Synthesis of coumermycin A1

Article abstract of DOI:10.1016/S0040-4039(02)02487-5

A concise synthesis of the antibiotic coumermycin A₁, a natural product isolated from streptomyces, was achieved. In a key step, a selectively protected noviose sugar was prepared from novobiocin through a transglycosylation reaction with aceto

Full text of DOI:10.1016/S0040-4039(02)02487-5

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 44 (2003) 61–63
Synthesis of coumermycin A1
Steven H. Olson* and Llnon H. Slossberg
Department of Medicinal Chemistry, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA
Received 21 October 2002; accepted 6 November 2002
Abstract—A concise synthesis of the antibiotic coumermycin A1, a natural product isolated from streptomyces, was achieved. In
a key step, a selectively protected noviose sugar was prepared from novobiocin through a transglycosylation reaction with acetone.
© 2002 Elsevier Science Ltd. All rights reserved.
Coumermycin A1 (1) and novobiocin (2) are potent
antibiotics isolated from Streptomyces1 that bind
reversibly and with high affinity to the amino-terminal
24K subdomain of the B subunit of bacterial DNA
gyrase (GyrB).2 This enzyme catalyzes the negative
supercoiling of closed-circular DNA and is essential for
bacterial replication and transcription. Coumermycin is
nearly dimeric, and equilibrium binding and gel filtra-
tion studies have established that it binds to 2 equiv. of
the GyrB protein.2 As expected, novobiocin binds with
a 1:1 stoichiometry.2 Lately, interest in GyrB inhibitors
has been renewed due to reports that coumermycin and
novobiocin are active against methicillin-resistant spe-
cies of staphylococci strains.3
ing targets make it a very useful tool6 for understanding
gene expression both in cell cultures and in vivo.
A prior synthesis of coumermycin was reported in 1966
by chemists at Hoffman–La Roche,7 but the route was
lengthy, and details of their work such as reagents and
yields were never published. To support our biological
efforts to control gene signaling, we wished to develop
an efficient synthesis of coumermycin A1. In developing
our synthetic plan, we decided to leave amide bond
construction until the final step to allow rapid prepara-
tion of coumermycin analogs in which the 3-methyl-
1H-pyrrole-2,4-dicarboxylic acid linking group could
be replaced with other dicarboxylic acids.8
Recent work at the University of Washington and
Merck has shown that coumermycin can mediate signal
transduction pathways by promoting the dimerization
of fusion proteins containing GyrB covalently bound to
a transcriptional protein.4,5 For example, coumermycin-
induced dimerization of a chimeric protein containing
GyrB linked to the Raf-1 serine/threonine kinase acti-
vated components of the MAP kinase cascade.5
Coumermycin’s pharmacokinetics, low toxicity in ani-
mal models, and lack of high-affinity eukaryotic bind-
The most readily available source of the noviose sugar
in coumermycin is novobiocin (Sigma). Initially, we
tried to directly convert novobiocin into coumermycin
by cleaving the benzamide and exchanging the carba-
mate at the C-3% position of the noviose sugar with
5-methyl-1H-pyrrole-2-carboxylate. This would give the
desired PNC-amine 10. Unfortunately, this approach
was plagued by poor yields and an inability to selec-
tively differentiate the C-2% and C-3% alcohols of the
noviose.9 Ultimately, we decided to cleave the glyco-
Keywords: coumermycin; noviose.
* Corresponding author. Tel.: (732)594-4831; fax: (732)594-9545; e-mail: steven olson@merck.com
–
0040-4039/03/$ - see front matter © 2002 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(02)02487-5

62
S. H. Olson, L. H. Slossberg / Tetrahedron Letters 44 (2003) 61–63
sidic linkage and protect C-2% by linking the protecting
group to the anomeric alcohol.
We surveyed a number of glycosylation reactions
between the noviose and various coumarin fragments,
and the most efficient was a Mitsunobu reaction
between 6 and 714 using the procedure of Laurin et al.
(Scheme 2).14 As expected, proton NMR studies
showed that the ratio of anomers in the noviose was
inversely related to the ratio of a- and b-glycoside
products. Nonpolar solvents favored the b-alcohol
and, thus, the desired a-glycoside. The diphenylmethyl
ether protecting group proved optimal, because it
ensured that the coumarin would be soluble in methyl-
ene chloride. After separating the isomers (a:b=3:1),
the desired product 8 was isolated in 49% yield. The
diphenylmethyl ether was cleaved by hydrogenolysis to
provide the enolic b-keto lactone 9. Installation of the
C-3 amine at an earlier stage of the synthesis hindered
the glycosylation, therefore, it was introduced on the
fully elaborated system by treatment of 9 with dia-
zobenzene. PNC-amine, 10, was prepared by a sodium
dithionate reduction of the diazotized intermediate
(Scheme 2).
Preparation of the noviose sugar is outlined in Scheme
1. An acid-catalyzed transglycosylation of 2 with acetone
provided the suitably protected noviose acetonide 3.10
With C-2% and C-3% reliably differentiated, the carbamate
was hydrolyzed with lithium hydroxide to give 4. The C-3%
hydroxyl proved to be extremely hindered, and acylation
proceeded very slowly. Ethyl 5-methyl-1H-pyrrole-2-car-
boxylate was easily prepared by the method of Curran11
and converted to the corresponding anhydride.12
Acylation of 4 with 5-methyl-1H-pyrrole-2-carboxylic
anhydride proceeded in good yield in the presence of
tributyl phosphine.13 The nucleophilicity and low basicity
of the tributyl phosphine made it an ideal catalyst for this
transformation. More basic catalysts, particularly pyri-
dine derivatives, were significantly inferior. Finally, the
acetonide in 5 was rapidly removed with wet tri-
fluoroacetic acid.
Scheme 1. Reagents and conditions: (a) acetone, p-toluenesulfonic acid, 60°C; (b) LiOH, THF, H2O, rt, 40°C; (c) 5-methyl-1H-
pyrrole-2-carboxylic anhydride, Bu3P, CH2Cl2, rt, 3 days; (d) trifluoroacetic acid, CH2Cl2, H2O, rt.
Scheme 2. Reagents and conditions: (a) DEAD, PPh3, CH2Cl2, rt; (b) H2, Pd/C, THF, MeOH; (c) aniline, NaNO2, NaOAc,
HCl(aq), MeOH, THF; (d) Na2S2O4, NaOAc, EtOH, H2O, THF; (e) 3-methyl-1H-pyrrole-2,4-dicarboxylic acid, O-(7-azabenzo-
triazol-1-yl)-N,N,N%,N%-tetramethyluronium hexafluorophosphate (HATU), 4-methylmorpholine, DMF, Ar.

S. H. Olson, L. H. Slossberg / Tetrahedron Letters 44 (2003) 61–63
63
Finally, coumermycin A1 was prepared from 3-methyl-
1H-pyrrole-2,4-dicarboxylic acid,15 2 equiv. of 9, and
HATU under oxygen-free conditions. The product was
purified by reverse-phase HPLC and was identical to
natural coumermycin (Sigma) by NMR, HPLC, mass
spectroscopy, and biological activity.
7. Berger, J.; Schocher, A. J.; Batcho, A. D.; Pecherer, B.;
Keller, O.; Maricq, J.; Karr, A. E.; Vaterlaus, B. P.;
Furlenmeier, A.; Speigelberg, H. Antimicrob. Agents
Chemother. 1966, 778.
8. Unpublished results.
9. Acyl and silyl group migration between the C-2% and C-3%
alcohols was a complicating factor.
10. All compounds were purified by silica gel chromatogra-
phy and characterized by NMR and mass spectroscopy.
11. Curran, T. P.; Keaney, M. T. J. Org. Chem. 1996, 61,
9068.
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