Biomimetic self-condensation of malonates mediated by nucleosides

Article abstract of DOI:10.1016/j.tetlet.2007.09.036

Nucleoside mediated Claisen condensation of malonates has been achieved under biomimetic weak acid conditions, pH 3 or 4, 0.15 M NaCl, and 0.125 M Mg²⁺. The result illustrates the catalyzing property of end-nucleosides of t-RNA in the RNA world

Full text of DOI:10.1016/j.tetlet.2007.09.036

Tetrahedron Letters 48 (2007) 8026–8028
Biomimetic self-condensation of malonates mediated by nucleosides
Qi Ji, Howard J. Williams,* Charles A. Roessner and A. Ian Scottz
Center for Biological NMR, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
Received 16 August 2007; revised 4 September 2007; accepted 5 September 2007
Available online 11 September 2007
Abstract—Nucleoside mediated Claisen condensation of malonates has been achieved under biomimetic weak acid conditions, pH 3
or 4, 0.15 M NaCl, and 0.125 M Mg2+. The result illustrates the catalyzing property of end-nucleosides of t-RNA in the RNA
world.
Ó 2007 Elsevier Ltd. All rights reserved.
It has been suggested that the most primitive organisms
used RNA’s rather than proteinaceous enzymes as cata-
lysts for their metabolic pathways.1,2 Molecular mecha-
nisms were proposed by Scott for carbon–carbon bond
forming processes (Fig. 1) in the RNA world leading
to the lipids necessary for the membranes.3 However,
to our knowledge, no self Claisen condensation of nucleo-
side malonates has been reported. In this work, self-con-
densation of nucleoside malonates has been explored.
Template RNA
RNA
RNA
RNA
RNA
RNA
RNA
Base
O
Base
OH
Base
OH
O
O
O
OH
O
O
O
O
O
B
H3C
A
O
O
HO
H3C
+
Mg2
Previous attempts to observe Claisen condensation
using solutions of adenosine malonate or deoxyadeno-
sine malonate under various conditions were unsuccess-
ful.4 As the active amino group of adenosine might
interfere with the condensation and accelerate the
hydrolysis of adenosine malonate, nucleoside malonates
with lower polarity (5a and 5b, Fig. 2) were used in the
condensation experiments.
RNA
RNA
Base
OH
O
(n-1) B
Polyketide
O
CH3
O
n
O
Figure 1. Mechanisms proposed for polyketide biosynthesis in the
The nucleoside malonates were synthesized from the
corresponding nucleosides as shown in Figure 2. Separa-
tion of the 20- and 30-isomers of the nucleoside malo-
nates was not possible because they immediately
reisomerized in solvents. NMR spectra confirmed that
the malonyl groups of nucleoside malonates were
switching between the 20- and 30-OH of the nucleosides.
RNA world.
A series of condensation experiments were carried out in
aqueous solution under acidic condition, as shown in
Table 1 and Figure 3. For some experiments, we added
Poly-U or Poly-A to see if the polynucleotides had some
template effect4,5 for the condensation. For most exper-
iments, Mg2+ was used as a catalyst. All the experiments
were carried out in 0.15 M NaCl solution, which is sim-
ilar in concentration to sea water. After 30 h incubation
at 37 °C, the reaction mixture was analyzed by TLC
(CHCl3/CH3OH = 2:1) to separate the products.
*
Corresponding author. Tel.: +1 979 845 4040; fax: +1 979 845
5992; e-mail: williams@cbnmr.chem.tamu.edu
Present address: Section of Molecular Genetics and Microbiology,
School of Biological Sciences, University of Texas at Austin, Austin,
TX 78712, USA.
z Deceased April 18, 2007.
As seen from Table 1, in the presence of Mg2+ (entries 1,
2, 5 and 6), the nucleoside malonates were converted
into the corresponding 1,3-acetonedicarboxylic acid
0040-4039/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2007.09.036

Q. Ji et al. / Tetrahedron Letters 48 (2007) 8026–8028
8027
B
HO
Pyridine
O
B
MeO
C
O
O
OH OH
1a, 1b
OH OH
MeO
C Cl
2a, 2b
B
B
O
O
HO
MeO
C
O
CCl3COOH
O
O
HO
O
OH O
OH O
O
O
DCC, DMAP
O
O
and 3'-isomer
3a, 3b
BnO
4a, 4b
BnO
CH3
N
N
B
H2 / Pd.BaSO4
HO
a: B =
b: B =
O
OH O
O
O
O
NH
and 3'-isomer
HO
N
O
5a, 5b
Figure 2. Synthesis of nucleoside 20- and 30-malonates.
Table 1. Conditions for condensation experiments
Entry
Substrate
Template
Condition
Product
Yield (%)
1
2
3
4
5
6
7
8
5a (50 mM)
5a (50 mM)
5a (50 mM)
5a (50 mM)
5b (50 mM)
5b (50 mM)
5b (50 mM)
5b (50 mM)
Poly-U (50 mM U)
None
Poly-U (50 mM U)
None
Poly-A (25 mM A)
None
Poly-A (25 mM A)
None
0.15 M NaCl, 0.125 M MgCl2, pH 4
0.15 M NaCl, 0.125 M MgCl2, pH 4
0.15 M NaCl, pH 4
6a
6a
93
90
None
None
6b
0.15 M NaCl, pH 4
0.15 M NaCl, 0.125 M MgCl2, pH 3
0.15 M NaCl, 0.125 M MgCl2, pH 3
0.15 M NaCl, pH 3
86
87
6b
None
None
0.15 M NaCl, pH 3
B
esters in yields of around 90% (Figure 3). No template
effects were observed in our experiment. Magnesium
cation, as a catalyst,6 was essential for successful con-
densation (entries 3, 4, 7 and 8). Generally, Claisen
condensations of malonate oxyesters happen only under
basic and harsher conditions. As a control experiment,
mono-benzylmalonate (Aldrich) was incubated under
the same reaction conditions and was unchanged after
30 h as indicated by a 13C spectrum of ether reaction
mixture extract. Our successful condensation experi-
ment under acidic and mild conditions (aqueous solu-
tion, no enzyme, no imidazole and body temperature)
may suggest that the malonate moiety can be highly
activated by linking to nucleosides and therefore can
easily undergo a biomimetic decarboxylative Claisen
condensation.
HO
O
OH O
O
O
CH3
B
HO
N
O
a: B =
b: B =
Mg2+
90%
OH
N
O
OH
O
N
O
B
HO
NH
O
O
HO
O
O
O
OH
and 2'-isomer
O
O
6a, 6b
OH
5a, 5b
Mg2+
Starting Material
Although some examples of biomimetic self Claisen
condensation of malonate esters had been reported,7–14
all used thioesters or amides as substrates, with the
exception of Scott13,14 in which malonate catechol esters
or monobenzyl malonates were used as substrates. Our
results are the first to show that malonate can be
activated simply by binding to nucleoside, and will pro-
O
O
O
OH
Figure 3. Decarboxylative Claisen condensation of nucleoside 20- and
30-malonates.

8028
Q. Ji et al. / Tetrahedron Letters 48 (2007) 8026–8028
2. The RNA World; Gesteland, R., Atkins, J. F., Eds.; Cold
Spring Harbor Press, 1993.
vide us to further understand the function of the end-
nucleosides of t-RNA.
3. Scott, A. I. Tetrahedron Lett 1997, 38, 4961.
4. Ryu, Y. Studies Toward Biomimetic Claisen Condensa-
tion Using Nucleic Acid Templates and Ribozyme Catal-
ysis. Ph.D. Dissertation, Texas A&M University, May
2004.
Acknowledgements
We thank NIH, Welch Foundation, and the Texas Ad-
vanced Technology Program for funding for this work.
5. Chung, S. K.; Copsey, D. B.; Scott, A. I. Bioorg. Chem.
1978, 300.
6. Scott, A. I.; Wiesner, C. J.; Yoo, S.; Chung, S.-K. J. Am.
Chem. Soc. 1975, 97, 6277.
7. Kobuke, Y.; Yoshida, J.-I. Tetrahedron Lett. 1978, 19,
367.
Supplementary data
8. Brooks, D. W.; Lu, L. D. L.; Masamune, S. Angew.
Chem., Int. Ed. Engl. 1979, 18, 72.
9. Sun, S.; Edwards, L.; Harrison, P. J. Chem. Soc., Perkin
Trans. 1 1998, 437.
Supplementary data includes synthetic procedures, char-
acterization and spectral data for compounds 2a–6a, 3b–
6b and 13C spectra of mono-benzylmalonate from Al-
drich (lower trace) and from an ether extract of a 30 h
incubation (upper trace). Supplementary data associated
with this article can be found, in the online version, at
doi:10.1016/j.tetlet.2007.09.036.
´
10. Sakai, N.; Sorde, N.; Matile, S. Molecules 2001, 6,
845.
11. Chen, H.; Harrison, P. H. M. Can. J. Chem. 2002, 80,
601.
12. Rock, C. O.; Heath, R. J. Nat. Prod. Rep. 2002, 19,
581.
References and notes
13. Ryu, Y.; Scott, A. I. Tetrahedron Lett. 2003, 44,
7499.
14. Ryu, Y.; Kim, K.-J.; Roessner, C. A.; Scott, A. I. Chem.
Commun. 2006, 1439.
1. Benner, S. A.; Ellington, A. D.; Tauer, A. Proc. Natl.
Acad. Sci. U.S.A. 1989, 86, 7054.