A novel class of H3 antagonists derived from the natural product guided synthesis of unnatural analogs of the marine bromopyrrole alkaloid dispyrin

Article abstract of DOI:10.1016/j.bmcl.2009.04.106

This Letter describes the natural product guided synthesis of unnatural analogs of the marine bromopyrrole alkaloid dispyrin, and the resulting SAR of H₃ antagonism. Multiple rounds of iterative parallel synthesis improved human H₃ I

Full text of DOI:10.1016/j.bmcl.2009.04.106

Bioorganic & Medicinal Chemistry Letters 19 (2009) 3204–3208
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
A novel class of H3 antagonists derived from the natural product guided
synthesis of unnatural analogs of the marine bromopyrrole alkaloid dispyrin
J. Phillip Kennedy a,d, P. Jeffrey Conn b,c,d, Craig W. Lindsley a,b,c,d,
*
a Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
b Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
c Vanderbilt Program in Drug Discovery, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37232, USA
d Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
This Letter describes the natural product guided synthesis of unnatural analogs of the marine bromopyr-
role alkaloid dispyrin, and the resulting SAR of H3 antagonism. Multiple rounds of iterative parallel syn-
thesis improved human H3 IC50 ꢀ33-fold, and afforded a new class of H3 antagonists based on the novel
bromotyramine core of dispyrin.
Received 24 February 2009
Revised 22 April 2009
Accepted 23 April 2009
Available online 3 May 2009
Ó 2009 Elsevier Ltd. All rights reserved.
Keywords:
H3 antagonist
Dispyrin
Marine natural product
Alkaloid
The neurotransmitter histamine exerts its action through four
distinct Class A GPCRs (H1–H4).1–7 The histamine H3 receptor, a
Gi/o-coupled receptor in the CNS, is a pre-synaptic auto- and het-
eroreceptor that not only controls the release of histamine, but also
other neurotransmitters (acetylcholine, noradrenaline, dopamine,
GABA and serotonin).1–7 Preclinically, H3 antagonists/inverse ago-
nists have demonstrated efficacy in a number of CNS pathologies
including schizophrenia, epilepsy, depression, pain, decreasing
food intake, drug abuse and addiction, sleep disorders/narcolepsy
and cognitive enhancement.1–7 Early reference H3 antagonists con-
tained imidazole moieties, such as thioperimide 1 and Perceptin
(GT-2331) 2 (Fig. 1). Effort from multiple companies then focused
on non-imidazole H3 antagonists and include compounds such as
UCL 1972 3, ABT-239 4, JNJ’s 5, Novo Nordisk’s 6, Eli Lilly’s 7 and
GSK189254 8 to exemplify a few (Fig. 1). This intense effort from
the pharmaceutical industry led to the evolution of a refined H3
antagonist pharmacophore model 9.1–8
We recently completed the first total synthesis of dispyrin
10,9 a bromopyrrole alkaloid with a novel bromotyramine core,
isolated by Crews in 200710 from the marine sponge Agelas dis-
par (Fig. 2). Upon recognition that dispyrin 10 possessed the ba-
sic features of the refined H3 pharmacophore model 9, we
evaluated our synthetic dispyrin against the human H3 receptor.
Gratifyingly, dispyrin was found to have modest activity as an H3
antagonist (IC50 = 2.35 lM, Ki = 1.04 l
M).9 Based on these data,
we initiated a natural product guided synthesis effort, employing
iterative parallel synthesis11 for molecular editing, aimed at
improving H3 inhibition and binding; moreover, we wanted to
validate the marine natural product dispyrin 10 as a viable lead
molecule due to the novel scaffold providing intellectual prop-
erty in extremely crowded chemical space.
The first generation 25-member library was based on a 5 Â 5
two-dimensional design wherein the core was held constant and
the amide R1 and aminoalkyl moieties R2 varied (Scheme 1). The li-
brary synthesis began with a simple DIC amide coupling employing
commercially available 3-bromo-4-methoxyphenylethylamine 11
with one of five heterocyclic carboxylic acids R1. These five scaf-
folds were then treated with BBr3 to remove the methyl ether lib-
erating the free phenols 13. Each of the five phenols 13 was then
alkylated with one of five aminoalkyl chlorides to install R2 under
microwave-assisted conditions to afford unnatural dispyrin ana-
logs 14 (Table 1).
This first generation library was highly informative. In gen-
eral, all R1s and R2s afforded modestly potent (Kis and IC50s in
the low micromolar range) H3 antagonists. Potent H3 antagonists
(Kis < 200 nM, IC50s < 430 nM) resulted for all of the heterocyclic
amides R1 in combination with the ethyl pyrrolidinyl R2 (14c,
14h, 14m, 14r and 14w). In contrast, the ethyl morpholino cong-
eners (14d, 14i, 14n, 14s and 14x) were uniformly weak
(Kis > 12
lM, IC50s > 29 lM). The most potent H3 antagonist from
* Corresponding author. Tel.: +1 615 322 8700; fax: +1 615 343 6532.
E-mail address: craig.lindsley@vanderbilt.edu (C.W. Lindsley).
the first generation library was 14r (R1 = 4-bromo-thiophene,
0960-894X/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2009.04.106

J. Phillip Kennedy et al. / Bioorg. Med. Chem. Lett. 19 (2009) 3204–3208
3205
O
S
H
N
N
N
H
N
O
H
N
HN
HN
1, Thioperimide
2, GT-2331
3, UCL 2190
CN
N
O
CF3
N
O
N
O
N
N
O
4, ABT-239
5
6
N
O
NH
N
MeHN
N
O
O
7
8, GSK189254
Polar Group
(H-donor/acceptor)
Central
Core
Basic Nitrogen
Spacer
Basic Nitrogen
Lipophilic
residue
9, Refined H3 Pharmacophore Model
Figure 1. Imidiazole and non-imidazole H3 antagonists 1–8 leading to a refined H3 pharmacophore model 9.
the next library maintained R1 = 4-bromo-thiophene and sur-
veyed functionalized pyrrolidines at R2 (Scheme 2).
Following Scheme 1, a large quantity of 15 was prepared.
Then, the phenol was alkylated with 2-bromo-1,1-dimethoxy
ethane to provide 16, which was then converted to the corre-
sponding aldehyde 17 by treatment with tosylic acid. Finally,
Br
H
N
H
3 IC50
H3 Ki
Br
O
N
H
2.35 µM
1.04 µM
O
N
10, dispyrin
Figure 2. Dispyrin 10, a novel bromopyrrole alkaloid from Agelas dispar with a
bromotyramine core unprecedented in marine natural products.
Table 1
Structures and activities of dispyrin analogs 14
H
R1
N
Br
O
R2
H
O
H2N
Br
O
R1
N
Br
O
a
b
14
O
a
Compd
R1
R2
H3 Kia
(l
m)
H3 IC50 (lm)
11
12
Br
N
H
H
14a
14b
14c
1.04
1.61
0.19
2.35
3.72
0.43
R1
N
Br
OH
R1
N
Br
N
H
c
O
O
R2
O
N
13
14
Scheme 1. First generation library synthesis. Reagents and conditions: (a) R1COOH,
DIC, HOBt, DIEA, DCM, rt, 12 h (69–99%); (b) BBr3, DCM, À78 °C–rt, 1.5 h (50–95%);
(c) 1.3 equiv ClR2, CsCO3, KI, DMF, mw, 160 °C, 20 min (72–93%). All analogs purified
to >98% by mass-directed preparative HPLC.12
N
N
O
14d
14e
12.9
1.33
29.1
2.94
N
R2 = ethyl pyrrolidine) with
180 nM—a 13-fold improvement over the parent natural product
dispyrin 10 (IC50 = 2.35 M, Ki = 1.04 M). Based on these data,
a Ki of 80 nM and an IC50 of
(continued on next page)
l
l

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J. Phillip Kennedy et al. / Bioorg. Med. Chem. Lett. 19 (2009) 3204–3208
Table 2
Table 1 (continued)
Structures and activities of dispyrin analogs 18
Compd
R1
R2
H3 Kia
(l
m)
H3 IC50
(lm)
a
Br
N
14f
1.36
1.55
2.92
3.43
N
H
N
H
Br
O
S
14g
N
N
O
N
R1
14h
14i
0.15
26.4
0.38
59.2
18
a
O
Compd
R1
H3 Kia
(lm)
H3 IC50 (lm)
N
18a
18b
18c
18d
(S)-2-Me
(S)-2-Me
(S)-3-F
0.31
0.33
1.10
1.15
0.71
0.75
2.11
2.52
N
N
14j
1.52
3.63
(S)-3-F
a
Average of three independent determinations.
14k
14l
1.76
2.13
3.99
4.54
N
N
N
14m
14n
0.13
17.6
0.31
39.6
reductive amination employing a functionalized pyrrolidine and
MP-B(OAc)3H provided analogs 18. As shown in Table 2, analogs
18 were weaker H3 antagonists than 14r, and there was no evi-
dence of enantioselective inhibition (18a vs 18b). In agreement
with the H3 pharmacophore model, incorporation of b-fluorine
atoms such as in 18c and 18d, which lowers the pKa on the pyr-
rolidine nitrogen from 11 to 9, afforded diminished H3
inhibition.13
We then prepared two singleton compounds following the syn-
thetic route depicted in Scheme 1 with the appropriate substitu-
tions, wherein the bromine in 14r was replaced with a chlorine
19 and a truncated version 20 (Fig. 3). A twofold diminution in po-
tency was noted for 19, relative to 14r, and the truncated benzyl
version lost over 13-fold compared to 14r; however, this high-
lighted that the heavy bromine atom was not required for H3
inhibition.
The final library iteration was directed at surveying a wider
range of alternative amides (heterocycles and functionalized aro-
matic moieties) while holding the preferred ethyl pyrrolidine ether
and bromotyramine core constant. The synthesis began with 11
and conversion to the phthalimide congener 21. Standard BBr3
deprotection provided 22 which was alkylated with chloroethyl
pyrrolidine to deliver 23. Hydrolysis of the phthalimide with
hydrazine, followed by amide coupling with a diverse collection
of aryl and heteroaryl carboxylic acids generated library 24
(Scheme 3).
O
N
N
N
14o
1.65
3.62
Br
14p
14q
14r
1.61
0.67
0.08
3.61
1.52
0.18
S
N
N
O
14s
14t
13.5
1.25
30.4
3.73
N
N
N
14u
14v
14w
Br
2.29
2.72
0.17
4.81
5.93
0.39
O
N
N
O
14x
32.5
2.11
73.2
4.56
N
This third generation library was uniformly active, providing
H3 antagonists in the sub-micromolar range. Six-member hetero-
cycles, such as pyridine 24a, were active, as were aryl amides
N
14y
a
Average of three independent determinations with human H3.
Br
Br
H
H
N
Br
O
N
Br
a
b
S
S
O
O
O
OH
O
16
15
Br
Br
H
N
H
N
Br
O
c
Br
O
S
S
O
O
O
N
R1
17
18
Scheme 2. Second generation library synthesis. Reagents and conditions: (a) BrCH2CH(OMe)2, Cs2CO32À, KI, DMF, reflux (70%); (b) TosOH, mw, 160 °C, 10 min (60%); (c)
functionalized pyrrolidine, MP-(OAc)3H, DCM, rt (40–85%). All analogs purified to >98% by mass-directed preparative HPLC.12

J. Phillip Kennedy et al. / Bioorg. Med. Chem. Lett. 19 (2009) 3204–3208
3207
Br
O
H
N
Cl
O
Cl
O
S
N
H
Br
O
N
S
N
20
Ki = 1.12 µM; IC50 = 2.45 µM
19
Ki = 0.16 µM; IC50 = 0.35 µM
Figure 3. Chlorinated version and chlorinated truncated version of 14r.
Table 3
O
Structures and activities of dispyrin analogs 24
H2N
Br
O
N
Br
O
a
b
H
R1
N
Br
O
O
O
N
11
21
24
O
O
a
Compd
R1
H3 Kia
(lm)
H3 IC50
0.56
(lm)
N
Br
N
Br
c
24a
0.27
O
O
N
F3C
N
OH
O
22
23
N
O
24b
24c
24d
24e
24f
0.03
0.43
0.03
0.12
0.25
0.21
0.44
0.08
0.97
0.07
0.26
0.55
0.45
0.98
H
R1
N
Br
d,e
N
N
O
N
N
H
O
24
N
Scheme 3. Third generation library synthesis. Reagents and conditions: (a) 1,2-
dicarboxybenzene, DIC, HOBt, DIEA, DCM, rt, 12 h (99%); (b) BBr3, DCM, À78 °C–rt,
1.5 h (95%); (c) 1.3 equiv Chloroethyl pyrrolidine, CsCO3, KI, DMF, mw, 160 °C,
20 min (93%); (d) (i) N2H4, mw, 160 °C; (ii) SCX; (e) R1COOH, DIC, HOBt, DIEA, DCM,
rt, 12 h (64–98%). All analogs purified to >98% by mass-directed preparative HPLC.12
S
S
N
Cl
with halogens (Cl and Br) or trifluoromethyl groups in the 3-po-
sition (24f–h). Five-member heterocycles (24b–e) proved opti-
mal, with a 5-oxazole 24b (Ki = 32 nM, IC50 = 83 nM) and 2-
thiazole 24d (Ki = 32 nM, IC50 = 72 nM) affording the most potent
H3 antagonists of the unnatural dispyrin analogs. For example,
24d improved the H3 Ki and IC50 ꢀ33-fold over the natural prod-
uct dispyrin, and required only three iterations of molecular
editing and 40 analogs. Moreover, as dispyrin represented a no-
vel chemotype, we were able to obtain composition of matter
patents for the dispyrin analogs as H3 antagonists within an
incredibly crowded intellectual property landscape.14 This effort
highlights the value of employing natural products as leads for
therapeutically relevant targets (Table 3).
24g
Br
24h
F3C
a
Average of three independent determinations.
Acknowledgements
The authors thank the Vanderbilt Department of Pharmacology
and the Vanderbilt Institute of Chemical Biology for support of this
In summary, a natural products guided synthesis effort in
molecular editing, employing iterative parallel synthesis, quickly
optimized the weak H3 antagonism of the marine natural prod-
uct dispyrin 10 over 30-fold to afford unnatural analog 24d with
low nanomolar potency and binding. By employing a novel nat-
ural product scaffold for lead optimization, we were able to
establish an intellectual property position in an incredibly
crowded intellectual property landscape. Although the role of
natural products drug discovery efforts within the pharmaceuti-
cal industry is being significantly reduced, despite overwhelming
success, the biological activity of dispyrin and its analogs argue
further that natural products are viable drug leads and offer pat-
enting advantages.
research. J.P.K. acknowledges
fellowship.
a
VICB predoctoral training
References and notes
1. Celanire, S.; Wijtmans, M.; Talaga, P.; Leurs, R.; de Esch, J. P. Drug Discovery
Today 2005, 10, 1613.
2. Esbenshade, T. A.; Brownman, K. E.; Bitner, R. S.; Strakhova, M.; Cowart, M. D.;
Brioni, J. D. Br. J. Pharmacol. 2008, 154, 1166.
3. Berlin, M.; Boyce, C. M. Exp. Opin. Ther. Patents 2007, 17, 675.
4. Stocking, E. M.; Letavic, M. A. Curr. Top. Med. Chem. 2008, 8, 988.
5. Jesudason, C. D.; Beavers, L. S.; Cramer, J. W.; Dill, J.; Finley, D. R.; Lindsley, C.
W.; Stevens, F. C.; Gadski, R. A.; Oldham, S. W.; Pickard, R. T.; Siedem, C. S.;
Sindelar, D. K.; Singh, A.; Watson, B. M.; Hipskind, P. A. Bioorg. Med. Chem. Lett.
2006, 16, 3415.

3208
J. Phillip Kennedy et al. / Bioorg. Med. Chem. Lett. 19 (2009) 3204–3208
6. Wijtmans, M.; Leurs, R.; de Esch, I. Exp. Opin. Invest. Drugs 2007, 16, 967.
7. Hudkins, R. L.; Raddatz, R. Ann. Reports Med. Chem. 2007, 42, 49.
8. Santora, V. J.; Covel, J. A.; Hayashi, R.; Hofilena, B. J.; Ibarra, J. B.; Pulley,
M. D.; Weinhouse, M. I.; Sengupta, D.; Duffield, J. J.; Semple, G.; Webb, R.
R.; Sage, C.; Ren, A.; Pereira, G.; Knudsen, J.; Edwards, J. E. L.; Suarez, M.;
Frazer, J.; Thomsen, W.; Hauser, E.; Whelan, K.; Grottick, A. J. Bioorg. Med.
Chem. Lett. 2008, 18, 1490.
10. Pina, I. C.; White, K. N.; Cabera, G.; Rivero, E.; Crews, P. J. Nat. Prod. 2007, 70, 613.
11. Kennedy, J. P.; Williams, L.; Bridges, T. M.; Daniels, R. N.; Weaver, D.; Lindsley,
C. W. J. Comb. Chem. 2008, 10, 345.
12. Leister, W. H.; Strauss, K. A.; Wisnoski, D. D.; Zhao, Z.; Lindsley, C. W. J. Comb.
Chem. 2003, 5, 322.
13. Fadeyi, O.; Lindsley, C. W. Org. Lett. 2009, 11, 943.
14. Provisional patent (61/059,975) filed June 9, 2008.
9. Kennedy, J. P.; Brogan, J. T.; Lindsley, C. W. J. Nat. Prod. 2008, 71, 1783.