New macrobicyclic receptors for amino acids

Article abstract of DOI:10.1016/S0040-4039(00)00488-3

Two new receptors, 9 and 13, have been prepared, utilising a pyridyl aryl ether unit in the rim of the macrobicyclic structure, and the crystal structures for both of these receptors are reported. The presence of the pyridyl unit provides additional hydrogen bonding functionality in comparison to earlier structures of this type, and 9 is an effective receptor for N- acetyl L-asparagine carboxylate in CH₂Cl₂. (C) 2000 Elsevier Science Ltd.

Full text of DOI:10.1016/S0040-4039(00)00488-3

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 41 (2000) 3963–3966
New macrobicyclic receptors for amino acids
Valerie Jullian, Emma Shepherd, Thomas Gelbrich, Michael B. Hursthouse and
Jeremy D. Kilburn ∗
Department of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
Received 3 March 2000; accepted 21 March 2000
Abstract
Two new receptors, 9 and 13, have been prepared, utilising a pyridyl aryl ether unit in the rim of the macrobicyclic
structure, and the crystal structures for both of these receptors are reported. The presence of the pyridyl unit
provides additional hydrogen bonding functionality in comparison to earlier structures of this type, and 9 is
an effective receptor for N-acetyl L-asparagine carboxylate in CH2Cl2. © 2000 Elsevier Science Ltd. All rights
reserved.
Keywords: host–guest; receptor; amino acid.
The development of synthetic receptors for biological substrates, particularly for peptides and amino
acids, continues to be an active area of research.1 We have been successful in developing receptors
for amino acids and peptidic substrates using a range of receptor structures and in particular using
C2 symmetric macrobicyclic receptors, such as 11a and 2,2 featuring a specific carboxylic acid, or
carboxylate, binding site at the base of a bowl-shaped cavity.3
Macrobicycle 1, for example, was found to be a selective receptor for the dipeptide Cbz L-Ala-
L-Ala-OH,1a while macrobicycle 2 was found to have the unusual property of binding N-acetyl L-
amino acid carboxylate salts (specifically alanine and phenylalanine) with the acetyl amide in the cis
configuration.2a A common feature of these receptors1a,2,3 has been the use of a biarylmethane unit to
∗
Corresponding author. E-mail: jdk1@soton.ac.uk (J. D. Kilburn)
0040-4039/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(00)00488-3
tetl 16767

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give a relatively rigid and well-defined, open rim to the bowl-shaped cavities. We wished to incorporate
additional hydrogen bonding functionality, which might in turn lead to more selective binding properties,
but without dramatically altering the gross structure of these receptors. We also wished to develop
an efficient route to such structures without the C2 symmetry, since this would greatly increase the
number of accessible macrobicyclic receptors of this type. In this paper we describe the successful and
straightforward synthesis of two new macrobicycles, 9 and 13, closely related to macrobicycle 2, but
with one or both of the biarylmethanes now replaced by a pyridyl aryl ether. We also describe the crystal
structures of 9 and 13, the first crystal structures of this class of macrobicyclic receptor, and preliminary
binding studies using receptor 9.
Following the successful strategy used previously for the synthesis of all of our macrobicyclic receptors
we aimed to prepare cyclisation precursors, which could ultimately undergo a double macrocyclisation,
by coupling the modified biaryl portion to a suitably protected lysine derivative, followed by formation
of a thiourea using the side-chain amino group of the lysines.
The desired modified biaryl amino acid derivative 6 was obtained by coupling4 methyl 4-
hydroxybenzoate, 3, with chloropyridine 4, to give the pyridyl aryl ether 5, followed by reduction
of the nitrile with H2/Pd/C5 (Scheme 1). Amine 6 was coupled to Nα-Boc-Nε-Cbz-L-lysine, and the
Nε-Cbz protecting group was removed by hydrogenolysis. Treatment of the resulting free amine 7 with
0.5 equiv. of thiophosgene, using aqueous K2CO3 as base, led directly to the symmetric thiourea 8, in
good yield. Hydrolysis of the methyl esters, formation of the corresponding pentafluorophenyl esters
and treatment with anhydrous TFA6 in dry CH2Cl2 gave the desired cyclisation precursor. Cyclisation
by slow addition of a solution of the precursor, in CH3CN, to a refluxing solution of DIPEA in CH3CN
yielded the C2 symmetric macrobicycle 9 in 28% yield.
Scheme 1. (i) NaH, DMSO, 120°C; (ii) H2, Pd/C, MeOH, NH3; (iii) Nα-Boc-Nε-CBz-L-lys, HOBT, 1-(3-dimethylamino
propyl)-3-ethyl carbodiimide (WSC), THF; (iv) H2, Pd, C; (v) 0.5 equiv. Cl2C_S, K2CO3, H2O, CHCl3, reflux; (vi) LiOH,
i
H2O, dioxane; (vii) C6F5OH, WSC, DMAP, THF; (viii) CF3CO2H, CH2Cl2, (1:1, v/v); (ix) Pr2EtN, CH3CN, reflux, high
dilution
Alternatively, amine 7 could be converted to the isothiocyanate 10 using 1.0 equiv. of thiophosgene,
again with aqueous K2CO3 as base (Scheme 2). Coupling with the previously described amine 11,2a gave
the unsymmetrical thiourea 12. Now an identical sequence of hydrolysis of the methyl esters, formation
of the corresponding pentafluorophenyl esters, removal of the Boc protecting groups with TFA, and
cyclisation, gave macrobicycle 13 in a particularly good yield of 54%.
The C2 symmetric compound 9 was recrystallised from MeOH and the non-symmetric compound 13
from DMSO/H2O to provide X-ray quality crystals.7 For both compounds the crystal structures (Fig. 1)
reveal a large open cavity, as desired, with the sulphur of the thiourea pointing into the cavity. The

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Scheme 2. (i) 1 equiv. Cl2C_S, K2CO3, CHCl3, reflux; (ii) 10, K2CO3, H2O, CHCl3, reflux; (iii) LiOH, H2O, dioxane; (iv)
C6F5OH, WSC, DMAP, THF; (v) CF3CO2H, CH2Cl2, (1:1, v/v); (vi) iPr2EtN, CH3CN, reflux, high dilution
main difference in the two structures comes from the different orientations of aromatic rings in the
biarylmethane fragment of 13 and the pyridyl aryl ether units with a more twisted arrangement for the
latter, which leads to a more open rim in the case of 9. For 9 the orientation of the thiourea, with the
sulphur pointing into the cavity, is stabilised by a pair of hydrogen bonds from both thiourea NH’s to
the benzamide C_O3 of an adjacent molecule of 9. For 13, the thiourea configuration is stabilised by
an intramolecular hydrogen bond from the thiourea sulphur to N4–H and one intermolecular hydrogen
bond from thiourea N1–H to the benzamide C_O3 of an adjacent molecule of 13. However, molecular
modelling of these compounds and of 2, and earlier binding studies on 2, make it very clear that the
thiourea, and the (CH2)4 chains that connect it to the macrobicyclic rim, are very flexible, allowing the
thiourea to orientate itself into or out of the cavity with little energetic penalty when in solution, so that
expected binding of amino acid derivatives within the cavity of the receptor can still be anticipated.
Fig. 1.
Some preliminary binding studies with macrobicycle 9 were carried out using UV titration expe-
riments, monitoring the absorption at 249.5 nm, with the tetrabutyl ammonium salts of N-acetyl L-
glutamine, N-acetyl L-asparagine and N-acetyl L-alanine as guests. Titration of 9, in CH2Cl2, with
glutamine or asparagine derivatives gave saturation curves with a good fit for the presumed 1:1 binding,8
and binding constants of 8.7×103 (±20%) M−1 (−∆Gass=22 kJ mol−1) and 5.5×104 (± 15%) M−1
(−∆Gass=27 kJ mol−1), respectively. The 1:1 stoichiometry of binding for both of these substrates
was confirmed by Job plots.9 Titration of the alanine derivative, however, gave a complex titration
curve, which indicated multiple binding equilibria, and a Job plot with this substrate confirmed that
the binding was not a simple 1:1 stoichiometry. A likely explanation for these preliminary observations
is that a number of modes of binding are possible for the N-acetyl L-alanine carboxylate salt (mirroring
the previous observations10 with the same substrate and macrobicycle 2) whereas, for the asparagine
substrate at least, incorporation of a pyridyl unit into the rim of the cavity provides additional hydrogen

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bonding functionality, as originally hoped, and thus a stabilising interaction with the CONH2 side-chain
functionality of this guest leading to predominantly one mode of binding.
Thus the strategy of modifying the structure of our original macrobicycles has been successfully
realised with efficient syntheses of 9 and 13, and the novel macrobicycles have been characterised by X-
ray crystallography. More detailed studies of the binding properties of both 9 and 13, including detailed
NMR studies of the 1:1 complexes, are now underway in our laboratory and will be reported in due
course.
Acknowledgements
We thank the Ministère des Affaires Etrangères (France) for a Lavoisier Fellowship (V.J.) and
AstraZeneca, Alderley Park, UK, and the EPSRC for a CASE studentship (E.S.). We also thank the
EPSRC for use of the X-ray crystallography facilities.
References
1. For recent examples, see: (a) Henley, P. D.; Kilburn, J. D. Chem. Commun. 1999, 1335; (b) Fessmann, T.; Kilburn, J. D.
Angew. Chem., Int. Ed. Engl. 1999, 38, 1993; (c) Xu, R.; Greiveldinger, G.; Marenus, L. E.; Cooper, A.; Ellman, J. A. J.
Am. Chem. Soc. 1999, 121, 4898; (d) Sirish, M.; Schneider, H.-J. Chem. Commun. 1999, 907 and references cited therein.
2. (a) Pernia, G. J.; Kilburn, J. D.; Essex, J. W.; Mortishire-Smith, R. J.; Rowley, M. J. Am. Chem. Soc. 1996, 118, 10220; (b)
Pernia, G. J.; Kilburn, J. D.; Rowley, M. Chem. Commun. 1995, 305.
3. For other examples of macrobicyclic peptide receptors of this type, see: (a) Henley, P. D.; Waymark, C. P.; Kilburn, J. D.;
Gillies, I. J. Chem. Soc., Perkin Trans. 1 2000, in press; (b) Waymark, C. P.; Kilburn, J. D.; Gillies, I. Tetrahedron Lett.
1995, 36, 3051.
4. For the preparation of related pyridyl aryl ethers, see: Markley, L. D.; Tong, Y. C.; Dulworth, J. K.; Steward, D. L.; Goralski,
C. T.; Johnston, H.; Wood, S. G.; Vinagradoff, A. P.; Bargar, T. M. J. Med. Chem. 1986, 29, 427.
5. Attempted reduction of nitrile 5 using borane, as successfully employed in the preparation of the original biarylmethane
spacer used in macrobicycles 1 and 2, led to cleavage of the pyridylaryl ether to give back the hydroxy benzoate.
6. We found that the use of rigorously dry TFA/CH2Cl2 was essential in the Boc deprotection step to avoid partial conversion
of the thiourea moiety to the corresponding urea.
7. The intensity data were collected on a Nonius Kappa CCD area-detector diffractometer at the window of a rotating
anode FR591 generator (Mo-Kα radiation, λ=0.71073 Å). The structures were solved by direct methods and refined
on F2 by full-matrix least-squares refinements. Full details have been deposited with the Cambridge Crystallographic
Data Centre as supplementary publication no. CCDC 140813 (9) and CCDC 140814 (13). 9: C39H42N8O6S. . .2
MeOH. T=293K, formula C41H50N8O8S, M=814.95, monoclinic, space group P21, Z=2, a=11.0792(2) Å, b=14.4360(3)
Å, c=13.6271(3) Å, β=110.547(1)°, V=2040.86(7) Å3, Dc=1.326 Mg/m3, µ(Mo-Kα)=0.14 mm−1. Colourless block,
crystal size 0.70×0.35×0.35 mm, θ range: 2.0−25.2°, 99.9% coverage, 7395 unique data and 612 parameters,
R1[F2>2σ(F2)]=0.042, wR2(all data)=0.111, Flack parameter=0.07(7). 13: C41H45N7O5S. . .3 H2O. T=120K, formula
C41H51N7O8S, M=801.95, monoclinic, space group P21, Z=4, a=9.0659(2) Å, b=17.6648(3) Å, c=26.1695(6) Å,
β=98.6819(7)°, V=4143.0(1) Å3, Dc=1.286 Mg/m3, µ(Mo-Kα)=0.14 mm−1. Colourless plate, crystal size 0.15×0.12×0.05
mm, θ range: 2.0−24.5°, 98.8% coverage, 13502 unique data and 1134 parameters, R1[F2>2σ(F2)]=0.061, wR2(all
data)=0.133, Flack parameter=0.11(8).
8. Binding constants were calculated by fitting the titration data to a 1:1 binding isotherm using NMRTit HG software, kindly
provided by Prof. C. A. Hunter, University of Sheffield. See: A. P. Bisson, C. A. Hunter, J. C. Morales, K. Young, Chem.
Eur. J. 1998, 4, 845–851.
9. (a) Connors, K. A. Binding Constants, The Measurement of Molecular Complex Stability; Wiley: 1987; pp. 24–28. (b) Job,
A. Annales de Chimie 1928, 9, 113.
10. With receptor 2, N-acetyl L-alanine carboxylate salt (and the corresponding phenylalanine carboxylate salt) was bound
predominantly within the bowl shaped cavity, utilising a carboxylate–thiourea interaction, but with the acetyl amide in
the cis configuration (with the cis amide stabilised by two hydrogen bonds from the rim of the macrobicycle to the acetyl
amide carbonyl). However detailed NMR studies (see Ref. 2a) revealed that there were additional modes of binding for
these substrates, involving the trans configuration of the acetyl amide.