Synthesis of a bis-amino acid that creates a sharp turn

Article abstract of DOI:10.1021/ol048585f

(Chemical Equation Presented) The synthesis of a new bis-amino acid 1 is presented. This monomer is designed to create a tightly curved structure when assembled into oligomers. The monomer is demonstrated to couple to the previously developed monomer 2 th

Full text of DOI:10.1021/ol048585f

ORGANIC
LETTERS
2004
Vol. 6, No. 19
3369-3371
Synthesis of a Bis-amino Acid that
Creates a Sharp Turn
Stephen A. Habay and Christian E. Schafmeister*
Department of Chemistry, UniVersity of Pittsburgh, Pittsburgh, PennsylVania 15260
meister@pitt.edu
Received July 21, 2004
ABSTRACT
The synthesis of a new bis-amino acid 1 is presented. This monomer is designed to create a tightly curved structure when assembled into
oligomers. The monomer is demonstrated to couple to the previously developed monomer 2 through pairs of amide bonds to create a strongly
bent spiro-ladder oligomer. The structure of oligomer 3 was determined in aqueous solution using two-dimensional NMR.
A systematic approach to the rapid synthesis of macromol-
ecules with designed shapes and functions would greatly
facilitate the development of biomimetic chemistry1 and
nanotechnology.2 Oligomer synthesis is an efficient approach
to macromolecules because it is modular and allows the rapid
assembly of large structures from a collection of small
monomers. Many groups are developing unnatural monomers
that are assembled through single bonds to form oligomers.3-5
Some of these oligomers have strong tendencies to form well-
defined secondary structures through the influence of weak
noncovalent interactions6-10 The development of a systematic
approach to oligomers with designed tertiary structures is
still elusive,11 however, because of the immense complexity
involved in predicting the folded structure of molecules with
even a few rotatable bonds.12
We are developing stereochemically pure, cyclic, bis-
amino acid monomers that couple through pairs of amide
bonds to form spiro-ladder oligomers that do not fold but,
instead, display complex shapes by virtue of their rich
stereochemistry and the well defined conformations of their
fused rings. Our long term goal is to rapidly design,
synthesize, and study macromolecules that have compact
tertiary structures and contain small molecule-sized cavities.
Toward this goal we have developed synthetic access to bis-
amino acid monomers that form rods and turns and are easily
coupled to each other. We have previously synthesized
monomer 2, named pro4(2S4S), and demonstrated that it is
easily assembled into homooligomers that form water-soluble
molecular rods of controlled lengths.13 We present here a
new monomer 1 that we have named hin(2S4R7R9R). This
monomer is designed to form a sharp turn, necessary for
constructing a compact tertiary structure. We present the
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10.1021/ol048585f CCC: $27.50 © 2004 American Chemical Society
Published on Web 08/20/2004

Scheme 1. Synthesis of hin(2S4R7R9R) Monomer
Scheme 2. Synthesis of a Short Oligomer Containing
hin(2S4R7R9R) and pro4(2S4S) Monomers
synthesis of monomer 1 and demonstrate that it assembles
into a heterosequence with our previous monomer 2. We
also present the solution structure of a three-mer of the
sequence pro4(2S4S)-hin(2S4R7R9R)-pro4(2S4S)-(L)-ty-
rosine and demonstrate that monomer 2 forms a turn.
Monomer 1 was synthesized on a 1.5 g scale from
inexpensive L-tyrosine in 10 steps (Scheme 1). The synthesis
uses chemistry developed by Wipf and co-workers14,15 to
convert L-tyrosine to ketone 5. Ketone 5 was reduced with
trichloromethyl anion to alcohol 6 with 10:1 stereoselectivity.
The major diastereomer 6 was crystallized from EtOAc/
hexanes and the stereochemistry confirmed using X-ray
crystallography. The trichloromethyl carbinol 6 was then
converted in a single step, with inversion of configuration,
to the azido methyl ester 7 using the modified Corey-Link
reaction developed by Dominguez and co-workers.16,17 This
remarkable reaction is considered to proceed via the gem-
dichloro-oxirane intermediate shown in Scheme 1.18 The
azide 7 was then reduced with Zn to the amine and protected
using the phenylfluorenyl (PhF) group19 to form 8. Finally,
the tertiary methyl ester was regioselectively hydrolyzed, in
the presence of the quaternary methyl ester, to carboxylate
1 due to the protective effect of the phenylfluorenyl-protected
amine. Monomer 1 contains two orthogonally protected
amino acid moieties suitable for sequential solid-phase
coupling.
resin.20 The sequence consisted of pro4(2S4S)-hin(2S4R7R9R)-
pro4(2S4S)-(L)-tyrosine. The role of the tyrosine is to provide
a UV-active chromophore and to enhance the lipophilicity
of the oligomer to allow C18 reverse-phase purification. We
have previously observed that oligomers that do not carry
lipophilic groups are too water soluble and refuse to bind to
a C18 reverse-phase column. Each monomer was activated
as the 1-hydroxy-7-azabenzotriazole (HOAt) ester.21 Quan-
titative coupling to the previous monomer was achieved
through double coupling of 2 equiv of activated monomer
with respect to the resin loading. Couplings were carried out
at room temperature for 90 min. After the three monomers
were coupled, the oligomer was functionalized with an Fmoc-
L-tyrosine residue. An extended, 2 h deprotection step was
then carried out to remove the N-terminal Fmoc group and
to accelerate the attack of the terminal amine on the methyl
ester of the pro4(2S4S) monomer that precedes it to form
the diketopiperazine 9. The oligomer was then cleaved from
the MBHA resin with simultaneous removal of all of the
carboxybenzoyl (Cbz) groups using a trifluoroacetic/tri-
fluoromethane sulfonic acid mixture. The flexible oligomer
10 was then converted into the rigidified scaffold 3 by
exposure to 20% piperidine/DMF over 10 days at 50 °C.22
The molecular mechanics package MOE23 was used to
carry out a stochastic conformational search24 of compound
3 to locate the lowest AMBER9425 energy minima in vacuo.
The modeled structure of the global energy minimum shows
We incorporated 1 into a heterosequence of three mono-
mers (Scheme 2) using standard solid-phase synthesis
techniques on a 16.5 µmol scale utilizing a MBHA‚LL HCl
(14) Wipf, P.; Kim, Y. T. Tetrahedron Lett. 1992, 33, 5477-5480.
(15) Wipf, P.; Methot, J. L. Org. Lett. 2000, 2, 4213-4216.
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Espada, M.; Pedregal, C. Tetrahedron Lett. 1998, 39, 9305-9308.
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239.
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chem: San Diego, 2004.
(21) Carpino, L. A. J. Am. Chem. Soc. 1993, 115, 4397-4398.
(22) Pedroso, E.; Grandas, A.; Delasheras, X.; Eritja, R.; Giralt, E.
Tetrahedron Lett. 1986, 27, 743-746.
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Org. Lett., Vol. 6, No. 19, 2004

SPARKY.26 The ROESY spectrum provided 26 cross-peaks
that correlated non-J-coupled protons. The cross-peaks were
ranked as strong, medium, and weak on the basis of their
relative intensity. The ROESY correlations were superim-
posed on top of the minimum energy structure and are
completely consistent with the model (Figure 1). The bent
conformation of the hin(2S4R7R9R) monomer is supported
by eight ROESY correlations, including a web of correlations
between the proton on N20 and protons on C4, C10, C13,
and C14, as well as strong correlations between the R-proton
on C22 and the proton of C16 (Figure 1). The diketopip-
erazines between monomers form shallow boats with their
substituents C11 and C23 occupying pseudoequatorial ori-
entations. The proline ring-based pro4(2S4S) monomers
adopt an envelope structure that avoids a 1,3-interaction
between the two substituents that are syn to each other on
the ring (C2 and N8, and C21 and N28). These conformations
are identical to what was seen in a previous NMR structure
that contained pro4(2S4S).13 The folded-back conformation
of the tyrosine side chain is also a feature that was seen in
a previous NMR structure and is probably due a hydrophobic
interaction between the aryl ring and the methylene of the
last pro4(2S4S) monomer.13
We have demonstrated the synthesis of monomer 1 and
that it can be assembled into a heterosequence with another
monomer 2. We have determined the solution structure of
this monomer in the context of a short oligomer, and, at 4
°C, it has a strong conformational preference to form a tight
curve. Combining this monomer with others to form longer
sequences should enable us to construct compact, water-
soluble macromolecules that contain cavities with controlled
size and shape for a variety of biomimetic and nanotech-
nology applications.
Figure 1. Stereoimage of the lowest energy conformation of 3.
Protons that are correlated in the 2D ROESY spectrum are
connected with lines (strong, medium, and weak ROESY correla-
tions are colored red, green, and blue, respectively).
that the molecule is strongly bent, with the cyclohexane ring
of the central “hin” monomer adopting a chair conformation
that places the amide nitrogen substituents N18 and N20 in
a 1,3-diaxial arrangement (Figure 1). This 1,3-diaxial ar-
rangement is reasonable because the planes of the two amides
are parallel to each other and are locked in an extended fused
ring system. The first low-energy minimum that displays a
different cyclohexane chair conformation is 2.4 kcal/mol
higher than the global energy minimum, indicating that
molecular mechanics predicts that this oligomer has a 4 times
greater kT preference for this conformation.
Acknowledgment. This work was supported in part by
the NIH/NIGMS (GM067866) and by the Research Corpora-
tion. We thank Dr. Steven Geib for X-ray structural analysis.
We thank Dr. Kasi Somayajula for assistance with LC/MS
and mass spectroscopy. We thank Dr. Fu Tyan Lin for
assistance with NMR.
To test this molecular mechanics prediction we determined
the solution structure of the three-mer 3 using two-
dimensional (2D) NMR. The solution structure was deter-
mined in H2O/D2O/CD3CN 80:10:10 at a concentration of 4
1
mM at 4 °C. The H and 13C resonances were assigned
through the interpretation of a collection of 2D spectra
including a COSY, an HMQC, an HMBC and a ROESY.
The assignment was carried out using the software package
Supporting Information Available: Experimental pro-
cedures, relevant NMR spectra, and characterization data for
new compounds. This material is available free of charge
via the Internet at http://pubs.acs.org.
(23) MOE, 2002.03 ed.; Chemical Computing Group, Inc.: Montreal,
2002.
(24) Ferguson, D. M.; Raber, D. J. J. Am. Chem. Soc. 1989, 111, 4371-
4378.
OL048585F
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M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman,
P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
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