Improved convergent synthesis of 5'-epi-analogues of muraymycin nucleoside antibiotics

Article abstract of DOI:10.1055/s-0029-1217742

Nucleoside antibiotics represent a promising class of natural products for the development of novel antibacterial agents, with particular respect to structurally simplified analogues maintaining biological activity. There are established truncated 5-epi-d

Full text of DOI:10.1055/s-0029-1217742

LETTER
2503
Improved Convergent Synthesis of 5¢-epi-Analogues of Muraymycin
Nucleoside Antibiotics
I
mprove
d
Synthesi
n
s
of
M
uraym
a
ycin Analo
t
gues ol P. Spork, Stefan Koppermann, Christian Ducho*
Institute of Organic and Biomolecular Chemistry, Department of Chemistry, Georg-August-University Göttingen,
Tammannstr. 2, 37077 Göttingen
Fax +49(551)399660; E-mail: cducho@gwdg.de
Received 8 June 2009
Dedicated to Professor Armin de Meijere on the occasion of his 70th birthday.
Streptomyces sp. as a collection of 19 compounds [e.g.,
muraymycin A1 (1), Figure 1].7 Following initial struc-
ture–activity relationship (SAR) studies using a semisyn-
thetic approach,8a a series of synthetic truncated
Abstract: Nucleoside antibiotics represent a promising class of nat-
ural products for the development of novel antibacterial agents,
with particular respect to structurally simplified analogues main-
taining biological activity. There are established truncated 5¢-epi-
derivatives of muraymycin nucleoside antibiotics with reported an- muraymycin analogues has been described.8b Some of
tibacterial properties, but the lengthy preparation of such com-
pounds is a major hurdle in more detailed structure–activity
these derivatives (e.g., compounds 2–6, Figure 1) were re-
ported to have remarkable activities against Staphylococ-
relationship (SAR) studies. A concise, improved synthesis of trun-
cus aureus and were identified as MraY inhibitors.8b
cated 5¢-epi-muraymycins based on a previously reported approach
However, SAR investigations on such muraymycin ana-
using sulfur ylide chemistry is reported here. The highly convergent
logues led to surprising results: firstly, the absolute con-
figuration at the 5¢-position was required to be R in order
to obtain good activities, that is, only 5¢-epi-analogues
with respect to the 5¢S-configured natural products were
active. Secondly, the presence of some synthetic protect-
ing groups [tert-butyl ester, tert-butyldimethylsilyl
(TBDMS) groups] turned out to be a prerequisite for anti-
bacterial potency. Only the para-methoxybenzyl (PMB)
group at the uracil-N-3 could be omitted without decreas-
ing the biological activity, which was demonstrated by the
pronounced antibacterial activity of muraymycin ana-
logue 6.
nature of this strategy will allow the efficient synthesis of novel mu-
raymycin analogues for thorough SAR investigations.
Key words: antibiotics, medicinal chemistry, MraY inhibitors, nat-
ural products, nucleosides
Due to emerging resistances of bacteria towards estab-
lished antibiotics,1 there is an urgent need to develop nov-
el antibacterial agents, ideally with new or yet unexploited
modes of action.2 One attractive target for new antibiotics
might be the bacterial membrane protein translocase I
(MraY), a key enzyme in the early stages of peptidoglycan
biosynthesis.3–5
The synthesis of 5¢-epi-muraymycin analogues was
reported either via aldol chemistry8b or via opening of an
epoxide. This epoxide, in turn, was prepared stereoselec-
tively from protected uridine 5¢-aldehyde using a sulfur
ylide.9 The reported aldol reaction gave moderate yields
Nucleoside antibiotics represent an interesting class of
natural products with often unusual nucleoside structures
and display inhibitory potency towards MraY.6 Muray-
mycin nucleoside antibiotics have been isolated from a
O
O
R5
NH
N
OR1
HO
O
O
O
R3
R4
O
N
O
N
O
O
O
H
H
N
OR2
O
OH
O
N
NH
N
H
NH
N
H
5'
5'
HO
N
H
H2N
O
O
OH OH
TBDMSO
OTBDMS
HN
O
1
HN
N
H
2 R3 = i-Pr, R4 = H, R5 = PMB
3 R3 = i-Pr, R4 = OH, R5 = PMB
4 R3 = R4 = H, R5 = PMB
H2N
=
NH
5 R3 = H2N(CH2)3, R4 = H, R5 = PMB
6 R3 = i-Pr, R4 = H, R5 = H
O
OH
R1
=
R2
N
NH2
11
OH
O
Figure 1 Naturally occurring nucleoside antibiotic muraymycin A1 (1) and synthetic truncated 5¢-epi-muraymycin analogues 2–6 displaying
antibacterial activity.8b Compound 2 has been chosen as target structure for this study.
SYNLETT 2009, No. 15, pp 2503–2507
x
x
.x
x
.2
0
0
9
Advanced online publication: 27.08.2009
DOI: 10.1055/s-0029-1217742; Art ID: G18709ST
© Georg Thieme Verlag Stuttgart · New York

2504
A. P. Spork et al.
LETTER
and stereoselectivities in our hands, requiring tedious alcohol 9 in nearly quantitative yield (Scheme 2). Howev-
chromatographic separation of the obtained diastereomer- er, this compound was found to be sensitive and instable,
ic mixtures. Hence, the objectives of this study were to and consequently, it had to be prepared freshly prior to
synthesise arbitrarily chosen target compound 2 following sulfur ylide reactions and was directly used without fur-
the sulfur ylide pathway9 and to possibly shorten and sim- ther purification. Employing the established strategy
plify this synthetic route to allow an efficient, convergent, (route A, Scheme 2), aldehyde 13 was reacted with a sul-
and modular access of 5¢-epi-muraymycins. Though the fur ylide generated in situ from sulfonium salt 1413 to give
methodology of the sulfur ylide approach was established, the epoxide 15 with excellent diastereoselectivity (dr >
it had not been applied to the synthesis of 2 before. Here 97:3 as judged by NMR) and good yield (85%). The an-
we describe the synthesis of this compound both via pre- ticipated trans stereochemistry of the epoxide moiety in
1
viously reported transformations9 and employing a signif- 15 could be unambiguously assigned based on H NMR
icantly shortened and improved procedure.
coupling constants, and the absolute configuration of the
two newly formed stereocentres had been determined be-
fore.9 However, further conversion of 15 into a suitable
building block for completion of the synthesis of 2 was
lengthy. After chemoselective oxidation of indoline
amide 15 to the indole amide 16 with DDQ (95% yield),
saponification of the amide moiety furnished an epoxy
carboxylic acid. Due to severe problems to purify this
compound, the crude product obtained from the saponifi-
cation reaction was directly converted into the tert-butyl
ester 17, which could be isolated in 59% yield over two
steps from 16 after chromatography. In summary, protect-
ed uridine derivative 9 could be converted into key inter-
mediate 17 in an overall yield of 47% over five steps via
this route.
Initially, two synthetic building blocks were required
(Scheme 1). In order to avoid an additional step for selec-
tive 5¢-O-trityl protection of the uridine derivative, trisily-
lated uridine 710 (which can be easily prepared from
uridine with TBDMS chloride and imidazole in pyridine
as solvent in quantitative yield) was converted into PMB-
protected derivative 8 in 85% yield. Selective acidic 5¢-O-
desilylation11 then gave the protected uridine building
block 912 (79% yield). For the construction of the peptidic
muraymycin side chain, commercially available mono-
Boc-protected 1,3-diaminopropane 10 was used in a stan-
dard peptide-coupling reaction with N-Cbz-protected L-
leucine to afford 11 in 93% yield, and acidic Boc depro-
tection then furnished the amino-acylated side-chain
building block 12 (99% yield).
This lengthy five-step transformation of 9 into the desired
epoxide 17 was expected to limit the convergence and
modularity of the synthetic strategy. Using a novel ap-
proach, the synthetic sequence could be significantly
shortened as the epoxide-forming reaction was conducted
with a sulfur ylide generated from sulfonium salt 18 (route
B, Scheme 2). This readily prepared tert-butyl ester deriv-
ative,14 which had found application in sulfur ylide chem-
istry before,15 provided efficient direct access to key
intermediate 17 in 79% yield from 13 (78% yield over 2
steps from 9, including only one chromatographic purifi-
cation).16,17 The excellent diastereoselectivity of the sulfur
ylide utilising step (vide supra) was retained, and the iso-
lated epoxide was spectroscopically (NMR) and chro-
matographically (HPLC coinjection) identical with the
material obtained via the reported route described above
(route A, Scheme 2).
For the application of the sulfur ylide route, protected uri-
dine 5¢-aldehyde 138b,12 was required, which could be
readily obtained either by Swern or by IBX oxidation of
O
NH
PMBCl, NaH,
DMF, 0 °C, 12 h
N
O
TBDMSO
O
85%
TBDMSO
OTBDMS
O
7
O
N
NPMB
NPMB
O
TFA, THF, H2O,
0 °C, 8 h
N
O
TBDMSO
HO
O
O
79%
Finally, assembly of the 5¢-epi-muraymycin structure was
accomplished by stereospecific regioselective opening of
epoxide 17 with amine 12 leading to 19 (64% yield,
Scheme 2). In the previous report on the sulfur ylide strat-
egy,9 epoxide opening was performed with derivatives of
1,3-diaminoalkanes in most cases. With respect to a high
convergence of the synthetic route, however, it was de-
sired to avoid additional steps and the late-stage introduc-
tion of the amino acid moiety. Monoaminoacyl 1,3-
diaminopropane 12 was therefore used as a nucleophile
for the reaction with epoxide 17. The diastereo- and regio-
selectivity of this reaction was unambigously proven by
NMR-spectroscopic investigation of isolated product 19.
Target compound 2 was then obtained after hydrogenolyt-
ic Cbz-deprotection of 19 in 95% yield for the final step
TBDMSO
OTBDMS
TBDMSO
OTBDMS
8
9
Cbz-L-Leu-OH,
EDC, HOBt,
CH2Cl2, r.t., 16 h
H2N
NHBoc
NH
O
NHBoc
93%
CbzHN
10
AcCl,
MeOH, EtOAc,
0 °C, 16 h
11
NH
NH
3 Cl
99%
CbzHN
12
O
Scheme 1
Synlett 2009, No. 15, 2503–2507 © Thieme Stuttgart · New York

LETTER
Improved Synthesis of Muraymycin Analogues
2505
O
Cl
S
N
O
N
O
N
O
N
14
NPMB
O
NPMB
O
NPMB
O
14, NaOH,
CH2Cl2, H2O,
0 °C, 2 h
Swern
or
O
O
IBX oxidation
HO
O
N
O
O
O
98%
85%
route A
TBDMSO
OTBDMS
TBDMSO
OTBDMS
TBDMSO
OTBDMS
13
15
9
18, NaH, THF,
r.t., 4 h, then
13, CH2Cl2,
0 °C, 4 h
O
79%
DDQ, benzene,
80 °C, 20 h
Br
S
95%
O
route B
O
18
O
1) LiOH, THF, H2O,
r.t., 10 min
2) t-BuOC(=NH)CCl3,
CH2Cl2, r.t., 4 d
NPMB
O
NPMB
12, DIPEA,
MeOH,
O
O
N
N
O
O
O
65 °C, 6 d
O
N
O
O
64%
59%
(over 2 steps)
TBDMSO
O
OTBDMS
TBDMSO
OTBDMS
17
16
O
NPMB
O
NPMB
O
O
O
O
O
H2, 10% Pd/C,
MeOH, r.t., 3 h
N
N
OH
O
OH
O
NH
N
NH
N
H
95%
CbzHN
H
H2N
O
O
TBDMSO
OTBDMS
TBDMSO
OTBDMS
19
2
Scheme 2
and in an overall yield of 32% over seven linear steps from
uridine.
Table 1 Reaction of Uridine Aldehydes 13 and 20 with Sulfur
Ylides Generated from Different Ester-Derived Sulfonium Salts
The use of different ester-derived sulfonium salts and nu-
cleoside derivatives in the sulfur ylide reaction would pro-
vide rapid access to 5¢-epi-muraymycin analogues with
different ester moieties and nucleoside structures, thus al-
lowing more detailed SAR studies. The scope of the novel
‘direct’ sulfur ylide approach was therefore further inves-
tigated (Table 1). A series of different sulfonium salts14
was used to generate sulfur ylides to be reacted with alde-
hyde 13. Yields varied and were found to be moderate
(e.g., 30% for R = Me, entry 2 in Table 1) to good (e.g.,
80% for R = Et, entry 3). 5¢-epi-Muraymycin analogues
without nucleobase protecting groups such as 6 (Figure 1)
were reported to be bioactive as well,8b and deprotection
of N-3-PMB-protected muraymycin derivatives with
CAN led to complex product mixtures in our hands. We
therefore also investigated the conversion of aldehyde 209
not bearing a nucleobase protecting group with the sulfur
ylide derived from sulfonium salt 18 and obtained the cor-
responding epoxy ester product in good yield (60%, entry
6, Table 1). As described before for epoxide 17, this reac-
tion product was found to be identical to the one synthe-
sised via the established route.18 All sulfur ylide reactions
depicted in Table 1 led to exclusive formation of just one
O
O
R2
O
R2
O
N
N
O
O
Br
S
N
N
R1O
O
R1O
O
O
O
TBDMSO
OTBDMS
13 R2 = PMB
TBDMSO
OTBDMS
20 R2 = H
Entry
Aldehyde R1
Yield of epoxy ester product (%)a
1
2
3
4
5
6
13
13
13
13
13
20
t-Bu
Me
Et
79
30
80
37
53
60
n-Pr
Bn
t-Bu
a Isolated yields in % with preparation of the aldehyde directly prior
to the sulfur ylide reaction.
Synlett 2009, No. 15, 2503–2507 © Thieme Stuttgart · New York

2506
A. P. Spork et al.
LETTER
(10) Hisamatsu, Y.; Hasada, K.; Amano, F.; Tsubota, Y.;
Wasada-Tsutsui, Y.; Shirai, N.; Ikeda, S.; Odashima, K.
Chem. Eur. J. 2006, 12, 7733.
(11) Zhu, X.-F.; Williams, H. J.; Scott, A. I. J. Chem. Soc., Perkin
Trans. 1 2000, 2305.
(12) Synthesis of 9 and 13 involving 5¢-O-dimethoxytrityl
protection: (a) Myers, A. G.; Gin, D. Y.; Widdowson, K. L.
J. Am. Chem. Soc. 1991, 113, 9661. (b) Myers, A. G.; Gin,
D. Y.; Rogers, D. H. J. Am. Chem. Soc. 1994, 116, 4697.
(13) Sarabia, F.; Sánchez-Ruiz, A.; Chammaa, S. Bioorg. Med.
Chem. 2005, 13, 1691.
(14) Synthesis of Ester-Derived Sulfonium Salts
A solution of the respective alkyl bromoacetate in degassed
dimethylsulfide (tert-butyl, n-propyl and benzyl esters) or in
acetone–dimethylsulfide (methyl ester) was stirred at r.t. for
2 d. The precipitated product was subsequently filtered off,
washed with n-hexane or PE, and dried in vacuo. With
exception of the tert-butyl ester derivative, the obtained
sulfonium salts still contained significant amounts of
trimethylsulfonium bromide, but could be used for sulfur
ylide generation in crude form. The ethyl ester derivative
was commercially available.
trans-epoxide diastereomer. The absolute configuration
of the two newly formed stereocentres, which had been in-
directly determined for the products of Table 1, entries 1
and 6 (vide supra), was proposed to be identical through-
out.9
In conclusion, we report an improved synthesis of 5¢-epi-
analogues of muraymycin nucleoside antibiotics using a
novel ‘direct’ sulfur ylide approach. This route bypasses
several steps of the previously reported methodology for
5¢-epi-muraymycin synthesis while retaining its excellent
stereoselectivity, therefore giving rise to a highly conver-
gent strategy. The longest linear sequence from uridine to
a target structure is comprised of seven steps only. The ap-
parent broad scope of the newly established ‘direct’ sulfur
ylide reaction will allow the rapid modular synthesis of
novel muraymycin analogues, which can then be screened
for MraY inhibitor activity.
Acknowledgment
(15) Examples: (a) Jiang, Y.; Ma, D. Tetrahedron: Asymmetry
2002, 13, 1033. (b) Oba, M.; Nishiyama, N.; Nishiyama, K.
Tetrahedron 2005, 61, 8456. (c) Tada, T.; Ishida, Y.; Saigo,
K. J. Org. Chem. 2006, 71, 1633.
(16) Synthesis of Epoxy Ester 17 via ‘Direct’ Sulfur Ylide
Reaction
We thank the Deutsche Forschungsgemeinschaft (DFG, SFB 803
‘Functionality controlled by organization in and between membra-
nes’) and the Fonds der Chemischen Industrie (FCI) for financial
support. Donation of laboratory equipment by the BASF SE is gra-
tefully acknowledged.
A solution of sulfonium salt 18 (430 mg, 1.67 mmol) in dry
THF (10 mL) was stirred over 4 Å MS at r.t. for 2 h to
remove any traces of H2O from the hygroscopic sulfonium
salt. Sodium hydride (60% suspension in mineral oil, 68 mg,
1.7 mmol) was then added at 0 °C, and the mixture was
stirred at r.t. for 4 h. After filtration and evaporation of the
solvent under reduced pressure, the obtained sulfur ylide was
dissolved in dry CH2Cl2 (2 mL). This solution of the sulfur
ylide was added in aliquots (0.5 mL each) at 0 °C over a
period of 4 h to a stirred solution of uridine aldehyde 13 (99
mg, 0.168 mmol, freshly prepared by IBX oxidation of
protected uridine 9 in MeCN) in dry CH2Cl2 (2 mL). After
addition of more CH2Cl2 (25 mL) and H2O (25 mL), the
aqueous layer was extracted with EtOAc (25 mL). The
combined organics were dried over Na2SO4, and the solvent
was evaporated under reduced pressure. The resultant crude
product was purified by column chromatography (PE–
EtOAc, 9:1) to give 17 (93 mg, 79%) as a colourless solid;
mp 71 °C. TLC: Rf = 0.50 (PE–EtOAc, 7:3). [a]D20 +31.6 (c
1.3, CHCl3). 1H NMR (300 MHz, C6D6): d = –0.06 (s, 3 H,
SiCH3), –0.01 (s, 3 H, SiCH3), 0.07 (s, 3 H, SiCH3), 0.09 (s,
3 H, SiCH3), 0.87 [s, 9 H, SiC(CH3)3], 0.93 [s, 9 H,
SiC(CH3)3], 1.33 [s, 9 H, OC(CH3)3], 3.24 (s, 3 H, OCH3),
3.39 (dd, J = 1.3, 1.3 Hz, 1 H, 5¢-H), 3.65 (d, J = 1.3 Hz, 1
H, 6¢-H), 3.97 (dd, J = 4.3, 4.3 Hz, 1 H, 3¢-H), 4.06 (dd,
J = 4.3, 1.3 Hz, 1 H, 4¢-H), 4.10 (dd, J = 4.3, 4.3 Hz, 1 H, 2¢-
H), 5.04 (d, J = 13.3 Hz, 1 H, PMB-CH2-Ha), 5.12 (d,
J = 13.3 Hz, 1 H, PMB-CH2-Hb), 5.46 (d, J = 8.1 Hz, 1 H, 5-
H), 6.10 (d, J = 4.3 Hz, 1 H, 1¢-H), 6.72 (d, J = 8.2 Hz, 2 H,
PMB-3-H, PMB-5-H), 7.42 (d, J = 8.1 Hz, 1 H, 6-H), 7.67
(d, J = 8.2 Hz, 2 H, PMB-2-H, PMB-6-H). 13C NMR (75
MHz, C6D6): d = –5.1 (SiCH3), –4.7 (SiCH3), –4.5 (SiCH3),
–4.5 (SiCH3), 18.2 [SiC(CH3)3], 25.9 [SiC(CH3)3], 26.0
[SiC(CH3)3], 27.8 [OC(CH3)3], 43.7 (PMB-CH2), 51.2 (C-
6¢), 54.6 (OCH3), 56.9 (C-5¢), 73.7 (C-3¢), 75.6 (C-2¢), 78.9
(C-4¢), 82.5 [OC(CH3)3], 89.2 (C-1¢), 102.7 (C-5), 114.0
(PMB-C-3, PMB-C-5), 129.8 (PMB-C-1), 131.5 (PMB-C-2,
PMB-C-6), 136.5 (C-6), 151.4 (C-2), 159.7 (PMB-C-4),
161.8 (C-4), 167.1 (ester C=O). MS (ESI+): m/z = 727.4 [M
References and Notes
(1) Taubes, G. Science 2008, 321, 356.
(2) Walsh, C. Nat. Rev. Microbiol. 2003, 1, 65.
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Med. Chem. 2005, 5, 1221. (b) Bugg, T. D. H.; Lloyd, A. J.;
Roper, D. I. Infect. Disorders Drug Targets 2006, 6, 85.
(4) Initial work on MraY and identification of the mraY gene:
(a) Struve, W. G.; Neuhaus, F. C. Biochem. Biophys. Res.
Commun. 1965, 18, 6. (b) Struve, W. G.; Sinha, R. K.;
Neuhaus, F. C.; Prime, M. S. Biochemistry 1966, 5, 82.
(c) Heydanek, M. G.; Struve, W. G.; Neuhaus, F. C.
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H. K.; Ishino, F.; Matsuhashi, M. J. Bacteriol. 1991, 173,
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180, 6429.
(5) More recent work on MraY including methodology for
activity assays: (a) Bouhss, A.; Mengin-Lecreulx, D.;
Le Beller, D.; van Heijenoort, J. Mol. Microbiol. 1999, 34,
576. (b) Lloyd, A. J.; Brandish, P. E.; Gilbey, A. M.; Bugg,
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Crouvoisier, M.; Blanot, D.; Mengin-Lecreulx, D. J. Biol.
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P.; Bouhss, A.; van Heijernoort, J.; Mengin-Lecreulx, D.;
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Chemother. 2004, 48, 897.
(6) Review: Kimura, K.-I.; Bugg, T. D. H. Nat. Prod. Rep. 2003,
20, 252.
(7) McDonald, L. A.; Barbieri, L. R.; Carter, G. T.; Lenoy, E.;
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Synlett 2009, No. 15, 2503–2507 © Thieme Stuttgart · New York

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Improved Synthesis of Muraymycin Analogues
2507
+ Na]+. HRMS (ESI+): m/z calcd. for C35H56N2O9Si2:
sulfur ylide from 18 was applied, epoxy ester 17 could also
be obtained, though in lower yield (60%).
(18) Aldehyde 20 was also converted into the respective epoxy
ester product using transformations according to route A in
Scheme 2 as reported previously.9
705.3597 [M + H]+; found: 705.3597 [M + H]+. IR (KBr):
n = 2932, 1671, 1514, 1456, 1392, 1250, 1162, 839, 778 cm–1.
UV (MeCN): lmax (lg e) = 194 (4.69), 222 (4.13), 262
(3.96).
(17) When a procedure similar to the one used for the synthesis
of 15 via route A (Scheme 2) with in situ generation of the
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