A convenient synthesis of difficult medium-sized cyclic peptides by Staudinger mediated ring-closure

Article abstract of DOI:10.1039/c2ob25996f

Novel, efficient and mild preparation of 7- and 8-membered cyclic di- and 10-membered cyclic tripeptides containing α-, β- or γ-amino acid residues is effected by a Staudinger-mediated ring closure. Medium-sized cyclic di- and tripeptides - recognized as

Full text of DOI:10.1039/c2ob25996f

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COMMUNICATION
A convenient synthesis of difficult medium-sized cyclic peptides by
Staudinger mediated ring-closure†
Khanh Ha,a Jean-Christophe M. Monbaliu,‡a,b Byron C. Williams,a Girinath G. Pillai,a Charles E. Ocampo,a
Matthias Zeller,c Christian V. Stevensb and Alan R. Katritzky*a,d
Received 22nd May 2012, Accepted 22nd August 2012
DOI: 10.1039/c2ob25996f
and often observed as undesired side-products in the synthesis
of peptide constructs.5 In sharp contrast, synthesis of their 7- and
8-membered analogs is much more challenging. As a rule of
thumb, di- and tripeptides possessing 7–15-membered rings are
less accessible and can frequently only be synthesized with diffi-
culty, whether using solution phase or polymer-supported stra-
tegies.6 The cyclization of linear peptides containing more than
seven amino acids usually proceeds well.7 The main hurdle to
the cyclization of peptides to afford 7- to 15-membered rings is
the preferential transoid alignment of amide bonds in their
acyclic precursors which leads to a preferred extended structure,
placing the termini which need to react far apart.8
Novel, efficient and mild preparation of 7- and 8-membered
cyclic di- and 10-membered cyclic tripeptides containing
α-, β- or γ-amino acid residues is effected by a Staudinger-
mediated ring closure. Medium-sized cyclic di- and tripep-
tides – recognized as difficult targets – were obtained in mod-
erate to good yields according to a straightforward sequence.
Empirical force-field calculations were undertaken to deter-
mine their conformational behaviors and showed high levels
of similarity with X-ray results. A computational study at the
B3LYP/6-31+G** level of theory afforded information
regarding the impact of the sequence, ring-size and substi-
tution on the activation barriers for the cyclization of azido
peptide thioesters.
Among other strategies, traceless Staudinger ligation has been
the focus of numerous attempts to overcome problems in the
coupling of large peptide fragments.7 Intramolecular traceless
Staudinger ligation has been applied to access cyclic poly-
peptides and medium-sized (7–10-membered) lactams, but this
methodology required protections of the phosphane-containing
auxiliary by a borane complex to avoid undesired premature
Staudinger reaction. The cleavage of the borane protecting
group can require harsh conditions and, importantly, the phos-
phinothioester peptide can undergo oxidation during the borane
deprotection process and produce undesired by-products.6e,9
Our group has recently reported a new entry to 2,5-diketopi-
perazines derivatives from protected dipeptidoyl benzotriazoles,
which has advantages over literature methods with regard to
reaction efficiency, atom economy and stereoflexibility.4a As part
of our ongoing research program dedicated to the development
of innovative and efficient cyclization procedures, we now report
a novel, straightforward, efficient and mild approach to the
preparation of 7- and 8-membered cyclic di- and 10-membered
cyclic tripeptides containing α- and β- or γ-amino acid residues
via a solution phase Staudinger-mediated ring closure (Fig. 1).
In the first phase of the project, the synthesis of 7- and 8-
membered cyclic dipeptides was investigated from azidopepti-
doyl thioesters. The general procedure for the synthesis of the
starting azidopeptidoyl thioesters 5a–f is illustrated in Scheme 1.
First, chloroalkylcarbonyl chlorides 1a–d were reacted with
amino acids 2a–e to form dipeptide derivatives 3a–f which with
an excess of sodium azide in DMF at 80 °C or MeOH at reflux,
afforded the corresponding azidoprotected dipeptides 4a–f.
Mixed anhydride coupling of 4a–f with 1.2 equiv. of thiophenol
Small cyclic peptides have attracted attention for decades.1 Due
to their metabolic stability and defined conformations, cyclic
peptides are a powerful source for new drug candidates. Natural
cyclic dipeptides possess diverse biological activities including
antibiotic/antifungal,2 plant growth retardation2b and cyto-
toxicity.2b–e Small cyclic peptides interact efficiently with opioid
receptors,3a show potent cytotoxic effects by a variety of
mechanisms3b–f and display neuroprotective properties.1a,3g
Ring size is a significant factor in the success of macrolacta-
misation in the synthesis of a cyclic peptide. Six-membered
dipeptides (2,5-diketopiperazines) are readily accessible1c,4a–d
aCenter for Heterocyclic Compounds, Department of Chemistry,
University of Florida, Gainesville, FL 32611-7200, USA.
E-mail: katritzky@chem.ufl.edu
bDepartment of Sustainable Organic Chemistry and Technology, Faculty
of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
cDepartment of Chemistry, Youngstown State University, Youngstown,
OH 44555, USA
dChemistry Department, King Abdulaziz University, Jeddah, 21589,
Saudi Arabia
†Electronic supplementary information (ESI) available: Detailed exper-
imental procedures and 1H and 13C NMR spectra of all intermediates
1a–d, 3a–f, 4a–f, 5a–f, 7–11; 1H and 13C NMR spectra of cyclic dipep-
tides 6a–e. 1H NMR and HPLC-MS for cyclic tripeptide 12. CCDC
881662 and 881663 (Cartesian coordinates for the TSs for the cycliza-
tion of azido dipeptide thioesters and computational details). For ESI
and crystallographic data in CIF or other electronic format see DOI:
10.1039/c2ob25996f
‡Jean-Christophe M. Monbaliu is Postdoctoral Fellow of the Research
Foundation-Flanders (FWO-Vlaanderen).
This journal is © The Royal Society of Chemistry 2012
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Table 1 En route to 7- and 8-membered cyclic dipeptides
From 5
X
n
m
R1
H
R2
H
6
Yield (%)
73
Fig. 1 Ring construction to form cyclic oligopeptides by Staudinger-
mediated ring closure.
a
Cl
1
1
b
c
Br
Cl
2
2
0
0
Bn
H
66
75
Me
Me
Scheme 1 Synthesis of starting azido dipeptide thioesters (see Table 1
for a–f designation).
d
Cl
2
1
H
H
55; 68a
furnished the azidopeptidoyl thioesters 5a–f (64% to 75%). Pre-
parative conditions for the Staudinger-mediated ring-closure
were first optimized on compound 5a: treatment with 1.5 equiv.
of PBu3 in dry THF under microwave heating at 50 °C and
50 W for 5 min. The desired cyclic peptide 6a was precipitated
from the crude mixture on addition of hexanes and obtained in
high purity (73% yield).
We then turned our attention to (S)-3-benzyl-[1,4]diazepane-
2,5-dione (6b), a challenging target difficult to obtain by direct
macrolactamization.6d,f Encouragingly, reaction of 5b with tribu-
tylphosphine using the optimized conditions described above
gave product 6b, isolated in 66% yield after purification. This
protocol was then applied to the synthesis of 3,3-dimethyl-1,4-
diazepane-2,5-dione (6c) by cyclization of precursor 5c. Novel
cyclic dipeptide 6c was obtained in 75% yield after purification.
These three examples show the advantages of our microwave-
assisted Staudinger-mediated cyclization for the synthesis of
difficult cyclic dipeptides. The higher yield in the reaction of 5a
in comparison to 5b suggests that the cyclization is sensitive to
steric congestion at the C-terminal fragment.10 The unexpected
high yield obtained for compound 5c is attributed to a Thorpe-
Ingold effect (Cα-dimethyl substitution).11
The few literature examples of 8-membered cyclic dipeptide
are endowed with promising biological activities.12 To broaden
the scope of our methodology, 1,4-diazocane-2,5-dione 6d and
1,5-diazocane-2,6-dione 6e were considered as potential targets.
The macrolactamizations of 5d–f were each initiated by treat-
ment with 1.5 equiv. of PBu3 in dry THF at room temperature.
The unfunctionalized 8-membered bislactams 6d and 6e were
isolated after purification in 55% and 57% yield, respectively.
The impact of the ring-size and the sequence onto the acti-
vation barrier were studied. Transition states for the cyclization
of model aza-ylide thioester intermediates (PH3 as model phos-
phine) were located at the B3LYP/6-31+G** level of theory and
the nature of the stationary points was determined by analytical
calculation of the Hessian. A model sequence N3-Gly-Gly-SPh
was selected as a reference. Its cyclization through a six-mem-
bered TS required an activation barrier of 16.3 kcal mol−1, while
the cyclization of the sequence N3-Gly-β-Ala-SPh through a
7-membered TS required 25.1 kcal mol−1. Interestingly, the
e
f
Cl
Cl
1
3
2
0
H
H
H
H
57
51
a The yield of 6d in italics was calculated from 1H NMR spectrum
(500 MHz) of the crude mixture.
cyclization of the reversed sequence (N3-β-Ala-Gly-SPh, leading
to 6a) proceeded with a lower activation barrier (ΔG‡
=
14.7 kcal mol−1). The conformational flexibility given to the
aza-ylide nucleophile by the β-Ala residue at the N-terminus of
the azido dipeptide thioester seemed to impact greatly on the
activation barrier. Incorporation of Cα-thioester substituent led to
slight increase of the activation barrier: 15.1 and 20.2 kcal mol−1
for the cyclization of N3-β-Ala-Phe-SPh (leading to 6b) and
for the N3-β-Ala-Aib-Sph (leading to 6c), respectively. The
cyclization of the eight-membered cyclic peptide 5d required
22.0 kcal mol−1
.
The procedure was then applied to the cyclization of azidotri-
peptidoyl thioester 11 for the synthesis of a cyclic 10-membered
tripeptide (12). Cyclotripeptides constitute a very important class
of compounds with high potential in drug rediscovery;12a,13 but
their synthesis using traditional enthalpy-activated carboxylic
acids occurs in low yield and is often accompanied by side-
products.12a Azido tripeptide thioester 11 was prepared accord-
ing to the strategy used for compounds 5a–f. The conditions for
the cyclization of 11 were similar to those used for the cycliza-
tion of 5d–f and gave cyclo(Gly-Phe-β-Ala) 12 in 48% yield
(Scheme 2).
Monocrystals were grown from acetone–methanol mixtures
for compounds 6a and 6c, the structures of which were un-
ambiguously assigned by X-ray diffraction.14 The conformational
behavior of medium-sized cyclic peptides has been rarely
studied in contrast to the decades of research dedicated to
medium-sized cyclic peptides.6f–k,15 We now find that, in cyclic
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thioesters yielding a small library of 7-, 8- and 10-membered
cyclopeptides, which could not be prepared efficiently using the
previously reported methods. A model of reactivity based on
ring size and sequence was drawn by using computational
chemistry. The conformational behavior of cyclodipeptides was
studied by X-ray on the homodiketopiperazine series. The con-
formers obtained by empirical force-field calculations showed
high levels of similarity with the X-ray results. Empirical force-
field calculations were also used to predict the conformational
behavior of diazocanes. Homodiketopiperazines have showed
envelope-like conformational preferences, while diazocanes
prefer chair-like conformations. Work is currently in progress to
expand this Staudinger-mediated cyclization approach to the
synthesis of other medium-sized cyclopeptides.
Scheme 2 Solution phase synthesis of
tripeptide.
a 10-membered cyclic
Notes and references
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powerful strategy towards small cyclic di- and tripeptides that
relies on a Staudinger-mediated ring closure. This was demon-
strated by the successful ring-closure of a series of azido peptide
This journal is © The Royal Society of Chemistry 2012
Org. Biomol. Chem., 2012, 10, 8055–8058 | 8057

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space, μ = 0.101 mm−1, Tmin = 0.6852, Tmax = 0.7462, structure solved
by direct methods and refined against F2 with a Full-matrix least-squares
algorithm using the SHELXL-97 software package, 164 parameters
refined, hydrogen atoms were treated using appropriate riding models,
goodness of fit = 1.039 for observed reflections, final residual values
R1(F) = 0.0353, wR(F2) = 0.0954 for observed reflections. CCDC
881663.
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8058 | Org. Biomol. Chem., 2012, 10, 8055–8058
This journal is © The Royal Society of Chemistry 2012