Total synthesis of pacidamycin D by Cu(I)-Catalyzed oxy enamide formation

Article abstract of DOI:10.1021/ol202124b

The first total synthesis of pacidamycin D, which is expected to be a good candidate as an antibacterial agent against P. aeruginosa, is described. The key elements of our approach feature an efficient and stereocontrolled construction of the Z-oxyvinyl iodide and copper-catalyzed crosscoupling with the tetrapeptide carboxamide.

Full text of DOI:10.1021/ol202124b

ORGANIC
LETTERS
2011
Vol. 13, No. 19
5240–5243
Total Synthesis of Pacidamycin D by
Cu(I)-Catalyzed Oxy Enamide Formation
Kazuya Okamoto,† Masahiro Sakagami,† Fei Feng,†, Hiroko Togame,†
Hiroshi Takemoto,† Satoshi Ichikawa,*,‡ and Akira Matsuda*,‡
Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11
Kita-ku, Sapporo 001-0021, Japan, and Faculty of Pharmaceutical Sciences,
Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
ichikawa@pharm.hokudai.ac.jp; matuda@pharm.hokudai.ac.jp
Received August 5, 2011
ABSTRACT
The first total synthesis of pacidamycin D, which is expected to be a good candidate as an antibacterial agent against P. aeruginosa, is described.
The key elements of our approach feature an efficient and stereocontrolled construction of the Z-oxyvinyl iodide and copper-catalyzed cross-
coupling with the tetrapeptide carboxamide.
Uridylpeptide antibiotics are nucleoside natural pro-
ducts sharing a common structural feature, namely, a
30-deoxyuridine with an enamide linkage at the 50-position
that is attached to a tetrapeptide moiety via a central R,β-
diaminobutyric acid that connects the N-terminal amino
acid, the ureadipeptide, and the 30-deoxyuridine moieties
(Figure 1).1,2 Among the class of uridylpeptide antibiotics,
the pacidamycins (1),3 isolated from the fermentation
broth of the Streptomyces coeruleorubiduns strain, showed
potent and selective antibacterial activity against strains
of Pseudomonas (MIC 1.5ꢀ12.5 μg/mL). The biological
target of the pacidamycins is believed to be phospho-
MurNAc-pentapeptide transferase (MraY),4,5 which is
responsibleforthe formation of lipid Iinthe peptidoglycan
biosynthesis pathway.6ꢀ9 Since MraY is an essential en-
zyme in bacteria,1,2 it is a potential target for the
† Shionogi & Co., Ltd.
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‡ Hokkaido University.
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mother. 1993, 37, 980–983.
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Targets 2006, 6, 85–106. (b) Kimura, K.; Bugg, T. D. H. Nat. Prod. Rep.
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J. Mol. Microbiol. 1999, 34, 576–585.
(8) Bouhss, A.; Trunkfield, A. E.; Bugg, T. D.; Mengin-Lecreulx, D.
FEMS Microbiol. Rev. 2008, 32, 208–33.
Present address: Faculty of Advanced Life Sciense, Hokkaido Univer-
sity, Kita-21, Nishi-11, Kita-ku, Sapporo 001-0021, Japan.
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r
10.1021/ol202124b
Published on Web 09/08/2011
2011 American Chemical Society

development of general antibacterial agents. Conse-
quently, uridylpeptide antibiotics which have a novel
mode of action are expected to be good candidates as
antibacterial agents effective against P. aeruginosa.
Scheme 1. Retrosynthetic Analysis of Pacidamycin D
tetrapeptide carboxamide 3. The tetrapeptide carboxa-
mide 3 contains a number of potentially reactive functional
groups that render selective synthetic modification diffi-
cult. We first planned to remove the allylic 30-hydroxyl
group at the uridine moiety by Barton deoxygenation after
the cross-coupling.
Preparation of the tetrapeptide is described in Scheme 2.
The carboxylic acid 520 and the pentafluorophenyl (Pfp)
ester of the unsymmetrical urea 721 were prepared as
previously described. Deprotection of the Boc group of 5
and the subsequent condensation of the liberated amine 6
with 7 gave the tripeptide 8. NꢀO Bond breakage was
achieved by catalytic hydrogenation, and the resulting
secondary amine 9 (quant. over three steps from 5) was
further reacted with the Pfp ester of N-Boc-L-Ala 10 to
afford the tetrapeptide carboxylic acid 11 in 69% yield.
Finally, the carboxyl group of 11 was converted to the
carboxamide (HATU, NH4Cl, NMM, DMF) to give 3 in
82% yield.
The Z-oxyvinyl ioide 4 was prepared as shown in
Scheme 3. After protecting group manipulation of the
uridine derivative 1222 (BOMCl, DBU, DMF, 99%,
TFAꢀTHFꢀH2O, 0 °C, 83%), the primary alcohol of
14 was converted to the iodide (I2, PPh3, pyridine, dioxane,
99%). Elimination of HI from 15 was promoted by DBU
to afford the exo-olefin 1623 in 93% yield. Previously, vinyl
halide derivatives of nucleoside were generally prepared
from an exo-olefin derivative by a rather lengthy conver-
sion, where the terminal hydrogen atom was substituted
sequentially with a phenylthio, a tributylstannyl, and an
Figure 1. Structure of uridylpeptide natural products.
Despite extensive efforts to prepare analogues of the
uridylpeptide antibiotics, including 1,10ꢀ16 no total synth-
esis has yet been accomplished. The difficulty in the
chemical synthesis 1 involves the Z-oxyenamide moiety,
which is chemically labile and therefore a challenging
chemical structure to construct. Moreover, analogues
having the enamide functionality have been prepared
only by semisynthesis from natural sources17 and by
biosynthesis.18 Herein we describe the first total synthesis
ofpacidamycinD (1). Scheme 1 highlightsthe key elements
of our retrosynthetic approach to the synthesis of 1, which
features an efficient and stereocontrolled construction of
the Z-oxyvinyl iodide 4 and a copper-catalyzed cross-
coupling19 of the iodide 4 with the highly functionalized
ꢀ
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Org. Lett., Vol. 13, No. 19, 2011
5241

Scheme 2. Preparation of the Tetrapeptide Carboxamide 3
Scheme 3. Initial Attempt to Synthesize 1
iodo group.24 Extensive efforts to obtain 4 directly from 16
revealed that the use of the iodonium dicollidinium
triflate25,26 (IDCT) was indeed effective. The desired
Z-vinyl iodide 4 was obtained in 79% yield as the sole
product when 16 was treated with 1.0 equiv of IDCT in
CH2Cl2 at room temperature. The geometry of the olefin
was confirmed by a 500 MHz NOE experiment in CDCl3,
where the correlation to H-30 was observed upon irradia-
tion at H-50 (7.2%).
Then, the key coupling of 4 with the tetrapeptide
carboxamide 3 was investigated. First, the iodide 4 was
reacted with 3 under the following conditions: 0.2 equiv of
CuI, 0.4 equiv of MeNHCH2CH2NHMe (A), Cs2CO3,
THF, 70 °C.27,28 However, a large amount of the iodide
remained unreacted, and only a trace amount of the
desired 17 was obtained. On the other hand, the tetrapep-
tide 3 was consumed, and cyclic products such as 18 were
obtained from the reaction mixture indicated by MS
analysis although not fully confirmed. In general, the
copper-mediated CꢀN cross-coupling reaction proceeds
through initial formation of the nitrogenꢀcopper complex
followed by an oxidative insertion into the halide and then
reductive elimination.29 It is presumed that if the oxida-
tive insertion is slow, the nitrogen atom, activated by
formation of the carboxamideꢀcopper(I) complex, reacts
with the tert-Bu ester at the C-terminus to form the cyclic
product 18. In order to suppress the approach of the
nitrogen atom to the tert-Bu ester, we increased the size
ofthe ligand coordinating tothe copper atom using ligands
such as B. As expected, the use of the ligand resulted in an
increased yield (32%). The yield of 17 was improved up
to 86% by increasing the catalyst loading (0.8 equiv). Of
note is the highly selective reaction at the N-unsubstituted
carboxamide moiety in spite of the presence of a number
of potential reactive sites, including the primary amide, the
carbamate, and the urea groups.
Next, a selective deoxygenation of the allylic 30-hydroxyl
group on the model cyclic thiocarbonate 2030 was then
investigated (Scheme 4). Thus, TBS groups of 19 were
removed (TBAF, THF, 99%), and the resulting diol was
reacted with phenyl chlorothionocarbonate to afford the
cyclic thiocarbonate 20 in 75% yield. However, exposure
of 20 to either Bu3SnH and AIBN in toluene at reflux or
Bu3SnH and V-7031 in CH2Cl2 at room temperature led to
a complex mixture of products, and the desired deoxyge-
nated compound 21 was not isolated.
Since the model study in Scheme 4 suggested that the
late stage deoxygenation of the 30-hydroxyl group may be
difficult, the total synthesis of 1 was pursued with the
30-deoxyvinyliodide 27(Scheme 5). Asin the synthesisof 4,
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ꢀ
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(30) The model compound 19 was prepared in 89% yield in a similar
manner to the synthesis of 17 from 4 and the corresponding dipeptide
carboxamide.
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Org. Lett., Vol. 13, No. 19, 2011

Scheme 4. Attempt of Deoxygenation with Model Com-
pound 20
Scheme 5. Total Synthesis of 1
the exo-olefin 26, which was obtained from 22,2 was
treated with IDTC in CH2Cl2. However a significant
amount of E-exo-olefin (10% yield) and endo-olefin
(39%) were also produced in addition to the desired
Z-exo-olefin 27(28%). The observed decrease in selectivity
could be attributed to the absence of the substituted
hydroxyl group at the 30-position. The yield of 27 was
improved up to 53% by conducting the reaction in MeCN
at ꢀ20 °C although the effect of solvent on the selectivity
remains unclear. The iodide 27 and the tetrapeptide 3 were
coupled using the optimized conditions (0.8 equiv of CuI,
1.6 equiv of ligand B, Cs2CO3, THF, 70 °C) to afford the
fully protected pacidamycin D 28 in 82% yield. Finally,
deprotection of the BOM, Cbz, and tert-Bu groups (BCl3,
potential epimerization, this approach provided ready
access to a range of uridylpeptide antibiotics and their
analogs simply by altering the tetrapeptide moiety. Results
of further studies will be forthcoming.
CH2Cl2, ꢀ78 °C) and the TBS group (5HF NEt3, 30%
3
over two steps) successfully afforded pacidamycin D (1).
Analytical data for the synthetic compound were in good
agreement with those reported for the natural material.3d
Preliminary biological evaluation indicated that 1 showed
potent inhibitory activity (IC50 22 nM) against isolated
MraY from S. aureus and antibacterial activity selectively
against a range of P. aeruginosa strains (MIC 16 μg/mL for
P. aeruginosa ATCC 25619 and P. aeruginosa SR 27156
and 64 μg/mL for P. aeruginosa PAO1, respectively).
In conclusion, the first total synthesis of pacidamycin D
(1) has been accomplished. By virtue of the assemblage, via
cross-coupling, of the Z-oxyvinylhalide 27 and the tetra-
peptide 3 at a late stage in the synthesis, and despite the
challengesthisimposes becauseofthe inherentlability with
Acknowledgment. We thank Mr. Kouichi Uotani
(Medicinal Research Laboratories, Shionogi & Co., Ltd.)
for evaluating the antibacterial activities and Ms. Fumiyo
Takahashi (Shionogi Innovation Center for Drug Discov-
ery, Shionogi & Co., Ltd) for evaluating the MraY inhibi-
tory activity.
Supporting Information Available. Full experimental
procedures and characterization data for all new com-
pounds are available. This material is available free of
charge via the Internet at http://pubs.acs.org.
Org. Lett., Vol. 13, No. 19, 2011
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