Synthesis and structure-activity studies of novel homomorpholine oxazolidinone antibacterial agents

Article abstract of DOI:10.1016/j.bmcl.2008.02.052

A novel series of oxazolidinones were synthesized in which the morpholine C-ring of linezolid was replaced with homomorpholine. In addition to investigating the effect of a homomorpholine C-ring on antibacterial activity, the effect of des-, mono-, di-, a

Full text of DOI:10.1016/j.bmcl.2008.02.052

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 19 (2009) 550–553
Synthesis and structure–activity studies of novel homomorpholine
oxazolidinone antibacterial agents
Ji-Young Kim,* Frederick E. Boyer, Allison L. Choy, Michael D. Huband,
Paul J. Pagano and J. V. N. Vara Prasad
Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA
Received 6 December 2007; revised 15 February 2008; accepted 21 February 2008
Available online 26 February 2008
Abstract—A novel series of oxazolidinones were synthesized in which the morpholine C-ring of linezolid was replaced with homo-
morpholine. In addition to investigating the effect of a homomorpholine C-ring on antibacterial activity, the effect of des-, mono-,
di-, and tri-fluoro substitution on the phenyl B-ring was investigated as well. Various C-5 functional groups were also examined,
including acetamides and triazoles and carboxamides.
Ó 2008 Elsevier Ltd. All rights reserved.
Oxazolidinones are a new class of totally synthetic anti-
biotics with activity against Gram-positive organisms
such as methicillin-resistant Staphylococcus aureus
CCH). It was also noted that recently reported oxazolid-
inone analogs with a novel C-5 carboxamide side chain
achieved improved myelotoxicity.5 Thus, homomorpho-
line analogs with the novel side chain (4, R1 = H, Me)
were synthesized in addition to investigate the effect of
such C-5 moiety on the antibacterial potency. The syn-
thesis and the antibacterial activity of our novel homo-
morpholine analogs are reported here.
(MRSA)
and
vancomycin-resistant
enterococci
(VRE).1 Linezolid (ZyvoxTM) 1 is the first drug of this
class to be approved for the treatment of infections
caused by such serious Gram-positive bacteria.2,3 In an
effort to investigate and expand the utility of oxazolidi-
nones as antibacterial agents, a series of analogs were
synthesized in which the morpholine C-ring of linezolid
was replaced with a homomorpholine ring as shown in
structures 2–4. The effect of the homomorpholine ring
on antibacterial activity in comparison to that of linezo-
lid was examined, as well as the effect of des-, mono-,
di-, and tri-fluoro phenyl B-ring substitution (2–4: X,
Y, Z = H; F) in the context of analogs with C-5 amides
(2, R1 = NHAc, NHCOEt). While investigating diverse
functionalities at the C-5 position, it was brought to
our attention that a number of oxazolidinone com-
pounds with the 1,2,3-triazole moiety at the C-5 position
reduced monoamine oxidase inhibition, a known side ef-
fect of oxazolidinones, while maintaining potency com-
parable to that of linezolid.4 It was therefore of interest
to see if the potency was maintained with homomorph-
oline analogs with the triazole moieties (3, R1 = H,
O
X
O
F
N
Y
O
N
O
N
O
Z
R1
N
O
O
2
N
H
X, Y, Z = H; F
1
R1 = NHAc; NHCOEt; NHCOOMe
Linezolid
O
O
X
X
Z
N
Y
N
O
O
N
Y
N
O
O
N
N
R1
Z
NHR1
N
3
4
O
X, Y, Z = H; F
X, Y, Z = H; F
R1 = H; CCH
R1 = H; Me
The synthesis of the C-5 acetamide analogs of the
homomorpholine series is shown in Scheme 1.6 Homo-
morpholine hydrochloride was reacted with 4-fluoroni-
trobenzene (5a), 3,4-difluoronitrobenzene (5b), 3,4,5-
tri-fluorobenzene (5c), and 3,4,5,6-tetrafluoronitroben-
Keywords: Oxazolidinone; Antibacterial agents; Homomorpholine;
Gram-positive; Linezolid; Synthesis of analogs; Structure–activity
relations.
*
Corresponding author. Tel.: +1 860 686 9320; fax: +1 860 686
0590; e-mail: ji-young.kim@pfizer.com
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.02.052

J.-Y. Kim et al. / Bioorg. Med. Chem. Lett. 19 (2009) 550–553
551
O
O
O
X
Z
X
Z
X
X
a
b
c
F
Y
N
Y
N
Y
N
Y
Cbz
NO2
N
H
NO2
NH2
Z
Z
5a: X = Y = Z = H
5b: X= F, Y = Z = H
5c: X = Y = F, Z = H
5d: X = Y = Z = F
6a: X = Y = Z = H
6b: X= F, Y = Z = H
6c: X = Y = F, Z = H
6d: X = Y = Z = F
7a: X = Y = Z = H
7b: X= F, Y = Z = H
7c: X = Y = F, Z = H
7d: X = Y = Z = F
8a: X = Y = Z = H
8b: X= F, Y = Z = H
8c: X = Y = F, Z = H
8d: X = Y = Z = F
X
Z
O
N
2a: X = Y = Z = H
2b: X= F, Y = Z = H
2c: X = Y = F, Z = H
2d: X = Y = Z = F
O
N
O
d
Y
OAc
Cl
NHAc
12:
NH
O
Scheme 1. Reagents and conditions: (a) homomorpholine hydrochloride, (i-Pr)2NEt; for 5a, NMP, 50 °C; for 5b and 5d, NMP, ꢀ20 °C; for 5c,
CH3CN, 0 °C; 88–100%; (b) Raney Ni, H2, THF, 50 psi, 95–100%; (c) CbzCl, pyr, CH2Cl2, rt, 70–100%; (d) (2S)-3-acetamido-1-chloropropan-2-yl
acetate 12, t-BuOLi, DMF, 0 °C, 17–62%.
zene (5d) to give the corresponding des-, mono-, di-, and
tri-fluoro nitroarene intermediates 6a–d, respectively.7
Subsequently following the reduction, the amine func-
tionality in anilines 7a–d was protected as a benzyl car-
bamate (8a–d). The benzyl carbamates 8a–d were then
reacted with (2S)-3-acetamido-1-chloropropan-2-yl ace-
tate 12 and lithium tert-butoxide in DMF to result in the
formation of both the oxazolidinone ring and the C-5
acetamide side chain in a single step (2a–d).
The synthesis of the C-5 triazole analogs (3a–d) is shown
in Schemes 3 and 4.4,8 Starting from the benzyl carba-
mates 8a and 8c, oxazolidinones 2q,r were prepared by
treatment with (2R)-glycidyl butryrate and n-butyllith-
ium. This step led to the closure of the oxazolidinone
ring and cleavage of the resulting butyric ester in one-
pot to form the C-5 primary alcohols. The C-5 primary
alcohol intermediates were converted to mesylates 9a,c
and then to the azide intermediates 10a,c. Subsequently,
the azides were reacted with bicyclo[2.2.1]hepta-2,5-
diene to provide the desired oxazolidinones with C-5 tri-
azole 3a,b.
The preparation of the C-5 ethyl amides (2o,p) and the
C-5 carbamate analogs (2m,n) was achieved by first
forming the tert-butyl carbamate intermediates 2e–h by
reacting the benzyl carbamates 8a–d with (2S)-tert-butyl
3-chloro-2-hydroxypropyl carbamate 13 and lithium
tert-butoxide in DMF. The tert-butyl carbamates 2e–h
were then cleaved with hydrogen chloride. The resulting
hydrochloride salts 2i–l were converted to the C-5
methyl carbamates 2m,n by treatment with methyl chlo-
roformate or to the C-5 ethyl amides 2o,p with propionic
anhydride, respectively (see Scheme 2).
The conversion of C-5-azidomethyl-3,5-difluorophenyl-
oxazolidinone 10c to the corresponding ethynyltriazolo-
3,5-difluorophenyl-oxazolidinone 3d was carried out
utilizing a regioselective Cu(I) catalyzed cycloaddition
as illustrated in Scheme 4.8 The transformation of azide
10c to the trimethylsilyl protected ethynyl triazole 3c
was carried out efficiently with trimethylsilyl 1,3-but-
adiyne, 2,6-lutidine and copper iodide with excellent
X
Z
O
X
Z
O
O
X
Z
b
N
Y
a
N
Y
O
O
N
O
N
Y
N
O
Cbz
N
H
NH2•HCl
NHBoc
2i: X = Y = Z = H
2j: X= F, Y = Z = H
2k: X = Y = F, Z = H
2l: X = Y = Z = F
8a: X = Y = Z = H
8b: X= F, Y = Z = H
8c: X = Y = F, Z = H
8d: X = Y = Z = F
2e: X = Y = Z = H
2f: X= F, Y = Z = H
2g: X = Y = F, Z = H
2h: X = Y = Z = F
2m: X = Y = Z = H, R1 = NHCO2Me
2n: X = Y = F, Z = H, R1 = NHCO2Me
2o: X = Y = F, Z = H, R1 = NHCOEt
2p: X = Y = Z = F, R1 = NHCOEt
X
O
c
N
Y
O
OH
N
O
Cl
NHBoc
13:
Z
R1
Scheme 2. Reagents and conditions: (a) (2S)-tert-butyl 3-chloro-2-hydroxypropyl carbamate 13, t-BuOLi, DMF, 0 °C, 39–97%; (b) 4 M HCl in
dioxane, THF, 0 °C, 48–100%; (c) for 2m,n, NaHCO3, methyl chloroformate, THF/H2O, rt; for 2o,p, NaHCO3, propionic anhydride, THF/H2O, rt;
85–95%.

552
J.-Y. Kim et al. / Bioorg. Med. Chem. Lett. 19 (2009) 550–553
O
X
Z
X
O
O
X
Z
a
b
N
Y
N
Y
N
Y
O
O
Cbz
N
N
O
O
N
H
Z
OMs
OH
8a: X = Y = Z = H
2q: X = Y = Z = H
2r: X = Y = F, Z = H
9a: X = Y = Z = H
8c: X = Y = F, Z = H
9c: X = Y = F, Z = H
X
X
Z
O
O
N
N
O
O
N
O
c
d
Y
N
Y
O
Z
N
N
N3
N
10a: X = Y = Z = H
3a: X = Y = Z = H
3b: X = Y = F, Z = H
10c: X = Y = F, Z = H
Scheme 3. Reagents and conditions: (a) (2R)-glycidyl butryrate, n-BuLi, THF, ꢀ78 °C, 47–82%; (b) NEt3, MsCl, CH2Cl2, 0 °C, 100%; (c) NaN3,
DMF, 75 °C, 84–100%; (d) bicyclo[2.2.1]hepta-2,5-diene, dioxane, 101 °C (reflux), 18–47%.
F
O
F
O
N
F
F
O
O
N
F
O
N
F
a
b
O
N
O
N
O
N
N
O
N
N
N
N
N
N3
TMS
10c
3c
3d
Scheme 4. Reagents and conditions: (a) TMS-1,3-butadiyne, 2,6-lutidine, CuI, CH3CN, rt, 62%; (b) KOH, MeOH, rt, 92%.
regioselectivity. No 1,5-regioisomers were detected in
this reaction. The TMS group in 3c was then cleaved
with potassium hydroxide to give the desired C-5 ethy-
nyl triazolo-3,5-difluorophenyl-oxazolidinone 3d.
The desired carboxamides 4a–h were then synthesized
by reacting the methyl esters 11a–d with either ammonia
or methyl amine.
The homomorpholine oxazolidinone analogs 2–4 were
tested against a panel of Gram-positive bacteria. Mini-
mum inhibitory concentration (MIC, in lg/mL) values
were determined by micro broth methodology.9 The
Escherichia coli in vitro transcription and translation
(TnT) assay was performed in 96-well microtiter plates
using a luciferase reporter system.10 The effects of fluo-
rine substitution on the phenyl ring (B-ring) as well as
the effects of various C-5 substitution on the antibacte-
rial activities are shown in Table 1. MIC data for linezo-
lid 1 are provided for comparison.
The synthesis of C-5 carboxamide analogs (4a–h) is
shown in Scheme 5. The resulting anilines were reacted
with (2R)-methyl glycidate followed by treatment with
1,10-carbonyldiimidazole to afford the corresponding
oxazolidinone C-5 methyl ester intermediates 11a–d.
X
Z
O
N
Y
O
O
X
Z
a
b
N
Y
N
O
NH2
Homomorpholine C-5 acetamide analogs with mono-,
di-, and tri-fluoro phenyl B-rings (2b–d) were roughly
equipotent in vitro as linezolid 1. On the whole, the
difluorophenyl analogs were shown to be more potent
in vitro compared to desfluoro, monofluoro, and tri-
fluorophenyl analogs, with desfluoro analogs generally
being least potent. The in vitro antibacterial activity of
C-5 carboxamide analogs (4a–h) was disappointing as
these compounds were all less potent than linezolid.
However, it has been demonstrated with several difluo-
rophenyl-oxazolidinone analogs that analogs with vari-
ous C-5 functionalities such as methyl carbamate 2n,
ethyl amide 2o, triazolo analog 3b, and ethynyl triazolo
analog 3d resulted in in vitro antibacterial activity com-
parable to linezolid. Overall, novel homomorpholine
oxazolidinones, in which linezolid’s morpholine C-ring
was replaced with the larger homomorpholine ring, have
OMe
O
7a: X = Y = Z = H
7b: X= F, Y = Z = H
7c: X = Y = F, Z = H
7d: X = Y = Z = F
11a: X = Y = Z = H
11b: X= F, Y = Z = H
11c: X = Y = F, Z = H
11d: X = Y = Z = F
4a: X = Y = Z = H, R1 = H
4b: X= F, Y = Z = H, R1 = H
4c: X = Y = F, Z = H, R1 = H
4d: X = Y = Z = F, R1 = H
4e: X = Y = Z = H, R1 = Me
4f: X= F, Y = Z = H, R1 = Me
4g: X = Y = F, Z = H, R1 = Me
4h: X = Y = Z = F, R1 = Me
X
Z
O
N
Y
O
N
O
NHR1
O
Scheme 5. Reagents and conditions: (a) i—(2R)-methyl glycidate,
LiOTf, t-BuOH, 70 °C; ii—CDI, CH2Cl2, rt, 20–59% for two steps; (b)
for 4a–d, NH3, MeOH, rt; for 4e–h, MeNH2, MeOH, rt; 35–39%.

J.-Y. Kim et al. / Bioorg. Med. Chem. Lett. 19 (2009) 550–553
553
Table 1. Minimum inhibitory concentrations (MICs, lg/mL) for compounds 1, 2a–g, 2j, 2m–r, 3a–d, 4a–h
Compound
X
Y
Z
R
EC TnT IC50 (lM)
S. a. MIC
S. p. MIC
S. py. MIC
E. f. MIC
1 linezolid
2a
2b
3.6
2
1
2
4
H
F
F
F
H
F
F
F
H
F
F
F
H
F
H
F
F
F
H
F
F
F
H
F
F
F
H
H
F
H
H
H
F
—
—
8
8
8
16
2
2.30
1.67
3.93
4
2
2
2c
2d
—
—
2
1
1
1
F
2
1
2
2
2e
H
H
F
H
H
H
H
H
H
H
F
—
—
16
32
8
16
32
16
>64
16
1
32
32
8
32
64
32
>64
16
2
2f
2g
—
—
2j
H
H
F
>64
16
2
>64
8
2m
2n
NHC(@O)OMe
NHC(@O)OMe
NHC(@O)Et
NHC(@O)Et
—
—
—
—
—
—
H
1.90
2.10
3.49
1
2o
2p
F
2
2
1
2
F
4
4
4
4
2q
H
F
H
H
H
H
H
H
H
H
H
F
>64
4
>64
4
>64
2
>64
8
2r
3a
H
F
16
2
16
2
8
32
2
3b
3c
1
F
>32
4
4
2
>32
2
3d
4a
F
2
2
H
H
F
32
8
32
16
4
64
8
64
16
8
4b
4c
H
H
5.87
23.4
4
4
4d
4e
F
H
16
32
16
4
16
32
8
16
32
8
32
64
16
8
H
H
F
H
H
H
F
Me
Me
Me
Me
4f
4g
6.37
18.9
4
16
4
16
4h
F
16
32
Strains: S. a., Staphylococcus aureus UC-76 SA-1; S. p., Streptococcus pneumoniae SV1 SP-3; E. f., Enterococcus faecalis MGH-2 EF1-1; S. py.,
Streptococcus pyogenes C-203.
M.; Pagano, P. J.; Ross, D.; Zhu, T.; Zurenko, G. E.;
Vara Prasad, J. V. N. J. Med. Chem. 2007, 50,
5886.
shown to retain antibacterial potency with in vitro activ-
ity of many compounds synthesized in this series compa-
rable to linezolid’s in vitro activity.
6. (a) For experimental details and 1H NMR data, see: Vara
Prasad, J. V. N.; Boyer, F. E.; Kim, J.-Y. WO 2007/
000644 A; (b) Barbachyn, M. R.; Brickner, S. J. WO 95/
07271 A; (c) Perrault, W. R.; Pearlman, B. A.; Godrej, D.
B.; Jegan-Herrnton, P. M.; Gadwood, R. C.; Chan, L.;
Lyster, M. A.; Maloney, M. T. Org. Process Res. Dev.
2003, 7, 533.
References and notes
1. For recent reviews of linezolid, see: (a) Wilcox, M. H.
Expert Opin. Pharmacother. 2005, 6, 2315; (b) Stevens, D.
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7. The nucleophilic aromatic substitution resulted only in the
desired regioisomers in high yields with no other regioi-
somers detected during the reaction. Highly regioselective
reactions of this type, indicated by extreme high yields of
the desired isomers, have been previously reported:
Barbachyn, M. R.; Harris, C. R.; Vara Prasad, J. V. N.
WO 2005/113520 A1.
8. Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless,
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2003, 42, 2010.
9. Clinical and Laboratory Standards Institute (formerly,
National Committee for Clinical Laboratory Standards).
Methods for Antimicrobial Susceptibility Testing of Anaer-
obic Bacteria; Approved Standard, 6th ed.; NCCLS
Document M11-A6; Vol. 24, No. 2.
10. (a) Murray, R. W.; Melchior, E. P.; Hagadorn, J. C.;
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Chem. 2005, 499.
5. Poel, T.-J.; Thomas, R. C.; Adams, W. J.; Aristoff, P.
A.; Barbachyn, M. R.; Blakeman, D. P.; Boyer, F. E.;
Brieland, J.; Brideau, R.; Brodfuehrer, J.; Choy, A. L.;
Dority, M.; Ford, C. W.; Gadwood, R. C.; Hamel, J.
C.; Huband, M. D.; Huber, C.; Kim, J.-Y.; Joseph,