5-(2-Pyrimidinyl)-imidazo[1,2-a]pyridines are antibacterial agents targeting the ATPase domains of DNA gyrase and topoisomerase IV

Article abstract of DOI:10.1016/j.bmcl.2009.07.141

Dual inhibitors of bacterial gyrB and parE based on a 5-(2-pyrimidinyl)-imidazo[1,2-a]pyridine template exhibited MICs (μg/mL) of 0.06-64 (Sau), 0.25-64 (MRSA), 0.06-64 (Spy), 0.06-64 (Spn), and 0.03-64 (FQR Spn). Selected examples were efficacious in mouse sepsis and lung infection models at <50 mg/kg (PO dosing).

Full text of DOI:10.1016/j.bmcl.2009.07.141

Bioorganic & Medicinal Chemistry Letters 19 (2009) 5302–5306
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
5-(2-Pyrimidinyl)-imidazo[1,2-a]pyridines are antibacterial agents targeting
the ATPase domains of DNA gyrase and topoisomerase IV
à
*
Jeremy T. Starr , Richard J. Sciotti , Debra L. Hanna, Michael D. Huband, Lisa M. Mullins, Hongliang Cai ,
Jeffrey W. Gage §, Mandy Lockard –, Mark R. Rauckhorst, Robert M. Owen ||, Manjinder S. Lall, Mark Tomilo ,
Huifen Chen àà, Sandra P. McCurdy, Michael R. Barbachyn §§
Pfizer Global Research and Development, 445 Eastern Point Rd., Groton, CT 06340, United States
a r t i c l e i n f o
a b s t r a c t
Article history:
Dual inhibitors of bacterial gyrB and parE based on a 5-(2-pyrimidinyl)-imidazo[1,2-a]pyridine template
Received 26 May 2009
Revised 29 July 2009
Accepted 30 July 2009
Available online 3 August 2009
exhibited MICs (lg/mL) of 0.06–64 (Sau), 0.25–64 (MRSA), 0.06–64 (Spy), 0.06–64 (Spn), and 0.03–64
(FQR Spn). Selected examples were efficacious in mouse sepsis and lung infection models at <50 mg/kg
(PO dosing).
Ó 2009 Elsevier Ltd. All rights reserved.
Keywords:
Antibacterial
Gyrase
Gram positive
GyrB
Fluoroquinolone (FQ) inhibitors of bacterial DNA gyrase and
topoisomerase IV have a long history characterized by the clinical
and commercial successes of Ciprofloxacin, Levofloxacin, and new-
er generations of the FQ class. However, resistance to FQs has
emerged1 and signals the need for discovery of medicines effective
against fluoroquinolone resistant (FQR) variants in the Gram-posi-
tive manifold where methicillin-resistant Staphylococcus aureus
(MRSA) is already a serious threat. FQs bind in the ‘Quinolone
Resistance Determining Region’ (QRDR) at the interface of the gyrA
and gyrB subunits in DNA gyrase, or the parC and parE subunits of
topoisomerase IV,2 inducing cell death by a complex cascade of
events involving cleavage of DNA.3a By contrast, coumerin natural
products such as novobiocin, inhibit type II topoisomerases by
binding in the ATPase domains of the gyrB subunit of DNA gyrase
and the parE subunit of topoisomerase IV, inhibiting the ATP
dependent step in the catalytic cycle.3b–d This leads to cell death
by loss of the respective supercoiling or decatenation functions
of DNA gyrase and topoisomerase IV. Dual gyrB/parE inhibitors,
therefore, present an alternative mechanistic approach to a classi-
cal enzyme target. Exploiting this mechanism would allow use of
the gyrase/topoisomerase IV pair as a therapeutic target while
retaining activity against FQR mutant organisms.
The opportunity for dual target inhibition and the availability of
high quality crystal structures4 of gyrB and parE has encouraged
numerous efforts to discover a new antibacterial drug based on
the gyrB/parE dual mechanism. Reports by many research groups,
among them, Vertex,5 Dainippon,6 Evotec,7 Quorex,8 Prolysis,9 As-
tra Zeneca10 and others,11 have yielded an array of novel antibacte-
rial chemical classes beyond the prototypical coumerin natural
products (Fig. 1). Our own work in this area identified triazolopyri-
dines12 similar to those reported by Evotec, and, 5-(2-pyrimidinyl)-
imidazo[1,2-a]pyridines (1)13 (Fig. 2), the subject of this report. The
latter are a novel class of dual gyrB/parE inhibitors that exhibit
excellent performance against important Gram-positive pathogens
including wild-type and methicillin-resistant Staphylococcus, and
wild-type and FQR Streptococcus and possess desirable in vivo
pharmacokinetic and efficacy properties.
* Corresponding author.
E-mail address: Jeremy.Starr@pfizer.com (J.T. Starr).
Present address: Walter Reed Army Institute of Research, 503 Robert Grant Ave.,
Silver Spring, MD, United States.
à
Present address: Pfizer Global Research and Development, 700 Chesterfield
Parkway, Chesterfield, MO 63017, United States.
§
Present address: 10634 McCrone, Milan, MI 48160, United States.
Present address: Wake Forest Institute for Regenerative Medicine, Medical Center
–
Blvd., Winston Salem, NC 27157, United States.
||
Present address: Pfizer Global Research and Development, Ramsgate Road, IPC
388, Sandwich, Kent CT13 9NJ, United States.
Present address: Compendia Bioscience, 110 Miller Ave., Ann Arbor, MI 48104,
United States.
àà
Present address: Department of Discovery Chemistry, Genentech, Inc., 1 DNA
Way, South San Francisco, CA 94080, United States.
Present address: AstraZeneca Pharmaceuticals LP, 35 Gatehouse Dr., Waltham,
MA 02451, United States.
Initially, 5-(2-pyrimidinyl)-imidazo[1,2-a]pyridines were syn-
§§
thesized according to the route outlined in Scheme 1.14 Conversion
0960-894X/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2009.07.141

J. T. Starr et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5302–5306
5303
N
N
N
N
O
O
O
O
NHEt
NHEt
NHEt
NHEt
N
S
N
N
N
N
N
NH
NH
NH
NH
N
N
N
N
H
F
N
N
N
O
NHEt
Pfizer
Vertex
Prolysis
Evotec
H
N
HO2C
N
NHEt
N
Me
N
O
H
N
O
NH2
Me
O
N
N
Me
Cl
O
Me
Me
N
O
Me
OH
Cl
Me
Cl
Cl
HO
Me
O
S
H
N
N
N
N
N
O
Me
O
O
N
N
H
N
O
N
N
O
N
S
N
O
O
N
Me
N
Me
Me
HN
H
HO2C
OH
Dainippon
Figure 1. Examples of GyrB inhibitors.
Astra Zeneca
Quorex
Novobiocin
N
thons in refluxing AcOH to give pyrimidines 4. Suzuki coupling
with the appropriate boronic acid or boronate ester installed the
desired heteroaryl substituent at C7. Hydrazinolysis of the remain-
ing ethyl ester (N2H4, MeOH) followed by azidation (NaNO2, aq
HCl), Curtius rearrangement in trifluoroethanol, and aminolysis
with ethylamine afforded final compounds 5.
O
7
NHEt
N
2
NH
N
N
5
N
Some analogs were synthesized by the shorter route shown in
Scheme 2.15 Conversion of 2-amino-4-bromo-6-ethoxycarbonyl-
pyridine 2 to the 2-H-imidazopyridine derivative was accom-
plished by reaction with chloroacetaldehyde (50% aq) in EtOH at
60 °C. The ethyl ester was aminolyzed with ammonia in MeOH at
the C5 position then dehydrated with TFAA in THF to give the cor-
responding C5 nitrile 6. Formation of the derived methyl imidate
under basic conditions (DBU in MeOH) followed by refluxing with
ammonium chloride in MeOH gave the amidine intermediate
which reacted with appropriately substituted 1,3-dicarbonyl syn-
thons in refluxing AcOH to give pyrimidines 7. Suzuki coupling
with the appropriate boronic acid or boronate ester installed the
desired heteroaryl substituent at C7. Direct installation of the ethyl
urea group at C2 by oxidation with Br2 or NBS in the presence of an
excess of ethyl urea completed the synthesis of final compounds 8.
R
1
Figure 2. 5-(2-Pyrimidinyl)-imidazo[1,2-a]pyridines.
Br
Ar
NH2
Br
N
a-c
CO2Et
N
N
d-e
CO2Et
CN
2
3
O
Br
NHEt
N
N
NH
CO2Et
f-j
N
N
N
N
N
N
Br
NH2
Br
R
R
N
a-c
5
4
N
N
d-e
Scheme 1. Reagents and conditions: (a) ethylbrompyruvate, EtOH, 75–99%; (b)
NH3, MeOH, 60 °C, 74%; (c) TFAA, pyr., 82%; (d) NH3, MeOH then NH4Cl, reflux; (e)
substituted b-aminoacrolein or 1,3-dicarbonyl, AcOH, reflux, 25–80%; (f) ArB(OR)2,
aq Na2CO3, Pd(dppf)Cl2, 50–75%; (g) N2H4, MeOH, 88%; (h) NaNO2, aq HCl, (i)
trifluoroethanol, reflux; (j) 70% aq EtNH2, DMSO, 80 °C, 25% over three steps.
CO2Et
CN
2
6
O
Ar
Br
NHEt
N
N
NH
f-g
N
N
N
of 2-amino-4-bromo-6-ethoxycarbonylpyridine 2 to the 2-ethoxy-
carbonyl-imidazopyridine derivative was accomplished by reac-
tion with ethyl bromopyruvate in EtOH at 60 °C. The diethylester
was selectively aminolyzed with ammonia in MeOH at the C5 po-
sition then dehydrated with TFAA in THF to give the corresponding
C5 nitrile 3. Formation of the derived methyl imidate under basic
conditions (NH3 or Et3N in MeOH) followed by refluxing with
ammonium chloride in MeOH gave the amidine intermediate
which reacted with appropriately substituted 1,3-dicarbonyl syn-
N
N
N
R
R
8
7
Scheme 2. Reagents and conditions: (a) chloroacetaldehyde, EtOH, 87%; (b) NH3,
MeOH, 60 °C, 85%; (c) TFAA, pyr., 60%; (d) DBU, MeOH then NH4Cl, reflux, 76%; (e)
substituted b-aminoacrolein or 1,3-dicarbonyl, AcOH, reflux, 65–85%; (f) ArB(OR)2,
aq. Na2CO3 or KF, Pd(dppf)Cl2, THF, 60–90%; (g) Br2 or NBS, EtNHCONH2, ACN then
aq NaHSO3, 10–50%.

5304
J. T. Starr et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5302–5306
Yields for this one pot procedure for direct installation of the urea
were typically modest (10–50%) but were competitive with the
overall yields for the four step Curtius rearrangement sequence
employed in the initial route (see Scheme 1). In practice, the direct
route became the preferred method due to the fewer number of
steps and greater tolerance of the 2-H intermediates for diverse
chemistry en route to final compounds.
the heterocycle. Polar functional groups at R3 or those with forced
3-dimensional geometry (entries 12, 15–16) exhibited reduced en-
zyme inhibition. These observations are consistent with docking in
the active site of Eco gyrB where a lipophilic surface associated
with the ILE-64 residue in the region of the ribose binding pocket
interacts with the planar C5 substituent. This region is similar in
the analogous domain of Eco parE.4e
The MIC16 and enzyme17 potencies of 5-pyrimidinyl-imidazo-
pyridines against Spn gyrB and parE, and five Gram positive organ-
isms (Sau, MRSA, Spy, Spn, and FQR Spn), are shown in Tables 1 and
2. Variation of the 4, 5, and 6 positions of the C5-pyrimidine (R2,
R3, R4), the heteroaryl group at C7 (R1, X), and the urea at C2
(R5) were investigated. Table 1 contains data for the C7-pyridyl
and C7-pyrimidinyl analogs. In general, deviation from ethyl urea
at C2 was found to be poorly tolerated (entries 22–26, 30) resulting
in >4-fold loss of enzyme potency in Spn gyrB and parE and >4-fold
loss of whole-cell activity across all the bacteria strains, compared
with the ethyl urea analogs. Substitution at R3 (entries 10–16, 22–
26, 28–29, 33, 35–37) conveyed improved whole-cell potency over
substitution at either R2 or R2 plus R4 (entries 17–21, 30–31).
However, tolerated substitution at R3 was limited to smaller axi-
ally symmetric groups or groups that could orient in plane with
Table 2 contains data obtained for C7-4-(2-pyridone) substi-
tuted analogs. Generally, C7 pyridones performed comparably to
or slightly better than C7 pyridyl or pyrimidine analogs, however,
greater disparity between Spn gyrB and parE inhibition was ob-
served with this substitution. The C7 pyridone having an anionic
group attached at the nitrogen (entry 42) was atypical in that en-
zyme potency was not translated to whole-cell activity. Poor cell
penetration may be prohibitive in this case.
Overall, achieving the goal of robust dual target pharmacology
was challenging across the imidazopyridines shown here and bal-
anced activity was seen only in isolated cases (entries 27, 29). Typ-
ically, Spn parE inhibition trailed Spn gyrB inhibition by >4-fold and
this gulf widened to >10-fold in the case of the C7-pyridones. Activ-
ity against MRSA (SA-1417) was similar to WT Staphylococcus aur-
eus (UC76) for most compounds that were tested. It is noteworthy
Table 1
Activity of selected C7-pyridyl and C7-pyrimidinyl examples
R1
N
O
R5
X
N
NH
N
N
N
R2
R4
R3
No.
Substitution
R3
Spn IC50
gyrB
(
l
M)
MICa
(lg/mL)
X
R1
R2
R4
R5
parE
S. au.
MRSA
S. py.
S. pn.
FQR S. pn.
Novobiocin
9
0.037
0.048
0.053
0.163
0.353
0.056
0.149
0.433
1.91
2.03
0.125
0.5
0.5
1
0.25
1
0.25
64
1
8
0.5
1
0.5
2
4
0.125b
0.5
0.5
1
8b
0.25
0.5
1
0.125
0.5
0.125
64
0.5
32
1
1
0.5
1
2
4b
0.125
0.125
0.5
0.06
0.125
0.06
8
0.25
16
0.125
0.5
0.25
0.25
1
4
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
CH
N
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
H
Me
Me
CF3
H
H
H
H
H
H
H
H
H
H
H
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHMe
Et
0.447
0.250
0.367
0.265
0.364
0.419
1.83
1.38
0.911
3.75
0.541
0.546
0.745
0.629
5
0.25
0.125
0.25
0.06
0.125
0.03
16
0.25
16
0.25
0.5
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
Me
CF3
Et
F
Cl
SO2Me
iPr
H
H
H
1
0.25
CO2Me
cPr
Me
CF3
CF3
H
H
H
H
H
H
H
H
Me
Me
H
H
H
0.052
0.33
8
0.5
4
1
4
0.198
0.216
0.242
0.092
0.255
0.295
0.261
0.368
0.044
0.096
0.117
1.38
0.113
0.137
0.524
0.075
0.036
0.132
0.244
H
H
0.125
0.125
0.25
16
Me
Me
Me
Me
Me
H
Me
Me
H
64
64
8
>64
>64
16
16
2
16
16
1
2
NHcPr
NHtBu
0.571
4.75
0.25
0.125
0.125
0.06
0.25
0.125
0.125
0.125
0.125
0.125
0.125
0.06
16
H
H
NHCH3CF3
NHEt
NHEt
NHEt
OEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
NHEt
0.504
0.119
0.373
0.147
6.22
0.424
0.611
1.38
8
4
0.25
0.06
0.5
0.25
0.5
0.25
0.125
0.25
0.125
0.25
16
Me
Me
OMe
Me2N
Me2N
Me2N
Me2N
H
0.25
0.5
0.5
64
0.5
1
0.25
0.25
0.5
0.25
0.25
0.25
0.5
0.5
0.5
32
1
2
N
N
N
N
N
N
N
H
H
Me
H
Me
Me
Me
H
H
H
H
1
4
0.28
0.258
3.64
0.5
0.25
16
0.5
H
MeO
C4H8N
H
H
H
1
>64
H
0.366
0.25
0.125
0.06
a
Strains: S. au. = Staphylococcus aureus UC76; MRSA = Staphylococcus aureus SA-1417; S. py. = Streptococcus pyogenes SP1-1; S. pn. = Streptococcus pneumoniae SP-3; FQR S.
pn. = Streptococcus pneumoniae SP-3765. ‘MIC’ refers to minimum inhibitory concentration and is the lowest concentration at which bacterial growth is inhibited.
b
MRSA = Staphylococcus aureus 01A-1095; S. py. = Streptococcus pyogenes C203; S. pn. = Streptococcus pneumoniae D39.

J. T. Starr et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5302–5306
5305
Table 2
Activity of selected C7-pyridone examples
O
R1
N
O
Me
NH
N
NH
N
N
N
Me
No.
Substitution
R1
Spn IC50
(l
M)
MIC (
lg/mL)
gyrB
parE
S. au.
MRSA
S. py.
S. pn.
FQR S. pn.
38
39
40
41
42
43
Me
Et
nPr
MeOC2H4
HO2CCH2
FC2H4
0.5
0.25
0.125
0.06
64
0.5
0.125
1
0.25
0.06
64
0.5
0.06
0.06
0.06
0.06
64
0.06
0.125
0.06
0.125
64
0.5
0.051
0.097
0.401
0.098
0.376
0.624
0.5
0.25
0.25
32
1.02
1.64
2.14
10
1
0.125
Table 3
In vivo activity and pharmacokinetics of selected compounds
No.
Mouse
Rat
Sepsisa (oral) PD50 (mg/kg)
Lungb (oral) PD50 (mg/kg)
Bioavailability (%F)
Clearance (mL/min/kg)
Volume of distribution (L/kg)
9
10
24
24
35
21
56
99
33
18
1.6
1.3
Infecting organism: (a) Streptococcus pyogenes SP1-1; (b) Streptococcus pneumoniae SV-1.
4. (a) Tsai, F. T. F.; Singh, O. M. P.; Skarzynski, T.; Wonacott, A. J.; Weston, S.;
Tucker, A.; Pauptit, R. A.; Breeze, A. L.; Poyser, J. P.; O’Brien, R.; Ladbury, J. E.;
Wigley, D. B. Proteins: Struct., Funct., Bioinf. 1997, 28, 41; (b) Brino, L.;
Urzhumstev, A.; Mousli, M.; Bronner, C.; Mitschler, A.; Oudet, P.; Moras, D. J.
Biol. Chem. 2000, 275, 9468; (c) Dale, G. E.; Kostrewa, D.; Gsell, B.; Stieger, M.;
D’Arcy, A. Acta Crystallogr., Sect. D 1999, 55, 1626; (d) Lewis, R. J.; Singh, O. M. P.;
Smith, C. V.; Skarzynski, T.; Maxwell, A.; Wonacott, A. J.; Wigley, D. B. EMBO J.
1996, 15, 1412; (e) Bellon, S.; Parsons, J. D.; Wei, Y.; Hayakawa, K.; Swenson, L.
L.; Charifson, P. S.; Lippke, J. A.; Aldape, R.; Gross, C. H. Antimicrob. Agents
Chemother. 2004, 48, 1856.
5. (a) Charifson, P. S.; Grillot, A.-L.; Grossman, T. H.; Parsons, J. D.; Badia, M.;
Bellon, S.; Deininger, D. D.; Drumm, J. E.; Gross, C. H.; LeTiran, A.; Liao, Y.; Mani,
N.; Nicolau, D. P.; Perola, E.; Ronkin, S.; Shannon, D.; Swenson, L. L.; Tang, Q.;
Tessier, P. R.; Tian, S.-K.; Trudeau, M.; Wang, T.; Wei, Y.; Zhang, H.; Stamos, D. J.
Med. Chem. 2008, 51, 5243; (b) Grossman, T. H.; Bartels, D. J.; Mullin, S.; Gross,
C. H.; Parsons, J. D.; Liao, Y.; Grillot, A.-L.; Stamos, D.; Olson, E. R.; Charifson, P.
S.; Mani, N. Antimicrob. Agents Chemother. 2007, 51, 657; (c) Mani, N.; Gross, C.
H.; Parsons, J. D.; Hanzelka, B.; Muh, U.; Mullin, S.; Liao, Y.; Grillot, A.-L.;
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that some potentiation of effect in an FQR resistant strain (SP-3765)
compared to wild-type occurred. Many compounds exhibited >2-
fold lower MIC against a FQR Spn strain compared to WT, consistent
with a fitness penalty associated with the FQR resistant DNA gyrase
or topoisomerase IV enzymes. An agent possessing this property
may be advantageous in patients at higher risk of FQR infection,
in coadministration with a FQ agent, or as follow-on therapy in
cases that are refractory to FQ treatment.
The 5-(2-pyrimidinyl)-imidazopyridines were efficacious
in vivo against murine Spy sepsis and Spn Lung models. Table 3
shows selected examples with oral PD50 and rat PK parameters.
Compound 10 was selected for additional study and will be high-
lighted individually in a future publication.
Acknowledgment
6. (a) Tanitame, A.; Oyamada, Y.; Ofuji, K.; Terauchi, H.; Kawasaki, M.; Wachi, M.;
Yamagishi, J.-i. Bioorg. Med. Chem. Lett. 2005, 15, 4299; (b) Tanitame, A.;
Oyamada, Y.; Ofuji, K.; Fujimoto, M.; Suzuki, K.; Ueda, T.; Terauchi, H.;
Kawasaki, M.; Nagai, K.; Wachi, M.; Yamagishi, J.-i. Bioorg. Med. Chem. 2004, 12,
5515; (c) Tanitame, A.; Oyamada, Y.; Ofuji, K.; Fujimoto, M.; Iwai, N.; Hiyama,
Y.; Suzuki, K.; Ito, H.; Terauchi, H.; Kawasaki, M.; Nagai, K.; Wachi, M.;
Yamagishi, J.-I. J. Med. Chem. 2004, 47, 3693; (d) Tanitame, A.; Oyamada, Y.;
Ofuji, K.; Suzuki, K.; Ito, H.; Kawasaki, M.; Wachi, M.; Yamagishi, J.-i. Bioorg.
Med. Chem. Lett. 2004, 14, 2863; (e) Tanitame, A.; Oyamada, Y.; Ofuji, K.; Kyoya,
Y.; Suzuki, K.; Ito, H.; Kawasaki, M.; Nagai, K.; Wachi, M.; Yamagishi, J. n-i.
Bioorg. Med. Chem. Lett. 2004, 14, 2857.
7. East, S. P.; White, C. B.; Barker, O.; Barker, S.; Bennett, J.; Brown, D.; Boyd,
E. A.; Brennan, C.; Chowdhury, C.; Collins, I.; Convers-Reignier, E.; Dymock,
B. W.; Fletcher, R.; Haydon, D. J.; Gardiner, M.; Hatcher, S.; Ingram, P.;
Lancett, P.; Mortenson, P.; Papadopoulos, K.; Smee, C.; Thomaides-Brears, H.
B.; Tye, H.; Workman, J.; Czaplewski, L. G. Bioorg. Med. Chem. Lett. 2009, 19,
894.
We thank Richard Miller (Pfizer Global Research and Develop-
ment) for assistance with manuscript preparation.
References and notes
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229; (b) Van Bambeke, F.; Reinert, R. R.; Appelbaum, P. C.; Tulkens, P. M.;
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2. Co-crystal structures of clinafloxacin and moxifloxacin bound with DNA and
Streptococcus pneumoniae topoisomerase IV were recently reported:
Laponogov, I.; Sohi, M. K.; Veselkov, D. A.; Pan, X.-S.; Sawhney, R.; Thompson,
A. W.; McAuley, K. E.; Fisher, L. M.; Sanderson, M. R. Nat. Struct. Mol. Biol. 2009,
16, 667.
3. For a recent discussion of the FQ mechanism see: (a) Drlica, K.; Malik, M.;
Kerns, R. J.; Zhao, X. Antimicrob. Agents Chemother. 2008, 52, 385; For the
novobiocin mechanism see: (b) Ali, J. A.; Jackson, A. P.; Howells, A. J.; Maxwell,
A. Biochemistry 1993, 32, 2717; (c) Maxwell, A. Mol. Microbiol. 1993, 9, 681; (d)
Kampranis, S. C.; Gormley, N. A.; Tranter, R.; Orphanides, G.; Maxwell, A.
Biochemistry 1999, 38, 1967.
8. Yager, K.; Chu, S.; Appelt, K.; Li, X. US patent appl. US 20050054697, 2005.
9. Haydon, D. R.; Czaplewski, L. G.; Palmer, N. J.; Mitchell, D. R.; Atherall, J. F.;
Steele, C. R.; Ladduwahetty, T. Int. Pat. Appl. WO 2007148093, 2007.
10. (a) Dumas, J.; Sherer, B. Int. Pat. Appl. WO 2009027733, 2009; (b) Basarab, G.;
Hill, P.; Zhou, F. Int. Pat. Appl. WO 2008152418, 2008.

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J. T. Starr et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5302–5306
11. Oblak, M.; Kotnik, M.; Solmajer, T. Curr. Med. Chem. 2007, 14, 2033. and
references therein.
12. Butler, D. C. D.; Chen, H.; Hegde, V. R.; Limberakis, C.; Rasne, R. M.; Sciotti, R. J.;
Starr, J. T. Int. Pat. Appl. WO 2006038116, 2006.
yl)imidazo[1,2-a]pyridine. (f) To a degassed solution of 7-bromo-5-(pyrimidin-
2-yl)imidazo[1,2-a]pyridine (0.820 g, 2.98 mmol) and pyridine-3-boronic acid
(0.550 g, 4.47 mmol) in 20 mL THF and 7.5 mL 2 N KF was added 0.041 g of
Pd(dppf)Cl2 and the reaction was heated to reflux for 3 h. The reaction was then
cooled to 23 °C and evaporated in vacuo to give a brown residue that was
partitioned between 1 M HCl and dichloromethane. The aqueous layer was
collected and the organic layer was extracted 2 Â 1 M HCl then the combined
aqueous layers were washed 1 Â dichloromethane. The combined aqueous
layers were then neutralized with sodium bicarbonate and extracted
3 Â dichloromethane. The combined organic extracts were dried over sodium
sulfate, evaporated in vacuo, and purified by silica gel chromatography (2–10%
isopropanol/dichloromethane) to give 0.540 g (66.3%) of 7-(pyridin-3-yl)-5-
13. Sciotti, R. J.; Starr, J. T.; Richardson, C.; Rewcastle, G. W.; Palmer, B. D.;
Sutherland, H. S.; Spicer, J. A.; Chen, H. Int. Pat. Appl. WO 2005089763, 2005.
14. For example, the synthesis of compound 32 is described in Ref. 13.
15. For example, the synthesis of compound 9: (a) To a stirring solution of ethyl 6-
amino-4-bromopicolinate (2) (30.11 g, 123 mmol) in 200 mL EtOH was added
50% aq chloroacetaldehyde (19 mL) and the reaction was heated to reflux. After
3 h, the solvent volume was reduced to ca. 100 mL in vacuo then the brown
solution was slowly poured into dil. aq sodium bicarbonate. The resulting slurry
was then vacuum filtered, the filter cake was rinsed 3 Â water, 1 Â ether, and
dried to give 28.90 g (87%) of ethyl 7-bromoimidazo[1,2-a]pyridine-5-
(pyrimidin-2-yl)imidazo[1,2-a]pyridine. (g) To
a preformed solution of
ethylurea (1.74 g, 19.7 mmol) and bromine (1.26 g, 7.90 mmol) in 20 mL
dichloromethane was added 7-(pyridin-3-yl)-5-(pyrimidin-2-yl)imidazo[1,2-
a]pyridine (0.540 g, 1.97 mmol) and the resulting red solution was stirred at rt
for 1 h. It was then poured into ice-cold aqueous sodium hydrogen sulfite
(200 mL Â 0.050 g/ml) and the bright yellow reaction was neutralized with
sodium bicarbonate and extracted 3 Â 10% isopropanol/dichloromethane.
The combined organic extracts were dried over sodium sulfate and evaporated
then purified by silica gel chromatography (5–30–60% isopropanol/
dichloromethane). Fractions containing desired product were combined and
washed 2 Â water to remove ethylurea and dried over sodium sulfate. The
solution was filtered and to this was added a solution of ca. 0.3 mL concd HCl in
10 mL IPA. Evaporation in vacuo and drying under hivac overnight gave 0.318 g
(37%) of compound 9 as the HCl salt. 1H NMR (400 MHz, DMSO-d6) d ppm 9.76 (s,
1H), 9.36 (s, 1H), 9.26 (s, 1H), 9.14 (s, 1H), 9.13 (s, 1H), 8.87 (d, J = 5.66 Hz, 2H),
8.59 (d, J = 1.95 Hz, 1H), 8.29 (d, J = 1.76 Hz, 1H), 8.02 (dd, J = 7.81, 5.85 Hz, 1H),
7.68 (t, J = 4.88 Hz, 1H), 3.16 (q, J = 7.22 Hz, 2H), 1.06 (t, 7.22, 3H); 13C NMR
(100 MHz, DMSO-d6) d ppm 159.55, 158.56, 154.58, 143.95, 142.83, 142.80,
141.58, 141.08, 136.00, 134.01, 131.68, 127.22, 121.90, 115.95, 113.83, 101.39,
34.79, 16.05; LCMS purity: 95%, MS(API): M+H = 360.1.
dicarboxylate as an amorphous powder. (b)
A solution of ethyl 7-
bromoimidazo[1,2-a]pyridine-5-dicarboxylate (15.0 g, 55.7 mmol) in 150 mL
2:1 THF/MeOH was treated with 150 mL 7 N NH3/MeOH and the reaction was
stirredat23 °Cfor3 h. Theresultingcopiousprecipitatewascollected byvacuum
filtration and the filtrate was allowed to continue reacting. The filter cake was
rinsed 1 Â MeOH and 1 Â ether then dried to give a first crop of 7.09 g of amide
product. After 24 h, additional precipitate had formed in the filtrate and an
additional 4.33 g was repetition of the collecting procedure described above to
give a combined yield of 11.42 g (85%) of 7-bromo-5-carboxamidoimidazo[1,2-
a]pyridine. (c) To
a suspension of 7-bromo-5-carboxamidoimidazo[1,2-
a]pyridine (7.09 g, 29.8 mmol) in 200 mL dichloromethane at 0 °C was added
triethylamine (16.5 mL, 118 mmol) followed by dropwise addition of
trifluoroacetic anhydride (5.2 mL, 37 mmol). The reaction was allowed to
warm to 23 °C and it gradually became a homogeneous bright yellow solution.
After 2 h, the reaction was washed 2 Â 1 N NaHSO4, 2 Â satd aq sodium
bicarbonate and dried over sodium sulfate. Evaporation in vacuo gave 5.59 g of
crude product that was recrystallized from ethylacetate to give 3.96 g (60%) of 7-
bromo-5-cyanoimidazo[1,2-a]pyridine (6). (d) To a suspension of 7-bromo-5-
cyanoimidazo[1,2-a]pyridine (6) (3.15 g, 14.2 mmol) in 75 mL MeOH was added
DBU (2.20 g, 14.5 mmol) and the reaction was stirred at 23 °C for 30 min. To the
reaction was then added 2.60 g ammonium chloride and the reaction was heated
to reflux. After 3 h, the reaction was uncapped and allowed to evaporate to 50%
volume. It was then cooled to 23 °C and poured into water. The resulting slurry
was vacuum filtered and the wetcake was rinsed 3 Â water. To the filtrate was
then added solid NaCl and the mixture was heated until the salt (and all other
solids) dissolved. Cooling in the freezer resulted in copious precipitation.
Vacuum filtration gave 1.31 g of tan solid after drying the filtercake.
The mother liquor was allowed to stand in the freezer for two more days and a
second crop of 1.27 g of tan solid was obtained. The combined solids were dried
16. Clinical and Laboratory Standards Institute Methods for Antimicrobial
Susceptibility Testing of Anaerobic Bacteria; Approved Standard, 6th ed.; NCCLS
Document M11-A6; Vol. 24, No. 2.
17. For gyrB see: (a) Miller, J. R.; Herberg, J. T.; Tomilo, M.; McCroskey, M. C.;
Feilmeier, B. J. Anal. Biochem. 2007, 365, 132; (b) For parE: Compounds to be
tested were solvated at 10–30 mM in DMSO then diluted into 10 mM Tris pH
7.5, 9 mM MgCl2, and 0.02% (v/v) Tween 20 and serial diluted. The serially
diluted compounds (10
To each well, 10 L of a solution consisting of 20 mM Tris, pH 7.5, 120 mM KCl,
1.5 mM MgCl2, 0.02% (v/v) Tween 20, 0.018% polyethyleneimine, 0.03%
butylperflorosulfonate, and 66 g/mL Streptococcus pneumoniae ParE. The
reaction was initiated by addition of 10 L of a solution containing 3 mM
ATP and 0.02% Tween 20 and allowed to proceed for 30 min. The ATPase
activity was quenched and orthophosphate detected by addition of 30 L of a
lL) were then transferred into a clear 384-well plate.
l
l
to give
carboximidamide. (e)
a
total yield of 2.58 g (76%) of 7-bromoimidazo[1,2-a]pyridine-5-
mixture of 7-bromoimidazo[1,2-a]pyridine-5-
l
A
carboximidamide (1.10 g, 4.64 mmol) and dimethylaminoacrolein (0.6 mL,
6 mmol) in 20 mL AcOH was refluxed for 3 h. The dark brown solution was
then evaporated to a viscous residue that was diluted with water and poured into
dil. aq sodium bicarbonate. The resulting yellow slurry was vacuum filtered and
the collected solid was dried to give 0.824 g (65%) of 7-bromo-5-(pyrimidin-2-
l
solution consisting of equal volumes of 4.2% (w/v) ammonium molybdate in
4 M HCl and 0.135% (w/v) malachite green in 20% (w/v) glycerol. The plate was
briefly shaken and the absorbance at 650 nm was determined using
Spectramax plate reader (Molecular Devices).
a