a moderate influence on the electronic
properties, but they interact quite differently with the receptor. In-
deed, knowing that the ether-oxygen is electron rich but a poor
acceptor, whereas the amine-nitrogen is a strong donor, and addi-
tionally looking at the homology model, it is very likely that this
The commercially available isomeric 6-hydroxy-naphthoic
acids 1 (6-hydroxy-1-naphthoic and 6-hydroxy-2-naphthoic) were
converted to their respective amides 2 by coupling with the appro-
priate amine and TBTU as the coupling reagent. Final conversion to
naphthalene derivatives 3 and 4 was achieved using a Mitsunobu
coupling protocol employing polymer-bound tri-phenyl phosphine
which allowed, after filtration, for easy purification by preparative
HPLC on reversed phase. Conversely, 6-amino-naphthoic acid 5
was first converted by reductive amination with 1-isopropyl-
piperidin-4-one and sodium tri-acetoxyborohydride to 6-(1-
isopropyl-piperidin-4-ylamino)-naphthalene-2-carboxylic acid
methyl ester 6, which was subsequently converted to naphthalene
derivatives 7 by saponification and coupling of the resulting acid
derivative with the appropriate amines under TBTU conditions.
Several hundred compounds in various sub-series have been syn-
thesized and tested for their binding activity towards the H3 recep-
tor.14 To illustrate the general structure activity trend, a few
compounds and their human binding affinity data are shown in
Figure 3.
ether oxygen has
a positive interaction with the sulfur of
CYS3.36, which the nitrogen cannot have.15 As can be seen from
Figure 4, naphthalene derivative 3b, optimized with AM1 in
MOE, fits perfectly the pharmacophore model using the new accep-
tor position. Since the binding is strongly driven by the interaction
between the basic amine and ASP3.32, it restrains the number of
possible fits. Distance-wise, the carbonyl function of the naphtha-
lene can only match the new acceptor feature (THR6.52). More-
over, compound 3c shows a very nice selectivity against all the
other histamine subtypes by displaying less than 25% inhibition
Naphthalenes 3a–c showed the highest potency in binding to-
wards the H3 receptor (functionally characterized as inverse ago-
nists by GTPcS assay, exemplified with 3c; EC50 = 21 nM) in the
R1
N
O
R2
O
O 1
O
R1
R1
1
1
HO
N
N
b)
a)
2
2
R2
2
R2
R3
R3
O
O
OH
OH
1
2
3
4
O
O
O
R1
MeO
N
N
N
d)
c)
HO
R2
N
N
NH2
H
H
5
7
6
Scheme 1. Reagents and conditions: (a) 1.2 equiv TBTU, 1.2 equiv HNR1R2, DMF, DIPEA. (b) 1.2 equiv R3-OH, 2 equiv di-tert-butyl azodicarboxylate, polymer bound TPP, THF.
(c) 1.2 equiv 1-isopropyl-piperidin-4-one, NaBH(OAc)3, THF. (d) 1—LiOHÁH2O, THF, H2O, 2—1.2 equiv TBTU, 1.2 equiv HNR1R2, DMF, DIPEA.

O. Roche et al. / Bioorg. Med. Chem. Lett. 18 (2008) 4377–4379
4379
O
O
O
O
N
N
H
N
N
N
N
O
O
O
N
3a Ki: 4nM
3b Ki: 57nM
3c Ki: 87nM
O
O
N
N
N
N
N
H
O
N
N
N
H
H
H
4a 57%inhibition @3uM
4b 61%inhibition @3uM
4c 45%inhibition @3uM
H
N
O
N
O
N
O
N
N
O
O
O
N
7a 52%inhibition @3uM
7b 53%inhibition @3uM
7c 58%inhibition @3uM
Figure 3. Selected compounds and their binding activity towards the human histamine H3 receptor.14
Figure 4. Molecules 3b and 4b in the pharmacophore model.
at 3 l
M against H1, H2 and H4.16 This selectivity was expected from
the model since THR6.52 is only present in the H3 receptor sub-
type. On the other hand, the fit of the isomeric naphthalene deriv-
ative 4b in Figure 4 is far less good, and that was confirmed by the
experimental values (3b: Ki: 57 nM, 4b: 61% inhibition at 3 lM),
and more broadly by the SAR of both sub-series.
In conclusion, we have refined our original five point pharmaco-
phore model for the H3 receptor with the addition of a new accep-
tor. The importance of this new acceptor feature for the binding
and the selectivity against H1, H2 and H4 has been validated using
a newly synthesized naphthalene series. With the SAR deduced
from several hundred naphthalene derivatives in various sub-clas-
ses, we have been able to elucidate the specific role of each phar-
macophoric feature by varying the geometry, size and charge of
the molecules. This led to the discovery of a highly potent and
selective new compound series.
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It is with real pleasure that we wish to thank all our collabora-
tors whose contributions made the described work possible and so
enjoyable, especially Drs. Jean-Marc Plancher, Susanne Raab, Hans
Richter, Sven Taylor and Christoph Ullmer.
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