Design, synthesis and membrane ion transport properties of cystine- and serine-based cyclo-4-oxa-heptane-1,7-bisamides

Article abstract of DOI:10.1016/S0040-4039(02)00979-6

A new class of cyclobisamides, having the general profile of amino acid (cystine or serine)-ether composites, as potentially efficient ion transporters has been designed and synthesized. In model membranes, the adamantane harboring composites exhibited 57-66% of gramicidin A activity in ion transport.

Full text of DOI:10.1016/S0040-4039(02)00979-6

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 43 (2002) 5145–5147
Design, synthesis and membrane ion transport properties of
cystine- and serine-based cyclo-4-oxa-heptane-1,7-bisamides
Darshan Ranganathan,a,* Manoj P. Samant,a R. Nagarajb and E. Bikshapathyb
aOrganic Division III, Discovery Laboratory, Indian Institute of Chemical Technology, Hyderabad 500 007, India
bCentre for Cellular and Molecular Biology, Hyderabad 500 007, India
Received 24 April 2002; accepted 17 May 2002
Abstract—A new class of cyclobisamides, having the general profile of amino acid (cystine or serine)–ether composites, as
potentially efficient ion transporters has been designed and synthesized. In model membranes, the adamantane harboring
composites exhibited 57–66% of gramicidin A activity in ion transport. © 2002 Elsevier Science Ltd. All rights reserved.
The design and synthesis of new macrocycles with
tailor-made structural and functional properties contin-
ues to attract the attention of synthetic chemists.1 Our
promising efforts in the novel domain of hybrid cyclic
peptides2,3 made it logical to explore systems that are
likely to be more effective in ion transport. In this
context, cyclic structures that incorporate facets of pep-
tide and ether were considered attractive. This commu-
nication reports the design and synthesis of
cystine-based 15-membered and serine-based 20-mem-
bered cyclo-4-oxa-heptane-1,7-bisamides and demon-
strates their ability to transport Na+ ions across model
membranes.
The cystine-based 15-membered cyclo-4-oxa-heptane-
1,7-bisamides (4a–c) were prepared by the condensation
of 14 with either the simple cystine diOMe (2a) or its
C,C%-extended bispeptides5 (2b–c) in the presence of
NEt3 under high dilution conditions (Scheme 1). The
precursor C,C%-extended bispeptides (2b–c) were pre-
O
CH2
H2C
O
CH2
O
H2C
O
O
O
Cl
Cl
1
NEt3, dry CH2Cl2
+
NH
HN
NH2
NH2
COR
X
CH
CH
R
R
ROC
CH2
H2C
2, 4; X = -S-S-
x
O
2a-c
3a-c
O
O
O
4a (75%); 4b (67%); 4c (69%)
5a (73%); 5b (67%); 5c (63%)
3, 5; X =
O
O
a: R = OCH3 ; b: R = LeuOMe ; c:
N
H
Scheme 1.
Keywords: amino acid; cyclobisamide; gramicidin A; ionophore; macrocycle; membrane.
* Corresponding author. Fax: +91-40-7160757; e-mail: rangan@iict.ap.nic.in
0040-4039/02/$ - see front matter © 2002 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(02)00979-6

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D. Ranganathan et al. / Tetrahedron Letters 43 (2002) 5145–5147
pared by DCC/HOSu coupling of bis Boc cystine with
either LeuOMe or 1-amino adamantane, followed by
Na-Boc deprotection using TFA/CH2Cl2.
Similarly, the serine-based 20-membered cyclo-4-oxa-
heptane-1,7-bisamides (5a–c) were prepared by the con-
densation of
1
with 1,3-adamantane bis-ser
depsipeptides (3a–c) (Scheme 1). The preparation of
1,3-adamantane bis-ser depsipeptides (3a–c) firstly
involves the condensation of an N,C-protected serine
amino acid or its peptide with 1,3-adamantane-dicar-
bonyl dichloride followed by Na-Z deprotection using
10% Pd/C/H2.
All cyclobisamides (4a–c and 5a–c) required purifica-
tion through a short column of silica gel with CHCl3/
1
MeOH as eluent and were fully characterized.6 In H
NMR variable-temperature (VT) studies, conducted in
DMSO-d6 between 303 and 343 K, there was no indica-
tion of any intramolecular hydrogen bonding of the
amide protons as shown by high temperature coefficient
values (dl/dT >5 ppb K−1).
Figure 1. The profiles (a) and (b) represent dissipation of
diffusion potential set up by valinomycin (lipid:Vm ratio=
1000:1) in small unilamellar vesicles (SUVs) of palmitoyl
oleoyl phosphatidyl choline (POPC) on addition of 4c (7.91
mM) and 5c (6.32 mM), respectively, as monitored by the
fluorescence of cyanine dye dis-C2 (5). SUVs were diluted into
a buffer (5 mM HEPES, pH 7.4) solution of 150 mM NaCl.
Vm and C, respectively, denote the points at which valino-
mycin and cyclobisamides were added. The increase in
fluorescence on addition of cyclobisamides indicates transport
of Na+ ions from the suspension medium into the vesicles.
The spikes seen on the profile at each point (Vm and C) result
from the opening of the chamber door.
The ability of cyclobisamides 4a–c and 5a–c to trans-
port ions across model membranes (small unilamellar
vesicles of palmitoyl oleoyl phosphatidylcholine) was
assessed by monitoring the decay of a valinomycin-
mediated K+ diffusion potential using the fluorescent
dye method.7 Of these, 4c and 5c were able to dissipate
the diffusion potential created by valinomycin (Vm),
indicating its ability to transport Na+ ions across the
lipid bilayer (Fig. 1). Compounds 4c and 5c were,
respectively, assessed as having 57 and 66% of grami-
cidin A activity, in ion transport. Other compounds in
the class exhibited a low profile. None of the cyclo-
bisamides were able to transport Ca2+ and Mg2+ ions.
The compounds 4c and 5c did not cause the release of
entrapped carboxyflorescein, indicating that the move-
ment of ions across the lipid bilayers was not due to the
formation of large pores or detergent-like action.8 The
ion flux may thus be ascribed to a carrier-type of
ion-transport mechanism like that of valinomycin.9
G. W.; Murillo, O. Acc. Chem. Res. 1996, 29, 425.
2. (a) Ranganathan, D.; Haridas, V.; Kurur, S.; Nagaraj, R.;
Bikshapathy, E.; Kunwar, A. C.; Sarma, A. V. S.; Vaira-
mani, M. J. Org. Chem. 2000, 65, 365; (b) Ranganathan,
D.; Haridas, V.; Madhusudanan, K. P.; Roy, R.; Nagaraj,
R.; John, G. B. J. Am. Chem. Soc. 1997, 119, 11578; (c)
Ranganathan, D.; Haridas, V.; Madhusudanan, K. P.;
Roy, R.; Nagaraj, R.; John, G. B.; Sukhaswami, M. B.
Angew. Chem., Int. Ed. Engl. 1996, 35, 1105.
The design delineated provides a straightforward entry
into a new class of amino acid anchored cyclobisamide
ionophores. The flexibility in the synthetic strategy with
the proper choice of ring-inserts is likely to provide
incentives for the design of cyclobisamide ionophores
with promise to act as selective hosts in molecular
recognition.
3. Ranganathan, D. Acc. Chem. Res. 2001, 34, 919.
4. Pratt, J. A. E.; Sutherland, I. O. J. Chem. Soc., Perkin
Trans. 1 1988, 13.
5. Ranganathan, D.; Samant, M. P.; Karle, I. L. J. Am.
Chem. Soc. 2001, 123, 5619.
6. General experimental procedure for the preparation of
cyclo-4-oxa-heptane-1,7-bisamides 4a–c and 5a–c: A solu-
tion of 1 (0.5 mmol, freshly prepared from the precursor
dicarboxylic acid by refluxing with 2 M excess of SOCl2
for 3 h, followed by drying in vacuo) in dry CH2Cl2 (10
mL) was added dropwise over a period of 0.5 h to a
well-stirred and ice-cooled solution of 2a–c or 3a–c (0.5
mmol) in dry CH2Cl2 (250 mL) containing NEt3 (1 mmol)
and the mixture stirred at room temperature for 12 h. The
reaction mixture was washed sequentially with 20 mL each
of ice-cold 2N H2SO4, H2O, and 5% aqueous NaHCO3
and the organic layer dried over anhydrous MgSO4 and
Acknowledgements
We are most grateful to Professor S. Ranganathan for
helpful discussions. Financial support from DST and
UGC, New Delhi is acknowledged.
References
1. (a) Comprehensive Supramolecular Chemistry; Pergamon,
Elsevier Science: Oxford, 1996; Vols. 1 and 2; (b) Gokel,

D. Ranganathan et al. / Tetrahedron Letters 43 (2002) 5145–5147
5147
evaporated in vacuo. The residue was purified on a short
column of silica gel using a mixture of CHCl3/MeOH as
eluent to afford the title cyclobisamides. Compound 4a:
mp 190–192°C; IR (KBr) wmax 3318, 2957, 2925, 2855,
-CH2CO), 2.76 (m, 2H, -CH2CO), 3.64–3.83 (s+m, 10H,
-CO2CH3+-OCH2), 4.32 (m, 2H, Ser CbH2s), 4.65 (m, 2H,
Ser CbH2s), 4.93 (m, 2H, Ser CaHs), 7.45 (d, J=7.3 Hz,
2H, Ser NHs); ES MS m/z 553 ([M+H]+, 100%). Anal.
calcd C26H36N2O11: C, 56.51; H, 6.57; N, 5.07. Found: C,
56.72; H, 6.88; N, 4.90. Compound 5b: mp 88–90°C; IR
1760, 1647, 1514 cm−1 1H NMR (200 MHz, CDCl3) l
;
2.56 (t, 4H, -CH2CO), 3.24 (d, J=6.4 Hz, 4H, Cyst
CbH2s), 3.66 (m, 2H, -OCH2), 3.76 (s, 6H, -CO2CH3), 3.92
(m, 2H, -OCH2), 4.93 (m, 2H, Cyst CaHs), 6.79 (d, J=8.0
Hz, 2H, Cyst NHs); FAB MS m/z 395 ([M+H]+, 100%).
Anal. calcd for C14H22N2O7S2: C, 42.63; H, 5.62; N, 7.10;
S, 16.26. Found: C, 42.15; H, 6.02; N, 6.56; S, 15.99.
Compound 4b: mp 195–197°C; IR (KBr) wmax 3394, 3300,
(KBr) wmax 3350, 2957, 2869 (sh), 1736, 1654, 1528 cm−1
;
1H NMR (500 MHz, DMSO-d6) l 0.83 (d, 6H, Leu CH3s),
0.88 (d, 6H, Leu CH3s), 1.49 (m, 2H, Leu CgHs), 1.59 (m,
4H, Leu CbH2s), 1.64–2.05 (m, 14H, Adm Hs), 2.27 (m,
2H, -CH2CO), 2.51 (m, 2H, -CH2CO), 3.54 (m, 2H,
-OCH2), 3.60 (s, 6H, -CO2CH3), 3.67 (m, 2H, -OCH2),
4.16 (m, 4H, Ser CbH2s), 4.29 (m, 2H, Leu CaHs), 4.67 (m,
2H, Ser CaHs), 7.98 (d, J=7.8 Hz, 2H, Ser NHs), 8.35 (d,
J=8.4 Hz, 2H, Leu NHs); ES MS m/z 779 ([M+H]+, 9%),
801 ([M+Na]+, 100%). Anal. calcd C38H58N4O13: C, 58.60;
H, 7.51; N, 7.19. Found: C, 58.22; H, 7.28; N, 6.92.
Compound 5c: mp 142–145°C; IR (KBr) wmax 3323, 2909,
2953, 2381, 2337, 1856, 1753, 1543 cm−1 1H NMR (200
;
MHz, CDCl3) l 0.92 (d, 12H, Leu CH3s), 1.65 (m, 6H,
Leu (CbH2s+CgHs)), 2.56 (m, 4H, -CH2CO), 3.13 (m, 2H,
Cyst CbH2s), 3.29 (m, 2H, Cyst CbH2s), 3.63 (m, 2H,
-OCH2), 3.73 (s, 6H, -CO2CH3), 3.94 (m, 2H, -OCH2),
4.52 (m, 2H, Leu CaHs), 4.79 (m, 2H, Cyst CaHs), 7.28 (d,
J=8.2 Hz, 2H, Cyst NHs), 7.33 (d, J=7.4 Hz, 2H, Leu
NHs); ES MS m/z 621 ([M+H]+, 100%). Anal. calcd for
C26H44N4O9S2: C, 50.30; H, 7.14; N, 9.03; S, 10.33.
Found: C, 50.15; H, 7.24; N, 8.59; S, 10.09. Compound 4c:
mp 173–175°C; IR (KBr) wmax 3304, 3073, 2908, 2851,
1
2853, 1734, 1652, 1522 cm−1; H NMR (200 MHz, CDCl3)
l 1.63–2.10 (m, 44H, Adm Hs), 2.40 (m, 2H, -CH2CO),
2.65 (m, 2H, -CH2CO), 3.69 (m, 4H, -OCH2), 4.21 (m, 2H,
Ser CbH2s), 4.58 (m, 2H, Ser CbH2s), 4.65 (m, 2H, Ser
CaHs), 6.15 (s, 2H, Adm NHs), 7.63 (d, J=7.4 Hz, 2H,
Ser NHs); ES MS m/z 792 ([M+H]+, 28%), 814 ([M+Na]+,
100%). Anal. calcd C44H62N4O9: C, 66.81; H, 7.90; N,
7.08. Found: C, 67.02; H, 8.28; N, 6.82.
1
1848, 1539 cm−1; H NMR (200 MHz, CDCl3) l 1.66–2.04
(m, 30H, Adm Hs), 2.52 (m, 4H, -CH2CO), 3.06 (m, 2H,
Cyst CbH2s), 3.27 (m, 2H, Cyst CbH2s), 3.55 (m, 2H,
-OCH2), 3.90 (m, 2H, -OCH2), 3.60 (m, 2H, Cyst CaHs),
6.05 (s, 2H, Adm NHs), 6.96 (d, J=8.4 Hz, 2H, Cyst
NHs); FAB MS m/z 633 ([M+H]+, 25%), 655 ([M+Na+],
100%). Anal. calcd for C32H48N4O5S2: C, 60.73; H, 7.64;
N, 8.85; S, 10.13. Found: C, 60.55; H, 7.82; N, 8.66; S,
9.98. Compound 5a: mp syrup; IR (neat) wmax 3366, 2941,
7. Sims, P. J.; Waggoner, A. S.; Wang, C. H.; Hoffman, J. F.
Biochemistry 1974, 13, 3315.
8. Allen, T. M.; Cleland, L. G. Biochim. Biophys. Acta 1980,
597, 418.
9. (a) Pioda, L. A. R.; Stankova, V.; Simon, W. Anal. Lett.
1969, 2, 665; (b) Jenny, H. B.; Riess, C.; Ammann, D.;
Mayyar, B.; Asper, R.; Simon, W. Mikrochim. Acta 1980,
2, 309.
1
2913, 2858, 1734, 1671, 1528 cm−1; H NMR (200 MHz,
CDCl3) l 1.66–2.13 (m, 14H, Adm Hs), 2.43 (m, 2H,