Application of substituted 2-(trimethylsilyl)ethyl esters to suppress diketopiperazine formation

Article abstract of DOI:10.1016/j.tetlet.2004.03.054

The use of differently substituted 2-(trimethylsilyl)ethyl esters for C-terminal protection in peptide synthesis has been investigated. While the use of the unsubstituted 2-(trimethylsilyl)ethyl ester resulted in a substantial amount of diketopiperazine a

Full text of DOI:10.1016/j.tetlet.2004.03.054

Tetrahedron
Letters
Tetrahedron Letters 45 (2004) 3585–3588
Application of substituted 2-(trimethylsilyl)ethyl esters to suppress
diketopiperazine formation
Katarzyna Borsuk,a Floris L. van Delft,a Ivo F. Eggen,b,* Paul B. W. ten Kortenaar,b
Annet Petersenb and Floris P. J. T. Rutjesa,*
aDepartment of Organic Chemistry, NSRIM, University of Nijmegen, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
bDiosynth BV, PO Box 20, NL-5340 BH Oss, The Netherlands
Received 9 February 2004; revised 4 March 2004; accepted 10 March 2004
Abstract—The use of differently substituted 2-(trimethylsilyl)ethyl esters for C-terminal protection in peptide synthesis has been
investigated. While the use of the unsubstituted 2-(trimethylsilyl)ethyl ester resulted in a substantial amount of diketopiperazine at
the dipeptide stage, use of the corresponding methyl-substituted silyl ester gave a significant reduction of this undesired pathway.
Both esters could be deprotected by fluoride-induced cleavage under mild conditions.
ꢀ 2004 Elsevier Ltd. All rights reserved.
A novel method for peptide manufacturing, called
DioRaSSP––Diosynth rapid solution synthesis of pep-
tides––has recently been introduced by Diosynth.1;2
DioRaSSP combines the advantages of the homoge-
neous character of classical solution phase synthesis
with the generic character and the amenability to auto-
mation of solid phase approaches. In the DioRaSSP
approach, the growing peptide is essentially anchored in
a permanent organic phase (generally EtOAc) by means
of its hydrophobic C-terminal and side-chain protecting
groups. Intermediates are not isolated, and excess
reagents and by-products are intermittently removed by
aqueous extractions. No organic waste streams are
generated during the performance of the synthesis.
Processes according to this highly efficient manufactur-
ing method are easy to scale up and yield products of
reproducibly high purity.
protecting group is removed by hydrogenolysis in each
cycle of the DioRaSSP process. In the case of peptides
with sulfur-containing residues––which are not com-
patible with hydrogenolysis––and in the case of long
peptides to reduce the risk of handling failures, a con-
vergent synthetic approach using peptide fragments can
be chosen. Such an approach requires the application of
a C-terminal ester function, which is orthogonal with
respect to both Z and tert-butyl type protection, that is
the said function should be completely stable during
hydrogenolysis––so all benzyl- and allyl-type functions
cannot be used––and its cleavage should not give rise to
premature loss of tert-butyl type protecting groups.
Moreover, the conditions for its cleavage should be mild
in order to preserve the integrity of the peptide chain.
For instance, saponification to cleave primary alkyl
esters cannot provide a general protocol, since this is
likely to result in side reactions at incorporated
Asp(OBut) residues.3 Logically, the ester function
should be stable under the conditions associated with
the DioRaSSP process. Taking these specifications into
account, the 2-(trimethylsilyl)ethyl (Tmse) ester was
selected as an orthogonal C-terminal protecting group in
our initial studies towards convergent DioRaSSP
approaches. This ester can be deprotected under rela-
tively mild conditions by fluoride-induced cleavage.4 Its
application, however, is associated with a serious
drawback. While peptide fragments in a convergent
approach are preferably selected to contain a Gly or Pro
residue in the C-terminal position to ensure the enan-
tiomeric purity of the ensuing product, such fragments
In a typical DioRaSSP process, the benzyloxycarbonyl
(Z) function is applied for temporary amine protection,
while tert-butyl type functions or functions of similar
lability are generally applied for the semi-permanent
protection of the C-terminal carboxylic function and
functional side chains of the growing peptide. The Z
Keywords: Solution phase peptide synthesis; Diketopiperazine forma-
tion; Protecting groups.
* Corresponding authors. Tel.: +31-412-66-3220; fax: +31-412-66-2563
(I.F.E.); tel.: +31-24-365-3202; fax: +31-24-365-3393 (F.P.J.T.R.);
e-mail addresses: ivo.eggen@diosynth.com; rutjes@sci.kun.nl
0040-4039/$ - see front matter ꢀ 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2004.03.054

3586
K. Borsuk et al. / Tetrahedron Letters 45 (2004) 3585–3588
ROH, DCC, 0.1 equiv DMAP
CH2Cl2
Boc-AA4-AA3-AA2-AA1-O
AA1 = Pro or Gly
Z-Pro-OH
Z-Pro-OR
SiMe3
R = Tmse
R = Tmsi
R = Tmst
1a
1b
1c
R = Tmse
R = Tmsi
R = Tmst
2a
2b
2c
R
N
O
R1
O
R1
O
H2, Pd/C
EtOAc
1. H2, Pd/C, EtOAc
H2N
O
O
+
Z-Trp-Pro-OR
N
R
SiMe3
2. Z-Trp-OH, EDC/HOBt
EtOAc
R2
N
H
R2
O
3a
3b
R = Tmse
R = Tmsi
1. Z-Asp(OBut)-OH
EDC/HOBt, EtOAc
O
R1
H
H-Trp-Pro-OR
+
DKP
N
N
R
SiMe3
2. H2, Pd/C, EtOAc
Z
R2
O
O
R = Tmse
R = Tmsi
4a
4b
Boc-Ala-OH
H-Asp(OBut)-Trp-Pro-OR
R1
R, R1 = H
R, R1 = -(CH2)3- (Pro)
(Gly)
EDC/HOBt, EtOAc
Z
R = Tmse
R = Tmsi
5a
5b
SiMe3
N
R
O
Scheme 1.
TBAF
Boc-Ala-Asp(OBut)-Trp-Pro-OH
Boc-Ala-Asp(OBut)-Trp-Pro-OR
R = Tmse 6a 89% (overall yield)
7
are extremely prone to diketopiperazine (DKP) forma-
tion at the dipeptide stage (Scheme 1).5
R = Tmsi
86% (overall yield)
6b
Scheme 3.
This propensity is most pronounced for primary esters.
The problem was indeed encountered in the synthesis of
the tripeptide Z-Asp(OBut)-Trp-Pro-OTmse according
to the DioRaSSP protocol, but could be suppressed to a
certain degree through addition of a molar equivalent of
hydrochloric acid at the end of the hydrogenolysis of the
intermediate dipeptide Z-Trp-Pro-OTmse. However, in
order to arrive at a more robust protocol, the synthesis
and application of secondary and tertiary analogues of
the Tmse ester have been explored in our groups
(Scheme 2).
was then applied in an investigation regarding DKP
formation. To this end, Boc-Ala-Asp(OBut)-Trp-Pro-
OTmsi was prepared in an analogous fashion to the
tetrapeptide Boc-Ala-Asp(OBut)-Trp-Pro-OTmse using
the DioRaSSP protocol8 (Scheme 3). During the hydro-
genolysis at the dipeptide stage, the rate of DKP for-
mation in the case of the Tmse and Tmsi esters 3a, b,
respectively, was studied and compared (Fig. 1). Clearly,
in the latter case the extent of DKP formation was
considerably reduced compared to the Tmse ester, which
is probably due to the sterically somewhat more con-
gested secondary ester function. Upon addition of a
stoichiometric amount of HCl after completion of the
hydrogenation reaction at ambient temperature, DKP
formation was almost completely suppressed (Fig. 2).
For model studies, we selected N-benzyloxycarbonyl-L-
proline (Z-Pro-OH), which was transformed into the
corresponding esters (2a–c). These reactions were car-
ried out using standard reaction conditions with the
commercially available alcohol 1a and the readily
available alcohols 1b and c,6 dicyclohexylcarbodiimide
(DCC) and a catalytic amount of DMAP7 (Scheme 3).
In the case of the Tmsi ester 2b, a mixture of diastereo-
isomers was obtained in a 1:1.3 ratio, and used as such
for further synthesis. The tertiary Tmst ester 2c could be
prepared, but was even cleaved under the mildly acidic
conditions of HPLC analysis (0.1% TFA in the eluent).
Consequently, we abandoned further investigations into
the tertiary ester, since it would then also be too labile
for use in the DioRaSSP methodology, which includes
multiple acidic aqueous washing steps. Z-Pro-OTmsi 2b
DKP formation with time
50
40
30
20
10
0
0
10
20
30
40
Time (h)
Tmse-ester
50
60
70
R = H, R1 = H: Tmse
AA
O
R
HN
Z
SiMe3
R = H, R1 = Me: Tmsi
R = Me, R1 = Me: Tmst
R1
O
Tmsi-ester
Scheme 2.
Figure 1.

K. Borsuk et al. / Tetrahedron Letters 45 (2004) 3585–3588
3587
further by the addition of HCl after completion of the
hydrogenolysis at the dipeptide stage. Additional
advantages of the Tmsi group include its complete sta-
bility under the DioRaSSP conditions and its facile
removal at the final stages of the desired sequence.
DKP formation with time after HCl addition
5
4
3
2
1
Acknowledgements
0
0
10
20
30
40
50
60
70
80
Diosynth B. V. is kindly acknowledged for providing a
research grant to K.B.
Time (h)
Tmse-ester
Tmsi-ester
Figure 2.
References and notes
We also investigated the deprotection of the Tmsi ester
compared to the Tmse ester on the tetrapeptides 6b and
6a, respectively. As anticipated, the 2-(trimethylsi-
lyl)ethyl and 2-(trimethylsilyl)isopropyl esters both
readily underwent fluoride-induced cleavage upon
treatment with an equimolar amount of tetra-n-butyl-
ammonium fluoride (TBAF) to afford the same tetra-
peptide 7 with a free C-terminal carboxylic acid. The
deprotection conditions for both esters were to some
extent optimized (Table 1) using varying amounts of
TBAF in combination with solvents that are compatible
with the DioRaSSP procedure.
1. (a) Presentations by Eggen, I. F. at IBC’s Tides 2003:
Oligonucleotide and Peptide Technology Conferences, at
IBC’s 4th Annual Conference: Eurotides and at the 8th
International Scientific Update Conference on Organic
Process Research and Development; (b) Speciality Chem-
icals Magazine 2003, 23, 42–44, SP2 2003, 2, 34–35.
2. (a) Eggen, I. F.; Ten Kortenaar, P. B. W.; Haasnoot, C. A.
G. U.S. Patent 2003/0018164 A1; (b) Eggen, I. F.; Ten
Kortenaar, P. B. W. U.S. Patent US 2003/0018163 A1.
3. Barany, G.; Merrifield, R. B. In The Peptides; Gross, E.,
Meienhofer, J., Eds.; Academic: New York, 1979; Vol. 2,
pp 1–284.
4. (a) Sieber, P. Helv. Chim. Acta 1977, 60, 2711; (b) Gerlach,
H. Helv. Chim. Acta 1977, 60, 3039.
The reaction was relatively slow when carried out in a
1:1 mixture of EtOAc and THF containing 4 equiv of
TBAF. The rate improved upon switching to pure THF
and increasing the amount of TBAF. It was generally
observed that deprotection occurred faster with the
Tmse ester than with the Tmsi ester; however, both
could be completely deprotected. Furthermore, depro-
tection of the Tmse ester occurred faster in pure THF
than in EtOAc/THF, while no such rate enhancement
was observed for the Tmsi ester. In all cases, the
deprotection proceeded in a clean fashion without the
formation of undesired side products.
ꢀ
5. Rothe, M.; Mazanak, J. Liebigs Ann. Chem. 1974, 439.
6. (a) Hauser, C. R.; Hance, C. R. J. Am. Chem. Soc. 1952,
74, 5091; (b) Davis, D. D.; Jacocks, H. M. J. Organomet.
Chem. 1981, 206, 33.
7. Strazzolini, P.; Scuccato, M.; Giumanini, A. G. Tetrahe-
dron 2000, 56, 3625.
8. Typical procedure for the preparation of tetrapeptide 6b
using the DioRaSSP protocol. Z-Trp-Pro-OTmsi 3b: A
solution of Z-Pro-OTmsi (1.75 g, 4.8 mmol) in a mixture of
EtOAc (17 mL) and water (0.89 mL) at 20 ꢁC was subjected
to a H2 atmosphere (1 bar) in the presence of 10% Pd/C
(180 mg) and N-methylmorpholine (NMM, 528 lL,
4.8 mmol). Upon completion of the reaction, the catalyst
was filtered off, and the residue was washed with EtOAc
(5 mL). Then to the organic layer––containing the H-Pro-
OTmsi derivative––were added 1-hydroxybenzotriazole
(HOBt, 649 mg, 4.8 mmol), Z-Trp-OH (1.35 g, 4 mmol) and
In conclusion, we have investigated the application of
differently substituted 2-(trimethylsilyl)ethyl esters as
orthogonal C-terminal carboxylic acid protecting
groups for peptide synthesis. The 2-(trimethylsilyl)iso-
propyl (Tmsi) ester proved most suitable for this pur-
pose, giving rise only to very low amounts of
diketopiperazine (DKP) formation in the peptide syn-
thesis. The DKP formation could be suppressed even
1-(30-dimethylaminopropyl)-3-ethylcarbodiimide
hydro-
chloride (EDC, 843 mg, 4.4 mmol). After stirring the
resulting solution for 1 h, an additional amount of EDC
(84 mg, 0.44 mmol) was added. After stirring of the
resulting solution until completion of the reaction, 3-
dimethylamino-1-propylamine (254 lL, 2 mmol) was
added. The mixture was stirred for 30 min and washed
with 10% aqueous Na2CO3 (11 mL), 10% aqueous KHSO4
(4·11 mL), 2·11 mL of 10% aqueous Na2CO3 (2·11 mL)
and 30% aqueous NaCl (3·11 mL).
Table 1
Entry Conditions
Reaction time for Reaction time for
Tmse deprotection Tmsi deprotection
H-Trp-Pro-OTmsi 4b: The organic layer containing the
protected dipeptide Z-Trp-Pro-OTmsi was subjected to
catalytic hydrogenolysis (H2 gas) at 30 ꢁC in the presence of
10% Pd/C (440 mg), water (1.14 mL) and NMP (0.69 mL).
After completion of the reaction, 340 lL of 36% HCl
(4 mmol) was added, the catalyst was filtered off and the
catalyst was washed with EtOAc (5 mL).
1
TBAF (4 equiv) 5–6 h 7–24 h
in ethyl acetate/
THF 1:1 (v/v)
2
3
TBAF (4 equiv) 3–4 h
in THF
7–24 h
1–1.5 h
TBAF (8 equiv) 15–30 min
in THF
H-Asp(OBut)-Trp-Pro-OTmsi 5b: To the organic layer
containing dipeptide 4b were added HOBt (649 mg,

3588
K. Borsuk et al. / Tetrahedron Letters 45 (2004) 3585–3588
4.81 mmol), Z-Asp(OBut)-OH (1.55 g, 4.81 mmol) and EDC
Boc-Ala-Asp(OBut)-Trp-Pro-OTmsi 6b: To the organic
layer containing the tripeptide 5b were added HOBt
(649 mg, 4.81 mmol), Boc-Ala-OH (910 mg, 4.81 mmol)
and EDC (843 mg, 4.41 mmol). After stirring the resulting
solution for 1 h, an additional amount of EDC (84 mg,
0.44 mmol) was added. After stirring the resulting solution
until completion of the reaction, 3-dimethylamino-1-prop-
ylamine (254 lL, 2.1 mmol) was added. The mixture was
stirred for 30 min and washed with 10% aqueous Na2CO3
(15 mL), 10% aqueous KHSO4 (2·15 mL), 10% aqueous
Na2CO3 (2·15 mL) and of 30% aqueous NaCl (3·15 mL).
The organic layer was evaporated to dryness to give the
desired protected in 86% overall yield (2.52 g) based on the
starting material Z-Trp-OH. Purity: 95.6 a/a % by reversed
phase HPLC (2 to 75% MeCN in 0.1% trifluoroacetic acid
in 48 min at 220 nm, 2.0 mL/min, 5 l C18 column). Iden-
tity: m=z 758.6 [M+H]þ, 702.6 [M)tBu+H]þ;
756.6 [M)H]ꢀ, 802.6 [M+HCOO]ꢀ both by electrospray
MS.
(843 mg, 4.41 mmol). The pH was adjusted to 5.2 using
NMM (400 lL, 3.6mmol). After stirring the resulting
solution for 1 h at pH 5.2, an additional amount of EDC
(84 mg, 0.44 mmol) was added. After stirring the resulting
solution until completion of the reaction, H-b-Ala-OBzl p-
tosylate (700 mg, 2.0mmol) and NMM (244lL, 2.2 mmol)
were added. The mixture was stirred for 30 min and washed
with 10% aqueous Na2CO3 (13 mL), 10% aqueous KHSO4
(4·13 mL), 10% aqueous Na2CO3 (2·13 mL) and 30%
aqueous NaCl (3·13 mL). The organic layer containing the
protected tripeptide Z-Asp(OBut)-Trp-Pro-OTmsi was then
subjected to catalytic hydrogenolysis (H2-gas) at 20 ꢁC in the
presence of 10% Pd/C (280 mg) and water (1.4 mL). Upon
completion of the reaction, 10% aqueous Na2CO3 (7.5 mL)
was added and the resulting suspension was filtered. The
residue was washed with EtOAc (5 mL) and the combined
filtrates were washed with 10% aqueous Na2CO3 (7.5 mL
and 15 mL) and 30% aqueous NaCl (3·15 mL).