Synthesis and antibacterial activity of novel bifunctional macrolides

Article abstract of DOI:10.1016/j.bmcl.2004.04.077

We report the discovery of a novel class of macrolide antibiotics that have improved antibacterial activity against Ery-resistant organisms.

Full text of DOI:10.1016/j.bmcl.2004.04.077

Bioorganic & Medicinal Chemistry Letters 14 (2004) 3809–3813
Synthesis and antibacterial activity of novel bifunctional macrolides
Irini Akritopoulou-Zanze,* Kathleen M. Phelan, Thomas G. Marron, Hong Yong,
Zhenkun Ma,ꢀ Greg G. Stone,ꢁ Melissa M. Daly, Dena M. Hensey,
Angela M. Nilius and Stevan W. Djuric
Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road,
Abbott Park, IL 60044, USA
Received 26 March 2004; revised 22 April 2004; accepted 26 April 2004
Available online 25 May 2004
Abstract—We report the discovery of a novel class of macrolide antibiotics that have improved antibacterial activity against Ery-
resistant organisms.
Ó 2004 Elsevier Ltd. All rights reserved.
Macrolide antibiotics such as erythromycin A (Fig. 1)
have been used for many years for the treatment of
respiratory tract infections. They exert their action by
selectively binding to domains II and V of the bacterial
ribosomal RNA and inhibiting protein biosynthesis.1
Many years of intense research resulted in macrolide
derivatives with improved activity and pharmacokinet-
ics, however continuous use of macrolide antibiotics has
also resulted in macrolide resistant bacteria. There are
two key mechanisms that contribute to macrolide
bacterial resistance.2 One is the dimethylation by erm
methyltransferases of an adenine group located at
the ribosome macrolide binding-site that prevents
tight macrolide binding (erm-resistance). The other is
the action of an efflux pump that recognizes and
removes macrolides from the bacterial cell (mef-resis-
tance).
Recently, substitution of the 3-cladinose sugar with a
keto-group resulted in a new class of drugs, the ketolides
as exemplified in Figure 1 by ABT-7733 and telithro-
mycin.4 These molecules have addressed macrolide
Figure 1. Chemical structures of erythromycin A and ketolides.
resistance by what is believed to be an alternative,
Keywords: Bifunctional macrolides; Macrolide resistance; Ketolides.
more effective interaction with domain II of the ribo-
somal RNA via anchoring units attached to various
sites on the macrolide molecule instead of the cladinose
sugar.5 Furthermore, several bifunctional macrolides
containing rigid anchoring units have also been
prepared.6
* Corresponding author. Tel.: +1-847-9375006; fax: +1-847-9350310;
e-mail: irini.zanze@abbott.com
ꢀ
Present address: Cumbre Inc., 1502 Viceroy Drive, Dallas, TX 75235,
USA.
ꢁ
Present address: Pfizer, Inc. MS-8118W-237, Groton Laboratories,
Groton, CT 06340, USA.
0960-894X/$ - see front matter Ó 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2004.04.077

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In an effort to probe the space around the macrolide
molecule and create additional interactions with a
secondary site on the ribosome we have prepared two
large lead generation libraries of macrolides attached to
a variety of tethers and potential secondary binders. We
decided to elaborate on two different scaffolds, based on
synthetic accessibility. One of the scaffolds allowed us
to build on C-3 of the macrolide molecule, the other on
C-9.
We selected diamines as the bifunctional units that
would link the macrolide and the secondary binder be-
cause they were readily available in a variety of lengths,
rigidity and polarity.
Secondary binders were selected to mimic parts of
known antibiotics that bind to domains II and/or V such
as chloramphenicol and anisomycin.7 Additionally,
aromatic and heterocyclic substituents were employed as
DNA-base surrogates8 in order to mimic antibiotics
containing DNA-bases such as puromycin9 and blas-
ticidin.7 A variety of other substituents were also se-
lected based on diversity to probe a large chemical
space. All possible combinations of tethers with sec-
ondary binders were carried out by a matrix parallel
synthesis approach.
The 3-O-carbamate analogs were prepared from
clarithromycin in seven steps as shown in Scheme 1.
Initially, the sugar hydroxyl groups were protected
selectively over the 11, 12 hydroxyls, which were
subsequently transformed to the carbamate 1.
Removal of the cladinose sugar with HCl and treatment
with 1,10-carbonyldiimidazole (CDI) provided the de-
sired intermediate 2 in large quantities. This compound
was further derivatized with various diamines, which
were acylated and deprotected to provide final analogs
3.10
Scheme 1. Reagents and conditions: (a) Bz2O, DMAP, Et3N, CH2Cl2,
55%; (b) 1. CDI, DBU, THF, DMF, 2. NH3, t-BuOK; (c) 2 M HCl,
EtOH, 45 °C, 78%; (d) CDI, THF, dichloroethane; (e) H2N–tether–
NH2, DMF, 74–85%; (f) RCO2H, PS-carbodiimide, HOBT, DMF,
then PS-trisamine; (g) MeOH, 5–72% in two steps.
The 9-oxime analogs were assembled as shown in
Scheme 2. Starting from ketolide 4, 9-oxime core 5 was
prepared in two steps in large scale and good overall
yields. Reactions of 3 equiv of various diamines with
bromide 5 in DMF proceeded in good yields to provide
the tethered molecules, which were subjected to reduc-
tive alkylation using Amberlite–BH4 as the reducing
agent. The presence of base was crucial to the success of
the reductive alkylation step, as without it the reaction
proceeded in very low yields and starting material was
recovered.
All compounds were tested in vitro against Staphylo-
coccus aureus NCTC 10649 (an erythromycin-susceptible
strain), S. aureus 1775 (a methicillin-resistant strain
(MRSA) bearing a constitutive erm (A) gene), Strepto-
coccus pneumoniae ATCC 6303 (an erythromycin-sus-
ceptible strain), S. pneumoniae 5649 (an efflux-resistant
strain bearing a mef (E) gene), S. pneumoniae 5979 (an
MLSB resistant stain bearing an erm (B) gene) and
Haemophilus influenzae GYR1435 (a fully susceptible
strain) by the broth microdilution method according to
the reference procedure of the National Committee for
Clinical Laboratory Standards.11
Scheme 2. Reagents and conditions: (a) NH2OHÆHCl, EtOH, NaOAc,
reflux, 99%; (b) dibromoethane, Bu4NBr, 10% NaOH, CH2Cl2, 40 °C,
2 d, 72%; (c) (3 equiv) H2N–tether–NH2, K2CO3, DMF, 69–85%; (d)
RCHO, DIEA, MeOH, Amberlite–BH4, 11–63%.

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3811
Table 1. In vitro antibacterial activity of 3-O-carbamate macrolides 3 (Scheme 1) and 9-oxime ketolides 6 (Scheme 2)
Compds
R
MIC (lg/mL)a
S. aureus S. aureus S. pneumo. S. pneumo. S. pneumo. H. flu
H2N
NH2
Tether
NCTC
10649
1775
ATCC
6303
5649
5979
GYR
1435
Eryb
Telic
ABT-773
4
0.25
0.06
0.12
0.5
>128
0.03
6 0.008
6 0.008
0.06
4
>128
2
2
>128
>128
>128
0.25
6 0.008
0.12
0.06
6 0.008
0.5
64
>128
NDd
>128
128
H2N
3a
64
>128
0.25
NH2
O
H2N
O
NH2
3b
8
>128
0.5
0.5
>128
16
13
O
O
O
6a
6b
6c
6d
6e
H2N
NH2
32
64
32
32
64
64
0.12
0.015
1
32
H2N
H2N
16
4
0.25
0.12
0.12
0.5
0.5
16
8
NH2
NH2
NH2
0.06
0.06
2
H2N
4
6 0.008
6 0.008
8
O
O
H2N
2
0.12
4
NH2
O
H2N
H2N
6f
1
>128
>128
6 0.008
0.12
0.25
2
1
4
NH2
O
NH2
6g
16
0.12
128
Cl
Cl
6h
6i
H2N
H2N
H2N
O
NH2
2
1
1
>128
>128
64
0.06
6 0.008
6 0.008
0.06
0.5
0.25
16
8
Cl
O
NH2
0.015
0.06
0.5
4
Cl
N
6j
O
NH2
4
8
F
N
6k
0.5
>128
0.25
64
H2N
H2N
O
O
NH2
NH2
O
6l
2
64
6 0.008
6 0.008
0.06
1
2
H2N
O
6m
32
>128
0.12
1
32
O
NH2
(continued on next page)

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Table 1 (continued)
Compds
R
MIC (lg/mL)a
S. aureus S. aureus S. pneumo. S. pneumo. S. pneumo. H. flu
H2N
NH2
Tether
NCTC
10649
1775
ATCC
6303
5649
5979
GYR
1435
O
O
6n
2
128
0.12
1
1
2
64
H2N
O
O
NH2
H2N
O
O
NH2
6p
2
128
0.25
2
32
O
a Minimum inhibitory concentrations.
b Erythromycin A.
c Telithromycin.
d ND not determined.
Table 1 summarizes the antibacterial activity of the most
potent compounds from each series. All 3-O-carbamate
analogs exhibited a weak antibacterial profile similar to
erythromycin, as exemplified by analogs 3a and 3b.
These compounds were not active against erm-resistant
strains and were weakly active against susceptible
strains.
taining phenyl groups suggesting a special interaction
between these units and the ribosome.
In conclusion we have identified numerous tether/sec-
ondary binder combinations that show comparable
antibacterial activity to optimized drugs or drug candi-
dates. The remarkable activity of these unoptimized
leads against resistant strains coupled with the fact that
the parent compound 4 exhibited only weak antibacte-
rial activity, suggests that additional interactions be-
tween the tether/secondary binders and the ribosome
take place.
The 9-oxime series on the other hand provided numer-
ous interesting analogs. Departing from the erythro-
mycin-like activity of the parent compound 4, analogs in
the 9-oxime series exhibited a distinct antibacterial
profile. The compounds were not as active in erythro-
mycin-susceptible S. aureus, however they showed im-
proved activity against the S. aureus strain having
the erm mechanism of resistance. They were also very
active against susceptible and resistant S. pneumoniae
strains.
Acknowledgements
The authors would like to thank the High Throughput
Purification Group for purifying all library compounds
and the Structural Chemistry group for obtaining NMR
and MS spectra.
A comparison of 9-oxime analogs with identical R
substituents such as 6a, 6b, 6c, 6l, 6n and 6p, revealed a
bell-shaped curve for antibacterial activity versus tether
length reaching an optimal tether length in compound
6l. This compound exhibited strong antibacterial activ-
ity against erythromycin-susceptible and resistant S.
pneumoniae strains that was better than erythromycin
and telithromycin. Antibacterial activity against the
erm-resistant S. aureus strain shifted the curve towards
smaller tethers. Compounds 6b and 6c exhibited a
greater than fourfold improvement against this strain
when compared with telithromycin and ABT-773.
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