Oligooxopiperazines as nonpeptidic α-helix mimetics

Article abstract of DOI:10.1021/ol1003143

Chemical Reaction Repretatio A new class of nonpeptidic α-helix mlmetics derived from a-amino acids and featuring chlral backbones is described. NMR and circular dichroism spectroscopies, in combination with molecular modeling studies, provide compelling evidence that ollgooxopiperazlne dimers adopt stable conformations that reproduce the arrangement of i, i+4, and i+7 residues on an α-helix.

Full text of DOI:10.1021/ol1003143

ORGANIC
LETTERS
2010
Vol. 12, No. 7
1588-1591
Oligooxopiperazines as Nonpeptidic
r-Helix Mimetics
Petra Tosˇovska´ and Paramjit S. Arora*
Department of Chemistry, New York UniVersity, 100 Washington Square East,
New York, New York 10003
arora@nyu.edu
Received February 5, 2010
ABSTRACT
A new class of nonpeptidic r-helix mimetics derived from r-amino acids and featuring chiral backbones is described. NMR and circular
dichroism spectroscopies, in combination with molecular modeling studies, provide compelling evidence that oligooxopiperazine dimers adopt
stable conformations that reproduce the arrangement of i, i+4, and i+7 residues on an r-helix.
R-Helices play fundamental roles in mediating protein-protein
interactions. Several approaches for stabilizing peptides in
helical conformations or mimicking this conformation with
nonnatural oligomers have been described.1 Examination of
complexes of proteins with other biomolecules reveals that
often one face of the helix featuring the i, i+4 and i+7
residues is involved in binding. Synthetic scaffolds that
display protein-like functionality and reproduce the arrange-
ment of key side chains on an R-helix would be invaluable
as inhibitors of selective protein interactions. In elegant
reports, Hamilton and others have successfully demonstrated
the utility of nonpeptidic helix mimetics based on aromatic
scaffolds.2 Here, we report a complementary approach that
affords nonaromatic helix mimetics which feature a chiral
backbone and are easily synthesized from R-amino acids.
We hypothesized that scaffolds that present chiral backbones,
as compared to the aromatic templates, may be more effective
in discriminating between chiral protein pockets.3 Molecular
modeling studies, 2D NMR, and circular dichroism spec-
troscopies provide strong support for our design features.
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5909–5911. (d) Ahn, J.-M.; Han, S.-Y. Tetrahedron Lett. 2007, 48, 3543–
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10.1021/ol1003143  2010 American Chemical Society
Published on Web 03/02/2010

We were attracted to the piperazine skeleton because it is
considered a privileged scaffold for peptidomimetic research
and drug discovery.4 Specifically, the 2-oxopiperazine and
the diketopiperazines have a rich history in medicinal
chemistry and are considered to be “drug-like” scaffolds.5
Although, the potential of oxopiperazine oligomers has not
been explored, we were intrigued by our computational
studies that predicted stable structures in these oligomers due
to the conformational constraints inherent in the system.
Molecular modeling studies indicate that an oxopiperazine
dimer spans the length of an 8mer R-helix and superimposes
amino acid functionality onto the i, i+4, and i+7 residues
of the helix (Figure 1). We began our analysis of oligoox-
insights regarding the φ and ꢀ dihedral angles favored in
the amino acid residue linking two piperazine rings and
corroborated our molecular modeling calculations (Figure
2). A full discussion of the accessible φ and ꢀ dihedral angles
in oxopiperazine dimers is included in the Supporting
Information.
Figure 2. (a) Rotatable bonds in oxopiperazine dimer. (b) Favored
chair and (c) amide bond geometries; values were calculated with
Macromodel MMFF force field in chloroform.
Molecular modeling studies of oxopiperazine dimers and
trimers composed of alanine residues, and examination of
the Cambridge Structural Database, suggest that piperazine
rings are well-defined and the overall folding of the oligomer
is determined by the geometry of the amide bond (ω dihedral
angle) that links piperazine rings (Figure 2). An oxopipera-
zine dimer features a tertiary amide bond that would be
expected to adopt trans and cis geometeries, as observed in
polyproline peptides. A trans-amide geometry would place
side chain groups on the dimer such as to reproduce the
arrangement of i, i+4, and i+7 residues on an R-helix. Only
constructs composed of alanine residues were modeled with
the expectation that flexible side chains would overcome
slight differences in backbone geometries. Modeling studies,
performed with Macromodel MMFF force field in chloro-
form,6 suggest that the trans conformation would be favored
by roughly 1 kcal/mol in oxopiperazine dimers composed
of alanine residues. The trans to cis ratio is expected to
increase in dimers built from bulkier amino acid residues.
Several synthetic routes to piperazines are known, which we
anticipated would allow rapid synthesis and evaluation of
the desired compounds.7
Figure 1. (a) Design of amino acid-derived oligooxopiperazines.
(b) An 8mer canonical R helix with side chain residues depicted
as green spheres (left). Predicted structure of an oxopiperazine dimer
with side chain residues depicted as orange spheres (right) and
overlay of the piperazine dimer and the R-helix (center). (c) Top-
down view of a canonical R-helix (left) and overlay of the i, i+4
and i+7 residues of the R-helix and side chain residues of
oxopiperazine dimer (right).
opiperazines by searching the Cambridge Structural Database
for examples of oxopiperazine derivatives. This search
resulted in five hits (CSD codes: KEMXUV, ZOZTUD,
ZARZOH, FOBFEH, and KEMXUV) of single piperazine
ring systems relevant to our system. Although this is a narrow
set to base hypotheses upon, these hits provided invaluable
In these initial studies, we report the design and synthesis
of three oxopiperazine dimers (Figure 3a), and evaluate their
potential to adopt a stable conformation in solution by NMR
and circular dichroism spectroscopies.
Org. Lett., Vol. 12, No. 7, 2010
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Figure 3. (a) Oxopiperazine helix mimetics designed for the current
study. (b) Synthesis of dimers 1a-c: (a) O3, (b) Me2S, (c) TFA
and triethylsilane. Combined yield for steps a-c: 3a, 81%; 3b, 80%;
3c, 85%; (d) Boc2O: 4a, 98%; 4b, 94%; 4c, 97%; (e) LiOH 3, DCC,
HOBt: 1a, 73%; 1b, 70%; 1c, 71%. a: R1 ) CH2CH(CH3)2, R2 )
CH3. b: R1 ) CH2Ph, R2 ) (CH2)4NHCbz. c: R1 ) CH2CH(CH3)2,
R2 ) CH2CH(CH3)2.
Figure 4. (a) Circular dichroism spectra of oxopiperazines 1a-c
in acetonitrile. (b) Effect of temperature on the stability of 1a-c.
CD spectra obtained in methanol are shown in the Supporting
Information.
Compounds 1a-c were designed to test the impact of
different side chain combinations on the stability of the
oxopiperazine dimer conformation. We evaluated several
routes for the synthesis of these compounds and eventually
found the reductive amination route described by Moeller
and co-workers to afford short oligomers in respectable yields
(Figure 3b).7b
The solution conformation of dimers 1a-c was investi-
gated by circular dichroism spectroscopy in methanol and
acetonitrile solutions. Figure 4 shows CD spectra in aceto-
nitrile; spectra in methanol are included in the Supporting
Information. The CD spectra of 1a-c display double minima
near 220 and 230 nm and maxima at 200 nm. Surprisingly,
the overall shape is reminiscent of CD spectra of R-helices;
although, the maxima and minima are red-shifted by 10 nm.
Although CD spectra of artificial systems are often difficult
to interpret,8 the spectra of 1a-c indicate a high degree of
preorganization. The thermal stabilities of 1a-c were
investigated by monitoring the temperature-dependent change
in the intensity of the 220 nm bands in the CD spectra (Figure
4b). We observe a gradual increase in the signal intensity at
220 nm with temperature, but the dimers retain over 70%
of their room-temperature elipticity at 75 °C. Similar
noncooperative denaturation behavior has been observed with
other conformationally defined oligomers.9 Overall, the CD
studies demonstrate that helix mimetics 1a-c adopt stable
conformations confirming our molecular modeling analysis.
We next utilized 2D NMR spectroscopy to analyze the
conformations adopted by 1a as a model oxopiperazine helix
mimetic, specifically we wanted to determine the geometry
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observe NOE crosspeaks between protons on neighboring
piperazine rings. This absence of NOEs is expected based
on the proposed low energy conformation in which these
protons lie outside the 5 Å distance typically required to
observe the nuclear Overhouser effect. Thus, the NOESY
studies strongly corroborate our modeling analysis. Signifi-
cantly, the NMR spectra did not display peaks indicative of
a minor cis-amide isomer, suggesting that the trans confor-
mation is substantially more stable than the cis analog.
In summary, through rational design and synthesis, we
have developed a new class of nonpeptidic R-helix mimetics.
NMR and circular dichroism spectroscopies provide compel-
ling evidence that oligooxopiperazine dimers adopt stable
conformations that reproduce the arrangement of i, i+4, and
i+7 residues on an R-helix. Given the importance of the helix
conformation in protein-protein interactions,10 and the
potential of nonpeptidic scaffolds that mimic this conforma-
tion, we believe that oxopiperazine scaffolds will offer
attractive new tools for chemical biology.11 In ongoing
studies, we are examining the potential of oxopiperazine helix
mimetics to disrupt chosen protein-protein interactions. The
results of these studies will be reported in due course.
Acknowledgment. We are grateful for financial support
from the NSF (CHE-0848410).
Figure 5. (a) Cross-section of the NOESY spectra of 1a in CDCl3.
(b) Overlay of key NOEs on the predicted oligooxopiperazine
conformation. (Side chain groups not shown for clarity.)
Supporting Information Available: Experimental pro-
cedures and structural characterization of compounds. This
material is available free of charge via the Internet at
http://pubs.acs.org.
adopted by the tertiary amide bond linking two piperazine
rings. A combination of COSY and NOESY spectroscopy
was used to assign 1H NMR resonances for 1a. The NOESY
spectrum reveals several NOEs in the two-ring system, which
would be expected from a trans-amide geometry in 1a but
not from the cis-amide conformation (Figure 5). We do not
OL1003143
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(b) Goodman, C. M.; Choi, S.; Shandler, S.; DeGrado, W. F. Nat. Chem.
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