An expeditious and atom-economic synthesis of lead-like, medicinally important 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones

Article abstract of DOI:10.1016/j.tetlet.2014.06.104

We have developed an expeditious and atom-economic synthesis of lead-like, privileged 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones, which is based on Sonogashira coupling and a two-step condensation with hydrazine hydrate leading to two ring-forming events, with full control over the two elements of diversity present.

Full text of DOI:10.1016/j.tetlet.2014.06.104

Accepted Manuscript
An expeditious and atom-economic synthesis of lead-like, medicinally impor-
tant 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones
Prashant Mujumdar, Alexander Sapegin, Mikhail Dorogov, Mikhail Krasavin
PII:
S0040-4039(14)01117-4
DOI:
http://dx.doi.org/10.1016/j.tetlet.2014.06.104
TETL 44829
Reference:
Tetrahedron Letters
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Received Date:
Revised Date:
Accepted Date:
11 May 2014
30 May 2014
26 June 2014
Please cite this article as: Mujumdar, P., Sapegin, A., Dorogov, M., Krasavin, M., An expeditious and atom-
economic synthesis of lead-like, medicinally important 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones, Tetrahedron
Letters (2014), doi: http://dx.doi.org/10.1016/j.tetlet.2014.06.104
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An expeditious and atom-economic synthesis of lead-like,
medicinally important 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones
Prashant Mujumdar, Alexander Sapegin, Mikhail Dorogov, Mikhail Krasavin*
Cl
O
5 steps
3 purifications
H2N
Cl
R1 CHO
H2N
N
NH2
O
N
R2
R1
N
R2
O
Cl
6 new bonds formed

An expeditious and atom-economic synthesis of lead-like,
medicinally important 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones
Prashant Mujumdar,a Alexander Sapegin,b Mikhail Dorogov,b Mikhail Krasavina, c, *
a
Eskitis Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111,
Australia
b The Ushinsky Yaroslavl State Pedagogical University, 108 Respublikanskaya St., Yaroslavl,
150000, Russian Federation
c
Department of Chemistry, St. Petersburg State University, 26 Universitetskyi Prospekt,
Peterhof 198504, Russian Federation
* Corresponding Author; phone: + 7 931 3617872, fax: +7 812 428 6939.
E-mail: m.krasavin@hotmail.com
Abstract: We have developed an expeditious and atom-economic synthesis of lead-like,
privileged 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones, which is based on Sonogashira
coupling and a two-step condensation with hydrazine hydrate leading to two ring-forming
events, with full control over the two elements of diversity present.
Keywords: propargylamine, Sonogashira coupling, ynone, pyrazole, intramolecular
alkylation, atom efficiency, lead-likeness, privileged structure
The choice of a synthetic target may not only be dictated by the current practical needs of a
specific research program, but may be a result of a chemist’s conscious effort to undertake a
creativity exercise in synthetic planning and identifying particularly simple ways to construct
structurally complex scaffolds with an underlying potential to exert biological activities.
Undertaking such an exercise regularly, besides its scholastic value, may very well be the
principal, if not the only driving force behind various scaffold-oriented efforts aimed at
increasing the volume and improving the quality of the chemical matter currently available
for biological screening.

Numerous ideas generated in the course of such an activity require some level of
prioritization before taking a decision to realize them in a laboratory setting. A scaffold idea
will be more likely to progress through the ‘paper exercise’ stage if it scores highly on such
basic criteria as novelty, medicinal relevance (i.e., availability of biological activity data for
related structural motifs) and, very importantly, the low number and practical simplicity of
synthetic manipulations required to translate the scaffold idea into a set of tangible
compounds.
Ample use of ring-forming transformations engaging multiple reactive centers within
synthetic precursors is a proven strategy to achieve convergent, atom-economic synthetic
planning, and thus shorten the sequence of synthetic operations.1 In the course of one of our
group’s brain-storming sessions, the idea of assembling ynone 1 was raised. It was
recognized as a versatile, triply electrophilic synthon and was expected to give rise to 4,5-
dihydropyrazolo[1,5-a]pyrazin-6-ones 2 on reaction with hydrazine, in which case, the latter
would act as an “N2-–N-” equivalent (Figure 1). A quick analysis of the literature available on
the pyrazolo[1,5-a]pyrazine scaffold revealed it to be relatively novel with the vast majority
of reports published in the last 3-5 years. At the same time, the scaffold appeared highly
relevant in terms of possible medicinal chemistry applications. In fact, based on the number
of diverse biological activities displayed by the compounds containing the pyrazolo[1,5-
a]pyrazine motif, it could be considered privileged, as defined by Evans.2 To support this
view, the following selected examples can be mentioned (Figure 2):
i.
the core was central to the design of Janssen’s BACE-1 inhibitors (exemplified by 3)
for treatment of Alzheimer’s disease;3
ii.
positive allosteric modulators of metabolic glutamate receptor 5 (mGluR5), such as 4,
have recently been disclosed by Janssen and Vanderbilt University;4
iii. a team from Millennium Pharmaceuticals developed selective HDAC6 inhibitors (e.g.,
5)5 that are essentially the pyrazolo[1,5-a]pyrazine scaffold decorated with a
pharmacophoric hydroxamic acid functionality;
iv. a large team of researchers from Shandong University discovered potent cytotoxic
agents such as 66 that have subsequently been found to act as apoptosis inducers;7
v.
Merck and Co. incorporated the pyrazolo[1,5-a]pyrazine scaffold in the design of their
selective MK2 inhibitors (e.g., 7);8
vi. the bicyclic heterocycle has appeared as part of a bioactive molecule’s unique periphery
in Genentech’s BTK inhibitors,9 in the selective TrkA inhibitors from Dr. Reddy’s

Laboratories,10 in Janssen’s SCD-1 inhibitors which are potentially useful as anti-
obesity drugs,11 in GSK’s inhibitors of NADPH oxidase II12 and
Pharmaceuticals’ calcium channel blockers for pain management.13
Zalizus
In addition to these considerations, the development of screening libraries based on the 4,5-
dihydropyrazolo[1,5-a]pyrazine scaffold would fill an important void in the currently
available screening collections – namely, the scarcity of so-called lead-like compounds.
According to a recent seminal account from GSK’s computational chemistry team,14 the
synthetic methods reported in the literature over recent decades appear to be unintentionally
biased toward producing more lipophilic (high logP) compounds of higher molecular weight
(Mw), whereas the chemistry space defined by Mw <350 and logP <3.0 and thus most
relevant to screening-based drug discovery efforts, remains alarmingly underpopulated
(Figure 3). The 4,5-dihydropyrazolo[1,5-a]pyrazine core itself resides very well within this
range (Mw = 137, clogP = -1.87),15 which leaves ample room (both in terms of lipophilicity
and heavy atom count) for growing the periphery of a compound during library development.
To access the key synthons (such as 1), two possibilities were considered (Figure 4). One of
them was described by Wipf16 and implied the generation, from an appropriately decorated
propargylamine synthon, of a lithium acetylide species and its addition to an aldehyde
followed by oxidation of the intermediate alcohol to the corresponding carbonyl compound.
The other possibility would be to invoke Sonogashira-type coupling of the same synthon with
an acyl chloride. The latter approach, being very well described by Cox,17 was chosen by us
due to its practical simplicity.
The overall synthetic scheme toward 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones 2a-m
developed based on this approach is presented in Scheme 1. Terminal alkyne synthon 8 was
prepared in three simple chemical operations (imine formation, imine reduction and capping
of the secondary amine with chloroacetyl chloride in the presence of a polymer-supported
piperidine base as an HCl scavenger) and purified chromatographically in good to excellent
yields. Sonogashira coupling with a set of acyl chlorides (aliphatic and aromatic) proved to
work very well under the conditions reported by Cox.17 Finally, condensation with hydrazine
hydrate was very quick under reflux conditions in ethanol, however, it did not lead, even over
prolonged reaction times and on using excess hydrazine hydrate, to the concomitant
piperazinone ring closure as we had hoped. We discovered, however, that once the initial
formation of the pyrazole nucleus was complete (according to TLC analysis), the desired

intramolecular alkylation could be relatively quickly brought about by the addition of an
equivalent amount of sodium ethoxide and continued heating at reflux (similarly to the
conditions for intramolecular pyrazole alkylation described by Janssen earlier).3 As can be
seen from Table 1, a set of diversely substituted 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones
2a-m was prepared in good to excellent overall yields.18 The synthesis is remarkably atom-
efficient (all the synthons used were almost entirely incorporated into the product structure
with the loss of condensation water and two equivalents of HCl), involves formation of five
chemical bonds and requires only three purifications. The resulting compounds are distinctly
lead-like as can be seen from their Mw/clogP profile (Figure 5).15
In summary, we have developed an expeditious and atom-economic synthesis of lead-like,
privileged 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones with full control over the two elements
of diversity present. The biological activity of these compounds will be studied extensively,
via a panel biological annotation approach, and any promising bioactivity leads identified
will be reported in due course.
Acknowledgements
Mikhail Krasavin acknowledges support from Griffith University.
References and notes
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M.; Bartolome-Nebreda, J. M.; Macdonald, G. J. PCT Int. Appl. WO2012078817, 2012;
Chem. Abstr. 2012, 157, 76803; (b) Conn, P. J.; Lindsley, C. W.; Stauffer, S. R.;
Bartolome-Nebreda, J. M.; Conde-Ceide, S.; Macdonald, G. J.; Tong, H. M.; Jones, C.

K.; Alcazar-Vaca, M. J.; Andres-Gil, J. I.; Malosh, C. PCT Int. Appl. WO2012083224,
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Y. Eur. J. Med. Chem. 2011, 46, 2359-2367.
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18. Characterization data for representative compounds: 2b – sticky white solid, mp = 116-
1
123 °C (broad); H NMR (400 MHz, CDCl3) δ 7.65-7.78 (m, 2H), 7.12-7.21 (m, 2H),
6.31 (s, 1H), 5.11 (s, 2H), 4.12 (s, 2H), 2.83 (d, J = 7.1 Hz, 2H), 1.62 (m, 1H), 0.57 (d, J

= 7.7 Hz, 6H); 13C NMR (100 MHz, CDCl3) δ 170.2, 163.5, (d, JC-F = 254.0 Hz), 150.2,
140.2, 127.5 (d, JC-F = 9.8 Hz), 126.9 (d, JC-F = 2.7 Hz), 115.6 (d, JC-F = 27.6 Hz), 101.6,
49.2, 48.3, 44.6, 28.0, 19.6; LC MS (EI) m/z [M+H]+ 288.3; anal. calcd for C16H18FN3O:
C, 66.88; H, 6.31; N 14.62; found: C, 67.02; H, 6.42; N, 14.68; 2h –white solid, mp =
163-165 °C; 1H NMR (400 MHz, CDCl3) δ 7.67-7.72 (m, 2H), 7.33 – 7.46 (m, 2H), 7.19
– 7.23 (m, 2H), 6.23 (m, 1H), 6.11 (s, 1H), 5.82 (d, J = 4.6 Hz, 1H), 5.08 (s, 2H), 4.63 (s,
2H), 4.21 (s, 2H); 13C NMR (100 MHz, CDCl3) δ 168.2, 150.3, 149.3, 142.4, 138.7,
130.8, 129.1, 127.5, 124.5, 111.8, 106.3, 100.4, 46.9, 45.8, 37.3; LC MS (EI) m/z
[M+H]+ 294.3; anal. calcd for C17H15N3O2: C, 69.61; H, 5.15; N 14.33; found: C, 69.53;
H, 5.07; N, 14.44; 2l –white solid, mp = 134-136 °C; 1H NMR (400 MHz, CDCl3) δ 7.67
(d, J = 7.8 Hz, 2H), 7.26 – 7.32 (m, 3H), 7.08 – 7.16 (m, 2H), 7.07 (d, J = 7.8 Hz, 2H),
6.23 (s, 1H), 4.98 (s, 2H), 4.18 (s, 2H), 3.57 (t, J = 7.0 Hz, 2H), 2.83 (t, J = 7.0 Hz, 2H),
2.37 (s, 3H); 13C NMR (100 MHz, CDCl3) δ 165.3, 154.5, 141.5, 139.6, 138.4, 129.6,
128.9, 128.7, 128.0, 126.7, 126.3, 100.9, 50.3, 49.1, 43.9, 33.8, 21.7; LC MS (EI) m/z
[M+H]+ 332.4; anal. calcd for C21H21N3O: C, 76.11; H, 6.39; N 12.68; found: C, 76.03;
H, 6.33; N, 12.74;

Figure 1. The idea for possible synthetic access to 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones
2 developed in this work.
-N N2-
H2N
NH2
Cl
N
O
N
R2
O
R1
N
N
R2
O
R1
2
1
Figure 2. Examples of bioactive pyrazolo[1,5-a]pyrazines reported in the literature.
H2N
N
O
N
N
Cl
N
HN
N
CF3
N
N
N
O
F
4
3
O
N
N
F
HN OH
O
N
N
N
N
N
N
N
HN
N
N
O
O
O
6
7
5
Figure 3. Distribution of Mw and clogP values for two sets of ~30,000 compounds selected
from two major screening library vendors – Enamine and ChemDiv (MK’s personal account).

Figure 4. Possible retrosynthetic considerations of synthon 1.
Sonogashira-type
coupling with an acyl
chloride
Li acetylide addition to
an aldehyde followed
by oxidation
R2
O
R2
O
Cl
R2
O
Cl
Cl
Li
H
Cl
N
N
N
1
O
O
O
R1
R1
R1
Figure 5. Mw/clogP profile15 of 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones 2a-m synthesized
in this work.
Scheme 1. Synthesis of 4,5-dihydropyrazolo[1,5-a]pyrazin-6-ones 2 developed in this work.
1) R1CHO, MgSO4
Cl
CH2Cl2, r.t., 3 h
2) NaBH4, CH2Cl2-MeOH
R1
O
r.t., 30 min
H2N
N
3) ClCH2COCl, PS-Piperidine
CH2Cl2, r.t., 1 h
8, 76-92%
R2COCl, THF
PdCl2(PPh3)2, CuI
Et3N, r.t., 1 h
Cl
.
1) N2H4 H2O, EtOH
reflux, 1 h
O
R1
O
N
N
R2
R2
O
R1
N
N
2) EtONa/EtOH
reflux, 3 h
2a-m
1, 64-93%

Table 1. 4,5-Dihydropyrazolo[1,5-a]pyrazin-6-ones 2 prepared in this work.
Entry
R1
R2
Yield of 8
(%)
Yield of 1
(%)
Yield of 2
(%)
Ph
4-MeC6H4
4-FC6H4
2-furyl
73
89
59
a
b
c
i-Pr
n-Pr
84
86
77
77
66
65
63
78
67
d
*
O
*
e
f
Ph
Me
92
77
64
71
75
57
3,5-F2C6H3
*
g
2,4-(MeO)2C6H3
81
70
75
*
2-furyl
Ph
Et
81
90
93
68
73
64
h
i
N
*
4-FC6H4
92
91
78
j
*
Bn
Bn
4-FC6H4
4-MeC6H4
i-Pr
77
83
90
90
83
71
81
63
48
k
l
m
*