Design and synthesis of a new bicyclic dipeptide isostere

Article abstract of DOI:10.1039/b101692j

The synthesis of a new Gly-Pro turn mimetic and the computational study of its ability to induce β-turn is reported.

Full text of DOI:10.1039/b101692j

Design and synthesis of a new bicyclic dipeptide isostere
Franca M. Cordero,* Silvia Valenza, Fabrizio Machetti and Alberto Brandi*
Dipartimento di Chimica Organica ‘Ugo Schiff’, Centro di Studio C.N.R. sulla Chimica e la Struttura
dei Composti Eterociclici e loro Applicazioni (CSCEA), Università di Firenze, via G. Capponi 9, I-50121
Firenze, Italy. E-mail: cordero@chimorg.unifi.it; Fax: +39-055-2476964
Received (in Cambridge, UK) 21st February 2001, Accepted 27th June 2001
First published as an Advance Article on the web 6th August 2001
The synthesis of a new Gly-Pro turn mimetic and the
computational study of its ability to induce b-turn is
reported.
the reactivity of the amino group towards the peptide synthesis
and to avoid the possible epimerization to the thermodynam-
ically more stable trans isomer. The two diastereomeric
tripeptides 10a and 10b were separated by chromatography on
silica gel and fully characterized.
To assign the absolute configuration of 10a and 10b, a
sample of the racemic cis alcohol 8 was resolved through the
formation of the corresponding diastereomeric esters of R-
Mosher acid, and one of the separated esters was analyzed by
single crystal X-ray crystallography.† Consequently, both the
diastereomeric esters were assigned their absolute configura-
tion. After hydrolysis and treatment with CH2N2 the enantio-
merically pure alcohols (2R,7aR)-8 and (2S,7aS)-8 were
obtained, and transformed into 10a and 10b, respectively,
through the previously described procedure.
The investigation of the turn-inducing potential of both the
enantiomers (2R,7aR)-2 and (2S,7aS)-2 has been carried out
through a simulation procedure run on model hexapeptides
according to the criteria recently proposed by Müller et al.6
The model hexapeptides Ac-Ala-Ala-GPTM-Ala-Ala-
NHMe 11 and 12 (Fig. 2), containing in the central position RR-
GPTM and SS-GPTM respectively, were examined for their
conformational freedom by Monte Carlo (global search
In recent years several strategies have been adopted to limit the
conformational space of peptide chains1 and many efforts have
been made to develop b-turn mimetics.2
It is known that a cis peptide moiety is geometrically suited
for inducing the peptide chain to bend and that b-turns of type
VI are characterized by a cis-Pro in the i + 2 position.3 The
control of the cis-prolyl amide geometry has been effectively
achieved by tethering the a-carbon of the N-terminal amino acid
residue to the proline 2-position.4 Particularly, the bicyclic
dipeptide analogues 1, in which the a positions are joined by a
two (X = –CH2CH2–) or three (X = –CH2NHCO–) atom
bridge, have been synthesized4 to serve as mimetics of dipeptide
cis-Xxx-Pro (Fig. 1). To reduce the conformational freedom of
dipeptide mimetics like 1, a shorter link could be introduced. In
this way the pyrrolizidine amino acids 1 (X = –CH2–),
containing the cis-Xxx-Pro residue, would result (Fig. 1).
In this communication we report the synthesis of the GPTM
(Gly-Pro Turn Mimetic) 2 (Fig. 1) either in racemic or
enantiomerically pure form and its successful coupling with
Boc-Phe-OH.
L
-
The 1,3-dipolar cycloaddition (1,3-DC) of nitrone 35 and an
acrylic acid derivative, followed by reductive opening of the
isoxazolidine ring and intramolecular cyclization was envis-
aged as a rapid route to afford the bicyclic lactam 9.
The 1,3-DC reaction was performed under different condi-
tions and the best results were obtained from 3 and acrylamide
(4) in water at 60 °C (Scheme 1) which afforded the
2-aminocarbonylhexahydropyrrolo[1,2-b]isoxazoles 5 and 6
and their 3-aminocarbonyl isomers 7 in 4+1 ratio and excellent
yield (98%). Although the endo–exo selectivity of the cycload-
dition was very low (6% de) this approach was synthetically
convenient because both the diastereomeric adducts 5 and 6
could be transformed into 9.
The pyrrolizidine 9 was obtained from 6 through the domino
process N–O bond hydrogenolysis/intramolecular trans-amida-
tion. Moreover, the cis substituted pyrrolizidine 8, analogously
derived from 5, could be quantitatively isomerized to the
corresponding trans hydroxy ester 9 by treatment with NaOH–
MeOH at 70 °C followed by methylation with CH2N2.
Therefore, the intermediate 9, possessing the bicyclic skeleton
of the GPTM 2, was achieved in 55% overall yield starting from
3 and 4 (Scheme 1).
The trans alcohol 9 was easily transformed into the
corresponding cis amine 2 by mesylation followed by a
nucleophilic displacement with NaN3 and reduction of the azido
group with Ni-Raney (Scheme 1). The lactam 2, was im-
Scheme 1 a: H2O, 60 °C, 14 h (5: 37%, 6: 42%, 7: 19%). b: Pd(OH)2 (cat),
MeOH, AcOH, H2, 12 h (98%). c: (i) NaOH, MeOH, 70 °C, 2 h; (ii) Dowex
50; (iii) CH2N2; (60%). d: (i) MsCl, py; (ii) NaN3, DMF; (87%). e: Ni-
Raney (80%). f:
L
-Boc-Phe-OH, PyBroP, DiPEA, CH2Cl2 (55%).
mediately coupled with an amino acid such as Boc- -Phe, to test
L
Fig. 1 Mimetics of cis-Xxx-Pro dipeptide and Gly-Pro turn mimetic.
Fig. 2 Model hexapeptides.
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Chem. Commun., 2001, 1590–1591
This journal is © The Royal Society of Chemistry 2001
DOI: 10.1039/b101692j

Fig. 4 Structures of two low energy conformers of 11 and 12. Legend: C:
black, N: pale grey, O: grey, H: white. For reasons of clarity only the H
atoms involved in hydrogen bondings (--) were depicted.
Fig. 3 Percentage distribution N of dN-O, dCa and qCa values in the
conformers of 4 and 5 within 6 kcal mol21 of the global minimum. (Each
column spans 0.3 Å or 6°.)
In conclusion both the enantiomers of GPTMs 2 were shown
to be potentially useful reverse turn mimics. Attractive features
of these new dipeptide surrogates were the reduced flexibility
compared to analogous bicyclic systems, the complementary
behavior of the two enantiomers in controlling the side-chain
orientation, the rapid access to these systems starting from
easily available compounds, the possibility of extending the
process to the synthesis of other Xxx-Pro analogues (XPTMs)
through the cycloaddition of nitrone 3 to 2-substituted acrylic
acid derivatives.
Some structural modifications of GPTMs 2 for their use in
solid phase syntheses and their incorporation into selected
bioactive peptides for structure–activity relationship studies are
currently under investigation in our laboratories.
MCMM) procedure.7 The following parameters were used to
establish the presence of a reverse turn: the donor–acceptor
NHAla5–COAla2 distance dN-O, the CaAla2–CaAla5 distance dCa
and the virtual torsion angle qCa (defined by CaAla2–CaGly3
–
CaPro4–CaAla5).3,6 The percentage distribution of dN-O, dCa and
q
Ca values in the calculated conformations within 6 kcal mol21
of the global minimum of 11 and 12 (318 and 170 conformers
respectively) were reported in Fig. 3. The histograms showed a
substantial restriction of the occupied conformational space of
hexapeptides incorporating GPTMs 2. Moreover, a very good
portion of conformers possessed the dCa and qCa values
characteristic of b-turn. In particular the percentages of
conformers of 11 and 12 with dCa less than 5 Å (one definition
of a tight b-turn) were 55 and 58%, respectively, while almost
all structures showed dCa less than 7 Å (11: 94%, 12: 96%).3 All
conformers had |qCa| under 50°, and |qCa| under 30° present in
54 and 75% conformers of 11 and 12, respectively.
This work was supported by the Ministry of University and
Scientific and Technological Research, Italy (Cofin 2000
Project Synthesis of Mimics and Analogs of Bioactive Natural
Compounds). S. V. acknowledges the receipt of a PhD stipend
from Menarini Ricerche S.p.A.
On the contrary, the presence of the hydrogen bonding
characteristic of classical b-turn (dN-O < 3.5 Å) was found in a
small fraction of conformers (11: 7%; 12: 5%). However, the
intramolecular hydrogen bond was not found critical for the
stability of a b-turn,3 and seems not to be necessary in peptides
Notes and references
† Crystallographic data for (2S,7aS)-3-oxo-2-[(2R)-3,3,3-trifluoro-2-
methoxy-2-phenylpropionyloxy]tetrahydro-1H-pyrrolizine-7a(5H)-car-
boxylic acid methyl ester: C19H20F3NO6, M = 415.36, orthorhombic, a =
8.2726(3), b = 11.9643(6), c = 19.746(2) Å, U = 1954.7(2) Å3, T = 293
K, space group P212121, Z = 4, m(Cu-Ka) = 1.067 mm21, 2168 reflections
incorporating mimics 2, because the three torsion angles (yGly3
,
wPro4 and oPro4) embedded in the 5,5-bicyclic structure and the
spatial orientation of the terminal amino and carboxylic groups
(on the same face of the bicyclic ring system) force the peptide
chain to fold back upon itself.
The whole set of computational data clearly showed that
bicyclic lactams like (2R,7aR)-2 and (2S,7aS)-2 were effective
turn restraints when incorporated in the hexapeptides 11 and
12.
The spatial arrangement of side chains is generally critical to
recognition and bioactivity of peptides and its control is one of
the goals of peptidomimetics. GPTMs (2R,7aR)-2 and (2S,7aS)-
2 were shown to promote complementary relative orientation of
the side chains of the residues near the reverse-turn.
As shown in Fig. 3, the qCa values were prevalently negative
in the conformers of 11, but positive in those of 12 because of
the enantiomeric relationship between the incorporated
GPTMs. The presence of opposite reverse turns resulted also in
an opposite orientation of the amino acid side chains as
illustrated by a structural comparison of two representative low
energy conformers of 11 and 12 (Fig. 4).
collected, 1992 independent (Rint
= 0.0318) which were used in all
calculations. The final R1 was 0.0399 and wR2 0.1177 (all data).
CCDC 166488. See http://www.rsc.org/suppdata/cc/b1/b101692j/ for
crystallographic data in .cif or other electronic format.
1 J. Gante, Angew. Chem., Int. Ed. Engl., 1994, 33, 1699; A. Giannis and
T. Kolter, Angew. Chem., Int. Ed. Engl., 1993, 32, 1244.
2 For a recent review see S. Hanessian, G. McNaughton-Smith, H.-G.
Lombard and W. D. Lubell, Tetrahedron, 1997, 53, 12 789.
3 G. D. Rose, L. M. Gierasch and J. A. Smith, Adv. Protein Chem., 1985,
37, 1; J. S. Richardson, Adv. Protein Chem., 1981, 34, 167; P. N. Lewis,
F. A. Momany and H. A. Scheraga, Biochim. Biophys. Acta, 1973, 303,
211; J. B. Ball, R. A. Hughes, P. F. Alewood and P. R. Andrews,
Tetrahedron, 1993, 49, 3467.
4 D. Gramberg, C. Weber, R. Beeli, J. Inglis, C. Bruns and J. A. Robinson,
Helv. Chim. Acta, 1995, 78, 1588; K. Kim, J.-P. Dumas and J. P.
Germanas, J. Org. Chem., 1996, 61, 3138; K. Kim and J. P. Germanas,
J. Org. Chem., 1997, 62, 2847; T. P. Curran and P. M. McEnaney,
Tetrahedron Lett., 1995, 36, 191.
Both the selected structures were characterized by the
presence of two intramolecular hydrogen bonds which indicated
the initiation of an antiparallel b-sheet interaction between the
two half-strands. In 11 the b-sheet hydrogen bonds were
5 S.-I. Murahashi and T. Shiota, Tetrahedron Lett., 1987, 28, 2383.
6 G. Müller, G. Hessler and H. Y. Decornez, Angew. Chem., Int. Ed., 2000,
39, 894.
7 The conformational search (61000 steps for each structure) was
performed with MacroModel v. 6.5 on Silicon Graphics O2 R10000
workstation using the AMBER* force field for energy minimization, the
GB/SA continuum model for water and the Polak-Ribiere conjugate
gradient (PRCG) minimization mode with the derivative convergence
criteria of 0.05 kJ Å21 mol21. F. Mohamadi, N. G. J. Richards, W. C.
Guida, R. Liskamp, M. Lipton, C. Caufield, G. Chang, T. Hendrickson
and W. C. Still, J. Comput. Chem., 1990, 11, 440.
contiguous (between NHAla6–COAla1 and NHAla1–COAla6
)
while in 12 were more distant (between NHAla2–COAla5 and
NHNHMe–COAc). In 11 the methyl groups of Ala2 and Ala5 were
situated under the back-bone plane (when the peptide chain was
oriented as shown in Fig. 4) and those of Ala1 and Ala6 over the
plane, while in 12 the opposite orientations occurred.
Chem. Commun., 2001, 1590–1591
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