Synthesis of β-lactam nucleoside chimera via Kinugasa reaction and evaluation of their antibacterial activity

Article abstract of DOI:10.1016/j.bmcl.2005.02.064

Several β-lactam nucleoside chimeras 1 (cis) and 2 (trans) were synthesized from the corresponding N-propargyl nucleobases via Kinugasa reaction in moderate yields. Initial screening for antibacterial activity against ampicillin sensitive E. coli showed weak activity for the uracil-β-lactam chimera.

Full text of DOI:10.1016/j.bmcl.2005.02.064

Bioorganic & Medicinal Chemistry Letters 15 (2005) 2015–2018
Synthesis of b-lactam nucleoside chimera via Kinugasa reaction
and evaluation of their antibacterial activity
Amit Basak* and Runa Pal
Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302, India
Received 4 January 2005; revised 17 February 2005; accepted 19February 2005
Abstract—Several b-lactam nucleoside chimeras 1 (cis) and 2 (trans) were synthesized from the corresponding N-propargyl nucleo-
bases via Kinugasa reaction in moderate yields. Initial screening for antibacterial activity against ampicillin sensitive E.coli showed
weak activity for the uracil-b-lactam chimera.
ꢀ 2005 Elsevier Ltd. All rights reserved.
Bioconjugates or the so-called dual acting drugs have
drawn significant interest in recent years. Several re-
search groups have applied this concept by combining
two different pharmacophores to successfully generate
chimeric molecules. For example, a chimera of classical
b-lactam antibiotics and gyrase inhibitors has given rise
to extremely potent antibiotics.1 Few years back, Ugi
and co-workers2 developed an elegant method for the
synthesis of b-lactam nucleoside chimeras by using the
well-known multicomponent Ugi reaction.3 Although
these molecules looked attractive targets owing to the
multi-faceted activity profiles of b-lactams4 and nucleo-
sides,5 the biological activity of these molecules has not
been reported. In this communication, we would like to
report an alternate approach to the synthesis of a struc-
turally different b-lactam nucleic base chimeras6 using
Kinugasa reaction7 between nitrones and various N-
propargyl nucleic acid bases. The results of initial
screening of these molecules as antibacterial agents are
also reported herein.
gyl bases, namely 3-propargyl adenine 3a, and 1-propar-
gyl uracil 3c, 1-propargyl thymine 3d and 3-propargyl
guanine 3e. Amongst these, propargyl uracil8 and thy-
mine, 3c and 3d, respectively, were synthesized by direct
alkynylation with propargyl bromide using DMF as a
solvent. For the synthesis of adenine-based alkyne, we
prepared both 3-propargyl adenine and its di-t-Boc ana-
logue 3b. The latter was synthesized to enhance the solu-
bility in organic solvents. The propargyl guanine,
however, could not be prepared; in our hands, the re-
ported acetylation followed by alkynylation ran into
problems.
With the propargyl nucleobases in hand, we proceeded
to do the Kinugasa reaction with the diphenyl nitrone
4 using our published procedure.9 N,N-di-t-Boc propar-
gyl adenine 3b was reacted in the first place for better
handling due to solubility. However, the reaction with
the nitrone 4 in the presence of CuI and Et3N in
DMF produced only the exo-methylene b-lactam 8 thus
showing the liability of the imidazoline ring as a nucleo-
fugal. At the same time, the fact that we could obtain a
b-lactam demonstrated that the initial cycloaddition be-
tween the nitrone and the in situ generated cuprous acet-
ylide was occurring; it is only during the rearrangement
of the intermediate isooxazoline 5 to the b-lactam 8,
concomitant elimination took place (route a).10 One
may, however, argue that the b-lactams 1b and 2b
were first formed via the standard mechanism. These
then underwent a base-induced elimination. In order
to establish the actual pathway, we synthesized the
di-Boc b-lactams 1b (cis) and 2b (trans) from the corre-
sponding adenine b-lactams. These were subjected to the
Since the nucleotide bases have reactive functional
groups, for the synthesis of the targeted b-lactams, a
method was required, which has a high functional group
tolerance. The Kinugasa reaction, which has drawn
significant attention in recent years, satisfies such a criteria.
Thus for our synthesis we needed the various N-propar-
Keywords: b-Lactam; Nucleoside; Chimera; Kinugasa reaction;
Antibacterial.
*
Corresponding author. Tel.: +91 322283300; fax: +91 322282252;
e-mail: absk@chem.iitkgp.ernet.in
0960-894X/$ - see front matter ꢀ 2005 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2005.02.064

2016
A.Basak, R.Pal / Bioorg.Med.Chem.Lett.15 (2005) 2015–2018
Table 1. Results of Kinugasa reaction of propargyl bases with the
phenyl nitrone
basic conditions employed in Kinugasa reaction. We
have not noticed any formation of the exo-methylene
b-lactam thus ruling out the latter mechanistic possibi-
lity as depicted in route b (Scheme 1).
Nitrone
Propargyl
base
Time Combined Ratio of cis
and trans
(h)
yield (%)
Phenyl (4) Adenine (3a)
Phenyl (4) Uracil (3c)
36
36
64
60
60
1:6
Realizing that the two t-butyloxy carbonyl groups at the
6-amino group enhance the electron withdrawing char-
acter of the imidazole ring in adenine, we decided to car-
ry out the reaction with propargyl adenine itself for
which the imidazole ring is not activated further by
the electron withdrawal from the adjacently fused
pyrimidine ring. On the contrary the presence of free
amine should reduce the electron withdrawing charac-
ter. Gratifyingly, the reaction was successful and we ob-
tained moderate yields of cis and trans b-lactams 1a and
2a, respectively (Scheme 2). The reaction of propargyl
uracil and thymine with the nitrone were also successful,
both producing a mixture of cis (1b,c) and trans b-lac-
tam (2b,c) in respectable yields (Table 1). NMR and
mass spectroscopy characterized the structures of the
various nucleoside-b-lactams chimeras. For example,
for the adenine-based b-lactam 1a, the characteristic sig-
nals for the ring hydrogens H-3 and H-4 appeared at d
4.39and 5.50 for the cis isomer with the H-4 appearing
as a doublet with a characteristic11 coupling constant of
6.0 Hz. For the corresponding trans isomer, H-4 ap-
2.5:1
2:1
Phenyl (4) Thymine (3d) 36
With the chimeras of b-lactam and nucleobases in hand,
we turned our attention to check their antibacterial
activities, if any. However, poor solubility of the materi-
als in many commonly used water miscible organic sol-
vents proved to be a problem. Finally, the activity could
be checked in DMF solution using the Ôholed-plateÕ as-
say12 against penicillin sensitive E.coli strain. The ura-
cil-b-lactam (initially given as a mixture of cis and
trans) was found to be active against the strain with
the activity potency of about 20% of that of ampicillin.
Similar activity was found when individual cis and trans
isomers 1c and 2c were used for antibacterial screening.
No firm conclusion could be drawn for the adenine and
thymine based b-lactams as these immediately precipi-
tates out upon contact with water present in the agar
medium.
peared as a doublet at d 5.01 with a characteristic11
J
In conclusion, we have demonstrated the utility of Kinu-
gasa reaction in the synthesis of b-lactam nucleobase
chimeras. The uracil-based chimera has been shown to
possess some activity, which may possibly be improved
value of 2.5 Hz. The H-3, shielded by the phenyl, ap-
peared as a multiplet at d 3.55. The other b-lactams
showed NMR spectra compatible with their structures.
H+
b
Ph
N
NH
N
Ph
N
N
N
N
Ph
H
a
a
R
R
R
R
+
N+
N
N
R
R
_
O
+
..
Ph
N
N
O
+
N
Cu
Ph
N
N
O
Cu
Ph
N
N
N
7
5
6
4
3b
b
Ph
Ph
Ph
Ph
N
N
N
N
N
R
R
N+
N
R
8
O
..
N
N
O
Ph
O
N
N
Cu
Ph
N
R
N
8
1b (cis) + 2b (trans)
9
R =
O
O
Scheme 1.
B
B
O
N
N
N
Ph
Ph
Ph
Ph
O
Ph
O
H
N
N
CuI / Et3N
DMF
HN
HN
O
+
N
O
N
N
O
N
N
O
O
H2N
N
HN
Ph
+
N
H3C
NH2
3d
3a
4
3e
2a, 2c, 2d
3c
1a, 1c, 1d
Scheme 2.

A.Basak, R.Pal / Bioorg.Med.Chem.Lett.15 (2005) 2015–2018
2017
by synthesizing water-soluble entities. Current efforts in
our laboratory are aimed towards that end.
trans b-Lactam with uracil (2c)
dH 3.39(1H, m), 4.27, 4.24 (2H, 2 · dd, J = 6.4, 7.4,
9.3 Hz), 5.00 (1H, d, J = 2.5 Hz), 5.71 (1H, dd, J = 2,
5.8 Hz), 7.48–7.04 (10H, m), 8.56 (1H, br s); dC 44.20,
45.83, 58.08, 102.81, 117.05, 124.38, 125.63, 128.75,
129.21, 129.38, 134.23, 136.77, 144.36, 150.93, 162.91
and 163.88; Mass (ES) 348 (MH+), 370 (MNa+);
HRMS: calcd for C20H17N3O3 + H+ 348.1349found
348.1342.
General procedure for preparation of b-lactam
To a solution of N-propargyl bases 3a, 3c or 3d
(1.1 mmol) in DMF, triethylamine (1.1 mmol) was
added under argon. The mixture was stirred for
30 min at 0 ꢁC. CuI (1 mmol) was added and stirring
was continued for 5 min at room temperature. Solution
of phenyl nitrone 4 (1 mmol) in DMF was added drop
wise for about 15 min. The reaction mixture was stirred
for 36 h at rt, after which it was poured into water and
filtered through Celite. The Celite bed was thoroughly
washed with EtOAc. The organic layer was washed with
saturated solution of NH4Cl, water and brine and dried
over Na2SO4. Filtration followed by removal of solvent
gave solid residue from which product was isolated by
column chromatography over Si-gel using hexane–
EtOAc or DCM–methanol (for adenine b-lactams) as
eluent.
cis b-Lactam with thymine (1d)
mmax 3432, 3154, 3028, 1750, 1701, 1676 cmÀ1; dH
1.80 (3H, s), 3.72, 3.61 (2H, 2 · dd, J = 7.4, 8.0,
14.9Hz), 4.21 (1H, m), 5.29 (1H, d, J = 5.7 Hz), 6.08
(1H, s), 7.43–7.09(10H, m), 8.20 (1H, br s); dC 12.02,
51.74, 54.95, 56.30, 107.81, 116.84, 123.89, 127.42,
128.61, 129.07, 129.27, 134.34, 137.14, 141.35, 150.87,
164.21, 164.88; Mass (ES) 362 (MH+), 384 (MNa+);
HRMS: calcd for C21H19N3O3 + H+ 362.1506 found
362.1492.
trans b-Lactam with thymine (2d)
Spectral data
m
max 3435, 3025, 1741, 1704, 1673 cmÀ1; dH 1.90 (3H, s),
1H NMR spectra were recorded at 200 MHz in CDCl3
unless otherwise mentioned while 13C NMR spectra
were recorded at 50 MHz in d6-DMSO.
3.40 (1H, m), 4.20, 4.35 (2H, 2 · dd, J = 5.2, 14.7,
6.6 Hz), 5.06 (1H, d, J = 2.4 Hz), 7.44–7.04 (10H, m),
9.05 (1H, br s); dC 12.01, 43.83, 44.26, 51.74, 108.36,
116.84, 125.89, 127.41, 128.60, 129.07, 129.26, 134.34,
138.14, 141.83, 151.07, 164.21 and 164.42; Mass (ES)
362 (MH+), 384 (MNa+); HRMS: calcd for
C21H19N3O3 + H+ 362.1506 found 362.1494.
cis b-Lactam with adenine (1a)
m
max 3304, 3136, 1744, 1664, 1597 cmÀ1; dH (d6-DMSO):
3.97, 4.20 (2H, 2 · dd, J = 5.7, 14.0, 7.9Hz), 4.39(1H,
m), 5.50 (1H, d, J = 6.0 Hz), 7.37–7.03 (10H, m), 8.08
(1H, s); dC 41.04, 56.27, 58.17, 116.78, 123.87, 125.91,
127.09, 128.37, 128.93, 129.17, 137.03, 137.17, 140.78,
149.49, 152.57, 155.95, 164.08; Mass (ES) 371 (MH+),
393 (MNa+); HRMS: calcd for C21H19N6O + H+
371.1623 found 371.1622.
trans-b-Lactam with di-Boc adenine (2b)
dH 1.41 (18H, s), 3.64 (1H, m), 4.73 (2H, d, J = 6.0 Hz),
5.04 (1H, d, J = 2.5 Hz, H-4), 7.43–7.00 (10H, m), 7.97
(1H, s), 8.44 (1H, s); Mass (ES) 571 (MH+).
Acknowledgements
trans b-Lactam with adenine (2a)
Author A.B. expresses thanks to the Department of Sci-
ence and Technology, Government of India for funding.
R.P. thanks Council of Scientific and Industrial Re-
search for fellowship.
mmax 3313, 3117, 1735, 1679, 1637, 1600 cmÀ1; dH 3.55
(1H, m), 4.73 (2H, app d, J = 6.0 Hz), 5.01 (1H, d,
J = 2.5 Hz, H-4), 5.82 (2H, br s), 7.43–7.00 (10H, m),
7.97 (1H, s), 8.44 (1H, s); dC 41.80, 58.34, 59.64,
116.78, 118.54, 123.87, 125.30, 128.28, 128.62, 128.75,
133.92, 136.06, 136.49, 140.38, 152.10, 155.08 and
163.55; Mass (ES) 371 (MH+), 393 (MNa+); HRMS:
calcd for C21H19N6O + H+ 371.1623 found 371.1625.
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cis b-Lactam with uracil (1c)
mmax 3390, 3041, 1744, 1673 cmÀ1; dH 3.65 (2H, d,
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5.48 (1H, dd, J = 1.8, 6.0 Hz), 6.50 (1H, d, J = 7.9Hz),
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164.96; Mass (ES) 348 (MH+), 370 (MNa+); HRMS:
calcd for C20H17N3O3 + H+ 348.1349found 348.1339.

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