Novel promising linezolid analogues: Rational design, synthesis and biological evaluation

Article abstract of DOI:10.1016/j.ejmech.2013.09.035

A new series of 5-substituted oxazolidinones derived from linezolid, having urea and thiourea moieties at the C-5 side chain of the oxazolidinone ring, were prepared and their in vitro antibacterial activity was evaluated. The compound 10f demonstrated high antimicrobial activity, comparable to that of linezolid against Staphylococcus aureus.

Full text of DOI:10.1016/j.ejmech.2013.09.035

Accepted Manuscript
Novel promising linezolid analogues: rational design, synthesis and biological
evaluation
Margherita De Rosa, Anna Zanfardino, Eugenio Notomista, Thomas A. Wichelhaus,
Carmela Saturnino, Mario Varcamonti, Annunziata Soriente
PII:
S0223-5234(13)00608-9
10.1016/j.ejmech.2013.09.035
EJMECH 6438
DOI:
Reference:
To appear in: European Journal of Medicinal Chemistry
Received Date: 6 June 2013
Revised Date: 12 September 2013
Accepted Date: 14 September 2013
Please cite this article as: M. De Rosa, A. Zanfardino, E. Notomista, T.A. Wichelhaus, C. Saturnino, M.
Varcamonti, A. Soriente, Novel promising linezolid analogues: rational design, synthesis and biological
evaluation, European Journal of Medicinal Chemistry (2013), doi: 10.1016/j.ejmech.2013.09.035.
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ACCEPTED MANUSCRIPT
Graphical Abstract
O
R
X
NH NH
O
N
N
O
F
NO2
O
NH
+
F
F

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Highlights
5-substituted oxazolidinones Linezolid analogues were synthesized.
Docking studies of linezolid (thio)urea-derivatives were performed.
Compound 10f demonstrated an activity comparable to that of Linezolid.

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Novel promising linezolid analogues: rational design, synthesis and biological
evaluation.
Margherita De Rosaa, Anna Zanfardinoc, Eugenio Notomistac, Thomas A. Wichelhausd, Carmela
Saturnino,b,* Mario Varcamontic,* and Annunziata Sorientea,*
a
Dipartimento di Chimica e Biologia, Università degli Studi di Salerno, via Giovanni Paolo II, 132, 84084 Fisciano
(SA), Italy.
b
Dipartimento di Farmacia, Università degli Studi di Salerno, via Giovanni Paolo II, 132, 84084 Fisciano (SA), Italy.
c
Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S. Angelo, Via
Cinthia, 80126 Napoli, Italy.
d
Institute of Medical Microbiology and Infection Control, Hospital of Goethe-University, Paul-Ehrlich-Str. 40, 60596
Frankfurt/Main, Germany
Abstract
A new series of 5-substituted oxazolidinones derived from Linezolid, having urea and thiourea
moieties at the C-5 side chain of the oxazolidinone ring, were prepared and their in vitro
antibacterial activity was evaluated. The compound 10f demonstrated high antimicrobial activity,
comparable to that of Linezolid against Staphylococcus aureus.
Keywords:
Linezolid
Oxazolidinone
Thiourea
Antibacterial
Structure-activity relationship
1.Introduction
Today, the rising incidence of multidrug resistance in Gram-positive bacterial pathogens
represents one of the most significant challenge for scientific communities worldwilde highlighting
the need for the search and discovery of new and more effective antibacterial agents. Linezolid
(ZYVOX, Figure 1) [1-3] is the only clinically used drug in the oxazolidinone class, a class of
totally synthetic antibacterials, and has a broad spectrum of activity against Gram-positive bacteria
[4-8]. It is highly effective for the treatment of serious infections caused by Gram-positive
pathogens resistant to other antibiotics including meticillin-resistant Staphylococcus aureus
(MRSA), vancomycin-resistant enterococci (VRE) and penicillin-resistant Streptococcus
pneumonia.
*Corresponding author.
Tel.: +39(089)969584; fax: +39(089)969663; E-mail address:titti@unisa.it (A. Soriente)

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F
O
N
O
N
O
5
A
H
N
O
Figure 1. Linezolid (Zyvox)
Significant to linezolid success are both favorable pharmacokinetic and toxic effect profiles
consistent with oral or intravenous dosing in humans along with near-complete oral bioavailability,
and a number of characteristics appropriate to mitigate against the occurrence of drug resistence. In
fact, linezolid is a completely synthetic drug; thus, no natural and pre-existing pool of resistance
genes would be expected to favor the appearance of resistance mechanisms. Furthermore, it has a
unique mechanism of action which targets bacterial ribosomal protein synthesis at an extremely
early stage and consequently, cross-resistance between the drug and commercially available
antimicrobials would be remote. Unfortunately, the emergence of linezolid-resistance in S. aureus
and other bacteria has already been observed [9-11] highlighting once again the need for finding
novel oxazolidinone-type drugs with improved potency, reduced toxicity and broader spectrum of
activity. Studies into new oxazolidinones with different structural modifications and improved
characteristic is ongoing and the research area is very active [12-17].
In this paper we describe the synthesis and antibacterial activity of previously unreported
linezolid analogues bearing the urea and thiourea functionality at the C-5 position. We used a
computational approach with the structure-activity relationship studies to gain insights into their
design in order to find new derivatives with improved activity.
2. Results and Discussion
2.1. Design and molecular modeling
Several research groups have tried to modify the four moieties of the linezolid molecule (figure
1) to obtain derivatives with improved activity on linezolid-resistant clinical strains. Different
strategies have been used to select changes to linezolid structure including isosteric replacements, in
particular in the case of rings A and C, and rational modelling based on the few available structures
of ribosome-linezolid complexes. Two very recent examples are described in references 18 e 19.
In order to design rationally linezolid derivatives with improved binding, particularly to
ribosomes carrying mutations which confer partial or complete resistance to linezolid, we have
selected as template the crystallographic structure of the 50S subunit of Haloarcula marismortui
ribosome with linezolid and acetyl-phenylalanyl-CCA, an analogue of formyl-methionyl-tRNA
(PDB code: 3CPW). The analysis of this complex suggested that the oxazolidinone ring, the
acetamide NH-CO, and the fluorophenyl ring make very close contacts with the ribosome and are
essential to preserve the optimal conformation for binding, whereas, the acetamide methyl group
and the morpholino ring make significantly less tight interactions. Moreover, the terminal methyl
group points toward a wide solvent accessible cavity (Fig. 2A) lined by linezolid itself (the
fluorophenyl moiety), the acetyl-phenylalanyl moiety and the nucleotides G2540, G2102, A2538,
A2100, A2103 which are relatively close to the acetamidomethyl group. Other nucleotides,

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contributing to the cavity but slightly more distant from linezolid, are A2099, G2646, and U2541.
As the mutations which confer resistance to linezolid increase the dimension and/or the flexibility
of the binding pocket, thus reducing the ribosome/linezolid contacts, we planned to replace the
acetyl moiety of linezolid with progressively larger groups in an attempt to compensate for the
reduced steric complementarity. In a first phase several groups were appended to the nitrogen atom
of linezolid and the resulting derivatives were manually docked into the pocket using linezolid in
3CPW as reference. These screening phase showed that substituted phenyl-(thio)ureas could fit well
into the cavity described above. It is worth noting that linezolid derivatives bearing a 5-thiourea, 5-
dithiocarbamate or 5-thiocarbamate group are effective antimicrobials[20-22] Therefore, three
phenyl-urea derivatives and the corresponding thiourea derivatives (Fig. 3) were select to perform
more accurate docking studies in the 50S subunit of Haloarcula marismortui ribosome using the
bound linezolid molecule as template. However, as it is known that (di)substituted ureas and
thioureas show a complex conformational behavior [18-22], preliminary to the docking studies we
have performed an accurate analysis of the six derivatives in the absence of the ribosome.
Disubstituted (thio)urea-derivatives can adopt the four conformations shown in Fig. 3. The anti-anti
conformer is strongly destabilized due to steric reasons, whereas, the stability of the remaining three
conformations, according to literature, should depend on several factors including the presence of
oxygen or sulphur, the nature of the substituents and the environment [23-27].
A
B
A2100
A2100
A2103
A2103
G2102
G2102
A2099
A2099
A2538
A2538
3.23 3.09
2.74
2.85
G2540
G2540
C
A2100
D
A2100
A2103
A2103
G2102
G2102
A2099
A2099
A2538
A2538
3.67
3.35
4.65
3.76
2.72
3.81
G2540
G2540

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Figure 2. Docking of linezolid (thio)urea-derivatives into the linezolid binding site of Haloarcula
marismortui ribosome (PDB code: 3CPW). Panel A shows the linezolid binding pocket solvent accessible
surface. Panels B-D show, respectively, the docking of the syn-anti conformer of the p-nitro-phenyl-thiourea
derivative, the anti-syn conformer and the syn-syn conformer of the p-nitro-phenyl-urea derivative. Nitrogen,
oxygen and fluorine atoms are colored blue, red and light cyan, respectively. Carbon atoms of ribosome,
linezolid, linezolid derivatives and acethyl-phenylalanyl-CCA are colored white, green, magenta and yellow,
respectively. Yellow lines show potential H-bond or van der Waals contacts; distances are in Å. Red lines
show distances lower than 3 Å. Labels are close to the N9 atoms of the corresponding nucleotides.
Unfortunately, the majority of the structural studies were done on crystals which introduce
intermolecular constrains due, for example, to hydrogen bonding. For this reason we have modelled
the compounds of Figure 3 using two different strategies: the semi-empirical method AM1 was used
to model 1-methyl-3-aryl(thio)ureas, whereas, the structures of the corresponding linezolid
derivatives were modelled in water by using a molecular mechanics strategy (Monte Carlo
minimization). The results are shown in Table 1 which reports the stability of the syn-anti and anti-
syn conformers relatively to that of the syn-syn conformer.
Table 1
Stability of the syn-anti and anti-syn conformers of (thio)urea derivatives of linezolid relatively to
that of the syn-syn conformer.
∆E
Groups
R-a
Ar-
AM1
MonteCarlo
urea thiourea
urea thiourea
Met-/linezolid NO2-Phe-
anti
syn
syn
anti
-0.99
-0.39
-2.26
-3.59
-1.44
0.35
-2.08
-3.14
Met-/linezolid Phe-
anti
syn
syn
anti
-1.30
-2.15
-2.46
-5.25
-1.66
0.87
-2.44
-3.85
Met-/linezolid MetO-Phe-
anti
syn
-0.95
-1.82
-2.37
-4.72
n.d.
n.d.
n.d.
n.d.
syn
anti
a R- was a methyl group in the case of the AM1 analysis and linezolid in the case of the MonteCarlo analysis.

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Both methods suggest a noteworthy difference between ureas and thioureas as already discussed
in several papers [23]. As for thioureas, both AM1 and MonteCarlo methods suggest that the syn-
anti conformer is the most stable, a result in agreement with several known structures of pure
compounds [23,24] but also with the structure of several thiourea/protein complexes (e.g. ligand
0M6 in PDB structure 2G8E; ligand URS in 1BUG; ligand PBD in 3PB7 and other six structures).
syn-syn
syn-anti
X
X
R
Ar
R
H
N
N
H
N
N
H
H
Ar
X
X
H
Ar
H
H
N
N
N
N
R
H
R
Ar
anti-syn
anti-anti
R = -CH3 or
O
O
N
O
N
CH -
2
Ar = phenyl, p-NO2-phenyl,
p-MetO-phenyl
Figure 3. Possible conformers of the 1-alkyl-3-aryl(thio)ureas studied in this paper.
Figure 4A shows the most stable conformation in water for the phenyl and the p-nitro-phenyl
derivatives. It is worth noting that these compounds are able to adopt a “folded conformation”
stabilized by a T shaped interaction between the two aromatic rings. The phenyl ring and the
thiourea moiety are not coplanar as already observed in models and structures [23-25]. In the case
of the urea derivatives it is more difficult to determine the most stable conformation for the lower
∆E values. A recent study on the conformation of symmetric 1,3-dialkyl ureas has shown that the
energy of the anti-syn/syn-anti conformer is only 0.5-0.7 kcal/mol higher than the syn-syn one [26].
On the contrary in the case of 1,3-diphenylurea the energy of the syn-syn conformer was found to
be about 2 kcal/mol higher than the anti-syn/syn-anti one [27]. Given the small ∆E values it is
reasonable to expect that environmental and conformational effect can influence the rotation along
the C-N bonds. Likely this could explain the disagreement between the AM1 and MonteCarlo
methods. According to the MonteCarlo method the anti-syn conformer is the most stable followed
by the syn-syn one.

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A
B
C
D
Figure 4. Monte Carlo minimized models of the (thio)urea linezolid-derivatives. Panel A shows the syn-
anti conformer of the phenyl and the p-nitro-phenyl thiourea derivatives. Panels B-D show, respectively, the
models of the anti-syn, the syn-anti and the syn-syn conformers of the p-nitro-phenyl-urea derivative.
Nitrogen, oxygen, carbon and fluorine atoms are colored blue, red, magenta and light cyan, respectively.
Carbon atoms of phenyl thiourea derivative are colored cyan.
Figure 4B-D show the three possible conformers of p-nitro-phenyl urea derivative modeled in
water. The corresponding conformers of the phenyl urea derivative adopt similar “folded
conformations”. It is interesting to note that the conformations of the urea derivatives, unlike the
thiourea derivatives, are characterized by staking interactions between the aromatic rings. Finally,
several known structures of 1-alkyl-3-arylurea/protein complexes in PDB database show the syn-
syn conformation but in the majority of these complexes the two NH groups make hydrogen bonds
with the same or two adjacent CO groups in the protein (e.g. ligand 0HD in PDB structure 3V8S;
ligand 0QJ in 4EKG; ligand AW0 in 4EQZ; ligand BDQ in 3L5C). On the basis of the energy
calculations and the available experimental structures, the syn-syn and the anti-syn conformers,
likely, are the most stable conformers of the aryl-urea derivatives of linezolid.
The syn-syn, the anti-syn and the syn-anti conformers were docked in the linezolid pocket of
3CPW (figure 2B-D). The syn-anti conformer of the p-nitro-phenyl-thiourea derivative fits
particularly well the cavity (figure 2B): the first NH of the thiourea moiety is still at hydrogen bond
distance from the oxygen of the phosphate of G2540 (about 3.1Å versus 2.85 Å in the case of
linezolid); the nitro-phenyl moiety makes Van der Waals contacts with the phosphate and the ribose
of G2540; the oxygen of the nitro group is at hydrogen bonding distance from the N6 of the adenine
moiety of A2099; one of the aromatic CH in meta to the NO2 group is at about 3.2 Å from the
oxygen of the phosphate of G2540 thus making favorable electrostatic interactions (according to
AM1 the partial charge on this hydrogen is 0.164).

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The anti-syn conformer of the p-nitro-phenyl-urea derivative fits less well (figure 2C) as the anti
conformation at the -CH2-NH- prevent the formation of the hydrogen bond with the phosphate of
G2540, the nitro group is to far from the N6 of the adenine moiety of A2099 to form an hydrogen
bond, the nitrophenyl moiety makes less tight Van der Waals contacts with the phosphate and the
ribose of G2540.
The syn-syn conformer of the p-nitro-phenyl-urea derivative (figure 2D) is still able to make the
hydrogen bond with the phosphate of G2540 but the nitrophenyl moiety makes prevalently intra-
molecular interactions maintaining a conformation similar to that adopted in water. Van der Waals
contacts are formed with the ribose of G2540, but the phenyl ring is too close to the acetyl moiety
of acethyl-phenylalanyl-CCA.
On the basis of these finding we decided to synthesize the three aryl-urea derivatives 10a-c and
the corresponding thiourea derivatives 10d-f.
2.2. Chemistry
The synthetic route to the target compounds 10a-f is shown in Scheme 1. They were prepared
from key intermediate 7 synthesized starting from commercially available morpholine 1 and 3,4-
difluoronitrobenzene 2 in good yield according to published procedure (Scheme 1)[1].
a
c
b
F
NO2
O
NH
+
O
N
NO2
O
N
NH2
F
F
F
3
2
4
1
O
O
d,e
O
O
N
N
H
O
N
N
O
OH
F
6
5
F
f
O
O
A
g
2
O
O
N
N
O
O
N
N
N3
OSO2CH3
4
5
F
F
8
7
h
O
O
R
h
X
O
N
N
O
N
N
O
O
NH2
NH NH
F
F
9
10a: X= O, R= H
10d: X= S, R= H
10b: X= O, R= OMe
10c: X= O, R= NO2
10e: X= S, R= OMe
10f: X= S, R= NO2
Scheme 1. Synthesis of 5-substituted oxazolidinone derivatives. Reagents and conditions: (a) i-Pr2EtN,
AcOEt; (b) HCO2NH4, 10% Pd/C, THF/MeOH; (c) benzyl chloroformate, NaHCO3, acetone/H2O; (d) n-
BuLi, THF, -78°C; (e) (R)-(-)-glycidyl butyrate, -78°C-rt; (f) MsCl, Et3N, CH2Cl2. (g) NaN3, DMF, 70°C;
(h) 10% Pd/C, H2, AcOEt; (i) RPhNCX, CH2Cl2, rt.

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The formation of oxazolidinone ring with defined stereochemistry at the A-ring C-5 position was
accomplished using n-butyllithium and (R)-(-)-glycidyl butyrate [1]. Derivatization of the alcohol 6
to the mesylate 7, followed by nucleophilic displacement of the mesyl group in the presence of
NaN3 in DMF gave the azide 8. Hydrogenation of the azide 8 over Pd/C (10%) in ethyl acetate at
room temperature afforded the amino derivative 9 in quantitative yield [2]. Compound 9 was
reacted with a range of different iso(thio)cyanate reagents to give the target compounds 10a-f in
high yield. All the reported compounds were characterized by analytical spectroscopic methods (1H
and 13C-NMR, MS) and elemental analysis.
2.3. Antimicrobial activity of linezolid analogues
The antimicrobial activities of the various linezolid analogues, all belonging to the class of
oxazolidinones, were tested against Staphylococcus aureus.
Table 2
MICs of Linezolid and linezolid analogues against S. aureus ATCC 29213
Compound
MIC* (µg/mL)
> 100
> 100
> 100
> 100
10
10a
10b
10c
10e
10d
2
10f
Linezolid
1
* MICs present the median of three experiments.
Minimal inhibitory concentrations (MICs) were determined for all linezolid analogues, i.e.
compounds 10a-f, against methicillin-susceptible S. aureus ATCC 29213. 10a-c and 10e showed a
MIC higher than 100 µg/mL, instead 10d was able to inhibit the S. aureus ATCC 29213 at a
concentration of 10 µg/mL. Finally 10f was the most active compound having a MIC of 2 µg/mL
comparable to the activity of Linezolid (Table 2). These finding are in agreement with the results of
the molecular modeling analysis of linezolid derivatives which suggests that urea and thiourea
derivatives should bind to the ribosome with very different orientations. The higher activity of 10f
with respect to 10d could be likely attributed to the additional interactions between the -NO2 group
and the purine ring of A2099. At the moment it is less clear why 10e is not active. A possible
explanation is that the methoxy moiety of 10e is not able to make the hydrogen bond with the N6 of

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A2099 and also is too close to the purine ring. Moreover, other features of 10e like, for example,
impaired penetration into the cells, could contribute to decrease the antimicrobial efficacy. More
accurate analysis will be necessary to address these aspects.
As 10f was considered the most promising candidate for further studies, we tested this linezolid
analogue also against methicillin-resistant S. aureus ATCC 43300 (table 3).
Table 3
MICs of Linezolid and 10f against S. aureus ATCC 29213 and S. aureus ATCC 43300
MIC* (µg/mL)
linezolid
10f
2
S. aureus ATCC 29213
S. aureus ATCC 43300
1
1
1
* MICs present the median of three experiments.
The experimental data indicate that 10f shows similar activity compared to linezolid against
methicillin-susceptible and methicillin-resistant S. aureus. After this important result, our studies
will be directed to the analysis of 10f activity against some linezolid-resistant strains and to the
comprehension of 10f mechanism of action.
3. Conclusion
In summary, a series of novel linezolid analogues has been designed, prepared and tested for
antibacterial activity. The approach based on molecular modeling has been useful and profitable for
the realization of an analog (10f) that we have shown to be highly active against methicillin-
susceptible and methicillin-resistant S. aureus. This result is very promising for the design of
further studies directed against strains of S. aureus resistant to linezolid and to achieve new
analogues starting from 10f.
4. Experimental section
4.1 Molecular modeling
The ZMM-MVM molecular modeling package (ZMM Software Inc.; http://www.zmmsoft.com)
was used for the conformational analysis of linezolid derivatives in water [29]. Atom-atom
interactions were calculated using the AMBER force field with a cutoff distance of 8 Å.
Conformational energy calculations included van der Waals, electrostatic, H-bonds, torsion

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components and hydration component [30]. Electrostatic interactions were calculated with an
environment- and distance-dependent relative dielectric constant. Linezolid derivatives were
prepared using the PyMOL software (DeLano Scientific LLC). Geometry was optimized using the
“Zl” module of ZMM. Partial charges were attributed using the AM1 method in the HyperChem
software (HyperCube Inc., http://www.hyper.com). Optimized derivatives were manually docked
into the linezolid binding site of ribosome structure (3CPW) using the PyMOL software. The
HyperChem software was also used to model 1-methyl-3-aryl(thio)ureas.
4.2 Chemistry. General methods
All reagents and anhydrous solvents were obtained from commercial sources and used without
further purification. All reactions requiring anhydrous conditions were performed under N2
atmosphere and all glassware were flame dried. Elemental analyses were performed on the FlashEA
1112 Series with Thermal Conductivity Detector (Thermo Electron Corporation). 1H and 13C
NMR spectra were recorded on a Bruker AM 250 (250.13 MHz for 1H, 62.89 MHz for 13C),
Bruker DRX 300 (300 MHz for 1H; 75 MHz for 13C) and Bruker DRX 400 (400 MHz for 1H; 100
MHz for 13C). J values are given in Hz. The 1H chemical shifts were referenced to the solvent
peak: CDCl3 (7.26 ppm), and the 13C chemical shifts were referenced to the solvent peak: CDCl3
(77.0 ppm). Mass spectra were recorded on a Micromass Quattro micro API mass spectrometer (EI,
70 eV). IR spectra were recorded on an FT-IR instrument (Bruker Vector 22). Melting points were
performed on DSC 2920 TA INSTRUMENTS. Thin-layer chromatography was performed on
Macherey-Nagel pre-coated aluminium sheets (0.20 mm, silica gel 60 with fluorescent indicator
UV254) in appropriate solvent. Column chromatography was carried out using silica gel 60 (70– 230
mesh ASTM, Merck).
Compounds 3-8 were prepared according to the previously described procedure [1] and their
spectral features matched with those reported in literature.
4.2.1. (S)-5-(aminomethyl)-3-(3-fluoro-4-morpholinophenyl)oxazolidin-2-one (9)
To a solution of azide 8 ( 140 mg, 0.44 mmol) in ethyl acetate (16.5 mL) 10% Pd(C) ( 16.5 mg)
were added. The reaction was carried out under H2 balloon condition and was vigorously stirred at
room temperature overnight. The solution was filtered through a plug of diatomaceous earth and
concentrated under reduced pressure to afford the title compound as white solid (137 mg) which
was used without purification. 1H NMR (CDCl3, 250 MHz): δ 7.45 (dd, 1H, J = 2.35 Hz, 14.5 Hz),
7.13-7.10 (m,1H), 6.91 (t, 1H, J= 9.2 Hz), 4.71- 4.61 (m, 1H), 4.00 (t, 1H, J= 8.7 Hz), 3.87-3.77 (
m, 5H), 3.14-2.87 (m, 6H), 1.7 (bs, 2H). 13C NMR (CDCl3, 62.89 MHz): δ 155.2 (d, J= 245.84 Hz),
154.4, 136.0 (d, J= 8.9 Hz), 133.1 (d, J= 10.5 Hz), 118.6 (d, J= 4.1 Hz), 113.5, 107.1 (d, J= 26.2
Hz), 73.6, 66.7,50.8, 47.4, 44.6. IR (KBr pellet, cm-1): ν 3401, 2952, 1726, 1225. MS: m/z 295
(M+).
4.2.2. Synthesis of 10a-f compounds. General method
In a round bottom flask equipped with a stir bar, to a solution of 9 ( 21 mg,0.07 mmol) in dry
CH2Cl2 (1.61 mL) the appropriate iso (thio)cyanate was added. The reaction was stirred at room
temperature overnight. The solvent was removed under reduced pressure and the resulting residue

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was purified by flash chromatography (CH2Cl2/MeOH) followed by preparative thin layer
chromatography to give the pure final compounds.
4.2.2.1
1-(((S)-3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)-3-phenylurea
(10a )
Purification by silica gel column chromatography (CH2Cl2/MeOH 95/5) gave a white solid
(90% yield), m.p. 218-222°C. [a]20D -18 ° (c 0.67, DMSO) 1H NMR (CDCl3, 400 MHz): δ 7.46 (dd,
1H, J = 2.60 Hz, 15.0 Hz), 7.32- 7.26 (m, 5H), 7.13-7.06 (m, 1H), 7.05-6.94 (m, 2H), 5.75 (bs, 1H),
4.93-4.81 (m, 1H), 4.08 (t, 1H, J= 8.8 Hz), 3.99- 3.88 (m, 5H), 3.84-3.57 (m, 2H), 3.19-3.05 (m,
4H). 13C NMR (CDCl3, 100.03 MHz): δ 156.0, 155.4 (d, J= 246.10 Hz), 154.9, 138.4 (x2), 129.1
(x2), 123.6 (x2), 122.30, 120.3 (x2), 114.2, 108.0 (d, J= 26.0 Hz), 72.8, 66.5 (x2), 51.2 (x2), 47.4,
42.1. IR (KBr pellet, cm-1): ν 3475, 2970, 1736, 1569, 1385. MS: m/z 414 (M+), 437 (M+ Na)+.
Anal Calcd for C21H23N4O4F: C: 60.86, H: 5.59, N: 13.52 . Found C: 60.88, H: 5.56, N 13.46.
4.2.2.2
1-(((S)-3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)-3-
(4-
methoxyphenyl)urea (10b ).
Purification by silica gel column chromatography (CH2Cl2/MeOH 99/1) gave a white solid
(95% yield), m.p. 198-201°C. [a]20D -25 ° (c 0.98, DMSO) 1H NMR (CDCl3, 300 MHz): δ 7.55 (dd,
1H, J = 2.6 Hz, 14.3 Hz), 7.14-7.07 (m, 3H), 6.95-6.86 (m, 3H), 5.28 (bs, 1H), 4.80-4.78 (m, 1H),
4.02 (t, 1H, J= 8.9 Hz), 3.92-3.86 (m, 5 H), 3.81 (s, 3H), 3.69- 3.65 (m, 2H), 3.07- 3.04 (m, 4H). 13C
NMR (CDCl3, 100.03 MHz): δ 155.3, 154.3 (d, J= 246.10 Hz), 147.2 (x2), 141.0 (x2), 136.2, 134.0,
125.5 (x2), 119.9, 117.4 (x2), 114.5, 106.8 (d, J= 31.9 Hz), 72.0, 66.3 (x2), 50.8 (x2), 47.3, 42.0. IR
(KBr pellet, cm-1): ν 3381, 3301, 2950, 1739, 1675, 1634, 1559, 1511, 1244. MS: m/z 467 (M+
Na) +. Anal Calcd for C22H25N4O5F: C: 59.45, H: 5.67, N: 12.61 . Found C: 59.50, H: 5.64, N 12.65.
4.2.2.3
1-(((S)-3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)-3-
(4-
nitrophenyl)urea (10c ).
Purification by silica gel column chromatography (CH2Cl2/MeOH 95/5) gave a yellow solid
1
(90% yield), m.p. 245-248°C. [a]20 -22 ° (c 0.67, DMSO) H NMR (DMSO, 300 MHz): δ 9.40
D
(bs, 1H), 8.13 (d, 2H, J = 12.2 Hz), 7.61 (d, 2H, J = 12.2 Hz), 7.50 (dd, 1H, J = 2.6 Hz, 14.3 Hz),
7.20-7.17 (m, 1H), 7.07-7.01(m, 2H), 4.88-4.75 (m, 1H), 4.11 (t, 1H, J= 9.1 Hz), 3.85-3.72 (m, 5
H), 3.49-3.35 (m, 2H), 2.91- 2.94 (m, 4H).13C NMR (DMSO, 75.5 MHz): δ 155.3, 155.2, 154.2,
150.7 (d, J= 246.10 Hz), 132.0, 130.7, 129.1, 123.8 (x2), 119.1, 114.5, 114.2 (x2), 107.7 (d, J= 26.0
Hz), 72.7, 66.8 (x2), 55.5, 51.1 (x2), 47.5, 42.4. IR (KBr pellet, cm-1): ν 3315, 2960, 1745, 1518,
1381. MS: m/z 460 (M+1) +. Anal Calcd for C21H22N5O6F: C: 54.90, H: 4.83, N: 15.24 . Found
C:54.78, H:4.81, N: 15.28.
4.2.2.4
1-(((S)-3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)-3-phenylthiourea
(10d ).
Purification by silica gel column chromatography (CH2Cl2/MeOH 99/1) gave a white solid
(86% yield), m.p. 163-166°C. [a]20D -26° (c 0.95, DMSO) 1H NMR (DMSO, 250 MHz): δ 9.75 (bs,
1H), 8.05 (bs, 1H), 7.52 (dd, 1H, J = 2.3 Hz, 14.8 Hz), 7.40-7.30 (m, 5H), 7.23-7.19 (m, 1H), 7.15-
7.03 (m, 1H), 4.96-4.88 (m, 1H), 4.13 (t, 1H, J= 9.2 Hz), 3.90- 3.84 (m, 2H), 3.75-3.71(m, 4H),

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3.40-3.34 (m, 1H), 2.94-2.97 (m, 4H). 13C NMR (DMSO, 75.5 MHz): δ 182.0, 154.9 (d, J= 243.9
Hz), 154.4, 139.3, 136.0, 135.9, 129.1 (x2), 124.8 (x2), 123.7, 119.7, 114.6, 107.1 (d, J= 26.1 Hz),
71.6, 66.5 (x2), 51.1 (x2), 47.5, 46.8. IR (KBr pellet, cm-1): ν 3343, 2980, 1736, 1591, 1385. MS:
m/z 430 (M+). Anal Calcd for C21H23 F N4O3S: C: 58.59, H: 5.39, N: 13.01 . Found C: 58.79, H:
5.34, N: 12.97.
4.2.2.5
1-(((S)-3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)-3-(4-
methoxyphenyl)thiourea (10e ).
Purification by silica gel column chromatography (CH2Cl2/MeOH 95/5) gave a white solid
(90% yield), m.p. 150-152°C. [a]20 -30° (c 0.93, DMSO) 1H NMR (DMSO, 250 MHz): δ 9.60 (bs,
D
1H), 7.87 (bs, 1H), 7.50 (dd, 1H, J= 2.1 Hz, 14.8 Hz), 7.22-7.19 (m, 3H), 7.07 (t, 1H, J= 9.5 Hz),
6.88 (d, 2H, J= 8.7 Hz), 4.94- 4.88 (m, 1H), 4.11 (t, 1H, J= 9.0 Hz), 3.90-3.87 (m, 2H), 3.75-3.72
(m, 7H), 2.98-2.94 (m, 5H).13C NMR (DMSO, 75.5 MHz): δ 182.0, 156.9, 154.5 (d, J= 243.9 Hz),
154.2, 135.7 (d, J= 8Hz), 133.4, 131.0, 126.2 (x2), 119.4, 114.4, 114.1 (x2), 106.9 (d, J=
26Hz),71.4, 66.3 (x2), 55.4, 50.8 (x2), 47.3, 46.7. IR (KBr pellet, cm-1): ν 3362, 2995, 1743, 1375.
+
MS: m/z 483 (M+Na) . Anal Calcd for C22H25 F N4O4S: C: 57.38, H: 5.47, N: 12.17 . Found
C:57.25, H:5.49, N: 12.15.
4.2.2.6
1-(((S)-3-(3-fluoro-4-morpholinophenyl)-2-oxooxazolidin-5-yl)methyl)-3-(4-
nitrophenyl)thiourea (10f).
Purification by silica gel column chromatography (CH2Cl2/MeOH 95/5) gave a yellow solid
1
(90% yield), m.p. 190-193°C. [a]20 -23° (c 0.95, DMSO) H NMR (DMSO, 300 MHz): δ 10.30
D
(bs, 1H), 8.55 (bs, 1H), 8.17 (d, 2H, J= 9.2 Hz), 7.82 (d, 2H, J= 9.2 Hz), 7.51 (dd, 1H, J= 2.3 Hz,
14.8 Hz), 7.23-7.20 (m, 1H), 7.07 (t, 1H, J= 9.6 Hz), 5.01- 4.93 (m, 1H), 4.15 (t, 1H, J= 9.0 Hz),
3.94-3.90 (m, 1H), 3.87- 3.81 (m, 1H), 3.74-3.71 (m, 4H), 2.97-2.94 (m, 5H) .13C NMR (DMSO,
62.89 MHz): δ 181.0, 154.7 (d, J= 243.9 Hz), 154.0, 146.0, 142.4, 135.6, 133.3, 124.5 (x2), 120.9
(x2), 119.3, 114.2, 106.7 (d, J=27 Hz), 71.0, 66.2 (x2),50.7 (x2), 47.2, 46.4. IR (KBr pellet, cm-1):
ν 3346, 3104, 1752, 1516, 1328. MS: m/z 475 (M+). Anal Calcd for C21H22FN5O5S: C: 53.04, H:
4.66, N: 14.73 . Found C:53.10, H:4.65, N: 14.76.
4. 3. Minimum Inhibitory Concentration (MIC) determination
Minimal inhibitory concentrations (MICs) of Linezolid and its various analogues were
determined according to microdilution method established by Clinical and Laboratory Standards
Institute (CLSI). Therefore, 95 microliters of cation-adjusted Mueller-Hinton broth supplemented
with the different compounds at various concentrations ranging from 128 to 0.06 µg/mL were added
to each well of a 96-well microtiter plate. Five microliters of a bacterial suspension were added to
each well to yield a final concentration of about 5 x 105 cells/mL. MICs were determined after 16
to 20 h of incubation at 35±2°C. (National Commitee for Clinical Laboratory Standards.
Performance standards for antimicrobial susceptibility testing; Ninth informational supplement.
NCCLS document M100-S9 [ISBN1-56238-358-2]. NCCLS, 940 West Valley Road, Wayne,
Pa19087-1898 USA, 1999.Ref.

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Acknowledgements
We are grateful for the financial support from the Ministero dell’Istruzione, dell’Università e della
Ricerca (MIUR). Our thanks to Dr. Ivano Immediata for experimental support in the characterization of new
compounds.
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