Novel oxazolidinone-quinolone hybrid antimicrobials

Article abstract of DOI:10.1016/j.bmcl.2003.07.021

Antimicrobial compounds incorporating oxazolidinone and quinolone pharmacophore substructures have been synthesized and evaluated. Representative analogues 2, 5, and 6 display an improved potency versus linezolid against gram-positive and fastidious gram-negative pathogens. The compounds are also active against linezolid- and ciprofloxacin-resistant Staphylococcus aureus and Enterococcus faecium strains. The MOA for these new antimicrobials is consistent with a combination of protein synthesis and gyrase A/topoisomerase IV inhibition, with a structure-dependent degree of the contribution from each inhibitory mechanism.

Full text of DOI:10.1016/j.bmcl.2003.07.021

Bioorganic & Medicinal Chemistry Letters 13 (2003) 4213–4216
Novel Oxazolidinone–Quinolone Hybrid Antimicrobials
Mikhail F. Gordeev,a,* Corinne Hackbarth,a Michael R. Barbachyn,b Lee S. Banitt,b
James R. Gage,b Gary W. Luehr,a Marcela Gomez,a Joaquim Trias,a Sara E. Morin,b
Gary E. Zurenko,b Christian N. Parker,b Jonathan M. Evans,b Richard J. Whitea
and Dinesh V. Patela
aVicuron Pharmaceuticals Inc., 34790 Ardentech Ct., Fremont, CA 94555, USA
bPharmacia Co., 7000 Portage Rd., Kalamazoo, MI 49001, USA
Received 5 May 2003; accepted 29 July 2003
Abstract—Antimicrobial compounds incorporating oxazolidinone and quinolone pharmacophore substructures have been synthe-
sized and evaluated. Representative analogues 2, 5, and 6 display an improved potency versus linezolid against gram-positive and
fastidious gram-negative pathogens. The compounds are also active against linezolid- and ciprofloxacin-resistant Staphylococcus
aureus and Enterococcus faecium strains. The MOA for these new antimicrobials is consistent with a combination of protein
synthesis and gyrase A/topoisomerase IV inhibition, with a structure-dependent degree of the contribution from each inhibitory
mechanism.
# 2003 Elsevier Ltd. All rights reserved.
Oxazolidinones are a new class of synthetic antibacterial
agents with a unique mechanism of bacterial protein
synthesis inhibition (for recent reviews, see refs 1–5).
The first drug in this class, Zyvox1 (linezolid), has been
widely accepted as a valuable addition to the chemo-
therapeutic armamentarium for treatment of serious
gram-positive infections.6,7 First generation oxazolidi-
nones as represented by linezolid are generally limited in
their antimicrobial spectrum to gram-positive species.1ꢀ7
An expanded spectrum and enhanced potency of newer
second generation oxazolidinones with activity against
gram-negative pathogens could expand the utility of this
class beyond the hospital setting into the treatment of
infections in the community.
microorganisms and achieve sufficient intracellular tar-
get exposure. From an SAR viewpoint, antibacterial
compounds of both classes feature a heterocyclic amine
presented as a popular C-ring in oxazolidinones1ꢀ3 and
a mandatory cyclic amine in position 7 of quinolones.8
We have envisaged a combination of substructures per-
mitted by SAR for both oxazolidinone and quinolone
antimicrobials (Fig. 1, structure I).9,10 Given a pre-
cedence of N1-aryl groups in quinolones (cf. tosu-
floxacin8), we have also hypothesized that the quinolone
N1 substituent may be supplanted by an oxazolidinone
pharmacophore (e.g., structure II). Based on these con-
siderations, we’ve set out to explore two distinct types
of the hybrid classes I and II with potential for a dual
MOA: protein synthesis inhibition (caused by the oxa-
zolidinone) and the gyrase A/topoisomerase IV inhibi-
tion (due a to the quinolone pharmacophore). In a
similar approach, quinolone–sulfonamide and quino-
lone–trimethoprim hybrids have been previously eval-
uated (see publications in refs 10 and 11 and refs cited
therein). The quinolone structures have been also
incorporated into ‘codrug’ cephalosporins designed to
release the quinolone component upon b-lactam opening
by bacterial enzymes.12,13
En route to novel oxazolidinones with an expanded
antibacterial spectrum and improved potency, we have
analyzed various drug classes with activity against
gram-negative microorganisms. The essentially gram-
positive spectrum of oxazolidinones can be partially
attributed to their limited ability to reach the cyto-
plasmic RNA target of gram-negative prokaryotes. In
contrast, quinolones possess a well-recognized capacity to
permeate through the cell membranes of gram-negative
Synthesis of the prototypical analogues 2, 5, 6, 13, 16,
and 19 is summarized in Schemes 1–4. The compounds
were tested against a panel of microorganisms including
*Corresponding author. Tel.: +1-510-739-3013; fax: +1-510-739-
3050; e-mail: mgordeev@vicuron.com
0960-894X/$ - see front matter # 2003 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2003.07.021

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M. F. Gordeev et al. / Bioorg. Med. Chem. Lett. 13 (2003) 4213–4216
ciprofloxacin-resistant Staphylococcus aureus and
Enterococcus faecium, and linezolid-resistant strains of
S. aureus (LRSA) and E. faecium (LREF; Table 1).
While the frequency of resistance to oxazolidinones is
low, several clinical observations of resistance to lin-
ezolid have been reported.14ꢀ18 It is expected that the
incidence of resistance may rise over time, and com-
pounds with LRSA and LREF coverage are of potential
interest.
incorporating ciprofloxacin, ofloxacin, and levofloxacin
quinolone substructures linked via a piperazine group
are highly potent against gram-positive strains: MICs
versus linezolid-susceptible S. aureus and E. faecium are
ꢁ1 mg/mL (see Table 1). Notably, the activity against
gram-positive strains is markedly superior cf. to line-
zolid as well as versus progenitor eperezolid (the latter is
equipotent to linezolid;2 data omitted from Table 1).
For example, compound 2 is ca. 8-fold more active than
linezolid and eperezolid against both S. aureus and E.
faecium. Analogues 2, 5, and 6 are also active against
linezolid resistant strains, with MICs versus LRSA and
LREF in the range of 2–4 and 0.5–4 mg/mL, respectively.
It is also noteworthy that the compounds maintain
Design of a tether connecting the oxazolidinone and
quinolone pharmacophores appears critical for anti-
bacterial activity. Thus, N1-linked tosufloxacin analogue
19 is inactive. In contrast, oxazolidinones 2, 5, and 6
Figure 1. Conceptual design of oxazolidinone–quinolone antimicrobials.
Scheme 1. Reagents and conditions: (a) 5-(S)-acetamidomethyl-3-[3-fluoro-(4-piperazine-1-yl)-phenyl]oxazolidinone, N-methylmorpholine, DMSO,
110 ꢂC; (b) aq HCl–AcOH, D; (c) TMSCHN2, MeOH, rt.
Scheme 2. Reagents and conditions: (a) Tf2O, Py, 0 ꢂC to rt; then BnOH, rt; (b) i-BuOCOCl, K2CO3, DCM, water, rt to Á; (c) 1,3-dibromo-5,5-
dimethylhydantoin, DCM, water, 39 ꢂC; (d) t-C5H11OLi, THF, ꢀ15 ꢂC; then pre-mixed at ꢀ25 ꢂC to 10 ꢂC (S)-3-chloro-1,2-propanediol, t-BuOK,
THF; (e) 3-NO2C6H4SO2Cl, TEA, DCM; (f) 29% NH4OH, MeCN, MeOH, sealed autoclave, 80 ꢂC; (f) di-t-butylcarbonate; (g) EtMgBr, TMEDA,
THF, ꢀ50 ꢂC; then BuLi, hexanes, B(OMe)3, then aq HCl; (h) 9, Pd(PPh3)2Cl2, aq K2HPO4, 1,2-dimethoxyethane, 90 ꢂC; (i) TFA, DCM; (j) Ac2O,
Py; (k) 10% Pd/C, H2, EtOH.

M. F. Gordeev et al. / Bioorg. Med. Chem. Lett. 13 (2003) 4213–4216
Table 1. Antimicrobial activity for oxazolidinone–quinolones (MICs, g/mL)21
4215
Compd
SA1009
CipR
SA1011
SA1012
LinR
EF4010
CipR
EF4008
LinR; CipR
EF4016
CipR
EF4011
LinR; CipR
HI1008
MC1002
EC1008
Linezolid
Ciprofloxacin
2
5
6
4
32
0.25
0.5
1
4
0.5
0.25
0.5
1
64
1
2
4
2
4
>64
0.125
0.25
0.5
16
>64
0.5
2
>64
0.125
0.25
0.5
8
>64
0.5
16
ꢁ0.06
8
8
4
8
0.03
4
4
4
>64
0.03
32
32
32
2
4
2
4
7
8
4
8
8
0.5
8
>64
1
8
>64
>64
8
—
32
>64
>64
>64
—
>64
>64
>64
4
—
64
>64
>64
>64
—
>64
>64
>64
>64
0.25
2
>64
>64
>64
2
16
>64
>64
>64
2
8
>64
>64
13
16
18
19
>64
>64
>64
>64
Scheme 3. Reagents and conditions: (a) CrO3, AcOH; (b) SOCl2,
DCM; (c) t-BuOLi, THF; (d) Fe, aq NH4Cl; (e) CbzCl, Py, DCM; (f)
(R)-glycidyl butyrate; (g) MsCl, TEA, DCM; (h) NaN3, DMF, 80 ꢂC;
(i) PPh3, THF, water, 55 ꢂC; (j) Ac2O, Py, DCM; (k) TFA, DCM, rt;
(l) PfpOCOCF3, Py, DMF; (m) norfloxacine, TEA, acetone.
Scheme 4. Reagents and conditions: (a) ethyl 3-dimethyl-aminoacryl-
ate, TEA, dioxane, rt; (b) 5-(S)-acetamidomethyl-3-(3-fluoro-4-amino-
phenyl)oxazolidinone, 4-methylmorpholine, NMP, 110 ꢂC; (c) DBU,
NMP, 85 ꢂC; (d) N-methylpiperazine, NMP, 80 ꢂC; (e) aq HCl, 80 ꢂC;
(f) Ac2O, polyvinylpyridine, MeCN.
activity against the quinolone-resistant S. aureus and E.
faecium strains. For example, while ciprofloxacin has
MIC of 32 mg/mL against the resistant S. aureus strain
SA1009, MICs of hybrids 2, 5, and 6 are 0.25, 0.5 and 1
mg/mL, respectively.
ciprofloxacin-resistant S. aureus SA1009 is suggestive of
an enhanced contribution of the quinolone MOA in this
analogue vs. piperazine-linked compounds 2, 5, and 6.
Indeed, compound 13 exhibits an IC50 of 12.5 mM in a
standard Escherichia coli DNA gyrase gel-based super-
coil assay22 (cf. to cipropfloxacin IC50 of 4.1 mM in the
same assay). The hybrid 13 also displays atypical for
oxazolidinones but expected for quinolones potency
against a wild-type E. coli strain (MIC 2 mg/mL). This
analogue is active against H. influenzae, M. catarrhalis,
and LRSA: MICs 0.25, 2, and 1 mg/mL, respectively.
Similar results were found for E. faecium. Thus, oxazo-
lidinone-ciprofloxacin hybrids 2, 5, and 6 are ca. 32- to
128-fold more active than ciprofloxacin against quino-
lone-resistant S. aureus and E. faecium strains (Table 1).
Furthermore, oxazolidinone-quinolone hybrids 2, 5,
and 6 are 2–4 times more active than linezolid against
two gram-negative respiratory tract pathogens, Haemo-
philus influenzae and Moraxella catarrhalis. However,
these compounds were not as active vs. latter strains as
the parent quinolones. The latter is likely reflective of a
sub-optimal pKa of the distal 7-amine group in the qui-
nolone fragment of the compounds (due to a reduced
basicity of N,N0-diarylpiperazine cf. to a mono-aryl
piperazine linkage of progenitor quinolones; cf. also
with only moderately active piperazine amide 16).
In summary, oxazolidinone and quinolone sub-
structures merged in a mutually SAR-compatible design
gave rise to a new class of antimicrobials with an
improved spectrum and potency over linezolid. Proto-
typical analogues 2, 5, and 6 represent an improvement
over linezolid against fastidious gram-negative patho-
gens H. influenzae and M. catarrhalis. These new leads
also maintain activity against linezolid- and/or cipro-
floxacin-resistant strains of S. aureus and E. faecium.
The enhanced potency and expanded antibacterial
spectrum of new analogues are consistent with antici-
pated dual oxazolidinone/quinolone MOA. In agree-
ment with the quinolone SAR, the activity of ester 7 is
inferior to that for corresponding acid 5. As expected, 3-
(S)-isomer 6 of the racemic (at quinolone) compound 5
appears somewhat more active than the latter against H.
influenzae. This parallels SAR in the progenitor quino-
lone series, wherein 3-(S)-enantiomer levofloxacin is
more potent than its racemic analogue, ofloxacin.19,20
Attenuated activity of the biaryl hybrid 13 against
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21. MICs determined following NCCLS guidelines. (National
Committee for Clinical Laboratory Standards. Methods for
Dilution Antimicrobial Susceptibility Tests for Bacteria that
Grow Aerobically; Approved Standard, 5th ed; NCCLS docu-
ment M7-A5; NCCLS: Wayne, PA, 2000). Bacterial strains
listed in Table 1 were obtained from Pharmacia Kalamazoo,
MI, USA) and include: SA1009: clinical isolate of S. aureus;
SA1011: ATCC29213; SA1012: in vitro selected linezolid-
resistant strain derived from SA1011; EF4010 and EF4016:
clinical isolates of E. faecium; EF4008 and EF4011: isogenic
linezolid-resistant strains isolated from same patient as
EF4010 and EF4016, respectively. HI1008: clinical isolate of
H. influenzae; MC1002: clinical isolate of M. catarrhalis;
EC1008: clinical isolate of E. coli.
22. A standard supercoiling assay using reagents and proto-
cols obtained from TopoGen Inc., Columbus, OH, USA, was
used to evaluate inhibitory activity of this compound.