Professional Documents
Culture Documents
odyssey
William Erb
*
a
and Jieping Zhu
*
b
Covering: 1975 to 2012
The rst members of the tiacumicin family of antibiotics, encompassing more than 40 compounds, were
isolated in 1975. Structurally, the core aglycon is an 18-membered macrolactone having two conjugated
diene units, one isolated double bond, 5 stereogenic centers and most often, at least one glycosidic
linkage. Tiacumicin B, a RNA synthesis inhibitor, is a narrow-spectrum antibiotic against clostridia. For
the treatment of Clostridium dicile infection (CDI), it has the same cure rate as vancomycin but with
lower relapse rate and was approved by the FDA in May 2011. The aim of this review is to present an
overview of the chemistry and biology of tiacumicins since their discovery.
1 Introduction
2 Isolation and characterization
2.1 Lipiarmycin from Actinoplanes deccanensis
2.2 Clostomicins from Micromonospora echinospora
2.3 Tiacumicins from Dactylosporangium aurantiacum
2.4 Lipiarmycin from Catellatospora
3 Biosynthesis
4 Biological activity
4.1 Biological activity
4.2 Mechanism of action
5 SAR studies
6 Synthesis
6.1 Homodichloro-orsellinic acid
6.2 2-O-Methyl-b-D-rhamnose
6.3 5-Methyl-b-rhamnose
7 Clinical application
8 Summary and outlook
9 Acknowledgements
10 References
1 Introduction
Microbial diversity represents an almost innite pool for the
discovery of novel compounds. There are more than 23 000
known microbial secondary metabolites, close to 60% of them
produced by bacteria, and their usefulness in drug development
is well established.
14
Actinomycetes are among the most morphologically diverse
prokaryotes and are widely distributed all around the Earth.
5,6
They arouse the attention of the scientic community due to the
great diversity and biological activities associated with the cor-
responding metabolites: antimicrobial, antifungal, immuno-
suppressive, antitumor, etc. Compounds such as erythromycin,
streptomycin, amphotericin B and rapamycin, all sold as drugs,
came from such strains,
7,8
and they are still considered as a
promising source of new antibiotics.
912
In 1975, Parenti and co-workers identied a new substance,
lipiarmycin, which exhibited a strong activity against gram-
positive bacteria from actinoplanaceae strains (a sub-class of
Actinomycetes). A few years later, related compounds were
isolated from parent strains and were named clostomicin and
tiacumicin. This eld remained broadly unexplored until the
late 90s when Optimer Pharmaceuticals began the commercial
development of one tiacumicin for the treatment of Clos-
tridium dicile infection (CDI). C. dicile is an important
nosocomial pathogen frequently diagnosed in infectious
hospital-acquired diarrhoeas whose cost is estimated from
433797 million dollars annually in the USA.
13
The research in
this eld turned out to be highly rewarding since tiacumicin B
has recently been approved by the FDA for the treatment of C.
dicile infection. The aim of this review is to present an
overview of the chemistry and biology of tiacumicin
compounds and their application to the treatment of C. dicile
associated infection.
1418
2 Isolation and characterization
2.1 Lipiarmycin from Actinoplanes deccanensis
In the 1970s, Parenti and co-workers reported the isolation of a
novel antibiotic from a new strain, isolated from a soil sample
collected in India, named Actinoplanes deccanensis ATCC
a
Laboratoire de Chimie Organique, ESPCI, 10 rue Vauquelin, 75231, Paris Cedex 05,
France. E-mail: w.erb@exchem.fr
b
Institut of Chemical Sciences and Engineering,
Ecole Polytechniques Federale de
Lausanne, EPFL-SB-ISIC-LSPN, CH-1015 Lausanne, Switzerland. E-mail: jieping.
zhu@ep.ch
Cite this: Nat. Prod. Rep., 2013, 30,
161
Received 24th July 2012
DOI: 10.1039/c2np20080e
www.rsc.org/npr
This journal is The Royal Society of Chemistry 2013 Nat. Prod. Rep., 2013, 30, 161174 | 161
NPR
REVIEW
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21983.
1921
Growth of the soil extract on agar led to the forma-
tion of sporangia that liberated spores by rupture of the wall
(Fig. 1). The major compound isolated from this strain was
named lipiarmycin, from leap year, because the strain was
isolated on February 29th 1972.
Initial analysis of lipiarmycin revealed the presence of two
chlorine atoms, at least one phenolic hydroxyl group, three
carbonyls (one saturated and two conjugated to double bonds),
a probable sugar moiety, and an aromatic nucleus, which was
determined to be homodichloro-orsellinic acid by degradation
studies.
A few years later, scientists from Gruppo Lepetit reported the
isolation of 2-O-methyl-4-O-homodichloroorsellinate-b-rham-
noside upon acid methanolysis of lipiarmycin.
22
This sugar was
also found in other natural antibiotics with either an a- or b-
glycosidic linkage.
2325
They also identied the second sugar in
lipiarmycin as 5-methyl-b-rhamnose. Note that the absolute
congurations of both sugars have not been established and
were shown articially in their L form.
Finally, in 1987, Nasini and co-workers reported that the
lipiarmycin known at that time was a mixture of two products,
lipiarmycin A3 (1) and A4 (2), in a 3 : 1 ratio, separable by
ash chromatography.
26
Chemical degradation and extensive
NMR studies allowed them to elucidate the structure of the
two lipiarmycins (Fig. 2). These molecules feature a 18-
membered macrolactone incorporating four stereogenic
centers (unkown conguration), two conjugated dienes and
one tri-substituted double bond. The macrolactone is glyco-
sylated by 2-O-methyl-b-D-rhamnose esteried in the 4th
position either by homodichloro-orsellinic acid (lipiarmycin
A3) or dichloro-orsellinic acid (lipiarmycin A4). The second
sugar link to the macrolactone is 4-O-isobutyrate-5-methyl-b-
rhamnose, whose absolute conguration was not determined
but shown as D form.
One year later, two novel lipiarmycins were isolated from the
same strain:
27
lipiarmycins B3 (3) and B4 (4), which dier from
the corresponding A3 and A4 by the position of the isobutyric
ester on the 2-O-methyl-b-D-rhamnose moiety (position 2
0 0
for
lipiarmycin B and 4
0 0
for A). Lipiarmycins B3 and B4 dier
through the substituent (methyl or ethyl) of the aromatic ring.
Fig. 1 Sporangium obtained on soil extract-agar. Magnication 800. Fig. 2 The structure of lipiarmycins.
William Erb studied chemistry
at the University of Paris-Sud XI.
He received his PhD in organic
chemistry under the guidance of
Pr. Jieping Zhu (Institut de Chi-
mie des Substances Naturelles)
in 2010. He then joined the
group of Pr. Varinder Aggarwal
at the University of Bristol,
working on organocatalysis and
its application to the synthesis of
natural products. He is currently
Attache Temporaire dEnseigne-
ment et de Recherche in the group of Janine Cossy in Paris, working
on total synthesis and metal-catalyzed reactions.
Jieping Zhu received his B. Sc
from Hangzhou Normal Univer-
sity and his M.Sc. degree from
Lanzhou University (P. R. China)
under the guidance of Professor
Li Yulin. He got his Ph.D. degree
from University Paris XI, France
under the supervision of
Professor H.-P. Husson and Pr. J.
C. Quirion. Aer 18 months
post-doctoral stay with Professor
Sir D. H. R. Barton at Texas A &
M University in USA, he joined
in the Institut de Chimie des Substances Naturelles, CNRS,
France as Charge de Recherche and was promoted to Director of
Research 2nd class in 2000 and then 1st class in 2006. He moved to
Ecole Polytechnique Federale de Lausanne (Swiss Federal Institute
of Technology Lausanne), Switzerland in September 2010 as a full
professor.
162 | Nat. Prod. Rep., 2013, 30, 161174 This journal is The Royal Society of Chemistry 2013
NPR Review
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2.2 Clostomicins from Micromonospora echinospora
In 1985,
~
Omura and co-workers isolated a strain of Micro-
monospora echinospora from a soil sample collected in a rice
eld in Japan.
28,29
Based on taxonomic studies, it appeared that
it was a new strain, subsequently named Micromonospora echi-
nospora subsp. armeniaca subsp. nov. KMR-593.
Fermentation yielded ve compounds: clostomicins A (5),
B1, B2 (6), C (7) and D (8). NMR studies revealed that closto-
micin B1 was identical to lipiarmycin A3 previously isolated and
that the dierence between clostomicins A and B2 resided in
the substitution pattern of the 5-methyl-b-rhamnose sugar: the
isobutyric ester substituent was proposed to be in the C
3
0 0
position for clostomicin A and in the C
2
0 0
for clostomicin B2.
Therefore it was concluded that the structure of clostomicin B2
is identical to lipiarmycin B3.
The IR spectrum of clostomicins C and D showed the pres-
ence of an additional carbonyl group compared to lipiarmycin
A3, which was attributed to a ketone at the C
18
position. The
13
C
NMR spectra of clostomicin C also reveals the absence of one
methyl carbon at 28.6 ppm assigned to the equatorial methyl
group of the 5-methyl-b-rhamnose sugar. Therefore, the struc-
ture of clostomicins C and D was assigned as shown in Fig. 3.
2.3 Tiacumicins from Dactylosporangium aurantiacum
In 1986, McAlpine and co-workers reported a newstrain isolated
from a soil sample collected in Connecticut, which was named
Dactylosporangium aurantiacum subsp. hamdenensis subsp. nov.
AB718C-41 (NRRL 18085).
3032
A rst fermentation experiment
using 20 litres of broth yielded three compounds named tia-
cumicins A (9), B (10) and C (11) (10 mg, 35 mg and 24 mg,
respectively). A second study using a much bigger broth (4500
litres) led to the isolation of three additional tiacumicins (D
(12), E (13) and F (14)) in very low yields (7 mg, 20 mg and 13 mg,
respectively) compared to tiacumicin B (3.82 g).
Extensive NMR studies allowed scientists to propose the
structure of tiacumicin B, which was found to be identical to
lipiarmycin A3 and clostomicin B1. Tiacumicins C and F are
dierent from tiacumicin B in the position of the isobutyric
ester on the 5-methyl-b-rhamnose moiety (respectively at C
2
0 0
and C
3
0 0 ). Tiacumicin D is another isomer of tiacumicin B in
which the 2-O-methyl-b-D-rhamnose is esteried in the C
3
0
position by homodichloro-orsellinic acid (Fig. 4). Tiacumicin E
is almost identical to tiacumicin C except for the ester moiety on
position C
2
0 0 , which is not an isobutyric ester but a propionate
one. Finally, tiacumicin A is a simpler analog without the 2-O-
methyl-b-D-rhamnose moiety and with an acetate ester on the 5-
methyl-b-rhamnose sugar. Note that although described with
the right conguration (2R, 3S, 4S, 5S, 6R) in the text, the 2-O-
methyl-b-D-rhamnose was written as its enantiomer in the nal
structure of tiacumicins.
31
The absolute conguration of the macrolactone was
assigned in 2005 by X-ray crystal structure analysis of tiacumicin
B. It was subsequently established that C
18
has the (R) cong-
uration for tiacumicin B and (S) conguration for lipiarmycin
A4.
33,34
Even though we cannot conclude denitively, it could be
assumed the conguration of C
18
to be (R) for other tiacumicins
and (S) for lipiarmycins. The C
18
conguration remained
unassigned for clostomicins.
Therefore, without taking into account the C
18
congura-
tion, lipiarmycin A3, clostomicin B1 and tiacumicin B seem to
be identical. So are lipiarmycin B3, clostomicin B2 and tiacu-
micin C or clostomicin A and tiacumicin F.
In the late 90s, with the aim of producing novel tiacumicin
analogs, McAlpine and co-workers replaced the potassium
chloride added to the broth with potassium bromide.
35,36
Using
the same Dactylosporangium aurantiacum strain as before, they
isolated four new compounds (Fig. 5, 1518) incorporating
bromide on the aromatic ring, whose structure have been
elucidated by mass spectroscopy and NMR studies.
In 2007, scientists from Optimer Pharmaceuticals, Inc.
reported seven new members of tiacumicin family (Fig. 6, 19
25), present in very low concentration in the fermentation
broth, as judged by the HPLC prole of the mixture and the
corresponding integrations (Fig. 6).
37,38
During formulation
studies, Optimer scientists also identied the new tiacumicin
derivative 26. It is identical to tiacumicn B except for the pres-
ence of carbonyl function at C
7
.
39
Although the conguration of
these new compounds has not been elucidated, they are
assumed to be the same as for tiacumicin B.
The most important library of tiacumicin analogs was
generated by Zhang and co-workers while working on the
elucidation of the biosynthesis of tiacumicin B.
4044
Indeed,
from dierent mutants of the Dactylosporangium aurantiacum
strain, they have been able to characterize 37 new analogs
(Fig. 7). We can note, based on published data, that 50 is the C
18
epimer of lipiarmycin A4 (2).
It is interesting to note that the yield of tiacumicin B
production by D. aurantiacum has been greatly improved over
the years by Optimer scientists.
45
Using a growth medium
mainly composed of sh powder, glucose, casamino acid, yeast
extract and some inorganic salts to support microorganism
growth, it is possible to obtain 100500 mg of crude tiacumicin
per litre of broth, much higher than the 18.8 mg L
1
initially
reported by McAlpine. The introduction of a resin able to trap Fig. 3 The structure of clostomicins.
This journal is The Royal Society of Chemistry 2013 Nat. Prod. Rep., 2013, 30, 161174 | 163
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macrocycles as they are formed in the broth increased the yield
of tiacumicin and facilitated the recovery of product by sieving
from the broth and elution with organic solvents. Purication is
mainly achieved by reversed-phase medium-pressure liquid
chromatography.
2.4 Lipiarmycin from Catellatospora
In 2008, during the course of a screening programme to identify
new anti-tuberculosis agents, scientists from Novartis reported
the isolation of lipiarmycin A3 from Catellatospora sp. Bp3323-
81, a strain from the companys screening library.
46
3 Biosynthesis
Despite more than 30 years of history, little was known about
the biosynthesis of tiacumicin until the work of Zhang and co-
workers in 2011.
40,41
In early studies, Parenti noted that the
source of chlorine could be the meat extract used in the broth or
the added sodium chloride and that omission of both chlorine
sources greatly reduce the yield of lipiarmycin.
19
Furthermore,
McAlpine has shown that addition of potassium bromide to the
broth allows the formation of brominated tiacumicin
analogs.
35,36
Apart fromfeeding experiments, the biosynthesis of
tiacumicin remained undetermined.
In 2011, Zhang and co-workers reported their studies on
the biosynthesis of tiacumicin based on a genetic approach
on Dactylosporangium aurantiacum hamdenensis NRRL
18085.
4750
Firstly, they targeted polyketide synthase (PKS) and
halogenase using probes to identify genes involved in the
biosynthesis of tiacumicin. They have been able to identify
the complete tia-gene cluster which comprised 50 orfs (Open
Reading Frame) and 110 633 bp (base pairing). In a rst
attempt, the putative functions of orfs have been deduced by
comparison with protein databases and a further renement
Fig. 4 The structure of tiacumicins.
Fig. 5 The structure of brominated tiacumicins.
Fig. 6 The structure of tiacumicin analogs.
164 | Nat. Prod. Rep., 2013, 30, 161174 This journal is The Royal Society of Chemistry 2013
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allowed them to eliminate some orfs, which are not involved
in tiacumicin biosynthesis. Thus the nal gene cluster con-
tained 31 orfs, from gene TiaG1 to TiaR2 for approximately
83 kb.
Genes TiaA1 to TiaA4 were predicted as modular polyketide
synthases, and inactivation experiments led to the conclusion
that they are responsible for the tiacumicin aglycone synthesis
(Fig. 8, A). The biosynthesis involved propionyl-CoA, malonyl-
CoA, (2S)-methylmalonyl-CoA and (2S)-ethylmalonyl-CoA.
Bioinformatic analysis of the TiaB gene revealed some
similarity to 6-methyl-salicylic acid synthase and thus it is
probably involved in the biosynthesis of the homo-orsellinic
acid part 69 from a propionyl-CoA starting unit (Fig. 8, B). The
aromatic moiety could then be transferred to the 2-O-methyl-D-
rhamnose residue by TiaF due to similarity to acyltransferases,
responsible for incorporation of aromatic parts into secondary
metabolites. Finally, the gene TiaM showed some similarity to
other halogenases and its selective inactivation led to the
formation of tiacumicin analogs lacking chlorine atoms,
therefore allowing the assignment of its function. It has also
been shown that instead of chlorine (from NaCl), TiaM is able
to transfer bromine atoms to the homo-orsellinic acid moiety
(from NaBr). However, F
and I