Selectivity profiling of novel indene H1-antihistamines for the treatment of insomnia

Article abstract of DOI:10.1016/j.bmcl.2010.02.055

A series of indene analogs of the H₁-antihistamine (-)-R-dimethindene was evaluated for selectivity in the search for potentially improved sedative-hypnotics. Variation of the 6-substitutent in the indene core in combination with a pendant electron rich heterocycle led to the identification of several potent H₁-antihistamines with desirable selectivity over CYP enzymes, the M₁ muscarinic receptor and the hERG channel. These compounds were candidates for further ADME profiling and in vivo evaluation.

Full text of DOI:10.1016/j.bmcl.2010.02.055

Bioorganic & Medicinal Chemistry Letters 20 (2010) 2629–2633
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Selectivity profiling of novel indene H1-antihistamines for the treatment
of insomnia
*
Bin-Feng Li, Wilna J. Moree , Jinghua Yu, Timothy Coon, Said Zamani-Kord, Siobhan Malany, Kayvon Jalali,
Jianyun Wen, Hua Wang, Chun Yang, Samuel R. J. Hoare, Robert E. Petroski, Ajay Madan, Paul D. Crowe,
*
Graham Beaton
Neurocrine Biosciences, 12780 El Camino Real, San Diego, CA 92130, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of indene analogs of the H1-antihistamine (À)-R-dimethindene was evaluated for selectivity in
the search for potentially improved sedative-hypnotics. Variation of the 6-substitutent in the indene core
in combination with a pendant electron rich heterocycle led to the identification of several potent H1-
antihistamines with desirable selectivity over CYP enzymes, the M1 muscarinic receptor and the hERG
channel. These compounds were candidates for further ADME profiling and in vivo evaluation.
Ó 2010 Elsevier Ltd. All rights reserved.
Received 12 January 2010
Revised 10 February 2010
Accepted 11 February 2010
Available online 18 February 2010
Keywords:
H1 receptor
H1-antihistamine
Insomnia
Indene
Histamine
SAR
First generation H1-antihistamines are sedating and are used in
over-the-counter sleep aids. These agents are functional antago-
nists of muscarinic receptors,1 a property thought to cause unde-
sirable side effects such as dry mouth, blurred vision,
constipation, tachycardia, urinary retention, and memory defi-
cits.2,3 Next-day impairment has also been observed with these
compounds, presumed to result from protracted CNS exposure.4,5
Thus, selective H1-antihistamines with appropriate duration of
CNS exposure may provide an alternative to current medications
for the treatment of insomnia.
liability for drug interactions, heterogeneity of CYP2D6 activity
within the general population raised the concern of extreme vari-
ability in pharmacokinetics for candidate compounds.8
PK variability in lead compounds was considered a significant
issue because of the potential for varying exposures to adversely
impact duration of action.
In this Letter we describe initial SAR around indene 4. The
objective of this work was to identify analogs of 2 and 3 that re-
tained suitable selectivity profiles to justify further metabolism
and pharmacokinetic profiling. It has been reported that substitu-
tions in the 6-position of the indene core are accommodated with-
in the H1 pharmacophore.9 Our previous studies also indicated the
requirement for a heteroaryl moiety in the substructure 4 to confer
selectivity versus CYP2D6 inhibition.7 We therefore elected to eval-
uate the effects of substituents in the 6-position of the indene core
in conjunction with substitutions of the heteroaryl moiety with
and without the presence of a chiral center (R2 = Me or H). Substi-
tutions at the 6-position would be anticipated to improve meta-
bolic stability and potentially modulate the biotransformation
pathways encountered as an issue for the CYP2D6 substrates 2
and 3. From our previous work modification of the heteroaryl moi-
ety and chiral center would be expected to further modify the
overall PK profile of candidate compounds.7.
Previously, we described the use of the selective (À)-R-dimeth-
indene6 as a starting point to generate novel selective and brain pe-
netrating H1-antihistamines with an improved pharmacokinetic
7
profile suitable for use as night-time sleep aids. In addition to
the benzothiophene 1 (Fig. 1) that was selected for clinical evalua-
tion, indenes 2 and 3 were discovered with suitable receptor selec-
tivity and demonstrated effects on NREM sleep in rats. However,
metabolism studies in human liver microsomes (HLM) of 2 and 3
demonstrated that the major portion of metabolism occurred at
the 6-position of the indene core via the CYP2D6 pathway (Supple-
mentary data). The characterization of these compounds as pre-
dominant CYP2D6 substrates presented two issues. Besides a
To achieve similar selectivity to that described earlier,7 candi-
date compounds were required to demonstrate high H1 binding
affinity (Ki <10 nM) with at least 100-fold binding selectivity
* Corresponding authors. Tel.: +1 858 336 4479 (W.J.M.); +1 858 337 1801 (G.B.)
E-mail addresses: wilna.moree@gmail.com (W.J. Moree), beaton.graham@gmail.
com (G. Beaton).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.02.055

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B.-F. Li et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2629–2633
Scheme 2. Reagents and conditions: (a) LDA, THF, 0 °C; (b) 20% HCl, reflux; (c)
Chiral separation by chiral HPLC or SFC.
Figure 1. Benzothiophene candidate (1), indene leads (2) and (3) from (À)-R-
dimethindene, and series (4) described in this Letter.
versus the representative muscarinic M1 receptor. Selectivity of the
order of 1000-fold was deemed acceptable for CYP enzyme inhibi-
tion. It is well known that several antihistamines are potent inhib-
itors of the hERG channel10 implicated in prolongation of cardiac
QTc and leading to cardiac arrhythmias. Although benzothiophene
1 had shown weak hERG channel inhibition (hERG IC50/H1 Ki selec-
tivity of 3367), in vivo characterization indicated an absence of car-
diovascular risks and safety margins significantly higher than
previous guidelines for the assessment of hERG inhibitors.10a Based
on these data we reasoned that hERG IC50/H1 Ki selectivity of 400 or
greater would be acceptable for candidate compounds.
Compounds were evaluated for H1 binding affinity, selectivity
versus M1 and inhibition of CYP2D6 and CYP3A4.7 We also
screened compounds in this series against hERG, initially using a
high-throughput dofetilide binding assay, followed by hERG chan-
nel current (patch clamp) analysis for the more promising
candidates.7
Various synthetic schemes were employed to generate indenes
(4) (Schemes 1–4). Indanone 5 was converted to 6 in either a single
step by alkylation with N,N-dimethyl-2-chloroacetamide or by a
four step process using a condensation with glycolic acid followed
by a reduction with Zn in acetic acid, acyl chloride formation and
an amide coupling. Simultaneous reduction of the amide and ke-
tone functionality in 6 with LiAlH4 to alcohol 7 was followed by
oxidation with benzophenone to indanone 8 or acid mediated
dehydration to give indene 9.
The lithium salts from various alkyl heteroaryls, generated by
treatment of alkyl heteroarenes with LDA, were added to indanone
8, followed by an acid mediated dehydration to afford indenes 10–
13. When R2 was a methyl group, the enantiomers were separated
by chiral HPLC or SFC. By analogy to (À)-R-dimethindine (1),6 the
(À) enantiomers (3, 14) were used for biological profiling.
Scheme 3. Reagents and conditions: (a) (i) n-BuLi, THF, À78 °C; (ii) BrCH(Me)CN,
À78 °C to rt; (b) iPrNH2, (NH4)2S, H2S, DMA, 60 °C or S@P(OEt)2S, HCl(g); (c) R3 = H:
BrCH2CH(OEt)2, concd H2SO4, dioxane/EtOH; R3 = Me:CH3COCH2Cl, EtOH, 80 °C; (d)
Chiral separation by chiral HPLC or SFC.
Indenes 4, containing a thiazole moiety were synthesized
using two different routes (Schemes 3 and 4). Alkylation of in-
dene 9 with 2-bromopropionitrile yielded nitrile 15. Conversion
of 15 to the corresponding thioamide 16 was followed by cycliza-
tion to thiazole 17. Enantiomers 18 were separated by chiral
HPLC or SFC.
When R1 was not hydrogen, alkylation of 9 not only generated
the desired R1 6-substituted indenes 15 but also the 5-substituted
regioisomers, which were difficult to separate. Therefore another
synthetic route (Scheme 4) was employed, using direct alkylation
of indanone 8 with the lithium salt of 2-ethyl-5-trimethylsilanyl-
Scheme 1. Reagents and conditions: (a) LDA, N,N-dimethyl-2-chloroacetamide, THF, À78 °C; (b) Glycolic acid (40% in H2O), concd H2SO4, dioxane, reflux; (c) Zn, HOAc, H2O,
100 °C; (d) (COCl)2, cat. DMF, DCM; (e) HNMe2, Et3N, DCM; (f) LiAlH4, THF, 0 °C; (g) Ph2CO, t-BuOK, benzene, reflux; (h) Concd HCl in HOAc, reflux.

B.-F. Li et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2629–2633
2631
Scheme 4. Reagents and conditions: (a) (i) n-BuLi, THF, À50 °C; (ii) 8; (b) 20% HCl, reflux; (c) aq HF in CH3CN; (d) Chiral separation by chiral HPLC or SFC.
Table 1
SAR of indenes with different heteroaryl groups
R2
H
HetAr
H1 Ki (nM)
M1 Ki (
lM)
CYP2D6c IC50
6.8
(
lM)
hERGd,e IC50
(lM)
a
b
Compd
N
2
4.0 0.3
19
5.4
N
N
N
11a
H
12
1
>10
6.0
NTf
N
11b
11c
H
H
63 30
>10
>10
22
NT
NT
N
N
35
3
3.2
N
OMe
N
11d
12a
H
H
2.2 0.5
7.7 1.5
15
17
0.9
7.6
NT
N
>10
N
N
N
N
13a
3
H
15
3
>10
20
>10
51
NT
1.4
N
N
Me
1.3 0.1
1.0 0.1
N
OMe
14a
Me
3.7
17
7.6
N
S
18a
18b
Me
Me
0.8 0.1
3.1 0.4
2.4
3.6
3.8
3.7
1.9
N
S
>10
N
a
b
c
d
e
f
Ki values derived from dose–response curves generated from triplicate or more data points.
Ki values derived from dose–response curves generated from duplicate data points.
CYP3A4 IC50 >10 lM for all compounds tested.
hERG patch clamp assay.
In hERG dofetilide binding assay all compounds had Ki >3
NT = not tested.
lM.
thiazole (19)11 followed by acid treatment to generate indene 20.
Aqueous HF mediated removal of the TMS group and subsequent
chiral HPLC or SFC gave the desired (À) enantiomers 21.
binding and was >1000-fold selective over M1, the CYP enzymes
tested, and the hERG channel. Incorporation of a methyl substitu-
ent at various positions in the pyrazine ring (11a–c) decreased
H1 affinity. In contrast, a 3-methoxy substituent (11d) demon-
strated similar H1 affinity compared to 2 with a slightly improved
selectivity profile versus M1 and hERG. However CYP2D6 inhibition
Effects of changes to the heteroarene and chiral center in the
absence of 6-substitution are shown in Table 1. Achiral indene 27
containing an unsubstituted 1,4-pyrazine, displayed potent H1

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B.-F. Li et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2629–2633
was increased to unacceptable levels. Alternative heterocyclic isos-
teres such as the pyridazine (12a) and pyrimidine (13a) had less
binding affinity for H1, although their selectivity profile was
acceptable. To increase H1 affinity and selectivity, a chiral center
was incorporated into the compounds with the most promising
profiles. Indeed, 3 and 14 demonstrated higher H1 binding affinity
than the achiral analogs 2 and 11d, improved selectivity versus
CYP2D6 inhibition, and comparable selectivity versus M1 and
hERG. Incorporation of the pyridine isostere, thiazole (18a),
provided a compound with sub-nanomolar H1 affinity and >2000
selectivity over the anti-targets screened. Addition of a methyl
group to the thiazole ring (18b) decreased H1 affinity, as was
observed for the 1,4-pyrazine series, although an acceptable
selectivity profile was maintained.
In initial studies, chlorine, fluorine, methoxy, and methyl sub-
stituents in the 6-position of the indene core were investigated
to explore the effects on both H1 affinity and selectivity, especially
with respect to the hERG channel. Comparisons were made with
the previously described achiral indenes shown to give the best
affinity and selectivity profile. (Table 2).
We previously demonstrated that chiral analogs were generally
more selective with a marginal increase in H1 affinity. Based on
these observations we decided to incorporate the chiral center to
improve H1 affinity in the less active 6-substituted indene core
(methoxy, methyl) and improve selectivity in the more active 6-
fluoro substituted indene core. The 6-chloro substituted indene
core was abandoned due to irreconcilable high hERG inhibition
(Table 3).
Introduction of a chiral center was a successful strategy for
improving H1 affinity and selectivity of 6-methyl and 6-methoxy
substituted indenes (14b and 14c), compared to the achiral analogs
(11g and 11h). 6-Methoxy substituted indenes indicated a trend to
improved hERG selectivity compared to the corresponding 6-
methyl indenes (comparisons of 14b–14c, 14d–14e and 21b–21c)
although 14d retained good selectivity for the channel. A similar
trend was observed for the achiral pair 11g and 11h. In the case
of analogs 14c–f and 21c, hERG selectivity was greater than
1000-fold versus H1. In general, the 3-methoxypyrazine moiety
led to comparable H1 affinity and improved hERG selectivity com-
pared to the corresponding pyrazine analogs (comparisons of 14b–
14d, 14c–14e, 14a–3). CYP2D6 inhibition in the methoxypyrazine
analogs was increased although the selectivity for these com-
pounds was still acceptable [CYP2D6 IC50/H1 Ki >1000]. Introduc-
tion of a chiral center appeared to be a general approach for
maintaining selectivity versus CYP2D6 inhibition in the 6-substi-
tuted series with the 3-methoxypyrazine feature (14d–f). While
the 3-methoxypyrazine contributed to significant CYP2D6 inhibi-
tion in achiral 6-fluoro indene (11l), this liability was removed in
the corresponding chiral analog (14f).
Methyl and methoxy groups (11g, 11h) led to a decrease in H1
affinity while the selectivity profile for M1 and CYP2D6 inhibition
was maintained. Methyl substitution (11g) led to a significant in-
crease in hERG potency. Electron-withdrawing chlorine and fluo-
rine substituents (11i, 11j) increased H1 binding, but also
significantly increased hERG inhibition. This effect was more pro-
found for chlorine than fluorine. Increases for hERG potency were
attributed to relative increases in hydrophobicity (substituent con-
tribution to clog P: chlorine > methyl > fluorine > methoxy, hydro-
gen12).
A
reduction in electron density to the indene also
The 6-fluoro indene in combination with the thiazole group
(21a) retained H1 binding affinity but increased hERG inhibition
relative to the thiazole analog with the unsubstituted indene core
(18a). A similar effect of the 6-fluoro substituent had been ob-
served for the pyrazine pair 2 and 11j. In contrast, 6-methoxy in-
dene 21c provided an excellent overall screening profile with
>10,000-fold selectivity over the hERG channel.
appeared to contribute to increased hERG activity. Despite these
observations, some compounds from the 6-fluoro series (11j and
12c) passed our in vitro criterion for hERG selectivity (hERG IC50
/
H1 Ki >400). Notably, the methoxy substituent in the pyrazine moi-
ety of 6-fluoro and 6-chloro substituted indenes (11k and 11l)
caused a significant increase in CYP2D6 inhibition compared to
11i and 11j. This phenomenon was also observed in the unsubsti-
tuted indene core (11d compared to 2).
These observations demonstrated that a desirable profile with
potent H1 binding and selectivity over hERG could be achieved
Table 2
Effect of R1 substituent in various indenes without a chiral center on H1 binding affinity and selectivity
R1
R3
H1 Ki (nM)
CYP2D6c,d IC50
(lM)
hERGc,e Ki (
l
M)
hERGf IC50
(lM)
a,b
Compd
2
11g
11h
11i
11j
11k
11l
H
H
H
H
H
4.0 0.3
11.9 0.5
8.9 0.6
1.4 0.3
1.4 0.3
1.5 0.4
0.8 0.2
2.1 0.3
1.7 0.2
6.8
6.6
5.3
36
>3.0
>3.0
>3.0
1.4
0.95
1.3
>3.0
0.38
>3.0
5.4
0.52
2.1
0.11
0.59
0.23
NTg
0.22
0.89
Me
OMe
Cl
F
Cl
F
H
15
OMe
OMe
H
0.69
0.32
12
12b
12c
Cl
F
H
12
a
b
c
d
e
f
Ki values derived from dose–response curves generated from triplicate or more data points.
M1 Ki >10 M for all compounds except 11k (Ki = 2.0 M).
Ki values derived from dose–response curves generated from duplicate data points.
CYP3A4 IC50 >10 M for all compounds tested.
hERG dofetilide binding assay.
hERG patch clamp assay.
NT = not tested.
l
l
l
g

B.-F. Li et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2629–2633
2633
Table 3
H1 binding affinity and selectivity of (À)-enantiomers with different R1 and heteroaryl groups
R1
R3
H1 Ki (nM)
CYP2D6c IC50
(lM)
hERGd Ki (
lM)
hERGe IC50
(lM)
a,b
Compd
14b
14c
14d
14e
14f
21a
21b
21c
Me
OMe
Me
OMe
F
H
H
OMe
OMe
OMe
—
4.2 1.1
3.1 0.4
2.7 0.3
1.3 0.1
0.7 0.1
0.3 0.1
2.2 0.2
2.5 0.1
22
12
11
1.9
6.4
1.0
1.4
5.6
5.1
>3
>3
>3
>3
1.2
>3
>3
0.36
3.4
3.8
5.0
1.8
NTf
0.62
22
F
Me
OMe
—
—
a
b
c
d
e
f
Ki values derived from dose–response curves generated from triplicate or more data points.
M1 Ki >10 M for all compounds except 21a (Ki = 3.5 M).
CYP3A4 IC50 >10 M for all compounds tested.
hERG dofetilide binding assay.
hERG patch clamp assay.
NT = not tested.
l
l
l
through the right balance between electron rich heterocycles,
the presence of a chiral center and 6-substitution in the indene
core.
References and notes
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3. Meoli, A. L.; Rosen, C.; Kristo, D.; Kohrman, M.; Gooneratne, N.; Aguillard, R. N.;
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Sukenik, E.; Harris, A. G. Arch. Intern. Med. 1997, 157, 2350.
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466.
In summary, detailed SAR around our lead indene 2 led to the
identification of several compounds with potent H1 affinity and
>1000-fold selectivity over M1, CYP2D6, and hERG. Optimization
of the 6-substituent in the indene core was required with each het-
erocycle to obtain the most beneficial balance between H1 affinity
and selectivity over the hERG channel. A chiral center typically led
to a small increase in H1 affinity and overall selectivity improve-
ment but was not always required to obtain the desired profile.
Numerous compounds with an acceptable in vitro profile were
identified. Additional metabolism studies and further selectivity
profiling, followed by in vivo evaluation of a subset of these com-
pounds led to the identification of our clinical backup compound.
These studies will be the subject of our next communication.
Acknowledgments
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The authors wish to thank John Harman, Shawn Ayube and
Chris DeVore for analytical support. Dr. Tao Hu and Mila Lagman
for chiral separations and Dr. John Saunders, Dr. Paul Conlon, and
Dr. H. Bozigian for program support.
11. 2-Ethyl-5-trimethylsilanyl-thiazole (19) was prepared by treatment of 2-ethyl-
thiazole with n-BuLi in THF at À50 °C for 30 min followed by addition of TMSCl
at À50 °C. The reaction was allowed to warm to room temperature prior to
workup.
12. Calculated using ACD/Log P and pKa DB, version 9.02, Advanced Chemistry
Development, Inc., Toronto, ON, Canada.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.bmcl.2010.02.055.