Synthesis and In Vitro Antibacterial Activity of Novel 3-Azabicyclo[3.3.0]octanyl Oxazolidinones

Article abstract of DOI:10.1111/j.1747-0285.2012.01404.x

We synthesized a series of oxazolidinone-type antibacterials in which morpholine C-ring of linezolid has been modified by substituted 3-azabicyclo[3.3.0]octanyl rings. Acetamide or 1,2,3-triazole heterocycle was used as C-5 side chain of oxazolidinone. The resulting series of compounds was then screened in vitro against panel of susceptible and resistant Gram-positive, Gram-negative bacteria, and Mycobacterium tuberculosis (Mtb). Several analogs in this series exhibited potent in vitro antibacterial activity comparable or superior to linezolid against the tested bacteria. Compounds 10a, 10b, 11a, and 15a displayed highly potent activity against M. tuberculosis. Selected compound 10b showed good human microsomal stability and CYP-profile, and showed low activity against hERG channel. We synthesized a series of oxazolidinone-type antibacterials in which morpholine C-ring of linezolid has been modified by substituted 3-azabicyclo[3.3.0]octanyl rings, and acetamide or 1,2,3-triazole heterocycle was used as C-5 side chain of oxazolidinone. Several analogs in this series exhibited potent in vitro antibacterial activity comparable or superior to linezolid against panel of susceptible and resistant Gram-positive, Gram-negative bacteria and Mycobacterium tuberculosis (Mtb). Compounds 10a, 10b, 11a, and 15a displayed highly potent activity against M. tuberculosis.

Full text of DOI:10.1111/j.1747-0285.2012.01404.x

ª 2012 John Wiley & Sons A/S
doi: 10.1111/j.1747-0285.2012.01404.x
Chem Biol Drug Des 2012; 80: 388–397
Research Article
Synthesis and In Vitro Antibacterial Activity of
Novel 3-Azabicyclo[3.3.0]octanyl Oxazolidinones
Deepak Bhattarai1,2, Sun H. Lee1,
active against multiresistant Gram-positive pathogens including
methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-
resistant Enterococci (VRE), and penicillin-resistant Streptococcus
pneumouniae (6,7). In addition, oxazolidinone class antibacterials
have good activity against multidrug resistant Mycobacterium
tuberculosis infections which are one of the most threatening and
Seon H. Seo1, Ghilsoo Nam1,
Soon B. Kang1, Ae N. Pae1, Eunice E. Kim1,
Taegwon Oh3, Sang-Nae Cho3 and
Gyochang Keum1,2,
*
1Center for Neuro-Medicine, Brain Science Institute, Korea Institute
of Science and Technology, Hwarangro 14-gil 5 Seongbuk-gu, Seoul
136-791, Korea
wide-spreading infectious diseases (8–10).
Linezolid binds to 50S ribosomal subunit at the translation step and
inhibits the formation of 70S complex, leading to the inhibition of
protein synthesis, and the binding mode was confirmed by X-ray
crystallography (11). Although linezolid has demonstrated clinical
success as synthetic unnatural antibacterials and is now in the
position of a last resort for the treatment of multi-resistant patho-
gens like vancomycin, clinical emergences of linezolid-resistant bac-
teria including Staphylococci and Enterococci have been reported
(12–14). The most common mechanism of linezolid resistance is
point mutations in the 23S rRNA peptidyl transferase region (15–
17), and recently, a new resistance mechanism mediated by cfr
gene has been reported (18,19). Thus, there is a significant need
for the development of new oxazolidinone series with an improved
potency and spectrum of antibacterial activity.
2Department of Biomolecular Science, University of Science and
Technology, Gajungro 217, Youseong-gu, Daejeon 305-350, Korea
3Department of Microbiology and the Brain Korea 21 Project for the
Medical Sciences, Yonsei University College of Medicine, Seoul
120-752, Republic of Korea
*Corresponding author: Gyochang Keum, gkeum@kist.re.kr
[Correction added on 09 July 2012, after first online publication:
Two additional authors have been added]
We synthesized a series of oxazolidinone-type anti-
bacterials in which morpholine C-ring of linezolid
has been modified by substituted 3-azabicy-
clo[3.3.0]octanyl rings. Acetamide or 1,2,3-triazole
heterocycle was used as C-5 side chain of oxazo-
lidinone. The resulting series of compounds was
then screened in vitro against panel of susceptible
and resistant Gram-positive, Gram-negative bacte-
ria, and Mycobacterium tuberculosis (Mtb). Sev-
eral analogs in this series exhibited potent in vitro
antibacterial activity comparable or superior to
linezolid against the tested bacteria. Compounds
10a, 10b, 11a, and 15a displayed highly potent
activity against M. tuberculosis. Selected com-
pound 10b showed good human microsomal sta-
bility and CYP-profile, and showed low activity
against hERG channel.
Four types of chemical modifications of linezolid and oxazolidinone-
type antibacterials have been reported (20–23), including modifica-
tions on each of the A, B, and C-rings as well as the C-5 side chain
of the A-ring substructure (20,24). Among them, recently, torezolid
(2, Figure 1) (25) and radezolid (26) are under clinical development.
We are interested in conformationally constrained azabicyclic isostere
of the morpholine ring (C-ring) of linezolid. Some oxazolidinones with
Key words: antibacterial agents, drug design, drug discovery,
Mycobacterium tuberculosis, oxazolidinone
Received 23 December 2011, revised 6 April 2012 and accepted for
publication 30 April 2012
Figure 1: Structures of linezolid and torezolid.
Because of innovation gap in the antibacterial drug development,
the growing incidence and prevalence of bacterial resistance to
clinically useful antibacterials are one of the most serious global
health threats of the last two decades (1–4). Oxazolidinones are a
new class of antibacterial agents used to overcome the gap. Linezo-
lid (1, Figure 1), marketed under the trade name Zyvoxꢀ in 2000, is
the first oxazolidinone antibacterials approved for the treatment of
Gram-positive bacterial infections in humans (5). It is consistently
Figure 2: Oxazolidinone analogs with 3-azabicyclo[3.3.0]octanyl
C-rings.
388

Novel 3-Azabicyclo[3.3.0]octanyl Oxazolidinones
bicyclic substituents are reported with good antibacterial activities in
panels of bacteria (27,28). In an effort to improve the potency and
broaden the spectrum of oxazolidinones as antibacterial agents, we
herein described the synthesis and biological evaluation of a series of
oxazolidinone-type antibacterials in which C-ring has been modified by
3-azabicyclo[3.3.0]octanyl ring systems with oxime or cyano group sub-
stituent at C-7 position. Cyano group was known to drastically enhance
the antibacterial activity as a substituent of oxazolidinones (29,30).
142.78, 142.66, 121.46, 115.25, 115.17, 112.73, 112.38, 74.34,
57.21, 41.99, 41.77, 40.81, 40.68; IR (film):ꢀt = 3350, 2952, 1605,
1525, 1491, 1380, 1319 ⁄ cm; HRMS (EI+) calcd for C13H15FN2NaO3
(M+): 289.0964, found: 289.0980.
2-(2-Fluoro-4-nitrophenyl)hexahydro-1H-
spiro[cyclopenta[c]pyrrole-5,2¢-[1,3]dioxolane]
(6)
Acetamide and 1,2,3-triazole are introduced as C-5 side chain of ox-
azolidinone rings. The structural skeleton of designed compounds is
shown in Figure 2, and the resulting library of compounds was then
screened against Gram-positive and Gram-negative bacteria, and
also Mycobacterium tuberculosis (Mtb) H37Rv.
DMSO (0.8 mL, 11.26 mmol) was dissolved in methylene chloride
(13 mL), and the solution was cooled down at )78 ꢂC under argon
environment. Oxalyl chloride (0.483 mL, 5.63 mmol) was added to it
slowly with stirring at the same temperature, and the mixture was
stirred for 1 h. The solution of compound 5 in methylene chloride
(1.00 g, 3.75 mmol) was added to reaction mixture slowly, and the
reaction mixture was stirred for another 2 h. Triethylamine
(2.63 mL, 18.77 mmol) was added to the reaction mixture, and the
temperature was allowed to increase up to room temperature. The
mixture was stirred for another 2 h at room temperature, water
was added to it, and the mixture was extracted with methylene
chloride three times. Combined organic layer was washed with
brine, dried over magnesium sulfate, and concentrated under
reduced pressure. The yellow solid was recrystallized in methanol
to provide 0.93 g (94%) pure compound.
Experimental
Reagents and analysis
Melting points were measured on MEL-TEMPꢁ 3.0 Laboratory
Devices INC, USA. 1H and 13C-NMR spectra were recorded on
Bruker DPX 300 MHz spectrophotometer using CDCl3, CD3OD, and
DMSO-d6 as NMR solvent. TMS was used as an internal standard,
and chemical shift data are reported in parts per million (ppm), and
s, d, t, and m are designated as singlet, doublet, triplet, and multi-
plet, respectively. Coupling constants (J) were reported in hertz (Hz).
Infrared spectra (IR) were recorded on Perkin Elmer 16F PC FT-IR
spectrometer, and frequencies are given in reciprocal centimeters.
Mass spectra were recorded on Waters Acquity UPLC ⁄ Synapt G2
QTOF MS mass spectrometer. The reaction progress was monitored
by thin layer chromatography (TLC).
The yellow crystal from above reaction was dissolved in benzene
(10 mL) with ethylene glycol (0.25 mL, 4.5 mmol) and p-toluene sul-
fonic acid monohydrate (49.9 mg, 0.26 mmol). Solution was refluxed
under argon environment for 3 h using Dean-Stark trap. Reaction mix-
ture was cooled down to room temperature and washed with satu-
rated aqueous sodium carbonate solution. Organic layer was dried in
magnesium sulfate, and the solvent was removed under reduced pres-
sure to provide yellow solid product. The product was purified by sil-
ica gel column using hexane and ethyl acetate (3:1) solution to
provide 0.92 g (80%) of pure compound: mp 117.0–118.5 ꢂC; 1H NMR
(CDCl3, 300 MHz) d 7.88 (m, 2H), 6.57 (t, J = 8.9 Hz, 1H), 3.92 (m, 4H),
3.74 (m, 2H), 3.52 (t, J = 4.5 Hz, 2H), 3.48 (t, J = 3.2 Hz, 1H), 2.86 (m,
1H), 2.17 (dd, J = 13.9, 8.7 Hz, 2H), 1.84 (dd, J = 13.9, 5.8 Hz, 2H);
13C NMR (CDCl3, 75 MHz) d 151.11, 147.86, 142.55, 142.43, 136.87,
136.76, 121.66, 114.10, 114.03, 113.46, 113.39, 112.91, 112.56,
112.44, 112.16, 55.70, 55.62, 54.93, 54.85, 50.09, 48.82, 42.40, 39.82,
39.80, 39.30, 38.88, 38.85; IR (film):ꢀt = 2949, 2882, 1741, 1605, 1525,
1490, 1379, 1321 ⁄ cm; HRMS (EI+) calcd for C15H17FN2NaO4 (M+):
331.1070, found: 331.1080.
2-(2-Fluoro-4-nitrophenyl)octahydrocyclopenta
[c]pyrrol-5-ol (5)
tert-Butyl 5-oxohexahydrocyclopenta[c]pyrrole-2(1H)-carboxylate (10.0 g,
44.4 mmol) was dissolved in methanol, and sodium borohydride
(3.36 g, 88.8 mmol) was added at 0 ꢂC. The reaction mixture was stir-
red at same temperature for 1 h, and then, 15 mL of concentrated
hydrochloric acid was added to it. The mixture was stirred for another
1 h at room temperature. The solvent was removed in reduced
pressure, and the white solid product was used directly without
purification.
The white solid product was dissolved in acetonitrile (100 mL). To
the solution, 3, 4-difluoronitrobenzene (4.91 mL, 44.4 mmol) and N,
N-diisopropylethylamine (23.20 mL, 133.2 mmol) were added, and
the mixture was refluxed for 6 h. It was cooled to room tempera-
ture, and the solvent was removed under reduced pressure. Residue
was dissolved in ethyl acetate and washed with water. Organic
layer was dried by magnesium sulfate. Solution was filtered, and
the solvent was removed under vacuum to provide 8.27 g (70%) of
yellow solid product. It was used for next step without further puri-
fication: mp 98.4–100.9 ꢂC; 1H NMR (CDCl3, 300 MHz) d 7.88 (m,
2H), 6.66 (t, J = 8.7 Hz, 1H), 4.34 (t, J = 4.8 Hz, 1H), 3.60 (m, 4H),
2.82 (m, 2H), 2.21 (m, 2H), 1.70 (t, J = 4.5 Hz, 1H), 1.65 (t,
J = 3.9 Hz, 1H); 13C NMR (CDCl3, 75 MHz) d 152.03, 148.77,
(5R)-3-(3-Fluoro-4-(tetrahydro-1H-spiro
[cyclopenta[c]pyrrole-5,2¢-[1,3]dioxolane]-2(3H)-
yl)phenyl)-5-(hydroxymethyl)oxazolidin-2-one (7)
Compound 6 (0.80 g, 2.61 mmol) was dissolved in ethyl acetate,
and 10% palladium on charcoal (139 mg, 0.13 mmol) was added to
it. Reaction mixture was stirred at room temperature for 6 h under
hydrogen gas environment. The reaction mixture was filtered
through celite, and the solvent was concentrated to provide pure
white solid product 0.72 g (95%).
The white solid product (0.69 g, 2.48 mmol) in above reaction was
dissolved in tetrahydrofuran, and saturated sodium bicarbonate
Chem Biol Drug Des 2012; 80: 388–397
389

Bhattarai et al.
solution (2.17 mL) was added. The temperature of reaction mix-
ture was lowered to 0 ꢂC in argon environment. Benzyl chlorofor-
mate (0.50 mL, 3.46 mmol) was added to it gradually, and the
temperature of reaction mixture was increased gradually to room
temperature. Mixture was stirred at room temperature for 4 h. The
reaction mixture was concentrated and extracted with ethyl acetate.
It was dried over magnesium sulfate, and the solvent was evapo-
rated to yield white solid product. The product was purified by sil-
ica gel column using hexane and ethyl acetate (3:1) solution to
provide 0.74 g (75%) of pure compound.
compound as white solid: mp 143.3–150.6 ꢂC; 1H NMR (CDCl3,
300 MHz) d 8.37 (dd, J = 15.3, 2.1 Hz, 1H), 7.05 (dd, J = 8.7,
2.7 Hz, 1H), 6.69 (t, J = 9.3 Hz, 1H), 4.77 (m, 1H), 4.03 (t,
J = 9.1 Hz, 1H), 3.93 (s, 4H), 3.69 (t, J = 6.6 Hz, 1H), 3.62 (m, 2H),
3.33 (t, J = 7.4 Hz, 2H), 3.23 (d, J = 9.1, 2H), 2.83 (br s, 2H), 2.11
(dd, J = 19.2, 8.1 Hz, 2H), 1.84 (dd, J = 19.5, 3.3 Hz, 2H); 13C NMR
(CDCl3, 75 MHz) d 153.99, 147.86, 134.53, 129.85, 118.55, 117.24,
117.17, 113.46, 107.95, 107.60, 70.57, 64.79, 64.04, 56.47, 53.09,
47.75, 41.02, 39.20; IR (film): ꢀt = 2947, 2105, 1729, 1519, 1519,
1478, 1426, 1318 ⁄ cm; HRMS (EI+) calcd for C19H22FN5NaO4 (M+):
426.1554, found: 426.1548.
The above-prepared pure compound (0.70 g, 1.75 mmol) was dis-
solved in tetrahydrofuran (7 mL). Temperature of the solution was
lowered to )78 ꢂC. n-BuLi (1.3 mL, 2.1 mmol) was added to the
solution gradually. The mixture was stirred at the same temperature
for 1 h. Then, (R)-glycidyl butyrate (0.28 mL, 2.1 mmol) was added
slowly. Temperature was raised to room temperature slowly, and
the reaction mixture was stirred for another 12 h at room tempera-
ture. The solvent was concentrated, and the residue was extracted
with ethyl acetate. Organic layer was washed with saturated
ammonium chloride solution. It was dried over magnesium sulfate,
and the solvent was evaporated to provide white solid product. The
product was purified by silica gel column chromatography using
methylene chloride and methanol (50:1) solution to provide 0.55 g
(82%) of pure compound: mp 173.9–175.8 ꢂC; 1H NMR (CDCl3,
300 MHz) d 7.83 (d, J = 1.2 Hz, 1H), 7.79 (d, J = 1.2 Hz, 1H), 7.23
(dd, J = 15.3, 2.4 Hz, 1H), 6.93 (dd, J = 8.7, 2.7 Hz, 1H), 6.65 (t,
J = 9.3 Hz, 1H), 5.07 (m, 1H), 4.81 (dd, J = 4.1, 1.4 Hz, 2H), 4.14 (t,
J = 9.0 Hz, 1H), 3.91 (dd, J = 9.5, 6.1 Hz, 1H), 3.61 (m, 2H), 3.31
(m, 2H), 3.07 (m, 2H), 2.60 (dd, J = 19.5, 9.0 Hz, 2H), 2.29 (m, 2H);
13C NMR (CDCl3, 75 MHz) d 153.99, 147.86, 134.53, 129.85, 118.55,
117.24, 117.17, 113.46, 107.95, 107.60, 70.57, 64.79, 64.04, 62.91,
56.47, 47.75, 41.02, 39.20; IR (film): ꢀt = 3405, 2959, 1741, 1706,
1523, 1479, 1437, 1318 ⁄ cm; HRMS (EI+) calcd for C19H23FN2NaO5
(M+): 401.1489, found: 401.1497.
N-(((5S)-3-(3-Fluoro-4-(tetrahydro-1H-spiro
[cyclopenta[c]pyrrole-5,2¢-[1,3]dioxolane]-2(3H)-
yl)phenyl)-2-oxo-oxazolidin-5-yl)methyl)
acetamide (9a)
Compound 8 (1.0 g, 2.48 mmol) was dissolved in ethyl acetate
(10 mL), and 10% palladium on charcoal (100 mg, 0.13 mmol), pyri-
dine (0.4 mL, 4.56 mmol), and acetic anhydride (0.35 mL,
3.72 mmol) were added to it. Reaction mixture was stirred at room
temperature for 6 h under hydrogen gas environment. The reaction
mixture was filtered through celite, and the solvent was concen-
trated. The white solid compound was purified by silica gel col-
umn chromatography using methylene chloride and methanol (30:1)
solution to provide 0.62 g (65%) of pure compound as white solid:
mp 177.5–178.4 ꢂC; 1H NMR (CDCl3, 300 MHz)
d 7.38 (dd,
J = 15.3, 2.1 Hz, 1H), 7.05 (dd, J = 8.7, 2.7 Hz, 1H), 6.69 (t,
J = 9.3 Hz, 1H), 6.24 (t, J = 5.7 Hz, 1H), 4.77 (m, 1H), 4.02 (t,
J = 9.1 Hz, 1H), 3.91 (s, 4H), 3.69 (t, J = 6.6 Hz 1H), 3.62 (m, 2H),
3.33 (t, J = 7.4 Hz, 2H), 3.23 (d, J = 9.1, 2H), 2.81 (br s, 2H), 2.11
(dd, J = 19.2, 8.1 Hz, 2H), 2.01 (s, 3H), 1.84 (dd, J = 19.5, 3.3 Hz,
2H); 13C NMR (CDCl3, 75 MHz) d 171.25, 154.78, 151.54, 134.62,
134.49, 129.97, 129.84, 118.54, 117.21, 117.13, 114.36, 107.95,
107.60, 71.93, 64.75, 64.04, 56.36, 47.83, 41.01, 39.20, 23.09; IR
(film): ꢀt = 3315, 2963, 1746, 1659, 1519, 1479, 1420, 1360,
1320 ⁄ cm; HRMS (EI+) calcd for C21H26FN3NaO5 (M+): 442.1754,
found: 442.1759.
(5R)-5-(Azidomethyl)-3-(3-fluoro-4-(tetrahydro-
1H-spiro[cyclopenta[c]pyrrole-5,2¢-
[1,3]dioxolane]-2(3H)-yl)phenyl)oxazolidin-2-one
(8)
(5R)-5-((1H-1,2,3-Triazol-1-yl)methyl)-3-(3-fluoro-
4-(tetrahydro-1H-spiro[cyclopenta[c]pyrrole-5,2¢-
[1,3]dioxolane]-2(3H)-yl)phenyl)oxazolidin-2-one
(9b)
Compound 7 (0.48 g, 1.27 mmol) was dissolved in methylene chlo-
ride, and the temperature was lowered to 0 ꢂC. Triethylamine
(0.45 mL, 3.17 mmol) was slowly added to the solution of alcohol
7, and then, methanesulfonyl chloride (0.2 mL, 2.54 mmol) was
added to the reaction mixture. Temperature was gradually increased
to room temperature, and the mixture was stirred for 4 h. Solvent
was removed in reduced pressure and was extracted with ethyl
acetate. Organic portion was dried in sodium sulfate and concen-
trated. The residue was used to next step directly.
Compound 8 (1 g, 2.48 mmol) was dissolved in vinyl acetate
(10 mL) and then refluxed for 48 h. Reaction mixture was cooled
down to room temperature. Distilled water was added, and then,
the mixture was extracted with ethyl acetate. Organic layer was
dried over magnesium sulfate, and the solvent was evaporated
under reduced pressure. The white solid compound was purified by
silica gel column chromatography using methylene chloride and
methanol (30:1) solution to provide 0.52 g (55%) of pure compound
as white solid: mp 191.1–192.9 ꢂC; 1H NMR (CDCl3, 300 MHz) d
7.80 (d, J = 0.8 Hz), 7.74 (d, J = 0.9 Hz), 7.20 (dd, J = 14.8, 2.5 Hz,
1H), 6.90 (dd, J = 8.8, 2.4 Hz, 1H), 6.68 (t, J = 9.2 Hz, 1H), 5.05 (m,
1H), 4.77 (dd, J = 4.2, 2.1 Hz, 2H), 4.11 (t, J = 9.1 Hz, 1H), 3.94 (s,
4H), 3.88 (t, J = 6.6 Hz 1H), 3.26 (t, J = 7.4 Hz, 2H), 3.19 (d,
J = 9.0, 2H), 2.78 (br s, 2H), 2.11 (dd, J = 19.2, 8.1 Hz, 2H), 1.79
The above product was dissolved in dimethylformamide, and sodium
azide (1.14 g, 17.5 mmol) was added. The mixture was stirred at
80 ꢂC for 4 h. The solvent was concentrated and then extracted
with ethyl acetate. Organic layer was dried over sodium sulfate,
and solvent was removed under reduced pressure. The product was
purified by silica gel column chromatography using methylene chlo-
ride and methanol (50:1) solution to provide 0.46 g (90%) of pure
390
Chem Biol Drug Des 2012; 80: 388–397

Novel 3-Azabicyclo[3.3.0]octanyl Oxazolidinones
(dd, J = 19.5, 3.3 Hz, 2H); 13C NMR (CDCl3, 75 MHz) d 153.59,
134.99, 134.85, 134.47, 129.14, 129.09, 125.06, 118.52, 117.13,
117.06, 114.86, 108.34, 108.0, 70.39, 64.75, 64.04, 56.36, 52.10,
47.65, 41.01, 39.20; IR (film): ꢀt = 3111, 2959, 1733, 1523, 1485,
1420, 1359, 1321 ⁄ cm; HRMS (EI+) calcd for C21H24FN5NaO4 (M+):
452.1710, found: 452.1709.
were added, and the mixture was stirred at room temperature for
18 h. Ethanol was removed under reduced pressure, and the aqueous
layer was extracted with methylene chloride. Organic layer was
washed with brine, dried over magnesium sulfate, and filtered. The
solvent was concentrated, and the compound was purified by column
chromatography using methylene chloride and methanol (20:1) solu-
tion to provide 21.2 mg (20%) of pure compound as white solid: mp
180.4–182.0 ꢂC (decomposed); 1H NMR (CD3OD, 300 MHz) d 7.40 (dd,
J = 15.6, 2.7 Hz, 1H), 7.10 (dd, J = 8.4, 3.0 Hz, 1H), 6.79 (t,
J = 9.3 Hz, 1H), 4.79 (m 1H), 4.12 (t, J = 9.0 Hz, 1H) 3.8 (dd, J = 9.0,
6.3 Hz, 1H), 3.58 (d, J = 4.8 Hz, 2H), 3.55 (m, 2H), 3.21 (m, 3H), 3.00–
2.70 (m, 4H), 2.44 (m, 2H), 2.00 (s, 3H); 13C NMR (CDCl3, 75 MHz) d
172.13, 165.62, 155.22, 153.71, 134.05, 125.19, 115.54, 114.88,
108.36, 108.01, 72.09, 55.73, 54.95, 41.95, 40.61, 35.01, 31.92, 22.42;
IR (film):ꢀt = 3314, 2952, 1736, 1650, 1526, 1417, 1353, 1323 ⁄ cm;
HRMS (EI+) calcd for C19H23FN4O4 (M+): 413.1601, found: 413.1604.
N-(((5S)-3-(3-Fluoro-4-(5-
oxohexahydrocyclopenta[c]pyrrol-2(1H)-
yl)phenyl)-2-oxo-oxazolidin-5-
yl)methyl)acetamide (10a)
Compound 9a (1.0 g) was dissolved in acetone:water (3:1) solution.
To the solution, p-toluene sulfonic acid was added, and the mixture
was refluxed for 6 h. The solution was cooled to room temperature.
Acetone was removed under reduced pressure. The aqueous layer
was extracted by using saturated aqueous sodium bicarbonate solu-
tion and ethyl acetate. Organic layer was dried over magnesium
sulfate, and the solvent was evaporated under reduced pressure.
The white solid compound was purified by silica gel column chro-
matography using methylene chloride and methanol (30:1) solution
to provide 0.67 g (75%) of pure compound as white solid: mp
154.6–155.7 ꢂC; 1H NMR (CDCl3, 300 MHz) d 8.37 (dd, J = 15.3,
2.1 Hz, 1H), 7.05 (dd, J = 8.7, 2.7 Hz, 1H), 6.69 (t, J = 9.3 Hz, 1H),
6.24 (t, J = 5.7 Hz, 1H), 4.77 (m, 1H), 4.03 (t, J = 9.1 Hz, 1H), 3.68
(m, 5H), 3.30 (d, J = 17.4 Hz, 2H), 3.07 (br s, 2H), 2.60 (dd,
J = 19.2, 8.1 Hz, 2H), 2.29 (dd, J = 19.5, 3.3 Hz, 2H), 2.05 (s, 3H);
13C NMR (CDCl3, 75 MHz) d 171.06, 154.48, 153.71, 153.62, 133.91,
133.78, 125.19, 116.00, 115.92, 114.58, 108.19, 107.84, 71.85,
55.96, 55.90, 47.89, 43.33, 42.02, 38.47, 23.08; IR (film):ꢀt = 3301,
2826, 1737, 1659, 1520, 1481, 1420, 1363, 1321 ⁄ cm; HRMS (EI+)
calcd for C19H22FN3NaO4 (M+): 398.1492, found: 398.1491.
(5R)-5-((1H-1,2,3-Triazol-1-yl)methyl)-3-(3-fluoro-
4-(5-(hydroxyimino)hexahydrocyclopenta
[c]pyrrol-2(1H)-yl)phenyl)oxazolidin-2-one (11b)
The compound was prepared according to compound 11a. Pure
compound was white solid, 20 mg (22.8%): mp 186.8–187.7 ꢂC
1
(decomposed); H NMR (DMSO-d6, 300 MHz) d 10.36 (s, 1H), 8.18
(s, 1H), 7.78 (s, 1H), 7.32 (dd, J = 16.1, 2.8 Hz, 1H), 7.04 (dd,
J = 8.9, 2.3 Hz, 1H), 6.75 (t, J = 9.4 Hz, 1H), 5.10 (m, 1H), 4.83 (d,
J = 5.1 Hz, 2H), 4.18 (t, J = 9.0 Hz, 1H), 3.83 (dd, J = 9.3, 5.4 Hz,
1H), 3.47 (m, 2H), 3.10 (m, 2H), 2.83 (m, 2H), 2.63 (m, 2H), 2.27 (m,
2H); 13C NMR (CDCl3, 75 MHz) d 172.23, 165.46, 154.32, 153.71,
134.43, 133.73, 125.46, 115.34, 108.36, 108.27, 70.61, 55.51, 54.72,
51.98, 49.23, 40.48, 34.76, 31.71; IR (film):ꢀt = 3150, 2850, 1738,
1566, 1519, 1483, 1365, 1330 ⁄ cm; HRMS (EI+) calcd for
C19H21FN6NaO3 (M+): 423.1557, found: 423.1555.
(5R)-5-((1H-1,2,3-Triazol-1-yl)methyl)-3-(3-fluoro-
4-(5-oxohexahydrocyclopenta[c]pyrrol-2(1H)-
yl)phenyl)oxazolidin-2-one (10b)
N-(((5S)-3-(3-Fluoro-4-(5-(methoxyimino)
hexahydrocyclopenta[c]pyrrol-2(1H)-yl)phenyl)-
2-oxo-oxazolidin-5-yl)methyl)acetamide (12a)
Compound 12a was prepared according to compound 11a. The reac-
tion time was 48 h. Pure compound was white solid, 100 mg (92.8%):
mp 153.4–154.4 ꢂC; 1H NMR (CD3OD, 300 MHz) d 7.39 (dd, J = 15.5,
2.9 Hz, 1H), 7.09 (dd, J = 8.7, 2.7 Hz, 1H), 6.77 (t, J = 9.3 Hz, 1H),
4.79 (m, 1H), 4.10 (t, J = 8.9 Hz, 1H), 3.83 (s, 3H), 3.78 (m, 1H), 3.57
(d, J = 5.4 Hz, 2H), 3.52 (m, 2H), 3.20 (m, 2H), 2.92 (m, 2H), 2.76 (m,
2H), 2.44 (m, 1H), 2.40 (m, 1H), 2.00 (s, 3H); 13C NMR (CD3OD,
75 MHz) d 172.90, 165.95, 155.71, 153.84, 150.64, 134.19, 129.54,
115.95, 115.10, 108.11, 107.76, 72.30, 60.57, 55.97, 55.26, 55.20,
42.03, 40.94, 40.71, 35.14, 32.39, 21.31; IR (film):ꢀt = 3296, 2954,
2437, 1731, 1642, 1523, 1479, 1421, 1364, 1323 ⁄ cm; HRMS (EI+)
calcd for C20H25FN4NaO4 (M+): 427.1758, found: 427.1759.
The compound was prepared according to compound 10a. Pure
compound was white solid, 0.88 g (98%): mp 145.7–146.9 ꢂC; 1H
NMR (CDCl3, 300 MHz) d 7.83 (d, J = 1.2 Hz, 1H), 7.79 (d,
J = 1.2 Hz, 1H), 7.23 (dd, J = 15.3, 2.4 Hz, 1H), 6.93 (dd, J = 8.7,
2.7 Hz, 1H), 6.65 (t, J = 9.3 Hz, 1H), 5.07 (m, 1H), 4.81 (dd, J = 4.1,
1.4 Hz, 2H), 4.14 (t, J = 9.0 Hz, 1H), 3.91 (dd, J = 9.5, 6.1 Hz, 1H),
3.61 (m, 2H), 3.31 (m, 2H), 3.07 (m, 2H), 2.60 (dd, J = 19.5, 9.0 Hz,
2H), 2.29 (m, 2H); 13C NMR (CDCl3, 75 MHz) d 171.56, 153.71,
153.62, 134.27, 134.15, 134.02, 128.70, 128.57, 125.19, 115.96,
115.88, 115.04, 108.45, 108.10, 70.51, 55.85, 55.78, 52.09, 47.67,
43.29, 38.40; IR (film): ꢀt = 3129, 2956, 1740, 1519, 1481, 1421,
1361, 1320 ⁄ cm; HRMS (EI+) calcd for C19H20FN5NaO3 (M+):
408.1448, found: 408.1453.
N-(((5S)-3-(3-Fluoro-4-(5-(hydroxyimino)
(5R)-5-((1H-1,2,3-Triazol-1-yl)methyl)-3-(3-fluoro-
4-(5-(methoxyimino)hexahydrocyclopenta
[c]pyrrol-2(1H)-yl)phenyl)oxazolidin-2-one (12b)
Compound 12b was prepared according to compound 11a. The
reaction time was 48 h. Pure compound was white solid, 98.2 mg
(92%): mp 172.6–174.7 ꢂC; H NMR (DMSO-d6, 300 MHz) d 8.18 (d,
hexahydrocyclopenta[c]pyrrol-2(1H)-yl)phenyl)-
2-oxo-oxazolidin-5-yl)methyl)acetamide (11a)
Compound 10a (0.1 g, 0.27 mmol) was dissolved in ethanol and dis-
tilled water (2:1). To the solution, sodium bicarbonate (24.6 mg,
0.29 mmol) and hydroxylamine hydrochloride (27.8 mg, 0.4 mmol)
Chem Biol Drug Des 2012; 80: 388–397
391

Bhattarai et al.
J = 0.9 Hz, 1H), 7.78 (d, J = 1.2 Hz, 1H), 7.32 (dd, J = 15.6, 2.4 Hz,
1H), 7.02 (dd, J = 8.7, 2.1 Hz, 1H), 6.75 (t, J = 9.3 Hz, 1H), 5.11 (m,
1H), 4.84 (d, J = 4.8 Hz, 2H), 4.19 (t, J = 9.3 Hz, 1H), 3.84 (dd,
J = 9.3, 6.0 Hz, 1H), 3.75 (s, 3H), 3.47 (m, 2H), 3.11 (m, 2H), 2.85
(m, 2H), 2.66 (m, 2H), 2.32 (m, 2H); 13C NMR (DMSO-d6, 75 MHz) d
165.15, 154.28, 153.36, 150.18, 134.33, 129.62, 116.70, 115.64,
108.23, 107.90, 71.42, 61.61, 56.61, 56.34, 55.65, 52.50, 48.01,
35.51, 33.13; IR (film): ꢀt = 3104, 2955, 2109, 1732, 1524, 1480,
1449, 1422, 1365, 1321 ⁄ cm; HRMS (EI+) calcd for C20H23FN6NaO3
(M+): 437.1713, found: 437.1709.
N-(((5S)-3-(4-(5-(Cyanomethyl)-3,3a,6,6a-
tetrahydrocyclopenta[c]pyrrol-2(1H)-yl)-3-
fluorophenyl)-2-oxo-oxazolidin-5-
yl)methyl)acetamide (14a)
Compound 10a (0.1 g, 0.27 mmol) and ammonium acetate (2 mg,
0.027 mmol) was dissolved in benzene, and cyanoacetic acid
(22.6 mg, 0.27 mmol) was added. The apparatus was fitted with
Dean-stark device, and the mixture was refluxed for 20 h. Tem-
perature was cooled down to room temperature, and the solvent
was removed under reduced pressure. The residue was extracted
with methylene chloride. Organic layer was washed with brine,
dried in magnesium sulfate, and filtered. The solvent was con-
centrated, and the compound was purified by column chromatog-
raphy using ethyl acetate and methanol (40:1) solution to provide
31 mg (30%) of pure compound as white solid: mp 167.2–
168.3 ꢂC; 1H NMR (CD3OD, 300 MHz) d 8.10 (d, J = 1.2 Hz, 1H),
7.79 (d, J = 1.2 Hz, 1H), 7.30 (dd, J = 15.0, 2.4 Hz, 1H), 7.02 (dd,
J = 9.0, 2.7 Hz, 1H), 6.84 (t, J = 9.0 Hz, 1H), 5.69 (d, J = 2.4 Hz,
1H), 5.14 (m, 1H), 4.89 (m, 2H), 4.25 (t, J = 9.3 Hz, 1H), 3.96
(dd, J = 9.3, 5.4 Hz, 1H), 3.51–3.08 (m, 6H), 2.78 (dd, J = 16.5,
8.1 Hz, 1H), 2.31 (dd, J = 16.8, 1.5 Hz, 1H); 13C NMR (CDCl3,
N-(((5S)-3-(4-(5-(Cyanomethylene)
hexahydrocyclopenta[c]pyrrol-2(1H)-yl)-3-
fluorophenyl)-2-oxo-oxazolidin-5-
yl)methyl)acetamide (13a)
Potassium t-butoxide (29.9 mg, 0.27 mmol) was dissolved in THF. The
temperature of the solution was lowered to )78 ꢂC. Diethyl cyanom-
ethyl phosphonate (233.9 mg, 0.33 mmol) was added to the solution
slowly, and the mixture was stirred at the same temperature for 1 h.
The solution of compound 10a (0.1 g, 0.27 mmol) in THF was added
to the reaction solution slowly. Reaction temperature was increased
slowly to room temperature. Solvent was removed under reduced
pressure, and the residue was extracted with methylene chloride.
Organic layer was washed with brine, dried in magnesium sulfate,
and filtered. The solvent was concentrated, and the compound was
purified by column chromatography using ethyl acetate and methanol
(40:1) solution to provide 88.1 mg (83%) of pure compound as white
solid: mp 90.8–91.6 ꢂC; 1H NMR (CDCl3, 300 MHz) d 7.31 (dd,
J = 15.0, 2.4 Hz, 1H), 7.06 (t, J = 6.0 Hz, 1H), 6.97 (dd, J = 8.9,
2.3 Hz, 1H), 6.61 (t, J = 9.0 Hz, 1H) 5.24 (t, J = 2.0 Hz, 1H), 4.74 (m,
1H), 3.97 (t, J = 9.0 Hz, 1H), 3.72 (dd, J = 8.7, 6.6 Hz, 1H), 3.6 (t,
J = 5.3 Hz, 2H), 3.45 (m, 1H), 3.43 (s, 1H), 3.14 (m, 2H), 2.90 (m, 3H).
2.78 (m, 1H), 2.56 (m, 1H), 2.46 (m, 1H), 2.00 (s, 3H); 13C NMR (CDCl3,
75 MHz) d 172.62, 171.79, 155.01, 154.10, 150.89, 134.12, 133.98,
129.77, 129.63, 117.30, 116.36, 116.29, 114.83, 108.33, 107.99, 91.97,
72.23, 56.11, 56.05, 55.97, 48.12, 42.21, 42.14, 41.86, 39.77, 38.85,
23.19; IR (film):ꢀt = 3313, 2955, 2215, 1746, 1659, 1519, 1480, 1420,
1365, 1320 ⁄ cm; HRMS (EI+) calcd for C21H23FN4NaO3 (M+): 421.1652,
found: 421.1646.
75 MHz)
d 171.02, 154.39, 153.10, 134.12, 132.85, 131.60,
129.63, 117.23, 114.24, 107.87, 107.52, 71.81, 57.86, 54.95,
49.36, 47.79, 42.03, 41.61, 40.16, 23.19, 19.68; IR (film):
ꢀt = 3292, 2920, 1746, 1658, 1518, 1478, 1415, 1365, 1319 ⁄ cm;
HRMS (EI+) calcd for C21H23FN4NaO3 (M+): 421.1652, found:
421.1647.
2-(2-(4-((R)-5-((1H-1,2,3-Triazol-1-yl)methyl)-2-
oxo-oxazolidin-3-yl)-2-fluorophenyl)-
1,2,3,3a,4,6a-hexahydrocyclopenta[c]pyrrol-5-
yl)acetonitrile (14b)
Compound 14b was prepared according to compound 14a. Pure
compound was white solid, 37 mg (35%): mp 99.0–100.6 ꢂC; 1H
NMR (CD3OD, 300 MHz) d 8.10 (d, J = 1.2 Hz, 1H), 7.79 (d,
J = 1.2 Hz, 1H), 7.30 (dd, J = 15.0, 2.4 Hz, 1H), 7.02 (dd, J = 9.0,
2.7, 1H), 6.84 (t, J = 9.0 Hz, 1H), 5.69 (d, J = 2.4 Hz, 1H), 5.14 (m,
1H), 4.90 (m, 2H), 4.25 (t, J = 9.3 Hz, 1H), 3.96 (dd, J = 9.3, 5.4 Hz,
1H), 3.49 (m, 1H), 3.39–3.08 (m, 6H), 2.78 (dd, J = 16.5, 8.1 Hz, 1H),
2.32 (d, J = 16.8, 1.5 Hz, 1H); 13C NMR (CD3OD, 75 MHz) d 156.09,
152.88, 135.88, 135.75, 135.23, 134.58, 131.81, 131.68, 131.54,
129.51, 127.25, 118.77, 118.57, 118.50, 116.27, 109.21, 108.86,
72.57, 59.09, 59.03, 56.41, 56.34, 53.47, 50.74, 42.42, 41.46; IR
(film): ꢀt = 3129, 2921, 1750, 1519, 1478, 1416, 1361, 1319 ⁄ cm;
HRMS (EI+) calcd for C21H21FN6NaO2 (M+): 431.1608, found:
431.1601.
2-(2-(4-((R)-5-((1H-1,2,3-Triazol-1-yl)methyl)-2-
oxo-oxazolidin-3-yl)-2-fluorophenyl)
hexahydrocyclopenta[c]pyrrol-5(1H)-
ylidene)acetonitrile (13b)
Compound 13b was prepared according to compound 13a. Pure
compound was white solid, 84.8 mg (80%): mp 72.9–74.0 ꢂC; 1H
NMR (CDCl3, 300 MHz) d 7.83 (s, 1H), 7.77 (s, 1H), 7.22 (dd,
J = 14.9, 1.6 Hz, 1H) 6.92 (dd, J = 8.7, 2.4 Hz, 1H), 6.63 (t,
J = 9.3 Hz, 1H), 5.28 (t, 1H), 5.06 (m, 1H), 4.81 (dd, J = 4.0, 1.4 Hz,
2H), 4.13 (t, J = 9.0 Hz, 1H), 3.89 (dd, J = 9.4, 6.1 Hz, 1H), 3.50(m,
2H), 3.19 (m, 2H), 2.80 (m, 2H), 2.60 (m, 2H); 13C NMR (CDCl3,
75 MHz) d 172.13, 153.58, 150.89, 134.57, 129.77, 125.08, 117.00,
116.09, 116.01, 115.05, 108.58, 108.23, 91.92, 70.34, 55.68, 52.10,
47.63, 42.06, 41.65, 39.50, 38.58; IR (film):ꢀt = 3129, 2955, 2214,
1750, 1519, 1480, 1420, 1362, 1321 ⁄ cm; HRMS (EI+) calcd for
C21H21FN6NaO2 (M+): 431.1608, found: 431.1606.
N-(((5S)-3-(4-(5-Cyano-3,3a,6,6a-
tetrahydrocyclopenta[c]pyrrol-2(1H)-yl)-3-
fluorophenyl)-2-oxo-oxazolidin-5-
yl)methyl)acetamide (15a)
Compound 10a (0.3 mg, 0.80 mmol) and indium bromide (30 mg,
0.085 mmol) was dissolved in methylene chloride. The tempera-
ture was lowered to 0 ꢂC. Trimethylsilyl cyanide (0.36 g,
3.6 mmol) was added dropwise to the reaction mixture and stir-
red for 20 h at room temperature. Mixture was washed with
392
Chem Biol Drug Des 2012; 80: 388–397

Novel 3-Azabicyclo[3.3.0]octanyl Oxazolidinones
saturated sodium bicarbonate solution, and the aqueous layer
was extracted with methylene chloride. Organic layer was
washed with brine, dried over magnesium sulfate, and filtered.
The solvent was concentrated, and the compound was purified
by column chromatography using ethyl acetate and methanol
(40:1) solution.
broth and diluted with the same fresh medium to a density of ca.
107 colony-forming units (CFU) ⁄ mL. Suspensions were applied to
Mueller–Hinton agar (MHA) plates containing serial dilutions of
antimicrobial agents using
a multipoint inoculator to yield
105 CFU ⁄ spot. Plates were incubated in air at 37 ꢂC for 18 h and
were examined for growth. The MIC was considered to be the low-
est concentration that completely inhibited growth on agar plates,
disregarding a single colony or a faint haze caused by the inocu-
lum.
The solid compound was dissolved in formic acid and was stirred
for 24 h at room temperature. Formic acid was removed under
reduced pressure. The residue was dissolved in pyridine, and the
temperature of the solution was lowered to 0 ꢂC. Phosphorus oxy-
chloride (0.17 g, 1.1 mmol) was added to it slowly, and the reac-
tion mixture was stirred at room temperature for 30 h. The
solvent was removed under reduced pressure. Compound was
extracted with methylene chloride. Organic layer was washed with
brine, dried over magnesium sulfate, and filtered. The solvent was
concentrated, and the compound was purified by column chroma-
tography using methylene chloride and methanol (30:1) solution to
provide 0.184 g (60%) of pure compound as white solid: mp
156.8–159.1 ꢂC; 1H NMR (CDCl3, 300 MHz) d 7.39 (dd, J = 15.1,
2.6 Hz, 1H), 7.05 (dd, J = 8.7, 1.8 Hz, 1H), 6.72 (t, J = 9.3 Hz, 1H),
6.52 (t, J = 9.1 Hz, 1H), 4.77 (m, 1H), 4.02 (t, J = 8.7 Hz, 1H), 3.77
(t, J = 4.3 Hz, 1H), 3.63 (m, 3H), 3.38 (m, 3H), 3.22 (m, 2H), 3.13
(m, 1H), 2.59 (dd, J = 16.2, 1.8 Hz, 1H), 2.01 (s, 3H); 13C NMR
(CDCl3, 75 MHz) d 171.50, 162.31, 155.21, 154.76, 151.96, 149.95,
133.90, 131.15, 117.62, 116.43, 115.10, 114.49, 108.11, 107.77,
72.19, 57.66, 54.25, 54.33, 50.73, 47.99, 42.20, 41.32, 39.63,
23.32; IR (film): ꢀt = 3311, 2925, 1738, 1659, 1520, 1481, 1420,
1365, 1321 ⁄ cm; HRMS (EI+) calcd for C20H21FN4NaO3 (M+):
407.1495, found: 407.1491.
Minimal inhibitory concentration determination
of Mycobacterium tuberculosis
The MICs of compounds against Mycobacterium tuberculosis (Mtb)
H37Rv was determined by the microplate Alamar Blue Assay (32).
Determination of CYP, microsomal stability,
and hERG profile of the compound 10a
CYP450 remaining test was conducted using Vividꢁ CYP450 Screen-
ing Kits Protocol (Invitrogen, Carlsbad, CA, USA), and hERG (human
ether-a-go-go-related gene) potassium channel assay for cardiac
toxicity test was conducted using an automated patch-clamp device,
NPC-16 Patchliner (Nanion Technologies, Munchen, Germany) (33),
and human hepatic microsomal stability test was conducted by
automated HPLC ⁄ Mass Spectrometry System (34).
Result and Discussion
Synthesis
The synthesis of oxazolidinone derivative 10a, in which morpholine C-
ring of linezolid was replaced with azabicyclic ketone, is shown in
Scheme 1. Also, the preparation of its triazole analog 10b additionally
replaced acetamide by triazole at the C-5 position of oxazolidinone
10a is described. Reduction in tert-butyl 3-azabicyclo[3.3.0]octane-7-
one 3-carboxylate 3, purchased from Hanchem (Daejeon, South Korea),
with sodium borohydride, and subsequent deprotection of tert-butyl-
oxycarbonyl (Boc) group by concentrate hydrochloric acid gave
3-azabicyclo[3.3.0]octane-7-one hydrochloride 4. SNAr reaction of
3,4-difluoronitrobenzene with 4 gave 5 in good overall yield. Swern
oxidation of the alcohol 5 and followed by the protection of the
corresponding ketone with ethylene glycol afforded the ketal 6. On
the other hand, attempts to prepare the ketone intermediate with-
out additional reduction and oxidation steps by SNAr reaction with
3-azabicyclo[3.3.0]octane-7-one, prepared from starting material 3
by N-Boc deprotection, were unsuccessful.
2-(4-((R)-5-((1H-1,2,3-Triazol-1-yl)methyl)-2-oxo-
oxazolidin-3-yl)-2-fluorophenyl)-1,2,3,3a,4,6a-
hexahydrocyclopenta[c]pyrrole-5-carbonitrile
(15b)
Compound 15b was prepared according to compound 15a. Pure
compound was white solid, 0.156 g (51%): mp 157.1–157.8 ꢂC; H
NMR (CDCl3, 300 MHz) d 7.82 (d, J = 1.2 Hz, 1H), 7.25 (dd,
J = 14.9, 2.2 Hz, 1H), 6.94 (dd, J = 8.9, 2.9 Hz, 1H), 6.69 (t,
J = 9.1 Hz, 1H), 5.06 (m, 1H), 4.80 (m, 2H), 4.13 (t, J = 9.0 Hz, 1H),
3.89 (dd, J = 9.4, 6.1 Hz, 1H), 3.39 (m, 1H), 3.21 (m, 3H), 3.21 (m,
2H), 3.12 (m, 1H), 2.58 (dd, J = 16.5, 2.1 Hz, 1H); 13C NMR (CDCl3,
75 MHz) d 155.07, 153.78, 151.83, 149.95, 134.73, 130.38, 125.36,
117.61, 117.53, 116.43, 115.09, 114.97, 114.92, 108.48, 108.14,
70.64, 57.65, 57.60, 54.27, 54.19, 52.30, 50.72, 47.76, 41.31, 39.62;
IR (film):ꢀt = 3138, 2931, 1751, 1570, 1517, 1436, 1361, 1322 ⁄ cm;
HRMS (EI+) calcd for C20H19FN6NaO2 (M+): 417.1451, found:
417.1452.
1
The preparation of oxazolidinone 7 from 6 was accomplished by
established procedure (35). Carbamate intermediate derived from
nitro reduction, and successive Cbz protection was deprotonated
with n-BuLi and followed by reaction with (R)-glycidyl butyrate to
give the oxazolidinone alcohol 7. Alcohol 7 was converted into the
corresponding azide 8 by the standard procedure in high yield.
Hydrogenation of azide 8 in the presence of acetic anhydride and
pyridine to provide the acetamide 9a in 65% yield. 1,2,3-Triazole
derivative 9b was also prepared by cycloaddition of azide 8 with
vinyl acetate and spontaneous elimination. Deprotection of ketal 9a
Biological assay
Minimal inhibitory concentration (MIC)
determination
Minimal inhibitory concentrations were determined by twofold agar
dilution as described by the Clinical and Laboratory Standards Insti-
tute (31). Test strains were grown for 18 h at 37 ꢂC in tryptic soy
Chem Biol Drug Des 2012; 80: 388–397
393

Bhattarai et al.
Scheme 1: (i) NaBH4, MeOH, 0 ꢂC, 1 h, then conc. HCl, rt, 1 h; (ii) DIEA, 3,4-difluoronitrobenzene, CH3CN, reflux, 6 h, 70% in two steps;
(iii) (COCl)2, DMSO, TEA, CH2Cl2, )78 ꢂC, 6 h, 94%; (iv) HOCH2CH2OH, p-TsOH, benzene, reflux, 1 h, 80%; (v) Pd ⁄ C, H2, EtOAc, 10 h, 95%; (vi)
CbzCl, sat. NaHCO3, THF, 0 ꢂC to rt, 12 h; (vii) n-BuLi, (R)-glycidyl butyrate, THF, )78 ꢂC, 12 h, 78% in two steps; (viii) MsCl, TEA, CH2Cl2,
0 ꢂC, 4 h; (ix) NaN3, DMF, 90 ꢂC, 4 h, 90% in two steps; (x) Pd ⁄ C, H2, Ac2O, pyridine, EtOAc, rt, 6 h, 65% (9a); (xi) vinyl acetate, reflux,
48 h, 55% (9b); (xii) p-TsOH, acetone ⁄ water (3:1), 6 h, 75% (10a), 98% (10b).
Scheme 2: (i) HONH2ÆHCl or CH3ONH2ÆHCl, NaHCO3, H2O, rt, 18–48 h, 20% (11a), 23% (11b), 99% (12a), 98% (12b); (ii) t-BuOK,
PO(OEt)2CH2CN, THF, )78 ꢂC to rt, 83% (13a), 80% (13b); (iii) NH4OAc, CH2(CN)CO2H, benzene, reflux, 20 h, 30% (14a), 35% (14b); (iv)
InBr3, TMSCN, CH2Cl2, 0 ꢂC to rt, 20 h; (v) HCO2H, rt, 24 h; (vi) POCl3, pyridine, 0 ꢂC to rt, 30 h, 60% (15a), 51% (15b) in three steps.
Table 1: In vitro antibacterial activities of oxazolidinone deriva-
tives against standard strains (MICs in lg ⁄ mL)
Table 2: In vitro antibacterial activity of oxazolidinone deriva-
tives against resistant strains and Mycobacterium tuberculosis
H37Rv (MICs in lg ⁄ mL)
Compound S.a.a
C.s.b
E.f.c
E.f.d
S.pe
S.p.f S.a.g H.i.h.
10a
11a
12a
13a
14a
15a
10b
11b
12b
13b
14b
15b
Linezolid
1.56
1.56
3.12
3.12
3.12
3.12
3.12
6.25
6.25
1.56
6.25
3.12
3.12
1.56
1.56
3.12
3.12
3.12
3.12
3.12
6.25
6.25
1.56
6.25
3.12
3.12
0.78 0.78 0.39 0.39
0.78 0.78 0.39 0.39
1.56 1.56 0.78 0.78
1.56 0.78 0.78 0.78
1.56 1.56 0.78 0.78
3.12 1.56 0.78 0.78
1.56 1.56 0.78 0.39
6.25 3.12 1.56 0.78
1.56 1.56 0.39 0.19
1.56 1.56 0.78 0.39
6.25 6.25 3.12 1.56
3.12 3.12 1.56 0.78
1.56 1.56 0.78 0.78
0.78
0.78
1.56
1.56
1.56
1.56
1.56
3.12
0.78
0.78
3.12
1.56
1.56
0.39
0.78
1.56
0.78
1.56
0.39
1.56
3.12
0.39
0.39
1.56
0.78
0.78
Compound
S.a.a
C.s.b
E.f.c
E.f.d
S.p.e
M.t.f
10a
11a
12a
13a
14a
15a
10b
11b
12b
13b
14b
15b
Linezolid
1.56
1.56
3.12
3.12
1.56
1.56
3.12
6.25
6.25
0.78
1.56
1.56
3.12
1.56
1.56
3.12
3.12
3.12
3.12
3.12
6.25
6.25
1.56
6.25
3.12
3.12
0.78
0.78
1.56
1.56
3.12
3.12
1.56
6.25
3.12
3.12
6.25
3.12
3.12
0.78
0.78
1.56
1.56
1.56
1.56
3.12
6.25
1.56
1.56
6.25
3.12
1.56
0.39
0.39
0.78
0.78
0.78
0.39
0.39
0.78
0.19
0.39
1.56
0.78
0.78
0.5
0.5
1
1
1
0.5
0.5
–
1
1
2
1
1
aMethicillin-susceptible Staphylococcus areus C463.
bMethicillin-susceptible Coagulase negative Staphylococi.
cVancomycin-susceptible Enterococcus faecalis C474.
dVancomycin-susceptible Enterococcus faecium C803.
ePenicillin-susceptible Streptococcus pneumonia C402.
fStreptococcus pyogenes ATCC 8736.
aMethicillin-resistant Staphylococcus areus.
bMethicillin-resistant Coagulase negative Staphylococi.
cVancomycin-resistant Enterococcus faecalis.
dVancomycin-resistant Enterococcus faecium.
ePenicillin-resistant Streptococcus pneumonia.
fMycobacterium tuberculosis H37Rv.
gStreptococcus agalactiae ATCC 2901.
hHameophilus influenza.
394
Chem Biol Drug Des 2012; 80: 388–397

Novel 3-Azabicyclo[3.3.0]octanyl Oxazolidinones
Table 3: The inhibitory effect of compound 10b on specific CYP enzyme in cDNA-expressed CYP microsomes, and its stability in human
hepatic microsome, and hERG channel activity
% Control of CYP-450 (at 10 lM)a
Compound
1A2
2D6
2C9
3A4
Microsomal stability (% remains after 30 min)
83.82
hERG (IC50, lM)
10b
Positive control
94.9 € 13.4
2.3b
107.7 € 1.3
11.1c
73.7 € 34.9
105.6 € 6.0
2.3e
80.5 € 6.0
)3.5d
aValues are remained % activities and the mean € SD of triplicate determinations.
ba-naphthoflavone.
cQuinidine.
dSulfaphenazole.
eKetoconazole.
and 9b by using p-toluene sulfonic acid catalyst in acetone and
water mixture (3:1) provided 3-azabicyclo[3.3.0]octane-7-one
derivative 10a and 10b having acetamide and 1,2,3-triazole moiety
at the C-5 position of the oxazolidinone, respectively.
Among C-5 triazole oxazolidinones 10b–15b, cyanomethylene
13b demonstrated highest activity. Thus, 13b resulted in compa-
rable or twofold higher activity against most of the strains, and
notably, fourfold higher activity against MRSA than linezolid.
Among the C-5 triazole derivatives, ketone 10b showed similar
activity, but oximes, 11b and 12b, and cyanomethyl compound
14b lost the activity slightly. O-Methyloxime 12b especially
exhibited highly potent activity against S. pneumonia and S. pyoge-
nes. In general, the replacement of acetamide with triazole at the
C-5 position of 3-azabicyclic oxazolidinone series led to less potent
compounds. Ketone 10a and nitrile 15a among C-5 acetamide
analogs, and O-Methyloxime 12b and cyanomethylene 13b
among triazole analogs showed higher activity against Gram-nega-
tive strain H. influenza than linezolid.
Then, azabicyclic ketone intermediates 10a and 10b were con-
verted into a variety of new oxazolidinone derivatives 11–15
bearing acetamide or 1,2,3-triazole ring moiety at the A-ring C-5
position as shown in Scheme 2. The preparation of hydroxime
(11a and 11b) and methoxime (12a and 12b) analogs was
achieved by treating the ketones 10a and 10b with hydroxyl-
amine hydrochloride and methoxyamine hydrochloride, respectively,
in the presence of saturated aqueous sodium carbonate solution.
Exo-cyanomethylene compounds 13a and 13b were prepared
from the ketones by employing Horner–Wadsworth–Emmons reac-
tion with diethyl cyanomethyl phosphonate and tert-butoxide.
Knoevenagel condensation and decarboxylation of ketones 10a
and 10b with cyanoacetic acid in the presence of ammonium ace-
tate provided cyanomethyl substituted hexahydrocyclopenta[c]pyrrole
compounds 14a and 14b. a,b-Unsaturated nitriles 15a and 15b
with one-carbon homologations were also prepared by InBr3-cata-
lyzed formation of trimethylsilyl cyanohydrin followed by dehydra-
tion with POCl3.
Furthermore, the new oxazolidinone derivatives possessing 3-azabi-
cyclo[3.3.0]octanyl moiety were evaluated for their antibacterial
activity against Mycobacterium tuberculosis H37Rv. Most of the
compounds examined, except 14b, showed comparable or higher
activity than linezolid against Mycobacterium tuberculosis as shown
in Table 2.
CYP, microsomal stability, and hERG profile of
the compound 10b
Biological activity
We selected the compound 10b from more active compounds
than linezolid against M. tuberculosis and evaluated for its CYP
profile, microsomal stability, and hERG inhibition as shown in
Table 3. The compound 10b was found to be stable in human
microsome and to have no-CYP-related liabilities, involved in drug
metabolism and drug interaction. The compound exhibits remaining
activities of minimum 73.6%, maximum 105.6% in the activity test
for four isozymes of CYP450 (1A2, 2D6, 2C9, 3A4), indicating that
it is not affected by CYP450 compared to positive control up to
10 lM concentrations. The compound 10b also showed low activ-
ity against hERG channel, which plays a crucial role on cardiac
side effects of drugs.
This series of oxazolidinone antimicrobial compounds prepared above
was screened against panel of susceptible and resistant bacteria.
MICs (lg ⁄ mL) of these compounds against standard strains were
summarized in Table 1, and linezolid was used as a reference com-
pound for comparison. The compounds were also tested against
drug-resistant strains such as MRSA, VRE (vancomycin-resistant
Enterococcus faecium), Coagulase negative Staphylococi, E. faecalis,
and S. pneumonia, and the results were shown in Table 2.
Most of the prepared compounds showed good activity against
Gram-positive and Gram-negative bacteria. Among C-5 acetamide
oxazolidinones 10a–15a, ketone and oxime analogs of 10a and
11a showed twofold higher activity against most of the tested
strains compared to linezolid, and particularly fourfold higher activ-
ity against VRE as shown in Table 2. The antibacterial activities of
O-methyloxime 12a and cyano compounds 13a–15a were similar
to linezolid. Acetamide analogs showed potent activity against
resistant strains such as S. areus and E. faecalis.
Conclusion
A new series of oxazolidinones having 3-azabicyclo[3.3.0]octanyl moi-
ety have been synthesized, and their in vitro antibacterial activities
were evaluated against Gram-positive, Gram-negative, and M. tuber-
Chem Biol Drug Des 2012; 80: 388–397
395

Bhattarai et al.
culosis including resistant strains of Staphylococi, Streptococci, and
Enterococci. Some of these analogs exhibited potent in vitro antibac-
terial activities comparable or superior to linezolid.
isolates in 23 countries. Diag. Microbiol Infect Dis;64:191–
204.
13. Gracia M.S., De la Torre M.A., Morales G., Pelaez B., Tolon
M.J., Domingo S., Candel F.J., Andrade R., Arribi A., Garcia N.,
Sagasti F.M., Fereres J., Picazo J. (2010) Clinical outbreak of
linezolid-resistant Staphylococcus aureus in an Intensive Care
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