Synthesis and antibacterial activity of the C-7 side chain of 3-aminoquinazolinediones

Article abstract of DOI:10.1016/j.bmcl.2008.07.117

A novel series of bacterial topoisomerase (3-aminoquinazolinediones) inhibitors are described. The side-chain SAR against Gram-positive and Gram-negative organisms as well as DNA gyrase activity is reported.

Full text of DOI:10.1016/j.bmcl.2008.07.117

Bioorganic & Medicinal Chemistry Letters 18 (2008) 5087–5090
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and antibacterial activity of the C-7 side chain
of 3-aminoquinazolinediones
Kim M. Hutchings a,b, , Tuan P. Tran a,b, Edmund L. Ellsworth a,b, Brian M. Watson a,b, Joseph P. Sanchez a,b
,
,
*
H. D. Hollis Showalter a,b, Michael A. Stier a,b, Martin Shapiro a,c, E. Themis Joannides a,c, Michael Huband a,c
Dai Q. Nguyen d, Samarendra Maiti d, Tingsheng Li d, Jyoti Tailor d, George Thomas d, Chan Ha d,
Rajeshwar Singh d
a Pfizer Global Research and Development, Michigan Laboratories, Ann Arbor Campus, 2800 Plymouth Road, Ann Arbor, MI 48105, USA
b Department of Chemistry, 4290-91A Street, Edmonton, Alta., Canada T6E5V2
c Department of Antibacterial Pharmacology, 4290-91A Street, Edmonton, Alta., Canada T6E5V2
d Naeja Pharmaceuticals, 4290-91A Street, Edmonton, Alta., Canada T6E5V2
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 bacterial topoisomerase (3-aminoquinazolinediones) inhibitors are described. The side-
chain SAR against Gram-positive and Gram-negative organisms as well as DNA gyrase activity is reported.
Ó 2008 Elsevier Ltd. All rights reserved.
Received 12 June 2008
Revised 29 July 2008
Accepted 31 July 2008
Available online 3 August 2008
Keywords:
Topoisomerase
Aminoquinazolinediones
Antibacterial
Fluoroquinolone
We recently reported a new class of antibacterial agents, the 3-
hydroxyquinazolinediones, which have been identified as bacterial
type-2 topoisomerase inhibitors.1 While this class exhibited good
potency against Escherichia coli gyrase, it possessed no in vivo effi-
cacy. Metabolism studies showed that this was attributed to rapid
clearance due to glucuronidation of the 3-hydroxy function. Fur-
ther investigation showed that replacement of the 3-hydroxy with
a 3-amino moiety retained potency and prevented this route of
metabolism, thus providing excellent in vivo efficacy in murine
infection models.2,3
This novel class of agents is similar in structure to the flu-
oroquinolones (i.e., ciprofloxacin). The acidic functionality of
the fluoroquinolones has historically been viewed as being
essential for binding to bacterial gyrase and topo IV (pKa
5.6–6.4).4,5 Although the 3-hydroxyquinazolinedione series re-
tains acidic functionality at the 3-position (pKa 6.3–7.0), the
3-aminoquinazolinediones are neither acidic nor basic at the
3-position. Notably, they share the same mechanism of action
as the fluoroquinolones. More specifically, the 3-amin-
oquinazolinediones inhibit the supercoiling of DNA, and, like
the fluoroquinolones, provide
a
linear cleavage complex.
Although these two classes share a similar mechanism of ac-
tion, we have shown that fluoroquinolone-resistant strains are
sensitive to the 3-aminoquinazolinediones. Sequencing of resis-
tant mutants grown in Neisseria gonorrhoeae identified muta-
tions in or near the quinolone-resistant determining regions
(QRDR) in gyrA or gyrB, suggesting that the binding site is near
to or overlapping that of the fluoroquinolones. This lack of
cross resistance to quinolone-resistant strains in addition to
the 3-aminoquinazolinedione’s exceptional activity makes this
an attractive new series for further evaluation. Our earlier re-
O
N
O
N
F
F
NH2
O
F
NH2
O
a
N
N
R2R1N
1
2
* Corresponding author at present address: AstraZeneca Pharmaceuticals, Infec-
tion chemistry, 35 Gatehouse Drive, Waltham, MA 02451, USA.
E-mail address: kim.hutchings@astrazeneca.com (K.M. Hutchings).
Scheme 1. Reagents and conditions: (a) TMG, DMSO, NR1R2, 80–100 °C, 30–60%.
0960-894X/$ - see front matter Ó 2008 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2008.07.117

5088
K. M. Hutchings et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5087–5090
We have previously published on the SAR around the 3-hydrox-
O
O
yquinazolinedione core.1 The work described here focuses on the
SAR of the C-7 position of the 3-aminoquinazolinediones. All com-
pounds reported in this Letter utilize the core with optimal substi-
tution at the C-1, C-6, and C-8 positions (Fig. 1). The results of this
effort are shown in Table 1. In general, the MICs against wild-type
E. coli are poor, although the MICs versus the TolC strain are signif-
icantly improved, suggesting that these compounds are substrates
for efflux. Both the pyrrolidine (6) and the piperidine (7) analogs
show good MICs against Gram-positive organisms, with pyrroli-
dine 6 exhibiting the best MICs overall. Similar to the fluoroquino-
lones, the 5- and 6-membered heterocycles demonstrate the best
activity in Gram-positive organisms and the piperazine side chain
has the best activity in wild-type E. coli.4
a
F
NH2
F
NH2
N
N
N
N O
N
N O
BocHN
H2N
3
4
Scheme 2. Reagents and conditions: (a) HCl, CH2Cl2 or EtOH, 80–90%.
ports profiled two compounds within the 3-aminoquinazolined-
ione series.2,3 In this Letter, a systematic SAR around the C-7
side chain is explored.
Historically, fluoroquinolones containing amino-substituted
pyrrolidines give improved Gram-positive activity.4 Therefore,
substitution of the pyrrolidine with an additional amino group
was explored and found to give significantly improved potency
(Table 2). The optimal positioning of an amino substituent was
determined by varying the distance of the terminal amino group
to the pyrrolidine. Although pyrrolidine 9 has excellent enzyme
activity, the aminomethyl-substituted pyrrolidine analog (10) dis-
plays the best overall activity with significantly better Gram-posi-
tive activity relative to its comparators.
The 3-aminoquinazolinediones (3-AQD) were prepared accord-
ing to Schemes 1 and 2. A substituted heterocyclic side chain was
coupled to the 3-AQD core6 in dimethylsulfoxide using 1,1,3,3-tet-
ramethylguanidine (TMG) providing the desired analogs in moder-
ate yields (unoptimized). In many cases, the functionalized side
chains contained Boc-protected nitrogens that were deprotected
using anhydrous hydrogen chloride in dichloromethane or ethanol
(Scheme 2). In these cases, the compounds were isolated and
tested as hydrochloride salts.
Having identified the methyl amino pyrrolidine side chain as
having the best activity, we then looked to further explore the
SAR around this template. Several analogs are shown in Table 3.
Many of these targets with substitution of the exocyclic meth-
ylene showed improved activity over the unsubstituted analog
10. Most notably, the larger ethyl and phenyl substituents (15
and 16) demonstrate superior enzyme activities. Disubstitution
of the exocyclicmethylene was also examined. While an addi-
tional methyl group (13 vs 12) gave a modest decrease in anti-
bacterial activity, incorporating the cyclopropyl group resulted
in one of the most active of the 3-aminoquinazolinediones
(compound 14).
Having determined that substitution at the methylene pro-
vided enhanced activity, the role of stereochemistry was also
explored examining the isomers of 12. A comparison of the en-
zyme activity of each of the four stereoisomers shows that the
stereocenter adjoining the pyrrolidine ring is the most impor-
tant for enhanced activity. Compounds 17 and 18 with the R
Many of the side chains included in this study are either
available commercially (R1 for compounds 5–11), or prepared
as reported in the literature (R1 for compounds 12–15, 17–
22).7–9 The side chain for compound 16 was prepared in six
steps from commercially available methyl N-benzyl-3-
pyrrolidinecarboxylate.10
The prepared 3-aminoquinazolinediones were tested according
to CLSI guidelines (formerly NCCLS)11,12 against representative
Gram-negative and Gram-positive strains using standard micro-
broth dilution methodology.13 The Gram-negative strains reported
here include E. coli MC4100, a wild-type strain, as well as E. coli
TolC, an efflux pump knock-out strain. The Gram-positive strains
represented here include Staphylococcus aureus, Streptococcus pyog-
enes, and Enterococcus faecalis. The minimum inhibitory concentra-
tions are summarized in Tables 1–4 and are compared to that of
ciprofloxacin.
The compounds were also tested for their inhibition of DNA
gyrase.14
Table 1
Structure–activity relationships of several heterocycles at the C-7 position
O
N
F
NH2
N
R1
O
Compound
R1
MICs (
lg/mL)
IC50 (lM)
E. coli MC4100
E. coli Tol C
E. faecalis MGH-2
S. aureus 29213
S. pyogenes C-203
E. coli gyrase
Ciprofloxacin
5
0.06
>64
0.06
2
0.4
64
0.5
32
2
64
0.4
12.5
N
6
7
8
16
>64
4
0.13
0.25
1
2
4
1
4
1
4
4
1.9
6.3
3.1
N
N
N
32
32
HN

K. M. Hutchings et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5087–5090
5089
Table 2
Structure–activity relationships of aminopyrrolidines at the R-7 position
O
N
F
NH2
O
N
R1
Compound
R1
E. coli MC4100
MICs (lg/mL)
IC50 (lM)
E. coli Tol C
E. faecalis MGH-2
S. aureus 29213
S. pyogenes C-203
E. coli gyrase
6
9
16
1
0.13
2
1
1
1.9
N
H2N
0.25
0.13
0.5
8
8
1
0.2
0.4
1.2
N
H2N
H2N
10
11
2
0.5
4
0.5
4
0.06
0.125
N
16
N
Table 3
Effect of substitution on the exomethylene of the pyrrolidine 10
O
F
NH2
N
R1
N
O
Compound
R1
MICs (
l
g/mL)
IC50 (lM)
E. coli MC4100
E. coli Tol C
E. faecalis MGH-2
S. aureus 29213
S. pyogenes C-203
E. coli gyrase
12
13
14
15
4
0.25
1
0.5
0.03
0.6
H2N
H2N
H2N
N
N
N
16
2
0.25
0.03
0.13
2
1
0.125
0.03
1.6
0.8
0.4
0.13
0.25
0.25
0.5
8
0.03
H2N
H2N
N
N
16
4
0.06
0.25
0.13
0.03
0.26
configuration at the pyrrolidine ring showed increased antibac-
terial activity in most strains versus their comparators 20 and
19. Of these two compounds, 17 has superior activity with min-
imally 4x better MICs in all organisms. Historically, the stereo-
center on the pyrrolidine ring had a profound effect on activity
in the fluoroquinolones as well, and as in the AQD series, the R
configuration is favored.4,15
showed similar activity to compound 17, larger groups showed a
decrease in activity, especially noticeable in Strep. pyogenes in com-
pound 22.
In conclusion, we have reported on the SAR of the C-7 position
of 3-aminoquinazolinediones, which has a remarkable similarity to
the fluoroquinolone SAR. A number of analogs were prepared
exhibiting good antibacterial activity, especially in Gram-positive
organisms. Further exploration in this series will be reported in
due course.
Finally, we explored the effect of substitution on the primary
amine of analog 17. Although methyl substitution on the nitrogen

5090
K. M. Hutchings et al. / Bioorg. Med. Chem. Lett. 18 (2008) 5087–5090
Table 4
Effect of stereochemistry and substitution on the distal nitrogen
O
N
F
NH2
O
N
R1
Compound
R1
MICs (lg/mL)
IC50 (lM)
E. coli MC4100
E. coli TolC
E. faecalis MGH-2
S. aureus 29213
S. pyogenes C-203
E. coli gyrase
NH2
H
17
18
19
20
21
22
0.5
0.03
0.13
0.13
0.13
0.03
0.13
0.06
0.13
0.015
0.2
N
N
N
N
N
NH2
H
2
2
4
4
8
0.5
0.5
1
0.06
0.25
0.5
0.3
0.8
0.6
0.2
0.9
NH2
H
0.25
2
NH2
H
2
NH
H
0.13
0.25
0.5
0.5
0.015
0.13
NH
H
N
7. Kimura, Y.; Atarashi, S.; Takahashi, M.; Hayakawa, I. Chem. Pharm. Bull. 1994,
42, 1442.
8. Fleck, T. J.; McWhorter, W. W., Jr.; DeKam, R. N.; Pearlman, B. A. J. Org. Chem.
2003, 6(8), 961.
9. Schroeder, M. C.; Kiely, J. S.; Laborde, E.; Johnson, D. R.; Szoteck, D. L.;
Domagala, J. M.; Stickney, T. M.; Michel, A.; Kampf, J. W. J. Heterocycl. Chem.
1992, 1481.
O
N
O
N
R3
O
4
6
F
F
CO2H
N
R7
8
N
1
HN
10. The side chain for compound 16 was prepared from methyl N-benzyl-3-
pyrrolidinecarboxylate. The ester was converted to the Weinreb amide via the
carboxylic acid using standard conditions. Addition of phenyl Grignard provided
the phenyl ketone, which was converted to the oxime. Reduction to the amine
followed by deprotection of the benzyl group gave the desired side chain.
R3=OH 3-Hydroxyquinazolinedione
R3=NH2 3-Aminoquinazolinedione
ciprofloxacin
Figure 1. Structural comparison.
Acknowledgments
O
O
OCH3
H2N
d,e,f
a,b,c
We thank Richard Zaniewski for providing enzyme data and
Lisa Mullins for performing several MIC determinations.
N
N
N
H
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