Cyclic carbo-isosteric depsipeptides and peptides as a novel class of peptidomimetics

Article abstract of DOI:10.1021/ol5003797

A novel and highly efficient cyclization method has been developed to access a new class of cyclic carbo-isosteric depsipeptides and carbo-isosteric peptides. Our strategy requires easily accessible C-terminal methyl ketone ester or amide functionalized l

Full text of DOI:10.1021/ol5003797

Letter
pubs.acs.org/OrgLett
Cyclic Carbo-Isosteric Depsipeptides and Peptides as a Novel Class of
Peptidomimetics
Stephanie M. Gueret,* Peter Meier, and Hans-Jorg Roth
́
́
̈
Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Novartis International AG, Postfach, CH-4002 Basel,
Switzerland
S
* Supporting Information
ABSTRACT: A novel and highly efficient cyclization method has
been developed to access a new class of cyclic carbo-isosteric
depsipeptides and carbo-isosteric peptides. Our strategy requires
easily accessible C-terminal methyl ketone ester or amide
functionalized linear precursors as starting materials. The well-
known reductive amination has then been used to afford cyclic
tetra- to octa-pseudopeptides via a selective intramolecular
formation of a glycine peptidomimetic unit under moderate dilution.
ver the years, both academic groups and the
pharmaceutical industry have extended their research
Scheme 1. Attempted Prior-Capture/Ring Contraction
Strategy Giving Rise to Cyclic Pseudopeptide via a Novel
Glycine Peptidomimetic Motif
O
toward peptide chemistry.1 Peptides with their high modularity
and potential diversity give rise to a high likelihood for strong
affinity for a broad range of biological targets. Consequently,
they have become interesting candidates for the development
of novel drug-like molecules.2 However, only a few of them
have reached the market due to their poor bioavailability and
lack of permeability and metabolic stability. Multiple factors are
known to improve the pharmacological properties of peptidic
drugs such as N-methylation,3,4 glycosylation,5 and the use of D-
amino-acids and CPP transporters.6 Head-to-tail cyclization of
peptides7−9 has additionally been performed to increase their in
vivo stability and proteolysis resistance.10,11 Another major
strategy is the use of pseudopeptidic motifs12,13 which mimic
the secondary structure of peptides and can modulate their
bioavailability.14,15 As a state of the art option, cyclic
peptidomimetics16 represent a very interesting and powerful
combination to access highly potent compounds with improved
pharmacokinetic properties.17
knowledge, never been reported in the literature to afford
cyclic pseudopeptides. Compared to the native cyclic peptide
scaffold 6, the obtained motif 5 displays the same number of
ring atoms with the methyl being a replacement for the
carbonyl unit and would presumably mimic the glycine amino
acid structure. Additionally, the resulting cyclic lactone 5
resembles the depsipeptide family consisting of a cyclic peptidic
structure containing a lactone unit. We therefore propose
herein to name our new peptidomimetic family, “carbo-
isosteric” depsipeptides (Scheme 1).
It is important to state that interesting syntheses of
depsipeptides have been reported in the literature.20,21 This
compound class exhibits remarkable biological activity (e.g.,
anticancer22,23 and antimicrobial24) and is widely investigated
for therapeutic applications. In general, the cyclic depsipeptides
have mainly been found in natural environments. For example,
Jaspamidine25 isolated from the indo-pacific sponge displays
cytotoxic, antifungal, and insecticidal activities. Petriellin A
With the aim of developing new methods to access
macrocyclic molecules, we focused on the possible modification
of the Tam ligation.18,19 Using a linear peptide functionalized
with a C-terminal methyl ketone ester 1, we first expected to
perform a head-to-tail cyclization via a reversible hemiaminal 2
formation which could then undergo a ring contraction to
afford, after spontaneous elimination, a native cyclic peptide 3
(Scheme 1). A wide range of conditions were studied.
Unfortunately, the ring contracted product 3 was never
observed and only the starting material 1 was detected. To
understand the lack of detectable product resulting from the
hemiaminal/ring contraction strategy, sodium cyanoboro-
hydride was added to the reaction mixture leading to the
formation of a cyclic amine in 100% conversion. Surprisingly,
only the monomeric product 5 was formed without
oligomerization. Even though the reductive amination is a
well-known transformation, it has, to the best of our
Received: February 5, 2014
Published: February 26, 2014
© 2014 American Chemical Society
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isolated from the organic extracts of a fungus, Petriella sordida,
also shows antifungal activity.26 In accordance, our first
disclosed carbo-isosteric depsipeptide family could represent a
valuable starting point for the development of new drug-like
molecules.
Table 2. Cyclic Carbo-Isosteric Depsipeptides 16a−f Using
Optimized Reductive Amination Conditions27
Encouraged by the above-mentioned observations and the
interest in the cyclic depsipeptide class of peptidomimetics, we
decided to apply this novel methodology to the synthesis of
various ring size carbo-isosteric depsipeptides. First, the methyl
ketone motif was introduced in linear peptides (Table 1).
Table 1. Synthesis of Methyl Ketone Ester Linear Peptidic
Precursors 14 and 15a−f
a
b
Final concentration in mM at step 3. Isolated yield over 3 steps after
c
preparative RP-HPLC. dr determined by RP-UPLC-MS or chiral-
HPLC analysis. For structures see Figure 1.
d
a
b
SM used in step 1 unless otherwise stated. Isolated yield over 2 steps
c
after preparative RP-HPLC. Complete racemization observed (dr
50:50 determined by RP-UPLC-MS analysis). Hydroxyacetone
d
(3 equiv), EDC·HCl (1.2 equiv), DMAP (0.3 equiv), DCM, 0 °C
e
to rt, o/n. Optimized conditions: 8 or 9a−c (2.5 equiv), HCTU (1.45
equiv), 2,6-lutidine (2.5 equiv), DCM/DMF 1:1, 0 °C to rt, o/n;
racemization was not observed using RP-UPLC-MS analysis.
Commercially available hydroxyacetone 8 was directly reacted
with linear peptide 10 using EDC·HCl and DMAP to give
product 14 as a 50:50 mixture of epimers at the C-terminal
leucine (entry 1). Using other coupling conditions did not
allow the formation of the desired product. Alternatively, N-
Boc-protected phenylalanine 7a was esterified without race-
mization using alcohol 8 and EDC·HCl and DMAP (entry 2).
The resulting phenylalanine 9a was then treated with hydrogen
chloride and coupled to peptide 10 using HCTU to afford
precursor 15a without observable epimerization. In a similar
fashion, compound 8 was reacted with N-Boc-protected alanine
7b and glycine 7c and introduced into tetrapeptide 10 to give
compounds 15b and 15c (entries 3 and 4).
To enhanced the ring closure study, linear peptides 11−13
were reacted with methyl ketone ester amino-acids 9a and 9b
to afford functionalized hepta-, tetra- and tripeptides 15d−f
(entries 5−7).
Our attention next focused on the use of our cyclization
method to afford various ring size carbo-isosteric depsipeptides
(Table 2 and Figure 1). After extensive experimentation, we
found the optimal conditions for the ring closing reductive
Figure 1. Structure of the obtained cyclic carbo-isosteric depsipeptides
and carbo-isosteric peptides.
amination to be 1% acetic acid in DMF followed by addition of
sodium cyanoborohydride and 25% MeOH onto the imine
intermediate. The desired monomeric cyclic hexapeptidomi-
metic 16a was successfully isolated in 74% yield (entry 1). It is
noteworthy that the cyclization was performed at relatively high
concentration (c = 8 mM) with respect to reported peptide
cyclizations. Even when the concentration was increased to
50 mM, the cyclic dimer was detected in only 21% conversion
and the desired cyclic monomer 16a was observed with 79%
conversion and isolated in 51% yield after purification by
preparative RP-HPLC (entry 2). Variation of the C-terminal
amino acid from phenylalanine to alanine or glycine did not
noticeably influence the yield of the cyclization (entries 1, 3,
and 4).
By increasing the linear precursor length to eight units, the
intramolecular reductive amination allowed the selective
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formation of cyclic carbo-isosteric octa-depsipeptide 16d in
good yield (entry 5). However, the lysine backbone amino acid
was protected to avoid side chain backbone cyclization.
Alternatively, the azide protecting group for lysine residue
would be compatible with our system.
Table 3. Synthesis of the Methyl Ketone Amide Linear
Peptidic Precursors 20a,b,e,f
By decreasing the ring size, constrained cyclic penta-
pseudopeptide 16e was successfully isolated in 85% yield.
From a more challenging aspect and knowing the difficulty in
accessing cyclic tetra-peptides using conventional amide bond
formation methods, we studied the feasibility of our concept to
access cyclic tetra-depsipeptide carbo-isosteres with the expect-
ation that the reversible prior-capture step of imine formation
could ease such difficult cyclizations. To our delight, cycle 16f
was obtained in an acceptable isolated yield of 40% without
observable oligomerization.
a
Optimized conditions: peptide (1 equiv), 19a or 19b (1 equiv),
As expected when the N-terminal amino acid differs from a
glycine unit, a slight induction toward one diastereoisomer was
achieved during the reduction of the imine intermediate
(entries 5 and 7). Remarkably for cyclic carbo-isosteric penta-
depsipeptide 16e containing a N-terminal phenylalanine, a
81:19 diastereoisomeric ratio was observed (entry 6). In the
case of cyclic pseudopeptides 16b, 16d, and 16e, each
diastereoisomer was successfully separated by preparative
chiral-HPLC or RP-HPLC (see Supporting Information).
However the absolute configuration could not be established
due to the lack of relevant NOE correlations.
HATU (1.45 equiv), 2,6-lutidine (1.22 equiv), DCM/DMF (3:1),
0 °C to rt, o/n. Isolated yield over 2 steps after preparative RP-
HPLC; racemization was not detected using RP-UPLC-MS analysis.
b
Table 4. Extension of Our Method to the Synthesis of Cyclic
Carbo-Isosteric Peptides 21a,b,e,f27
The last part of our study aimed to enrich our cyclic
pseudopeptidic family by expanding the lactone unit to a lactam
group to increase the pool of peptidomimetic scaffolds. We
focused our feasibility study on four selected lactone analogues.
Starting with the synthesis of the methyl ketone amide motif,
N-Boc-protected phenylalanine 7a and alanine 7b were coupled
with commercially available amino-alcohol 17 to give alcohols
18a and 18b, respectively. Subsequent Dess-Martin periodinane
oxidation afforded the amide methyl ketones 19a28 and 19b29
in good yield (Scheme 2).
a
b
Isolated yield over 3 steps after preparative RP-HPLC. dr
c
determined by chiral-HPLC analysis. See Figure 1 for structures.
d
Desired monomeric product was not observed; cyclic dimer was
isolated in 16% yield as a complex mixture of four diastereoisomers.
Scheme 2. Synthesis of the Methyl Ketone Amide
Functionalized Amino Acids 19a and 19b
yield with a 88:12 diastereoisomeric ratio, and the two
diastereoisomers were isolated by preparative chiral-HPLC
(entry 3). In analogy to its carbo-isosteric depsipeptide
analogue 16e, a similar yield and diastereoisomeric ratio were
obtained.
Unfortunately, highly challenging cyclic tetra-pseudopeptide
21f could not be obtained and only the dimer (cyclic octa-
peptidomimetic) was isolated in 16% yield (entry 4).
Alternative methods, conditions, and different sequences for
the ring closing reductive amination of cyclic carbo-isosteric
tetra-peptides will have to be studied in the future. However, as
a preliminary remark, the replacement of the lactone by a
lactam decreases the ring flexibility which in the case of a cyclic
tetramer is extremely critical and does not give rise to the
desired cyclic monomer.
To further demonstrate the impact of our cyclization
method, the synthesis of a native cyclic hexapeptide cyclo[-
GGFLAG-], an analogue of the obtained pseudopeptide 21b,
was attempted by cyclization of a linear peptide Boc-GGFLAG-
OH using standard coupling reagents with a concentration of
1 mM. By using PyOxP,30 the ring closure was achieved in only
4% yield. The maximum yield was obtained using the HATU/
HOAt system, but in that case, even at 1 mM the cyclic peptide
could only be isolated in 35% yield. In contrast, its carbo-
After Boc deprotection of precursors 19a and 19b and using
the optimal coupling conditions (see Table 1), the free amine
unfortunately self-reacted with the ketone to form as the major
product the corresponding methylpyrazinone after rearrange-
ment. After extensive experimentation, HATU and 2,6-lutidine
with a 1:1 acid/amine ratio gave the desired methyl ketone
amide linear peptides 20a,b,e,f in good yields without
epimerization and only traces of the unwanted side product
(Table 3, entries 1−4).
Finally, the ring closing reductive amination was performed
with the methyl ketone amide analogues using the previously
optimized conditions. Cyclic carbo-isosteric hexa-peptides
containing either phenylalanine 21a or alanine 21b as C-
terminal amino acids were isolated in 70% and 54% yield
respectively (Table 4, entries 1 and 2). The constrained cyclic
penta-lactam 21e was also successfully obtained in excellent
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isosteric peptide analogue 21b was successfully isolated in 54%
yield at 8 mM (entry 2).
To conclude, we have developed a powerful method to
access novel cyclic peptidomimetics. Our strategy affords cyclic
carbo-isosteric penta- to octa-depsipeptides and peptides in
high yields under moderate dilution. Importantly, a constrained
cyclic lactone tetra-pseudopeptide was successfully isolated in
good yield. In our study, N-Boc-protected linear peptides were
arbitrarily chosen. However, the precursors could be replaced
by Fmoc protected linear peptides without affecting the efficacy
of our reductive amination cyclization strategy. From a
structural aspect, the resulting α-methyl secondary amine
provides an interesting chemical handle to diversify the
obtained cyclic peptidomimetic structure. Future work will
investigate the scope and limitation of our strategy. Computa-
tional and NMR conformational studies will be performed to
understand the rules that govern the intramolecular selectivity
and diastereoselectivity of our novel methodology. Their
potential biological applications will additionally be inves-
tigated.
ASSOCIATED CONTENT
■
S
* Supporting Information
Experimental procedures and characterization data for all
compounds. Analytical RP-UPLC-MS profiles for 14 and
reaction mixtures of 16a at c = 8 and 50 mM. Complete
analytical RP-UPLC-MS profiles for the synthesis of cyclic
carbo-isosteric depsipeptide 16e. Analytical RP-UPLC-MS or
analytical chiral-HPLC profiles for the final cyclic peptidomi-
(18) Liu, C. F.; Tam, J. P. J. Am. Chem. Soc. 1994, 116, 4149−4153.
(19) Tam, J. P.; Miao, Z. W. J. Am. Chem. Soc. 1999, 121, 9013−
9022.
(20) Nguyen, M. M.; Ong, N.; Suggs, L. Org. Biomol. Chem. 2013, 11,
1167−1170.
(21) Rajesh, B. M.; Iqbal, J. Curr. Pharm. Biotechnol. 2006, 7, 247−
259.
1
metic products (16a,b,d,e,f and 21b,e). Copies of H and 13C
NMR spectra for the precursors and the cyclic peptidomimetic
compounds. This material is available free of charge via the
Internet at http://pubs.acs.org.
(22) Ghosh, A. K.; Xu, C. X. Org. Lett. 2009, 11, 1963−1966.
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Beilstein J. Org. Chem. 2012, 8, 1344−1351.
AUTHOR INFORMATION
■
Corresponding Author
(25) Zabriskie, T. M.; Klocke, J. A.; Ireland, C. M.; Marcus, A. H.;
Molinski, T. F.; Faulkner, D. J.; Xu, C. F.; Clardy, J. C. J. Am. Chem.
Soc. 1986, 108, 3123−3124.
*E-mail: stephanie.gueret@novartis.com; stephanie.gueret@
gmail.com.
(26) Sleebs, M. M.; Scanlon, D.; Karas, J.; Maharani, R.; Hughes, A.
B. J. Org. Chem. 2011, 76, 6686−6693.
Notes
(27) It is worth noting that even if the RP-HPLC isolated yields are
moderate for some cyclic peptidomimetic, cyclic dimers or side
products were never observed. LC-MS analysis of the reaction mixture
after the required reaction time showed 100% conversion to the
desired cyclic monomer peptidomimetic unless otherwise noted.
(28) Adam, I.; Orain, D.; Meier, P. Synlett 2004, 2031−2033.
(29) Bogevig, A.; Pastor, I. M.; Adolfsson, H. Chem.Eur. J. 2004,
10, 294−302.
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
The authors acknowledge Dr. Felix Thommen and Urs
Rindisbacher (Global Discovery Chemistry, NIBR, Novartis,
Basel) for the RP-HPLC purification and Nicole Battaglia
(Global Discovery Chemistry, NIBR, Novartis, Basel) for the
synthesis of 18a. We are also grateful to Dr. Eric Francotte, Dan
Huynh, and Paul Richert (Global Discovery Chemistry, NIBR,
Novartis, Basel) for the chiral-HPLC analysis and purification.
Finally, the authors thank the Novartis Education Office for
funding of a Presidential Postdoctoral Fellow (PostDoc
fellowship granted to S.M.G.).
(30) Subiros-Funosas, R.; El-Faham, A.; Albericio, F. Org. Biomol.
Chem. 2010, 8, 3665−3673.
REFERENCES
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