Chiral centers in the side chains of α-amino acids control the helical screw sense of peptides

Article abstract of DOI:10.1002/anie.200460420

Chirality on the side suffices: The screw sense of 3₁₀- and α-helices formed by the oligopeptides 1, which have no α-carbon chiral centers, is controlled by the chiral centers in their side chains. These results imply that just the side chain c

Full text of DOI:10.1002/anie.200460420

Communications
Helical Structures
Chiral Centers in the Side Chains of a-Amino
Acids Control the Helical Screw Sense of
Peptides**
Masakazu Tanaka,* Yosuke Demizu, Mitsunobu Doi,
Masaaki Kurihara, and Hiroshi Suemune*
Understanding the secondary structures of peptides and
proteins, for example, the a-helix, b-sheet, and reversed-
turn, is important as they play a vital role in molecular
biology, the life sciences, and drug discovery.[1] The a-helices
and the 310-helices in proteins almost always form a right-
handed (P) helical screw, which is believed to result from the
asymmetry of the a-carbon (S enantiomer) in terrestrial l-a-
amino acids.[1a] Among proteinogenic l-a-amino acids, only
isoleucine and threonine possess an additional chiral center at
the side-chain b-carbon besides the a-carbon. However, so far
it has not been clear howchiral centers in the side chain affect
the secondary structure of peptides.[2] Here we describe how
the asymmetric centers of the a-amino acid side chain alone
control the screwsense of the helices formed by oligopeptides
made up of amino acids without a chiral center at the a-
carbon.
Replacement of the a-hydrogen atom of an a-amino acid
with an alkyl substituent results in an a,a-disubstituted a-
amino acid (dAA), such as 2-aminoisobutyric acid (Aib),
diethylglycine (Deg), 1-aminocycloalkanecarboxylic acid
(Acnc, n = ring size), and isovaline.[3] Oligopeptides contain-
ing dAAs showstable secondary structural preferences, such
as b-turns, 310-helices, and extended planar C5 conformations.
We designed a chiral cyclic dAA [(S,S)-Ac5cdOM], in which the
a-carbon does not have an asymmetric center but has two side
chain g-carbons that are asymmetric centers. In the case of
Ac5cdOM homopeptides, the asymmetric centers do not lie
along the main-chain backbone of the peptides but rather in
the side chain cyclopentane ring. Thus, the secondary
[*] Prof. Dr. M. Tanaka, Y. Demizu, Prof. Dr. H. Suemune
Graduate School of Pharmaceutical Sciences
Kyushu University
Fukuoka 812-8582 (Japan)
Fax: (+81)92-642-6545
E-mail: mtanaka@phar.kyushu-u.ac.jp
suemune@phar.kyushu-u.ac.jp
Prof. Dr. M. Doi
Osaka Universityof Pharmaceutical Sciences
Osaka 569-1094 (Japan)
Dr. M. Kurihara
Division of Organic Chemistry
National Institute of Health Sciences
Tokyo 158-8501 (Japan)
[**] This work was partlysupported bya Grant-in-Aid for Scientific
Research (C) from the Japan Societyfor the Promotion of Science
and also bythe Sasakawa Scientific Research Grant from the Japan
Science Society.
Supporting information for this article is available on the WWW
under http://www.angewandte.org or from the author.
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DOI: 10.1002/anie.200460420
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structure is affected by the side chain chiral centers of (S,S)-
Ac5cdOM peptides but not by the a-carbons.[4]
exposed NH group). This suggests the absence of two
intramolecular hydrogen bonds at these NH groups and
thus indicates that the peptides assume a helical structure in
The optically active (S,S)-Ac5cdOM was synthesized from
dimethyl-l-(+)-tartrate as follows (Scheme 1): Dimethyl-l-
1
CDCl3 solution.[6] Also, the ROESY H NMR spectrum of 8
shows a complete series of sequential dNN cross peaks of
NOEs, from the N-terminal NH1 to the C-terminal NH6,
characteristic of a helical secondary structure.[6]
The CD spectra of 8–10 in 2,2,2-trifluoroethanol (TFE)
showpositive maxima and intensity for two bands at 222 nm
and 208 nm, indicating that the screwsense of the helix is left-
handed (M) (Figure 1a). The ratio of R [q222/q208] suggests that
Scheme 1. Synthesis of (S,S)-Ac5cdOM and its homopeptides. Reagents
and conditions: a) dimethyl malonate, KOtBu; b) 1. NaOH, 2. DPPA,
3. BnOH; c) NaOH; d) 1. Pd/C, H2, 2. EDC, HOBt, 4, MeCN, RT;
e) 1. Pd/C, H2, 2. EDC, HOBt, 6, MeCN, RT. Cbz=benzyloxycarbonyl,
EDC=2-(3-dimethylaminopropyl)-1-ethylcarbodiimide, HOBt=1-hy-
droxy-1H-benzotriazole.
(+)-tartrate was converted into a diiodide 1 by conventional
procedures;[5] then dimethyl malonate was alkylated with 1 to
give the cyclic diester 2. Monohydrolysis of 2 followed by
Curtius rearrangement with diphenylphosphoryl azide
(DPPA) afforded the C- and N-terminal protected Cbz-
(S,S)-Ac5cdOM-OMe 3. Hydrolysis with an alkaline solution
gave the N-protected Cbz-(S,S)-Ac5cdOM-OH 4. Homopep-
tides Cbz-[(S,S)-Ac5cdOM]n-OMe (up to the decamer; n = 2, 4,
6, and 10) were prepared by coupling the N-terminal free
peptides and C-terminal free dipeptide 6 by solution-phase
methods.[6] Octapeptide 9 and decapeptide 10 can be dis-
solved in water (10: > 5 mgcmÀ1) because of the hydrophilic
ethereal groups at the cyclopentane.[7]
The preferred secondary structure of the homopeptides in
the CDCl3 solution was first studied by FT-IR and H NMR
spectroscopies. In the IR spectra, the weak bands in the
region 3420–3440 cmÀ1 are assigned to free (solvated) peptide
NH groups, and the strong bands at 3320–3370 cmÀ1 to
1
Figure 1. CD spectra of Cbz-[(S,S)-Ac5cdOM]n-OMe 8–10 (n=6, 8, 10)
(0.5 mm) a) in TFE solution, b) in H2O.
the secondary structure of 8 is a 310-helix, and that those of 9
and 10 are a-helices.[8] Interestingly, the intensity of the CD
spectra of 9 and 10 in water become stronger, indicating that
these peptides are more helical when dissolved in water than
in TFE (Figure 1b).
À
=
peptide NH groups with N H···O C intramolecular hydro-
gen bonds of differing strengths. As the length of the peptide
chain increases, the strong band observed at 3370 cmÀ1 in 7
shifts to slightly lower wave numbers (3320 cmÀ1 in 10), and
the relative intensity of this band gradually increases.[6] These
IR spectra are very similar to those of achiral Ac4c peptides,
which form 310-helices in solution,[3c] but very different from
those of Deg peptides, which form extended planar confor-
mations.[3b]
The molecular and crystal structures of the terminally
protected hexapeptide
8 (Figure 2) and octapeptide 9
(Figure 3) were determined by X-ray crystallographic analy-
sis. In the crystal structure of 8 three crystallographically
independent molecules A, B, and C exist in the asymmetric
unit. All three molecules are left-handed (M) 310-helices
(mean value: f= 58.58, y = 30.58), showing small differences
in the conformation of the side chains, and four intra-
molecular hydrogen bonds are found in each molecule. The
molecules A, B, and C are connected by two intermolecular
In the 1H NMR spectra measured after addition of DMSO
or the free radical 2,2,6,6-tetramethyl-1-piperidinoxyl
(TEMPO), as well as at different peptide concentrations,
the two NH signals [NH1 and NH2] of the hexapeptide 8 and
octapeptide 9, respectively, are very sensitive (solvent-
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Figure 2. a) Illustrative structure of 8 (molecules A, B and C) as viewed perpendicular to the 310-helical axis; b) ORTEP drawing of molecule A as
viewed along the 310-helical axis.
310-helix but an a-helix, exists along with three water
molecules. Five intramolecular hydrogen bonds exist in the
a-helical molecule, and in the packing mode the chains of
intermolecularly hydrogen-bonded (M) a-helices are formed
by means of the water.
The conformational search calculation with Macromodel
(AMBER*) produced left-handed (M) a-helices as a global
minimum-energy conformation for both 8 and 9. The (M) 310-
helix of 8, which is similar to those in the crystal, was obtained
as
molÀ1).[6]
We have efficiently synthesized a newchiral cyclic dAA
a local minimum-energy conformation (+ 3.22 kcal
and studied the secondary structure of (S,S)-Ac5cdOM homo-
peptides. It is notable that: 1) Chiral centers in the side chain
of the a-amino acid strongly control the helical screwsense of
its peptides; 2) The (M) a-helix of the (S,S)-Ac5cdOM peptides
is stable even in water; 3) The transition from the 310-helix
into the a-helix occurs for longer (S,S)-Ac5cdOM peptides; and
4) The a-helix is formed in dAA homopeptides without a
natural a-amino acid in the solid state.
These results strongly imply that the side chain chiral
centers of isoleucine and threonine would affect the secon-
dary structure of their oligopeptides; albeit, these residues
also exhibit a strong screw-sense bias due to their chiral a-
carbon atom, and they are poorly helicogenic residues.
Preparation of the enantiomer and incorporation of (S,S)-
Ac5cdOM into natural a-amino acid sequences are currently
underway.
Figure 3. a) Illustrative structure of 9 as viewed perpendicular to the a-
helical axis; b) ORTEP drawing as viewed along the a-helical axis (a-
helical wheel).
hydrogen bonds, forming
a head-to-tail alignment of
(··A···B···C···A···B···C··) chains.[9]
Received: April 23, 2004
In the asymmetric unit of 9 one left-handed (M) helical
structure (mean value: f= 60.98, y = 46.88),[10] which is not a
Published Online: July 7, 2004
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Chemie
Keywords: amino acids · chirality· conformation analysis ·
.
helical structures · peptidomimetics
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[2] Chiral N-alkylated glycine oligopeptides (peptoids) form a one-
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[4] Tonioloꢀs group reported that homopeptides of a C2-symmetric
binaphthyl dAA with only axial chirality form one-handed 310-
helices in solution. See: J. P. Mazaleyrat, K. Wright, A. Gaucher,
M. Wakselman, S. Oancea, F. Formaggio, C. Toniolo, V. Setnicka,
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[5] I. Takahashi, K. Odashima, K. Koga, Tetrahedron Lett. 1984, 25,
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[6] See the Supporting Information for synthetic procedures,
spectroscopic data of newcompounds, IR spectra, 1H NMR
experiments (DMSO, TEMPO, concentration effects, and the
ROESY spectrum), molecular mechanics calculations, torsion
angles, and hydrogen-bond parameters.
[7] M. Tanaka, Y. Demizu, M. Doi, M. Kurihara, H. Suemune, Pept.
Sci. 2003 (Proceedings of the 40th JPS) 2004, 109 – 110.
[8] a) C. Toniolo, A. Polese, F. Formaggio, M. Crisma, J. Kamphuis,
J. Am. Chem. Soc. 1996, 118, 2744 – 2745; b) P. Pengo, L.
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[9] CCDC-236749 and CCDC-236750 contain the supplementary
crystallographic data for this paper. These data can be obtained
free of charge via www.ccdc.cam.ac.uk/conts/retrieving.html (or
from the Cambridge Crystallographic Data Center, 12, Union
Road, Cambridge CB2 1EZ, UK; fax: (+ 44) 1223–336–033 or
deposit@ccdc.cam.ac.uk). Crystal data: 8: 3(C57H88N6O21), Mr =
3579.99 (1193.33), space group P21, a = 22.889, b = 11.9061, c =
33.711 ꢁ, b = 91.8878, V= 9182.0 ꢁ3, Z = 6, T= 90 K, m(MoKa) =
0.99 cmÀ1, 31196 reflections measured, 29355 unique reflections
(Rint = 0.0326) R1 (I > 2s) = 0.0775, wR2 (I > 2s) = 0.1972,
GOF = 1.095. 9: C73H114N8O27·3H2O, Mr = 1589.77, space group
P21, a = 15.639, b = 16.431, c = 15.989 ꢁ, b = 95.858, V= 4087 ꢁ3,
Z = 2, T= 123 K, m(MoKa) = 1.0 cmÀ1, 16850 reflections mea-
sured, 12478 unique reflections (Rint = 0.0609) R1 (I > 2s) =
0.0579, wR2 (I > 2s) = 0.1401 (I > 2s), GOF = 1.031.
[10] The signs of f, y torsion angles at the C-terminus are opposite to
those of the preceding residues. The average is amino acid
residues (1–7).
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