Synthesis of the C1-C5 and C6-C24 fragments of the RNA polymerase inhibitors ripostatin A and B

Article abstract of DOI:10.1055/s-2006-926263

The enantioselective synthesis of the C1-C5 and C6-C24 fragments of the ripostatins utilize a Negishi coupling, two Nagao acetate aldol reactions followed by a Denmark vinylogous aldol reaction and Stille couplings as key C-C bond forming steps. Georg Thi

Full text of DOI:10.1055/s-2006-926263

LETTER
419
Synthesis of the C1–C5 and C6–C24 Fragments of the RNA Polymerase
Inhibitors Ripostatin A and B
Synthesis of the
C
h
1–C5 and
C
r
6–C24
F
i
ragmen
s
ts of Ripo
t
statin
o
A and
B
f Kujat, Martin Bock, Andreas Kirschning*
Institut für Organische Chemie, Universität Hannover, Schneiderberg 1b, 30167 Hannover, Germany
E-mail: andreas.kirschning@uni-hannover.de
Received 14 November 2005
to note as ripostatins are now regarded to be good lead
structures for new antibiotics.2 So far, no partial or total
synthesis of any of the ripostatins has been reported. Due
to the highly attractive biological properties of the ri-
postatins, we initiated a synthetic research program,
which ultimately should yield derivatives, which are more
potent than the parent natural product.
Abstract: The enantioselective synthesis of the C1–C5 and C6–
C24 fragments of the ripostatins utilize a Negishi coupling, two
Nagao acetate aldol reactions followed by a Denmark vinylogous
aldol reaction and Stille couplings as key C–C bond forming steps.
Key words: natural product synthesis, antibiotics, RNA poly-
merase inhibitors, vinylogous aldol reaction, Nagao aldol reaction
vinylogous Mukaiyama
In 1995 ripostatin A, B and C were isolated from
Sorangium cellulosum, strain So ce 377 by Höfle and
Reichenbach.1 Ripostatin A and B (Figure 1) show activ-
ity against Gram-positive bacteria (e.g. Staphylococcus
aureus) by inhibiting the eubacterial RNA polymerase,
which is essential for bacterial growth. RNA polymerase
is a very attractive biological target for antibiotics as cur-
rently only one drug, namely rifampin, is in clinical use
that targets RNA polymerase.
aldol reaction
RCM
O
O
COOH
O
OH
Negishi
coupling
esterification
OR OR
OR
O
+
HO
OR
fragment C
fragment D
O
O
COOH
O
OH
OR OR
O
OTBS
OEt
+
Ripostatin A (1a)
X
fragment A
fragment B
(R)
Scheme 1 Retrosynthetic analysis
HO
O
(S)
COOH
O
We reckoned that the particular synthetic challenge of the
ripostatins is associated with the stereochemically well
defined deconjugated olefinic double bonds in association
with two C=O bonds from the carboxylic moieties in the
eastern half. This setup of p bonds should be prone to
isomerisation of positions as well as stereochemistry
under basic as well as acidic conditions. In addition,
ripostatin A was found to undergo elimination as the
lactone ester group is an ideal leaving group.1 These con-
siderations were taken into account for the retrosynthetic
analysis. Key steps of the planned synthesis are an esteri-
fication thus coupling fragments C and D followed by
ring-closing metathesis, which should yield the macrolac-
tone (Scheme 1). Fragment C is planned to be synthesized
from fragment A via a vinylogous aldol reaction. The
aromatic subunit is introduced by carbalumination of an
alkyne and subsequent Negishi coupling starting from
benzyl bromide.
(R)
OH
Ripostatin B (1b)
Figure 1 Structures of ripostatin A and B
Other known natural products, which inhibit this bacterial
enzyme are sorangicin A, streptolydigin, thiolutin, holo-
mycin and corallopyronin. Most importantly it was shown
that no cross-resistance between ripostatin A and rifampin
exists.2 Obviously, ripostatin A binds to a different loca-
tion on the protein than rifampin. This aspect is important
SYNLETT 2006, No. 3, pp 0419–0422
Advanced online publication: 06.02.2006
DOI: 10.1055/s-2006-926263; Art ID: G34605ST
© Georg Thieme Verlag Stuttgart · New York
1
5.
0
2.
2
0
0
6

420
C. Kujat et al.
LETTER
d–f
a–c
OH
O
I
OTBS
89%
80%
OEt
a
2
TBSO
OPiv
3
46%
HO
O
S
O
g
OH
O
OPiv
N
S
6
OTBS
82%
4
5
8 (dr = 93:7)
TBSO
OPiv
b–d
e, f
S
h–m
49%
O
OAc
O
60%
N
S
48%
TBDPSO
TBDPSO
OPiv
OTBS
OH
6 (resembles fragment A)
7a
OTBS
S
O
9
10 (resembles fragment C)
N
S
7b
Me
O
OTBS
OEt
g
N
O
Scheme 2 Reagents and conditions: a) TBSCl, imidazole, DMF;
b) Me3Al (3 equiv), H2O (0.8 equiv), Cp2ZrCl2 (0.4 equiv), CH2Cl2,
–23 °C, 4 h; c) I2, THF; d) PhCH2ZnBr, 5% Pd(PPh3)4, THF–DMF
(2:1); e) TBAF, THF; f) Dess–Martin periodinane, CH2Cl2; g) 7a,
Sn(OTf)2, 1-ethyl piperidine, CH2Cl2; h) TBSOTf, 2,6-lutidine,
CH2Cl2; i) DIBAL-H, toluene; j) 7b, Sn(OTf)2, 1-ethyl piperidine,
CH2Cl2; k) MeONHMe·HCl, AlMe3, CH2Cl2; l) Piv-Cl, 4-DMAP,
pyridine, CH2Cl2, 3 d, r.t.; m) DIBAL-H, THF, –78 °C.
P
N
N
(CH2)5
2
76%
OEt
Me
11
12
Scheme 3 Reagents and conditions: a) (R,R)-12, DIPEA, SiCl4,
CH2Cl2, 11, TBAI, 4 d, –40 °C (dr = 93:7); b) TBDPSCl, imidazole,
4-DMAP, DMF, r.t., 3 d; c) DIBAL-H, THF, –78 °C to –50 °C; d)
AcCl, 2,4,6-collidine, 0 °C; e) Bu3Sn(vinyl), cat. Pd2(dba)3, LiCl,
DMF, 60 °C, 16 h; f) DIBAL-H, CH2Cl2, –78 °C to –50 °C; g)
TBSCl, LDA, HMPA, THF.
The synthesis of the major fragment C via fragment A
starts from alkinol 2 which was transformed into vinylio-
dide 3 by carbalumination3 followed by iodination of the
intermediate vinyl anion (Scheme 2). Negishi coupling
and functional group manipulation yielded aldehyde 4,
which was sequentially subjected to two Nagao acetate al-
dol reactions.4 As protecting group for the second aldol-
derived alcohol we chose the pivaloate ester. This second
aldol product was further transformed into aldehyde 6 (re-
sembles fragment A) via the Weinreb amide. In the fol-
lowing, aldehyde 6 was converted into triene 10
(resembles fragment C) after employing the Denmark
variant of the asymmetric vinylogous Mukaiyama
reaction5–7 followed by transforming the ethyl ester 88 into
allyl acetate 9, which was vinylated by a Stille-type cross
coupling reaction. Finally, the pivaloate protection was
removed under reducing conditions to yield fragment C9
(Scheme 3).
O
OH
a, b
c, d
Cl3C
O
OBn
84%
82%
13
14
O
RO
OBn
15 R = TCE
16 R = H
e (74%)
fragment D
Scheme 4 Reagents and conditions: a) BnBr, NaH, THF; b) BuLi,
Troc-Cl, THF; c) LiI, AcOH; d) Bu3Sn(allyl), Pd(PPh3)4, benzene;
e) Zn, AcOH, THF.
In addition, fragment D was prepared from alkinol 13,
which was converted into trichloroethylester 14. Iodina-
tion according to a protocol by Lu et al.10 afforded the Z
alkene which was coupled with allyl stannane under Stille
conditions to yield diene 15. Finally, fragment D 168 was
collected after reductive removal of the trichloroethyl
(TCE) protection (Scheme 4).
Esterification of fragment 10 and 16 has turned out to be
a challenge so far, because of the sterically demanding
protecting groups in the close neighbourhood. Additional-
ly, building block 16 is prone to double bond iso-
merization and migration under basic conditions. Work is
in progress to complete the total synthesis of 1a,b and
derivatives in order to establish structure–activity
relationships.
In conclusion, we prepared key fragments 10 and 16 for
the convergent synthesis of ripostatins. Our synthetic
approach includes several Pd-catalyzed cross-coupling
reactions as well as the efficient use of the Nagao acetate
aldol reaction and Denmark vinylogous aldol reaction.
Acknowledgment
The work was supported by the Fonds der Chemischen Industrie.
We thank Solvay Pharmaceutical Research Laboratories, Hanno-
ver, for the donation of chemicals.
Synlett 2006, No. 3, 419–422 © Thieme Stuttgart · New York

LETTER
Synthesis of the C1–C5 and C6–C24 Fragments of Ripostatin A and B
421
(8) Analytical Data for Compounds 8 and 16:
References and Notes
Compound 8: Aldehyde 6 (17 mg, 36 mmol) was dissolved
in CH2Cl2 (0.3 mL) under nitrogen. Bisphosphoramide
(R,R)-12 (3 mg, 3.5 mmol), TBAI (5 mg, 13.5 mmol) and
DIPEA (5 mL, 30 mmol) were added and the solution was
cooled to –78 °C. Then, 1 M SiCl4 in CH2Cl2 (100 mL, 100
mmol) was added. Ketene acetal 11 (50 mL, 0.2 mmol) was
added dropwise. The solution was stirred at –40 °C for 4 d
and then poured into a rapidly stirring 1:1 sat. aq KF–
KH2PO4 (1.0 M) solution (10 mL). This biphasic mixture
was stirred vigorously for 2 h at r.t. The aqueous phase was
extracted several times with CH2Cl2. The combined organic
phases were dried with MgSO4, concentrated in vacuo and
purified by flash column chromatography (PE–EtOAc, 10:1
to 7:1) to yield aldol product 8 (10 mg, 16.6 mmol, 46%
yield). [a]D20 –13.0 (c 1,CHCl3). 1H NMR (400 MHz,
CDCl3, TMS = 0 ppm): d = 0.02 (s, 3 H, TBS), 0.03 (s, 3 H,
TBS), 0.88 (s, 9 H, TBS), 1.18 (s, 9 H, Piv), 1.27 (t, J = 7.2
Hz, 3 H, OEt), 1.52–1.84 (m, 6 H, H-6, H-8, H-10), 1.71 (d,
J = 0.8 Hz, 3 H, H-19), 1.96–2.12 (m, 2 H, H-11), 2.17 (d,
J = 1.0 Hz, 3 H, H-20), 2.22 (dd, J = 13.3, 8.2 Hz, 1 H, H-4),
2.33 (dd, J = 13.3, 4.1 Hz, 1 H, H¢-4), 3.35 (d, J = 7.1 Hz, 2
H, H-14), 3.70 (m, 1 H, H-9), 3.86 (dddd, J = 12.3, 8.2, 4.1,
4.1 Hz, 1 H, H-5), 4.14 (q, J = 7.2 Hz, 2 H, OEt), 5.01 (m, 1
H, H-7), 5.35 (tq, J = 7.1, 0.8 Hz, 1 H, H-13), 5.71 (d, J = 1.0
Hz, 1 H, H-2), 7.14–7.21 (m, 3 H, Ph), 7.24–7.31 (m, 2 H,
Ph) ppm. 13C NMR (100 MHz, CDCl3, CDCl3 = 77 ppm):
d = –4.7, –4.1, 14.2, 16.3, 18.0, 18.8, 25.9, 27.1, 34.2, 34.7,
36.4, 38.8, 42.3, 42.9, 49.0, 59.6, 66.8, 68.8, 69.8, 118.4,
123.1, 125.7, 2 × 128.3, 135.9, 141.6, 155.9, 166.4, 178.4
ppm. HRMS: m/z calcd for C35H59O6Si [M + H]+: 603.4081;
found: 603.4110.
Compound 16: Allyl tributyltin (2.65 mL, 8 mmol, 1.1
equiv) and Pd(PPh3)4 (356 mg, 0.3 mmol, 0.04 equiv) were
added to a solution of crude vinyliodide (3.24 g, 7.0 mmol,
1 equiv) in benzene (70 mL) and stirred overnight at 70 °C.
After cooling to r.t. acetone (10 mL) and a sat. KF solution
(20 mL) were added and stirring was continued for
additional 2 h. The precipitate was removed by filtration
through CeliteTM and the filtrate was washed with sat. NH4Cl
solution. Drying (MgSO4), evaporation and flash column
chromatograpghy (PE–EtOAc, 25:1) yielded diene 15 (2.40
g, 6.3 mmol, 90%).
This trichloroethyl ester 15 (43 mg, 0.11 mmol) was
dissolved in glacial AcOH (5 mL). Zinc (75 mg, 1.14 mmol)
and H2O (2 drops) were added and the resulting suspension
was sonicated for 30 min. After stirring for 3 d at 60 °C the
suspension was cooled to r.t., filtered through a pad of
CeliteTM and washed several times with MTBE. The solvent
was removed and the crude product was azeotropically dried
several times with toluene. Acid 16 was obtained after flash
column chromatography (PE–EtOAc, 4:1) in 73% yield (20
mg, 0.08 mmol). 1H NMR (400 MHz, CDCl3, CDCl3 = 7.26
ppm): d = 2.50 (dt, J = 0.9, 6.6 Hz, 2 H, CH2CH2), 3.45 (d,
J = 6.7 Hz, 2 H, CCH2CH), 3.64 (t, J = 6.6 Hz, 2 H,
CH2OBn), 4.51 (s, 2 H, CH2Ar), 5.07 (dd, J = 1.6, 10.1 Hz,
1 H, CHtransHcisCH), 5.11 (dd, J = 1.6, 17.1 Hz, 1 H,
CHtransHcisCH), 5.78 (br s, 1 H, CHCO2), 5.81 (tdd, J = 6.8,
10.2, 17.0 Hz, 1 H, CHtransHcisCH), 7.27–7.39 (m, 5 H, Ar)
ppm. 13C NMR (100 MHz, CDCl3, CDCl3 = 77.0 ppm):
d = 36.9, 38.0, 67.7, 73.0, 2 × 116.8, 2 × 127.7, 128.4, 134.6,
138.0, 160.5, 171.1 ppm. HRMS: m/z calcd for C15H18O3
[M – H]–: 245.1178; found: 245.1176.
(1) (a) Irschik, H.; Augustiniak, H.; Gerth, K.; Höfle, G.;
Reichenbach, H. J. Antibiot. 1995, 48, 787.
(b) Augustiniak, H.; Irschik, H.; Reichenbach, H.; Höfle, G.
Liebigs Ann. 1996, 1657.
(2) O’Neill, A.; Oliva, B.; Storey, C.; Hoyle, A.; Fishwick, C.;
Chopra, I. Antimicrob. Agents Chemother. 2000, 44, 3163.
(3) Wipf, P.; Lim, S. Angew. Chem. 1993, 105, 1095.
(4) (a) Nagao, Y.; Hagiwara, Y.; Kumagai, T.; Ochiai, M. J.
Org. Chem. 1986, 51, 2391. (b) Nagao, Y.; Hagiwara, Y.;
Kumagai, T.; Ochiai, M. J. Org. Chem. 1986, 51, 2391.
(5) Denmark, S. E.; Beutner, G. L. J. Am. Chem. Soc. 2003, 125,
7800.
(6) The pivaloate protection was beneficial for high diastereo-
selectivity (dr = 93:7). In contrast, the corresponding TBS-
protected aldehyde gave the vinylogous aldol product in
only 4:1 dr.
(7) (a) The configuration of the newly formed stereogenic center
was further proven for acetonide 17 according to
Rychnovsky et al. Acetonide 17 was prepared after DIBAL-
H reduction of 8 followed by protection of the 1,3-diol
moiety (Figure 2). See: Rychnovsky, S. D.; Rogers, B. N.;
Richardson, T. I. Acc. Chem. Res. 1998, 31, 9.
HO
O
20.1 ppm
O
98.4 ppm
30.3 ppm
OTBS
17
Figure 2
(b) Experimental Procedure.
DIBAL-H (50 mL, 1 M) in hexane (0.05 mmol) was added to
a stirred solution of ethyl ester 8 (3 mg, 0.005 mmol) in abs.
CH2Cl2 (1 mL) at –78 °C. After 20 min sat. Na,K-tartrate
solution (5 mL) was added and stirred rapidly at r.t. for 1 h.
The aqueous phase was extracted several times with CH2Cl2.
The combined organic phases were dried with MgSO4 and
concentrated in vacuo to yield 2.5 mg of the triol which was
used without further purification for the next step.
The crude product was dissolved in 2,2-dimethoxypropane
(1 mL) and PPTS (1 mg, 4 mmol) was added. After stirring
for 1 h at r.t. aq phosphate buffer solution (pH = 7, 5 mL) was
added. The aqueous phase was extracted several times with
CH2Cl2. The combined organic phases were dried with
MgSO4, concentrated in vacuo and purified by flash
chromatography (PE–EtOAc, 10:1 to 2:1) to yield acetonide
17 (1 mg, 2 mmol, 40% yield). 1H NMR (400 MHz, CDCl3):
d = 0.04 (s, 3 H, TBS), 0.05 (s, 3 H, TBS), 0.88 (s, 9 H,
TBS), 1.25 (s, 3 H, H-20), 1.35 (s, 3 H, H-22), 1.42 (s, 3 H,
H-23), 1.42–1.73 (m, 6 H, H-6, H-8, H-10), 1.70 (s, 3 H, H-
19), 2.00–2.05 (m, 2 H, H-11), 2.07 (dd, J = 13.7, 6.3 Hz, 1
H, H-4), 2.26 (dd, J = 13.7, 6.3 Hz, 1 H, H-4), 3.35 (d,
J = 7.3 Hz, 2 H, H-14), 3.88–4.01 (m, 3 H, H-5, H-7, H-9),
4.16 (d, J = 6.8 Hz, 1 H, H-1), 4.17 (d, J = 6.8 Hz, 1 H, H-1),
5.33 (t, J = 7.3 Hz, 1 H, H-13), 5.45 (t, J = 6.8 Hz, 1 H, H-
2), 7.14–7.20 (m, 3 H, Ph), 7.23–7.30 (m, 2 H, Ph) ppm. 13
C
NMR (100 MHz, CDCl3): d = –4.5, –4.0, 16.3, 16.9, 18.1,
20.1, 25.9, 30.3, 34.1, 34.3, 36.5, 37.5, 44.3, 46.3, 59.3, 65.7,
67.4, 68.1, 98.4, 123.1, 125.7, 125.8, 2 × 128.3, 136.0, 136.4,
141.7 ppm.
Synlett 2006, No. 3, 419–422 © Thieme Stuttgart · New York

422
C. Kujat et al.
LETTER
(9) Analytical Data for Compound 10.
J = 17.0, 10.2, 6.7 Hz, 1 H, 2-H), 7.14–7.21 (m, 3 H, Ph),
7.23–7.32 (m, 2 H, Ph), 7.32–7.45 (m, 6 H, TBDPS), 7.66–
7.76 (m, 4 H, TBDPS) ppm. 13C NMR (100 MHz, CDCl3,
CDCl3 = 77 ppm): d = –4.6, –4.4, 15.7, 16.2, 18.1, 19.2,
25.9, 26.9, 32.2, 34.2, 35.4, 35.6, 43.2, 44.8, 48.2, 66.7, 70.2,
72.0, 114.3, 123.0, 124.8, 125.7, 127.4, 127.7, 2 × 128.3,
129.5, 129.8, 132.9, 133.5, 134.2, 135.9, 136.0, 136.1,
137.0, 141.7 ppm. HRMS: m/z calcd for C46H67O3Si2 [M –
H]–: 723.4629; found: 723.4622.
[a]D20 –7.3 (c 0.4, CHCl3). 1H NMR (400 MHz, CDCl3,
TMS = 0 ppm): d = 0.07 (s, 3 H, TBS), 0.09 (s, 3 H, TBS),
0.90 (s, 9 H, TBS), 1.03 (s, 9 H, TBDPS), 1.15 (d, J = 0.8 Hz,
3 H, 22-H), 1.43–1.50 (m, 2 H, 12-H), 1.53–1.68 (m, 4 H, 8-
H, 10-H), 1.70 (s, 3 H, 21-H), 1.94–2.16 (m, 4 H, 6-H, 13-
H), 2.60 (t, J = 6.7 Hz, 2 H, 3-H), 3.35 (d, J = 7.2 Hz, 2 H,
16-H), 3.50 (s, 1 H, OH), 3.90–4.02 (m, 2 H, 7-H, 11-H),
4.07 (m, 1 H, 9-H), 4.88 (dd, J = 10.2, 1.7 Hz, 1 H, 1-H),
4.91 (dd, J = 17.0, 1.7 Hz, 1 H, 1-H¢), 5.02 (tq, J = 6.7, 0.8
Hz, 1 H, 4-H), 5.33 (t, J = 7.2 Hz, 1 H, 15-H), 5.68 (ddt,
(10) Ma, S.; Lu, X. J. Chem. Soc., Chem. Commun. 1990, 1643.
Synlett 2006, No. 3, 419–422 © Thieme Stuttgart · New York