Synthesis and antibacterial activity of potent heterocyclic oxazolidinones and the identification of RBx 8700

Article abstract of DOI:10.1016/j.bmcl.2007.10.061

Several potent oxazolidinone antibacterial agents were obtained by systematic modification of the linker between the five-membered heterocycle and the piperazinyl ring of RBx 7644 (Ranbezolid, 1) and its thienyl analogue 2, leading to the identification of an expanded spectrum compound RBx 8700 (6b).

Full text of DOI:10.1016/j.bmcl.2007.10.061

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 17 (2007) 6714–6719
Synthesis and antibacterial activity of potent heterocyclic
oxazolidinones and the identification of RBx 8700
Sonali Rudra,a,* Ajay Yadav,a A. V. S. Raja Rao,a A. S. S. V. Srinivas,a Manisha Pandya,b
Pragya Bhateja,b Tarun Mathur,b Sunita Malhotra,b Ashok Rattan,b
Mohammed Salman,a Anita Mehta,a Ian A. Cliffea and Biswajit Dasa
aDepartment of Medicinal Chemistry, New Drug Discovery Research, Ranbaxy Laboratories Limited, R&D III, Plot No. 20,
Sector-18, Udyog Vihar Industrial Area, Gurgaon, Haryana 122015, India
bDepartment of Infectious Diseases, New Drug Discovery Research, Ranbaxy Laboratories Limited, R&D III, Plot No. 20, Sector-18,
Udyog Vihar Industrial Area, Gurgaon, Haryana 122015, India
Received 25 May 2007; revised 16 October 2007; accepted 16 October 2007
Available online 22 October 2007
Abstract—Several potent oxazolidinone antibacterial agents were obtained by systematic modification of the linker between the five-
membered heterocycle and the piperazinyl ring of RBx 7644 (Ranbezolid, 1) and its thienyl analogue 2, leading to the identification
of an expanded spectrum compound RBx 8700 (6b).
Ó 2007 Elsevier Ltd. All rights reserved.
O
Oxazolidinones have emerged as a new class of anti-
bacterial agents active against Gram-positive nosoco-
mial infections. Linezolid1 (ZyvoxTM, Pfizer) is the
only drug from the oxazolidinone class of com-
pounds to be approved for use in humans. Linezolid
is active against Gram-positive pathogens such as
strains of methicillin-resistant Staphylococcus aureus
(MRSA), methicillin-resistant Staphylococcus epide-
rmidis (MRSE), vancomycin-resistant Enterococcus
faecium (VRE), Streptococcus pyogenes (S. pyogenes)
and Streptococcus pneumoniae (S. pneumoniae).2 Lin-
ezolid is inactive against Gram-negative bacilli and
has modest activity against fastidious Gram-negative
bacteria such as Haemophilus influenzae (H. influen-
zae). Linezolid exhibits its antibacterial activity by
inhibiting bacterial protein synthesis via binding to
the 50S ribosomal subunit and interfering with the
fMet-tRNA binding to the P-site of the ribosomal
peptidyltransferase centre.3
O
O
N
N
NHCOCH3
F
Linezolid (ZyvoxTM/Pfizer)
O
O
N
N
N
O2N
X
NHCOCH3
F
1: X = O (HCl salt), (RBx 7644, Ranbezolid)
2: X = S
We have been interested in furyl and thienyl heterocyclic
derivatives of oxazolidinones,4–8 and have previously
reported the discovery of Ranbezolid9 (RBx 7644, 1)
as a lead molecule active against Gram-positive patho-
gens. RBx 7644 has a 5-nitrofuryl ring linked with a
methylene linker to the piperazin-1-yl-3-phenyloxazoli-
din-2-one core. Herein, we describe the synthesis and
antibacterial activity of a series of compounds 3–6
(Table 1) obtained by varying the linker between the
piperazine and five-membered heterocycle of the furyl
and thienyl compounds 1 and 2, respectively. Compound
Keywords: Antibacterial; Oxazolidinone; RBx 8700; RBx 7644; Ran-
bezolid; Nitrothiophene; Nitrofuran.
*
Corresponding author. Tel.: +91 124 2342001–10x5156; fax: +91 124
2343544; e-mail: sonali.rudra@ranbaxy.com
0960-894X/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2007.10.061

S. Rudra et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6714–6719
Table 1. Structures of compounds (3–11)
6715
R"
O
O
N
N
N
R
W
X
n
NHCOCH3
R'
Compound
X
O
R
W
n
R0
F
R00
H
H
3a
NO2
1
1
1
1
1
CH3
H
3b
4a
4b
5a
S
NO2
NO2
NO2
NO2
F
F
F
F
H
H
H
H
CH3
O
S
O
O
O
O
5b
6a
6b
7
S
O
S
S
S
S
S
S
NO2
NO2
NO2
1
0
0
0
0
0
0
0
F
F
F
F
F
F
F
H
H
H
H
H
H
H
F
O
Direct bond
Direct bond
Direct bond
Direct bond
Direct bond
Direct bond
Direct bond
COCH3
CN
8
9
CHO
NO2
10
11
NO2
H
6b (RBx 8700, Table 1) has a five-membered 5-nitrothi-
ophene attached directly to the piperazine ring, and mod-
ification of this lead compound led to compounds 7–11.
sodium borohydride. These secondary alcohols were
converted to triflate derivatives 14a–b using triflic
anhydride. The triflate derivatives were used to alkylate
the piperazin-1-yl-3-phenyloxazolidin-2-one compound
1511 to give compounds 3a and 3b. Using achiral reverse
phase HPLC (C18 KromasilTM column, UV detector),
compounds 3a and 3b were found to have purities of
96.1% (mobile phase: 20 mM sodium acetate, pH 5.5,
The synthesis of compounds 3–1110 is depicted in
Schemes 1–3. As shown in Scheme 1, 2-acetyl-5-nitrofu-
ran (12a) and 2-acetyl-5-nitrothiophene (12b) were
reduced to their corresponding alcohols (13a–b) with

6716
S. Rudra et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6714–6719
(a)
(b)
O2N
O2N
X
O2N
X
X
OH
O
OTf
12a: X = O
12b: X = S
13a: X = O
13b: X = S
14a: X = O
14b: X = S
O
(c)
O
N
O2N
N
N
O
X
NHCOCH3
O
HN
N
N
F
NHCOCH
3
F
15
3a: X = O
3b: X = S
Scheme 1. Reagents and conditions: (a) NaBH4, THF-H2O, 0 °C, 3 h; (b) triflic anhydride, triethylamine, dichloromethane, 0 °C to rt, 6 h (for 14a),
3 h (for 14b); (c) 15, triethylamine, THF, 0 °C to rt, 24 h, 31% (for 3a), 30% (for 3b).
O
(a)
O
OH
N
N
N
O2N
S
O2N
X
NHCOCH3
O
O
F
16
4a: X = O
4b: X = S
(b)
(c)
Cl
OH
O2N
O
19
O2N
O
O
O
18
O
(a)
O
OH
N
N
N
O2N
O2N
X
X
NHCOCH3
O
O
F
17a: X = O
17b: X = S
5a: X = O
5b: X = S
Scheme 2. Reagents and conditions: (a) 15, EDAC, NMM, HOBt, DMF, 0 °C to rt, 18 h, 93% (for 4b), 35% (for 5a), 13% (for 5b); (b) SO2Cl2, Et3N,
dichloromethane, 0 °C to rt, 4 h; (c) 15, K2CO3, DMF, rt, 18 h, 21%.
R"
O
(a)
(b)
O
N
N
N
R
Br
O2N
R
Br
X
S
X
NHCOCCH3
20: R = NO2
21: R = CHO
20: X = S
24: X = O
R'
(c)
6a: X = O, R = NO2, R' = F, R" = H
6b: X = S, R = NO2, R' = F, R" = H
7: X = S, R = COCH3, R' = F, R" = H
R
Br
8: X = S, R = CN, R' = F, R" = H
9: X = S, R = CHO, R' = F, R" = H
10: X = S, R = NO2, R' = F, R" = F
S
25: R = COCH3
26: R = CN
11: X = S, R = NO2, R' = H, R" = H.
Scheme 3. Reagents and conditions: (a) 15 (trifluoroacetate salt) or 22, N-ethyldiisopropylamine, acetonitrile, 60 °C, 4 h, 46% (for 6b); 80 °C, 30 h,
<10% (for 9); 60 °C, 17 h, 55% (for 10); (b) 23, K2CO3, DMSO, 18 h, 16% (for 11), rt; 15 (hydrochloride salt), NaOH, DMF, 18 h, 59% (for 6a), rt; (c)
15 (trifluoroacetate salt), racBINAP, Cs2CO3, Pd2(dba)3, DMF, 95 °C, 10 h, 12% (for 7), <10% (for 8).
and methanol, 60–40–60% gradient) and 88.8% (mobile
phase: 20 mM sodium acetate, pH 5.5, and methanol,
80–20–80% gradient), respectively, with no other major
peak >5% being detected. The diastereomeric purities
of compounds 3a and 3b were not determined.
An amide bond was formed between the N-piperazinyl
group of compound 15 and 5-nitrothiophene-2-carbox-
ylic acid (16), 3-(5-nitro-2-furyl)acrylic acid (17a) and
3-(5-nitro-2-thienyl)acrylic acid (17b), respectively,
using N-(3-dimethylaminopropyl)-N0-ethylcarbodiimide

S. Rudra et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6714–6719
6717
hydrochloride (EDAC), N-methylmorpholine (NMM)
and 1-hydroxy-benzotriazole (HOBt) to obtain com-
pounds 4b, 5a and 5b (Scheme 2). 5-Nitrofuran-2-car-
boxylic acid (18) was treated with thionyl chloride to
generate the acid chloride 19, which was then used to
acylate the compound 15 to produce compound 4a.
gave amides 4a and 4b which were very active in vitro
and in vivo, with the thienyl analogue 4b being several
fold more active than its methylene analogue 2. Exten-
sion of the oxo linker to an acryloyl linker produced
highly active in vitro compounds (5a and 5b), but with
loss of in vivo activity. The absence of a linker, wherein
a 5-nitrofuryl or 5-nitrothienyl ring is attached directly
to the piperazine compound 15, led in the case of the thi-
ophene analogue to a compound (6b, RBx 8700) having
high activity against staphylococci, enterococci and
streptococci strains, and in the case of the furan ana-
logue to a compound (6a) having low activity.
The synthesis of compounds 6–11 is shown in Scheme
3. Nucleophilic substitution of the bromine of 2-bro-
mo-5-nitrothiophene (20) and 5-bromothiophene-2-car-
boxaldehyde (21) by compound 15 (trifluoroacetate
salt) using N-ethyldiisopropyl amine in acetonitrile at
elevated temperatures led to the synthesis of com-
pounds 6b and 9, respectively. Similarly, nucleophilic
substitution of 20 by the difluorophenyl analogue 22
((S)-N-[[3-[3,5-difluoro-4-(piperazin-1-yl)phenyl]-2-oxo-
5-oxazolidinyl]methyl]-acetamide trifluoro-acetate) led
to the compound 10. For nucleophilic substitution of
20 by the phenyl without fluorine analogue 23((S)-N-
[[3-[4-(piperazin-1-yl)phenyl]-2-oxo-5-oxazolidinyl]methyl]
-acetamide trifluoroacetate), and 2-bromo-5-nitrofuran
(24) by 15 (hydrochloride salt), the reaction was carried
out with inorganic bases such as potassium carbonate
or sodium hydroxide at room temperature to produce
compounds 11 and 6a, respectively. Buchwald’s meth-
od of C–N bond formation12,13 was employed for the
reaction of 2-acetyl-5-bromothiophene (25) or 2-bro-
mo-5-cyanothiophene (26) with compound 15 (trifluo-
roacetate salt) to give compounds 7 and 8, respectively.
In the in vitro experiments, the rank order of potencies
of the thienyl analogues was 6b (the linker is –), 4b
(–CO–) > 5b (–CH2@CH2CO–), ꢀ3b (–CH(CH3)–) > 2
(–CH2–). For the furyl analogues, the rank order was
5a (–CH2@CH2CO–) > 1 (–CH2–), ꢀ3a (–CH(CH3)–) >
4 (–CO–) > 6a (–). It is speculated that the observed
decrease in activity in the thiophene series may be asso-
ciated with a decrease in the planarity of the heterocy-
cle–linker–piperazinyl system. The decrease in activity
in the furan series appears to be less associated with
the presence of mesomeric interactions between the het-
erocycle, linker and piperazinyl groups, and more
related to either a decrease in the steric size of the linker
group (and a concomitant decrease in the size of the
heterocycle–linker–piperazinyl system) or a decrease in
the flexibility of the linker.
The in vitro14 activity (against a panel of resistant and
susceptible Gram-positive pathogens) and in vivo15
activity (against MRSA 562) of the compounds are pre-
sented in Table 2. Replacing the methylene linker of
RBx 7644 (1) or the thienyl analogue 2 with a 1-alkyl-
methylene linker gave the highly active in vitro com-
pounds 3a and 3b. Compound 3a was also active
in vivo. Changing the methylene linker to an oxo linker
A comparison of the furan-containing compounds with
their thiophene analogues reveals some interesting dif-
ferences. In the case of compounds 6a and 6b, in which
there exists a direct attachment of the piperazine ring
nitrogen atom to the 2-position of the 5-membered het-
eroaromatic ring, the thienyl compound 6b has higher
potency. It may be that the activity seen correlates with
charge delocalization from the 5-membered heteroaro-
Table 2. In vitro and in vivo activity
Compound
MIC (lg/ml) (organisms)a
ED50 mg/kg (po) MRSA 562
S.a 25923
MRSA 562
MRSA 33
VRE 6A
E.fa 29212
S.py 19615
S.pn 6303
1
1
1
2
2
2
0.125
1
0.125
8
4.33
>25
9.1
2
3a
8
8
8
8
8
1
1
1
0.25
0.5
1
0.125
0.5
1
0.06
2
1
3b
4a
0.5
1
0.5
n.d.
0.06
0.25
1
0.5
0.5
0.06
0.25
0.5
8
2
>25
8.24
9.77
>25
>25
n.d.
11.15
n.d.
n.d.
>25
>25
n.d.
5.6
2
2
4b
5a
0.125
0.5
0.5
16
0.25
>16
4
0.5
<0.125
0.5
8
0.5
0.5
1
0.125
<0.125
0.5
0.5
0.5
1
5b
6a
16
0.25
>16
2
8
4
4
6b
7
0.25
>16
2
0.25
>16
n.d.
1
0.25
>16
2
0.125
>16
0.25
0.5
0.125
>16
0.5
0.5
0.5
0.5
2
8
9
10
1
0.5
0.25
1
0.5
0.25
1
<0.25
0.25
1
0.25
2
0.25
1
0.5
0.5
11
Linezolid
Vancomycin
2
2
0.5
2
0.5
2
>16
2
2
0.5
1
4
0.5
8.8 (s.c.)
a Organisms: S.a 25923, Staphylococcus aureus ATCC 25923; MRSA 562, methicillin-resistant Staphylococcus aureus 562; MRSA 33, methicillin-
resistant Staphylococcus aureus 33; VRE 6A, vancomycin-resistant Enterococcus faecium 6A; E.fa 29212, Enterococcus faecalis ATCC 29212; S.py
19615, Streptococcus pyogenes ATCC 19615; S.pn 6303, Streptococcus pneumoniae ATCC 6303.

6718
S. Rudra et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6714–6719
matic ring into the 5-nitro group. Such an effect is more
favoured in a 5-nitrothiophene than a 5-nitrofuran be-
cause the development of positive charge (in the ground
state) on the heteroatom is more favourable with thio-
phene than with furan. The charge delocalization is ex-
pected to be assisted by the presence of the 2-amino
group. In compounds 4a and 4b, the thienyl compound
4b also has higher potency. Once again, delocalization
of charge from the heteroaromatic ring into the 5-nitro
group is anticipated, but in this case such delocalization
can also occur into the 2-carboxamido group. As ex-
plained above, the amount of delocalization will be
greater for the thiophene compound, but here the expla-
nation is confused by the possible existence of rotational
isomers arising from the presence of syn and anti
amide groups, leading to the possibility that the
two compounds may adopt different ground-state
conformations.
oxazolidinones.18 Compound 6b was also highly active
against sensitive and multi-drug resistant (MDR) Myco-
bacterium tuberculosis (M. tuberculosis) strains19,20 with
MIC90 values of 0.25 and 1 lg/ml, respectively.
Compound 6b exhibited an expanded range of microbi-
ological activity, so the nitro group was replaced with
other electron-withdrawing groups (compounds 7–9).
The results were disappointing with the acetyl derivative
7 showing no activity at less than 16 lg/ml, the nitrile
derivative 8 showing only modest activity, and the for-
myl derivative 9 showing high activity but no activity
in vivo. Changing the fluorophenyl ring of 6b to a
difluorophenyl ring gave a compound (10) with similar
in vitro activity but reduced in vivo activity. The simple
phenyl analogue 11 was inferior to the monofluorophe-
nyl compound 6b in all aspects.
In summary, changing the methylene linker of com-
pounds 1 (RBx 7644) and 2 led to many compounds
with superior in vitro activities. Compound 6b (RBx
8700) exhibited an expanded spectrum in vitro activity
along with in vivo efficacy.
The furan-containing compound 1 is the more potent of
the pair of methylene-linked compounds 1 and 2. Whilst
mesomeric interactions between the piperazine nitrogen
atoms and the heteroaromatic groups cannot occur in
these cases, the 5-aminomethyl group would be expected
to have an electron-withdrawing inductive effect upon
the aromatic ring. Of more importance, however, may
be the conformational differences arising from rotation
around the methylene linker bonds. Branching of the
methylene linkers by a methyl group results in equipo-
tent compounds, with the thienyl analogue 3b being one-
fold more potent than the furyl analogue 3a against
staphylococci, and 3a being one- or more fold potent
than 3b against enterococci and streptococci. The signif-
icant gain in potency of compounds 3a and 3b over their
methylene counterparts 1 and 2 cannot be explained by
electronic effects, and the introduction of the methyl
groups is probably having a profound effect upon the
compounds, conformational preferences. In addition,
compounds 3a and 3b may exist as diastereoisomers,
and it may be that the isomers possess differing antibac-
terial activities.
Acknowledgments
We thank Drs. Pradip Bhatnagar and Dharam Vir,
Ranbaxy Laboratories Ltd, and Professor Upendra K.
Pandit, University of Netherlands, for their valuable
comments and suggestions; and the Analytical Chemis-
try group for providing the analytical data.
References and notes
1. Brickner, S. J.; Hutchinson, D. K.; Barbachyn, M. R.;
Manninen, P. R.; Ulanowicz, D. A.; Gammon, S. A.;
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4. Mehta, A.; Arora, S. K.; Das, B.; Ray, A.; Rudra, S.;
Rattan, A. PCT WO 02/06278, 2002.
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008389, 2003.
Compounds 5a and 5b were essentially equipotent, and
it is speculated that a complex mixture of mesomeric,
steric and conformational effects is playing major roles
in defining the compounds, activities. It is interesting
to note that Lohray et al.17 have reported on a series
of compounds containing a phenyl group linked to a
piperazine ring nitrogen atom via an extended conju-
gated linker and shown that electron-donating substitu-
ents such as methoxy and electron-withdrawing
substituents such as acetamido have no effect on anti-
bacterial activity.
7. Mehta, A.; Rudra, S.; Raja Rao, A. V. S.; Yadav, A.;
Rattan, A. PCT WO 04/014392, 2004.
8. Salman, M.; Das, B.; Rudra, S.; Yadav, A.; Rattan, A.
PCT WO 05/082899, 2005.
In the in vivo experiments, compounds 3a, 4a, 4b and 6b
were all active against MRSA 562, but slightly less po-
tent than Ranbezolid. The reasons for the potency dif-
ferences were not investigated further, but may be due
to differing pharmacokinetic and metabolic profiles.
Compound 6b showed moderate activity against fastid-
ious Gram-negative bacteria such as H. influenzae
(MIC50 = 8 lg/ml) and good activity against M. catarrh-
alis (MIC50 = 2 lg/ml), thus extending the spectrum of
9. Das, B.; Rudra, S.; Yadav, A.; Ray, A.; Raja Rao, A. V.
S.; Srinivas, A. S. S. V.; Soni, A.; Saini, S.; Shukla, S.;
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S. K.; Rattan, A.; Mehta, A. Bioorg. Med. Chem. Lett.
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10. Analytical data of (6b): 1H NMR (300 MHz, CDCl3) d
7.80 (d, 1H, J = 4.8 Hz, thienyl-H), 7.5 (dd, 1H, Ar-H),
7.11 (dd, 1H, Ar-H), 6.97 (t, 1H, J = 9.1 Hz, Ar-H), 6.01
(d, 1H, J = 4.8 Hz, thienyl-H), 5.94 (t, 1H, NH), 4.77 (m,

S. Rudra et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6714–6719
6719
1H, C5-H), 4.02 (t, 1H, J = 9 Hz), 3.85–3.5 (m, 7H), 3.23
(m, 4H, piperazinyl-H), 2.03 (s, 3H, –COCH3); MS m/z
[rel. int.]: (M+H)+ = 464.1 [30%]; (M+Na)+ = 486.1,
[65%]; (M+K)+ = 502.2, [35%]; (MꢁNO2)+ = 418.3
[100%]; HPLC purity = 98.44%; mp = 171–174 °C.
11. Hutchinson, D. K.; Brickner, S. J.; Gammill, R. V.; Patel,
M. V. U.S. Patent 5700799, 1997.
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and 4 h post infection. The ED50 values were calculated
by the Spearman Karber16 method on day 7 post
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14. In vitro: Minimum inhibitory concentration (MIC) was
determined by an agar dilution method (NCCLS meth-
odology) using doubling dilutions in cation adjusted
Mueller Hinton agar over a concentration range of 16–
0.015 lg/ml with incubation in air at 35 °C for 24 h.
15. In vivo: Swiss albino mice weighing 20 2 g were used in
the study. There were six mice in each group and water
and rodent feed were provided ad libertum throughout.
Lethal systemic infection was caused in mice by injecting
intraperitoneally MLD inoculum of methicillin-resistant
Staphylococcus aureus (MRSA) 562 mixed with 1:1 10%