Endohedral peptide lining of a self-assembled molecular sphere to generate chirality-confined hollows

Article abstract of DOI:10.1021/ja073629b

At the interior of a ca. 5 nm-sized self-assembled coordination sphere, 24 amino acids (or peptides) are lined to generate chirality-confined protein-mimic cavities, whose structures are well-characterized by spectroscopy and X-ray analysis. Copyright

Full text of DOI:10.1021/ja073629b

Published on Web 08/09/2007
Endohedral Peptide Lining of a Self-Assembled Molecular Sphere To
Generate Chirality-Confined Hollows
Kosuke Suzuki, Masaki Kawano, Sota Sato, and Makoto Fujita*
Department of Applied Chemistry, School of Engineering, The UniVersity of Tokyo and CREST, Japan Science and
Technology Agency (JST), 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
Received May 21, 2007; E-mail: mfujita@appchem.t.u-tokyo.ac.jp
Enzyme pockets are chiral cavities surrounded by amino acid
residues, where highly elaborated molecular recognition and
chemical transformations take place.1 Although there are many
reports on the de novo design and control of peptide 3D-structures,2,3
the construction of chiral pockets fully surrounded by amino acid
residues has been seldom achieved. In the present study, peptide
fragments are tethered to the interior of an M12L24 nanosized
spherical complex4,5 to generate peptide-lined chiral cavities. The
shell of the spherical complex self-assembles from 12 Pd(II) ions
and 24 bent bridging ligands with dangling peptide fragments
Figure 1. CSI-MS spectrum of complex 2a (CH3CN, OTf- salt).
(Scheme 1). In this simple way, we succeeded in decorating the
interior surface of the 4 nm shell with 24-96 amino acid residues.
As the ligand synthesis is modular, we expect that the combinatorial
replacement of peptide residues enables the artificial evolution of
enzymelike pockets.
(n ) 5-13). For example, intense peaks at m/z 1860.6, 1637.2,
and 1458.7 were assigned to [2a-(OTf-)8]8+, [2a-(OTf-)9]9+, and
[2a-(OTf-)10]10+, respectively (Figure 1).
The structure of complex 2a was unambiguously determined by
single-crystal X-ray diffraction.7 Single crystals suitable for X-ray
Scheme 1
crystallographic analysis were obtained by the slow vapor diffusion
of 1,4-dioxane into an acetonitrile solution of 2a. Despite the severe
disorder of solvent molecules and some of the triflate counterions,
synchrotron X-ray irradiation with high flux and low divergence
provided high quality data, from which the structure of M12L24
spherical complex with a diameter of 4.6 nm was revealed (Figure
2). The locations of the L-alanine moieties on the interior surface
were precisely determined. The positions of the t-Boc protection
groups, however, could not be clearly observed because of disorder.
The accumulation of 24 asymmetrical amino acid moieties
generates a chiral environment within the spherical shell. The
intensity of the circular dichromism (CD) spectra of ligands 1a
We designed bent ligands 1a-i with amino acids or peptides
attached at the benzene core. The ligands were synthesized in one
step by the condensation reactions of 2,6-bis(4-pyridylethynyl)-
phenol and N-protected amino acids or peptides using N,N′-
dicyclohexylcarbodiimide as a condensation agent. When a mixture
of L-alanine anchored ligand 1a (5.0 µmol) and Pd(CF3SO3)2 (2.5
µmol) in CD3CN (1 mL) was stirred for 4 h at 50 °C, the
quantitative formation of a single and highly symmetric product,
1
2a, was indicated by H NMR spectroscopic analysis. The large
downfield shift of the product signals as compared to ligand 1a,
particularly for pyridyl R-hydrogen atoms (∆δ ) 0.33 ppm), is
attributed to the metal-pyridine coordination. Cold-spray ionization
Figure 2. Crystal structure of complex 2a. Counterions and solvent
mass spectrometry (CSI-MS)6 clearly confirmed the M12L24 stoi-
chiometry from a series of prominent peaks of [2a-(OTf-)n]n+
molecules are omitted for clarity (Pd, yellow; C, blue; N, purple; O, red;
H, gray).
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J. AM. CHEM. SOC. 2007, 129, 10652-10653
10.1021/ja073629b CCC: $37.00 © 2007 American Chemical Society

C O M M U N I C A T I O N S
Figure 4. CSI-MS spectrum of M12L24 spherical complex self-assembled
from the mixture of ligand 1a (Ala) and 1c (Phe). The ratio of 1a/1c was
10:1 (CH3CN, OTf- salt).
binding pockets for asymmetric molecular recognition and reactions.
We also demonstrated the dynamic combinatorial libraries of
spherical cavities by combining two or more different ligands
bearing amino acids. Although the ratio of amino acids within the
complexes is statistical, we expect that the ratio and position of
amino acid residues can be controlled by template molecules and
external environment and that the interior confined in the sphere
can be ultimately evolved toward artificial enzyme pockets.
Figure 3. (a) CD spectra and (b) UV spectra of ligand 1a (L-Ala, 24 µM),
1b (D-Ala, 24 µM) and complex 2a,b (1 µM) in CH3CN at 25 °C with a 1
cm cell. The CD spectra of 1a,b were multiplied by a factor of 24 for
comparison. ∆ꢀ ) molar circular dichroism.
(L-Ala) and 1b (D-Ala) is very weak (Figure 3). After complexation,
however, sphere 2a shows distinct Cotton effects in the absorptive
region of the complex framework. At equimolar concentration of
alanine moieties of 1a and 2a, the intensity of the Cotton effects
of 2a was about thirty times higher than that of 1a. Mirror image
Cotton effects were exhibited for 2a and 2b, reflecting the absolute
configurations of L- and D-alanine moieties. We believe that the
Cotton effects stem from the chiral conformation of the ligand
frameworks.8 Namely, the chirality of 24-amino acids is transferred
to the backbone of the spherical complex, resulting in twisting of
the coordinated ligands in solution.
In addition to the alanine-lined spherical complexes, we obtained
spheres endo-functionalized with various types of amino acids or
peptides. Ligands 1c-i were assembled into spherical complexes
2c-i, whose structures were characterized by NMR and CSI-MS.
These complexes contain 24- (2c-f), 48- (2g), 72- (2h), and 96-
(2i) amino acid residues, respectively (Figure S1). When the
5-residue peptide (Ala-Val-Phe-Ala-Gly) was tethered to the ligand,
the spherical complex was no longer formed as a single product,
probably because of the limitation of the cavity volume. These
results reveal that the spherical shell (4.6 nm in diameter) can
contain up to ca. 100 amino acid residues, corresponding to small
proteins in size and the number of amino acid residues.
The interior of the spheres can be combinatorially functionalized
with a variety of amino acid residues. For the simplest demonstra-
tion, we examined the self-assembly of the spherical complex from
two different ligands. When the mixture of ligand 1a and 1c
(10:1) was treated with Pd(CF3SO3)2, CSI-MS analysis indicated
the formation of several isomers of M12L24 spherical complexes
containing Ala and Phe residues in 24/0 to 20/4 ratios (Figure 4).
In a similar way, the Ala-lined sphere can incorporate a few
L-proline residues of 1e that potentially show organocatalysis for
some organic transformations.9 Since the sphere formation is a
thermodynamic process, the spherical shell assembling from two
or more ligands constitutes a dynamic combinatorial library10 of
amino acid residues at the interior.
Acknowledgment. This research was partially supported by the
Ministry of Education, Culture, Sports, Science and Technology
of Japan. This work has been approved by the Photon Factory
Program Advisory Committee (Proposal No. 2006G284).
Supporting Information Available: Preparation and physical
properties of 1a-i and 2a-i, and crystallographic data of 2a. This
material is available free of charge via the Internet at http://pubs.acs.org.
References
(1) (a) Jencks W. P. Catalysis in Chemistry and Enzymology; McGraw-Hill:
New York, 1969. (b) Stryer, L. Biochemisty, 4th ed.; W. H. Freeman and
Company: New York, 1995.
(2) (a) Blanco, F. J.; Jime´nez, M. A.; Herranz, J.; Rico, M.; Santoro, J.; Nieto,
J. L. J. Am. Chem. Soc. 1993, 115, 5887-5888. (b) Haque, T. S.; Gellman,
S. H. J. Am. Chem. Soc. 1997, 119, 2303-2304. (c) Mutz, M. W.; Case,
M. A.; Wishart, J. F.; Ghadiri, M. R.; McLendon, G. L. J. Am. Chem.
Soc. 1999, 121, 858. (d) Hamuro, Y; Schneider J. P.; DeGrado W. F. J.
Am. Chem. Soc. 1999, 121, 12200-12201.
(3) Controlling with synthetic receptors: (a) Peczuh, M. W.; Hamilton, A.
D.; Sa´nchez-Quesada, J.; Mendoza, J.; Haack, T.; Giralt, E. J. Am. Chem.
Soc. 1997, 119, 9327-9328. (b) Tashiro, S.; Tominaga, M.; Yamaguchi,
Y.; Kato, K. Fujita, M. Angew. Chem., Int. Ed. 2006, 45, 241-244. (c)
Tashiro, S.; Kobayashi, M.; Fujita, M. J. Am. Chem. Soc. 2006, 128,
9280-9281.
(4) Tominaga, M.; Suzuki, K.; Kawano, M.; Kusukawa, T.; Ozeki, T.;
Sakamoto, S.; Yamaguchi, K.; Fujita, M. Angew. Chem., Int. Ed. 2004,
43, 5621-5625.
(5) Functionalizaton of M12L24 complex: (a) Tominaga, M.; Suzuki, K.;
Murase, T.; Fujita, M. J. Am. Chem. Soc. 2005, 127, 11950-11951. (b)
Sato, S.; Iida. J.; Suzuki, K.; Kawano, M.; Ozeki, T.; Fujita, M. Science
2006, 313, 1273-1276. (c) Murase, T.; Sato, S.; Fujita, M. Angew. Chem.,
Int. Ed. 2007, 46, 1083-1085. (d) Kamiya, N.; Tominaga, M.; Sato, S.;
Fujita, M. J. Am. Chem. Soc. 2007, 129, 3816-3817.
(6) CSI-MS is quite effective for analyzing the solution structures of metal
complexes: (a) Sakamoto, S.; Fujita, M.; Kim, K.; Yamaguchi, K.
Tetrahedron 2000, 56, 955-964. (b) Yamaguchi, K. J. Mass Spectrom.
2003, 38, 473-490.
(7) For the crystal data, see Supporting Information. The final R factor was
converged to a high value of 0.2595, because the crystal diffracted very
weakly owing to a large amount of highly disordered molecules of
solvents, triflate anions, and t-Boc groups in the amino acid chains. The
detail is described in a cif file deposited in CCDC (No. 644915).
(8) (a) The small twisting of pyridyl rings around each Pd ion center was
observed. (b) Amino acid induced Cotton effects in the aromatic
framework: Pantos, G. D.; Pengo, P.; Sanders J. K. M. Angew. Chem.,
Int. Ed. 2007, 46, 194-197.
(9) (a) List, B.; Lerner, R. A.; Barbas, C. F., III. J. Am. Chem. Soc. 2000,
122, 2395-2396. (b) Northup, A. B.; Macmillan, D. W. C. J. Am. Chem.
Soc. 2002, 124, 6798-6799.
(10) (a) Lehn, J.-M. Chem.sEur. J. 1999, 5, 2455-2463. (b) Otto, S.; Furlan,
R. L. E.; Sanders, J. K. M. Curr. Opin. Chem. Biol. 2002, 6, 321-327.
In summary, we have constructed 4.6 nm-sized spherical
complexes containing up to 96 amino acid residues. The number
and the sequence of amino acid residues are modified and
controlled. These peptide-lined complexes generate chiral hollow
cavities, similar to enzyme pockets, which could be utilized as
JA073629B
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