Design, synthesis, and antibacterial activities of novel 3,6-bicyclolide oximes: Length optimization and zero carbon linker oximes

Article abstract of DOI:10.1016/j.bmcl.2008.07.118

We designed and synthesized a series of novel 3,6-bicyclolide oximes, possessing linkers of varying lengths to the secondary binding site. The E isomers exhibited excellent antibacterial profiles against a broad spectrum of resistant pathogens.

Full text of DOI:10.1016/j.bmcl.2008.07.118

Bioorganic & Medicinal Chemistry Letters 18 (2008) 5078–5082
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Design, synthesis, and antibacterial activities of novel 3,6-bicyclolide oximes:
Length optimization and zero carbon linker oximes
*
Datong Tang , Yonghua Gai, Alexander Polemeropoulos, Zhigang Chen, Zhe Wang, Yat Sun Or
Enanta Pharmaceuticals, Inc., 500 Arsenal Street, Watertown, MA 02472, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
We designed and synthesized a series of novel 3,6-bicyclolide oximes, possessing linkers of varying
lengths to the secondary binding site. The E isomers exhibited excellent antibacterial profiles against a
broad spectrum of resistant pathogens.
Received 19 June 2008
Revised 30 July 2008
Accepted 31 July 2008
Available online 3 August 2008
Ó 2008 Elsevier Ltd. All rights reserved.
Keywords:
Antibacterial
Bicyclolide
Oxime
MIC
The development of novel, effective, and safe antibacterial
agents is urgently needed to control infectious disease caused
by antibiotic-resistant bacteria. Macrolide antibiotics are an
important class of therapeutic agents against bacterial infec-
tions.1 However, the extensive clinical use of macrolide antibiot-
ics has resulted in an increasing MLSB-resistance in respiratory
pathogens. In our laboratories, we have been pursuing new gen-
erations of macrolides. Recently, EP-1304,2 a 6,11-bicyclolide
core, was discovered. Subsequent chemistry efforts based on this
core structure resulted in EDP-420 (EP-013420),3 our first-in-
class bicyclolide antibiotic clinical candidate, currently in phase
II clinical trial for the treatment of community acquired pneumo-
nia. In continuation of our efforts, we have designed and synthe-
sized 3,6-bicyclolide oxime derivatives possessing linkers of
varying lengths attached to the secondary aromatic binding mo-
tifs4 (see Fig. 1).
6f as mixtures in similar E/Z ratios. The final desired 3,6-bicyclolide
E-oximes 7a–7f were isolated by either crystallization or prepara-
tive reverse-phase HPLC chromatography.5
The structure of ketolide 7b was confirmed by the X-ray crystal-
lography (Fig. 2).
The 3,6-bicyclolides 7a–7f and the reference compound, eryth-
romycin A, were tested against a panel of representative respira-
tory pathogens. Various macrolide- and multidrug-resistant
isolates were included in the panel in order to identify potent ana-
logues that could overcome macrolide resistance. Staphylococcus
aureus 29213, Streptococcus pyogenes 19615, and Streptococcus
pneumoniae 49619 are erythromycin-susceptible strains. Staphylo-
coccus aureus 27660 is an inducibly MLSB-resistant strain encoded
by an ermA gene. Staphylococcus aureus 33591 is an MRSA. Strepto-
coccus pyogenes 2912 is constitutive MLSB-resistant strain encoded
The synthesis of 3,6-bicyclolide oxime is outlined in Scheme 1.
Key intermediate 11,12-carbamate 3,6-bicyclolide 2 was prepared
from 1 in 85% yield in a three-step one-pot fashion. The following
Osmium tetraoxide and sodium periodate mediated olefin cleavage
provided diketone compound 3 in 94% yield. The acid catalyzed
oxime formation was carried out using diketone 3 and hydroxyl-
amine 4a–4f in an aqueous alcoholic media at room temperature.
Oxime formation at C-9 ketone was not observed under these reac-
tion conditions. The resulting oximes 5a–5f were usually about 3
to 1 E/Z mixtures, which underwent 20-deacetylation to give 6a–
N
N
O
O
N
N
N
N
O
N
O
N
O
O
O
O
O
O
O
O
HO
O
HO
O
HO
HO
O
O
O
EP-1304
EDP-420
* Corresponding author. Tel.: +1 617 607 0716; fax: +1 617 6070532.
E-mail address: dtang@enanta.com (D. Tang).
Figure 1. Structure of 6,11-bicyclolide EP-1304 and EDP-420.
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.07.118

D. Tang et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5078–5082
5079
O
O
O
H
1) CDI, NaHMDS,
DMF-THF, rt, 22 h
2) NH (l), sealed tube
3
N
O
N
O
HO
HO
N
O
AcO
O
O
AcO
O
O
O
DMF-THF, rt, 22 h
O
O
3)
t
BuOK
DMF-THF, rt, 2 h
O
O
O
1
2
O
ONH
n
2
O
H
N
O
4a-4f
N
O
OsO , NaIO
O
AcO
4
4
O
Acetone/H O
2
HCl (aq, 1M), EtOH/H O
2
rt, 15 min
O
O
O
Yield: 94%
O
3
O
O
O
O
H
H
N
O
N
N
O
N
O
O
AcO
O
O
HO
MeOH
60 ºC, 2 h
O
O
O
O
O
O
N
O
N
n
O
O
O
6a-6f
5a-5f
n
O
O
H
N
N
4a-7a: n=0
4b-7b: n=1
4c-7c: n=2
4d-7d: n=3
4e-7e: n=4
4f -7f : n=5
O
HO
O
O
prep HPLC purification
O
O
O
N
n
O
O
7a-7f
Scheme 1. Synthesis of 3,6-bicyclolide oximes.
by an ermA gene, and S. pneumoniae 700906 is resistant strain
encoded by an erm gene. Streptococcus pyogenes 1323 and S. pneu-
moniae 7701 are efflux-resistant strains encoded by mefA genes.
Haemophilus influenzae 33929 is an ampicillin-resistant strain with
a b-lactamase positive determinant. The in vitro antibacterial
activities are reported as minimum inhibitory concentrations
(MICs), which were determined utilizing the broth-microdilution
method as per CLSI standards. The in vitro antibacterial activities
of 3,6-bicyclolides 7a–7f and reference compound are shown in
Table 1.
Figure 2. X-ray single crystal structure of 3,6-bicyclolide 7b.

5080
D. Tang et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5078–5082
Table 1
In vitro antibacterial activities of 3,6-bicyclolide oximes—length optimization
O
O
H
N
O
N
HO
O
O
O
O
O
N
O
O
(CH2)n
Organism
MIC (lg/ml)
7a (n = 0)
7b (n = 1)
7c (n = 2)
7d (n = 3)
7e (n = 4)
7f (n = 5)
Ery A
S. aureus 29213
S. aureus 27660
S. aureus 33591
Ery S
MLS Ri
MRSA
60.06
60.06
>64
60.06
60.06
32
60.06
60.06
4
60.06
60.06
>64
60.06
60.06
>64
60.06
0.125
4
0.125
0.125
>64
60.06
60.06
16
60.06
0.125
8
0.125
0.125
>64
60.06
60.06
4
60.06
60.06
8
0.25
0.25
64
60.06
0.125
4
60.06
0.25
16
0.25
0.25
>64
60.06
0.125
8
60.06
0.125
8
0.5
>64
>64
60.06
4
>64
0.015
16
S. pneumoniae 49619
S. pneumoniae 7701
S. pneumoniae 700906
S. pyogenes 19615
S. pyogenes 1323
S. pyogenes 2912
H. influenzae 33929
H. influenzae
Ery S
Ery R-mef
Ery R-erm
Ery S
Ery R-mef
Ery R-erm
Amp R
>64
4
4
1
2
2
2
2
2
2
2
4
8
4
4
Amp S
M. catarrhalis
60.06
60.06
60.06
0.125
0.25
0.25
0.13
Table 2
well as H. influenzae strains. These results strongly suggested that
each of the 3,6-bicyclolide oximes are good templates for further
modifications.
In vitro antibacterial activities of 3,6-bicyclolide oximes—E/Z isomer comparison
O
To overcome S. pneumoniae and S. pyogenes erm resistant
strains, zero carbon linker 3,6-bicyclolide oximes 13g–13n
were synthesized as shown in Scheme 2. Boronic acids 9g–
9n were reacted with N-hydroxyl phthalimide via copper (II)
acetate-catalyzed coupling condition to give 10g–10n.6 Treat-
ing 10g–10n with ammonia in methanol provided zero carbon
linker O-hydroxylamine 11g–11n. Oxime formation reactions
from diketone 3 and 11g–11n were carried out in a similar
fashion as previously described to give 3,6-bicyclolide E/Z
oxime mixtures 12g–12n. Finally, 20-deacetylation followed
by preparative reverse-phase chromatography provided the
desired zero carbon 3,6-bicyclolide E-oximes 13g–13n
(see Table 3).
O
H
O
N
O
N
O
O
H
HO
O
O
N
O
N
O
O
HO
O
O
O
O
O
N
O
O
N
O
O
7b
8
Organism
MIC (
l
g/ml)
7b
8
Compared to its phenyl analog, 3-pyridyl oxime 13g showed
slight antibacterial improvement against S. pneumoniae erm and
Haemophilus influenzae. Among the three chlorophenyl derivatives
13h, 13i, and 13j, the meta-substituted oxime 13i showed the most
potent antibacterial profile against the resistant strains. Further-
more, the three biphenyl analogs 13k, 13l, and 13m appeared to
give similar antibacterial activity pattern. Meta-biphenyl oxime
13l gave the most balanced antibacterial profile and it even exhib-
ited good potency against S. aureus resistance strain MRSA. These
zero carbon 3,6-bicyclolides represent a novel and promising mac-
rolide series.
S. aureus 29213
S. aureus 27660
S. aureus 33591
Ery S
MLS Ri
MRSA
60.06
60.06
>64
60.06
60.06
>64
60.06
0.125
4
2
0.5
0.5
>64
60.06
0.125
>64
60.06
0.25
64
S. pneumoniae 49619
S. pneumoniae 7701
S. pneumoniae 700906
S. pyogenes 19615
S. pyogenes 1323
S. pyogenes 2912
H. influenzae 33929
H. influenzae
Ery S
Ery R-mef
Ery R-erm
Ery S
Ery R-mef
Ery R-erm
Amp R
16
8
0.125
Amp S
2
M. catarrhalis
60.06
In conclusion, we designed and synthesized a series of no-
vel 3,6-bicyclolide oximes, possessing linkers of varying
lengths to the secondary binding site. Further modifications
of zero carbon linker 3,6-bicyclolide oximes improved antibac-
The undesired Z-oxime isomer 8 was isolated and subjected to
in vitro antibacterial test together with the corresponding E-oxime
isomer 7b (Table 2). This direct comparison clearly showed that the
E-oxime was much more potent than the Z-oxime.
All 3,6-bicyclolide oximes 7a–7f showed good antibacterial
activities against the susceptible strains, mef resistant strains, as
terial activities against
a broad panel of macrolide-resistant
bacterial strains. Good overall antibacterial activities of 3,6-
bicyclolide oximes warrant further efforts on this novel class
of antibiotics.

D. Tang et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5078–5082
5081
O
HO
N
O
Ar
NH in MeOH
3
O
Ar
Ar B(OH)
O N
2
O NH
2
Cu(OAc) , Py
2
rt, o/n
4A mol sieves
O
C H Cl , rt
2
4
2
11g-11n
9g-9n
10g-10n
O
O
O
O
H
H
N
O
N
Ar
11g-11n
2
N
O
N
O
O NH
O
AcO
O
O
AcO
O
HCl (aq, 1M), EtOH/H O
2
rt, 15 min
O
O
O
O
O
O
N
O
O
O
Ar
12g-12n
3
O
Ar = 3-pyridyl
9g-13g:
9h-13h: Ar = 2-Cl-phenyl
O
H
N
N
O
Ar = 3-Cl-phenyl
Ar = 4-Cl-phenyl
Ar = 2-biphenyl
Ar = 3-biphenyl
Ar = 4-biphenyl
9i-13i:
9j-13j:
9k-13k:
9l-13l:
HO
O
1) MeOH, 60 ºC, 2 h
2) prep HPLC purification
O
O
O
O
O
N
9m-13m:
O
9n-13n: Ar = 2-napthyl
13g-13n
Ar
Scheme 2. Synthesis of zero carbon linker 3,6-bicyclolide oximes.
Table 3
In vitro antibacterial activities of 3,6-bicyclolide oximes—length optimization
O
O
H
N
O
N
O
HO
O
O
O
O
N
O
O
Ar
Organism
MIC (l
g/ml)
7a
13g
13h
13i
13j
13k
13l
13m
13n
Ery A
Ar=
Ph
3-Pyridyl
2-Cl-Ph
3-Cl-Ph
4-Cl-Ph
2-Ph-Ph
3-Ph-Ph
4-Ph-Ph
2-Napthyl
S. aureus 29213
S. aureus 27660
S. aureus 33591
Ery S
MLS Ri
MRSA
60.06
60.06
>64
60.06
60.06
32
60.06
60.06
4
0.125
0.125
>64
0.125
0.125
16
60.06
0.25
4
60.06
60.06
64
60.06
60.06
32
60.06
60.06
4
60.06
60.06
32
60.06
60.06
8
60.06
60.06
1
60.06
60.06
>64
60.06
60.06
16
60.06
60.06
2
0.5
0.5
16
60.06
0.5
16
60.06
0.5
16
0.125
0.125
4
60.06
60.06
2
60.06
0.125
4
0.5
0.5
16
60.06
0.125
0.25
60.06
0.25
2
0.25
0.25
32
60.06
0.125
0.5
60.06
0.125
2
0.5
>64
>64
60.06
4
>64
0.015
16
>64
4
S. pneumoniae 49619
S. pneumoniae 7701
S. pneumoniae 700906
S. pyogenes 19615
S. pyogenes 1323
S. pyogenes 2912
H. influenzae 33929
H. influenzae
Ery S
Ery R-mef
Ery R-erm
Ery S
Ery R-mef
Ery R-erm
Amp R
1
2
1
1
2
2
2
2
4
4
8
8
4
4
8
8
8
4
Amp S
4
M. catarrhalis
60.06
60.06
60.06
60.06
60.06
0.5
0.125
1
0.25
0.13
Korkhin, Y.; Phan, L. T.; Or, Y. S. 43rd ICAAC, Chicago, IL, USA, 2003; Poster F-
1193.
Acknowledgment
3. (a) Scorneaux, B.; Arya, A.; Polemeropoulos, A.; Lillard, M.; Han, F.; Amsler, K.;
Sonderfan, A.; Busuyek, M.; Wang, G.; Phan, L.; Or, Y. S. 43rd ICAAC, Chicago, IL,
USA, 2003; Poster F-1191.; (b) Wang, G.; Niu, D.; Qiu, Y.; Phan, L. T.; Chen, Z.;
Polemeropoulos, A.; Or, Y. S. Org. Lett. 2004, 6, 4455.
We thank Dr. Emil Lobkovsky from Cornell University for help
with the X-ray structures of compounds 7b.
4. Tang, D.; Sun, Y.; Gai, Y.; Xu, G.; Liu, D.; Polemeropoulos, A.; Chen, Z.; Wang, Z.;
Or, Y. S. 46th ICAAC, San Francisco, CA, USA, 2006; Poster F1-1989.
References and notes
5. Synthesis of 3,6-bicyclolide 7b and 8: To a solution of O-benzyl-hydroxylamine
(18 mg, 0.15 mmol, 1.5 equiv) and 1.0 M aqueous hydrochloric acid (0.2 ml,
0.2 mmol, 2.1 equiv) in ethanol (0.25 ml) was added a solution of bridged ketone
3 (67 mg, 0.10 mmol) in acetonitrile (0.25 ml) dropwise at room temperature.
After stirring for 15 min at room temperature the mixture was quenched with
saturated aqueous sodium bicarbonate solution and extracted with EtOAc twice.
1. For recent reviews, see: (a) Zhanel, G. G.; Dueck, M.; Hoban, D. J.; Vercaigne, L.
M.; Embil, J. M.; Gin, A. S.; Karlowsky, J. A. Drugs 2001, 61, 443; (b) Ma, Z.;
Nemoto, P. Curr. Med. Chem. Anti-Infect. Agents 2002, 1, 15.
2. Wang, G.; Qiu, Y.; Niu, D.; Vo, N. H.; Haley, T.; Polemeropoulos, A.;
Scorneaux1, B.; Arya, A.; Schlünzen, F.; Harms, J. M.; Albrecht, R.; Yonath, A.;

5082
D. Tang et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5078–5082
The combined organic extracts were washed with brine, dried, filtered, and
concentrated in vacuo to give an E/Z oxime mixture 5b as a tan foam. MS (ESI):
m/z 802.15 [M+H].
The above residue was dissolved in methanol (1 ml) and stirred at room
temperature for 21 h. The reaction mixture was in vacuo to give E/Z (2:1 ratio by
HPLC) oxime mixture 6b as a tan foam. MS (ESI): m/z 760.10 [M+H].
The above residue was purified by HPLC to afford the desired E-oxime 7b and Z-
oxime 8.
Compound 7b : 13C NMR (CDCl3) d 217.0, 177.6, 158.0, 157.8, 137.9, 128.6, 128.2,
128.1, 104.8, 84.5, 80.8, 80.5, 79.2, 76.8, 76.5, 70.6, 69.6, 66.3, 66.1, 61.0, 58.3, 44.4,
44.2, 43.0, 40.6, 39.0, 37.4, 23.0, 21.5, 21.4, 19.9, 13.9, 13.5, 11.6, 11.4, 11.0 ppm.
Compound 8: 13C NMR (CDCl3) d 217.1, 177.3, 158.5, 157.7, 137.7, 128.6, 128.5,
128.1, 103.4, 84.4, 82.3, 81.0, 80.9, 76.6, 76.3, 73.1, 70.0, 68.2, 67.2, 58.6, 44.4, 44.1,
43.3, 41.4, 40.5, 39.5, 37.3, 32.0, 22.6, 21.7, 21.0, 20.1, 14.1, 13.4, 12.3, 11.3,
11.1 ppm.
6. Petrassi, H. M.; Sharpless, K. B.; Kelly, J. W. Org. Lett. 2001, 3, 139.