Maximizing the stereochemical diversity of spiro-ladder oligomers

Article abstract of DOI:10.1021/ol060902q

We introduce all stereoisomers of a bis-amino acid building block derived from trans-4-hydroxy-L-proline. This small library of monomers allows arbitrary stereochemical configuration at any chiral center within our spiro-ladder oligomers. Three tetramer o

Full text of DOI:10.1021/ol060902q

ORGANIC
LETTERS
2006
Vol. 8, No. 13
2807-2810
Maximizing the Stereochemical Diversity
of Spiro-Ladder Oligomers
Christopher G. Levins, Zachary Z. Brown, and Christian E. Schafmeister*
Department of Chemistry, UniVersity of Pittsburgh, Pittsburgh, PennsylVania 15260
meister@pitt.edu
Received April 13, 2006
ABSTRACT
We introduce all stereoisomers of a bis-amino acid building block derived from trans-4-hydroxy-
L
-proline. This small library of monomers
allows arbitrary stereochemical configuration at any chiral center within our spiro-ladder oligomers. Three tetramer oligomers containing
several combinations of the monomers 1−4 were synthesized; we explored the effect of monomer sequence on scaffold conformation by
NMR.
The ability to fashion nonnatural macromolecules that have
designed tertiary structure and that precisely align chemical
functionality in three-dimensional space would be valuable
for biomimetic and nanotechnology applications.1 Oligomer
synthesis represents one strategy toward this end, as diverse
sequences may be compiled from a small library of mono-
mers. Foldamers are oligomers that adopt well-defined
secondary structures with short sequences.2 Most foldamers
are assembled from monomers connected through single
bonds and rely on hydrogen bonding and other noncovalent
interactions to define their secondary structure.3,4 Despite
intense effort, there still is no systematic way to create
oligomers with defined tertiary structure.4
We have devised a modular strategy toward the synthesis
of water-soluble oligomeric molecules of designed shape.5-7
We synthesize heterocyclic bis-amino acid monomers and
couple them through pairs of amide bonds to form fused-
ring spiro-ladder oligomers that lack rotational flexibility.
Our long-term goal is to develop a library of monomers that
can be assembled into any sequence and to develop func-
tional oligomers by programming the sequence of monomers.
(1) (a) Breslow, R. Acc. Chem. Res. 1995, 28, 146-153. (b) Merkle, R.
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5447.
Previously, we described the synthesis of monomers 3 and
4 (Figure 1) gram-scale.7 Both are derived from inexpensive
(3) Hill, D. J.; Mio, M. J.; Prince, R. B.; Hughes, T. S.; Moore, J. S.
Chem. ReV. 2001, 101, 3893-4011.
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9008. (b) Levins, C. G.; Schafmeister, C. E. J. Am. Chem. Soc. 2003, 125,
4702-4703.
10.1021/ol060902q CCC: $33.50
© 2006 American Chemical Society
Published on Web 05/23/2006

using a mild two-step procedure described previously.9 The
amine of 7 was converted to the Fmoc derivative 8 by the
method described by Bolin,10 and the carboxylic acid was
converted efficiently to the methyl ester 9 using TMS-
CHN2. The tert-butyl ester 9 was cleaved with TFA in CH2-
Cl2, and the Cbz protecting group was exchanged for a Boc
group,11 yielding the desired monomer 1. Monomer 2 was
generated from 6 by the same route and with comparable
yield.
Figure 1. Stereochemistry of monomers 1-4.
The three oligomers described in this work are shown in
Figure 2. For oligomer 13, monomers 3, 1, 2, and 4 were
and commercially available trans-4-hydroxy-L-proline; we
have named 3 pro4(2S,4S) and 4 pro4(2R,4R). Herein, we
report the gram-scale synthesis of 1 and 2 (the pro4(2S,4R)
and pro4(2R,4S) monomers, respectively), the final stereoi-
somers of the pro4 monomer class. This library of four
monomers enables complete control over the stereo-
chemistry at any chiral center of the oligomer and provides
the means to direct hydrogen bonding groups in three-
dimensional space along the length of the molecule.
We synthesized three tetramers; each sequence was a
permutation of all four members of the pro4 monomer class.
The composition of each oligomer was verified by HRMS,
whereas connectivity and stereochemistry were confirmed
unambiguously through NMR experiments. We examined
the three-dimensional structure of these oligomers in aqueous
solution using two-dimensional NMR spectroscopy.
Scheme 1. Monomer Synthesis
Figure 2. Structure of oligomers 13-15. Backbone C-H-N atom
numbering is labeled on 13 in blue (the same system is used for
14 and 15). Stereochemistry is indicated in red. Heterocycle naming
is labeled on 14 in cyan; relative pyrrolidine ring atom naming is
illustrated in green on 15.
coupled sequentially to solid support, followed by Fmoc-L-
tyrosine. The synthesis was carried out on 100 mg of Rink
Amide AM resin (0.64 mmol/g loading) using standard Fmoc
solid-phase peptide synthesis methodology (Scheme 2). Each
coupling was achieved using 2 equiv of monomer, 2 equiv
of HATU,12 and 4 equiv of diisopropylethylamine; double
coupling was used to achieve quantitative yield. Tyrosine
was added as a UV tag and to ease purification by increasing
the lipophilicity of the oligomer.
The product was cleaved from the resin by treatment with
8% triflic acid in TFA for 1.5 h in an ice bath. The crude
“open form” product 10 was precipitated from diethyl ether
and dissolved in a solution of 20% piperidine in N-
Hydantoins 5 and 6 (Scheme 1) are the minor products of
the Bucherer-Bergs reaction8 performed during the synthesis
of 3 and 4.7 Hydantoin 5 was hydrolyzed to amino acid 7
(9) Hammarstro¨m, L. G. J.; Fu, Y.; Vail, S.; Hammer, R. P.; McLaughlin,
M. L. Org. Synth. 2005, 81, 213-224.
(10) Bolin, D. R.; Sytwu, I.-I.; Humiec, F.; Meienhofer, J. Int. J. Pept.
Protein Res. 1989, 33, 353-359.
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89. (b) Ware, E. Chem. ReV. 1950, 46, 403-470.
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Org. Lett., Vol. 8, No. 13, 2006

on the face of the pyrrolidine ring opposite to HR) are closer
to one another than Hâa and Hδa (on the same face as HR).
This encodes a unique pattern of transannular ROESY
interactions that enables us to distinguish this conformation
from other pyrrolidine conformations. The minimized con-
formations we judged to be most consistent with the ROESY
correlations are depicted in Figure 3. 13 and 15 are bent; 14
has a linear shape.
Scheme 2. Oligomer Synthesis
methylpyrrolidinone to accelerate the closure of the second
amide bond between adjacent residues. After approximately
48 h, the desired product 13 was precipitated in ether and
purified by reverse-phase HPLC on a C18 column. Oligomers
14 and 15 were prepared in a similar fashion, as described
in Scheme 2.
For the NMR experiments, the oligomers were dissolved
in 10% D2O/H2O; the aqueous solution contained 0.01 M
acetic acid (d4)/ammonium acetate (d8) to neutralize TFA
salts and to raise the pH to slow amide hydrogen/deuterium
exchange. Experiments were performed at 4 °C. The two-
dimensional NMR spectra (COSY, ROESY, HMQC, HMBC)
were assigned using SPARKY;13 the NMR data confirmed
the expected connectivity and stereochemistry of 13-15.
Compared with less stereochemically-diverse pro4 oligomers
we have synthesized,7 there is good chemical shift dispersion
in the proton spectra of these molecules, particularly for the
δ protons of the pyrrolidine rings.
The ROESY data were used to select oligomer conforma-
tions generated by an in Vacuo stochastic search with the
Amber94 force field14 within MOE.15 ROESY correlations
between non-J-coupled protons were sorted by intensity,
classified as strong, medium, and weak, and superimposed
upon the energy-minimized conformers.
Figure 3. Conformations of 13-15 generated by molecular
mechanics calculations that agree with observed ROESY correla-
tions. The thin red, green, blue, and cyan cylinders represent strong,
medium, weak, and undefined ROESY correlations, respectively.
In the lowest-energy conformers, diketopiperazine (DKP)
rings are shallow boats, whereas the pyrrolidine rings assume
an envelope conformation where atom Câ is positioned out
of the plane defined by CR, Cγ, Cδ, and the pyrrolidine N
atom. In this conformation, Hâb and Hδb (Hâ and Hδ atoms
The structure shown for 13 in Figure 3 is identical to the
Amber94 minimum energy conformation except for pyrro-
lidine ring E. The integrated intensities of the Hâb-Hδb
correlations across pyrrolidine rings A, C, and G (H4b-
H6b, H11b-H13b, H19b-H21b, H28b-H29b) are 4-5
times greater than those for the corresponding Hâa-Hδa
correlations, supporting the Câ displaced conformation. The
expected ROESY correlations across DKP ring D of 13 are
occluded due to overlap, but the H10-H4a correlation
(13) Goddard, T. D.; Kneller, D. G. Sparky 3, version 3.111; University
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(14) Cornell, W. D.; Cieplak, P.; Bayly, C. I. et al. J. Am. Chem. Soc.
1995, 117, 5179-5197.
(15) MOE 2005.06, Chemical Computing Group: Montreal, 2005.
Org. Lett., Vol. 8, No. 13, 2006
2809

suggests the predicted boat conformation of DKP ring B and
provides additional evidence for the Câ displaced conforma-
tion of pyrrolidine A. Correlations between H27a and H27b
with H39 and H40 evince the predicted boat conformation
of DKP ring H and suggest that the aromatic ring of the
tyrosine residue is folded back against the backbone of the
oligomer.
The conformation of pyrrolidine ring E of 13 (Cδ displaced
rather than Câ, with Hâa closer to Hδa than Hâb is to Hδb)
is unexpected. The integrated intensity of the H19a-H21a
correlation is 2 times greater than the intensity of the H19b-
H21b correlation, and the H26-H21b correlation across DKP
ring F is 4 times the integrated intensity of the H26-H21a
correlation.
its pyrrolidine ring prefers the Cδ displaced conformation.
This suggests that the preferred envelope conformation of a
particular residue may be context dependent.
We carried out quantum mechanics calculations to calcu-
late energy differences between the two envelope conforma-
tions of the pyrrolidine rings that would give rise to the
different transannular ROESY correlation patterns that we
observe. Density functional theory minimizations were
performed on every contiguous trimer within oligomers 13-
15 using Gaussian 0316 (B3LYP/6-31G*, see Supporting
Information). At this level of theory, we found that the
differences in energy between pyrrolidine conformations
were small (<1 kcal/mol), with no strong preferences for
one ring conformation over the other. Our NMR observations
suggest that the oligomers do have strong conformational
preferences; the difference between experiment and theory
may be due to solvent stabilization of one conformation over
the other.
We synthesized all possible stereoisomers of the pro4
monomer and demonstrated the assembly of oligomers
incorporating all four monomers in different sequences. We
solved the solution-phase NMR structures of three oligomers
and established that the connectivity and stereochemistry for
each was as designed. We are currently exploring new
methods to probe the shape and rigidity of these oligomers,
such as labeling the scaffolds with spin probes to study their
shapes and dynamics by electron spin resonance.17
For compound 14, the ROESY correlations were consistent
with the minimum-energy Amber94 structure shown in
Figure 3. The four Hâb-Hδb correlations (H4b-H6b,
H11b-H13b, H19b-H21b, H27b-H29b) are 3-5 times
greater in integrated intensity than the corresponding Hâa-
Hδa correlations, suggesting the Câ displaced conformation
for every pyrrolidine ring. As with 13, correlations across
DKP ring D are overlapped. Nevertheless, the strong H10-
H6a correlation supports the illustrated conformation of DKP
ring B, and the strength of this correlation relative to H10-
H6b (visibly weaker but overlapped, preventing integration)
supports the depicted conformation of pyrrolidine ring A.
Furthermore, the correlation H26-H19a, across DKP ring
F, is 10 times the intensity of the correlation H26-H19b,
which lends support to the conformation of DKP ring F and
the envelope conformation of E shown in Figure 3.
The structure of 15 shown in Figure 3 is consistent with
its Amber94 predicted minimum-energy structure, except for
pyrrolidine ring C. The Hâb-Hδb correlations across rings
A, E, and G (H4b-H6b, H19b-H21b, H27b-H29b) are
visibly stronger than the corresponding Hâa-Hδa interac-
tions (though the integrated intensities are greater only by
factors of 1.2-2.1) supporting the predicted Câ displaced
conformations. For pyrrolidine ring C, the correlation H11a-
H13a is slightly more intense (1.1 times) than H11b-H13b,
suggesting the unexpected Cδ displaced conformation. The
integrated intensities of the Hâa-Hδa correlations in 15 were
similar to those between Hâb and Hδb, contrasting with the
results for 13 and 14 and providing only weak support for
the conformation of 15 shown. There are very clear ROESY
correlations across all of the DKP rings of 15 (H10-H6a,
H18-H13b, and H26-H21a which are 5, 9, and 2 times
the intensity of H10-6Hb, H18-H13b, and H26-H21b,
respectively) supporting the illustrated conformation of DKP
rings B, D, and F and pyrrolidine rings A, C, and E.
In 14, the pro4(2R,4S) residue is clearly in the Câ
displaced conformation; it precedes a pro4(2S,4R) residue
in this oligomer. In both 13 and 15, where pro4(2R,4S)
precedes a pro4(2R,4R) residue, there is strong evidence that
Acknowledgment. The authors are very thankful for
financial support from the National Institute of Health/
NIGMS (GM067866).
Supporting Information Available: Experimental pro-
cedures for the synthesis of monomers 1 and 2, oligomers
13-15, characterization of new compounds, and 2D NMR
spectra. This material is available free of charge via the
Internet at http://pubs.acs.org.
OL060902Q
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