Synthesis and antibacterial activity of novel 4″-O-arylalkylcarbamoyl and 4″-O-((arylalkylamino)-4-oxo-butyl)carbamoyl clarithromycin derivatives

Article abstract of DOI:10.1016/j.bmcl.2010.04.051

Novel series of novel 4″-O-arylalkylcarbamoyl and 4″-O-((arylalkylamino)-4-oxo-butyl)carbamoyl clarithromycin derivatives were designed, synthesized and evaluated for their in vitro antibacterial activities. These derivatives retained excellent activity against the erythromycin-susceptible strains and showed significantly improved activity against all of the tested erythromycin-resistant strains. Among them, compound 4c was the most effective (0.06 μg/mL) against Streptococcus pneumonia encoded by the erm gene and compound 4a was had the most potent activity (0.25 μg/mL) against S. pneumonia encoded by the erm and mef genes.

Full text of DOI:10.1016/j.bmcl.2010.04.051

Bioorganic & Medicinal Chemistry Letters 20 (2010) 3272–3274
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and antibacterial activity of novel 400-O-arylalkylcarbamoyl and
400-O-((arylalkylamino)-4-oxo-butyl)carbamoyl clarithromycin derivatives
Yongjing Ju a, Ruiqing Xian b, Ling Zhang a, Ruixin Ma c, Jichao Cao a, Shutao Ma a,
*
a Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, 44, West Culture Road, Jinan 250012, PR China
b Shandong Institute for Drug Control, Jinan 250000, PR China
c Affiliated Hospital of Medical College, Qingdao University, Qingdao 266003, PR China
a r t i c l e i n f o
a b s t r a c t
Novel series of novel 400-O-arylalkylcarbamoyl and 400-O-((arylalkylamino)-4-oxo-butyl)carbamoyl clari-
thromycin derivatives were designed, synthesized and evaluated for their in vitro antibacterial activities.
These derivatives retained excellent activity against the erythromycin-susceptible strains and showed
significantly improved activity against all of the tested erythromycin-resistant strains. Among them,
Article history:
Received 15 January 2010
Revised 14 March 2010
Accepted 13 April 2010
Available online 24 April 2010
compound 4c was the most effective (0.06 lg/mL) against Streptococcus pneumonia encoded by the
erm gene and compound 4a was had the most potent activity (0.25
by the erm and mef genes.
lg/mL) against S. pneumonia encoded
Keywords:
Clarithromycin derivatives
Synthesis
Ó 2010 Elsevier Ltd. All rights reserved.
Antibacterial activity
Bacterial resistance
Second-generation macrolides such as clarithromycin1 (CAM)
(Fig. 1) and azithromycin2 (AZM) have been widely used for the
treatment of upper and lower respiratory tract infections, as well
as genital infections due to their superior antibacterial activity
and pharmacokinetic properties, and fewer gastrointestinal side ef-
fects compared with first-generation macrolide erythromycin
(EMA). Their mechanism of action has been elucidated that these
macrolides reversibly bind to the nucleotide A2058 in domain V
of the 23S rRNA in the ribosomal 50S subunit and block protein
synthesis.3 However, the therapeutic utility of macrolides has been
severely compromised by the emergence of widespread bacterial
resistance which become a serious medical problem worldwide.4
The most important mechanism of macrolide resistance are medi-
ated by erm-encoded methylation of 23S rRNA. Expression of an
erm-resistant determinant in bacteria results in production of a
methyltransferase which modifies the key nucleotide A2058,
thereby conferring resistance to macrolides.5
To address the problems of the bacterial resistance, third-gener-
ation macrolides known as ketolides exemplified by telithromycin
and cethromycin have been investigated. The ketolides are
characterized by excellent activity against several types of macro-
lide-resistant organisms and may offer alternative therapy for
Gram-positive infections attributable to resistant pathogens.6
Their mechanism of action has been reported to interact with a
secondary ribosomal binding site A752 directly in domain II of
the 23S rRNA by the C-11,12 carbamate side chain or the C-6 side
chain in the ketolides in addition to the main interaction of the
drugs in domain V, which leads to tighter binding to bacterial ribo-
somes and imparts some activity against erm-resistant organ-
isms.7,8 The tighter binding also inhibits the mef-mediated
mechanism by creating an influx rate of the ketolide that exceeds
its efflux rate.
While significant efforts have gone into the discovery of
increasingly potent ketolides, a substantial amount work has also
been carried out on the next-generation macrolides to effectively
cope with bacterial resistance. These investigations have led to
the discovery of C-400-modified macrolides9–13 such as A-663329
and CP-54437210 (Fig. 1). In particular, CP-544372 containing a
long anchor group at the C-400 position of 9(S)-erythromycylamine,
exhibits excellent in vitro and in vivo activity against macrolide-
resistant strains encoded by the erm gene with competitive bind-
ing to chloramphenicol, suggesting that the anchor group can
reach the chloramphenicol-binding sites in the peptide tunnel.14
Its long anchor group is six atom distances from 400-oxygen atom
to the benzene ring. Therefore, the C-400-modified macrolides dis-
play a higher affinity for the ribosomes of resistant bacteria, which
is due to the additional interaction mediated by the C-400 side
chain.
The study of high-resolution X-ray co-crystal structures has re-
vealed that the binding sites of clarithromycin, clindamycin and
chloramphenicol differ from each other, but they show some over-
lapping nucleotides in the peptide tunnel.15 Particularly, the high
nucleotide content in the peptide tunnel gives rise to a number
* Corresponding author. Tel.: +86 531 88382009; fax: +86 531 88911612.
E-mail address: mashutao@sdu.edu.cn (S. Ma).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.04.051

Y. Ju et al. / Bioorg. Med. Chem. Lett. 20 (2010) 3272–3274
3273
N
N
N
HO
H2N
HO
HO
HO
OH
O
HO
OMe
O
O
O
′
′
′
2
2
2
9
OH
9
9
HO
HO
HO
HO
O
6
3
6
3
6
3
O
O
O
11
11
12
11
12
12
O
4
O
4
O
4
O
O
O
O
O
O
O
O
″
″
″
N
O
O
O
OH
OMe
O
O
N
H
OMe
OMe
OCH3
A-66332
CP-544372
Clarithromycin (CAM)
Figure 1. Structures of clarithromycin, A-66332 and CP-544372.
of possible interactions such as hydrogen bonding,
p
-stacking as
resistant strains whose resistance were encoded by the erm gene,
the mef gene and the erm and mef genes, respectively.
well as electrostatic interactions. Therefore, a reasonably long
group at the C-400 position is helpful for the interaction with the
nucleotides in the peptide tunnel. To probe the effect of different
lengths of C-400 side chains in antibacterial activity, we designed
novel structural series of C-400-modified clarithromycins with C-
400-prolonged side chains from 400-oxygen atom to aromatic ring
is three, four, eight and nine atom distances, respectively.
The two series of C-400-modified clarithromycins showed excel-
lent activity against erythromycin-susceptible S. pneumonia
ATCC49619. Among them, compounds 3c, 3d and 4a–e were found
to be the most potent activity (MIC 0.03 lg/mL) comparable to
those of EMA, CAM and AZM. As for the activity against the eryth-
romycin-resistant S. pneumonia, most of the series 3 showed im-
proved activity in comparison with the references. Among them,
The novel series of C-400-modified clarithromycins were designed
and synthesized from CAM as a starting material. Acetylation of the
20-hydroxyl group of CAM with acetic anhydride (Ac2O) was fol-
lowed by transformation of the 400-hydroxyl group to the acyl imid-
azole utilizing 1,10-carbonyldiimidazole (CDI) and triethylamine
(Et3N) to give 400-O-acylimidazolide (2). These reactions proceeded
very smoothly at room temperature in 79% yield. The 400-O-aryl-
alkylcarbamoyl clarithromycin derivatives (3a–g) were obtained in
yields ranging from 62% to 67% by condensation of 2 with the
corresponding arylalkylamines in the presence of 1,8-diazabicy-
clo[5.4.0]undec-7-ene (DBU) at 60 °C, followed by selective removal
of the 20-O-acetyl group by heating with methanol (Scheme 1).
Similarly, the 400-O-((arylalkylamino)-4-oxo-butyl)carbamoyl clari-
thromycin derivatives (4a–e) were prepared by condensation of 2
with the corresponding arylalkylcarbamoyl butylamines in the pres-
ence of DBU at room temperature and subsequent methanolysis at
55 °C (Scheme 2).The yields were within the range of 69–76%.
The two series of C-400-modified clarithromycins 3a–g and 4a–e
prepared above, as well as EMA, CAM and AZM as references, were
tested for in vitro antibacterial activity against four phenotypes of
Gram-positive strains. The activities are reported in Table 1 as min-
imum inhibitory concentrations (MICs) determined using the broth
microdilution method. Streptococcus pneumonia ATCC49619 are an
erythromycin-susceptible strain, and S. pneumoniae B1, S. pneu-
moniae A22072 and S. pneumoniae AB11 are three erythromycin-
compounds 3a, 3c and 3g were the most effective (0.25 lg/mL)
against S. pneumoniae A22072 encoded by the mef gene, and com-
pounds 3a and 3b displayed greatly improved activity against
S. pneumoniae encoded by the erm gene or the erm and mef genes,
showing 16-fold and 16-fold higher activity than the parent CAM,
respectively. In contrast, the series 4 had much better activity than
the series 3 against S. pneumoniae encoded by the erm gene or the
erm and mef genes, but the both series showed similar activity
against S. pneumoniae encoded by the mef gene. Among all of the
tested series, compound 4c was the most effective (0.06 lg/mL)
against S. pneumoniae B1encoded by the erm gene, showing 267-
fold higher activity than the corresponding 3c, and compound 4a
had the most potent activity (0.25 lg/mL) against S. pneumoniae
AB11encoded by the erm and mef genes, showing 32-fold better
activity than the corresponding 3a.
The results described above suggested that introduction of the
arylalkyl group at the C-400 position of CAM not only retains good
activity against the erythromycin-susceptible strains, but also
shows remarkably improved activity against all of the tested eryth-
romycin-resistant S. pneumonia. In particular, introduction of the
prolonged 400-O-arylalkyl group further increase activity against
S. pneumoniae encoded by the erm gene, and the erm and mef
genes. The prolonged 400-O-arylalkyl group with eight to nine atom
distances from 400-oxygen atom to aromatic ring might reach the
N
N
O
N
HO
AcO
O
O
O
HO
OMe
O
OMe
OMe
HO
HO
HO
HO
HO
HO
O
O
a, b
c, d
N
O
O
O
O
O
O
O
O
O
O
O
O
O
R1
O
O
O
OH
OMe
N
H
O
N
O
OMe
OMe
2
3
CAM
3a R1 = benzyl
3b
3c
R
1 = 4-fluorobenzyl
R1 = 4-methoxybenzyl
3d R1 = 4-hydroxyphenethyl
R1 = 2-chlorophenethyl
3f R1 = phenethyl
3g
3e
R1 = 3,4-methylenedioxyphenethyl
Scheme 1. Reagents and conditions: (a) Ac2O, Et3N, CH2Cl2, rt, 24 h, 85%; (b) CDI, CH2Cl2, rt, 24 h, 93%; (c) R1NH2, DBU, DMF, 60 °C, 7 h; (d) CH3OH, 45 °C, 12 h, 62–67% for two
steps.

3274
Y. Ju et al. / Bioorg. Med. Chem. Lett. 20 (2010) 3272–3274
N
N
O
HO
AcO
O
O
OMe
OMe
HO
HO
HO
HO
O
O
R1 = benzyl
a, b
N
O
4a
4b R1 = 4-fluorobenzyl
O
O
O
O
O
O
4c
O
O
R1 = 4-methoxybenzyl
H
N
4d R1 = 4-hydroxyphenethyl
R1
O
O
N
H
O
O
N
R1 = 2-chlorophenethyl
4e
OMe
OMe
O
2
4
Scheme 2. Reagents and conditions: (a) corresponding amine hydrochloride, DBU, DMF, rt, 24 h; (b) CH3OH, 55 °C, 24 h, 69–76% for two steps.
Table 1
In vitro antibacterial activity of 400-O-arylalkylcarbamoyl and 400-O-((arylalkylamino)-4-oxo-butyl)carbamoyl clarithromycin derivatives
Strains/compounds
MICs (lg/mL)
3a
3b
3c
0.03
16
0.25
32
3d
0.03
16
1
3e
3f
0.06
16
0.5
32
3g
0.06
32
0.25
64
4a
4b
4c
4d
4e
0.03
32
1
EMA
0.03
128
8
CAM
0.03
64
4
AZM
0.03
128
4
S. pneumoniae ATCC49619a
S. pneumoniae B1b
0.25
4
0.25
8
0.06
4
0.5
8
0.12
0.03
2
0.5
0.25
0.03
1
0.25
2
0.03
0.06
0.25
1
0.03
0.25
0.5
1
128
4
128
S. pneumoniae A22072c
S. pneumoniae AB11d
64
32
256
128
256
a
b
c
S. pneumoniae ATCC49619: erythromycin-susceptible strain.
S. pneumoniae B1: erythromycin-resistant strain encoded by the erm gene.
S. pneumoniae A22072: erythromycin-resistant strain encoded by the mef gene.
d
S. pneumoniae AB11: erythromycin-resistant strain encoded by the erm and mef genes.
chloramphenicol-binding sites and interact with them, resulting in
a higher affinity to the resistant ribosome.
Supplementary data
In conclusion, two series of novel 400-O-arylalkylcarbamoyl and
400-O-((arylalkylamino)-4-oxo-butyl)carbamoyl clarithromycin
derivatives were designed, synthesized and evaluated for their
in vitro antibacterial activities. These derivatives retained excellent
activity against the erythromycin-susceptible strains and showed
significantly improved activity against the erythromycin-resistant
strains. Especially, the series 4 displayed much higher activity than
the series 3 against S. pneumoniae encoded by the erm gene or the
erm and mef genes. Among all of the tested series, compound 4c
was the most effective against S. pneumoniae encoded by the erm
gene, and compound 4a had the most potent activity against
S. pneumoniae encoded by the erm and mef genes. It is noteworthy
that both compounds have a prolonged 400-O-arylalkyl group with
eight to nine atom distances from 400-oxygen atom to aromatic ring.
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.bmcl.2010.04.051.
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Acknowledgements
This research was financially supported by Major R&D Program
of New Drugs–National S&T Key Special Subject of China
(2009ZX09103-115) and National Natural Science Foundation of
China (20872081).