Synthesis and antibacterial activity of 7-(1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones

Article abstract of DOI:10.1016/j.bmcl.2009.07.087

A novel series of 7-(1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones has been designed and synthesized in which the heterocyclic side chain is attached to the quinolone core through a carbon-carbon linkage. The antibacterial activity of the compo

Full text of DOI:10.1016/j.bmcl.2009.07.087

Bioorganic & Medicinal Chemistry Letters 19 (2009) 4933–4936
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and antibacterial activity of 7-(1,2,3,4-tetrahydropyrrolo[1,2-a]-
pyrazin-7-yl) quinolones
*
Bin Zhu , Brett A. Marinelli, Raul Goldschmidt, Barbara D. Foleno, Jamese J. Hilliard, Karen Bush,
Mark J. Macielag
Research & Early Development, Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Welsh and McKean Roads, Spring House, PA 19477, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
A novel series of 7-(1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones has been designed and syn-
thesized in which the heterocyclic side chain is attached to the quinolone core through a carbon–carbon
linkage. The antibacterial activity of the compounds was determined against a panel of Gram-positive
and Gram-negative pathogens. Compounds 1b and 1e, bearing an 8-methoxy group as well as unsubsti-
tuted and (3S)-methyl substituted 1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-7-yl side chains, respectively,
demonstrated notable activity against ciprofloxacin-resistant clinical isolates of Streptococcus
pneumoniae.
Received 1 July 2009
Revised 15 July 2009
Accepted 17 July 2009
Available online 22 July 2009
Keywords:
Antibacterial agent
Quinolone
Ó 2009 Elsevier Ltd. All rights reserved.
Since the discovery of nalidixic acid1 over four decades ago, the
quinolones have evolved into an important class of antibacterial
agents.2 Several of the quinolones, including ciprofloxacin3 and lev-
ofloxacin,4 are widely used in the clinic to treat multiple bacterial
infections. The quinolones act against bacteria by selectively inhib-
iting the type II topoisomerases DNA gyrase and topoisomerase IV,
enzymes that play a critical role in bacterial cell growth and divi-
sion.2c However, extensive clinical use of these agents has led to
increasing bacterial resistance to the available quinolones.2d Thus,
it is a continuing challenge to discover and develop newer quinolone
antibacterial agents with activity against resistant organisms,
including the respiratory pathogen, Streptococcus pneumoniae.
The general chemical structure of the quinolone antibacterial
agents consists of a 4-quinolone/naphthyridone-3-carboxylic acid
nucleus and a nitrogen-containing side chain, which is attached
to the C7 position of the heterocyclic core. While the side chain
is typically attached to the quinolone core through a nitrogen
atom, there have been a limited number of examples wherein a
carbon–carbon linkage was utilized.5 One of the most noteworthy
examples is garenoxacin6 (Fig. 1), which exhibits a broad spectrum
antibacterial profile and is among the newer quinolones to have
advanced into late stage clinical trials.
antibacterial activity of a series of 7-(1,2,3,4-tetrahydropyrrol-
o[1,2-a]pyrazin-7-yl) quinolones 1 (Fig. 1).
The general synthetic route to the 7-(1,2,3,4-tetrahydropyrrol-
o[1,2-a]pyrazin-7-yl) quinolones is outlined in Scheme 1. The key
O
O
O
N
O
Y
OH
OH
R3
X
N
R1
HN
N
O
HN
F
F
R2
X = N, CR;Y = H, F
garenoxacin
7-(1,2,3,4-tetrahydropyrrolo[1,2-a]
pyrazin-7-yl) quinolone (1)
Figure 1.
O
O
Y
Z
O
B
OEt
Pd-mediated
coupling
R3
O
+
X
N
R1
N
BocN
R2
Z = Br, Cl, OTf
Investigating quinolone analogs with a carbon–carbon linkage
between the quinolone core and the C7 side chain is one of the strat-
egies we employed in the search for new and more effective quino-
lone antibacterial agents. Herein we report the synthesis and
3
2
O
O
O
O
Y
Y
OEt
OH
oxidation
de-protection
R3
R3
X
N
X
N
R1
R1
N
N
BocN
R2
HN
R2
4
1
* Corresponding author. Tel.: +1 215 628 7943.
E-mail address: bzhu@its.jnj.com (B. Zhu).
Scheme 1.
0960-894X/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2009.07.087

4934
B. Zhu et al. / Bioorg. Med. Chem. Lett. 19 (2009) 4933–4936
HO
HO
O
O
R2
6
Bn
N
b
O
B
Y
Z
a
OEt
MeO
CO2Me
+
a
NHBn
CO2H
O
N
N
+
O
R2
X
N
R1
O
Boc
Boc
N
BocN
R2
5
7
X = N, CR;Y = H, F
Z = Br, Cl, OTf
O
OH
OH
O
c
e
d
3a
2
N
N
N
Bn
N
Bn
N
O
O
Bn
N
O
O
Y
Y
O
R2
OEt
R2
R2
OEt
b
10
9
8
X
N
X
N
R1
R1
O
OTf
O
B
N
N
BocN
R2
BocN
R2
OH
g
f
O
N
13
N
14
Boc
N
Boc
N
O
O
N
Boc
N
R2
R2
Y
c, d
R2
12
11
3a
X
N
R1
Scheme 2. Reagents and conditions: (a) DCC, CH2Cl2; (b) (I) CF3CO2H, CH2Cl2; (II) aq
NaHCO3, THF, rt; (c) LiAlH4, THF, reflux; (d) EDCI, DMSO, PyTFA, CH2Cl2; (e) (I)
CH3CH(Cl)OC(O)Cl, CH3CN; (II) aq NaHCO3, THF rt; (III) Boc2O, THF; (f) KN(SiMe3)2,
PhNTf2, THF, ꢀ78 °C to 0 °C; (g) bis(pinacolato)diboron, Pd(PPh3)2Cl2, PPh3, KOPh,
toluene, 55 °C.
N
HN
R2
1a-j
Scheme 3. Reagents and conditions: (a) Pd(PPh3)4, CsF, THF, reflux; (b) Pd/C, air,
MeOH, rt; (c) aq 1 N NaOH, MeOH, THF; (d) 4 N HCl in dioxane, CH2Cl2.
step is a palladium-mediated coupling reaction between 7-halo/7-
trifloxy-quinolone-3-carboxylic ester 2 and 1,2,3,4,6,8a-hexahy-
O
dropyrrolo[1,2-a]pyrazin-7-yl boronic ester
3 to form the
H2N
OMe
OTBS
N
HO
OTBS
N
carbon–carbon bond between the quinolone core and the side
chain. The resulting 7-(1,2,3,4,6,8a-hexahydropyrrolo[1,2-a]pyra-
zin-7-yl)-quinolone-3-carboxylic ester 4 could then be oxidized
and deprotected to give the 7-(1,2,3,4-tetrahydropyrrolo[1,2-
a]pyrazin-7-yl) quinolone 1.
R2
d
a, b
c
17
N
CO2H
OMe
N
O
O
Boc
Boc
Boc
OTBS
5
15
16
R
N
+
Inspired by the side-chain structure of garenoxacin, we focused
primarily on the unsubstituted 1,2,3,4-tetrahydropyrrolo[1,2-
a]pyrazine side chain and those with small R2 substituents, such
as a methyl group. The synthesis of side-chain intermediate 3a is
illustrated in Scheme 2. Commercially available (4R)-hydroxy-N-
BocN
OTBS
R2
CO2Me
OTBS
N
20
R2
f, g
e
NH
OTBS
N
HN
R2
S
Boc
O
N
BocN
R2
Boc-L
-proline 5 was coupled with N-benzyl-glycine (R2 = H) methyl
18
19
21
ester or N-benzyl-alanine [R2 = (S)-CH3 or (R)-CH3] methyl ester
under standard peptide coupling conditions [N,N0-dicyclohexylcar-
bodiimide (DCC), CH2Cl2] to give amide 7. The Boc protecting group
of 7 was removed by treatment with trifluoroacetic acid, and the
resulting amine was cyclized under basic conditions (aq NaHCO3,
THF) to give the bicyclic di-amide compound 8. Both amide groups
of 8 were then reduced by treatment with LiAlH4 to give compound
9, the hydroxyl of which was then oxidized to give the correspond-
O
R3
O
h, i
same as
B
R3
O
20 or 21
N
BocN
Scheme 2
N
BocN
R2
R2
22 R3 = (R)-CH3
3b R3 = (R)-CH3
or
3c R3 = (S)-CH3
or
23 R3 = (S)-CH3
O
O
ing ketone 10 using
a modified Pfitzner–Moffat procedure
Y
[N-(3-dimethylaminopropyl)-N0-ethylcarbodiimide hydrochloride
(EDCI), DMSO, pyridinium trifluoroacetate].7 The benzyl protecting
group of 10 was removed by treatment with 1-chloroethyl chloro-
formate, and the resulting secondary amine was re-protected with
a Boc group to give compound 11. Compound 11 was reacted with
potassium bis(trimethylsilyl)amide at ꢀ78 °C, followed by addition
of N-phenyl-bis(trifluoromethane-sulfonimide) (PhNTf2) to con-
vert the ketone to vinyl triflate 12. Transforming the vinyl triflate
group of 12 to a boronic ester group proved to be a challenging
task, mainly due to the ease with which the pyrroline was oxidized
to the pyrrole. Gratifyingly, after a number of attempts, the desired
boronic ester 3a was prepared by modifying a procedure reported
by Miyaura et al.8 Vinyl triflate 12 was reacted with bis(pinacola-
to)diboron under Pd(PPh3)2Cl2 catalysis in the presence of potas-
sium phenoxide in toluene at elevated temperature (55 °C) to
give vinyl boronic ester 3a.
OH
R3
same as
Scheme 3
X
N
R1
N
HN
R2
1k-q R3 = (S)-CH3
or
1r-u R3 = (R)-CH3
Scheme 4. Reagents and conditions: (a) CH3NH(OCH3) HCl, Et3N, DCC, CH2Cl2; (b)
TBSCl imidazole, DMF, rt; (c) CH3MgBr, THF, 0 °C to rt; (d) NaCNBH3, HOAc, MeOH,
rt; (e) (I) CF3CO2H, CH2Cl2; (II) aq NaHCO3, THF; (f) LiAlH4, THF, rt; (g) (I) Boc2O,
THF; (II) chromatography separation; (h) HF (aq 48%), CH3CN; (i) EDCI, DMSO,
PyTFA, CH2Cl2.
a]pyrazin-7-yl) quinolone 14. Hydrolysis under basic conditions
(aq NaOH, MeOH, THF) converted the ethyl ester of 14 to the car-
boxylic acid. Finally, deprotection of the side chain amine under
acidic condition (4 N HCl in dioxane, CH2Cl2) led to 7-(1,2,3,4-tet-
rahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones 1a–j (Scheme 3).
Scheme 4 outlines the synthesis of side-chain intermediates 3b
The coupling of side-chain intermediate 3a and quinolone core
29 was catalyzed by Pd(PPh3)4, in the presence of CsF in refluxing
THF to give 7-(1,2,3,4,6,8a-hexahydropyrrolo[1,2-a]pyrazin-7-yl)
quinolone 13, which was then subjected to Pd/C catalyzed air-oxi-
dation to yield the corresponding 7-(1,2,3,4-tetrahydropyrrolo[1,2-
and 3c. (4R)-Hydroxy-N-Boc-L-proline 5 was reacted with N,O-dim-

B. Zhu et al. / Bioorg. Med. Chem. Lett. 19 (2009) 4933–4936
4935
ethylhydroxylamine hydrochloride in the presence of Et3N and
The hydroxy group was then protected as a t-butyldimethylsilyl
ether (TBSCl, imidazole, DMF) to give compound 15. The Weinreb
N,N0-dicyclohexylcarbodiimide (DCC) to form the Weinreb amide.
Table 1
In vitro antibacterial activity of 7-(1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones 1
O
O
Y
6
OH
7
8
1
R7
X
N
R1
1
Compd
Y
R7
X
R1
MIC (lg/ml)
A
B
C
D
E
F
Cipro
F
C–H
0.12
1
>16
1
>16
8
>16
0.03
HN
HN
N
1a
H
C–OCHF2
0.06
0.5
N/A
0.25
N
1b
1c
F
F
C–OCH3
0.03
0.5
0.25
2
1
1
1
0.12
1
>16
>16
>16
O
CH3
HN
S
1d
1e
1f
H
F
F
F
F
F
F
C–OCHF2
C–OCH3
CH
0.12
0.03
0.06
0.25
0.06
0.12
0.03
1
1
8
1
1
N
0.12
0.5
1
0.5
2
1
0.5
2
0.25
0.12
0.5
0.25
2
4
1g
1h
1i
4
8
4
O
CH3
N
0.5
1
2
8
8
F
N
16
1
16
2
16
1
F
HN
R
1j
C–OCH3
0.25
0.5
N
1k
H
C–OCHF2
0.5
1
4
16
4
2
HN
S
N
1l
F
F
F
F
F
F
H
F
F
F
C–OCHF2
C–OCH3
CH
0.25
0.12
0.25
0.25
0.5
2
1
8
2
2
1m
1n
1o
1p
1q
1r
0.5
1
2
4
1
0.5
0.5
0.5
1
4
16
8
4
1
4
4
O
CH3
N
1
8
8
8
F
N
1
4
>16
4
>16
16
16
16
8
>16
8
8
F
C–OCHF2
C–OCH3
CH
0.5
1
4
HN
R
N
1s
0.25
0.25
0.12
2
8
>16
8
2
1t
1
4
0.25
1
R
HN
S
1u
C–OCH3
1
2
N/A
N
(A) Staphylococcus aureus subsp. aureus ATCC13709; (B) Streptococcus pneumoniae ATCC49619; (C) Streptococcus pneumoniae OC5462; (D) Streptococcus pneumoniae OC5458;
(E) Streptococcus pneumoniae OC5465; (F) Escherichia coli ATCC25922. Strains C, D, and E are ciprofloxacin-resistant clinical isolates of Streptococcus pneumoniae that contain
different representative constellations of amino acid substitutions in the QRDR regions of DNA gyrase and DNA topoisomerase IV.

4936
B. Zhu et al. / Bioorg. Med. Chem. Lett. 19 (2009) 4933–4936
Table 2
amide was converted to the methyl ketone by treatment with
In vivo efficacy of 1e in the S. aureus murine lethal systemic infection model
CH3MgBr. The resulting ketone 16 was subjected to a reductive
amination reaction with glycine methyl ester (R2 = H) or
L-alanine
Compd
ED50 (mg/kg)
methyl ester [R2 = (S)-CH3] in the presence of NaCNBH3 to give
compound 18 as a mixture of two diastereomers. Removal of the
Boc group using trifluoroacetic acid, followed by cyclization under
basic conditions (aq NaHCO3, THF) afforded the cyclized amide 19.
The amide group was reduced to a tertiary amine by treatment
with LiAlH4. Protecting the secondary amine with a Boc group gave
a mixture of two diastereomers 20 and 21, which could be easily
separated by standard chromatography. The TBS protecting group
of 20 and 21 was removed by treatment with aq HF in CH3CN,
and the resulting hydroxyl was oxidized to the corresponding ke-
tones 22 and 23, respectively.
Compounds 22 and 23 were first converted to boronic esters 3b
and 3c, which were then coupled with the quinolone derivative 2.
The final products 1k–q and 1r–u were obtained after oxidation,
hydrolysis and de-protection under the same conditions as those
described in Scheme 3.
Oral
Subcutaneous
Cipro
1e
10.8
4.0
1.4
<1.25
Compound 1e was selected for further evaluation in a murine
lethal systemic infection model ( S. aureus subsp. aureus
ATCC13709),11 and exhibited more potent in vivo efficacy (oral
ED50 = 4.0 mg/kg; subcutaneous ED50 <1.25 mg/kg) than ciproflox-
acin (Table 2).
In summary, we have designed and synthesized a series of novel
7-(1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones with a
carbon–carbon linkage between the quinolone nucleus and the C7
side chain. The antibacterial activity of these compounds was eval-
uated against ciprofloxacin-susceptible and ciprofloxacin-resistant
bacteria. One of the best analogs of this series (compound 1e) also
demonstrated good in vivo efficacy. Further studies of the antibac-
terial activity of this series of quinolone compounds will be re-
ported in the future.
The in vitro antibacterial activity of the 7-(1,2,3,4-tetrahydro-
pyrrolo[1,2-a]pyrazin-7-yl) quinolones 1 was determined against
both ciprofloxacin-susceptible and ciprofloxacin-resistant bacteria.
Data for representative compounds, along with ciprofloxacin, are
presented in Table 1 as the minimum inhibitory concentration
(MIC; lowest concentration of compound inhibiting visible
growth)10 against an abbreviated panel of six bacterial strains,
including ciprofloxacin-susceptible Staphylococcus aureus subsp.
aureus ATCC13709 (A), S. pneumoniae ATCC49619 (B), and Esche-
richia coli ATCC25922 (F), as well as ciprofloxacin-resistant clinical
isolates of S. pneumoniae OC5462 (C), OC5458 (D) and OC5465 (E).
Compared to ciprofloxacin, the 7-(1,2,3,4-tetrahydropyrrol-
o[1,2-a]pyrazin-7-yl) quinolones listed in Table 1 showed similar
in vitro activity against the ciprofloxacin-susceptible Gram-posi-
tive bacteria, S. aureus subsp. aureus ATCC13709 (A) and S. pneumo-
niae ATCC49619 (B), whereas they were generally less active
against the ciprofloxacin-susceptible Gram-negative bacteria,
E. coli ATCC25922 (F). In contrast, the majority of the 7-(1,2,3,4-tet-
rahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones exhibited lower
MIC values against all or some of the three ciprofloxacin-resistant
S. pneumoniae strains C, D and E than ciprofloxacin. The data indi-
cated that substituents at the 1- and 8-positions of the quinolone
core as well as the C7 side chain all played crucial roles in deter-
mining the antibacterial activity of the corresponding quinolone
compounds. Among various 1,2,3,4-tetrahydropyrrolo[1,2-a]pyra-
zine side chains investigated, the combination of a C-8 methoxy
group (X = C-OCH3) and a N-1 cyclopropyl group (R1 = cyclopropyl)
generally led to analogs with better antibacterial activity, as dem-
onstrated by compounds 1b, 1e, and 1m. For methyl substituted
1,2,3,4-tetrahydropyrrolo[1,2-a]pyrazine side chains, the position
of the methyl group on the tetrahydropyrazine ring was important
(1d–1i vs 1k, 1m–1q), as well as the stereochemistry (1e vs 1j; 1m
vs 1s). The (S)-configuration of the methyl group seemed to be pre-
ferred. Accordingly, incorporation of a second methyl group of the
(R)-configuration into the tetrahydropyrazine ring did not improve
antibacterial activity (1u vs 1e). The unsubstituted 1,2,3,4,-tetrahy-
dropyrrolo[1,2-a]pyrazine (1a–1c) and the (S)-methyl substituted
1,2,3,4,-tetrahydropyrrolo[1,2-a]pyrazine (1d–1i) side chains are
apparently optimal for this series. In fact, among the 7-(1,2,3,4,-
tetrahydropyrrolo[1,2-a]pyrazin-7-yl) quinolones evaluated, 1b
and 1e are the most potent compounds in terms of in vitro antibac-
terial activity against ciprofloxacin-susceptible and ciprofloxacin-
resistant strains.
Acknowledgment
The authors wish to thank Ellyn Wira for contributions to
in vitro testing.
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group of infected mice not treated with drug served as controls.