Design, synthesis, and self-assembly of an ether and amide linkage-based cyclic lipid

Article abstract of DOI:10.1055/s-0029-1217756

A novel 48-membered cyclic lipid, in which two ether and two amide groups serve as a linker between its hydrophilic and hydrophobic moiety, was synthesized starting from d-1,2-O-isopropylidene-sn-glycerol. The synthetic scheme is featured by the selective

Full text of DOI:10.1055/s-0029-1217756

LETTER
2651
Design, Synthesis, and Self-Assembly of an Ether and Amide Linkage-Based
Cyclic Lipid
Ether and
Amide Link
o
d
C
t
L
i
pid nari Shibakami,* Shin Miyoshi, Makoto Nakamura, Rie Goto
Institute of Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST),
Central 5th, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
Fax +81(29)8614547; E-mail: moto.shibakami@aist.go.jp
Received 27 May 2009
ones with four amide bonds (tetraamide), which are also
Abstract: A novel 48-membered cyclic lipid, in which two ether
resistant to degradation (Figure 1).6 All the cyclic lipids
and two amide groups serve as a linker between its hydrophilic and
hydrophobic moiety, was synthesized starting from D-1,2-O-isopro-
pylidene-sn-glycerol. The synthetic scheme is featured by the selec-
that have been synthesized, including ours, use the same
type of linkers within each molecule.4,5 Unlike these cy-
tive removal of protecting groups, followed by the introduction of clic lipids, little attention has been paid to the cyclic ones
mesylate and carboxylic acid, which sequentially leads to the for-
containing two types of linkers. We think that the synthet-
mation of ether and amide bonds, respectively. Transmission elec-
ic strategy that adopts two types of linkages within a mol-
tron microscopic observation confirmed that this lipid forms
ecule is expected to expand the design possibility of cyclic
submicrosized helical ribbons.
lipids, since each linker has different physical and chemi-
cal properties. With this background in mind, we have re-
cently started a program aiming at synthesizing a novel
Key words: lipids, macrocycles, ether bond, amide bond, self-
assembly
cyclic lipid that contains ether and amide linkers as an ex-
ample of the cyclic ones having two types of linkers. Here
we report the synthesis of a novel cyclic lipid 1 that con-
Common structural features of the membrane lipids ob-
served in eukaryotes and eubacteria contain ester groups
tains ether and amide bonds. The self-assembly of this lip-
that link hydrophilic and hydrophobic moieties.1 Unlike
id is also discussed.
these membrane lipids, cyclic ones of archaea, the third
First, the halves of the long alkyl chains that connected
biome that were found in 1977, use ether bonds instead of
two glycerols were synthesized. The synthetic approach is
ester ones.2 It is generally presumed that this structural
summarized in Scheme 1. Here, two types of terminal
feature contributes to maintain integrity of these microor-
acetylenes 2 and 3 were prepared. One is mesylate 2,
ganisms even in harsh environments such as high temper-
which was obtained by acetylene migration from 3-decyn-
ature and acidic conditions, since ether bonds have higher
1-ol with NaH and 1,3-diaminopropane (DAP)7a, fol-
resistance to hydrolysis than ester ones.3,4a Thus, there has
lowed by the treatment with methanesulfonyl chloride
been considerable research on the synthesis of the cyclic
(MsCl) and Et3N. This mesylate was used for the forma-
lipids that mimic archaeal membrane ones from both syn-
tion of the ether linkage. Another is carboxylic acid 3,
thetic and material chemistry standpoints.4,5 Our own ef-
forts in this area have focused on the cyclic lipids
which was synthesized from 9-decyn-1-ol using Jones re-
agent (CrO3, concd H2SO4), which was used for the amide
containing four ether bonds (tetraether) as well as cyclic
linkage.
O
O
Me3N+
+NMe3
O
P
O
O
P
O
O–
O–
O
O
O
O
6
6
6
6
tetraether cyclic lipid
OH
OH
OH
OH
H
N
H
N
O
O
6
6
6
6
6
O
O
O
N
H
N
H
N
H
N
H
6
6
6
O
O
O
1
tetraamide cyclic lipid
Figure 1 Structures of typical tetraether, tetraamide cyclic lipid, and 1
SYNLETT 2009, No. 16, pp 2651–2654
x
x
.x
x
.2
0
0
9
Advanced online publication: 04.09.2009
DOI: 10.1055/s-0029-1217756; Art ID: U05709ST
© Georg Thieme Verlag Stuttgart · New York

2652
M. Shibakami et al.
LETTER
The next step was to combine the long alkyl chains and In essence, the selective removal of PMB was accom-
glycerols. The synthetic scheme is outlined in Scheme 2. plished using 2,3-dichloro-5,6-dicyano-1,4-benzoquino-
This part started with the protection of the hydroxy group ne (DDQ) to give diol 8 in 46% yield.8 A key step in the
of D-1,2-O-isopropylidene-sn-glycerol with p-methoxy- present synthesis is the introduction of amine, which can
benzyl chloride (PMBCl). Protection, deprotection, and be converted into the amide group. Our synthetic strategy
coupling processes yielded diacetylene compound 7 ac- is as follows. First, the hydroxy groups of 8 were substi-
cording to the method previously described in the litera- tuted by mesyl (Ms) groups by using MsCl, followed by
ture.6a,7 Compound 7 is featured by the protection of its the displacement of the resulting Ms groups with an azide
hydroxy groups with two different protecting groups, i.e., ion which afforded azide 9 in 63% yield.6c,9 The reduction
trityl (Tr) and p-methoxybenzyl (PMB) groups. This of 9 with triphenylphosphine (PPh3), followed by the con-
structure allows us to perform the selective removal of the densation with carboxylic acid 3 using EDC–HOBt–Et3N,
protective groups, which leads to the sequential formation without further purification of the resulting amine, yielded
of different types of bonds.
amide 10 in 47% yield.10 The subsequent subjection of 10
to a Glaser coupling method [Cu(OAc)2 in pyridine] af-
forded 11 in 62% yield, which shows that a Glaser cou-
pling reaction proceeded in a similar way as that
previously reported.6 Finally, the removal of the Tr groups
with p-toluenesulfonic acid (p-TsOH) gave diol 1 in 72%
yield as a white solid. The structure of 1 was confirmed on
b
MsO
8
2
a
HO
HO
5
2
8
O
1
the basis of H NMR, 13C NMR and TOF mass spec-
c
3-decyn-1-ol
9-decyn-1-ol
trum.11,12 This scheme is applicable to the synthesis of ste-
reoisomers of 1. For example, the synthesis that uses
L-1,2-O-isopropylidene-sn-glycerol as a starting material
theoretically can give an isomer bearing R,R configura-
tion.
HO
7
3
Scheme 1 Reagents and conditions: (a) NaH, DAP, 100 °C, 16.5 h,
81%; (b) MsCl, Et3N, CHCl3, 0 °C, 1 h, 94%; (c) CrO3, concd H2SO4,
H2O–acetone, –5 °C, 2.5 h, 61%
OTr
O
OH
OTr
O
OH
a
OH
b
c
O
8
OH
OPMB
OPMB
OPMB
D-1,2-O-isopropylidene
-sn-glycerol
4
5
6
OTr
OTr
OTr
OTr
d
O
O
O
O
e
6
6
6
6
OPMB
PMBO
OH
HO
7
8
OTr
OTr
OTr
OTr
g
f
O
O
O
O
6
6
6
6
6
N3
N3
N
H
N
H
6
O
O
9
10
OTr
OTr
OH
OH
O
O
O
O
h
i
6
6
6
6
6
6
N
N
N
H
N
H
H
H
6
6
O
O
O
O
11
1
Scheme 2 Reagents and conditions: (a) (i) p-TsOH, MeOH, r.t., 16 h; (ii) PMBCl, KOH, DMSO, r.t., 3 h, 80%; (b) TrCl, DMAP, pyridine,
80 °C, 5 h, 96%; (c) 2, NaH, TBAI, DMF, 0 °C to r.t., 19 h, 94%; (d) Cu(OAc)2, pyridine, reflux, 5 h, 60%; (e) DDQ, CH2Cl2, phosphate buffer
solution (pH 7.2), 0 °C, 3 h, 77%; (f) (i) MsCl, Et3N, CH2Cl2, –20 °C, 1 h; (ii) NaN3, DMSO, 60 °C, 8 h, 63%; (g) (i) PPh3, H2O–THF, r.t., 25.5
h; (ii) 3, EDC·HCl, HOBt·H2O, Et3N, CH2Cl2, 0 °C to r.t., 19 h, 42%; (h) Cu(OAc)2, pyridine, reflux, 5.5 h, 62%; (i) p-TsOH, CHCl3–MeOH,
22 h, 72%; DMAP = 4-dimethylaminopyridine, TrCl = triphenylmethyl chloride or trityl chloride, TBAI = tetrabutylammonium iodide, EDC =
1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride, HOBt = 1-hydroxybenzotriazole
Synlett 2009, No. 16, 2651–2654 © Thieme Stuttgart · New York

LETTER
Ether and Amide Linkage-Based Cyclic Lipid
2653
Course, Promotion Budget for Science and Technology from Mini-
stry of Education, Culture, Sports, Science and Technology.
We examined the self-assembly of lipid 1 by the hydra-
tion/sonication of the thin film made from 1. In brief, 0.5
mg of 1 was dissolved in 1 mL of a mixture of chloroform
and methanol (4:1), and an aliquot of the solution was
transferred into a small test tube. After removing the or-
ganic solvent using a nitrogen stream, the resulting thin
film was dried under reduced pressure (overnight). Then,
Milli-Q water (1 mL) was added to the resulting film, and
the solution was incubated at 60 °C for 1 hour. After add-
ing Milli-Q water (1 mL) to the supernatant, the solution
was subjected to sonication for 3 min with a Branson
Sonifier S-250A homogenizer. Transmission electron mi-
croscope (TEM) images revealed that the solution con-
tained microsized helical ribbons with a width of ca. 100
nm (Figure 2). It is important to note that the polymeriza-
tion of diacetylene compounds proceeds by external stim-
uli such as UV irradiation when diacetylenes are arranged
in a lattice with an appropriate geometry.13 Also, it is
known that diacetylene amphiphiles with chiral head-
groups often form nonspherical structures such as helices
and tubules.13f Thus, we think that the observed helical
ribbons may be prepared by the polymerization of the lip-
id aggregates induced by TEM electron beam irradia-
tion,14,15 which suggests that it is likely that the structure
of the lipid architecture composed of 1 in the aqueous so-
lution is different from that on the TEM grid. Finally, giv-
en the fact that the aqueous solution, which has been left
sequentially at room temperature over years and at 0 °C
for several months, contains broken pieces of the ribbons,
we think that the essential structure of this assembly is
considerably stable.17
References and Notes
(1) Gennis, R. B. Biomembranes: Molecular Structure and
Function; Springer: New York, 1989.
(2) (a) Woese, C. R.; Fox, G. E. Proc. Natl. Acad. Sci. U.S.A.
1977, 74, 5088. (b) Tornabebe, T. G.; Langworthy, T. A.
Science 1979, 203, 51. (c) De Rosa, M.; Gambacorta, A.;
Gliozzi, A. Microbiol. Rev. 1986, 50, 70. (d) Comita, P. B.;
Gagosian, R. B.; Pang, H.; Costello, C. E. J. Biol. Chem.
1984, 254, 15234.
(3) (a) van de Vossenberg, J. L. C. M.; Driessen, A. J. M.;
Konings, W. N. Extremophiles 1998, 2, 163. (b) Daniel, R.
M. Cell Mol. Life Sci. 2000, 57, 250. (c) DeLong, E. F.
Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 6417.
(4) For recent reviews on synthetic archaeal membrane lipid
analogues, see: (a) Benvegnu, T.; Brard, M.; Plusquellec, D.
Curr. Opin. Colloid Interface Sci. 2004, 8, 469.
(b) Benvegnu, T.; Lemiègre, L.; Cammas-Marion, S. Eur. J.
Org. Chem. 2008, 28, 4725.
(5) (a) Menger, F. M.; Chen, X. Y. Tetrahedron Lett. 1996, 37,
323. (b) Menger, F. M.; Chen, X. F.; Brocchini, S.; Hopkins,
H. P.; Hamilton, D. J. Am. Chem. Soc. 1993, 115, 6600.
(c) Yamauchi, K.; Sakamoto, Y.; Moriya, A.; Yamada, K.;
Hosokawa, T.; Higuchi, T.; Kinoshita, M. J. Am. Chem. Soc.
1990, 112, 3188. (d) Moss, R. A.; Li, J. M. J. Am. Chem.
Soc. 1992, 114, 9227. (e) Fuhrhop, J.-H.; David, H. H.;
Mathieu, L.; Liman, U.; Winter, H. J.; Boekema, E. J. Am.
Chem. Soc. 1986, 108, 1785. (f) Meglio, C. D.; Rananavare,
S. B.; Svenson, S.; Thompson, D. H. Langmuir 2000, 16,
128. (g) Kim, J. M.; Thompson, D. H. Langmuir 1992, 8,
637. (h) Ladika, M.; Fisk, T. E.; Wu, W. W.; Jons, S. D.
J. Am. Chem. Soc. 1994, 116, 12093. (i) Eguchi, T.;
Arakawa, K.; Terachi, T.; Kakinuma, K. J. Org. Chem.
1997, 62, 1924. (j) Eguchi, T.; Ibaragi, K.; Kakinuma, K.
J. Org. Chem. 1998, 63, 2689. (k) Patwardhan, A. P.;
Thompson, D. H. Org. Lett. 1999, 1, 241.
(6) (a) Miyawaki, K.; Takagi, T.; Shibakami, M. Synlett 2002,
1326. (b) Miyawaki, K.; Goto, R.; Takagi, T.; Shibakami,
M. Synlett 2002, 1467. (c) Miyawaki, K.; Harada, A.;
Takagi, T.; Shibakami, M. Synlett 2003, 349.
(d) Nakamura, M.; Tadokoro, T.; Goto, R.; Shibakami, M.
J. Colloid Interface Sci. 2007, 310, 630. (e) Ono, Y.;
Namekata, M.; Goto, R.; Nakamura, M.; Shibakami, M.
Synlett 2009, 759.
Figure 2 TEM images of helical ribbons composed of 1: (left) a
low-magnification image, where the bar represents 0.5 mm, and
(right) a high-magnification image, where the bar represents 100 nm
(7) (a) Carvalho, J. F.; Prestwich, G. D. J. Org. Chem. 1984, 49,
1251. (b) Qin, D.; Byun, H.; Bittman, R. J. Am. Chem. Soc.
1999, 121, 662. (c) Hirth, G.; Barner, R. Helv. Chim. Acta
1982, 65, 1059.
(8) Oikawa, Y.; Yoshioka, T.; Yonemitsu, O. Tetrahedron Lett.
1982, 23, 885.
(9) (a) Uenishi, J.; Hiraoka, T.; Yuyama, K.; Yonemitsu, O.
Heterocycles 2000, 52, 719. (b) Taylor, E. C.; Macor, J. E.;
Pont, J. L. Tetrahedron 1987, 43, 5145.
(10) Hayashi, Y.; Kinoshita, Y.; Hidaka, K.; Kiso, A.; Uchibori,
H.; Kimura, T.; Kiso, Y. J. Org. Chem. 2001, 66, 5537.
(11) To a solution of 11 (15.9 mg, 12.9 mmol) in MeOH (0.5 mL)
and CHCl3 (1 mL) was added p-TsOH·H2O (250 mg, 1.3
mmol). After stirring at r.t. for 22 h, the reaction was diluted
with CHCl3 (20 mL). The solution was then washed
subsequently with sat. aq NaHCO3 (10 mL) and brine (10
mL). The organic layer was dried over anhyd Na2SO4 and
concentrated under reduced pressure. Purification of the
residue was done by flash chromatography (silica, CHCl3–
In this study, we have developed the synthetic scheme of
a unique ether and amide linkage-based cyclic lipid.
Based on the fact that much attention has been mainly
paid to headgroup species and long alkyl chain structures
when cyclic lipids are newly designed, we think that this
synthesis is a fresh reminder that linkers are also a tunable
structure.
Acknowledgment
This research was supported by an Industrial Technology Research
Grant from the New Energy and Industrial Technology Develop-
ment Organization (NEDO) of Japan. It was also financially sup-
ported by the AIST Upbringing of Talent in Nanobiotechnology
Synlett 2009, No. 16, 2651–2654 © Thieme Stuttgart · New York

2654
M. Shibakami et al.
LETTER
[M + H]+ calcd for C84H103N2O6: 1235.78107; found:
MeOH, 20:1) on a Biotage SP1 flash system to give 1 (6.8
mg, 72%) as a white solid.
1235.76957. Compound 1: Rf 0.32 (CHCl3–MeOH, 20:1).
1H NMR (CDCl3): d = 5.90 (br s, 2 H), 3.32–3.69 (m, 14 H),
3.21 (br s, 2 H), 2.17–2.34 (m, 12 H), 1.48–1.68 (m, 16 H),
1.24–1.44 (m, 28 H). 13C NMR (CDCl3–CD3OD, 20:1): d =
78.03, 77.37, 69.89, 65.30, 60.81, 50.17, 49.30, 39.58,
36.48, 29.86, 29.12, 28.91, 28.87, 28.63, 28.52, 28.47,
28.09, 28.04, 25.93, 25.59, 19.03. MS (TOF): m/z [M]+ calcd
for C46H74N2O6: 750.55414; found: 750.54743.
(12) All new compounds gave satisfactory analytical and spectral
data. Selected physical data are as follows. Compound 9: Rf
0.57 (hexane–EtOAc, 10:1). 1H NMR (CDCl3): d = 7.43 (d,
J = 7.0 Hz, 12 H), 7.30 (t, J = 7.5 Hz, 12 H), 7.24 (t, J = 7.3
Hz, 6 H), 3.29–3.56 (m, 10 H), 3.14–3.24 (m, 4 H), 2.22 (t,
J = 7.0 Hz, 4 H), 1.46–1.59 (m, 8 H), 1.24–1.38 (m, 16 H).
13C NMR (CDCl3): d = 143.72, 128.52, 127.72, 126.97,
86.71, 78.31, 77.37, 77.26, 70.56, 65.28, 63.11, 52.29,
29.87, 29.29, 29.15, 28.90, 28.65, 28.20, 27.37, 26.57,
25.88, 19.07. MS (TOF): m/z [M + Na]+ calcd for
(13) (a) Tieke, B. Adv. Polym. Sci. 1985, 17, 79. (b) Ringsdorf,
H.; Schlarb, B.; Venzmer, J. Angew. Chem., Int. Ed. Engl.
1988, 27, 113. (c) Okada, S.; Peng, S.; Spevak, W.;
Charych, D. H. Acc. Chem. Res. 1998, 31, 229.
C64H72N6O4Na: 1011.55073; found: 1011.54383.
Compound 10: Rf 0.29–0.44 (hexane–EtOAc, 2:1; tailing).
1H NMR (CDCl3): d = 7.44 (d, J = 7.3 Hz, 12 H), 7.30 (t,
J = 7.5 Hz, 12 H), 7.24 (t, J = 7.2 Hz, 6 H), 5.76 (br s, 2 H),
3.11–3.59 (m, 14 H), 2.05–2.25 (m, 8 H), 2.08 (m, 4 H), 1.93
(m, 2 H), 1.20–1.75 (m, 44 H). 13C NMR (CDCl3): d =
172.94, 143.72, 128.60, 127.81, 127.04, 86.72, 84.59, 77.44,
70.10, 68.12, 65.26, 63.76, 40.62, 36.73, 29.97, 29.29,
29.08, 29.04, 28.76, 28.50, 28.35, 28.28, 26.12, 25.63,
19.14, 18.31. MS (TOF): m/z [M + Na]+ calcd for
(d) O’Brien, D. F.; Armitage, B.; Benedicto, A.; Bennet,
D. E.; Lamparksi, H. G.; Lee, Y.-S.; Srisri, W.; Sisson, T. M.
Acc. Chem. Res. 1998, 31, 861. (e) Carpick, R. W.; Sasaki,
D. Y.; Marcus, M. S.; Eriksson, M. A.; Burns, A. R. J. Phys.:
Condens. Matter 2004, 16, R679. (f) Reppy, M. A.;
Pindzola, B. A. Chem. Commun. 2007, 4317.
(14) We often observed that the aggregates made from
diacetylenic cyclic lipids were frizzling on the grid during
the TEM observations. Thus we think that the electron beam
irradiation triggered the formation of the helical ribbons.
(15) Similar helical ribbons were observed in our previous
studies, although they differed in size.6c,16
(16) Shibakami, M.; Miyawaki, K.; Goto, R.; Shigeno, M. Jpn. J.
Appl. Phys. 2004, 43, 4655.
(17) One reason for such a high degree of stability of the ribbons
is the polydiacetylene structure that was formed during the
first TEM observation.
C84H104N2O6Na: 1259.77866; found: 1259.77685.
Compound 11: Rf 0.65 (hexane–EtOAc, 1:1). 1H NMR
(CDCl3): d = 7.44 (d, J = 7.6 Hz, 12 H), 7.30 (t, J = 7.6 Hz,
12 H), 7.23 (t, J = 7.2 Hz, 6 H), 5.80 (br s, 2 H), 3.30–3.74
(m, 8 H), 3.08–3.24 (m, 6 H), 2.03–2.34 (m, 12 H), 1.44–
1.69 (m, 16 H), 1.24–1.42 (m, 28 H). 13C NMR (CDCl3): d =
172.92, 143.77, 128.65, 127.83, 127.06, 86.75, 70.11, 65.40,
63.83, 40.70, 36.84, 30.01, 29.31, 29.08, 28.80, 28.72,
28.63, 28.28, 28.23, 26.26, 25.74, 19.16. MS (TOF): m/z
Synlett 2009, No. 16, 2651–2654 © Thieme Stuttgart · New York