Selective synthesis of 1-substituted 4-chloropyrazolo[3,4-d]pyrimidines

Article abstract of DOI:10.1021/ol4005382

Strategies for carrying out the reaction of 4,6-dichloropyrimidine-5- carboxaldehyde with various hydrazines to generate 1-substituted 4-chloropyrazolo[3,4-d]pyrimidines in a selective and high-yielding manner are presented. For aromatic hydrazines, the reaction is performed in the absence of an external base, which promotes exclusive hydrazone formation. The hydrazones subsequently cyclize at an elevated temperature to form the desired pyrazolo[3,4-d]pyrimidine products. For aliphatic hydrazines, the reaction sequence proceeds as a single step in the presence of an external base.

Full text of DOI:10.1021/ol4005382

ORGANIC
LETTERS
XXXX
Vol. XX, No. XX
000–000
Selective Synthesis of 1‑Substituted
4‑Chloropyrazolo[3,4‑d]pyrimidines
Suresh Babu, Christie Morrill, Neil G. Almstead, and Young-Choon Moon*
PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield,
New Jersey 07080, United States
ymoon@ptcbio.com
Received February 26, 2013
ABSTRACT
Strategies for carrying out the reaction of 4,6-dichloropyrimidine-5-carboxaldehyde with various hydrazines to generate 1-substituted
4-chloropyrazolo[3,4-d]pyrimidines in a selective and high-yielding manner are presented. For aromatic hydrazines, the reaction is performed
in the absence of an external base, which promotes exclusive hydrazone formation. The hydrazones subsequently cyclize at an elevated temperature
to form the desired pyrazolo[3,4-d]pyrimidine products. For aliphatic hydrazines, the reaction sequence proceeds as a single step in the presence of an
external base.
Pyrazolo[3,4-d]pyrimidines are frequently employed
as structural units in drug discovery programs. Com-
pounds containing this structure have been developed
for the treatment of Parkinson’s disease,1 as well as
various inflammatory and autoimmune diseases.2
Pyrazolo[3,4-d]pyrimidines are also present as a core
structure in inhibitors of numerous oncogenic targets.3
Both the 1- and 4-positions of these subunits have been
used as points of structural diversification.
We recently became interested in synthesizing a series
of 1-substituted 4-chloropyrazolo[3,4-d]pyrimidines. The
most efficient known route to obtain these structures
involves the direct condensation of commercially available
4,6-dichloropyrimidine-5-carboxaldehyde (1) with a sub-
stituted hydrazine (2) in the presence of an external base
(Scheme 1).4 This procedure can potentially be carried out
in a single step. Unfortunately the reaction can generate
several products, including hydrazone 3, 1-substituted
pyrazolo[3,4-d]pyrimidine 4, and 2-substituted pyrazolo-
[3,4-d]pyrimidine 5. Product mixtures have been observed
for similar reactions,3e,4a but achieving high selectivity
remains a challenge. Herein, we report (1) observations
regarding the factors that influence selectivity in the reac-
tion of 1 with 2 and (2) optimized reaction conditions to
generate 1-substituted pyrazolo[3,4-d]pyrimidine 4 selec-
tively and in high yield.
(1) Neustadt, B. R.; Hao, J.; Lindo, N.; Greenlee, W. J.; Stamford,
A. W.; Tulshian, D.; Ongini, E.; Hunter, J.; Monopoli, A.; Bertorelli, R.;
Foster, C.; Arik, L.; Lachowicz, J.; Ng, K.; Feng, K. I. Bioorg. Med.
Chem. Lett. 2007, 17, 1376–1380.
(2) (a) Das, J.; Moquin, R. V.; Pitt, S.; Zhang, R.; Shen, D. R.;
McIntyre, K. W.; Gillooly, K.; Doweyko, A. M.; Sack, J. S.; Zhang, H.;
Kiefer, S. E.; Kish, K.; McKinnon, M.; Barrish, J. C.; Dodd, J. H.;
Schieven, G. L.; Leftheris, K. Bioorg. Med. Chem. Lett. 2008, 18, 2652–
2657. (b) Baraldi, P. G.; Bovero, A.; Fruttarolo, F.; Romagnoli, R.;
Tabrizi, M. A.; Preti, D.; Varani, K.; Borea, P. A.; Moorman, A. R.
Bioorg. Med. Chem. 2003, 11, 4161–4169.
(3) (a) Curran, K. J.; Verheijen, J. C.; Kaplan, J.; Richard, D. J.;
Toral-Barza, L.; Hollander, I.; Lucas, J.; Ayral-Kaloustian, S.; Yu, K.;
Zask, A. Bioorg. Med. Chem. Lett. 2010, 20, 1440–1444. (b) Verheijen,
J. C.; Richard, D. J.; Curran, K.; Kaplan, J.; Lefever, M.; Nowak, P.;
Malwitz, D. J.; Brooijmans, N.; Toral-Barza, L.; Zhang, W. G.; Lucas,
J.; Hollander, I.; Ayral-Kaloustian, S.; Mansour, T. S.; Yu, K.; Zask, A.
J. Med. Chem. 2009, 52, 8010–8024. (c) Tan, T. M. C.; Yang, F.; Fu, H.;
Raghavendra, M. S.; Lam, Y. J. Comb. Chem. 2007, 9, 210–218. (d)
Link, W.; Oyarzabal, J.; Serelde, B. G.; Albarran, M. I.; Rabal, O.;
ꢀ
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Cebria, A.; Alfonso, P.; Fominaya, J.; Renner, O.; Peregrina, S.; Soilan,
D.; Ceballos, P. A.; Hernandez, A. I.; Lorenzo, M.; Pevarello, P.;
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Granda, T. G.; Kurz, G.; Carnero, A.; Bischoff, J. R. J. Biol. Chem.
2009, 284, 28392–28400. (e) Deng, X.; Okram, B.; Ding, Q.; Zhang, J.;
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Choi, Y.; Adrian, F. J.; Wojciechowski, A.; Zhang, G.; Che, J.;
Bursulaya, B.; Cowan-Jacob, S. W.; Rummel, G.; Sim, T.; Gray, N. S.
(4) (a) Boyd, S.; Campbell, L.; Liao, W.; Meng, Q.; Peng, Z.; Wang,
X.; Waring, M. J. Tetrahedron Lett. 2008, 49, 7395–7397. (b) Slavish,
P. J.; Price, J. E.; Hanumesh, P.; Webb, T. R. J. Comb. Chem. 2010, 12,
807–809.
J. Med. Chem. 2010, 53, 6934–6946.
r
10.1021/ol4005382
XXXX American Chemical Society

was resubjected to the reaction conditions (Scheme 3).6
Cyclization to form 4a was not observed. This result indi-
cates that, at 65 °C in the presence of an external base, 4
arises from intermediate 6, rather than through hydrazone
3. Although 3 can form under these conditions (Table 1,
entries 2À4), it does not cyclize.
Scheme 1. Direct Condensation of 1 with 2
These observations suggest that the reaction conditions
have a significant impact on selectivity. Use of an external
base favors the initial displacement of the chloro substi-
tuent of 1, which inherently leads to product mixtures. In
the absence of an external base, however, 2 preferentially
undergoes initial condensation with the aldehyde moiety
of 1, allowing only the 1 f 3 f 4 pathway to proceed.
Thus we postulated that 4 could be selectively synthesized
by performing the condensation reaction in the absence
of an external base, which would quantitatively form 3.
A subsequent cyclization reaction would then generate 4.
Our initial efforts focused on the reaction of 15 with
various phenylhydrazines using the conditions reported
in the literature (NEt3, 65 °C, 1 h).4a The major products
were pyrazolo[3,4-d]pyrimidines 4 and 5 (Table 1, entries
1À4). Small quantities of hydrazone 3 were also observed.
Electron-rich hydrazines favored the formation of 4(entry1),
whereas electron-poor hydrazines favored the formation of 5
(entry 4). Performing these reactions without triethylamine
led to dramatically different results: hydrazone 3 was almost
the sole product (entries 5À8).
Scheme 2. Possible Reaction Pathways
Table 1. Initial Reactions of 1 with Phenylhydrazinesa
NEt3
1
(%)c
3
(%)c
4
(%)c
5
(%)c
entry
R
(equiv)
1
2
3
4
5
6
7
8
4-MeO-C6H4 (a)
Ph (b)
2.1
2.1
2.1
2.1
0
ND
ND
2
ND
2
91
63
40
8
9
35
4-Cl-C6H4 (c)
4-CF3-C6H4 (d)
4-MeO-C6H4 (a)
Ph (b)
7
51
9
9
74
3
92
96
98
79
5
ND
ND
ND
ND
0
4
ND
ND
ND
Our next task was to optimize the synthesis and isolation
of hydrazone 3. Having established reaction conditions to
generate 3 selectively at 65 °C (Table 1, entries 5À8), we
screened additional solvents at rt. Nucleophilic solvents such
as isopropanol were not compatible with 1, as they readily
displaced its chloro substituents. The conversion of 1into 3did
proceed cleanly in THF, dioxane, acetonitrile, acetic acid, and
DMF. The reaction was the most efficient in DMF, exhibiting
essentially quantitative conversion within 2 h. Either the free
base or the HCl salt of 2 was a viable starting material, but for
electron-poor hydrazines such as 2d, reactions involving the
HCl salt progressed more slowly. Adding cold aqueous
sodium bicarbonate to the crude reaction mixture and filtering
the resultant precipitate led to the isolation of 3. Purification
via column chromatography was not necessary. Table 2 shows
the conversion of 1 into a variety of aromatic hydrazones
(3aÀn) using our optimized reaction conditions. The reaction
worked efficiently for electron-rich substrates (entries 1 and
5À6), electron-poor substrates (entries 3À4 and 8À10), steri-
cally hindered substrates (entries 5, 8, and 11), and heteroaro-
matic substrates (entries 12À14).
4-Cl-C6H4 (c)
4-CF3-C6H4 (d)
0
2
0
21
a 0.2 M in THF, 1.05 equiv of 2, 0.3À0.6 mmol scale. b HCl salt.
c Determined from relative 1H NMR ratios in the crude reaction
mixture. ND = not detected.
Scheme 2 illustratesthe various pathwaysthrough which
the reaction of 1 with 2 can proceed. Selectivity issues arise
due to the presence of two different electrophilic sites on
1 and two different nucleophilic sites on 2. Three inter-
mediates are possible: 3, 6, and 7. Initial condensation with
the aldehyde moiety of 1 can only proceedwith the external
nitrogen of 2, generating 3, which then can cyclize to form
4. Initial displacement of the chloro substituent of 1, on the
other hand, can occur with either nitrogen of 2, generating
both 6 and 7, which in turn form 4 and 5, respectively.
Entries 5À8 of Table 1 suggest that 3 does not readily
cyclize to form 4 at 65 °C in the absence of an external base.
Formation of 4 did readily occur when an external base
was used (entries 1À3). To provide insight into the path-
way through which 4 formed in these cases, hydrazone 3a
(5) 1 was unstable at rt for extended time periods. Commercially
purchased 1 was initially purified and stored in the refrigerator. See the
Supporting Information for further details.
(6) To fully mimic the original reaction conditions, HCl (1.05 equiv)
was added, since 2a was an HCl salt. H2O (1 equiv) was also added, since
formation of 3a generated 1 equiv of H2O.
B
Org. Lett., Vol. XX, No. XX, XXXX

Table 2. Optimized Conversion of 1 into 3a
Scheme 3. Resubjection of 3a to Original Reaction Conditionsa
a 0.2 M in THF, 2.1 equiv of NEt3, 1.05 equiv of HCl, 1 equiv of H2O,
0.3 mmol scale. b Only 3a was detected in the crude reaction mixture by
1H NMR.
entry
R
isolated yield (%)
1
4-MeO-C6H4 (a)
Ph (b)
87
97
93
99
93
92
94
92
89
96
92
85
88
91
2
3
4-Cl-C6H4 (c)
4-CF3-C6H4 (d)c
2-MeO-C6H4 (e)
4-Me-C6H4 (f)
4-F-C6H4 (g)
With hydrazones 3aÀn in hand, we needed to find
reaction conditions under which they would efficiently
cyclize to form 4aÀn. Hydrazones such as 3 tend to re-
sist cyclization, presumably because they exist in the
E-configuration.4a,7 Heating at elevated temperatures
can sometimes facilitate the process.4a,8 Cyclizations
that have been reported in the literature for other
heterocyclic systems generally involved heating the
substrates under neat reaction conditions or in polar
solvents (e.g., water, alcohols).8 Unfortunately these
reaction conditions are not compatible with pyrazolo-
[3,4-d]pyrimidine 4, due to its highly labile chloro sub-
stituent. We found, however, that heating 3aÀn at
200 °C, in solvents such as THF, dioxane, or acetonitrile,
led to quantitative cyclization to form 4aÀn within
20 min (Table 3).9 Both microwave and conventional
heating (sealed tube) were evaluated, and no difference
was observed between the two methods in terms of the
reaction efficiency. Dioxane was utilized as the solvent
for reactions involving conventional heating, due to its
higher boiling point. Acetonitrile, on the other hand,
was the preferred solvent for the microwave reactions
because it reached 200 °C more readily in our microwave
reactor compared to THF or dioxane. Pyrazolo[3,4-d]-
pyrimidine products 4aÀn were isolated by adding cold
aqueous sodium bicarbonate and filtering the resultant
precipitate. Purification via column chromatography
was again not necessary.
4
5
6
7
8
2-Cl-C6H4 (h)
3-Cl-C6H4 (i)
9
10
11
12
13
14
4-Br-C6H4 (j)
1-naphthyl (k)
2-pyridyl (l)d
2-quinoxalyl (m)d
2-benzo[d]oxazolyl (n)d
a 0.3À1 M in DMF, 1.05 equiv of 1, 0.5À3 mmol scale. b HCl salt
unless otherwise noted. c Free base of 2 was used. d Bis-HCl salt of 2 was
generated in situ using 4 M HCl in dioxane (2 equiv).
yield in the presence of an external base (Table 4).10
Essentially quantitative conversion to 4 was observed
within 1 h at rt, and isomeric product 5 was not detected.
The products (4oÀs) were cleanly isolated after an aqueous
workup without the use of column chromatography. We
obtained significantly higher isolated yields than those
reported in the literature for the corresponding reactions
to form 4p, 4q, and 4s carried out at 65 °C.4a We suspect
that, in the case of aliphatic substrates, some decomposi-
tion of 4 occurs at elevated temperatures, which could
account for the higher yields observed in our studies.11
The difference in product selectivity between aliphatic
and aromatichydrazines in thepresenceof anexternalbase
is striking. Aliphatic substrates selectively generate 4
(Table 4), whereas aromatic substrates generate mixtures
of 3, 4, and 5 (Table 1, entries 1À4). We attribute this
observation to the difference in reactivity between the
nitrogen atoms of 2. For the aliphatic hydrazines, the
internal nitrogen is likely more nucleophilic than the
external nitrogen. It has been previously observed that
the internal nitrogen of methylhydrazine (2p) is more
nucleophilic than the external nitrogen.12 This increased
reactivity of the internal nitrogen ensures that the 1f6f4
pathway (Scheme 2) will predominate in reactions involv-
ing aliphatic hydrazines.
Finally, we investigated the reaction of 1 with aliphatic
hydrazines. Unlike the aromatic hydrazines (Table 1, en-
tries 1À4), these substrates selectively generated 4 in high
(7) Hayes, R.; Meth-Cohn, O. TetrahedronLett. 1982, 23, 1613–1616.
(8) (a) Quiroga, J.; Trilleras, J.; Insuasty, B.; Abonıa, R.; Nogueras,
´
M.; Marchal, A.; Cobo, J. Tetrahedron Lett. 2008, 49, 3257–3259. (b)
Quiroga, J.; Diaz, Y.; Insuasty, B.; Abonia, R.; Nogueras, M.; Cobo, J.
Tetrahedron Lett. 2010, 51, 2928–2930. (c) Mali, J. R.; Pratap, U. R.;
Jawale, D. V.; Mane, R. A. Tetrahedron Lett. 2010, 51, 3980–3982. (d)
Paul, S.; Gupta, M.; Gupta, R.; Loupy, A. Tetrahedron Lett. 2001, 42,
3827–3829.
(9) We also attempted to perform the reaction sequence illustrated in
Tables 2 and 3 as a one-pot procedure by heating a mixture of 1 and 2 at
200 °C for 20 min. Selective formation of 4 was observed. However, a
significant amount of 4 decomposed via chloride hydrolysis, presumably
due to the water that was generated in situ. Further optimization of this
one-pot process is currently underway.
(11) Another possible explanation is that the isolated yields reported
in ref 4a were obtained after silica gel chromatography, whereas those
reported in Table 4 were not. We observed that the products shown in
Table 4 were partially unstable to silica gel chromatography, observing
an approximately 25% loss of material when this purification method
was attempted.
(10) We also investigated the corresponding reactions of 2pÀs in the
absence of an external base. In cases where 2 was an HCl salt (2rÀs),
exclusive formation of hydrazone 3 was observed. When 2 was used in its
free base form (2pÀq), a mixture of 1 and 4 (ca. 1:2) was observed, as well
as several unidentified minor byproducts. When 2.1 equiv of 2pÀq were
used instead of 1.05 equiv, 4 formed quantitatively. In the latter case
2pÀq presumably functioned as the external base, thus leading to similar
results as those obtained in Table 4.
(12) Nigst, T. A.; Antipova, A.; Mayr, H. J. Org. Chem. 2012, 77,
8142–8155.
Org. Lett., Vol. XX, No. XX, XXXX
C

Table 3. Optimized Cyclization of 3 to Form 4a
Table 4. Reaction of 1 with Aliphatic Hydrazinesa
entry
R
NEt3 (equiv)
isolated yield (%)
entry
R
isolated yield (%)
1
2
3
4
5
H (o)
1
1
1
2
3
74
92
81
84
95
Me (p)b
1
4-MeO-C6H4 (a)
Ph (b)
97
91
97
96
85
98
99
94
92
86
92
90
92
92
2
CH2CH2OH (q)
cyclohexyl (r)c
benzyl (s)d
3
4-Cl-C6H4 (c)
4-CF3-C6H4(d)
2-MeO-C6H4 (e)
4-Me-C6H4 (f)
4-F-C6H4 (g)
2-Cl-C6H4 (h)b
3-Cl-C6H4 (i)
4
5
6
a 0.3À0.8 M in THF, 1.05 equiv of 2, 0.5À0.8 mmol scale. b Diiso-
propylethylamine was used instead of NEt3. c HCl salt of 2 was used.
d Bis-HCl salt of 2 was used.
7
8
9
10
11
12
13
14
4-Br-C6H4 (j)
1-naphthyl (k)
2-pyridyl (l)c
or aliphatic hydrazines. Each type of hydrazine has its own
optimal set of conditions under which 4will form selectively.
For aromatic substrates, selectivity is achieved by utilizing a
two-step procedure carried out in the absence of an external
base, which preferentially promotes the initial condensation
reaction of 2 with the aldehyde moiety of 1. For aliphatic
substrates, selectivity can be attained through a single-step
reaction performed in the presence of an external base.
Initial displacement of the chloro substituent of 1 is favored,
but the greater nucleophilicity of the internal nitrogen
of 2 ensures selectivity. This chemistry can thus be used to
rapidly generate a structurally diverse array of 1-substituted
4-chloropyrazolo[3,4-d]pyrimidines (4) in a selective and high-
yielding manner. In addition, the highly reactive 4-chloro
substituent of 4 is preserved throughout all of the reactions
reported herein. These 4-chloropyrazolo[3,4-d]pyrimidine
substrates are therefore poised to readily undergo fur-
ther diversification through substitution reactions at the
4-position.
2-quinoxalyl (m)
2-benzo[d]oxazolyl (n)
a 0.5 M in CH3CN using microwave heating (entries 1À4) or 0.5 M
in dioxane using conventional heating in a sealed tube (entries 5À14),
0.5 mmol scale. b 40-min reaction time. c 4 was isolated as the HCl salt.
Witharomatichydrazines, onthe otherhand, we suggest
that the two nitrogens of 2 react in a more competitive
fashion, and thus product mixtures arise when an external
baseis present. Product selectivity becomes highly sensitive
to the substrate’s electronic properties. Electron-rich hy-
drazines such as 2a behave more similarly to the aliphatic
hydrazines, favoring initial chloride displacement by the
internal nitrogen (Table 1, entry 1). With electron-poor
hydrazines such as 2d, however, the external nitrogen
becomes the preferred site for initial chloride displacement,
and the product distribution reverses (Table 1, entry 4).
Thus for aromatic hydrazines, the most general strategy
for attaining selectivity is to perform the reactions in the
absence of an external base, which favors the initial con-
densation of2 withthe aldehyde moietyof1 (i.e., favorsthe
1f3f4 pathway in Scheme 2). The above discussions
provide a rationale to explain our observations, which
canserveasapredictivemodelforothersystems. However,
further mechanistic studies are required in order to more
fully determine the operative reaction pathways.
Acknowledgment. The authors wish to thank Dr.
Joseph M. Colacino (PTC Therapeutics, Inc.), Dr. Ramil
Baiazitov (PTC Therapeutics, Inc.), and Prof. Scott E.
Denmark (University of Illinois, UrbanaÀChampaign)
for helpful discussions and Jane Yang (PTC Therapeutics,
Inc.) for analytical support.
Supporting Information Available. Experimental details
and characterization data for compounds 3aÀn and 4aÀs.
This material is available free of charge via the Internet at
http://pubs.acs.org.
In summary, we have developed efficient procedures
to selectively convert 4,6-dichloropyrimidine-5-carbox-
aldehyde (1) and various hydrazines (2) into 1-substituted
4-chloropyrazolo[3,4-d]pyrimidines (4), usingeitheraromatic
The authors declare no competing financial interest.
D
Org. Lett., Vol. XX, No. XX, XXXX