Tandem deprotection-dimerization-macrocyclization route to C2 symmetric cyclo-tetrapeptides

Article abstract of DOI:10.1002/chem.201304262

Dimerization-macrocyclization has been a long-standing problem in the cyclization of peptides since, together with the desired cyclic product, many cyclic oligomers and linear polymers may also be formed during the reaction. Therefore, the development of a process that affords the cyclic dimer predominantly is difficult. A novel and versatile strategy for the synthesis of symmetric cyclo-tetrapeptides by palladium-promoted tandem deprotection/cyclo- dimerization from readily available Cbz-dipeptidoyl benzotriazolides is reported (Cbz=carboxybenzyl).

Full text of DOI:10.1002/chem.201304262

DOI: 10.1002/chem.201304262
Communication
&
Macrocyclization
Tandem Deprotection–Dimerization–Macrocyclization Route to C2
Symmetric cyclo-Tetrapeptides
Khanh Ha,[a] Iryna Lebedyeva,[a] Sadra Hamedzadeh,[a] Zhiliang Li,[a] Ryan QuiÇones,[a]
Girinath G. Pillai,[a, b] Byron Williams,[a] Amir Nasajpour,[a] Kristin Martin,[a]
Abdullah M. Asiri,[c, d] and Alan R. Katritzky*[a, d]
Chem. Eur. J. 2014, 20, 4874 – 4879
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ficult lactamizations in the construction of peptide macrocy-
cles.[16,17] Several tandem click reactions have facilitated difficult
lactamization reactions in the construction of modified cyclic
peptides.[18,17,19] For macrolactamization of a linear precursor,
such an approach improved yields from 42 to 90%[20,17,21]
(Figure 1).
Abstract: Dimerization–macrocyclization has been a long-
standing problem in the cyclization of peptides since, to-
gether with the desired cyclic product, many cyclic oligo-
mers and linear polymers may also be formed during the
reaction. Therefore, the development of a process that af-
fords the cyclic dimer predominantly is difficult. A novel
and versatile strategy for the synthesis of symmetric cyclo-
tetrapeptides by palladium-promoted tandem deprotec-
tion/cyclo-dimerization from readily available Cbz-dipep-
tidoyl benzotriazolides is reported (Cbz=carboxybenzyl).
Cyclic tetrapeptides represent a unique class with a wide diver-
sity in both structural detail and biological activity.[1,2] Tetrapep-
tide macrocycles have shown potential applications ranging
from nanomaterials to drug discovery. The first cyclic tetrapep-
tide nanotubes composed of b-amino acid residues were re-
ported by Seebach.[3,4] Due to the additional carbon atom in
the backbone of each residue, multiple conformers of the mac-
rocycles permit hydrogen bonding and strong tubular arrays
can be formed. Many naturally occurring cyclic tetrapeptides
show biological activity,[5,3,6] and are highly selective in a wide
range of therapeutic areas including: inhibition of histone de-
acetylase,[2,6] and tyrosinase,[7] cytotoxicity,[8,9] antimalaria,[7] and
antibiotic activity.[10]
Figure 1. Contemporary ring construction strategies to form symmetrical
Cyclic tetrapeptides are a rich source of drug-like molecules
due to their low molecular weight, favorable pharmacokinetic
characteristics, and unique cyclic backbone, which provides
a rigid framework able to support a wide range of functional
groups.[6,11] Despite their interesting properties, the application
of cyclic tetrapeptides is limited by synthetic difficulty.
The cyclization event often poses a great challenge,[12,11]
since direct macrolactamization to form cyclo-tetrapeptides by
activation of a carboxylic acid is hampered by ring strain.[1] The
primary reason for ineffective cyclization of a linear tetrapep-
tide originates from the difficulty of bringing the termini suffi-
ciently close for cyclization.[11,12,13] Peptide bonds preferentially
adopt trans conformations, and linear peptides prefer more ex-
tended conformations.[14,15]
cyclic peptides and peptide-mimetic.
A
dimerization–macrocyclization approach using penta-
fluorophenyl diphenylphosphinate (FDPP) as a coupling re-
agent was successfully applied to the synthesis of sugar amino
acid based 24-membered macrocyclic C2-symmetric cationic
peptides.[16] In addition, the utility of the dimerization–macro-
cyclization method was demonstrated in the synthesis of C2-
symmetrical decapeptide derivatives of the natural product
pentapeptide Sansalvamide A and cyclo-(Lys-Lys-Pro-Tyr-Ile-
Leu-)2 using HBTU.[22,23]
On the other hand, designing a dimerization–macrocycliza-
tion process to form C2-symmetrical cyclic peptides can be a se-
rious challenge: cyclization is a concentration-dependent reac-
tion and many cyclo-oligomers or linear polymers can be
formed (Figure 2).[24,25] A cyclic dimer is normally the predomi-
nant product at low concentration (10À2–10À4 m) and the per-
centage of linear polymers rises as concentration of the sub-
strate increases.
Among contemporary strategies for peptide and peptido-
mimetic macrocyclization, a tandem dimerization–macrocycli-
zation approach has proved to be a powerful tool to force dif-
[a] K. Ha, Dr. I. Lebedyeva, S. Hamedzadeh, Z. Li, R. QuiÇones, G. G. Pillai,
B. Williams, A. Nasajpour, K. Martin, Prof. Dr. A. R. Katritzky
Center for Heterocyclic Compounds, Department of Chemistry
University of Florida, Gainesville, FL 32611-7200 (USA)
E-mail: katritzky@chem.ufl.edu
Using
a Pd-promoted tandem deprotection/cyclization
dimerization method, we were able to control the cyclization
reaction and selectively convert open chain N-Cbz-dipeptidoyl
benzotriazole sequences into the corresponding C2 symmetri-
cal 14- and 16-membered cyclic tetrapeptides (Scheme 1).
As outlined in Scheme 1, C2 symmetrical cyclic tetrapeptide
[b-Ala-l-Pro-]2 5a was selected as our first target. Compound
5a was synthesized in a four-step procedure starting from
1a.[26,27] Cbz-N-protected b-amino acid 1a was first converted
into the benzotriazolide 2a (Cbz=Carboxybenzyl); reaction of
2a with proline gave 3a, which was converted into Cbz-dipep-
[b] G. G. Pillai
Department of Chemistry, University of Tartu, Tartu, 50411 (Estonia)
[c] Prof. Dr. A. M. Asiri
Center of Excellence for Advanced Material Research
King Abdulaziz University, Jeddah, 21589 (Saudi Arabia)
[d] Prof. Dr. A. M. Asiri, Prof. Dr. A. R. Katritzky
Chemistry Department, King Abdulaziz University
Jeddah, 21589 (Saudi Arabia)
Supporting information for this article is available on the WWW under
http://dx.doi.org/10.1002/chem.201304262.
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Communication
tail cyclization methods.[30] Using our tandem depro-
tection/cyclization dimerization method, compound
5b was synthesized in 82% yield from 4b or 86%
from 4bb with a product selectivity of 92%. To prove
the generality of the method, 1-N-Cbz-benzotriazolyl
dipeptides 4c and d were cyclo-dimerized to give
cyclic tetrapeptide products 5c and d in 52 and 77%
yield, respectively.
Cyclization of linear N-Cbz-dipeptidoyl benzotriazo-
lide 4e employing similar conditions as for 4a–d
(10 wt% Pd/C in MeOHdry) afforded cyclic peptide 5e
in 37% yield after HPLC purification.
Figure 2. Challenges in dimerization-macrocyclization reaction to form cyclic peptides.
The few literature examples of 16-membered cyclic
tetrapeptides are endowed with promising biological
activities. Cyclic peptides bearing aliphatic side
tidoyl benzotriazolide 4a.[28,29] Stirring at a concentration of
12 mm under hydrogen in the presence of Pd/C (10 wt%) at
208C for 48 h, 4a afforded 5a (Scheme 1) by tandem dimeriza-
tion–macrocyclization: HPLC-MS confirmed the major product
is symmetrical cyclic tetrapeptide cyclo-(b-Ala-l-Pro-)2 5a
which, after purification by gradient chromatography (MeOH/
ether) was obtained in 70% isolated yield. Similarly, 5a was
synthesized in 72% yield by deprotection/cyclo-dimerization of
Cbz-l-Pro-b-Ala-Bt 4aa.
chains attached to a 16- membered ring are more favorable
with respect to the binding affinity.[31] To broaden the scope of
our methodology, 16-membered cyclic tetrapeptides 5 f–i were
considered as potential targets. The macrolactamizations of
4 f–i were each initiated by treatment with Pd/C (10 wt%) at
208C for 24–36 h in dry MeOH at room temperature. The un-
functionalized 16-membered symmetrical cyclo-tetrapeptides
5 f–i were isolated in high purities after separation by gradient
chromatography (Scheme 1).
Next, we turned our attention to cyclo-(d,l-b-Phe-d-Pro-)2
5b, whose diastereomer was isolated from Roccella canarien-
sis.[30] Peptide 5b is inaccessible or can only be prepared with
great difficulty by traditional step-wise coupling and head-to-
To rationalize the reaction pathways of Cbz-dipeptidoyl ben-
zotriazolides and gain further insight into the Pd-assisted
tandem deprotection/cyclization macrocyclization process, we
employed theoretical calculations. Scheme 1 implies that Cbz-
Scheme 1. Tandem deprotection-dimerization-macrocyclization of Cbz-dipeptidoyl benzotriazoles.
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deprotection of Cbz-1-N-benzotriazolyl dipeptide 4a forms
intermediate I (Figure 3) that cyclises intermolecularly in a “di-
merization–macrocyclization” pathway to 5a, with benzotria-
zole as leaving group. On the other hand, unprotected dipep-
tide intermediate I can also cyclise “head-to-tail” to form intra-
molecular lactamization product 5a’ (Figure 3), which was de-
tected as a trace component in the reaction mixture by HPLC-
MS analysis.
and the solvation was not considered. Steric energy refers to
energy associated with a bond being stretched or compressed.
Since, there is no intermolecular interaction in the gas phase,
bond lengths between b(C-N) and b(O-H) have to be signifi-
cantly different from those between same atoms when the
molecule is complexed. Steric energies are calculated using
molecular mechanics with MMX[41] forcefield in PCModel[42]
(Figure 3). Our calculation results suggest that 5a has lower
steric energy than 5a’; therefore,
formation of 5a would be more
favoured.
Another factor contributing to
the more favourable formation
of 5a may be the relative ener-
gies of transition state (TS)-II. Co-
ordination of the N-unprotected
dipeptide I to the Pd could form
(I)2Pd complex II, which in-turn
could lower the activation
Figure 3. Energy diagram for the formation of 5a.
energy in the formation of the
intermolecular dimerization/cy-
clization product 5a (Scheme 2).
These two products 5a and a’ differ mainly in ring sizes.
Compound 5a’ is a 7-membered cyclic dipeptide and 5a is
To test this hypothesis, unprotected dipeptidoyl benzotriazo-
lide I was synthesized by boc-deprotection of compound 6
using previously reported method,[43] and dissolved in MeOH.
The reaction mixture was treated with one equivalent of N,N-
diisopropylethylamine (DIPEA) and stirred for 48 h at 208C
(Scheme 3). Interestingly, the HPLC-MS analysis of the reaction
mixture revealed that the major components were linear oligo-
a
14-membered symmetrical cyclo-tetrapeptide. Molecular
structures of the unprotected dipeptide intermediate I and the
structures of products 5a and a’ were drawn using Marvin
Sketch,[32] and geometries were optimized using the semi-em-
pirical program MOPAC2012[33,34] under PM6[35,36] parameteriza-
tion. Further, the optimized geometry is considered
for calculating the heat of formation and reaction
energy using Turbomole[37,38] (A development of Uni-
versitꢁt Karlsruhe (TH) and Forschungszentrum Karls-
ruhe GmbH, 1989–2007, TURBOMOLE GmbH, since
2007. The Turbomole program package can be ob-
tained from COSMOlogic GmbH&Co.) Later, calcula-
tions performed under DFT level of theory, B3LYP
function[39] and def-TZVP[40] basis set. We considered
large basis set, as this is the only one with more real-
istic predictions of energies for compounds with Pd
(Palladium), even though def-TZVP basis set took
more computation time and power. For the reaction
of 4a to form 5a and a’, assuming compound I is
Scheme 2. Ring-construction events in the formation of 5a.
the intermediate as shown in Figure 3, we calculated
relative energies (taken as differences of total elec-
tronic energies) of the two reaction pathways: I) in-
termolecular dimerization/macrocyclization leading
to the isolated 14-membered cyclic tetrapeptide 5a; II) intra-
molecular cyclization leading to the macrocycle 5a’. It is seen
that the total energy of product 5a lies 9.29 kcalmolÀ1 lower
than the intermediate I. As for the intramolecular pathway I–
5a’, it can be considered as an isodesmic reaction involving
two disjoint products: cyclic structure 5a’ and benzotriazole.
The reaction energy of this isodesmic reaction was calculated
to be À205.54 kcalmolÀ1, which means that reaction pathway
I–5a is 110.13 kcalmolÀ1 and they are more favorable than
pathway I–5a’. The calculations were carried out in vaccum
mers, which shows that Pd plays an important role in the ring-
construction leading to formation of the intermolecular cyclo-
dimerization product.
The approach of tandem dimerization–macrocyclization can
also be applied to the synthesis of unsymmetrical cyclic pep-
tide sequences by taking advantage of the statistical product
distribution from the reaction of two different linear precur-
sors. As an example, subjecting an equimolar mixture of pep-
tides 4a and b or d to the standard reaction conditions should
give a mixture of homo- and heterodimeric products. This ap-
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Peptide 1
Peptide 2
Heterodimer, ratio[a] (homo[b]/hetero)
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We thank the University of Florida and the Kenan Foundation
for financial support. This paper was also funded in part by
support from King Abdulaziz University under grant no. (D-
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Keywords: benzotriazoles · cyclodimerization · lactamization ·
macrocycles · peptides
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Received: October 31, 2013
Revised: December 24, 2013
Published online on April 2, 2014
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