The synthesis of a cubane-substituted dipeptide

Article abstract of DOI:10.1071/CH12179

Amino acids and peptides bearing cyclic hydrocarbon side-chains are of interest in the development of a wide range of bioactive molecules. The preparation of an amino acid and a dipeptide derivative bearing an unfunctionalised cubane substituent is described. Attempts to prepare a cubylalanine derivative via the corresponding dehydroalanine were unsuccessful due to the high sensitivity of this vinyl cubane compound. Conversely, the addition of cubyllithium to a (RS)-glyoxylate sulfinimine led to an effective synthesis of a cubylglycine derivative and a cubane-substituted dipeptide in diastereomerically pure form. CSIRO 2012.

Full text of DOI:10.1071/CH12179

CSIRO PUBLISHING
Aust. J. Chem. 2012, 65, 690–693
Communication
http://dx.doi.org/10.1071/CH12179
The Synthesis of a Cubane-Substituted Dipeptide
A
A
B
Quentin I. Churches, Roger J. Mulder, Jonathan M. White,
A
A C
,
John Tsanaktsidis, and Peter J. Duggan
A
CSIRO Materials Science and Engineering, Private Bag 10, Clayton South,
Vic. 3169, Australia.
B
School of Chemistry and Bio21 Molecular Science and Biotechnology Institute,
University of Melbourne, Parkville, Vic. 3010, Australia.
C
Corresponding author. Email: peter.duggan@csiro.au
Amino acids and peptides bearing cyclic hydrocarbon side-chains are of interest in the development of a wide range of
bioactive molecules. The preparation of an amino acid and a dipeptide derivative bearing an unfunctionalised cubane
substituent is described. Attempts to prepare a cubylalanine derivative via the corresponding dehydroalanine were
unsuccessful due to the high sensitivity of this vinyl cubane compound. Conversely, the addition of cubyllithium to a
(RS)-glyoxylate sulfinimine led to an effective synthesis of a cubylglycine derivative and a cubane-substituted dipeptide in
diastereomerically pure form.
Manuscript received: 2 April 2012.
Manuscript accepted: 2 May 2012.
Published online: 24 May 2012.
Non-natural amino acids continue to attract attention as analo-
gues of bioactive amino acids and for the incorporation into
peptides for the purpose of developing metabolically stable,
bioavailable peptides and peptidomimetics. Amino acids bear-
ing cyclic hydrocarbon side-chains in particular have been
pursued as analogues of glutamate and hydrophobic amino acids
such as isoleucine. An interesting example of a peptide deriv-
ative bearing cyclic hydrocarbon side-chains is SEN304
(1, Fig. 1) which has been developed as a potential treatment for
Alzheimer’s disease.[1]
O
O
H
N
H
N
ϩ
H3N
NH2
N
H
N
CH3
O
O
O
1
HO
Conformationally rigid cyclic a-amino acids are of particular
interest and are the subject of a detailed review by Komarov
et al. published in 2004.[2] There are very few examples of the
incorporation of such amino acids into peptides; cyclopropyl-
and cyclobutyl-substituted amino acids appear to be the most
common. The synthesis of amino acids with b-quaternary
centres, however, can be challenging.[3] Adamantyl-substituted
peptides are an intriguing class of bioactive molecules as they
apparently benefit from an enhanced ability to penetrate biolog-
ical membranes. Peptides bearing adamantyl side-chains have
been investigated for their anti-tumour[4] and antimicrobial
activities.[5] Cubane, structurally similar to adamantane, is a
unique spherical saturated hydrocarbon molecule with eight
methine units (C-H) arranged at the corners of a cube. Cubane
possesses octahedral symmetry (Oh), is highly strained (strain
Fig. 1. The structure of SEN304, a mimic of the peptide sequence LVFFL,
which has been investigated as a potential treatment for Alzheimer’s
disease.[1]
NH2
CO2H
HO2C
2
Fig. 2. The structure of a carboxyl-substituted cubylglycine investigated
for its neuroprotective properties.[6]
energy of 695 kJ molꢀ1 [6]
)
but stable, and has a density of
substituents are likely to be more appropriate mimics of hydro-
phobic amino acids such as leucine, isoleucine, and phenylala-
nine. Herein we report the first synthesis of an amino acid
derivative bearing an unfunctionalised cubane side-chain and
the first synthesis of a dipeptide derivative bearing a cubane side
chain.
1.29 g cmꢀ1. To date, only one cubyl amino acid has been
described, 4-carboxyl-cubylglycine (2, Fig. 2); this compound
has been investigated for its neuroprotective properties.[7] To the
best of our knowledge, there have been no reports of peptides
bearing cubyl side-chains and there have been no cubane-
substituted amino acids described where the cubane moiety is
unfunctionalised. Amino acids bearing unfunctionalised cubane
Our first approach to an unfunctionalised cubyl amino acid
employed a Horner-Wadsworth-Emmons reaction to install an
Journal compilation Ó CSIRO 2012
www.publish.csiro.au/journals/ajc

The Synthesis of a Cubane-Substituted Dipeptide
691
a,b-dehydroamino acid functionality. It was envisioned that
asymmetric hydrogenation could be used to generate the desired
cubylalanine derivative in enantiomerically enriched form.
In order to obtain the required aldehyde precursor,
cubylmethanol 3 (Scheme 1) was prepared from dimethyl 1,4-
cubanedicarboxylate[8] in four steps via published procedures,[9]
then cleanly oxidized to the cubane carbaldehyde 4 using
tetrapropylammonium perruthenate catalyst (TPAP) and
N-methyl morpholine-N-oxide (NMO). The resulting aldehyde
4 was found to be quite unstable, especially in concentrated
form, and so was used in the next step without purification. The
Horner-Wadsworth-Emmons reaction with glycine phospho-
nate 5 and potassium t-butoxide afforded the protected cubyl-
dehydroalanine 6 in 69 % overall yield over two steps. Analysis
of the product by 1H and 13C NMR spectroscopy indicated that
only one geometrical isomer was present and the alkene was
shown to have Z-geometry by X-ray crystallography (Fig. 3).
Cubane is known to undergo rearrangement reactions in the
presence of several transition metals including rhodium (I),
silver (I), and palladium (II),[10] so initial attempts to reduce
the double bond present in 6 involved the use of NaBH4,
CoCl2/NaBH4,[11] and diimide.[12] In all of these cases only
starting material was recovered. When the dehydroalanine
derivative was subjected to hydrogenation using Pd/C and
ammonium formate, rapid formation of the rearranged cyclooc-
tatetraene derivative 7 was observed (Scheme 2 – the cyclooc-
tatetraene derivative is assumed to have Z-configuration). The
ease with which 6 undergoes rearrangement may relate to the
slightly polarised nature of the vinyl substituent, which is
thought to encourage such reactions in substituted
cubanes.[13,14] An alternative is ruthenium catalysed hydrogena-
tion, but for this to work efficiently a free pendant carboxylate or
N-acyl functionality is required for coordination to the
ruthenium.[15] The cubyldehydroalanine derivative 6 was hence
saponified to provide the free carboxylate and the reaction
mixture carefully neutralised. This process led, however, to
complete decomposition, again demonstrating the instability of
this type of vinyl cubane derivative.
Given the difficulties experienced with the cubane
dehydroalanine system, we turned to the synthesis of a
suitably protected cubylglycine derivative. Accordingly,
iodocubane 8, which was prepared in three steps from dimethyl
NHCbz
O
O
P
CO2Me
MeO
CbzHN
CO2Me
CbzHN
OMe
O
CH2OH
CHO
5
Pd/C
TPAP, NMO
t-BuOK,CH2Cl2
NH4HCO2
4 Å mol. sieves
CH2Cl2, 20 min
69 % (2 steps)
THF/MeOH 9:1
3
7
4
6
Scheme 1. Synthesis of protected cubyldehydroalanine 6 and attempted hydrogenation.
O2
C19
C20
O4
C12
C11
C9
N1
C15
C16
C14
C13
O1
C3
C18
C10
C2
C17
O3
C1
C7
C6 C4
C5
C8
Fig. 3. View of 6, with ellipsoids at 20 % probability, showing the alkene to have Z-geometry.
O
O
S
S
I
NH
NH
i) t-BuLi, Et2O,
LiOH
dioxane/H2O
OEt
Ϫ78ЊC
OH
99 %
O
O
O
S
ii)
8
10
69 %
11
N
OEt
1.1:1.0 d.r.
9
O
Scheme 2. Synthesis of cubylglycine derivative 11.

692
Q. I. Churches et al.
1,4-cubanedicarboxylate,[16] was lithiated with tert-butyl lithium
then treated with the (RS)-glyoxylate sulfinimine 9[17] to afford
the corresponding amino ester 10 in good yield (Scheme 2). The
nucleophilic addition to the chiral sulfinimine showed low
diastereoselectivity (1.1 : 1.0). While the diastereoselective
addition of organometallic nucleophiles into chiral sulfinimines
is commonly reported,[18] examples of additions of tertiary alkyl
lithium nucleophiles into these systems are rare. To investigate
whether the low diastereoselectivity we observed is unique to
the cubyl system or if it is a general characteristic of the addition
of tertiary organolithium nucleophiles to 9, we investigated the
addition of tert-butyllithium to the sulfinimine. Interestingly,
this reaction also proceeded in poor diastereoselectivity
(1.5 : 1.0, Scheme 3). In selected cases, when the addition of
nucleophiles into chiral sulfinimines has resulted in low diaster-
eoselectivity, Ellman’s group has been able to improve the
diastereoselectivity by the use of Lewis acids such as BF3ꢁEt2O
or trimethylaluminium.[19] In this instance, however, the use of
either BF3ꢁEt2O or trimethylaluminium additives in the addition
reaction of cubyllithium to 9 led to complex reaction mixtures.
Hydrolysis of cubylglycine ethyl ester 10 with lithium
hydroxide afforded the corresponding amino acid 11 in near
quantitative yield. Previously it has been noted that
t-butylsulfinamide amino acid diastereomers can have signifi-
cantly different solubility, and this trait can be used to diaster-
eomerically enrich a diastereomeric mixture.[20] Accordingly,
the carboxylic acid 11 could be diastereomerically enriched to
.9 : 1 d.r. by trituration with acetone. With a method for
resolving the diastereomers in hand, we then sought to confirm
the absolute stereochemistry of the major diastereomer of 11
following enrichment. An enriched mixture of the cubylglycine
derivative 11 was hence converted to the corresponding phe-
nylglycine dipeptide 13 by standard HBTU (O-(benzotriazol-1-
yl)-N,N,N0,N0-tetramethyluronium hexafluorophosphate) coupling
conditions with (R)-phenylglycine methyl ester (Scheme 4). By
examination of the 1H NMR spectra of the two diastereomers of
13, we were able to use Yabuuchi and Kusumi’s model[21,22] to
assign the major diastereomer of 13 as (Rs,S,R) since, relative to the
1
minor isomer, the H NMR peaks corresponding to the cubane
moiety appeared upfield and the peaks corresponding to the t-butyl
moiety appeared downfield, as a result of the ring current effect of
the phenyl moiety (see Fig. 4 and Supplementary Material). By
implication, the minor diastereomer was assigned to have (Rs,S,R)
configuration.
The generality of 11 to serve as a precursor for cubane-
substituted peptides was then demonstrated through the prepa-
ration of the L-leucine dipeptide 14 (Scheme 5) which was
obtained in diastereomerically pure (Rs,S,R) form via chroma-
tography over silica.
At the present time a suitable method for unmasking of the
N-terminal nitrogen has not been identified. Treatment of 14
with standard acidic conditions[23] gave no reaction, whereas
increased reaction time and/or the application of heat led to
decomposition of the peptide. In order to obtain more informa-
tion about potential methods for the cleavage of the
N-sulfinamide moiety we investigated the deprotection of
the cubylglycine ester 10. No reaction was observed when the
standard deprotection conditions (0.4 M HCl in methanol)
were applied to this substrate, and increased acid concentration
and excess (20 eq) or extended reaction times (4 days) gave the
same result. Hydrochloric acid promoted deprotection of the
t-butylsulfinamide group is reliant on nucleophilic attack of
chloride to displace the sulfinyl moiety.[24] It is reasonable to
expect that the bulky nature of the cubane substituent might
prevent this nucleophilic displacement from occurring. It was
envisaged that oxidation of the t-butylsulfinamide group to the
acid labile t-butylsulfonamide (BUS-derivative), might facili-
tate cleavage of the S-N bond and so the sulfinamide 10 was
cleanly oxidized to the corresponding sulfonamide 15 using
standard m-chloroperbenzoic acid (m-CPBA) conditions
(Scheme 6).[25] Attempts were then made to cleave the
t-butylsulfonamide of 15 involving the use of triflic acid/
anisole, triflic acid/trifluoroacetic acid, or AlCl3/anisole,[26,27]
all of which led to recovered starting material. It is clear that
O
PGME
O
S
O
H
N
S
ϩ0.005
ϩ0.086
ϩ0.139
NH
O
C
H
O
H
Li
S
HN
OEt
Et2O,
Ϫ78ЊC
O
N
H
9
O
12
H
O
Ϫ0.139
37 %
1.5:1.0 d.r.
Fig. 4. Diastereomeric d NMR values and predicted conformation of
cubylglycine-R-phenylglycine dipeptide 13a according to Yabuuchi and
Kusumi’s model.[21,22] PGME: phenylglycine methyl ester.
Scheme 3. The addition of tert-butyl lithium to the glyoxylate
sulfinimine 9.
O
O
Rs
Rs
S
S
O
O
NH
NH
H
N
H
HBTU, DIEA
DMF, 2 h, rt
R
R
N
11
7.0:1.0 d.r.
OMe
OMe
S
R
ϩ
O
O
O
ClH3N
OMe
Major
Minor
13a
13b
Scheme 4. Synthesis of cubylglycine-phenylglycine dipeptide derivative 13. DIEA: diisopropylethylamine.

The Synthesis of a Cubane-Substituted Dipeptide
693
O
S
O
O
NH
11, HBTU
HOBt, DIEA
H
N
ClH3N
OMe
OMe
THF, 2 h
45 %
O
14
Scheme 5. Synthesis of Rs,S,S-cubylglycine-leucine dipeptide 14. HOBt: 1-hydroxybenzotriazole.
[4] S. Horvat, K. Mlinaric´-Majerski, L. Glavasˇ-Obrovac, A. Jakas,
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A. Milostic´-Srb, J. Med. Chem. 2006, 49, 3136. doi:10.1021/
JM051026þ
O
S
NH
O
m-CPBA
OEt
10
[5] (a) A. D. Knijnenburg, V. V. Kapoerchan, E. Spalburg, A. J. de
Neeling, R. H. Mars-Groenendijk, D. Noort, G. A. van der Marel,
H. S. Overkleeft, M. Overhand, Bioorg. Med. Chem. 2010, 18, 8403.
doi:10.1016/J.BMC.2010.09.018
CH2Cl2, rt
45 min, 99 %
O
15
(b) V. V. Kapoerchan, A. D. Knijnenburg, M. Niamat, E. Spalburg,
A. J. de Neeling, P. H. Nibbering, R. H. Mars-Groenendijk, D. Noort, J.
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S. Overkleeft, M. Overhand, Chem. – Eur. J. 2010, 16, 12174. doi:10.
1002/CHEM.201001686
Scheme 6. Conversion of the N-sulfinamide derivative of cubylglycine
ester 10 to the N-sulfonamide 15.
sulfinamide and sulfonamide derivatives of cubylglycine are
remarkably resistant to cleavage.
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In summary, we have synthesised the first cubyl amino acid
derivative bearing an unfunctionalised cubane moiety 11 and
prepared the first known example of a cubyl-substituted peptide
14. The tolerance of cubylglycine derivatives to harsh reaction
conditions such as concentrated Lewis and Bronsted acids has
been shown, but cubyldehydroalanine derivatives were found to
readily decompose or rearrange to the corresponding cyclooc-
tatetraene derivatives in the presence of palladium or acid.
While the use of the enantiomerically pure glyoxylate
sulfinimine 9 in the addition reaction of cubyllithium did not
lead to a high diastereoselectivity, the presence of the chiral
t-butylsulfinamide group in the product allowed for the simple
enrichment of one of the diastereomers of the cubylglycine
derivative 11. Coupling of a diastereomerically enriched form of
this acid with R-phenylglycine facilitated the determination of
the configuration of the two diastereomers of 11 through the use
of Yabuuchi and Kusumi’s 1H NMR method.
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7588. doi:10.1021/JA00096A016
Experimental procedures and characterisation data for all new
compounds as well as the cif file for 6 are available on the
Journal’s website.
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Acknowledgements
This work was funded by CSIRO’s Preventative Health Flagship. Mike
Falkiner and Chris Hallam, CSIRO Materials Science and Engineering, are
thanked for providing dimethyl 1,4-cubanedicarboxylate.
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