Effects of positional and geometrical isomerism on the biological activity of some novel oxazolidinones

Article abstract of DOI:10.1016/j.bmcl.2004.10.073

Some novel oxazolidinone derivatives have been synthesized and tested for antibacterial activity. Compound 13 was found to be active against Gram-positive pathogens whereas compound 14 was less active. Either less active or inactive molecules were obtained, when benzotriazole was replaced with benzimidazole, benzthiazole, or benzoxazole. However, thioacetamide analogue of 13 produced a potent molecule similar to linezolid in vitro. Some novel oxazolidinone derivatives with benzotriazole as pendant have been synthesized and tested for antibacterial activity. Linearly attached benzotriazole derivative showed more potency compared to angular one in vitro. Out of E/Z-isomers of angularly attached derivatives E-isomer was found to be more potent than Z-isomer. Either less active or inactive molecules were obtained, when benzotriazole was replaced with benzimidazole, benzthiazole, or benzoxazole. Finally, thioacetamide analogue of linear compound gave a lead having activity similar to linezolid in vitro.

Full text of DOI:10.1016/j.bmcl.2004.10.073

Bioorganic & Medicinal Chemistry Letters 15 (2005) 337–343
Effects of positional and geometrical isomerism on the
biological activity of some novel oxazolidinonesI;II
Jagattaran Das,* C. V. Laxman Rao, T. V. R. S. Sastry, M. Roshaiah, P. Gowri Sankar,
Abdul Khadeer, M. Sitaram Kumar, Arundhuti Mallik, N. Selvakumar,
Javed Iqbal and Sanjay Trehan
Discovery Research, Dr. Reddy’s Laboratories Ltd, Miyapur, Hyderabad 500 049, India
Received 9 August 2004; revised 25 October 2004; accepted 25 October 2004
Abstract—Some novel oxazolidinone derivatives with benzotriazole as pendant have been synthesized and tested for antibacterial
activity. Linearly attached benzotriazole derivative showed more potency compared to angular one in vitro. Out of E/Z-isomers
of angularly attached derivatives E-isomer was found to be more potent than Z-isomer. Either less active or inactive molecules were
obtained, when benzotriazole was replaced with benzimidazole, benzthiazole, or benzoxazole. Finally, thioacetamide analogue of
linear compound gave a lead having activity similar to linezolid in vitro.
ꢀ 2004 Elsevier Ltd. All rights reserved.
1. Introduction
organisms such as methicillin-resistant Staphylococcus
aureus (MRSA), vancomycin-resistant Enterococci
(VRE), and glycopeptide intermediate resistant
S. aureus (GISA). Oxazolidinones bind selectively to 50S
ribosomal subunit thereby inhibiting bacterial protein
biosynthesis at an early stage.2 Linezolid is the first drug
from this class of compounds launched in 2000 by
Pharmacia. Subsequently it was tested against 249 clini-
cal isolates of rapidly growing mycobacteria and MIC of
4lg/mL was reported against most of the strains
studied.3 However, thiomorpholine analogue of linezo-
lid, PNU 100480 (Fig. 1) was found to be more potent
having MIC of 0.125lg/mL against mycobacterial
strains.4
Tuberculosis is one of the leading causes of death due to
infection worldwide. Today, nearly one third of world
population is infected with Mycobacterium tuberculosis;
and according to WHO report this number is increasing
every year.1 Both the developed and developing coun-
tries are facing a challenge to combat this disease. The
complexity is multifold in the case of immunocompro-
mised patients acquiring Mycobacterium avium complex
(MAC) infections. The emergence of multidrug resistant
(MDR) M. tuberculosis poses a serious threat to the cur-
rent therapies used for the treatment of tuberculosis.
Therefore, there is an urgent need to develop novel
drugs for tuberculosis.
We have a long-standing interest to develop drugs for
tuberculosis and oxazolidinone class fits well into our
objectives for its unique mechanism of action. Moreover
oxazolidinones are completely synthetic class of mole-
cules having less possibility of developing resistance.5
Oxazolidinones, a completely synthetic antibacterial
class, elicited lots of interest amongst medicinal chemists
because of its activity against resistant Gram-positive
Keywords: Oxazolidinones; E–Z-isomers; Positional isomers; Antibac-
terial; Benzotriazole.
q DRL Publication No. 220-A.
qq A part of this work was presented in 42nd Interscience Conference
on Antimicrobial Agents and Chemotherapy, September 27–30,
2002, San Diego, USA.
O
F
O
N
N
X
H
N
O
X = O, Linezolid
X = S, PNU 100480
*
Corresponding author. Tel.: +91 040 23045439; fax: +91 040
23045438; e-mail: jagat@drreddys.com
Figure 1.
0960-894X/$ - see front matter ꢀ 2004 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2004.10.073

338
J. Das et al. / Bioorg. Med. Chem. Lett. 15 (2005) 337–343
X
benzaldehyde was achieved with NiCl2 and NaBH4 to
obtain the amino alcohol 5. Protection of amine as benz-
ylcarbamate and alcohol as TBDMS ether gave
Y
Z
X
Z
CN
CN
Y
M
M
X,Y,Z = N, C; M = 2 H, CR2, CHR, PhCH, p-NO2C6H4CH, p-NR2C6H4CH etc.
N
N
N
Figure 2.
H
10
Literature search revealed the following common struc-
tures having antituberculosis activity (Fig. 2).6,7
a
2:7
N
N
The combination of two antibacterial agents with differ-
ent mechanisms of action into a single entity to achieve
drugs with dual action has received considerable atten-
tion in the literature.8 We deliberated on the above
chemical structures and decided to hybridize them with
oxazolidinones to explore the antituberculosis activity of
the resulting molecules (Fig. 3).
CN
N
N
N
N
CN
11
12
b
c
N
N
N
N
N
CN
CN
N
O
O
2. Chemistry
N
N
O
O
14
The key step involved in the synthesis of this series of
compounds is the Knoevenagel condensation of alde-
hyde 1 with acetonitrile derivative 2 to give the hybrid
molecule 3 (Scheme 1).
13
NH
NH
O
O
Scheme 3. Reagents and conditions: (a) ClCH2CN, TEA, DMF,
110ꢁC, 50%; (b) ald. 1, benzoic acid, piperidine, toluene, reflux, 40%;
(c) same as (b), 50%.
Synthesis of aldehyde 1 has been depicted in Scheme 2.
Reduction of both nitro and aldehyde groups of 4-nitro-
O
O
O
O
N
Y
X
H
N
X
Z
H
N
Z
N
Y
CN
CN
O
O
X,Y,Z = N, C, O, S
Figure 3.
O
Knoevenegal
Condensation
O
CN
X
X
Z
Y
Z
O
OHC
N
Y
CN
+
O
H
N
H
N
N
O
1
2
3
O
Scheme 1.
OHC
c
TBSO
OHC
O
b
a
TBSO
HO
N
NHCbz
NH2
O
NO2
4
5
6
7
OH
O
TBSO
O
TBSO
f
O
e
d
N
N
O
N
O
O
1
8
9
NH
NH
O
N3
O
Scheme 2. Reagents and conditions: (a) NaBH4, NiCl2, 71%; (b) 1. Cbz–Cl, NaHCO3, 2. TBDMS–Cl, Im, 43%; (c) n-BuLi, (R)-glycidyl butyrate,
À78ꢁC to rt, 55%; (d) 1. MsCl, TEA, 2. NaN3, 76%; (e) MeCOSH, 66%; (f) 1. TBAF, 2. PDC, 63%.

J. Das et al. / Bioorg. Med. Chem. Lett. 15 (2005) 337–343
339
NH2
NH2
compound 6. This compound was converted to 9 follow-
ing well known methods in the literature.9 Deprotection
of TBDMS ether and subsequent oxidation of the result-
ing alcohol with PDC produced the required aldehyde 1.
N
N
(b)
(a)
N
H
CN
N
CN
Me
15
16
17
19
N
N
N
(c)
Initially we decided to synthesize benzotriazole deriva-
tives 3 (Scheme 1, X = Y = Z = N) becau se both the regio-
isomers of benzotriazole 11 and 12 are readily available
and a systematic study of E- and Z-isomers involving 11
and 12 with substituted benzaldehydes have been carried
out by Sanna et al.7 Acetonitrile derivatives 11 and 12
were obtained from benzotriazole and chloroacetonitrile
in 2:7 ratio.7 These two compounds were separated
by column chromatography and spectral data were
compared with the reported values. Compounds 11
and 12 were then condensed with aldehyde 1 under
Knoevenagel conditions to give 13 and 14, respectively,
and only E-isomers were isolated in both the examples
(Scheme 3).
+
+
Cl
CN
N
H
CN
CN
18
NH2
SH
N
S
(d)
(e)
NC
NC
CN
CN
20
21
23
NH2
OH
N
+
O
CN
22
Scheme 4. Reagents and conditions: (a) CNCH2COOH, 4N HCl,
50%; (b) K2CO3, DMF, MeI, 75%; (c) TEA, DMF, 50%; (d) acetic
acid/ethanol, 20%; (e) same as (d), 35%.
N
N
N
H
CN
CN
N
16
H
a
O
N
O
24
NH
N
O
N
N
CN
CN
N
Me
17
Me
b
O
N
O
25
NH
N
N
N
OHC
O
O
N
CN
19
CN
c
N
O
O
NH
N
O
1
26
O
NH
N
S
O
N
CN
CN
S
21
d
O
N
O
27
NH
O
N
O
N
CN
CN
23
O
d
O
N
O
28
NH
O
Scheme 5. Reagents and conditions: (a) KF, dry ethanol, 52%; (b) same as (a), 41%; (c) TEA, toluene, reflux, 50%; (d) CsF, dry ethanol, 15%.

340
J. Das et al. / Bioorg. Med. Chem. Lett. 15 (2005) 337–343
Various acetonitrile derivatives were then prepared for
condensation with aldehyde 1 (Scheme 4). 1,2-Phenylene-
diamine was converted to C-linked imidazol derivative
16 by heating with cyanoacetic acid in 4N HCl, which
was further methylated with methyl iodide to give com-
pound 17. N-Linked imidazol derivative 19 was pre-
pared from imidazol and chloroacetonitrile in DMF
with triethyl amine as base. Benzthiazole derivative 21
and benzoxazole derivative 23 were synthesized from
o-aminothiophenol 20 and o-aminophenol 22, respec-
tively, with malononitrile in ethanol and acetic acid.
Condensation of acetonitrile derivatives with aldehyde 1
under Knoevenagel condition was tried with different
base/solvent combinations. However, Knoevenagel con-
densation was base sensitive and a single base/solvent
combination could not be utilized for all the conver-
sions.10 Compound 16 was condensed with aldehyde 1
N
N
N
N
N
N
NO2
CN
CN
N
N
a
b
+
N
CN
OHC
30
29
12
NO2
NH2
N
N
N
N
N
N
CN
CN
e
c
d
O
31
32
N
O
NHCBz
OH
N
N
N
CN
N
NC
N
+
N
O
O
O
N
N
O
34
N3
33
N3
1.5:1
f
f
N
N
N
CN
N
NC
N
N
O
N
O
O
N
O
NH
NH
14
35
O
O
Scheme 6. Reagents and conditions: (a) TEA, toluene, 50%; (b) NiCl2/NaBH4, 84%; (c) CbzCl, NaHCO3, 57%; (d) n-BuLi, (R)-glycidyl butyrate,
À78ꢁC to rt, 50%; (e) 1. MsCl, TEA, 2. NaN3, DMF, 51%; (f) CH3COSH, 65%.
F
F
39
O
F
F
MeO2C
MeO2C
HO2C
H3C
c
b
a
NO2
NH2
NO2
NO2
36
37
38
F
OH
F
TBDMSO
f
F
OH
F
OHC
e
d
N
O
NHCBz
NHCBz
NH2
42
40
41
43
NH
O
Scheme 7. Reagents and conditions: (a) Na2Cr2O7, H2SO4, 90ꢁC, 70%; (b) MeOH, H2SO4, 93%; (c) PtO2/H2, 95%; (d) LAH, 60%; (e) CbzCl,
NaHCO3, 93%; (f) TBDMSCl, TEA, DMAP, 63%.

J. Das et al. / Bioorg. Med. Chem. Lett. 15 (2005) 337–343
341
F
N
N
OHC
N
N
O
CN
a
N
N
+
N
CN
O
O
44
11
43
NH
F
N
O
O
NH
N
N
N
N
O
CN
CN
N
N
b
O
O
13
45
N
N
O
O
NH
NH
O
S
Scheme 8. Reagents and conditions: (a) KF/dry ethanol, 15%; (b) Lawessonꢀs reagent, dioxane, 41%.
1
to produce 24 in dry ethanol and KF. Similarly com-
pound 17 gave 25 under identical conditions whereas
compound 26 was obtained from 19 and aldehyde 1 with
triethylamine as base. Compounds 21 and 23 could not
be condensed under both the conditions. However, com-
pounds 27 and 28 could be obtained in modest yields on
treatment with CsF in dry ethanol (Scheme 5).
acterized by higher d values for vinylic protons7 in H
NMR and also by 3JC–H (13–14Hz) coupling for vinylic
H and nitrile C by using the ꢁgate decouplingꢀ tech-
1
nique.11 The H NMR values for vinylic protons of all
the compounds have been compiled in Table 1. The
vinylic proton peaks in H NMR appeared at d 8.21–
1
8.70 for all the E-isomers in accordance with the re-
ported values except compound 14. In this case the vinyl-
ic proton appeared at d 6.08. The upfield shift of vinylic
proton for compound 14 was abnormal compared to
other E-isomers. However, the vinylic proton for Z-iso-
mer was found to appear at d 6.22 as expected. The rea-
son for the abnormal behavior of compound 14 is not
clear to us at this moment. In order to prove that com-
pound 14 is really E-isomer we have isolated both E-
and Z-isomers from mixtures of 29 (Scheme 6) by care-
ful column chromatography along with mixture of E-
and Z-isomers and identified them on the basis of spec-
tral data reported.7 Both the isomers were then con-
verted to 14 and 35 following the same sequence of
reactions as depicted in Scheme 6 independently.
Z-Isomer of 14 was prepared following the sequence de-
scribed in Scheme 6. Knoevenagel condensation of 12
with 4-nitrobenzaldehyde gave a mixture of E- and Z-
isomers 29. The mixture of isomers was reduced to the
corresponding mixture of amines 30 with NiCl2Æ6H2O
and NaBH4. Isomeric amines 30 were converted to cor-
responding azidomethyl oxazolidinones 33 and 34 in 3:2
ratio following the known sequence of reactions
(Scheme 2); and at this stage isomers could be separated
by column chromatography. Finally, both E- and Z-iso-
mers 14 and 35 were obtained from azides 33 and 34,
respectively, on treatment with thiolacetic acid.
Synthesis of fluoro derivative of 13 is described in
Scheme 7. 2-Fluoro-4-nitro toluene 36 was oxidized to
2-fluoro-4-nitro benzoic acid 37, which was then esteri-
fied with methanol to give 38. Reduction of both ester
and nitro groups of 38 to amino alcohol 40 in one pot
could not be accomplished. Therefore reduction of nitro
group to amine 39 was carried out with PtO2/H2 and
then to alcohol 40 by lithium aluminum hydride. Amino
group of compound 40 was protected as benzylcarb-
amate (41) and hydroxy group as TBDMS ether to give
compound 42. Aldehyde 43 was then obtained following
the same procedure for aldehyde 1.
3. Biology
All the compounds listed in Table 1 were tested against
Mycobacterium smegmatis MTCC 006 in addition to the
panel of organisms consisted of six reference Gram-pos-
itive bacteria including both sensitive and resistant
strains: S. aureus ATCC 29213 (MSSA), S. aureus
Table 1. 1H NMR (d) values for vinylic protons
Entry
Compd no
d values
Condensation of acetonitrile derivative 11 with aldehyde
43 in presence of KF in dry ethanol yielded 44, the
fluoro analogue of 13. In a separate reaction, 13 was
converted to thioacetamide derivative 45 using Lawes-
sonꢀs reagent (Scheme 8).
1
2
13
14
35
24
25
26
27
28
44
45
8.55
6.08
6.22
8.31
8.22
8.45
8.21
8.32
8.70
8.52
3
4
5
6
It is our observation that Knoevenagel condensation of
aromatic aldehydes with the acetonitrile derivatives dis-
cussed here produced in most of the cases the E-isomer
as the only isolable product. E-Isomers have been char-
7
8
9
10

342
J. Das et al. / Bioorg. Med. Chem. Lett. 15 (2005) 337–343
Table 2. In vitro potency of oxazolidinones
Entry Compd Compound
no
MIC (lg/mL)
M.sma 006 S.a 29213 S.a 49951 S.a 33591 E.f 29212 E.f 12201 E.fm 12202
structure
O
CN
N
N
1
2
3
4
5
6
7
8
13
>32
>32
>32
>32
>32
>32
>32
>32
8
16
8
16
8
16
8
32
8
32
8
32
O
H
N
N
N
H
O
O
CN
N
N
N
O
H
N
N
14
24
25
26
27
28
35
H
O
O
CN
N
O
H
N
N
H
N
>32
>32
16
>32
>32
16
>32
>32
16
>32
>32
32
>32
>32
32
>32
>32
32
H
O
O
CN
N
O
H
N
N
N
Me
H
O
O
CN
N
N
O
H
N
N
H
O
O
CN
N
S
O
O
H
N
N
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
>32
H
O
O
O
CN
N
O
H
N
N
H
N
N
O
N
NC
O
H
N
N
H
O
O
O
CN
N
N
N
N
H
N
N
9
44
45
>32
8
16
16
32
32
32
H
F
O
S
O
CN
N
N
O
H
N
N
10
>32
2
2
2
4
4
4
H
11
12
Linezolid
Streptomycin
2
0.5
2
4
2
2
2
>32
2
>32
2
>32
2
32
a M.sm 006: Mycobacterium smegmatis MTCC 006; S.a 29213: S. aureus ATCC 29213 (MSSA); S.a 49951: S. aureus ATCC 49951 (Smith strain); S.a
33591: S. aureus ATCC 33591 (MRSA); E.f 29212: E. faecalis ATCC 29212; E.f 12201: E. faecalis NCTC 12201 (VREf); E.fm 12202: E. faecium
NCTC 12202 (VREfm).
ATCC 49951 (Smith), S. aureus ATCC 33591 (MRSA),
E. faecalis ATCC 29212, E. faecalis NCTC 12201
(VREf) E. faecium NCTC 12202 (VREfm). MIC was
determined by brothmicro dilution as per the guidelines
prescribed by NCCLS.12 Doubling dilution of the test
compound, in the range of 32–1lg/mL, was carried
out in Mueller Hinton Medium (Difco). The organisms
were inoculated to obtain a final concentration of 1–
5 · 105 cfu/mL and the microtiter plates were incubated
overnight, in ambient air, at 35ꢁC. Linezolid and strep-
tomycin were included as controls.
4. Results
Our hypothesis to hybridize oxazolidinones with frag-
ments having antituberculosis activity to achieve better
molecules for the treatment of tuberculosis was found
to be illusive. None of the compounds tested showed
antibacterial activity against M. smegmatis (Table 2).
However, some of these compounds were found to be
active against the Gram-positive strains mentioned
above. Benzotriazole derivative 13, having attachment
through middle nitrogen (linear attachment), exhibited

J. Das et al. / Bioorg. Med. Chem. Lett. 15 (2005) 337–343
343
moderate activity (MIC, 8lg/mL). On the other hand
compound 14, a positional isomer of 13 (having attach-
ment through terminal nitrogen, i.e., angular attach-
ment), was found to be less active than the linear one.
C-Linked benzimidazole derivative 24 and its methyl
derivative 25 did not show antibacterial activity against
the strains tested whereas N-linked benzimidazole deriv-
ative 26 retained the activity of analogues compound 14.
Derivatives of benzthiazole 27 and benzoxazole 28
were found to be inactive against the strains tested.
Compound 35, Z-isomer of 14 was found to be inactive
too. It is a general observation in oxazolidinone series
that replacement of hydrogen of central aromatic ring
with fluorine, having meta relationship with oxazolidi-
none group, is beneficial as far as MIC is concerned.
However, in this series compound 44, fluoro analogue
of 13, showed reduced antibacterial activity. On the
other hand, thioacetamide analogue (45) of 13 was
found to poses good antibacterial activity (MIC, 2–
4lg/mL) and was the most potent amongst the mole-
cules screened.
R. Rajagopalan for their constant encouragement into
this project.
References and notes
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5. Conclusion
We have synthesized various oxazolidinone derivatives
having positional and geometrical substitutions with
benzotriazole, benzimidazole, benzthiazole, and benz-
oxazole. Contrary to our expectations none of the com-
pounds showed antimycobacterial activity. However,
some of them showed antibacterial activity against
Gram-positive pathogens. Compound having linear
attachment with benzotriazole was found to be the most
potent among the compounds tested. Deviation from
the position of attachment or the geometry of the mole-
cule has dramatic effect on the activity. Heterocycle,
other than benzotriazole, was also not tolerated. Finally,
a lead molecule having activity comparable to linezolid
has been identified.
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Acknowledgements
We are thankful to the analytical department of Discov-
ery Research, particularly Dr. Moses Babu for their
help. We would like to thank Drs. K. Anji Reddy and