flexible oligomer 12 was then converted into the rigidified
scaffold 3 by treatment with 1,3-dicyclohexylcarbodiimide
(DCC) and N-hydroxy succinimide (NHS) in the presence
of base (DIPEA) in NMP at room temperature for 24 h.
NMR in H2O/D2O 90:10 at 25 °C. The 1H and 13C resonances
were assigned through the interpretation of a collection of
two-dimensional spectra, including a DQF-COSY, a TOCSY,
an HMQC, an HMBC and a ROESY spectrum. The
assignment was carried out using the software package
SPARKY.24 For protons that were correlated to several other
protons in the ROESY spectrum, the relative intensity of
the cross-peaks was assigned as strong, medium, or weak
on the basis of the integrated intensity. The chair conforma-
tion of each pipecolic acid ring was indicated by the
correlation of three axial protons syn to each other on each
ring. On the B ring of 3, correlations are seen between H3,
H5R, and H7R, and the axial orientation of the amine
substituent N11 is indicated by the correlation between H11
and H4â. On the D ring of 3, protons H13, H15R, and H17R
are correlated, and the axial orientation of N20 is seen in
the correlation between H20 and H14â. In the F ring of 3,
correlations are seen between H22, H24R, and H26R. The
amine substituent N29 is not the part of a diketopiperazine
ring and can rotate freely. However, we observe a correlation
between H29 and H23â, suggesting that N29 is axial to ring
F. These observations are consistent with rings B, D, and F
To our surprise, an earlier version of the oligomer
assembled using only the methyl ester monomer 2 did not
undergo intramolecular aminolysis between adjacent mono-
mers on treatment with 20% piperidine in dimethylforma-
mide. These are conditions that have proven to be effective
in the synthesis of oligomers containing 4 pro4(2S4S)13 and
5 hin(2S4R7R9R)14 monomers. The secondary amines of the
pip5(2S5S) monomers appear to be much less nucleophilic
than the secondary amines of the pro4(2S4S) and hin-
(2S4R7R9R) monomers. By replacing the methyl ester of the
monomer with a benzyl ester, we were able to simultaneously
deprotect the carboxybenzoyl groups and the benzyl esters
of the oligomer to form a free amine and a free carboxylic
acid between each adjacent pair of monomers (see compound
12). When the carboxylic acids were activated in situ using
DCC/NHS, intramolecular amide formation took place
between each adjacent pair of monomers. This in situ
coupling reaction simultaneously forms three diketopipera-
zine rings and produces a single pure product as determined
by C18 reverse-phase HPLC and NMR. This indicates that
the diketopiperazine rings form faster than any other mac-
rocycles that would result from one of the three amines N8,
N18, or N27 attacking one of the other activated carbonyl
groups at C9, C19, or C28.
The molecular mechanics package MOE21 was used to
carry out a stochastic conformational search22 of the three-
mer sequence gly-pip5(2S5S)-pip5(2S5S)-pip5(2S5S)-gly in
order to locate the lowest energy minima in vacuo using the
AMBER9423 force field. The modeled structure at the global
energy minimum suggests that the sequence forms a helical
rod and that each pipecolic acid ring has a strong preference
for a chairlike conformation, placing the amide nitrogens
N11, N20, and N29 in the axial positions (Figure 1).
Figure 2. Stereoimage of the lowest energy conformation of 3.
Protons that are correlated in the two-dimensional ROESY spectra
are connected by lines (strong, red; medium, yellow; weak, green;
unassigned, gray). The tyrosine residue and pivalic group have been
omitted for clarity.
Figure 1. Structures of three synthetically accessible bis-amino
acid monomers.
each being in a chair conformation. The conformation of
the diketopiperazine ring C is not clear because the only
correlation seen across this ring is a very weak correlation
between H11 and H13. A correlation is seen between H17â
and H23â, suggesting that the diketopiperazine ring E is in
a boat conformation that places C23 and C17 in a pseudo-
axial orientation. Combining these conformational prefer-
We determined the conformational preferences of the
component rings of compound 3 using two-dimensional
(21) MOE, 2002.03 ed.; Chemical Computing Group, Inc.: Montreal,
Canada, 2002.
(22) Ferguson, D. M.; Raber, D. J. J. Am. Chem. Soc. 1989, 111, 4371-
4378.
(23) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K.
M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman,
P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
(24) Goddard, T. D.; Kneller, D. G.; University of California: San
Francisco, 1989.
Org. Lett., Vol. 7, No. 14, 2005
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Gupta, Sharad
