High-yield synthesis of pyrrolidinyl PNA monomers

Article abstract of DOI:10.1016/j.tetlet.2011.08.167

Two monomers for the syntheses of conformationally restricted peptide nucleic acids were synthesized through a simple procedure, involving an asymmetric 1,3-dipolar cycloaddition chemistry as a key step, from common starting materials in 3 and 5 steps, and 58.8% and 30.5% overall yields, respectively.

Full text of DOI:10.1016/j.tetlet.2011.08.167

Tetrahedron Letters 52 (2011) 6003–6006
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Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
High-yield synthesis of pyrrolidinyl PNA monomers
Pedro Merino a, , Graziella Greco a,b, Tomás Tejero a, Ugo Chiacchio b, Antonino Corsaro b,
⇑
Venerando Pistarà b, Giovanni Romeo c
a Laboratorio de Síntesis Asimétrica, Departamento de Química Orgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Universidad de Zaragoza,
CSIC E-50009, Zaragoza, Aragon, Spain
b Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, Catania 95125, Italy
c Dipartimento Farmaco-Chimico, Università di Messina, Via, SS Anunziata, Messina 98168, Italy
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 25 July 2011
Revised 26 August 2011
Accepted 30 August 2011
Available online 10 September 2011
Two monomers for the syntheses of conformationally restricted peptide nucleic acids were synthesized
through a simple procedure, involving an asymmetric 1,3-dipolar cycloaddition chemistry as a key step,
from common starting materials in 3 and 5 steps, and 58.8% and 30.5% overall yields, respectively.
Ó 2011 Elsevier Ltd. All rights reserved.
Keywords:
Pyrrolidines
Nitrones
Dipolar cycloaddition
Nucleoside analogues
Peptide nucleic acids
The discovery of the remarkable biological profiles of peptide
nucleic acids (PNA) in 1991 by Nielsen and co-workers1 has led
to the preparation of several types of conformationally restricted
cyclic congeners in which an additional bond is introduced into
the aminoethyl glycine backbone.2 From the several possibilities
for constraining the conformation of PNA by including pyrrolidine
rings into their backbone,3 the constrained structure pyr-PNA 2
(Fig. 1), firstly reported by Nielsen and co-workers4 in 2001, has
two stereogenic centers in the monomeric unit of the PNA mole-
cule so, up to 4 different diastereomers could be prepared.
NH
O
NH
O
N
N
O
O
NH
NH
N
N
N
O
O
O
B
B
O
O
B
B
B
PNA, 1
NH
O
NH
O
N
In their original paper,4 Nielsen and co-workers prepared both
(3R,5R) and (3S,5R) monomers 4 in 13 and 15-step sequences
and 2.53% and 2.29% overall yields (Scheme 1), respectively, start-
ing from 3 (prepared from pyroglutamic acid in five steps and 49%
yield). Compounds 4 were used for preparing the corresponding
conformationally restricted PNA and it was found that pyr-PNA 2
derived from (3S,5R) isomer had the highest affinity toward RNA,
recognizing both RNA and PNA better than DNA.4
Since the Nielsen’s report no other synthetic approaches have
been communicated to obtain compounds 4 in a more efficient
way. In this context, we have recently reported5 the synthesis of
isoxazolidinyl nucleosides as building blocks for PNA analogues
through a strategy based on asymmetric nitrone 1,3-dipolar cyclo-
addition reactions. The same strategy has also been applied in our
O
B
pyr-PNA, 2
Figure 1. PNA and conformationally restricted analogue pyr-PNA.
laboratories for the synthesis of pyroglutamic acid derivatives6
thus demonstrating the synthetic utility of nitrone chemistry for
the construction of pyrrolidines.7
In this Letter we wish to report a direct asymmetric entry to
compounds 4 through an enantioselective 1,3-dipolar cycloaddi-
tion between an easily accessible nitrone A and a chiral acrylate
B (Scheme 2). DFT calculations have also been carried out in order
to rationalize the stereochemical outcome of the reaction.
Nitrone 8 was generated in situ from commercially available
aldehyde 5 and hydroxylamine 6. Compound 6 was obtained in
⇑
Corresponding author.
E-mail address: pmerino@unizar.es (P. Merino).
0040-4039/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2011.08.167

6004
P. Merino et al. / Tetrahedron Letters 52 (2011) 6003–6006
regio-(3,5), diastereo-(trans), and enantioselectivities (3S,5R). In-
5 steps
(49%)
deed, after column chromatography of the reaction mixture only
one isomer could be detected by NMR. The reduction (N–O cleav-
age) of compound 9 was first attempted with Zn in acetic acid, a
procedure successfully used in our laboratory for promoting the
transformation of 5-carboxy isoxazolidines into 3-hydroxy-2-pyr-
rolidines.13 However, under typical reaction conditions (THF,
60 °C, 5 h) a low yield (20%) was obtained. Fortunately, the cata-
lytic hydrogenation of 9 using Pd(OH)2–C (Pearlman’s catalyst) at
2000 psi for 48 h14 took place in high yield to provide pyrrolidin-
2-one 10.15 The last step consisting of the introduction of the base
moiety (adenine) into the pyrrolidine ring was carried out under
Mitsunobu conditions (PPh3, DIAD, CH3CN) with the free heterocy-
clic base. After 16 h at rt compound (3S,5R)-11 was obtained in 80%
yield (3 steps, 58.8% overall yield).16
HO2C
O
O
N
H
N
H
RO
L-pyroglutamic acid
3 (R = TBDPS)
13 steps
(2.53%)
15 steps
(2.29%)
Az
Az
Az: Bz-adenine
O
O
N
N
BocHN
BocHN
CO2H
CO2H
(3S,5R)-4
(3R,5R)-4
Scheme 1. Synthesis of pyr-PNA monomers by Nielsen and co-workers.4
In order to obtain the (3R,5R) isomer compound 10 was
subjected to
a
typical Mitsunobu reaction17 to afford, after
saponification (NaOEt, EtOH) of the intermediate benzoate 12 the
pyrrolidin-2-one 13.18 Introduction of the base moiety as described
for compound 11 furnished 14 in 81% yield. Globally, compound 14
has been obtained in 4 steps and 30.5% overall yield.19
The relative configuration of compounds 10–14 was ascertained
by conventional NMR techniques including 1D NOE, 2D NOESY,
COSY, and HMBC experiments. The absolute configuration and ste-
reochemical integrity of compounds 10 and 13 were determined
by preparing the corresponding Mosher esters.20 Analysis of the
400 MHz NMR spectra of those esters showed the presence of only
one diastereomer in each case, at the limit of detection indicating
the enantiomeric purity >98%.
B
OH
*
*
O
O
* N
* N
BocHN
BocHN
BocHN
CO2H
CO2R
4
*
CO2Xc
*
BocHN
*
Xc
O
N
O
* N
For a successful application of Kakisawa’s rule21 it is needed a
comparison between the values corresponding to a pair of isomers
having an opposite configuration. In consequence, we prepared the
corresponding Mosher esters derived from (R)- and (S)-Mosher
acids22 (Scheme 4) and the 1H NMR spectra of the pure esters were
recorded to calculate the differences in the chemical shift.
According to Kakisawa’s rule21 the methylene group (H4a and
O
CO2R
CO2R
A
B
Scheme 2. Retrosynthetic analysis for pyr-PNA monomers 4.
three steps from diethyltartrate by sequential treatment with peri-
odic acid8 to form ethyl-2-oxoacetate, hydroxylamine hydrochlo-
ride, and further reduction of the resulting oxime with borane in
pyridine.9 Based on the previous results from our10 and other11
laboratories we chose N-acryloyl-(2R)-bornane-10,2-sultam 7 as
the dipolarophile. The reaction between the three reagents 5, 6,
and 7 in a sealed tube using toluene as a solvent afforded after
18 h at 60 °C compound 9 in 76% yield12 (Scheme 3) and complete
H
4b) is selectively shielded by the phenyl group when the two
groups are located on the same plane containing H3 and the car-
bonyl group (compounds 15a and 16a). By defining d as indicated
D
in Scheme 4 (dS and dR refers to chemical shifts of (S)- and (R)-
MTPA esters, respectively) positive values would indicate a 3R con-
figuration, whereas negative values indicate a 3S configuration.
According to the values illustrated in Scheme 4 it was confirmed
O
O
toluene
BocHN
NHOH
7
N
NHBoc
N
N
O
NHBoc
S
O
O
sealed tube
60 °C, 18 h
CO2Et
6
S
O
O
N
CO2Et
O
O
5
7
8
9
CO2Et
(75%, ds >98%)
2, Pd(OH)2-C
2000 psi, 48 h
BH3·Py
H
O
H2NOH·HCl
H5IO6
NOH
CO2Et
Diethyl
tartrate
(93%)
HO
CO2Et
H2N
N
O
H2N
N
N
O
N
N
RO
N
N
Ph3P, DIAD,
adenine, rt, 16 h
NHBoc (80%)
PhCO2H, Ph3P, DIAD
THF, rt, 16 h
Ph3P, DIAD,
N
O
N
N
adenine, rt, 16 h
(81%)
O
N
N
NHBoc
NHBoc
EtO2C
NHBoc
EtO2C
EtO2C
EtO2C
14
12
13
R = PhCO
R = H
NaOEt, EtOH
(54%, 2 steps)
10
11
Scheme 3. Synthesis of PNA monomers 11 and 14.

P. Merino et al. / Tetrahedron Letters 52 (2011) 6003–6006
6005
Table 1
(R)-MTPA, DCC
(S)-MTPA, DCC
10
Total and relative energies for the four possible transition structures corresponding to
DMAP, CH2Cl2
DMAP, CH2Cl2
the reaction illustrated in Figure 2.a
Total energyb
Rel. energyc
2.62
TS
Attack
Product
2.67
H4a
O
H4a
CO2Et
O
TS1
TS2
TS3
TS4
Si endo
Si exo
Re-endo
Re-exo
(3R,5S)
(3R,5R)
(3S,5R)
(3S,5S)
ꢀ1583.003196
ꢀ1583.002915
ꢀ1583.002396
ꢀ1583.001658
0.00
0.18
0.50
0.97
OMe
CO2Et
Ph
N
R
O
Ph
O
N
MeO
F3C
R
R
R
NHBoc
R
F3C
S
NHBoc
H4b
1.72
O
H3
H4b
O
H3
1.94
a
Energies values calculated at B3LYP/6-311+G(d,p) //B3LYP/6-31G(d) level of
theory. For details on coordinates of TS1, TS2, TS3 and TS4 see Supplementary data.
15b
15a
H4a H4b
b
In hartrees.
In kcal/mol.
Δδ = δS - δR 0.05 0.22
c
(R)-MTPA, DCC
(S)-MTPA, DCC
13
DMAP, CH2Cl2
2.62
DMAP, CH2Cl2
favored of the four possible transition structures corresponding to
exo and endo attacks by the Re and Si faces of the nitrone (Table 1).
In conclusion, a high-yield synthesis of PNA monomers 11 and
14 has been achieved in 55.8% and 30.5% overall yields, respec-
tively, with considerable enhancement of the synthetic efficiency
when compared with the previous and only reported procedure
ten years ago4 (2.53% and 2.29% overall yield for similar
compounds). The approach has been based on a completely
(regio-, diastero-, and enantio-) selective 1,3-dipolar cycloaddition
of a nitrone generated in situ from common products. The relative
and absolute configurations have been assigned by NMR
techniques and DFT calculations are in agreement with the
observed experimental results.
2.60
H4a
O
H4a
N
O
CO2Et
CO2Et
H3
OMe
H3
O
N
R
R
Ph
NHBoc
Ph
F3C
S
MeO
F3C
NHBoc
S
H4b
2.31
O
H4b
2.10
R
S
16a
16b
O
O
H4a H4b
Δδ = δS - δR -0.02 -0.21
Scheme 4. Mosher esters of compounds 10 and 13.
Acknowledgments
O
O
Me
N
*
N
N
Thanks are due to the Spanish Ministry of Science and Innova-
tion (MICINN Madrid, Spain, Project CTQ2010-19606), FEDER Pro-
gram and the Government of Aragón (Group E-10, Zaragoza,
Spain). We thank the MIUR (Italy) and the CNMPS (Italy) for their
financial support. G.C. thank MICINN for a contract and the Univer-
sity of Palermo for a pre-doctoral grant.
S
O
*
O
Me
S
O
O
N
CO2Me
O
O
A
7
CO2Me
four channels studied: Si-endo; Si-exo; Re-endo and Re-exo
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.tetlet.2011.08.167.
a
b
References and notes
1. Nielsen, P. E.; Egholm, M.; Berg, R. H.; Buchardt, O. Science 1991, 254, 1497–
1500; Nielsen, P. E. Chem. Biodiversity 2010, 7, 786–804; Nielsen, P. E. In The
Chemical Biology of Nucleic Acids; Mayer, G., Ed.; Wiley: Hoboken, 2010. pp. 103-
113.
TS1
*
Xc
2. (a) Kumar, V. A. Eur. J. Org. Chem. 2002, 2021–2032; (b) Kumar, V. A.; Ganesh, K.
N. Acc. Chem. Res. 2005, 38, 404–412.
3. (a) Efimov, V. A.; Aralov, A. V.; Chakhmakhcheva, O. G. Russ. J. Bioorg.Chem.
2010, 36, 663–683; (b) Efimov, V. A.; Chakhmakhcheva, O. G. Coll. Czech. Chem.
Commun. 2006, 71, 929–955.
4. Püschl, A.; Boesen, T.; Zuccarello, G.; Dahl, O.; Pitsch, S.; Nielsen, P. E. J. Org.
Chem. 2001, 66, 707–712.
5. Merino, P.; Tejero, T.; Mates, J.; Chiacchio, U.; Corsaro, A.; Romeo, G.
Tetrahedron: Asymmmetry 2007, 18, 1517–1520.
6. (a) Merino, P.; Anoro, S.; Franco, S.; Merchan, F. L.; Tejero, T.; Tuñon, V. J. Org.
Chem. 2000, 65, 1590–1596; (b) Merino, P.; Revuelta, J.; Tejero, T.; Chiacchio,
U.; Rescifina, A.; Piperno, A.; Romeo, G. Tetrahedron: Asymmetry 2002, 13, 167–
172.
7. (a) Merino, P.; Anoro, S.; Merchan, F.; Tejero, T. Heterocycles 2000, 53, 861–875;
(b) Merino, P.; Franco, S.; Merchan, F. L.; Romero, P.; Tejero, T.; Uriel, S.
Tetrahedron: Asymmetry 2003, 14, 3731–3743.
Me
O
O
a: 2.044
b: 2.381
N
CO2Me
Si endo attack
Figure 2. Optimized (B3LYP/6-31G(d) level) low-energy transition structure (TS1)
for the 1,3-dipolar cycloaddition between nitrone and alkene 7. Ethyl and
A
BocNHCH2 groups have been replaced by methyl groups. For energy values of the
four transition structures at B3LYP/6-311G+(d,p)//B3LYP/6-31G(d) level see Table 1.
Distances of a and b forming bonds are given in amstrongs.
8. Schuda, P. F.; Ebner, C. B.; Potlock, S. J. Synthesis 1987, 12, 1055–1057.
9. Hercheid, J. D. M.; Ottenheijm, H. C. J. Tetrahedron Lett. 1978, 51, 5143–5146.
10. Tejero, T.; Dondoni, A.; Rojo, I.; Merchan, F. L.; Merino, P. Tetrahedron 1997, 53,
3301–3318. See also Ref. 6a.
11. (a) Gefflaut, T.; Bauer, U.; Ariola, K.; Koskinen, A. M. P. Tetrahedron: Asymmetry
1996, 7, 3099–3102; (b) Kim, B. H.; Lee, J.-Y. Tetrahedron: Asymmetry 1991, 2,
1359–1370; (c) Kanemasa, S.; Onimura, K.; Wada, E.; Tanaka, J. Tetrahedron:
Asymmetry 1991, 2, 1185–1188; (d) Curran, D. P.; Kim, B. H.; Daugherty, J.;
Heffner, T. A. Tetrahedron Lett. 1988, 29, 3555–3558.
as a 3R configuration for compound 10 and 3S for compound 13.
This confirmation served to ascertain the absolute configuration
of the only observed product of the cycloaddition, compound 9
as (3R,5R).
Indeed, DFT calculations23 carried out at B3LYP/6-31G(d) and
B3LYP/6-311+G(d,p)//B3LYP/6-31G(d) levels of theory for the mod-
el of the reaction illustrated in Figure 2 predicted TS1 as the most

6006
P. Merino et al. / Tetrahedron Letters 52 (2011) 6003–6006
12. Data for compound 9: oil; ½a D25
ꢁ
ꢀ73 (c 1.00, CHCl3); 1H NMR (400 MHz, CDCl3)
119.8, 146.7, 147.2, 152.9, 155.4, 156.1, 169.3, 172.4. HRMS m/z [M+Na+]
Calculated for C19H27N7NaO5: 456.1971. Found: 456.1973. Anal. Calcd for
d 0.96 (s, 3H), 1.13 (s, 3H),1.27 (t, 3H, J = 6.9 Hz), 1.33–1.40 (m, 2H), 1.42 (s, 9H),
1.87–1.92 (m, 3H), 2.02–2.12 (m, 2H), 2.43–2.49 (m, 1H), 2.65 (dt, 1H, J = 7.1,
13.7 Hz), 3.08–3.15 (m, 1H), 3.19–3.25 (m, 1H), 3.41 (d, 1H, J = 13.8 Hz), 3.44–
3.47 (m, 1H), 3.50 (d, 1H, J = 13.8 Hz) 3.56 (d, 1H, J = 16.5 Hz), 3.88 (dd, 1H),
3.96 (d, 1H, J = 16.5 Hz), 4.20 (q, 2H, J = 6.9 Hz), 5.05 (dd, 1H, J = 7.1, 8.0 Hz),
5.20 (br s, 1H). 13C NMR (100 MHz, CDCl3) d 14.1, 19.9, 20.9, 26.4, 28.4, 32.9,
38.2, 40.1, 42.2, 44.7, 47.8, 48.9, 52.9, 59.5, 60.9, 71.5, 77.5, 79.4, 85.5, 156.6,
168.9, 171.1. HRMS m/z [M+Na+] Calcld for C24H39N3NaO8S: 552.2356. Found:
552.2350. Anal. Calcd. for C24H39N3O8S: C, 54.42; H, 7.42; N, 7.93. Found: C,
54.29; H, 7.51; N, 8.11.
C
19H27N7O5: C, 52.65; H, 6.28; N, 22.62. Found: C, 52.49; H, 6.39; N, 22.42.
17. Hughes, O. L. Org. React. 1992, 42, 335–656.
18. Data for compound 13: oil; ½a D25
ꢁ
+2 (c 1.00, CHCl3); 1H NMR (400 MHz, CDCl3) d
1.21 (t, 3H, J = 7.1 Hz), 1.36 (s, 9H), 2.01–2.09 (m, 1H), 2.32–2.38 (m, 1H), 2.99–
3.03 (m, 1H), 3.40–3.45 (m, 1H), 3.67–3.69 (m, 1H), 3.79 (d, 1H, J = 17.8 Hz),
4.13 (q, 2H, J = 7.1 Hz), 4.20 (d, 1H, J = 17.8 Hz), 4.23 (m, 1H), 5.56 (br s, 2H, ex.
D2O). 13C NMR (100 MHz, CDCl3) d 14.3, 28.5, 31.9, 41.8, 43.7, 58.2, 61.7, 68.4,
79.6, 156.4, 169.3, 176.3. HRMS m/z [M+Na+] Calcld for C14H24N2NaO6:
339.1532. Found: 339.1535. Anal. Calcd for C14H24N2O6: C, 53.15; H, 7.65; N,
8.86. Found: C, 53.21; H, 7.80; N, 8.66.
13. Merino, P.; Mates, J. A.; Revuelta, J.; Tejero, T.; Chiacchio, U.; Romeo, G.;
Iannazzo, D.; Romeo, R. Tetrahedron Asymmetry 2002, 13, 173–190. See also
Ref.6a.
19. Data for compound 14: oil; ½a D25
ꢁ
ꢀ3 (c 1.00, MeOH); 1H NMR (400 MHz, CDCl3)
d 1.29 (t, 3H, J = 7.1 Hz), 1.46 (s, 9H), 2.62 (ddd, 1H, J = 14.2, 8.8, 7.7 Hz), 2.88
(ddd, 1H, J = 14.2, 10.9, 8.5 Hz), 3.29 (ddd, 1H, J = 1.7, 3.1, 14.6 Hz), 3.69–3.76
(m, 1H), 3.81 (d, 1H, J = 17.9 Hz), 4.18–4.24 (m, 3H), 4.56 (d, 1H, J = 17.9 Hz),
5.17 (dd, 1H, J = 8.8, 10.9 Hz), 5.67 (br s, 3H), 7.84 (s, 1H), 8.38 (s, 1H). 13C NMR
(100 MHz, CDCl3) d 14.3, 27.3, 28.7, 40.9, 42.3, 53.6, 55.5, 61.8, 79.7, 120.2,
146.8, 147.1, 152.8, 155.6, 156.7, 169.7, 171.9. HRMS m/z [M+Na+] Calcld for
14. Merino, P.; Padar, P.; Delso, I.; Thirumalaikumar, M.; Tejero, T.; Kovacs, L.
Tetrahedron Lett. 2006, 47, 5013–5016.
15. Data for compound 10: oil; ½a D25
ꢁ
+59 (c 0.95, CHCl3); 1H NMR (400 MHz, CDCl3)
d 1.27 (t, 3H, J = 7.0 Hz), 1.42 (s, 9H),1.77 (dt, 1H, J = 7.2, 13.4 Hz), 2.52 (ddd, 1H,
J = 7.2, 8.5,13.4 Hz), 3.30–3.41 (m, 2H), 3.77–3.83 (m, 1H), 3.98 (m, 1H), 4.16–
4.22 (m, 2H), 4.37 (q, 2H, J = 7.0 Hz), 5.27 (br s, 2H, ex. D2O). 13C NMR
(100 MHz, CDCl3) d 13.9, 28.4, 30.8, 41.1, 42.6, 55.2, 61.7, 68.9, 79.8, 156.2,
168.8, 175.9. HRMS m/z [M+Na+] Calcd for C14H24N2NaO6: 339.1532. Found:
339.1534. Anal. Calcd for C14H24N2O6: C, 53.15; H, 7.65; N, 8.86. Found: C,
53.06; H, 7.77; N, 8.93.
C
19H27N7NaO5: 456.1971. Found: 456.1974. Anal. Calcd for C19H27N7O5: C,
52.65; H, 6.28; N, 22.62. Found: C, 52.81; H, 6.11; N, 22.58.
20. Mancuso, A. J.; Huang, S.-L.; Swern, D. J. Org. Chem. 1978, 43, 2480–2482. See
also ref.10
.
21. (a) Ohtani, I.; Kusumi, T.; Kashman, Y.; Kakisawa, H. J. Am. Chem. Soc. 1991, 113,
4092–4096; (b) Kusumi, T.; Fukushima, T.; Ohtani, I.; Kakisawa, H. Tetrahedron
Lett. 1991, 32, 2939–2942.
22. This methodology is equivalent to that of preparing the esters of racemic
mixtures using an only enantiomerically pure Mosher acid.
23. For details see Supplementary data.
16. Data for compound 11: oil; ½a D25
ꢁ
ꢀ1 (c 0.75, MeOH); 1H NMR (400 MHz, CDCl3)
d 1.32 (t, 3H, J = 7.0 Hz), 1.49 (s, 9H), 2.64–2.79 (m, 2H), 3.23 (dt, 1H, J = 4.8,
14.9 Hz), 3.60–3.66 (m, 1H), 3.96–4.0 (m, 2H), 4.25 (m, 2H), 4.44 (d, 1H,
J = 7.0 Hz), 5.39 (m, 1H), 5.67 (br s, 3H, ex. D2O), 7.84 (s, 1H), 8.29 (s, 1H). 13C
NMR (100 MHz, CDCl3) d 14.2, 28.6, 30.6, 42.0, 44.4, 54.7, 57.8, 61.9, 77.0,