Synthesis, SAR, and antibacterial activity of novel oxazolidinone analogues possessing urea functionality

Article abstract of DOI:10.1016/j.bmcl.2007.09.024

The syntheses of a number of novel oxazolidinone analogues possessing an urea functionality are reported. While the urea derivatives possessing aliphatic and aromatic groups were prepared by the more conventional isocyanate method, the derivatives possess

Full text of DOI:10.1016/j.bmcl.2007.09.024

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 18 (2008) 856–860
Synthesis, SAR, and antibacterial activity of novel
oxazolidinone analogues possessing urea functionalityq
N. Selvakumar,* G. Govinda Rajulu, K. Chandra Shekar Reddy, B. Chandra Chary,
P. Kalyan Kumar, T. Madhavi, K. Praveena, K. Hari Prasada Reddy, Mohammed Takhi,
Arundhuti Mallick, P. V. S. Amarnath, Sreenivas Kandepu and Javed Iqbal
Anti-infectives Discovery Group, Discovery Research, Dr. Reddy’s Laboratories Ltd, Miyapur, Hyderabad 500 049, India
Received 13 March 2007; revised 25 August 2007; accepted 5 September 2007
Available online 8 September 2007
Abstract—The syntheses of a number of novel oxazolidinone analogues possessing an urea functionality are reported. While the
urea derivatives possessing aliphatic and aromatic groups were prepared by the more conventional isocyanate method, the deriva-
tives possessing heterocyclic rings were synthesized by a relatively uncommon but otherwise efficient carbamate chemistry. Though
the SAR resulted in novel compounds possessing in vitro activity equivalent to Linezolid, the compounds possess a range of sub-
stituents that are amenable for altering physicochemical properties of the resultant drug. The antibacterial activity was found to be
not sensitive to the functional groups attached to the urea site regardless of the size and electronic characteristics. Based on in vivo
results, one molecule has been identified as a candidate and additional work such as salt selection, scale-up, etc., are currently under-
way to take the molecule further through development.
Ó 2008 Published by Elsevier Ltd.
The emergence of bacterial resistance to the antibiotics
poses a serious concern for medical professionals during
the last decade.1 In particular, multi-drug-resistant
Gram-positive bacteria2 including methicillin-resistant
Staphylococcus aureus (MRSA)3 and Staphylococcus
epidermidis (MRSE), and vancomycin resistant entero-
cocci (VRE) are of major concern.4 Oxazolidinones are
a new class of synthetic antibacterials with activity
against Gram-positive bacteria and anaerobic bacte-
ria.5,6 They have shown to selectively bind to the 50S
ribosomal subunit and inhibit bacterial translation at
the initiation phase of the protein synthesis.7 This class
of compounds is particularly active against Gram-posi-
tive organisms such as MRSA, MRSE, and VRE. The
novel mechanism of action combined with the biological
activity against resistant organisms aroused widespread
attention and stimulated others to explore chemistry in
the oxazolidinone class.4
(Fig. 1). Owing to certain toxicity concerns, develop-
ment of Eperozolid 2 was terminated and Linezolid 1
became the first compound commercialized worldwide
from oxazolidinone class of antibacterials.8 Further
chemistry in this class of compounds involved modifica-
tions on the right-hand side acetamide group and
changes on the left-hand side piperazine ring. After hav-
ing thoroughly studied the SAR on the acetamide func-
tional group, we turned our attention to modify the
piperazine ring.4 As Eperozolid 2 was said to be toxic
and as Linezolid 1 has not been approved for long-term
F
O
O
N
O
N
H
N
Me
Linezolid, 1
O
Linezolid 1 and Eperozolid 2 were jointly taken for
development by the erstwhile Pharmacia and Upjohn
F
O
O
N
N
N
H
HO
N
Me
O
Keywords: Oxazolidinones; Antibacterial; Linezolid; Urea.
q
DRF Publication No. 639.
Corresponding author. Tel.: +91 40 23045439; fax: +91 40
23045438; e-mail: selvakumarn@drreddys.com
O
Eperozolid, 2
*
Figure 1.
0960-894X/$ - see front matter Ó 2008 Published by Elsevier Ltd.
doi:10.1016/j.bmcl.2007.09.024

N. Selvakumar et al. / Bioorg. Med. Chem. Lett. 18 (2008) 856–860
857
therapy owing to myelosuppression issues, we envi-
sioned that altering the piperazine ring with a more
drug-like urea functionality would provide an answer
for the continous search for safer second generation
oxazolidinone drug. Toward such a goal, we have de-
signed urea functionality on the piperazine nitrogen with
a range of substituents on the urea function that have
the potential to lead to analogues having varied physico-
chemical properties. In this letter, we report our results
on the antibacterial activity of the novel oxazolidinone
molecules possessing the said urea functionality.
A number of new molecules (compounds 4–22) having
substituted urea functionality have been synthesized
and summarized in Tables 1–3 along with their
in vitro antibacterial activity. The syntheses of the
Table 1. In vitro (MIC, lg/mL)a and in vivo (ED50, mg/kg) antibacterial activity of novel urea oxazolidinone compoundsb,c
F
O
H
R
N
N
N
N
O
H
N
Me
O
O
Entry
Compound
R
S.a. 035
S.a. 019
S.a. 446
E.f. 034
E.f. 153
E.fm 154
ED50
13.8
1
2
3
4
5
4
5
6
7
8
H
OH
4
4
2
4
4
8
4
2
2
4
8
4
2
4
4
8
2
2
2
2
4
2
2
2
4
4
4
Me
COCH3
CNHCH3
4
16
4
6
9
16
8
8
8
4
4
7
10
8
8
8
4
4
4
8
9
11
12
4
4
4
2
4
2
4
2
2
2
4
2
MeO
Cl
10
13
4
4
4
4
2
4
11
12
Linezolid
Vancomycin
2
1
2
2
2
1
2
2
2
>32
2
>32
3.91
3.93d
a S.a. 035 = Staphylococcus aureus ATCC 29213; S.a. 019 = Staphylococcus aureus ATCC 33591 (methicillin resistant); S.a. 446 = Staphylococcus
aureus (clinical isolate); E.f. 034 = Enterococcus faecalis ATCC 29212 (vancomycin sensitive); E.f. 153 = Enterococcus faecalis NCTC 12201
(vancomycin resistant) and E.fm 154 = Enterococcus faecium ATCC 12202 (vancomycin resistant).
b The MIC and ED50 values were determined as described previously.4
c All the compounds were prepared by Method A (Scheme 1).
d The ED50 values are for oral route of administration but for vancomycin (SC route).
Table 2. In vitro (MIC, lg/mL)a and in vivo (ED50, mg/kg) antibacterial activity of novel aromatic urea oxazolidinonesb
R2
R3
F
O
H
R1
N
N
N
N
O
H
N
Me
O
O
Entry
Compound
R1
R2
R3
S.a. 035
S.a. 019
S.a. 446
E.f. 034
E.f. 153
E.fm 154
ED50
1
2
3
4
5
6
7
8
14
15
H
H
F
H
4
4
2
4
4
2
2
1
4
2
2
4
2
1
2
2
2
2
2
4
2
2
2
1
2
2
2
2
2
2
2
2
2
1
2
2
>10
18.4
9.1
H
H
16
17
H
H
H
H
H
OCH3
OCH3
Cl
2
2
OCH3
H
Cl
2
4
18
19
2
2
Cl
1
2
>10
Linezolid
Vancomycin
2
>32
2
>32
3.91
3.93c
a See the footnote given in Table 1 for the details about the organisms.
b Compound 15 was prepared as per Method A and the rest of the compounds as per Method B (Scheme 1).
c The ED50 values are for oral route of administration but for vancomycin (SC route).

858
N. Selvakumar et al. / Bioorg. Med. Chem. Lett. 18 (2008) 856–860
Table 3. In vitro (MIC, lg/mL)a (ED50, mg/kg) antibacterial activity of novel heterocyclic urea oxazolidinonesb
F
O
H
R
N
N
N
N
O
H
N
Me
O
O
Entry
1
Compoundb
R
S.a. 035
4
S.a. 019
4
S.a. 446
4
E.f. 034
2
E.f. 153
2
E.fm 154
4
E.fm 154
20
N
O
N
2
3
21
22
2
2
2
2
2
2
1
1
1
1
1
1
18.4
S
N
4
5
Linezolid
Vancomycin
2
1
2
2
2
1
2
2
2
>32
2
>32
3.91
3.93c
a See the footnote given in Table 1 for the details about the organisms.
b All the compounds were prepared by Method A (Scheme 1).
c The ED50 values are for oral route of administration but for vancomycin (SC route).
compounds 4–22 were accomplished, starting from the
known intermediate 3,8 by following two methods
(Scheme 1).9,10 The first method involved the treatment
of the intermediate 3 with phenylcarbamates of appro-
priate amines in DMSO. This method is versatile that
the syntheses of carbamate reagents and the subsequent
treatment of these reagents with the intermediate 3 have
been performed in parallel. It is important to note that
this method of preparing urea is relatively uncommon,
which renders access to important heterocyclic deriva-
tives such as 20, 21, and 22 that are otherwise difficult
to prepare by conventional methods. While all the new
compounds were synthesized using this carbamate meth-
od, the aromatic urea compounds disclosed in the Table
2 were synthesized by a rather conventional method
which involved the treatment of the intermediate 3 with
the corresponding aryl isocyanates. In addition to the
above two methods, it is interesting to note that the syn-
thesis of compound 7 warranted the hitherto unknown
acetyl carbamate which was prepared by treating acetyl
isocyanate11 with phenol.
The analogues of Eperozolid 2 prepared above possess-
ing the substituted urea functionality were screened for
in vitro activity against a panel of Gram-positive organ-
isms and the results are summarized in Tables 1–3. The
unsubstituted urea compound 4 exhibited activity equiv-
alent to Linezolid having MIC values ranging 2–4 lg/
mL. The hydroxyl and methyl substituted compounds
5 and 6 were found to have activity slightly inferior to
that of Linezolid. However, the acetyl urea compound
7 was found to possess poor activity (4–16 lg/mL).
But, it is interesting to note that the corresponding imi-
date compound 8 exhibited activity equivalent to Lin-
ezolid. The in vitro activity of the cycloalkyl
substituted compounds 9–11 suggests the larger cyclo-
alkyl ring (compound 11) to be better than the smaller
ones. The substituted benzyl urea compounds 12 and
13 were also found to be good having same activity as
that of Linezolid.
F
O
O
N
HN
N
H
N
Me
3
Having accomplished preparing many analogues pos-
sessing activity equal to Linezolid, we turned our atten-
tion toward molecules having aryl substituted urea
functionality (Table 2) and heterocycles substituted urea
functionality (Table 3). The substituted aryl urea com-
pounds 14–19 exhibited activity equivalent to Linezolid
irrespective of aryl ring substituents such as fluorine,
methoxy, and chlorine. However, the heterocycle substi-
tuted urea compounds 20–22 showed improved activity.
In particular, the MIC values of vancomycin sensitive
and resistant Enterococcus faecalis and Enterococcus
faecium of the compounds 21 and 22 were one dilution
better (1 lg/mL) compared to Linezolid. This observa-
O
Method A
Method B
RNHCOOPh,
DMSO, rt to 80 ºC
RNCO,
DCM, 0 ºC to rt
F
O
H
O
N
R
N
N
N
H
N
Me
O
4-22
O
Scheme 1.

N. Selvakumar et al. / Bioorg. Med. Chem. Lett. 18 (2008) 856–860
859
6. For a comprehensive list of activities in this area: Phillips,
O. A. Curr. Opin. Invest. Drugs 2003, 4, 117.
7. Swaney, S. M.; Aoki, H.; Ganoza, M. C.; Shinabarger, D.
L. Antimicrob. Agents Chemother. 1998, 42, 3251, and the
references cited therein.
tion indicates the possibility of getting even superior
compounds if a SAR is carried out on the thiazole and
pyridine ring of the compounds 21 and 22.
It is important to note that most of the new analogues
possessing substituted urea functionality were exhibiting
activity equal to Linezolid. Based on the in vitro activ-
ity, the compounds 4, 14, 15, 16, 19, and 21 were scaled
up and subjected for in vivo studies in mice by systemic
infection model.4 The ED50 values of the in vivo exper-
iments following the oral route of administration for all
these compounds were >10 mg/kg except for compound
16 for which the value was 9.1 mg/kg.
8. Brickner, S. J.; Hutchinson, D. K.; Barbachyn, M. R.;
Manninen, P. R.; Ulanowicz, D. A.; Garmon, S. A.;
Grega, K. C.; Hendges, S. K.; Toops, D. S.; Ford, C. W.;
Zurenko, G. E. J. Med. Chem. 1996, 39, 673.
9. Representative experimental procedure: a solution of the
intermediate 3 (100 mg, 0.3 mmol) and phenyl carbamate
(50 mg, 0.36 mmol) in DMSO (2 mL) was stirred at 60 °C
over 3 h. After ascertaining the completion of the reaction
by TLC, the reaction mixture was allowed to attain room
temperature and diluted with half saturated brine (4 mL).
The resultant mixture was extracted with DCM and the
organic extract was washed with water, brine, and dried.
The residue obtained upon evaporation of the solvents
was purified by silica gel chromatography to afford the
urea compound 4 (85 mg, 75%) as a colorless solid. Mp
In conclusion, a number of new oxazolidinone mole-
cules having substituted urea functionality have been
synthesized following an uncommon method of treating
the compound 3 with various carbamates and evaluated
for their antibacterial activity. It was found that most of
the new analogues were exhibiting activity equal to Lin-
ezolid suggesting that the antibacterial activity is not
sensitive to the functional groups attached to the urea
site regardless of the size and electronic characteristics.
Selected compounds were subjected to in vivo studies
that revealed the compound 16 to possess acceptable
ED50 value. Further work, to develop this compound,
such as salt selection, PK, scale-up, and then toxicity
studies, is currently underway.
1
201 °C. IR (KBr) 1738, 1518, 1234, 990 cmÀ1. H NMR
(400 MHz, DMSO-d6) d 8.22 (br t, J = 5.6 Hz, 1H), 7.48
(dd, J = 15.0, 2.7 Hz, 1H), 7.17 (dd, J = 8.7, 2.4 Hz, 1H),
7.16–7.07 (m, 1H), 6.02 (s, 2H), 4.72–4.68 (m, 1H), 4.10–
4.05 (m, 1H), 3.70 (dd, J = 9.1, 6.4 Hz, 1H), 3.45–3.38 (m,
6H), 2.91–2.90 (m, 4H), 1.83 (s, 3H). 13C NMR (DMSO-
d6) d 170.0, 158.0, 154.7 (d, J = 242.4 Hz, 1C), 154.0, 135.5
(d, J = 8.7 Hz, 1C), 133.5 (d, J = 10.6 Hz, 1C), 119.7 (d,
J = 4.2 Hz, 1C), 114.0 (d, J = 2.7 Hz, 1C), 106.6 (d,
J = 26.2 Hz, 1C), 71.5, 50.4 (2C), 47.3, 43.5 (2C), 41.4,
22.4. MS (Electrospray) 380 (M++1), 337. HRMS: (Elec-
trospray method for Na adduct) Calcd for C17H22N5O4F-
Na 402.1554, found 402.1553. HPLC (System 1)4 99.41%
purity.
Acknowledgments
10. Spectral data for selected compounds: compound 14: Mp
245 °C. IR (KBr) 1722, 1660, 1537, 1242 cmÀ1. H NMR
1
We are indebted to Dr. K. Anji Reddy for his constant
support and encouragement. The help extended by Dr.
R. Rajagopalan is greatly acknowledged. We appreciate
the services extended by the Analytical Research Depart-
ment of Discovery Research, Dr. Reddy’s Laboratories
Ltd, for having carried out all the analytical work.
(400 MHz, DMSO-d6)
d 8.59 (s, 1H), 8.22 (br t,
J = 5.9 Hz, 1H), 7.52–7.46 (m, 3H), 7.25–6.91 (m, 5H),
4.72–4.68 (m, 1H), 4.10–4.06 (m, 1H), 3.71 (dd, J = 9.0,
6.6 Hz, 1H), 3.62–3.59 (m, 4H), 3.41–3.39 (m, 2H), 3.00–
2.90 (m, 4H), 1.83 (s, 3H). 13C NMR (50 MHz, DMSO-
d6) d 170.0, 154.9, 154.6 (d, J = 242.4 Hz, 1C), 154.0,
140.5, 135.4 (d, J = 8.8 Hz, 1C), 133.6 (d, J = 10.7 Hz,
1C), 128.3 (2C), 121.8, 119.8, 119.7 (2C), 114.0 (d,
J = 2.7 Hz, 1C), 106.6 (d, J = 25.8 Hz, 1C), 71.6, 50.4
(2C), 47.3, 43.9 (2C), 41.4, 22.4. MS (Electrospray) 456
(M++1), 337. HRMS: (Electrospray method for Na
adduct) Calcd for C23H26N5O4FNa 478.1867, found
478.1870. HPLC (System 1)4 98.39% purity. Compound
Supplementary data
The spectral data of all the final compounds are pro-
vided as supplementary data and can be found in the on-
line version. Supplementary data associated with this
article can be found, in the online version, at
doi:10.1016/j.bmcl.2007.09.024.
21: Mp 217 °C. IR (KBr) 1730, 1656, 1425 cmÀ1
.
1H
NMR (400 MHz, DMSO-d6) d 10.97 (br s, 1H), 8.21 (br
t, J = 5.6 Hz, 1H), 7.49 (dd, J = 14.8, 2.4 Hz, 1H), 7.34
(br s, 1H), 7.19–7.00 (m, 3H), 4.72–4.68 (m, 1H), 4.10–
4.06 (m, 1H), 3.72–3.60 (m, 5H), 3.41–3.38 (m, 2H),
2.98–2.95 (m, 4H), 1.83 (s, 3H). 13C NMR (50 MHz,
DMSO-d6) d 170.0, 162.2, 154.8, 154.7 (d, J = 242.4 Hz,
1C), 154.0, 135.4 (d, J = 9.1 Hz, 1C), 133.7 (d,
J = 4.5 Hz, 1C), 119.9, 119.8, 114.0 (d, J = 2.7 Hz, 1C),
111.8, 106.6 (d, J = 26.2 Hz, 1C), 71.6, 50.3 (2C), 47.3,
43.6 (2C), 41.4, 22.4. MS (Electrospray) 463 (M++1),
337. HRMS: (Electrospray method for M++1 peak)
Calcd for C20H24N6O4FS 463.1564, found 463.1569.
HPLC (System 1)4 98.61% purity.
References and notes
1. Service, R. F. Science 1995, 270, 724.
2. Swartz, M. N. Proc. Natl. Acad. Sci. U.S.A. 1994, 91,
2420.
3. Tomasz, A. N. Engl. J. Med. 1994, 330, 1247.
4. For a comprehensive list of references for this area, see: (a)
Selvakumar, N.; Srinivas, D.; Khera, M. K.; Kumar, M.
S.; Mamidi, N. V. S. R.; Sarnaik, H.; Chandrasekar, C.;
Rao, B. S.; Raheem, M. A.; Das, J.; Iqbal, J.; Rajagopa-
lan, R. J. Med. Chem. 2002, 45, 3953; (b) Selvakumar, N.;
Reddy, B. Y.; Kumar, G. S.; Khera, M. K.; Srinivas, D.;
Kumar, M. S.; Das, J.; Iqbal, J.; Trehan, S. Bioorg. Med.
Chem. Lett. 2006, 16, 4416.
11. The acetyl isocyanate was prepared as reported (Deng,
M.-Z.; Caubere, P.; Senet, J. P.; Lecolier, S. Tetrahedron
1988, 44, 6079) and was treated in situ with phenol to
generate the carbamate (colorless solid) as shown below,
which on treatment with compound 3 following Method A
led to the analogue 7. It is pertinent to note that the
5. Brickner, S. J. Curr. Pharm. Des. 1996, 2, 175.

860
N. Selvakumar et al. / Bioorg. Med. Chem. Lett. 18 (2008) 856–860
F
O
PhOH
O
O
3
H
Me
N
N
N
Me
NCO
N
O
Me
DMSO
H
O
O
7
treatment of acetyl isocyanate in situ with compound 3 as
per Method B did not yield even trace of compound 7,
which neccessitated the preparation of the carbamate as
above for the route A.