Synthesis of pyrimido[4,5-c]azepine- and pyrimido[4,5-c]oxepine-based γ-secretase modulators

Article abstract of DOI:10.1016/j.bmcl.2016.02.016

This Letter describes an efficient ring-closing metathesis approach to 2-chloro-4-amino-pyrimido[4,5-c]azepines and 2-chloro-4-amino-pyrimido[4,5-c]oxepines. These chlorides were applied to the synthesis of several potent γ-secretase modulators (GSMs).

Full text of DOI:10.1016/j.bmcl.2016.02.016

Bioorganic & Medicinal Chemistry Letters 26 (2016) 1554–1557
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis of pyrimido[4,5-c]azepine- and pyrimido[4,5-c]oxepine-
based
c
-secretase modulators
⇑
Yong-Jin Wu , Yunhui Zhang, Jeremy H. Toyn, John E. Macor, Lorin A. Thompson
Research and Development, Bristol-Myers Squibb Company, 5 Research Parkway, Wallingford, CT 06492, United States
a r t i c l e i n f o
a b s t r a c t
Article history:
This Letter describes an efficient ring-closing metathesis approach to 2-chloro-4-amino-pyrimido[4,5-c]
azepines and 2-chloro-4-amino-pyrimido[4,5-c]oxepines. These chlorides were applied to the synthesis
of several potent c-secretase modulators (GSMs).
Received 17 January 2016
Revised 4 February 2016
Accepted 6 February 2016
Available online 8 February 2016
Ó 2016 Elsevier Ltd. All rights reserved.
Keywords:
c
-Secretase modulator (GSM)
2-Chloro-pyrimido[4,5-c]azepin-4-amine
2-Chloro-pyrimido[4,5-c]oxepin-4-amine
Ring-closing metathesis (RCM)
There is substantial evidence to suggest that b-amyloid (Ab)
peptide, particularly the longer 42 amino acid form, Ab42, plays
a critical role in the progression of Alzheimer’s disease (AD).1–4
Ab is derived from the b-amyloid precursor protein (APP) by prote-
olysis. Cleavage of APP by b-site APP cleaving enzyme-1 (BACE1)
results in shedding of the APP ectodomain, and the remaining
membrane bound C-terminal fragment, C99, is further processed
lowering the total amount of Ab secreted using ELISAs that detect
all Ab species.10
Our early efforts in the GSM area led to diaminotriazine 1 which
exhibited good potency for inhibition of Ab1–42 production (IC50
:
29 nM) and no effect on total Ab production.11 In an effort to
increase potency through conformational restriction, we sought
to prepare pyrimido[4,5-c]azepine analogs 2a/b (Fig. 1). The fused
bicyclic ring system is somewhat related to the well-known benzo-
diazepine drugs, and may contribute to desired brain penetration.
In terms of a heterocyclic head group, we chose 4-chloroimidazole
instead of 4-methylimidazole as present in lead compound 1
because the former results in an improved CYP 3A4 inhibition
profile.11
by c-secretase (GS) to produce Ab peptides of lengths varying from
37 to 43 amino acids. Accumulation and aggregation of the toxic Ab
peptide, particularly the 42-amino acid form Ab42, initiates neu-
ronal dysfunction that eventually leads to brain atrophy, dementia,
and death. Thus, inhibition of BACE1 or GS to reduce Ab production
is a plausible approach to test the amyloid hypothesis.5–7 Recently,
the GS inhibitors (GSIs) semagacestat and avagacestat were dis-
continued in clinical trials presumably due to side effects such as
toxicity related to inhibition of other GS substrates and decline
in cognition.8,9 A viable alternative to direct GS inhibition is GS
modulation. GS modulators (GSMs) reduce the level of longer, neu-
rotoxic Ab peptides (Ab42 and Ab43) by shifting the APP processing
The synthesis of 2a/b required easy access to pyrimido[4,5-c]
azepines 3a/b (Fig. 1). Surprisingly, azepines of this type are
unknown in the literature. In contrast, the corresponding benzo
[c]azepines 4 are common intermediates that have been widely
used in the synthesis of benzazepine agents for the treatment of
central nervous system disorders.12–15 In general, two methodolo-
gies exist for the preparation of benzo[c]azepines 4 (Scheme 1).
The first one (Roche synthesis) involves palladium-catalyzed cou-
pling of iodide 5 with propargylphthalimide 6 to give the acetyle-
nic benzophenone 7.12,13 Removal of the phthaloyl protecting
group leads to a free primary amine 8, which undergoes partial
hydrogenation followed by spontaneous ring closure to furnish
benzazepine 10 (Scheme 1). The alternative procedure makes use
of the unprotected (Z)-3-(tributylstannyl)allylamine (12).14 The
palladium-catalyzed cross-coupling reaction of 12 with bromide
11 affords the substituted cis allylic amine 13, which cyclizes
by
c-secretase towards shorter isoforms (such as Ab37, Ab38)
without blocking GS processing. Because GS activity is not blocked,
this modulating mechanism does not inhibit intracellular signaling
resulting from GS activity, and should offer a differentiated safety
profile versus GSIs. GSMs are distinguished in cell assays by
combining lowering of secreted Ab42 in specific ELISAs without
⇑
Corresponding author.
E-mail address: Yong-Jin.wu@bms.com (Y.-J. Wu).
http://dx.doi.org/10.1016/j.bmcl.2016.02.016
0960-894X/Ó 2016 Elsevier Ltd. All rights reserved.

Y.-J. Wu et al. / Bioorg. Med. Chem. Lett. 26 (2016) 1554–1557
1555
R
R
R
N
OMe
NH
N
N
N
OMe
N
N
N
N
6
12
or
N
N
Br
O
Cl
N
N
N
N
N
Ph
N
N
N
H
N
N
H
Cl
Cl
Ph
Ph
: R = Me
3b: R = H
Ph
2a/b
a: R = H; b: R = Me
a: R = H
b: R = Me
3a
1
IC50: 29 nM
15a/b
R
N
Scheme 3. Initial approach to pyrimido[4,5-c]azepines 3a/b.
N
R
R
N
Cl
N
N
N
Cl
N
N
Ph
3a: R = H
: R = Me
R
4
b
a
N
N
N
3b
Cl
N
Cl
N
16
Cl
CO2Me
CO2Me
CO2H
17a/b
18a/b
Figure 1. Retrosynthesis of bicyclic GSMs.
a: R = H
b: R = Me
R
N
R
N
N
Br
c
O
N
d
e
X
PdCl2, Ph3P,
CuI, Et2NH
I
N
N
OMe
OMe
N
15a/b
N
Cl
N
Cl
+
O
Cl
46%
O
O
20a/b
O
Ph
19a/b
5
6
O
Scheme 4. Reagents and conditions: (a) dimethylamine or methylamine, 89–95%;
(b) lithium hydroxide, THF, H2O, rt, 79–85%; (c) N,O-dimethylhydroxylamine
hydrochloride, HATU, Hünig’s base, rt, 78–94%; (d) NBS, toluene, 80 °C, 3 h, 78–
94%; (e) PhMgBr or PhLi, THF or ether, various temperatures.
NH2
N
MeNH2
97%
O
O
O
Cl
Cl
Ph
Ph
R
R
7
8
N
N
N
N
b
a
N
N
OMe
N
10% Pd/C
BaSO4, H2
20a/b
Ph
NH2
92%
Cl
Cl
N
O
Cl
Cl
O
O
22a/b
21a/b
Ph
Ph
a: R = H
b: R = Me
10
9
R
R
Scheme 1. Roche synthesis of benzo[c]azepines.
N
N
N
N
c
d
N
N
N
N
Cl
Cl
Pd(PPh3)4
toluene
reflux
NH2
Br
Ph
Ph
3a/b
23a/b
+
NH2
O
O
SnBu3
Scheme 5. Reagents and conditions: (a) tributylvinyltin, Pd(PPh3)4, toluene, 80 °C,
sealed vial, 10 h, 74–79%; (b) PhMgBr, THF, rt, 92–97%; (c) allylamine, TiCl4, rt, 48–
84%; (d) Grubbs II (5 mol %), toluene, 80 °C, 15 min, 92–98%.
11
13
12
86%
N
phenyllithium under numerous conditions failed to produce the
desired phenyl ketones 15a/b due to decomposition of the starting
material.
14
Scheme 2. Corriu synthesis of benzo[c]azepines.
Due to the difficulty in accessing intermediates 15a/b we con-
sidered alternative approaches that could intercept our existing
intermediates. Thus, we decided to investigate a ring-closing
metathesis (RCM) approach which could leverage our existing
intermediates 20a/b.16 Despite its simplicity, this approach has
never been utilized to construct benzo[c]azepine compounds.17
Scheme 5 describes our RCM approach to azepines 3a/b. Weinreb
amides 20a/b underwent Stille coupling with tributyl(vinyl)stan-
nane to give vinylpyrimidines 21a/b in good yields. These com-
pounds were also prepared via Suzuki coupling with 2,4,6-
trivinyl-1,3,5,2,4,6-trioxatriborinane, but the yields were signifi-
cantly lower (<30%). In contrast to our results with the bromo-sub-
stituted Weinreb amides 20a/b, addition of phenylmagnesium
bromide to the vinyl-substituted Weinreb amides 21a/b proceeded
cleanly to give phenyl ketones 22a/b. Condensation of 22a/b with
allylamine was performed in the presence of titanium tetrachlo-
ride, and the resulting imines 23a/b were sufficiently stable that
spontaneously to give benzazepine 14 (Scheme 2). We started our
work hoping to leverage this existing methodology for the synthe-
sis of 3a/b, and both methods required access to the bromopyrim-
idinyl phenyl ketones 15a/b (Scheme 3) as starting materials.
Scheme 4 describes our approach to phenyl ketones 15a/b.
Addition of methylamine and dimethylamine to the readily avail-
able methyl 2,6-dichloropyrimidine-4-carboxylate (16) gave 6-
methylamino- and 6-dimethylamino-pyrimidines 17a and 17b,
respectively. Both esters were hydrolyzed with aqueous lithium
hydroxide to furnish free carboxylic acids 18a/b, which were cou-
pled with N,O-dimethylhydroxylamine hydrochloride to afford
Weinreb amides 19a/b. Bromination of 19a/b with NBS was carried
out smoothly in toluene at 80 °C to afford Weinreb amides 20a/b.
However, treatment of 20a/b with phenylmagnesium bromide or

1556
Y.-J. Wu et al. / Bioorg. Med. Chem. Lett. 26 (2016) 1554–1557
R
N
N
N
N
N
OMe
N
N
N
a
Cl
N
N
b
N
N
N
N
Cl
Cl
NH
Cl
N
N
H
Ph
Ph
Ph
Ph
a
23b
24
2a
(R = H)
IC50: 5 nM
2b (R = Me) IC50: 21 nM
N
N
c
N
N
N
OMe
N
N
OMe
b,c
N
N
Cl
Cl
Cl
N
N
Cl
N
N
Boc
Boc
Ph
NH
N
H
N
26
NH2
25
30
Ph
31
IC50: 36 nM
Scheme 6. Reagents and conditions: (a) NaBH3CN, HOAc, MeOH; (b) Boc2O, Hünig’s
base, CH2Cl2, 78% from 22b; (c) Grubbs II (5 mol %), toluene, 80 °C, 15 min, 92%.
a
OMe
N
N
N
O
N
H
N
N
N
N
Ph
b
a
32
IC50: 56 nM
N
N
N
OH
O
Cl
Cl
N
Cl
Scheme 8. Reagents and conditions: (a) 3a or 3b or 29, dioxane, acetic acid, 100 °C,
5 h, 16% (2a); 23% (2b); 21% (29); (b) 26, Pd2(dba)3 (4 mol %), Xantphos (10 mol %),
cesium carbonate, dioxane, 100 °C, 12 h, 40%; (c) TFA, CH2Cl2, rt, 71%.
Ph
Ph
22b
27
N
N
N
c
pyrimido[4,5-c]azepine core structure. The dimethylamino-substi-
tuted analog 2b (IC50: 21 nM) was 4-fold less active than the
monomethylamino-substituted counterpart 2a. Accordingly, we
speculate that the side chain nitrogen atom may serve as a hydro-
gen-bond donor instead of an acceptor to a residue on GS. Azepine
N
O
O
N
Cl
Ph
Ph
28
29
Scheme 7. Reagents and conditions: (a) NaBH4, MeOH, rt, 95%; (b) allyl bromide,
sodium hydride, DMF, rt, 92%; (c) Grubbs II (5%), toluene, 80 °C, 15 min, 92%.
31 (IC50: 36 nM) was comparable to its imine analog 2b (IC50
21 nM), but about twice as active as oxepine 32 (IC50: 56 nM).
:
Despite their potent cellular inhibitory activity, compounds 2a/
b demonstrated only marginal reduction in brain Ab peptides in
rodents relative to the vehicle treated control even at 30 mg/kg
PO. The brain exposure data (not shown) indicated low exposure
of the compounds in rat brain, explaining the lack of in vivo
activity.
In summary, we have developed an efficient route to 2-
chloropyrimido[4,5-c]azepines 3a/b and 26 as well as 2-chloropy-
rimido[4,5-c]oxepine 29. These chlorides were incorporated into
several GSMs, and the activity of azepine 2a (IC50: 5 nM) suggested
that this type of conformational constriction is a viable approach to
the discovery of potent GSMs.
they could be purified using standard silica gel chromatography,
and they showed no appreciable decomposition when exposed to
air at room temperature for a few months. Treatment of either
23a/b with the Grubbs II catalyst in toluene at 80 °C for 15 min
brought about a clean RCM transformation to give 3a/b in excellent
yield.18 In the case of RCM substrate 23a, the free secondary amine
functionality required no protection, thus leading to a direct syn-
thesis of 3a.
We also used imine 23b in the synthesis of the related N-Boc
protected azepine 26 (Scheme 6). The secondary amine in the
GSMs derived from 26 (see 31, Scheme 8) offered additional polar-
ity and a potential avenue for substitution. Reduction of 23b with
sodium cyanoborohydride furnished secondary amine 24, which
was converted to the N-Boc derivative 25. Exposure of 25 to the
Grubbs II catalyst led to the azepine 26 in good yield.19
We also extended the RCM approach to the synthesis of pyrim-
ido[4,5-c]oxepine 29 (Scheme 7).20 Reduction of ketone 22b with
sodium borohydride afforded alcohol 27, and subsequent O-allyla-
tion furnished allyl ether 28. Metathesis of 28 using the Grubbs II
catalyst gave oxepine 29 in excellent yield.21
The azepine and oxepine intermediates were utilized in the
synthesis of GSMs similar to other analogs we have reported
(Scheme 8).11 Treatment of aniline 30 with 3a/b or 29 with acetic
acid in dioxane at 100 °C afforded 2a/b and 32, respectively, in
moderate yields (not optimized). The palladium-catalyzed cou-
pling of azepine 26 with 30 and subsequent removal of the N-
Boc group gave 31 in good yield. We also attempted hydrogenation
of the olefinic double bond in these analogs, but without success.
The monomethylamino-substituted pyrimido[4,5-c]azepine 2a
Acknowledgements
We thank Dr. Nicholas Meanwell for critically reviewing this
manuscript. We thank Rudy Krause, Alan Xu Lin, and Tracey Hall
for various biological evaluations.
References and notes
1. Koh, J.-Y.; Yang, L.-L.; Cotman, C. W. Brain Res. 1990, 533, 315.
2. Haass, C.; Selkoe, D. J. Nat. Rev. Mol. Cell Biol. 2007, 8, 101. and references
therein.
3. Kennedy, M. E.; Rajendran, L.; Wong, P. C.; Vassar, R.; Kuhn, P.-H.; Haass, C.;
Lichtenthaler, S. F. J. Neurochem. 2014, 130, 4.
4. larson, M. E.; Lesne, S. E. J. Neurochem. 2012, 120, 125.
5. De Strooper, B.; Vassar, R.; Golde, T. Nat. Rev. Neurol. 2010, 6, 99.
6. Stamford, A.; Strickland, C. Curr. Opin. Chem. Biol. 2013, 17, 320.
7. Yan, R.; Vassar, R. Lancet Neurol. 2014, 13, 319.
8. Doody, R. S.; Raman, R.; Sperling, R. A.; Seimers, E.; Sethuraman, G.; Mohs, R.;
Farlow, M.; Iwatsubo, T.; Vellas, B.; Sun, X.; Ernstrom, K.; Thomas, R. G.; Aisen,
P. S. Alzheimers Res. Ther. 2015, 7, 1.
9. Coric, V.; Salloway, S.; van Dyck, C. H.; Dubois, B.; Andreasen, N.; Brody, M.;
Curtis, C.; Soininen, H.; Thein, S.; Shiovitz, T.; Pilcher, G.; Ferris, S.; Colby, S.;
Kerselaers, W.; Dockens, R.; Soares, H.; Kaplita, S.; Luo, F.; Pachai, C.; Bracoud,
L.; Mintun, M.; Grill, J. D.; Marek, K.; Seibyl, J.; Cedarbaum, J. M.; Albright, C.;
Feldman, H. H.; Berman, R. M. JAMA Neurol. 2015, 1–10.
was shown to be a potent inhibitor of Ab1-42 production (IC50
:
5 nM), and was approximately 6-fold more potent than the lead
compound 1. Since the 4-methylimidazole head group contributes
to activity to the same extent as 4-chloroimidazole, the potency
enhancement observed with azepine 2a likely results from its rigid
10. (a) Oehlrich, D.; Berthelot, D. J.-C.; Gijsen, H. J. M. J. Med. Chem. 2011, 54, 669;
(b) Pettersson, M.; Stepan, A. F.; Kauffman, G. W.; Johnson, D. S. Expert Opin.

Y.-J. Wu et al. / Bioorg. Med. Chem. Lett. 26 (2016) 1554–1557
1557
Ther. Patents 2013, 23, 1349; (c) Toyn, J. H.; Thompson, L. A.; Lentz, K. A.;
Meredith, J. E., Jr.; Burton, C. R.; Sankaranararyanan, S.; Guss, V.; Hall, T.; Iben,
L. G.; Krause, C. M.; Krause, R.; Lin, X. A.; Pierdomenico, M.; Polson, C.;
Robertson, A. S.; Denton, R. R.; Grace, J. E.; Morrison, J.; Raybon, J.; Zhuo, X.;
Snow, K.; Padmanabha, R.; Agler, M.; Esposito, K.; Harden, D.; Prack, M.; Varma,
S.; Wong, V.; Zhu, Y.; Zvyaga, T.; Gerritz, S.; Marcin, L. R.; Higgins, M. A.; Shi, J.;
Wei, C.; Cantone, J. L.; Drexler, D. M.; Macor, J. E.; Olson, R. E.; Ahlijanian, M. K.;
Albright, C. F. Int. J. Alzheimers Dis. 2014, 431858/1–431858/23.
11. Shi, J.; Zuev, D.; Xu, L.; Lentz, K. A.; Grace, J. E.; Toyn, J. H.; Olson, R. E.; Macor, J.
E.; Thompson, L. A. Biororg. Med. Chem. 2016. in press.
12. Trybulski, E. J.; Reeder, E.; Blount, J. F.; Fryer, R. I. J. Org. Chem. 1982, 47,
2441.
13. Trybulski, E. J.; Fryer, R. I.; Reeder, E.; Vitone, S.; Todaro, L. J. Org. Chem. 1986,
51, 2191.
14. Corriu, R. J. P.; Geng, B.; Moreau, J. J. E. J. Org. Chem. 1993, 58, 1443.
15. Isaacson, E. J. Central Nervous System Depressants in Textbook of Organic
Medicinal and Pharmaceutical Chemistry In Delgado, J. N., Remers, W. A., Eds.;
Lippincott-Raven, 1998. Chapter 14.
18. 3a: 1H NMR (CDCl3, 500 MHz) d d 7.51–7.46 (m, 2H), 7.41–7.32 (m, 3H), 6.64
(d, J = 9.5 Hz, 1H), 6.32 (dt, J = 9.5, 6.7 Hz, 1H), 4.06–3.67 (m, 1H), 3.85–3.46 (br
s, 1H), 3.27 (s, 6H). 13C NMR (CDCl3, 125 MHz) d 166.3, 165.0, 159.5, 156.9,
139.2, 130.0, 129.6, 129.5, 127.9, 126.2, 118.1, 41.5 and 29.8. Exact mass calcd
for C16H16ClN4 (M+H): 299.1064; found: 299.1056. 3b: 1H NMR (500 MHz,
CD3OD) d 7.51–7.31 (m, 1H), 6.76 (d, J = 9.5 Hz, 1H), 6.47 (dt, J = 9.7, 6.4 Hz,
1H), 4.8–3.4 (2H, br S), 3.07 (s, 3H). 13C NMR (CD3OD, 125 MHz) d 167.4, 162.1,
157.6, 157.5, 138.6, 133.6, 130.0, 129.5, 128.0, 122.8, 117.3, 49.0, and 27.6.
Exact mass calcd for C15H14ClN4 (M+H): 285.0907; found: 285.0900.
19. 26: at room temperature, this compound appears as
a
ꢀ5:2 mixture of
rotamers. 1H NMR (400 MHz, CDCl3) d 7.34–7.22 (m, 3H), 7.10–7.01 (m, 2H),
6.31 (s, 1H), 6.08–6.00 (m, 1H), 5.71 (dt, J = 12.3, 3.3 Hz, 1H), 4.78–4.65 (m, 1H),
3.37 (dt, J = 19.6, 2.4 Hz, 1H), 3.11 (6H, s), 1.39 (s, 9H). Peaks corresponding to
the minor rotamer are present at: d 6.49 (s, 1H), 6.13–6.05 (m, 1H), 5.71 (dt,
J = 12.3, 3.3 Hz, 1H), 5.69 (dt, J = 12.3, 3.3 Hz, 1H), 4.56 (d, J = 19.9 Hz, 1H), 3.10
(6H, s), 1.47 (s, 9H). MS (M+H): 401.20.
20. For
a RCM approach to 1,3-dihydrobenzo[c]oxepines, see: Pathak, R.;
Panayides, J.; Jeftic, T. D.; de Koning, C. B.; van Otterlo, W. A. L. Synlett 1859, 12.
21. 29: 1H NMR (500 MHz, CDCl3) d 7.41–7.31 (m, 3H), 7.23–7.11 (m, 2H), 6.20 (dt,
J = 12.4, 2.2 Hz, 1H), 5.89–5.82 (m, 2H), 4.46 (dt, J = 18.9, 2.6 Hz, 1H), 4.16 (dt,
J = 18.9, 2.4 Hz, 1H), 3.15 (s, 6H). 13C NMR (CDCl3, 125 MHz) d 170.8, 166.3,
156.1, 135.4, 132.7, 129.2, 128.5, 122.4, 122.7, 84.4, 67.3, 41.4, 21.1. Exact mass
calcd for C16H167ClN3O (M+H): 302.1060; found: 302.1054.
16. Grubbs, R. H.; Chang, S. Tetrahedron 1998, 54, 4413.
17. The RCM approach to 2,3-dihydro-1H-benzo[c]azepine has been reported, see:
Bradshaw, R.; Evans, P.; Fletcher, J.; Lee, A. T. L.; Mwashimba, P. G.; Oehlrich, D.;
Thoms, E. J.; Davies, R. H.; Allen, B. C. P.; Broadley, K. J.; Hamrouni, A.;
Escargueil, C. Org. Biomol. Chem. 2008, 6, 2138.