Solvent dependent selective alkylation of a bis(sulfonamide) for the synthesis of a DNA-binding chiral polyamine

Article abstract of DOI:10.1016/j.tetlet.2005.02.141

A new optically active linear polyamine has been efficiently prepared and its DNA binding abilities studied by UV melting experiments. The key step for this synthesis was the selective monoalkylation of the corresponding bis(sulfonamide). Thus, it is poss

Full text of DOI:10.1016/j.tetlet.2005.02.141

Tetrahedron
Letters
Tetrahedron Letters 46 (2005) 2783–2787
Solvent dependent selective alkylation of a bis(sulfonamide)
for the synthesis of a DNA-binding chiral polyamine
Carmen Pen˜a,a Ignacio Alfonso,b Nicolas H. Voelckerc and Vicente Gotora,*
a
´ ´ ´ ´
Departamento de Quımica Organica e Inorganica, Facultad de Quımica, Universidad de Oviedo,
Julian Claverıa, 8, E-33006 Oviedo, Spain
´
´ ´ ´
Departamento de Quımica Inorganica y Organica, ESTCE, Universidad Jaume I, Campus del Riu Sec, Avenida Sos Bainat,
´
b
´
s/n, E-12071 Castellon, Spain
cSchool of Chemistry, Physics and Earth Sciences, Flinders University of South Australia, Bedford Park, SA 5042, Australia
Received 12 January 2005; revised 23 February 2005; accepted 24 February 2005
Abstract—A new optically active linear polyamine has been efficiently prepared and its DNA binding abilities studied by UV melt-
ing experiments. The key step for this synthesis was the selective monoalkylation of the corresponding bis(sulfonamide). Thus, it is
possible to obtain mono or dialkylated compounds by simply changing the reaction conditions. These results are explained in terms
of conformational preferences and solvophobic effects.
Ó 2005 Elsevier Ltd. All rights reserved.
Polyamines are polycations at physiological pH and
play an essential role for many biological processes,1
ranging from stabilization of membrane and mitochon-
dria functions to facilitation of DNA transfection by
phage.2 Thus, this family of compounds has a great thera-
peutic potential for neurological diseases,3 in the devel-
opment of new antidiarrheals in AIDS related cases4
and as anticancer agents.5 Many of the biological appli-
cations of polyamines are related to their ability to inter-
act with polyanions such as nucleic acids. For instance,
spermine is known to stabilize DNA duplex and triplex,6
and to promote conformational changes of duplex
DNA, like B–Z transitions.7 There is also a structure–
function relationship, as different molecular architec-
tures display different spatial dispositions of the cationic
ammonium groups, which are able to interact with the
phosphate chain of the oligonucleotides. Most of the
structural changes studied to date8 rely on spatial sepa-
ration of nitrogen atoms,9 alkylation of terminal amino
groups, or the construction of dendritic structures.10
Conformational restricted analogues have also been pre-
pared and tested for biological activities.11 Especially,
derivatives bearing optically active pyrrolidyl moiety
stabilize DNA duplexes and triplexes, in a different ex-
tent depending on the absolute configuration of the chi-
ral centers.12 In spite of all these studies, there is not yet
a clear picture of the requirements for the polyamine–
DNA supramolecular structures. In particular, the ques-
tion how chirality on the polycationic polyamine can
affect the stability of its corresponding nucleic acid com-
plexes has not been investigated thoroughly.13
On the other hand, chiral cyclohexane-1,2-diamine has
been used for the preparation of receptors based on
macrocyclic polyamines for the molecular recognition
of optically active polyanions.14 Compounds bearing
this diamine are also known to induce helices of different
topicity depending on the cyclohexane-1,2-diamine
absolute configuration.15 Continuing our earlier studies,
we envisioned that optically active linear polyamines
could be interesting synthetic targets for the complex-
ation of chiral anions.
Inspired by preliminary molecular modeling, we decided
to prepare open chain polyamines with three cyclohex-
ane-1,2-diamine fragments joined by linkers of different
length. For this purpose, one of the key synthetic inter-
mediates should be a monoalkylated protected diamine
(Fig. 1). To achieve secondary amino groups in the final
product, protection of the diamine is desirable. Among
Keywords: Cyclohexane-1,2-diamine; Bis-sulfonamide; Chiral poly-
amines; DNA-binding.
*
Corresponding author. Tel./fax: +34 98 510 3448; e-mail addresses:
vgs@fq.uniovi.es; vgs@sauron.quimica.uniovi.es
0040-4039/$ - see front matter Ó 2005 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2005.02.141

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C. Pen˜a et al. / Tetrahedron Letters 46 (2005) 2783–2787
tivity on the electrophilic center. Thus, when the
reaction was carried out with O-trityl derivative (Table
1, entry 2), the monoalkylated sulfonamide (R,R)-2b
was obtained as the major product.18 This result could
be initially explained by steric hindrance between Ts
and Tr protecting groups. We extended the process
using O-Tr-a,x-bromoalcohols with different number
of methylenes (n = 1–5). Surprisingly, in all the tested
examples, the reaction was highly selective towards the
formation of the monoalkylated products, showing min-
or variations in yield with increasing length of the alkyl
chain.
R
R
N
H
NH
NH
n
n
PG
NH
NH
NH
X
N
PG
n
H
N
PG = protecting group
X = leaving group
Figure 1. Retrosynthetic analysis of the target chiral polyamines.
Considering the flexibility of aliphatic linear chains, we
ruled out steric repulsion as the only source for this
selectivity. We then suspected that the conformation of
the monoalkylated sulfonamide 2 could play an impor-
tant role in the reactivity of the second NH group. With
the alkyl chain in an extended conformation (I in Fig. 2),
Tr group would be far away from the second sulfon-
amide. However, in a folded conformation (II), aro-
matic rings of Ts and Tr groups would be close to
each other. This arrangement would protect the free
NH group in 2 from reaction with a second electrophile.
different options, we found tosyl (Ts) as the most suit-
able protecting group for our purposes. Despite that
monoalkylation or monoprotection of cyclohexane-1,2-
diamine is not an easy task,16 here we report an easily
tunable methodology for obtaining mono- or dialkyl-
ated bis(sulfonamide) in high yields and selectivity
depending on the reaction conditions. Finally, we have
used this strategy for the synthesis of a DNA-binding
chiral polyamine.
In a previous paper,17 we had carried out the alkylation
of (R,R)-1 with 3-bromopropanol (Table 1, entry 1).
Over all the reaction conditions tested, we always ob-
tained a mixture of mono and dialkylated bis(sulfon-
amide), readily separable after flash chromatography.
An experimental evidence for the existence of folded
conformations of the monoalkylated derivatives was
obtained from 1D NOESY experiments on (R,R)-2e
(n = 4). For instance, selective pulse field gradient irradi-
ation on the ortho protons of the Tr group yielded NOE
effects on ortho protons of the Ts group of the non-
alkylated sulfonamide and on both Tosyl-CH3 (Fig. 3).
This would set the two protecting groups at a distance
However, for selectively obtaining mono- or dialkylated
compounds in good yields, a more elaborated synthetic
strategy had to be found. We firstly checked if protec-
tion of the terminal hydroxy group could affect the reac-
shorter than 5 A, 19 supporting the folded conformation
˚
of (R,R)-2e.
The above-mentioned conformational equilibrium is
expected to be highly dependent on the polarity of the
medium. Polar solvents (such as acetonitrile) would
Table 1. Alkylation of bis(sulfonamide) (R,R)-1
Ts
NH
+
NH
Ts
OR
Br
n
R=H,Tr
n=1-5
(R,R)-1
Tr
O
Ts
NH
Ts
K2CO3
NH
Ts
NH
Ts
N
N
Ts
n
Tr
O
N
Ts
n
OR
OR
+
n
n
I
II
OR
N
Ts
N
Ts
n
Figure 2. Proposed equilibrium between extended (I) and folded (II)
conformations of 2.
(R,R)-2a (R=H, n=1)
(R,R)-3a (R=H, n=1)
(R,R)-3b-f (R=Tr, n=1-5)
(R,R)-2b-f (R=Tr, n=1-5)
Entry
n
R
H
Solvent
Yield 2a (%)
Yield 3a (%)
1
1
C(Ph)
CH3CN
CH3CN
CH3CN
CH3CN
CH3CN
CH3CN
21b
70
80
75
67
75
—
—
50b
11
—
—
12
5
21
3
3
3
2C(Ph)
4
3
4
5
1
5
C(Ph)3
C(Ph)3
C(Ph)3
C(Ph)3
C(Ph)3
5
6
c
7
PhCH3
72
82
c
8
PhCH3
a Isolated yields after flash chromatography.
b Taken from Ref. 17.
c A catalytic amount of n-Bu4NBr was added.
Figure 3. NOE contacts obtained from 1D NOESY experiments on
(R,R)-2e (CDCl3, 500 MHz).

C. Pen˜a et al. / Tetrahedron Letters 46 (2005) 2783–2787
2785
favor folded conformers while hydrophobic environ-
ments would stabilize extended structures. When run-
ning the reaction (for both the shortest and longest
electrophiles) in an aromatic hydrophobic solvent, only
dialkylated derivatives were isolated in good yields (Ta-
ble 1, entries 7 and 8). We thus demonstrated that the
effect of Tr group depends on the hydrophobicity of
the medium. Solvophobic effects governing conforma-
tion20 and reactivity21 have been previously reported in
the literature and it is a critical parameter for protein
folding.22 We present here an interesting example of
solvophobic effects where a terminal group prevents
the reaction in a remote center of the molecule.
From the synthetic point of view, the interest of this effect
is the possibility of selectively obtaining mono- or dialkyl-
ated bis(sulfonamide) by simply changing the solvent.
nitrogen alkylation of (R,R)-2b, followed by Tr cleavage
and mesylation of the resulting alcohol led to (R,R)-6 in
very high overall yield. Coupling of (R,R)-1 with 2
equivalents of (R,R)-6 in Cs2CO3/CH3CN afforded the
hexatosylated polyamine (R,R,R,R,R,R)-7 in ca. 50%
yield. Applying the same rational than for the alkylation
reaction, the isolated yield of this coupling process was
increased up to 70% by using toluene as solvent. Acidic
deprotection of all the Ts groups led to the desired poly-
amine which was isolated as the hydrochloride salt.23
1
Both H and 13C NMR spectra revealed C2 symmetry
in solution, supporting the lack of epimerization
throughout the synthetic sequence.
The DNA binding ability of (R,R,R,R,R,R)-8 has also
been investigated. The presence of the polyamine in-
creased the UV-melting temperatures of three different
oligonucleotides up to DTm = 7.3 °C (Table 2 and Fig.
4). Addition of sodium chloride decreased the stabiliza-
tion produced by the polycation, and the effect was even
more pronounced when ionic strength was increased and
dicationic metal salts were added. This suggests that
the interaction is mainly electrostatic and agrees with
reported data in related systems.
As the final goal, we attempted to use one of the mono-
alkylated compounds for the synthesis of a new optically
active polyamine (n = 1, R = Me in Fig. 1). The syn-
thetic procedure is outlined in Scheme 1. Conventional
Ts
N
a
Me
At this moment, it remains unknown if there is any con-
formational preference for the polyamine to bind the
(R,R)-2b
X
N
Ts
(R,R)-4 (X=OTr)
(R,R)-5 (X=OH)
(R,R)-6 (X=OMs)
b
c
N
R
NR
NR
NR
NR
d
(R,R)-1
+ 2 (R,R)-6
R
N
(R,R,R,R,R,R)-7 (R=Ts)
(R,R,R,R,R,R)-8 (R=H)
e
Figure 4. UV-melting profiles of B1/B1C DNA oligonucleotides (2 lM
in 20 mM Tris buffer, pH 7.4): (a) alone (black); (b) +0.1 mM
(R,R,R,R,R,R)-8 (red); (c) 20 mM NaCl (green); (d) like in (c)
+0.1 mM (R,R,R,R,R,R)-8 (blue); (e) 100 mM NaCl, 1 mM MgCl2,
1 mM CaCl2 (brown); (f) like in (e) +0.1 mM (R,R,R,R,R,R)-8
(yellow).
Scheme 1. Synthesis of (R,R,R,R,R,R)-8. Reagents and conditions: (a)
MeI, Cs2CO3, PhCH3, n-Bu4NBr, 110 °C (90%). (b) TFA, CH2Cl2,
MeOH (80%). (c) MsCl, NEt3, CH2Cl2 (quantitative). (d) Cs2CO3,
PhCH3, n-Bu4NBr (70%). (e) HBr (aq), PhOH (60%).
Table 2. UV (260 nm) melting temperatures (Tm in °C) of DNA (2 lM) sequences in the absence (ꢀ) and in the presence (+) of 0.1 mM
(R,R,R,R,R,R)-8
20 mM Tris (pH 7.4)
20 mM Tris, 20 mM NaCl
(pH 7.4)
20 mM Tris, 100 mM
NaCl, 1 mM MgCl2,
CaCl2 (pH 7.4)
ꢀ
+
ꢀ
+
ꢀ
+
A16/T16
B1/B1C
Hairpin
34.0
56.3
42.7
37.240.0
63.6
45.2
40.9
39.239.3
59.8
46.8
63.270.6
47.0
70.2
53.3
54.1
B1: dCCTGTCGCCTCGCACATAGCC.
B1C: GGACAGCGGAGCGTGTATCGGd.
Hairpin: dAGTCTATGGGTTAGACT.

2786
C. Pen˜a et al. / Tetrahedron Letters 46 (2005) 2783–2787
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of isomeric polyamino derivatives for binding assays,
which would give us interesting information about the
supramolecular structure. Other structural variables
such as the terminal alkylating group or separation
between conformationally rigid moieties will be also
investigated.
In summary, we report here a selective alkylation of the
bis(sulfonamide) (R,R)-1. The corresponding mono- or
dialkylated derivatives can be easily prepared by simply
changing the reaction conditions. These results have
been rationalized in terms of conformational preferences
and solvophobic effects. The applications of the ob-
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synthesis of a new optically active open chain poly-
amine, which is able to interact with DNA molecules.
Further synthetic studies are underway for the prepara-
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non-viral gene transfection technology.24
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Acknowledgments
Financial support from the Spanish Ministerio de Cien-
´
cia y Tecnologıa (PPQ-2001-2683), the Principado de
Asturias (GE-EXP01-03) and the Australian Research
Council (DP0344118) is gratefully acknowledged. I.A.
´
16. Kaik, M.; Gawronsky, J. Tetrahedron: Asymmetry 2003,
14, 1559.
17. Alfonso, I.; Rebolledo, F.; Gotor, V. Tetrahedron: Asym-
metry 1999, 10, 367.
´
thanks MCYT for personal financial support (Ramon
y Cajal Program).
18. General procedure for the alkylation reaction. In a flask
under nitrogen atmosphere 2mmol of ( R,R)-1 and 20
mmol of anhydrous K2CO3 were suspended in 12mL of
dry CH3CN and the mixture heated to 70 °C for half an
hour. Then, 8 mmol of the corresponding electrophile
were added drop wise and the obtained mixture stirred at
70 °C for 2days (TLC AcOEt:Hexan 3:2). After that, the
reaction was allowed to room temperature, acidified with
15 mL of 3 N HCl and extracted with CH2Cl2. The
combined organic layers were dried and evaporated to
dryness. The final monoalkylated product was isolated by
flash chromatography. For obtaining the dialkylated
compound, the reaction was carried out like in the
monoalkylation procedure but in dry toluene and a
catalytic amount of tetrabutylammonium bromide was
also added.
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578
decompose without melt; ½aꢁHg ꢀ 48:4, (c = 0.5, MeOH);
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1.98–2.67 (m, 10H), 2.69 (s, 6H), 2. 99–3.22 (m, 4H), 3.22–
3.64 (bm, 10H); 13C NMR (D2O, 75 MHz) d (ppm) 21.22
(CH2), 21.33 (CH2), 21.39 (CH2), 22.86 (CH2), 24.80
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´
(CH2), 42.58 (CH2), 57.04 (CH), 57.52(CH), 57.62(CH);
HRMS/EI calculated for C26H54N6: 450,4410; found
450,4414.
´
24. (a) Kirby, A. J.; Camillery, P.; Engberts, J. B. F. N.;
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