Antibacterial activity of pyrrolopyridine-substituted oxazolidinones: synthesis and in vitro SAR of various C-5 acetamide replacements

Article abstract of DOI:10.1016/j.bmcl.2006.06.023

A series of pyrrolopyridine-substituted oxazolidinones containing various C-5 acetamide isosteres was synthesized and the structure-antibacterial activity relationships determined against a representative panel of susceptible and resistant Gram-positive b

Full text of DOI:10.1016/j.bmcl.2006.06.023

Bioorganic & Medicinal Chemistry Letters 16 (2006) 4537–4542
Antibacterial activity of pyrrolopyridine-substituted oxazolidinones:
synthesis and in vitro SAR of various C-5 acetamide replacements
Steven D. Paget, Christine M. Boggs, Barbara D. Foleno, Raul M. Goldschmidt,
Dennis J. Hlasta, Michele A. Weidner-Wells, Harvey M. Werblood,
Karen Bush and Mark J. Macielag*
Johnson & Johnson Pharmaceutical Research and Development, L.L.C., Route 202, PO Box 300, Raritan, NJ 08869, USA
Received 6 April 2006; revised 7 June 2006; accepted 8 June 2006
Available online 27 June 2006
Abstract—A series of pyrrolopyridine-substituted oxazolidinones containing various C-5 acetamide isosteres was synthesized and
the structure–antibacterial activity relationships determined against a representative panel of susceptible and resistant Gram-posi-
tive bacteria.
Ó 2006 Elsevier Ltd. All rights reserved.
Introduction of the oxazolidinone class of antimicrobial
agents has provided a means for the healthcare commu-
nity to combat the increasing incidence of drug-resistant
Gram-positive bacteria found in both the hospital and
community settings. Linezolid, the first and only
FDA-approved drug in the class, is indicated for both
hospital and community-acquired pneumonia, skin infec-
tions including cases due to methicillin-resistant Staphy-
lococcus aureus (MRSA), and infections associated with
vancomycin-resistant Enterococcus faecium (VREF),
including cases of bloodstream infection.1 However, if
the healthcare community wishes to stay ahead of bacte-
rial innovation, such as the development of resistance to
vancomycin2,3 and b-lactam antibiotics,4 the discovery
of novel members of this class will be crucial.
(1, Fig. 1) as the optimal template for antibacterial activ-
ity, we next shifted our focus to the modification of the
C-5 acetamide moiety as a means of increasing potency
and enhancing efficacy. A handful of strategies have
been employed to replace the acetamide group of oxazo-
lidinone antibacterial agents with varying success;11–15
some of these same approaches were utilized in the pres-
ent study. The effect of novel isosteric replacements on
antibacterial activity was also investigated.16
The synthesis of the key intermediates, 8 and 9, in the
preparation of acetamide isosteres is depicted in Scheme
1. To begin the sequence an inverse electron demand
Diels–Alder reaction of acyclic precursor 2 with extru-
sion of hydrogen cyanide provided the regioisomeric
pyrrolopyridines 3 and 4.17 Separation of the desired
regioisomer by column chromatography followed by
acid hydrolysis of the carbamate protecting group of 3
provided the pyrrolopyridine salt 5. Following the work
of the Upjohn group18 an SNAr reaction of 3,4-difluoro-
nitrobenzene with 5, followed by transfer hydrogenation
of the nitro group with palladium on carbon and
ammonium formate and benzyloxycarbonylation of
the resulting amine furnished the Cbz-protected aniline
6. Nucleophilic attack of the lithium anion of 6 on
(R)-glycidyl butyrate provided oxazolidinone carbinol
derivative 7. Mesylation of 7 provided the first key
intermediate 8. Intermediate 9 was accessed by displace-
ment with potassium phthalimide and subsequent
hydrazinolysis.
In previous publications from this group, various pyr-
roloaryl-substituted oxazolidinones were detailed,5–10
several of which had superior in vitro antimicrobial
activity to linezolid. Following the identification of the
pyrrolo[3,4-b]pyridinyl oxazolidinone core structure
Keywords: Pyrrolopyridine-substituted oxazolidinones; Antibacterial
agents; C-5 acetamide isosteres; Methicillin-resistant Staphylococcus
aureus; Vancomycin-resistant Enterococcus faecium.
*
Corresponding author. Tel.: +1 609 655 6950; fax: +1 609 655
6930; e-mail: mmaciela@prdus.jnj.com
Present address: Johnson & Johnson Pharmaceutical Research and
Development, L.L.C., Welsh and McKean Roads, Spring House, PA
19477, USA.
0960-894X/$ - see front matter Ó 2006 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2006.06.023

4538
S. D. Paget et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4537–4542
O
O
O
O
5
O
N
N
N
N
H
N
H
N
N
F
F
O
O
Figure 1. Linezolid and pyrrolo[3,4-b]pyridinyl oxazolidinone (1) structures.
NCO Et
2
N
N
N
b
c, d
a
3
NCO Et
2
HCl
NH
N
+
2
5
NCO Et
2
N
4
O
f
e
N
NHCbz
O
N
N
N
N
OH
O
N
F
F
6
7
O
g, h
O
N
O
N
N
N
OSO Me
NH
2
2
N
F
F
8
9
Scheme 1. Reagents and conditions: (a) undecane, 180 °C; separate isomers (3, 60%; 4, 23%); (b) concd aq HCl, reflux (97%);
(c) 3,4-difluoronitrobenzene, DIPEA, DMF, 60 °C (94%); (d) 10% Pd/C, HCOONH4, THF, MeOH; CbzCl, NaHCO3, H2O, acetone (97%);
(e) n-BuLi, THF then (R)-glycidyl butyrate, À78 °C to rt (92%); (f) MsCl, Et3N, DMF (95%); (g) potassium phthalimide, DMF, 50 °C; (h) H2NNH2,
MeOH, reflux.
Reaction of amine 9 with various acyl chloride or chlo-
roformate reagents, or alternatively with methanesulfo-
nyl chloride in the case of sulfonamide 17, provided a
range of simple amide (10–12 and 15) or carbamate
(13 and 14) derivatives (Scheme 2). Acetyloxyacetamide
15 was saponified with K2CO3 in methanol to supply
hydroxyacetamide 16. More exotic isosteres such as N-
cyano-ethanimidamide 18,19 methyl N-cyano-carbimi-
dothioate 19,20 and N-nitro-guanidine 2021 were pre-
pared by the literature procedures.
susceptible (MSSA); S. aureus OC 2878 is methicillin-
resistant (MRSA); Enterococcus faecalis ATCC 29212
and E. faecium OC 3312 are susceptible and resistant
to vancomycin, respectively. Compounds were also test-
ed against S. aureus OC 4172 in the presence of 50%
mouse serum to gauge the extent of protein binding or
inactivation due to serum. Broth microdilution MIC
(lowest concentration of compound inhibiting visible
growth) determinations were performed according to
National Committee for Clinical Laboratory Standards
methods.22
A series of alkoxyheterocycles was constructed by reac-
tion of mesylate 8 with the sodium salt of the hydroxy-
heterocycle of interest. In general the displacement
proceeded smoothly to provide analogs 21–26 but at
times gave the alternate N-linked regioisomer, exempli-
fied by compound 27, in which the amide is constrained
to a ‘transoid’ conformation (Scheme 3). This side prod-
uct, while unintended, gave an additional isosteric struc-
ture for investigation.
Within this series of C-5 acetamide analogs (Table 1)23
the lead compound, 1, was the most active, with MIC
values fourfold lower than linezolid against the four
organisms tested. Although 1 was slightly less active
when tested in the presence of mouse serum, it was still
twofold more potent than linezolid. Among simple
amide replacements, propionamide 10 and cyclopropyl-
carboxamide 11 were about equally active as linezolid
but, like acetamide 1, they were slightly less potent in
the presence of mouse serum. Further increase in the size
and lipophilicity of the C-5 amide substituent, as in cyc-
lobutylcarboxamide analog 12, had a detrimental effect
on antibacterial activity. Similarly, introduction of polar
functionality reduced antibacterial activity. In particular
Minimum inhibitory concentrations (MIC) were mea-
sured against a panel of susceptible and resistant strains
of Gram-positive bacteria with linezolid as a standard.
A set of four strains was used as the primary screening
panel: S. aureus OC 4172 (Smith strain) is methicillin-

S. D. Paget et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4537–4542
4539
O
O
a
O
O
N
N
N
N
NH2
X
N
N
F
F
1, 10, 11, 12, 13, 14
9
X
O
OAc 15
N
b
H
O
S
OH
16
17
18
19
N
H
O
O
c
d
e
f
Me
N
H
N
HN
N
Me
N
HN
N
SMe
NO2
HN
20
N
H
NH
Scheme 2. Reagents and conditions: (a) R1COCl, Et3N, DMF (25–87%); (b) K2CO3, MeOH; (c) MsCl, pyridine, CH2Cl2 (38%);
(d) (EtO)(Me)C@N–CN, Et3N, CH3CN; (e) (MeS)2C@N–CN, toluene, reflux (20%); (f) (MeS)(NH2)C@N–NO2, MeOH, reflux (24%).
O
O
a
O
O
N
N
N
N
HO
OSO2Me
O
N
X
N
X
N
N
F
F
8
21- 26
+
O
O
N
N
N
N
F
O
27
Scheme 3. Reagents: (a) NaH, DMF (22–26, 15–93%; 21, 5%; 27, 30%).
the MIC values of acetoxyacetamide 15 and hydroxyac-
etamide 16 were 32- to 512-fold higher than 1.
mouse serum have limited efficacy in a S. aureus Smith
murine systemic lethal infection model, and therefore
these compounds were not pursued beyond susceptibility
testing.
Other acetamide isosteres (13, 14, and 17–20) were also
investigated but of these only methyl carbamate 13,
N-cyano-ethanimidamide 18, and methyl N-cyano-car-
bimidothioate 19 had MIC values of 4 lg/mL or less
against all bacterial strains tested in the absence of ser-
um. With the exception of N-nitro-guanidine analog
20, the antibacterial activity of these isosteric replace-
ments decreased 4- to 8-fold in the presence of mouse
serum, likely due to protein binding. We have found that
oxazolidinones with MIC values P8 lg/mL in 50%
In exploring C-5 substituents with proven success, the
acetamide was replaced with alkoxyheterocycles, a strat-
egy employed by researchers at AstraZeneca in the 4-
tetrahydropyridinyl and 4-dihydropyranyloxazolidinone
series.13,14 This approach was ineffective in the current
pyrrolopyridine oxazolidinone series; alkoxyheterocycle
compounds (21–26) were generally poorly active with
the notable exception of thiadiazolyloxy analog 26,

4540
S. D. Paget et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4537–4542
Table 1. Antibacterial activity (MICa values in lg/mL) for pyrrolo[3,4-b]pyridine-substituted oxazolidinones
O
O
N
N
X
N
F
Compound
X
E. faecalis
E. faecium
MRSA
MSSA in broth
MSSA + 50%
mouse serum
Linezolid
1
2
0.5
2
2
0.5
2
1
0.25
1
2
0.5
2
2
1
NHCOMe
NHCOEt
10
11
12
13
14
15
16
17
18
19
20
4
NHCOcyclopropyl
NHCOcyclobutyl
NHCO2Me
2
2
2
2
4
8
8
4
8
32
16
64
32
32
16
8
4
2
2
4
NHCO2Et
8
8
4
8
NHCOCH2OAc
NHCOCH2OH
NHSO2Me
16
32
8
16
16
4
128
16
2
32
32
4
N@C(Me)–NH–CN
N@C(SMe)–NH–CN
NHC@NH(NH–NO2)
4
4
2
2
4
16
2
2
2
8
16
8
8
8
O
N
21
22
23
24
25
26
27
>64
>32
>16
>32
>32
8
>64
>64
>64
>32
16
32
>128
>64
>32
8
>128
>128
>64
>32
>32
2
>128
>128
>64
>32
>64
8
O
O
N
N
Me
N
O
N
N
N
O
O
O
S
N
N
2
1
O
>32
>32
16
>32
64
N
a The variance in the determination of MIC values is twofold such that an MIC difference of at least fourfold is significant.
which had an MIC range of 1–8 lg/mL. The reasons for
the generally poor antibacterial activity of the O-linked
heterocycles in this series are not entirely clear. The cal-
culated logP values (Advanced Chemistry Development
Software V8.19 for Solaris) of AstraZeneca’s lead oxa-
zolidinone, AZD-2563,24 and compound 25, both of
which contain a 3-isoxazolyloxy acetamide replacement,
are 1.60 and 2.32, respectively. Thus, it is unlikely that
differences in physicochemical properties are responsi-
ble. Instead, the structure–activity relationships of the
C5-substituent would appear to be dependent on the
structure of the heterocyclic moiety appended to posi-
tion 4 of the phenyl ring. Interestingly, a similar trend
has recently been reported for a series of arylpiperazinyl
oxazolidinone antibacterial agents.25 The N-linked
pyridone analog 27 was also found to be poorly active,
possibly due to increased steric demand, the need for an
H-bond donor, or conformational factors.
Oxidation of select pyrrolo[3,4-b]pyridinyl oxazolidi-
nones with manganese dioxide26 provided the corre-
sponding fully aromatic pyrrolopyridinyl oxazol-
23
idinones 28–40 (Scheme 4).
In general, oxidation of the heterocycle proved to
be detrimental to antibacterial activity (Table 2). MIC
values for analogs 28–34 were 2- to greater than 32-fold
higher than for the corresponding analogs in the dihy-
dro series. The effect on antibacterial activity was espe-
cially apparent for the C-5 sulfonamidomethyl
derivative (32), in which MIC values increased by more
than eightfold compared to the dihydro analog (17)
against all bacteria in the testing panel. In select cases,
antibacterial activity improved for alkoxyheterocycle
analogs in the fully aromatic series compared to the par-
ent series. In particular, the MIC value of pyrazine 37
against the MRSA strain was at least fourfold lower

S. D. Paget et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4537–4542
4541
O
O
a
O
O
N
N
N
N
X
X
N
N
F
F
1, 10, 11, 13, 17, 19, 20, 22-27
Scheme 4. Reagents: (a) MnO2, CH2Cl2 (4–64%).
28-40
Table 2. Antibacterial activity (MICa values in lg/mL) for pyrrolopyridine-substituted oxazolidinones
O
O
N
N
X
N
F
Compound
X
E. faecalis
E. faecium
MRSA
MSSA in broth
MSSA + 50% mouse serum
Linezolid
2
1
2
1
1
0.5
2
1
2
2
28
29
30
31
32
33
34
NHCOMe
NHCOEt
16
16
16
>64
8
16
8
16
32
8
32
16
NHCOcyclopropyl
NHCO2Me
NHSO2Me
8
16
16
>64
8
16
>64
8
32
>64
8
>64
64
N@C(SMe)–NH–CN
NHC@NH(NH–NO2)
32
32
>128
64
128
O
N
Me
35
36
37
38
39
40
>64
>32
64
>128
>64
64
>64
>64
8
>128
>128
>32
8
>128
>128
>32
64
O
N
N
O
N
N
N
O
O
16
8
4
O
S
N
N
4
4
2
8
16
O
>128
>128
>128
>128
>128
N
a The variance in the determination of MIC values is twofold such that an MIC difference of at least fourfold is significant.
than the analogous compound 24, and the antibacterial
activity of isoxazole 38 was at least twofold better than
25 against all strains tested.
(MIC values of 2–16 lg/mL) with the remainder of the
alkoxyheterocycles (35–38) and the pyridone analog
(40) significantly less potent.
Despite the overall weaker antibacterial activity of the
fully aromatic series (28–40) compared to the parent ser-
ies, the SAR trends were generally quite similar but with
greater sensitivity to structural alteration of the C-5
acetamide substituent. Once again, acetamide 28 was
the most potent analog in this series, with MIC values
twofold lower than linezolid. Increasing substituent size
and lipophilicity produced an increase in the MIC value,
as was evident from the 16- to 32-fold increase in MIC
for propionamide 29 compared to acetamide 28, for
example. In the alkoxyheterocycle subseries the thiadia-
zole analog, 39, showed modest antibacterial activity
In summary, although diverse strategies were employed
to identify a replacement for the C-5 acetamide func-
tionality, no improvement was found over the lead
compound (1) in the pyrrolo[3,4-b]pyridinyl oxazolidi-
none series of antibacterial agents. Compound 1 and
the oxidized congener, 28, exhibited the best antibacteri-
al profile in our abbreviated testing panel with MIC
ranges of 0.25–0.5 lg/mL and 0.5–1 lg/mL, respectively,
against staphylococci, including MRSA, and 0.5 and
1 lg/mL, respectively, against enterococci, including
VRE. Unfortunately, many analogs with larger amide
or other isosteric replacements for the C-5 acetamide

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S. D. Paget et al. / Bioorg. Med. Chem. Lett. 16 (2006) 4537–4542
Interscience Conference on Antimicrobial Agents and
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were significantly less potent than the lead compound
(1), although propionamide 10 and cyclopropylcarboxa-
mide 11 were equally active as linezolid against the
bacterial strains tested. In contrast to the AstraZeneca
series of 4-tetrahydropyridinyl- and 4-dihydropy-
ranyloxazolidinones,13,14 pyrrolopyridinyl analogs with
C-5 alkoxyheterocycle substituents were poorly active
with the exception of the thiadiazoles 26 and 39. This
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oxazolidinone antibacterial agents is not only narrow
in terms of acceptable replacements but also highly
dependent on the nature of other substituents in the
molecule.
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