Symmetrical and unsymmetrical α,ω-nucleobase amide-conjugated systems

Article abstract of DOI:10.3762/bjoc.6.34

We present the synthesis and selected physicochemical properties of several novel symmetrical and unsymmetrical α,ω-nucleobase mono-and bis-amide conjugated systems containing aliphatic, aromatic or saccharidic linkages. The final stage of the synthesis i

Full text of DOI:10.3762/bjoc.6.34

Symmetrical and unsymmetrical α,ω-nucleobase
amide-conjugated systems
Sławomir Boncel1, Maciej Mączka1, Krzysztof K. K. Koziol2,
Radosław Motyka1 and Krzysztof Z. Walczak*1
Preliminary Communication
Open Access
Address:
Beilstein Journal of Organic Chemistry 2010, 6, No. 34.
1Silesian University of Technology, Department of Organic Chemistry,
Biochemistry and Biotechnology, Krzywoustego 4, 44-100 Gliwice,
Poland, Tel.: +48 32 237 1792, Fax: +48 32 237 2094 and 2University
of Cambridge, Department of Materials Science and Metallurgy,
Pembroke Street, Cambridge CB2 3QZ, United Kingdom, Tel.: +44
1223 334 356, Fax: +44 1223 334 567
doi:10.3762/bjoc.6.34
Received: 20 January 2010
Accepted: 23 March 2010
Published: 12 April 2010
Associate Editor: S. Flitsch
Email:
Krzysztof Z. Walczak* - krzysztof.walczak@polsl.pl
© 2010 Boncel et al; licensee Beilstein-Institut.
License and terms: see end of document.
* Corresponding author
Keywords:
amides; antiprotozoal agents; coupling; nucleosides; self-assembly
Abstract
We present the synthesis and selected physicochemical properties of several novel symmetrical and unsymmetrical α,ω-nucleobase
mono- and bis-amide conjugated systems containing aliphatic, aromatic or saccharidic linkages. The final stage of the synthesis
involves condensation of a subunit bearing carboxylic group with an amine subunit. 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methyl-
morpholinium chloride (DMT-MM) was found to be a particularly effective condensing agent. The subunits containing carboxylic
groups were obtained by acidic hydrolysis of N-1 Michael adducts of uracils or N-9 Michael adducts of 6-chloropurine with methyl
acrylate. The amines used were aliphatic/aromatic diamines, adenine, 5-substituted 1-(ω-aminoalkyl)uracils and 5′-amino-2′,5′-
dideoxythymidine. The title compounds may find application as antiprotozoal agents. Moreover, preliminary microscopy TEM
studies of supramolecular behaviour showed that target molecules with bolaamphiphilic structures were capable of forming highly
ordered assemblies, mainly nanofibres.
Introduction
There are numerous reports on the synthesis and application of We have previously reported compounds containing 5-substi-
symmetrical and unsymmetrical α,ω-nucleobase amide-conjug- tuted uracil-1-yl subunits bound via short (I, II) or extra-short
ated systems (Figure 1) [1-6]. These molecules are constructed (III) amide-linkages [1]. These compounds exhibited medium
usually via amide bond(s) from two subunits containing nucleo- antiprotozoal activity; thus I and III exhibited growth inhibi-
bases or their analogues (B1, B2) bearing various linkages (A1, tion of parasities – Leishmania donovani and Plasmodium
A2).
falciparum – at levels of 21.4 and 30.6%, respectively [2].
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Beilstein Journal of Organic Chemistry 2010, 6, No. 34.
Figure 1: Examples of symmetrical and unsymmetrical α,ω-nucleobase amide-conjugated systems.
Compound II reduced the Plasmodium falciparum population rical derivatives. Interestingly, considering the physicochem-
by only 17.4%, although it was the most active derivative ical aspect of our work, two of the compounds synthesised
against it within the group tested. Very recently, Accetta et al. containing aliphatic long-chain linkages revealed a tendency to
reported remarkable symmetrical amide-conjugated bis-α,ω- self-assemble in the initial TEM studies.
uracil based systems (IV). These compounds exhibited anti-
proliferative and erythroid differentiation induction properties Results and Discussion
towards human chronic myelogenous leukaemia K562 cells [3]. The subunits containing carboxylic groups were obtained by
Moreover, α,ω-nucleobase amide-conjugated molecules pos- acidic hydrolysis of N-1 Michael adducts of uracils or N-9
sess the tendency to form meta-stable complexes with DNA and Michael adducts of 6-chloropurine with methyl acrylate
thus can perturb the cell replication. For example, amide-linked (Scheme 1A) [1]. Uracil derivatives were obtained via the fully
heterodimer synthons consisting of acyclic nucleoside units and regioselective one-step procedure as previously reported
5′-amino-2′,5′-dideoxythymidine are PNA/DNA chimeras (V) [11,12]. To construct systems containing modified purinic
[4]. Furthermore, amide-conjugated systems of solely biologic- nucleobase, we synthesised the N-9 adduct (1ea) of 6-chlorop-
ally active units may be utilised in combined anti-HIV therapy, urine with methyl acrylate in 90% yield using Hünig’s base
e.g. 2′,3′-dideoxycytidine and 1-[(2-hydroxyethoxy)methyl]-6- (diisopropylethylamine) as a deprotonating agent (Scheme 1B)
(phenylthio)thymine conjugate (ddC-HEPT) (VI) [5].
(see Supporting Information File 1).
In addition, Shimizu et al. in 2001 reported structures, which
are formally α,ω-nucleobase bolaamphiphiles (VII), capable of
forming extraordinary nanotopologies [6].
In order to synthesise a new group of modified, mainly
pyrimidinic nucleosides, we employed a simple and effective
synthetic pathway based on the catalytic aminolysis of
carboxylic acids. Our synthetic approach surpasses all the
procedures previously reported, not only in terms of higher
yields, even although earlier reports of the synthesis of symmet-
rical α,ω-nucleobase amide-conjugated systems were based on a
similar strategy. These methods involved two-step procedures
such as catalytic condensation, e.g. in the presence of a suitable
coupling agent – N,N′-dicyclohexylcarbodiimide (DCC) [7], or
acylation of appropriate amines with acyl halides [3] or “active
esters” [6]. Monoacylation of aliphatic diamines, either in the
presence of MgCl2 [8,9] or 9-borabicyclo[3.3.1]nonane
(9-BBN) [10], has been used for the synthesis of unsymmet-
Scheme 1: Synthesis of main acidic subunits, precursors of both
symmetrical and unsymmetrical α,ω-nucleobase amide-conjugated
systems: A – 5-substituted uracil-based [11] – (i) methyl acrylate (2
equiv), TEA (1 equiv), DMF, 20 °C, 24 h, (ii) 5% HClaq, reflux, 0.5 h; B
– 6-chloropurine-based – (i) methyl acrylate (2 equiv), Hünig’s base (1
equiv), 20 °C, 24 h, (ii) 5% HClaq, reflux, 1 h.
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Beilstein Journal of Organic Chemistry 2010, 6, No. 34.
X-ray analysis confirmed the structure of this regioisomer
(Figure 2) [13]. This simple method appears to be the most N-9
regioselective process compared to other methods [14-16].
Figure 3: DMT-MM in its presumably more stable conformation [20].
We have previously used this catalyst successfully in our search
for unsymmetrical α,ω-nucleobase molecules, which are struc-
turally related to the title compounds, i.e. short linkage amide-
[1] and ester-conjugated systems [12].
Figure 2: X-ray structure of 1ea shown as thermal ellipsoids at 50%
probability [17,18].
Symmetrical α,ω-nucleobase amide-conjug-
The N-7 adduct of 6-chloropurine (1eb) was also isolated in ated systems
10% yield. Hydrolysis of the N-9 adduct under acidic condi- The first set of compounds – symmetrical aliphatic and
tions (5% HClaq) gave 9-(2-carboxyethyl)-6-chloro-9H- aromatic α,ω-nucleobase amide-conjugated systems (4–15,
purinium-3 chloride (1e). As amine components, readily access- Table 1) – was synthesised from 3-(5-substituted-uracil-1-
ible amines such as aliphatic α,ω-diamines, phenylene di- yl)propionic acids 1a–d and the appropriate aliphatic α,ω-di-
amines, adenine, 5-substituted 1-(ω-aminoalkyl)uracils and amines 2a–e, and the aromatic diamines 3a–c in DMF (see
5′-amino-5′-deoxythymidine were chosen.
Supporting Information File 1).
To accomplish the synthesis of the title compounds, we The yields vary from moderate to good. The lower yields noted
developed a simple and effective method of coupling the in the table arise as a result of the method of isolation (see
carboxylic subunit with an amino compound. As condensing Supporting Information File 1). Despite its susceptibility to
agent, 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmor- nucleophilic attack, 5-nitrouracil acid derivative 1d also reacted
pholinium chloride (DMT-MM) was found to be very with aliphatic diamines and gave the expected diamides 7 and
convenient and efficient (Figure 3) [19].
12.
Table 1: Symmetrical aliphatic and aromatic α,ω-nucleobase amide-conjugated systems.
Acidic subunit
X
Amine subunit
R
Product
Yield [%]
1c
1a
1b
1d
1b
1c
1a
1b
1d
1c
1c
1a
Br
H
2a
2b
2b
2b
2c
2c
2d
2e
2e
3a
3b
3c
(CH2)2
(CH2)3
4
5
57
64
60
55
67
31
74
59
67
35
37
68
CH3
NO2
CH3
Br
(CH2)3
6
(CH2)3
7
(CH2)6
8
(CH2)6
9
H
(CH2)9
10
11
12
13
14
15
CH3
NO2
Br
(CH2)10
(CH2)10
o-phenylene
m-phenylene
p-phenylene
Br
H
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Beilstein Journal of Organic Chemistry 2010, 6, No. 34.
Unsymmetrical α,ω-nucleobase amide-
conjugated systems
Two different acidic and three different amine subunits – syn-
thesised according to known procedures – were utilised in the
The second group – unsymmetrical α,ω-nucleobase amide- synthesis of 19, 20 and 23–25. The acidic subunits used were
conjugated systems and their synthetic precursors (Table 2) – (2S,3S,5R)-3-hydroxy-5-[5-methyl-2,4-dioxo-3,4-dihydro-
was synthesised from monoacid and monoamine derivatives pyrimidin-1(2H)-yl]tetrahydrofuran-2-carboxylic acid (1f) [21]
with the exception of mono-amine precursor 16 which was syn- and 4-({(2R,3S,5R)-3-acetoxy-5-[5-methyl-2,4-dioxo-3,4-di-
thesised from 1,6-hexylenediamine.
hydropyrimidin-1(2H)-yl]tetrahydro-furan-2-yl}methoxy)-4-
oxobutanoic acid (1g) [22]. The amine subunits employed were
This synthesis was based on the classical approach of half- 3-[5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl]propan-1-
conversion of the bifunctional reactant with the monofunctional aminium trifluoroacetate (2g) [23], 6-[5-nitro-2,4-dioxo-3,4-di-
compound by using an excess of diamine (3 equiv) with respect hydropyrimidin-1(2H)-yl]hexan-1-aminium trifluoroacetate
to the acidic reactant. Nevertheless, this procedure led to prob- (2h) [23] and 1-[(2R,4S,5R)-5-(aminomethyl)-4-hydroxytet-
lems in the purification step and partial decomposition of DMT- rahydrofuran-2-yl]-5-methylpyrimidine-2,4-(1H,3H)-dione (2l)
MM during the reaction. This was especially significant when [24]. The synthesis of the amine subunit 2j was carried out
compared to the synthesis of N-Boc monoprotected amine according to the known procedure [25]. The unprotected
reactant 17 (See Supporting Information File 1).
hydroxyl group in sugar moieties, as expected, was entirely
unreactive towards the carboxylic group when compared to the
The compounds in this second group were obtained in yields of amine functionality, and consequently nucleosides with a
31–95%. The synthesis of nucleosides containing aliphatic link- saccharide moiety (23, 25) were successfully synthesised.
ages (19–22) presented no difficulties on work-up.
Table 2: Unsymmetrical α,ω-nucleobase amide-conjugated systems based on aliphatic or saccharidic linkages and their exemplary synthetic
precursors.
B1A1–COOH
H2N–A2B2
Pro-
duct
B1A1−CONH−A2B2
Yield
[%]
1c
1b
2c
16
17
33
99
2ba
1b
2f
18
68
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Beilstein Journal of Organic Chemistry 2010, 6, No. 34.
Table 2: Unsymmetrical α,ω-nucleobase amide-conjugated systems based on aliphatic or saccharidic linkages and their exemplary synthetic
precursors. (continued)
1c
1c
2g
2h
19
20
90
83
1e
1e
2i
2j
21
22
95
44
1f
2h
2k
2l
23
24
25
85
31
92
1g
1c
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Beilstein Journal of Organic Chemistry 2010, 6, No. 34.
Self-assembly of aliphatic long-chain
symmetrical α,ω-nucleobase amide-conjug-
ated systems
For the microscopic studies, we selected the two model com-
pounds 11 and 12. The supramolecular behaviour of conjugated
nucleobase-based bolaamphiphiles was examined by TEM. A
JEOL 200 FX, operating at 200 kV, was used to obtain the
typical images as shown in Figure 4. For the microscopic
studies, saturated ethanolic solutions of 11 and 12 prepared by
ultrasonication were subjected to slow vaporisation at −20 °C.
Microcrystalline assemblies were grown directly on copper
grids for TEM analyses. This procedure of growth accom-
panied by careful investigations revealed that thymine- (A, B)
and 5-nitrouracil-based (C) bolaamphiphiles derived from 1,10-
diaminodecane may form nanofibres of 80–300 nm diameter for
thymine and 15–100 nm for 5-nitrouracil derivatives, respect-
ively.
Figure 4: TEM images of symmetrical α,ω-nucleobase amide-conjug-
ated systems: A – two splitting nucleoside nanofibres growing out from
crystalline phase (11), the rectangular area (A) shows “twin fibres”; B –
“twin fibres” growing out from microcrystalline “lizard tail” (11); C –
nanofibres in bulky microcrystalline area (12).
system could also be involved [26]. This fact is reflected in the
presence of residual electron diffraction patterns, which are in
particular visible in the case of so-called “twin fibres” (B)
growing out from the microcrystalline phase – “lizard tail”. A
The electron diffraction patterns in the case of 11 indicate single complete model of the nanofibre is presented in Figure 5C
crystal fibre diffraction (Figure 4A). A simplified model for the along with its longitudinal cross-section (D).
formation of multilayered nanofibres is shown in Figure 5.
Conclusion
A proposal of simplified models of micro- and nanofibres is We have synthesised a novel group of twelve symmetrical and
based on the π-stacking and hydrogen bonding interactions ten unsymmetrical α,ω-nucleobase amide-conjugated systems
between thymine units. Amide bonds, on the other hand, may using DMT-MM as the condensing agent. These two groups of
be crucial in the inter-layer hydrogen bonding. A linear system compounds will be investigated for antiprotozoal activity within
of hydrogen bonding appears as a thermodynamically favour- the framework of the Drugs for Neglected Diseases initiative
able (A). Nevertheless, a less favourable “bent” (or “wobble”) (DNDi). These investigations are currently in progress.
Figure 5: Models of micro- and nanofibres based on hydrogen bonding interactions between thymine units; (A) thermodynamically favourable linear
system of hydrogen bonds; (B) less favourable “bent” system of hydrogen bonds; (C) π-stacking and hydrogen bonding based nanofibre; (D) longitud-
inal cross-section of a particular nanofibre.
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Beilstein Journal of Organic Chemistry 2010, 6, No. 34.
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pounds. Their supramolecular nature was revealed since they
form nanofibres during low temperature crystal growth. These
experiments were reproducible, but further studies are required.
13.Crystallographic data of this compound was deposited in The
Cambridge Crystallographic Data Centre under the reference number
CCDC-728242. This data can be obtained free of charge via
http://www.ccdc.cam.ac.uk/data_request/cif
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Experimental Section
Supporting Information File 1
The data provides general remarks, procedures, physical
properties and 1H and 13C NMR spectra of all newly
synthesised compounds.
17.KM-4 Users Guide, Ver. KM4B8; Kuma Diffraction Ltd.: Wroclaw,
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Acknowledgements
doi:10.1016/S0040-4020(99)00809-1
The authors would like to thank the Institute of Tropical
Diseases in Geneva, Switzerland for performing the initial tests
of antiprotozoal activity for the unsymmetrical short-linkage
α,ω-nucleobase amide-conjugates. These investigations were
conducted within the framework of the Drugs for Neglected
Diseases initiative (DNDi).
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