Design of peptides with α,β-dehydro residues: Pseudo-tripeptide N-benzyloxycarbonyl-ΔLeu-L-Ala-L-Leu-OCH3

Article abstract of DOI:10.1107/S0108270101016468

The title peptide N-benzyloxycarbonyl-ΔLeu-L-Ala-L-Leu-OCH₃ [methyl N-(benzyloxycarbonyl)-α,β-dehydroleucyl-L-alanyl-L-leucinate], C₂₄H₃₅N₃O₆, was synthesized, in the solution phase. The peptide adopt

Full text of DOI:10.1107/S0108270101016468

organic compounds
Acta Crystallographica Section C
Crystal Structure
Communications
yet been fully de®ned. In order to establish the design rules
with ꢀ,ꢁ-dehydro residues at the (i+1) position, a tripeptide,
N-benzyloxycarbonyl(Cbz)±ÁLeu±l-Ala±l-Leu±OCH3, (III),
was synthesized and its three-dimensional structure deter-
mined by X-ray diffraction.
ISSN 0108-2701
Design of peptides with a,b-dehydro
residues: pseudo-tripeptide
N-benzyloxycarbonyl±DLeu±L-Ala±
L-Leu±OCH3
The structure of peptide Cbz±ÁLeu±l-Ala±l-Leu±OCH3
shows that the side chain of the ÁLeu residue adopts the
expected geometry, with the vinyl H atom on the same side of
the adjacent carbonyl group. The C1AÐC1B bond length of
Jyoti Makker, Sharmistha Dey, Pravindra Kumar and Tej P.
Singh*
Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar,
New Delhi 110 029, India
Ê
1.322 (5) A is in agreement with the average value of
Ê
1.323 (2) A quoted for this bond (Benedetti, 1977). The
Correspondence e-mail: tps@aiims.aiims.ac.in
planarity imposed by the ꢀ,ꢁ-double bond should promote an
electronic delocalization, with shrinking of the C1AÐN1 and
C1AÐC1P bonds, and lengthening of the carbonyl double
bond (Table 1). The C1AÐN1 and C1AÐC1P bond lengths of
Received 11 June 2001
Accepted 7 December 2001
Online 12 March 2002
Ê
1.413 (4) and 1.500 (4) A, respectively, are in accordance with
the expected values reported for dehydro residues (Singh &
The title peptide N-benzyloxycarbonyl±ÁLeu±l-Ala±l-Leu±
OCH3 [methyl N-(benzyloxycarbonyl)-ꢀ,ꢁ-dehydroleucyl-l-
alanyl-l-leucinate], C24H35N3O6, was synthesized in the
solution phase. The peptide adopts a type II0 ꢁ-turn
conformation which is stabilized by an intramolecular 4 ! 1
NÐHÁ Á ÁO hydrogen bond. The crystal packing is stabilized by
two intermolecular NÐHÁ Á ÁO hydrogen bonds.
Ê
Narula, 1996). The C1PÐO1P bond length of 1.217 (4) A
seems to be only slightly in¯uenced by electronic effects. The
bond angles N1ÐC1AÐC1P, N1ÐC1AÐC1B and C1AÐ
C1BÐC1G in the ÁLeu residue deviate from the standard
value of 120ꢀ (Table 1). The opening of the C1AÐC1BÐC1G
angle helps in releasing the constraints caused by the changes
introduced in an amino acid as a result of dehydrogenations at
the C1A and C1B atoms.
A perspective view of the title molecule is shown in Fig. 1.
Selected torsion angles are given in Table 1. The peptide
adopts a type II0 ꢁ-turn conformation characterized by torsion
Comment
The conformational preferences of amino acid side chains
govern the folding of peptides. These preferences differ from
one amino acid to another, as observed in protein crystals
(Chandrasekaran & Ramachandran, 1970; Janin et al., 1978;
Bhat et al., 1979) and oligopeptides (Benedetti et al., 1983),
and as determined theoretically by means of conformational
energy computations (Zimmerman et al., 1977; Vasquez et al.,
1983). Short-range interactions involving the atoms of the side
chains with the atoms of the backbone, as well as the atoms of
the two neighbouring peptide units, determine the confor-
mational preferences in peptides. Thus, the peptides can adopt
a large number of conformations in order to gain preferred
side-chain±backbone and side-chain±side-chain interactions.
This makes the design strategy rather weak and impractical. In
order to develop an effective design tool, it is necessary to
restrict the number of preferred conformations to a minimum.
This can be achieved through introduction of well de®ned
steric constraints with ꢀ,ꢁ-dehydro residues. So far, it has been
shown that the dehydro residues, such as dehydrophenyl-
alanine (ÁPhe), dehydroleucine (ÁLeu) and dehydro-ꢀ-
aminobutyric acid (ÁAbu), induce a type II ꢁ-turn confor-
mation when placed at the (i+2) position (Singh & Narula,
1996). However, the conformational contributions of these
dehydro residues when placed at the (i+1) position have not
angles '1 = 47.9 (4)ꢀ, = 137.2 (3)ꢀ, '2 = 87.2 (3)ꢀ and
1
Figure 1
A perspective view of the title peptide. Displacement ellipsoids are drawn
at the 50% probability level.
o212 # 2002 International Union of Crystallography
DOI: 10.1107/S0108270101016468
Acta Cryst. (2002). C58, o212±o214

organic compounds
acetate solvate, (II), isobutyl chloroformate (IBCF; 2.14 ml, 16 mmol)
and N-methylmorpholine (NMM; 1.75 ml, 16 mmol) were added to a
precooled solution (263 K) of Boc±l-Ala±OH (3.0 g, 16 mmol) in
dichloromethane (DCM) and the resulting solution stirred for
20 min. To this, a precooled solution of l-Leu±OCH3ÁHCl (2.75 g,
19 mmol) in DCM and NMM (2.1 ml, 19 mmol) was added and
stirred for 3 h at 263 K and then at room temperature overnight.
l-Amino acids were used in all the syntheses. The resulting solution
was evaporated, taken up in ethyl acetate and washed three times
with 10% sodium bicarbonate and three times with 5% citric acid and
water, dried over anhydrous sodium sulfate and then evaporated to
yield Boc±l-Ala±l-Leu±OCH3, which was dissolved in 1:1 (v/v)
DCM±TFA (tri¯uoroacetic acid) and stirred for 1 h at room
temperature. The resulting solution was concentrated in vacuo and
triturated with dry ether to give (II) [yield 3.51 g (10.6 mmol), 66.7%;
m.p. 388 K]. For the synthesis of Cbz±ÁLeu±l-Ala±l-Leu±OCH3,
(III), triethylamine (TEA; 0.11 ml, 0.8 mmol) and IBCF (0.1 ml,
0.8 mmol) were added to a precooled solution of (I) (200 mg,
0.8 mmol) in tetrahydrofuran and the resulting solution stirred for
20 min at 263 K. To this, a precooled solution of (II) in TEA (320 mg,
0.96 mmol) was added and stirring continued for 3 h at 283 K and
then at room temperature overnight. The ®nal solution was worked
up as outlined for (II) and the ®nal compound was recrystallized from
an ethyl acetate±petrol solution (yield: 180 mg).
Figure 2
The molecular packing viewed along the a axis.
= 10.2 (4)ꢀ, and an intramolecular N3ÐH3Á Á ÁO0P 4 ! 1
2
Ê
hydrogen bond [N3Á Á ÁO0P
=
3.181 (7) A and N3Ð
H3Á Á ÁO0P = 151ꢀ]. The side-chain conformation of the ÁLeu
residue, with ꢂ11
=
0.4 (6), ꢂ21;1 = 111.1 (5) and ꢂ21;2
=
127.3 (5)ꢀ, is different from that found in the saturated
leucine residue. The two sets of values of the side-chain
torsion angles in Leu are 60, 60 and 180ꢀ, and 180, 180 and
60ꢀ, with the ®rst combination being observed more
frequently. It may be mentioned here that this is the ®rst
complete sequence with a dehydro residue at the (i+1) posi-
tion which shows the formation of a type II0 ꢁ-turn confor-
mation. In an earlier structure with the sequence N-Ac±
ÁPhe±l-Val±l-Val±OCH3, the peptide adopted an open
conformation (Narula et al., 1991), presumably due to the
presence of branched ꢁ-carbon residues in the sequence. The
structure of the present peptide indicates that peptides with a
dehydro residue at the (i+1) position tend to form a type II
ꢁ-turn conformation in the presence of a non-ꢁ-branched
residue at the (i+2) position.
Crystal data
3
C24H35N3O6
Mr = 461.55
Monoclinic, P21
Dx = 1.185 Mg m
Cu Kꢀ radiation
Cell parameters from 25
re¯ections
Ê
a = 10.2550 (15) A
Ê
b = 9.5090 (14) A
ꢃ = 0±25ꢀ
ꢄ = 0.70 mm
T = 293 (2) K
1
Ê
c = 13.4550 (14) A
ꢁ = 99.715 (11)ꢀ
3
Ê
V = 1293.9 (3) A
Z = 2
Prism, colourless
0.3 Â 0.2 Â 0.1 mm
Table 1
Selected geometric parameters (A, ).
ꢀ
Ê
N1ÐC1A
C1AÐC1B
C1AÐC1P
1.413 (4)
1.322 (5)
1.500 (4)
C1PÐN2
N2ÐC2A
1.341 (4)
1.451 (4)
The packing of the molecules in the crystal is shown in Fig. 2
and details of the hydrogen bonds are given in Table 2. Two
intermolecular hydrogen bonds are formed, involving the NH
and CO groups of screw-related ÁLeu and Ala residues. The
packing is also stabilized by hydrophobic regions involving the
benzene ring of the Cbz group, the side chain of the ÁLeu
residue and the terminal OCH3 group.
O0PÐC0PÐN1
C0PÐN1ÐC1A
C1BÐC1AÐN1
C1BÐC1AÐC1P
125.2 (3)
121.6 (3)
123.3 (3)
120.9 (3)
N1ÐC1AÐC1P
O1PÐC1PÐN2
O1PÐC1PÐC1A
N2ÐC1PÐC1A
115.5 (3)
123.1 (3)
121.1 (3)
115.7 (3)
C0PÐN1ÐC1AÐC1P
N1ÐC1AÐC1BÐC1G
C1AÐC1BÐC1GÐC1D2 127.3 (5)
C1AÐC1BÐC1GÐC1D1 111.1 (5)
47.9 (4)
0.4 (7)
N2ÐC2AÐC2PÐN3
C2PÐN3ÐC3AÐC3P
N3ÐC3AÐC3BÐC3G
C3AÐC3BÐC3GÐC3D2
10.2 (4)
60.3 (4)
73.0 (4)
77.1 (5)
N1ÐC1AÐC1PÐN2
C1PÐN2ÐC2AÐC2P
137.2 (3)
87.2 (3)
C3AÐC3BÐC3GÐC3D1 160.1 (4)
N3ÐC3AÐC3PÐO3P
149.4 (5)
Experimental
Compound (I), Cbz±ÁLeu±OH, was synthesized by the condensation
of 3-methyl-2-oxopentanoic acid (0.9 g, 7.8 mmol) with benzyl
carbamate (1.4 g, 9.4 mmol) and p-toluenesulfonic acid (0.27 g,
9.4 mmol) in dry benzene. The reaction mixture was re¯uxed for 8 h
at 373 K using a Dean±Stark water remover. The solution was then
extracted with saturated sodium bicarbonate. The extracts were
neutralized by adding concentrated hydrochloric acid dropwise to
yield a white solid, which was ®ltered off and recrystallized from
benzene. The solid product of Cbz±ÁLeu±OH was obtained in a yield
of 67%. For the synthesis of NH3±l-Ala±l-Leu±OCH3 tri¯uoro-
Table 2
Hydrogen-bonding geometry (A, ).
ꢀ
Ê
DÐHÁ Á ÁA
DÐH
HÁ Á ÁA
DÁ Á ÁA
DÐHÁ Á ÁA
N1ÐH1Á Á ÁO1Pi
N2ÐH2Á Á ÁO2Pii
N3ÐH3Á Á ÁO0P
0.86
0.86
0.86
2.08
2.01
2.40
2.904 (4)
2.848 (4)
3.181 (7)
159
165
151
Symmetry codes: (i) 2 x; 12 ‡ y; z; (ii) 1 x; 21 ‡ y; z.
ꢁ
Acta Cryst. (2002). C58, o212±o214
Jyoti Makker et al. C24H35N3O6 o213

organic compounds
Data collection
The authors thank the Council of Scienti®c and Industrial
Research, New Delhi, for ®nancial support.
Enraf±Nonius CAD-4
diffractometer
!±2ꢃ scans
Absorption correction: empirical
via scans (SDP; Enraf±Nonius,
1979)
Tmin = 0.845, Tmax = 0.932
2887 measured re¯ections
2731 independent re¯ections
2363 re¯ections with I > 2ꢅ(I)
Rint = 0.051
ꢃ
max = 75.0ꢀ
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: DE1174). Services for accessing these data are
described at the back of the journal.
h = 0 ! 12
k = 0 ! 11
l = 16 ! 16
3 standard re¯ections
frequency: 60 min
intensity decay: none
References
Benedetti, E. (1977). Peptides, edited by M. Goodman & J. Meinhofer, p. 257.
New York: John Wiley and Sons Inc.
Benedetti, E., Morelli, G., Nemethy, G. & Scheraga, H. A. (1983). Int. J. Pept.
Protein Res. 22, 1±15.
Bhat, T. N., Sasisekaran, V. & Vijayan, M. (1979). Int. J. Pept. Protein Res. 13,
170±180.
Chandrasekaran, R. & Ramachandran, G. N. (1970). Int. J. Pept. Protein Res.
2, 223±233.
Re®nement
Re®nement on F2
R[F2 > 2ꢅ(F2)] = 0.056
wR(F2) = 0.162
S = 1.20
2731 re¯ections
w = 1/[ꢅ2(Fo2) + (0.1P)2]
where P = (Fo2 + 2Fc2)/3
(Á/ꢅ)max = 0.006
3
Ê
Áꢆmax = 0.21 e A
3
Ê
0.20 e A
Áꢆmin
=
Enraf±Nonius (1979). Structure Determination Package. Enraf±Nonius, Delft,
The Netherlands.
Flack, H. D. (1983). Acta Cryst. A39, 876±881.
294 parameters
H-atom parameters constrained
Absolute structure: Flack (1983)
Flack parameter = 0.0 (4)
Janin, J., Wodak, S., Levitt, M. & Margret, B. (1978). J. Mol. Biol. 125, 357±386.
Narula, P., Khandelwal, B. & Singh, T. P. (1991). Biopolymers, 31, 987±992.
Sheldrick, G. M. (1997). SHELXL97 and SHELXS97. University of
H atoms were re®ned as riding, with CÐH distances in the range
Ê
0.93±0.98 A.
È
Gottingen, Germany.
Singh, T. P. & Narula, P. (1996). Prog. Biophys. Mol. Biol. 66, 141±165.
Spek, A. L. (1999). PLUTON. University of Utrecht, The Netherlands.
Vasquez, M., Nemethy, G. & Scheraga, H. A. (1983). Macromolecules, 16,
1043±1049.
Zimmerman, S. S., Pottle, M. S., Nemethy, G. & Scheraga, H. A. (1977).
Macromolecules, 10, 1±9.
Data collection: SDP (Enraf±Nonius, 1979); cell re®nement: SDP;
data reduction: SDP; program(s) used to solve structure: SHELXS97
(Sheldrick, 1997); program(s) used to re®ne structure: SHELXL97
(Sheldrick, 1997); molecular graphics: PLUTON (Spek, 1999); soft-
ware used to prepare material for publication: SHELXL97.
ꢁ
o214 Jyoti Makker et al.
C24H35N3O6
Acta Cryst. (2002). C58, o212±o214