Synthesis and structure-activity relationships of antitubercular 2-nitroimidazooxazines bearing heterocyclic side chains

Article abstract of DOI:10.1021/jm901378u

Recently described biphenyl analogues of the antituberculosis drug PA-824 displayed improved potencies against M. tuberculosis but were poorly soluble. Heterobiaryl analogues of these, in which the first phenyl ring was replaced with various 5-membered ring heterocycles, were prepared with the aim of identifying potent new candidates with improved aqueous solubility. The compounds were constructed by coupling the chiral 2-nitroimidazooxazine alcohol with various halomethyl-substituted arylheterocycles, by cycloadditions to a propargyl ether derivative of this alcohol, or by Suzuki couplings on haloheterocyclic methyl ether derivatives. The arylheterocyclic compounds were all more hydrophilic than their corresponding biphenyl analogues, and several showed solubility improvements. 1-Methylpyrazole, 1,3-linked-pyrazole, 2,4-linked-triazole, and tetrazole analogues had 3- to 7-fold higher MIC potencies against replicating M. tb than predicted by their lipophilicities. Two pyrazole analogues were >10-fold more efficacious than the parent drug in a mouse model of acute M. tb infection, and one displayed a 2-fold higher solubility. 2009 American Chemical Society.

Full text of DOI:10.1021/jm901378u

J. Med. Chem. 2010, 53, 855–866 855
DOI: 10.1021/jm901378u
Synthesis and Structure-activity Relationships of Antitubercular 2-Nitroimidazooxazines Bearing
Heterocyclic Side Chains
Hamish S. Sutherland,*,† Adrian Blaser,† Iveta Kmentova,† Scott G. Franzblau,‡ Baojie Wan,‡ Yuehong Wang,‡
Zhenkun Ma,§ Brian D. Palmer,† William A. Denny,† and Andrew M. Thompson†
†Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142,
New Zealand, ‡Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street,
Chicago, Illinois 60612, and Global Alliance for TB Drug Development, 40 Wall Street, New York, New York 10005
§
Received September 16, 2009
Recently described biphenyl analogues of the antituberculosis drug PA-824 displayed improved
potencies against M. tuberculosis but were poorly soluble. Heterobiaryl analogues of these, in which
the first phenyl ring was replaced with various 5-membered ring heterocycles, were prepared with the
aim of identifying potent new candidates with improved aqueous solubility. The compounds were
constructed by coupling the chiral 2-nitroimidazooxazine alcohol with various halomethyl-substituted
arylheterocycles, by cycloadditions to a propargyl ether derivative of this alcohol, or by Suzuki
couplings on haloheterocyclic methyl ether derivatives. The arylheterocyclic compounds were all more
hydrophilic than their corresponding biphenyl analogues, and several showed solubility improvements.
1-Methylpyrazole, 1,3-linked-pyrazole, 2,4-linked-triazole, and tetrazole analogues had 3- to 7-fold
higher MIC potencies against replicating M. tb than predicted by their lipophilicities. Two pyrazole
analogues were >10-fold more efficacious than the parent drug in a mouse model of acute M. tb
infection, and one displayed a 2-fold higher solubility.
Introduction
6-nitroimidazo[2,1-b][1,3]oxazole, OPC-67683 (2),10 are cur-
rently in phase II clinical trials for the treatment of drug-
susceptible and drug-resistant TB,11 with the aim of reducing
the duration and frequency of drug treatment required. A
recent report12 of a phase IIa early bactericidal activity (EBA)
study of 1 given as a single agent to TB patients once daily for
14 days (dosing orally at 200, 600, 1000, or 1200 mg) showed
that the drug was essentially equivalent to the standard, four-
drug TB treatment protocol in reducing the number of live
M. tb in the sputum (∼0.1 log decrease in CFUs per day for 14
days) and was well-tolerated (but equally efficacious) at all
dose levels. The use of a dry powder inhaler as an alternative
drug delivery system for 1 has now been reported to provide
increased lung concentrations for longer times than that
achieved following oral administration (guinea pig model).13
We recently described6 a structure-activity relationship
(SAR) study of biphenyl analogues of 1, which showed that
many derivatives (I) (including 3-linked, but particularly
4-linked examples, such as 3) had improved potencies against
both replicating and nonreplicating M. tb in culture. Some of
these displayed particularly notable efficacies in a mouse
model of acute M. tb infection (e.g., 3 was >205-fold more
effective than 1). The study also showed that aerobic MIC
values correlated positively both with overall lipophilicity and
with the electron-withdrawing properties of substituents on
the terminal phenyl ring. However, these biphenyl analogues
had concomitantly lower aqueous solubilities than 1 (e.g., the
solubility of 3 was at least 16-fold less than 1), which could
negatively impact on their oral bioavailability at higher doses.
This is likely given that 1 itself is 94% protein bound in human
plasma14 and because absorption issues were noted during
Over the last two decades, there has been a global resur-
gence of tuberculosis (TBa), fuelled by an enhanced suscept-
ibility in HIV patients, the increasing incidence of multidrug-
resistant (MDR) TB, and the recent emergence of extensively
drug resistant (XDR) strains.1,2 The current second-line drugs
used in lengthy combination therapies to treat MDR-TB
(typically over 2 years2) mostly have reduced potency and/
or greater toxicity than existing first-line agents and may be
largely ineffective against XDR-TB,2 underscoring the urgent
need for new treatments. In the past decade, the general class
of (6S)-2-nitroimidazo[2,1-b][1,3]oxazines bearing lipophilic
side chains at the 6-position, typified by PA-824 (1),3 has
shown potent activity against both replicating and nonrepli-
cating cultures of Mycobacterium tuberculosis (M. tb),3-6 the
causative agent of TB. Recent work suggests that an impor-
tant component of the activity of these compounds against
nonreplicating M. tb is due to an unusual route of reductive
metabolism of the nitroimidazole ring,7,8 leading to the release
of nitric oxide as a toxic species.9 Both 1 and the related
*To whom correspondence should be addressed. Phone: (þ649) 923
4441. Fax: (þ649) 373 7502. E-mail: h.sutherland@auckland.ac.nz.
a Abbreviations: TB, tuberculosis; MDR, multidrug-resistant; XDR,
extensively drug resistant; M. tb, Mycobacterium tuberculosis; EBA,
early bactericidal activity; SAR, structure-activity relationship; MIC,
minimum inhibitory concentration; SD, standard deviation; MLB,
meta-linked biphenyl; CFU, colony forming unit; THP, tetrahydropyr-
anyl; APCI MS, atmospheric pressure chemical ionization mass spectro-
metry; DMF, N,N-dimethylformamide; THF, tetrahydrofuran; TBAF,
tetra-n-butylammonium fluoride; DMSO, dimethyl sulfoxide; PAR,
peak area ratio; IS, internal standard.
r
2009 American Chemical Society
Published on Web 12/07/2009
pubs.acs.org/jmc

856 Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2
Sutherland et al.
clinical trials of the much more lipophilic 2 that necessitated a
change in drug formulation for this compound.15 Unfortu-
nately, attempts to solubilize the biphenyl class via amino-
alkoxy substituents resulted in a dramatic loss in activity,
particularly in vivo.6
Scheme 1a
a Reagents and conditions: (i) NaH, DMF, 0 °C, 2 h; (ii) ArB(OH)2,
toluene, EtOH, 2 M K2CO3, PdCl2(dppf) under N2, reflux, 0.5-1 h.
Scheme 2a
In work aimed at identifying new, potent heterobiaryl
analogues of 1 with better aqueous solubilities than the
biphenyl class, we now report the synthesis and evaluation
of 11 different subseries in which the proximal phenyl ring
of I was replaced by more hydrophilic 5-membered ring
heterocycles.
a Reagents and conditions: (i) ArB(OH)2, toluene, EtOH, 2 M
K2CO3, PdCl2(dppf) under N2, reflux, 2 h; (ii) LiAlH4 or LiPyrrBH3,
THF, 0 or 20 °C, 1-2 h; (iii) SOCl2, reflux, 0.5 h; (iv) 61, NaH, DMF,
0 °C, 2 h.
Chemistry
The 5-arylthiophene and 2-arylthiazole analogues (9-19
and 20-25, respectively) were prepared by base-catalyzed
alkylation of the known16 chiral alcohol 61 with the 2-halo(5-
or 4-halomethyl) heterocycles 6217 or 64,18 followed by Suzuki
coupling of the products (63 and 65) with appropriate aryl-
boronic acids (Scheme 1). Similar base-catalyzed alkylation
of alcohol 61 with (3-bromo-1-propynyl)(tert-butyl)dim-
ethylsilane19 (87) gave (after desilylation) the propargyl ether
88, which underwent cycloaddition20 with known21-24
N-hydroxy-arylcarboximidoyl chlorides (89a-f) to give the
3-arylisoxazole derivatives 40-45 directly (Scheme 5). Alter-
natively, treatment of 88 with known25-28 aromatic azides
alcohols 73a-c, which yielded the desired bromides on treat-
ment with phosphorus tribromide.
The synthesis of 1-aryl-4-linked-pyrazoles 34-36 began
with the condensation of ethyl (2E)-2-cyano-3-ethoxy-2-pro-
penoate (75) and 4-substituted phenylhydrazines 76a-c to
give the expected34 substituted ethyl 5-amino-1-phenylpyrazole-
4-carboxylates (77a-c) (Scheme 4). Deamination with isoamyl
nitrite35 provided the esters 78a-c, which were successively
reduced and brominated as above to furnish the required
1-aryl-4-(bromomethyl)pyrazoles 80a-c. Synthesis of the iso-
meric 1-aryl-3-linked-pyrazoles 37-39 commenced with the
reaction of ethyl 2-chloroacetoacetate (81) and known36,37
4-substituted benzenediazonium tetrafluoroborates (82a-c) to
give38 the intermediate arylhydrazonoyl chlorides 83a-c
(Scheme 4). These underwent a [3 þ 2] cycloaddition with
bicyclo[2.2.1]hepta-2,5-diene, followed by a retro Diels-Alder
reaction (in refluxing xylenes), to form39,40 the ethyl 1-arylpyr-
azole-3-carboxylates 84a-c, which were elaborated to the
1-aryl-3-(bromomethyl)pyrazoles 86a-c in similar fashion.
2-(Chloromethyl)-5-(4-fluorophenyl)-1,3,4-oxadiazole (92),
employed in the preparation of the oxadiazole analogue 46,
was prepared directly41 by chlorination (POCl3) of N0-(chloro-
acetyl)-4-fluorobenzohydrazide42 (91), obtained by chloroace-
tylation of 4-fluorobenzohydrazide (90) (Scheme 5). The
2-aryl-4-(bromomethyl)-1,2,3-triazoles (99a-d) required for
the preparation of 2-aryl-4-linked-1,2,3-triazoles 53-56 were
synthesized by the condensation of 2-oxopropanedial diox-
ime43 (94) and arylhydrazines (95a-d) to give the intermediate
dioximes 96a-d (Scheme 6). These dioximes were successively
acetylated (Ac2O), cyclized with cesium carbonate, and treated
29
(93a, 93c-g) in the presence of CuI/Cu(OAc)2 gave the
1-aryl-1,2,3-triazole derivatives 47-52.
The rest of the compoundswere synthesized bythe coupling
of alcohol 61 with various fully constructed side chains
(arylheterocycles bearing a halomethyl substituent). These
were prepared by a variety of different routes. The 2-aryl-
5-(chloromethyl)-1-methylimidazole hydrochlorides 69a-e
required for the synthesis of 2-arylimidazole analogues
26-30 were formed by Suzuki coupling of methyl 2-bromo-
1-methyl-1H-imidazole-5-carboxylate30 (66) with arylboronic
acids, subsequent reduction (LiAlH4) of the resulting esters
(67a, 67c-e, or LiPyrrBH331 reduction in the case of 67b) to
give alcohols 68a-e, and finally chlorination with thionyl
chloride (Scheme 2). The 3-aryl-5-(bromomethyl)-1-methyl-
pyrazoles 74a-c employed in the synthesis of 3-arylpyrazole
analogues 31-33 were constructed by Pd-catalyzed four-
component coupling32 of THP-protected prop-2-yn-1-ol
(70)33 with 4-substituted iodobenzenes 71a-c, aqueous methyl-
hydrazine, and carbon monoxide to give the THP-protected
1-methylpyrazole derivatives 72a-c (Scheme 3). Deprotection
under forcing conditions (4M HCl/THF/80 °C/16 h) gave

Article
Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2 857
Scheme 5a
Scheme 3a
a Reagents and conditions: (i) MeNHNH2.H2SO4, aq NaHCO3, CuI,
PdCl2(PPh3)2, THF, 20 °C, 48 h under CO; (ii) 4 M HCl, THF, 80 °C,
16 h; (iii) PBr3, Et2O, 0-20 °C, 16 h; (iv) 61, NaH, DMF, 0 °C, 2 h.
Scheme 4a
a Reagents and conditions: (i) NaH, DMF, 0 °C, 1 h, then TBAF,
THF, 0 °C, 1 h; (ii) Et3N, THF, 0-20 °C, 16 h; (iii) ClCH2COCl, EtOAc,
reflux, 30 min; (iv) POCl3, reflux, 2 h; (v) 61, NaH, DMF, 0 °C, 0.5 h;
(vi) CuI, Cu(OAc)2, THF, 50 °C, 16 h (then, for 48: TFAA, THF,
reflux, 2 h).
Scheme 6a
a Reagents and conditions: (i) NaOAc, aq AcOH, 100 °C, 15 h; (ii)
isoamyl nitrite, THF, reflux, 20 h; (iii) LiAlH4, Et2O, 0-20 °C or reflux,
1-2 h; (iv) PBr3, Et2O, 0-20 °C, 2-17 h; (v) 61, NaH, DMF, 0 °C, 2 h;
(vi) aq pyridine, -5 °C, 0.5 h; (vii) bicyclo[2.2.1]hepta-2,5-diene, Et3N,
toluene, 70 °C, 1 h, then xylenes, reflux, 2 h.
with paraformaldehyde (rather than s-trioxane as reported44)
to give the triazole aldehydes 97a-d, which were further
elaborated to the required bromides. Finally, the 2-aryl-
5-(bromomethyl)tetraazoles 103a-d needed for the prepara-
tion of 2-aryltetrazole analogues 57-60 were obtained from
the known45 2-(2-arylhydrazono)acetic acids (100a-d) by
base-catalyzed reaction46 with 2-azido-1,3,5-tribromoben-
zene,47 followed by esterification with diazomethane, to give
2-aryltetrazole esters 101a-d. Following ester reduction, the
alcohols (102a-d) were brominated using either PBr3 or NBS/
Ph3P (Scheme 6).
a Reagents and conditions: (i) EtOH, 70 °C, 0.5 h; (ii) Ac2O, 20 °C, 0.5
h, then Cs2CO3, THF, 20 °C, 0.5 h, then (CH2O)n, 2 M HCl, reflux, 2 h;
(iii) NaBH4, MeOH, 20 °C, 0.5 h; (iv) PBr3, Et2O, 0-20 °C, 15-16 h or
NBS, PPh3, CH2Cl2, -40 °C, 2 h; (v) 61, NaH, DMF, 0 °C, 1-2 h; (vi)
NaOEt, EtOH, 2,4,6-triBrPhN3, reflux, 5 h, then aq HCl, then CH2N2,
Et2O, MeOH, 20 °C; (vii) LiAlH4, Et2O, 0 °C, 1 h.
Results and Discussion
and 3. The lipophilicities of the compounds were estimated by
CLogP values, calculated using ACD LogP/LogD prediction
software (version 8.0, Advanced Chemistry Development
Inc., Toronto, Canada), as described for the biphenyl series.6
The comparative effects of the heterocyclic groups on com-
pound CLogP values were evaluated using the reference set of
biphenyl analogues (4-8) and determining, for each aryl-
heterocyclic subseries, the average difference in CLogP values
between compounds in the reference and subseries sets
bearing the same substituents (Table 2). All of the arylhetero-
cyclic compounds were more hydrophilic than their MLB
Table 1 provides data on 11 subseries related to the
previously described biphenyl analogues, in which the phenyl
ring proximal to the 2-nitroimidazooxazine chromophore was
replaced by different 5-membered ring heterocycles. These
ranged from monoheterocyclic species (thiophene; class A),
through various N, mixed N/S, and N/O di- and trihetero-
cycles, to a tetraheterocycle (tetrazole; class K). For compar-
ison, previous data6 are given for five meta-linked biphenyl
(MLB) analogues (4-8) which have the most similar side
chain geometry tothe new analogues, together withdata6 for1

858 Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2
Sutherland et al.
Table 1. Continued
Table 1. Physicochemical Properties and MIC Values for Arylhetero-
cyclic Analogues of 1
MIC (μM)c
compd Fm
R
sola CLogPb
108 0.65
MABA
LORA
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
H
I
4-F
2.4 ( 0.8
0.11 ( 0.02
0.89 ( 0.04
1.2 ( 0.2
17 ( 0
3.4 ( 0.2
11 ( 5
4-CF3
4-CN
4-F
4.6 1.91
0.77
1.39
I
I
6.9 ( 3.4
I
4-OCF3
3-F, 4-OCH3
3-aza, 4-OCH3
H
2.29 0.075 ( 0.015 3.3 ( 0.2
1.25
0.44
I
0.86 ( 0.13
1.6 ( 0.4
0.25 ( 0.04
0.05 ( 0.01
0.17 ( 0.06
0.03 ( 0
1.2 ( 0.2
0.20 ( 0.03
0.29 ( 0.17
8.7 ( 1.2
12 ( 6
I
J
1.34
2.2 ( 0.9
2.1 ( 1.2
1.4 ( 0.2
1.6 ( 0.2
5.7 ( 2.4
1.4 ( 0.6
3.4 ( 0.1
J
4-CF3
4-F
1.0 1.91
1.39
2.29
J
J
4-OCF3
H
K
K
K
K
1.27
5.0 1.84
1.32
4-CF3
4-F
4-OCF3
2.22 0.035 ( 0.005 1.3 ( 0.4
a Solubility (μg/mL) in water at pH = 7 and 20 °C, determined by
HPLC (see Experimental Section, Method A). b CLogP values, calcu-
lated using the ACD LogP/LogD prediction software (version 8.0,
Advanced Chemistry Development Inc., Toronto, Canada). c Minimum
inhibitory concentration, determined under aerobic (MABA)50 or anae-
robic (LORA)49 conditions. Each value is the mean of at least two
independent determinations (29 determinations for 1) ( SD.
MIC (μM)c
compd Fm
R
sola CLogPb
19 2.70
MABA
LORA
1
3
0.50 ( 0.30
2.6 ( 1.4
analogues, but there was substantial variation across the
heterocyclic subseries. The thiophene and thiazole classes
(A and B) showed the least lipophilicity differences to MLB
analogues, with average ΔCLogP values of -0.20 and -0.43,
respectively. All of the other heterocyclic classes were much
more hydrophilic and fairly similar, with average ΔCLogPs
ranging from -1.90 (3,5-linked-1-methylpyrazole; class D) to
-2.79 (2,5-linked-1,3,4-oxadiazole; class H).
1.2 4.36 0.035 ( 0.015 1.3 ( 0.1
4
M
M
M
M
M
A
A
A
A
A
A
A
A
A
A
A
B
4-CF3
4-CN
4-F
2.8 4.48
2.83
0.12 ( 0.01
0.23 ( 0.01
2.9 ( 1.4
4.8 ( 1.1
5
6
1.8 3.44 0.077 ( 0.034 3.8 ( 0.7
7
4-OCF3
3-F, 4-OCH3
4-CF3
4.36
3.30
0.11 ( 0.05
0.19 ( 0.10
0.16 ( 0
2.2 ( 0.5
2.2 ( 0.5
1.0 ( 0.4
8
9
0.7 4.29
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
38
39
40
41
42
43
44
45
4-CN
4-F
2.63 0.055 ( 0.005 1.7 ( 0.6
The compounds were evaluated for their ability to inhibit
M. tb in two assays (Table 1) in order to derive SAR for both
aerobic and anaerobic activity, as described in previous
studies.4-6 The MABA (aerobic) assay evaluated the activity
of compounds against replicating M. tb in an 8 day micro-
plate-based assay using Alamar blue reagent (added on
day 7).48 The LORA (anaerobic) assay (luminescence-based
low-oxygen-recovery assay) screened for activity against bac-
teria in a nonreplicating state that models clinical persistence,
using an 11 day high-throughput format and M. tb containing
a plasmid with an acetamidase promoter driving a bacterial
luciferase gene, where the bacteria had first been adapted to
low oxygen conditions by extended culture.49 Activity was
quantified by the minimum inhibitory concentration (MIC):
the lowest compound concentration effecting a growth inhibi-
tion of >90%. The values recorded in Table 1 represent the
mean of at least two separate determinations ((SD). Because
the arylheterocyclic compounds were significantly different in
structure from 1 and the biphenyl analogues previously de-
scribed,6 assessment of mammalian cell cytotoxicity was also
important. This was done50 using VERO cells (CCL-81, Ameri-
can Type Culture Collection) in a 72 h exposure, using a
tetrazolium dye assay, against which all of the compounds were
relatively nontoxic, with IC50s >128 μM (data not shown).
The 5-arylthiophene derivatives9-19 (class A) hadbroadly
similar lipophilicities and MIC values to the corresponding
MLB analogues (4-8). The mean MABA and LORA MICs
for compounds 9-13 were 0.24 and 1.6 μM respectively,
compared with 0.15 and 3.2 μM for compounds 4-8
(Table 2). However, the 4-CF3Ph-thiophene 9 showed a
4-fold lower solubility than the corresponding biphenyl
analogue 4 (0.7 versus 2.8 μg/mL, Table 1). Therefore, the
3.25
4.16
0.05 ( 0.01
0.85 ( 0.01
0.06 ( 0
1.9 ( 0.5
2.6 ( 0.5
1.0 ( 0.3
4-OCF3
3-F, 4-OCH3
4-OCF2H
3-aza, 4-OCH3
2-aza, 5-CF3
3-aza, 4-CF3
3-aza, 4-F
3-aza, 5-F
4-CF3
3.10
3.31
0.86 ( 0.01 0.58 ( 0.20
2.2 2.50
2.94
0.22 ( 0.02
0.28 ( 0.16
0.05 ( 0
0.86 ( 0.04
0.87 ( 0.05
1.4 ( 0.3
0.67 ( 0.31
0.35 ( 0.13
1.2 ( 0.6
0.20 ( 0.04
1.4 ( 0.4
4.5 ( 0.7
1.7 ( 0.2
4.4 ( 2.3
2.3 ( 0.7
2.3 ( 0.3
3.0 ( 0.3
3.2 ( 0.3
2.8 ( 1.0
1.5 ( 0.1
1.7 ( 0.3
4.5 ( 0.9
9.7 ( 4.0
>32
8.9 3.37
1.99
2.01
2.8 3.74
2.43
2.99
B
4-CN
4-F
B
B
4-OCF3
3-F, 4-OCH3
3-aza, 4-OCH3
4-CF3
3.97
3.14
B
B
2.55
C
C
C
C
C
D
D
D
E
16
2.00
0.69
0.65 ( 0.16
2.8 ( 1.1
4-CN
4-F
1.28
2.24
1.9 ( 0.1
31 ( 0
4-OCF3
3-F, 4-OCH3
4-CF3
1.1 ( 0.1
1.4 ( 0.4
7.4 ( 1.2
>32
1.40
1.4 2.58
1.54
2.46
0.06 ( 0
0.36 ( 0.02
0.06 ( 0
0.54 ( 0.30
0.80 ( 0.13
0.15 ( 0.03
4.1 ( 0.2
4.0 ( 0.5
0.58 ( 0.20
2.3 ( 0.6
3.9 ( 0.8
1.8 ( 0.2
4-F
4-OCF3
4-CF3
4-F
4.9 2.22
1.70
2.60
E
E
4-OCF3
4-CF3
4-F
F
5.4 2.22 0.045 ( 0.005 1.0 ( 0.1
F
1.70
2.60
0.11 ( 0.02
7.2 ( 2.4
F
4-OCF3
4-CF3
4-CN
0.05 ( 0.01 0.61 ( 0.41
G
G
G
G
G
G
0.5 2.19
0.53
1.15
0.17 ( 0.01
1.4 ( 0.5
1.5 ( 0.9
0.55 ( 0.19
1.1 ( 0.3
2.0 ( 1.1
2.6 ( 1.0
6.2 ( 2.1
1.9 ( 0.6
1.2 ( 0.5
2.0 ( 0
4-F
4-OCF3
3-F, 4-OCH3
3-aza, 4-OCH3
2.07
1.00
0.40
4.1 ( 0.9

Article
Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2 859
Table 2. Summary of Calculated Lipophilicity Differences and Mean MICs for Compound Subsets
mean MICs ( μM)
observed
predictedc
compd
subseries
ΔCLogPa
nb
MABA
LORA
MABA
ratioc
4-8
M: m-linked biphenyl
A: (2,5)-thiophene
B: (2,4)-thiazole
5
5
5
5
3
3
3
5
1
5
3
3
0.15
0.24
0.76
1.6
3.2
1.6
2.4
9-19
20-25
26-30
31-33
34-36
37-39
40-45
46
-0.20d
-0.43d
-2.16d
-1.90e
-1.92e
-1.92e
-2.29d
-2.79 f
-2.16d
-2.23e
-2.30e
0.17
0.19
0.52
0.45
0.45
0.45
0.56
0.75
0.52
0.54
0.56
1.4
4.0
C: (2,5)-1-Me-imidazole
D: (3,5)-1-Me-pyrazole
E: (1,4)-pyrazole
>22
3.1
0.16
0.50
0.068
0.94
2.4
2.9
2.7
2.9
2.8
1/2.8
1.1
F: (1,3)-pyrazole
G: (3,5)-isoxazole
1/6.6
1.7
H: (2,5)-1,3,4-oxadiazole
I: (1,4)-1,2,3-triazole
J: (2,4)-1,2,3-triazole
K: (2,5)-tetrazole
17
3.2
1.2
47-52
53-56
57-60
0.63
0.083
0.18
6.7
1.7
2.0
1/6.5
1/3.1
a Mean difference in CLogP values between the heterocyclic subseries and the biphenyl reference compounds. b Number of compounds from which
mean MICs were calculated. c Predicted mean MABA MICs based on eq 1 (see text), using mean observed MABA MIC data for 4-8 and ΔCLogP values
for each subseries. Ratio is observed/predicted value. d Calculations based on data from CF3, CN, F, OCF3, and 3-F, 4-OMe analogues. e Calculations
based on data from CF3, F, OCF3 analogues. f Calculations based on data from F analogue only.
aza-containing compounds 15-19 were also prepared, aiming
for compounds of higher solubility. While this objective was
achieved (compound 17 displayed a 13-fold higher solubility
than 9), overall, these aza-containing compounds had poorer
MICs, with mean MABA and LORA values of 0.46 and
3.0 μM, respectively (the exception being the 3-aza, 4-CF3
analogue 17, with an aerobic MABA MIC value of 0.05 μM).
The slightly more hydrophilic 2-arylthiazole derivatives
20-25 (class B) were comparable to the corresponding
MLB analogues in the LORA assay but were overall about
5-fold less potent than the latter in the MABA assay (mean
MABA MIC values 0.76 versus 0.15 μM, Table 2). The
4-CF3Ph derivative 20 was also found to have equivalent
aqueous solubility to the MLB analogue 4. Thus these two
classes of arylheterocycles did not offer any significant
advantages over the original biphenyl analogues.
The 2-aryl-1-methylimidazole derivatives 26-30 (class C)
were much more hydrophilic, with a mean ΔCLogP value 2.2
units lower than the reference MLB analogues, and this
translated into much higher aqueous solubility (16 μg/mL
for the 4-CF3Ph derivative 26). However, these compounds
had average MIC potencies about an order of magnitude
poorer than for MLB analogues (mean MICs: MABA,
1.6 μM, LORA, >22 μM). We have previously shown a
negative correlation between hydrophilicity and MABA MIC
analogues) showed more promising results. The 3-aryl-1-
methylpyrazole derivatives 31-33 (class D) were equipotent
to the MLB analogues overall (3-fold more active in MABA
than expected based on their lipophilicity, Table 2), with one
analogue, 33 (4-OCF3Ph), highly effective in both assays
(MICs of 0.06 and 0.58 μM in MABA and LORA,
respectively). The 1-aryl-4-linked-pyrazole derivatives 34-
36 (class E) retained similar LORA potencies but were gen-
erally about 3-fold less potent in the MABA assay (average
MABA MIC of 0.50 μM, equivalent to their predicted mean
potency). The 1-aryl-3-linked-pyrazole derivatives 37-39
(class F) displayed the highest average MABA potency of
all the 11 subseries (0.068 μM; about 7-fold better than
expected based on their lipophilicity), with the 4-OCF3Ph
derivative (39) displaying particularly high potencies, similar
to 33 in both assays. Encouragingly, the 4-CF3Ph derivatives
in both 1-arylpyrazole classes (E and F: 34 and 37, re-
spectively) also showed about 2-fold higher solubilities than
the biphenyl analogue 4 (whereas 31, class D, showed a 2-fold
lower solubility than 4).
The 3-arylisoxazole derivatives 40-45 (class G) were more
hydrophilic than the above pyrazoles (mean CLogP value
2.3 units lower than for MLB analogues), but in this case the
aqueous solubility of the 4-CF3Ph derivative 40 was rather
poor (0.5 μg/mL, Table 1). Like the thiazoles (class B), these
compounds were significantly less potent overall in the
MABA assay (6-fold less than MLB analogues, slightly worse
than predicted, Table 2) but retained LORA potency. Only a
single 5-aryl-1,3,4-oxadiazole derivative (46, 4-FPh, class H)
was evaluated. This heterocycle provided the highest hydro-
philicity (ΔCLogP -2.79) and the highest aqueous solubility
(108 μg/mL) but the poorest activity of all the subseries (the
measured MABA MIC was 1.65 μM higher than that esti-
mated by eq 1), so was not investigated further.
values for a large set of substituted biphenyls (eq 1).6
X
logðMICMABAÞ ¼ -0:25CLogP -0:52 σ -0:014 (1Þ
Using this equation, a predicted mean MABA MIC value
of 0.52 μM could be estimated for the 2-aryl-1-methylimida-
zoles (Table 2). This is an average increase, due to their lower
lipophilicity, of about 3.5-fold compared with the MLB
analogues 4-8. However, the mean measured MABA MIC
value (1.6 μM) was about 3-fold poorer than that, suggesting
little further interest in these compounds. It is possible that the
significantly reduced potency of this particular class (in both
assays) may arise from an unfavorable steric effect associated
with the N-methyl group located betweenthe 5-methyleneand
2-aryl substituents (cf. class D below), which could result in a
less optimal binding to the nitroreductase; studies are under-
way to evaluate such effects in more detail.
Finally, two 1,2,3-triazole-based subseries were evaluated,
the 1-aryl-4-linked (47-52; class I) and the 2-aryl-4-linked
(53-56; class J), together with some 2-aryltetrazole analogues
(57-60; class K). These compounds all showed very similar
hydrophilicities to the 2-aryl-1-methylimidazole derivatives
26-30 (class C) and the 3-arylisoxazole derivatives 40-45
(class G). The class J triazoles were the more active isomer
series (mean MICs 2-fold better than for MLB analogues
in both assays, about 6.5-fold better than predicted on
Three classes of pyrazoles (D-F) of slightly less hydro-
philicity (mean ΔCLogP 1.9 units lower than for MLB

860 Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2
Sutherland et al.
lipophilicity grounds and 4- to 8-fold better than for class I),
with the 4-OCF3Ph derivative 56 being the most potent of all
the compounds in the MABA assay (MIC 0.03 μM). The
2-aryltetrazoles displayed mean MIC potencies comparable
to the MLB analogues (about 3-fold higher than predicted),
although 4-OCF3Ph derivative 60 was essentially as active
as triazole 56. For these three subseries, the 2-aryltetrazole
(class K) and 1-aryl-4-linked-1,2,3-triazole (class I) showed
modest improvements in aqueous solubility (about 1.6- to
1.8-fold for the 4-CF3Ph derivatives 47 and 58 over the
biphenyl analogue 4), whereas the 2-aryl-4-linked-triazoles
(class J) were less soluble.
Overall then, four heterocyclic subseries (5-arylthiophene,
3-arylisoxazole, 1-aryl-4-linked-pyrazole, and 1-aryl-4-linked-
1,2,3-triazole derivatives) showed aerobic (MABA) potencies
similar to those expected based on their lipophilicities
(Table 2), three subseries (2-arylthiazole, 2-aryl-1-methylimi-
dazole, and 5-aryl-1,3,4-oxadiazole derivatives) showed
slightly poorer MABA activities than predicted (3- to 4-fold),
while a further four subseries (3-aryl-1-methylpyrazole, 1-aryl-
3-linked-pyrazole, 2-aryl-4-linked-triazole, and 2-aryl-5-
linked-tetrazole analogues) were 3- to 7-fold more potent than
expected (MABA assay). Of these latter four, the 1-aryl-3-
linked-pyrazoles, class F, and the 2-aryltetrazoles, class K,
provided compounds with both lower lipophilicities and mod-
estly (2-fold) improved aqueous solubilities, compared to the
original biphenyl analogues. Interestingly, from an anaerobic
(LORA) potency perspective, only two heterocyclic subseries
(2-aryl-1-methylimidazole and 5-aryl-1,3,4-oxadiazole de-
rivatives) were significantly different from the MLB analogues
(5- to >7-fold less active). This is consistent with results from
previous studies,4-6 which describe different SAR for aerobic
and anaerobic activity with various nitroimidazole analogues
and may indicate that a different mechanism of activation
applies under aerobic and anaerobic conditions.
Broadly, the results above also suggest that compound
lipophilicity (alone) is much less strongly correlated with aero-
bic potency for this diverse set of heterobiaryl analogues of 1
than for the earlier biphenyl compounds.6 Indeed, eq 2 shows
an identical coefficient to eq 1 (suggesting a similar trend),
although the correlation itself had low statistical significance:
logðMICMABAÞ ¼ -0:25CLogP þ 0:059
(2Þ
n ¼ 52
R ¼ 0:41
F ¼ 9:9
While some uncertainties in the estimated CLogP values
and measured MIC data (or possibly, in the case of the 2-aryl-
1-methylimidazoles, the influence of subtle steric effects) may
inpart explain such findings, the unexpectedlyhighpotency of
certain nitrogen heterocyclic subseries suggests that there is
more to learn about the nature of the proposed5 hydrophobic
binding areas in the nitroreductase, which could be explored
in further studies.
The presence of several subsets of compounds bearing the
same terminal substituents also permitted an evaluation of the
comparative utility of these substituents, especially any differ-
ential effects on replicating versus nonreplicating bacteria.
Table 3 gives “average” rankings for the up to six common
substituent patterns, obtained by ranking the MIC potencies
of the compounds bearing them within each subseries (e.g., 1,
2, 3,...), and then averaging these rankings. To compensate for
a smaller set of common substituents (3) across five subseries
(classes D, E, F, J and K), separate analyses were performed
for these and for the fivelarger-sized subseries (classes A, B, C,
G, and I), generating two rankings (A and B). For activity in
the MABA assay across the full substituent set (ranking A),
3-F, 4-OCH3, and 4-CF3 were slightly better than 4-OCF3 and
4-F (with 3-aza, 4-OCH3 clearly the least effective), whereas
for the smaller substituent set (ranking B) 4-OCF3 was slightly
superior to 4-CF3 and 4-F was less effective. The rankings in
LORA were more pronounced and consistent, with 4-OCF3
clearly the best for both substituent set sizes, while 4-CN and
3-aza, 4-OCH3 were the least effective.
Table 3. Average Ranking of Substituents According to MABA and
LORA Activity
ranking Aa
ranking Bb
substituent
4-F
4-OCF3
MABA
LORA
MABA
LORA
3.4
3.0
2.6
2.6
3.6
5.5
3.0
1.8
2.6
2.8
4.6
5.8
3.0
1.2
1.6
2.4
1.2
2.4
4-CF3
3-F, 4-OCH3
4-CN
3-aza, 4-OCH3
A subset of compounds was evaluated for their stabilities in
a metabolism screen with human and mouse liver microsome
preparations (Table 4; data for 1 and biphenyl analogue 3 are
also provided for comparison). We have previously found at
least moderate microsomal stability (>50% remaining after 1 h)
to be a prerequisite to achieve in vivo efficacies better than 1.6
a Value obtained by ranking the MIC potencies of the different
substituted compounds in the five largest subseries (1 = most potent,
6 = least potent, for classes A, B, C, G, I) and averaging these
“substituent” rankings (see text). b Similar value (see footnote a) ob-
tained for the five subseries having only three common substituents
(classes D, E, F, J, K).
Table 4. Microsomal Stability and in Vivo Efficacy Data for Selected Analogues
microsomes (% remaining at 1 h)
compd
subseries
substituent
TD sola
Hb
Mc
in vivo efficacyd (ratio vs 1)
1
11
<0.5
82
97
85
85
86
87
87
99
97
94
96
54
77
81
64
67
74
81
1.00
>205
0.02
2.3
3
p-linked biphenyl
(2,5)-thiophene
(2,5)-thiophene
(3,5)-1-Me-pyrazole
(1,4)-pyrazole
OCF3
CN
10
17
33
36
39
50
60
3-aza, 4-CF3
OCF3
OCF3
OCF3
OCF3
OCF3
0.88
23
12
1.5
(1,3)-pyrazole
(1,4)-1,2,3-triazole
(2,5)-tetrazole
41
0.34
4.3
a Thermodynamic solubility (μg/mL) in water at pH = 7.4 and 20 °C, determined by HPLC (see Experimental Section, Method B). b Pooled human
liver microsomes. c Pooled CD-1 mouse liver microsomes. d Fold reduction in lung CFUs for compound compared with the fold CFU reduction for 1 in a
mouse model of acute TB infection (see text).

Article
Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2 861
All compounds assayed were found to be very stable
toward human microsomes (>80% remaining after incuba-
tion at 37 °C for 1 h), and most (except perhaps the thiophene
analogue 10) were adequately stable toward mouse micro-
somes (although less stable than 1 and 3). These compounds
were further evaluated for their antitubercular effects in a
mouse model of acute M. tb infection, using a once daily oral
dose of 100 mg/kg for 5 days a week for 3 weeks, following
established protocols.50 The clinical trial drug 1 was employed
as an internal standard, with activity recorded as the ratio of
the fold decrease in colony forming units (CFUs) recovered
from the lungs of compound-treated mice compared to the
corresponding fold CFU decrease achieved by treatment with
1, to allow interexperiment comparisons (Table 4). Examples
derived from six of the 11 heterocyclic subseries were evalu-
ated. The most active compound was the 1-aryl-3-linked-
pyrazole 39, which showed a 41-fold greater efficacy than 1
in this model. Two further compounds, the 3-aryl-1-methyl-
pyrazole 33 and the 2-aryltetrazole 60, also showed significant
in vivo activity in this assay (respectively 12-fold and 4-fold
greater than 1). Finally, accurate (thermodynamic) solubility
determinations were obtained on the two best candidates, 39
and 33, together with reference compounds 1 and 3 (Table 4).
The 1-aryl-3-linked-pyrazole 39 was twice as soluble as 1
(23 vs 11 μg/mL) and >45-fold more soluble than biphenyl
analogue 3. However, 3-aryl-1-methylpyrazole 33 was
12.5-fold less soluble than 1.
obtained on a Bruker Avance 400 spectrometer at 400 MHz for
1H and are referenced to Me4Si. Chemical shifts and coupling
constants are recorded in units of ppm and Hz, respectively. Low
resolution atmospheric pressure chemical ionization (APCI)
mass spectra were measured for organic solutions on a Thermo-
Finnigan Surveyor MSQ mass spectrometer, connected to a
Gilson autosampler. Thin-layer chromatography was carried
out on aluminum-backed silica gel plates (Merck 60 F254) with
visualization of components by UV light (254 nm) or exposure to
I2. Column chromatography was carried out on silica gel (Merck
230-400 mesh). Tested compounds were g95% pure, as deter-
mined by combustion analysis, or by HPLC conducted on an
Agilent 1100 system, using a reversed phase C8 column with
diode array detection.
Procedure A. (6S)-6-[(5-Bromo-2-thienyl)methoxy]-2-nitro-
6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (63) (Scheme 1).
NaH (60% w/w, 0.60 g, 15.0 mmol) was added to a solution
of (6S)-2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazin-6-ol16
(61) (2.00 g, 10.8 mmol) and 2-bromo-5-(bromomethyl)-
thiophene17 (62) (3.20 g, 12.5 mmol) in anhydrous DMF
(40 mL) at 0 °C. The mixture was stirred at 0 °C for 2 h and
then poured onto ice and extracted with EtOAc (2 ꢀ 200 mL).
The organic layer was dried and evaporated, and then column
chromatography of the residue using a gradient (1:1 hexanes:
EtOAc to EtOAc) gave 63 (2.985 g, 77%) as a white solid: mp
139-140 °C. 1H NMR [(CD3)2SO] δ 8.00 (s, 1 H), 7.11 (d, J =
3.7 Hz, 1 H), 6.95 (d, J = 3.7 Hz, 1 H), 4.79 (d, J = 13.2 Hz, 1 H),
4.76 (d, J = 13.2 Hz, 1 H), 4.60 (dt, J = 12.0, 1.6 Hz, 1 H), 4.44
(d, J = 12.0 Hz, 1 H), 4.25-4.19 (m, 3 H). Anal. (C11H10-
BrN3O4S) C, H, N.
Procedure B. (6S)-2-Nitro-6-({5-[4-(trifluoromethyl)phenyl]-
2-thienyl}methoxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (9).
A mixture of 63 (0.205 g, 0.569 mmol) and 4-(trifluoro-
methyl)phenylboronic acid (0.130 g, 0.684 mmol) in toluene
(10 mL), EtOH (6 mL), and aqueous K2CO3 (2M, 2 mL) was
purged with N2 for 5 min. PdCl2(dppf ) (10 mg, 0.014 mmol) was
added, and the mixture was refluxed under N2 for 0.5 h. The
resulting solution was partitioned between EtOAc and water, and
the organic layer was dried (MgSO4) and concentrated under
reduced pressure. Column chromatography of the residue using
a gradient (1:1 hexanes:EtOAc to EtOAc) gave 9 (0.161 g, 67%) as
Conclusions
Theresultsofthis study showedthatheterobiarylanalogues
of 1 were more hydrophilic than the related biphenyl series (I),
as determined by calculated ΔCLogP values, but that there
was no overall correlation between hydrophilicity and mea-
sured aqueous solubility for the 4-CF3Ph-substituted analo-
gues across the 10 major subseries. However, six of the
heterocycles did provide significant increases in solubility
(e.g., 6-fold for the N-methylimidazole analogue 26, 60-fold
for the 1,3,4-oxadiazole derivative 46). A quantitative correla-
tion found previously between MIC potencies against repli-
cating M. tb (MABA assay) and compound lipophilicity was
employed to calculate the predicted activities of various
heterocyclic subseries for comparison with measured values.
The results showed thatcompound lipophilicity was muchless
strongly correlated with aerobic potency for this diverse set of
heterobiarylanalogues of1 than for the earlier biphenyl series.
However, four subseries (3-aryl-1-methylpyrazole, 1-aryl-3-
linked-pyrazole, 2-aryl-4-linked-triazole, and 2-aryl-5-linked-
tetrazole analogues) were identified from this work as having
excellent potencies against both replicating M. tb (MABA
assay) and nonreplicating M. tb (LORA assay). In terms
of both retaining good activity and improving solubility, the
1-aryl-3-linked-pyrazole and 2-aryltetrazole subseries seemed
to offer the most potential. Representatives of these two classes
(pyrazole 39 and tetrazole 60), together with a 1-methylpyra-
zole analogue (33), showed significantly greater efficacy than 1
(4- to 41-fold) in a mouse model of acute M. tb infection, and
the best of these (pyrazole 39) was 2-fold more soluble than 1.
1
a white solid: mp 210-211 °C. H NMR [(CD3)2SO] δ 8.04 (s,
1H),7.84(d,J= 8.3 Hz, 2 H), 7.74 (d, J=8.3Hz,2H),7.56(d,J=
3.7 Hz, 1 H), 7.15 (d, J = 3.7 Hz, 1 H), 4.88 (d, J = 13.8 Hz, 1 H),
4.85 (d, J = 13.8 Hz, 1 H), 4.65 (dt, J = 12.0, 1.3 Hz, 1 H), 4.47 (d,
J = 11.5 Hz, 1 H), 4.30-4.22 (m, 3 H). Anal. (C18H14F3N3O4S) C,
H, N.
See Supporting Information for details of the syntheses of
related compounds 10-19 from bromothiophene 63.
(6S )-6-[(2-Chloro-1,3-thiazol-4-yl)methoxy]-2-nitro-6,7-dihy-
dro-5H-imidazo[2,1-b][1,3]oxazine (65) (Scheme 1). Reaction of
alcohol 61 with 2-chloro-4-(chloromethyl)-1,3-thiazole18 (64)
(1.01 equiv) and NaH in DMF, using procedure A, followed
by column chromatography (eluting with EtOAc) gave 65
(27%) as
a
cream solid: mp 161-163 °C. 1H NMR
[(CD3)2SO] δ 8.01 (s, 1 H), 7.59 (s, 1 H), 4.71-4.61 (m, 3 H),
4.47 (d, J = 12.0 Hz, 1 H), 4.30-4.19 (m, 3 H). APCI MS m/z
317, 319 [M þ H]þ.
(6S)-2-Nitro-6-({2-[4-(trifluoromethyl)phenyl]-1,3-thiazol-4-yl}-
methoxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (20). Reac-
tion of 65 and 4-(trifluoromethyl)phenylboronic acid under the
Suzuki coupling conditions described in procedure B for 1 h gave
20 (51%) as a white solid: mp 170-172 °C. 1HNMR [(CD3)2SO] δ
8.14 (d, J = 8.1 Hz, 2 H), 8.03 (s, 1 H), 7.85 (d, J = 8.1 Hz, 2 H),
7.75 (s, 1 H), 4.84 (dd, J = 12.9, 0.8 Hz, 1 H), 4.80 (dd, J = 12.9,
0.8 Hz, 1 H), 4.69 (dt, J = 12.0, 2.5 Hz, 1 H), 4.50 (d, J = 11.9 Hz,
1 H), 4.38-4.34 (m, 1 H), 4.32 (dt, J = 13.5, 2.1 Hz, 1 H), 4.25 (dd,
J = 13.5, 3.3 Hz, 1 H). Anal. (C17H13F3N4O4S) C, H, N.
See Supporting Information for details of the syntheses of
related compounds 21-25 from chlorothiazole 65.
Experimental Section
Combustion analyses were performed by the Campbell Micro-
analytical Laboratory, University of Otago, Dunedin, New
Zealand. Melting points were determined on an Electrothermal
2300 melting point apparatus and are as read. NMR spectra were

862 Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2
Sutherland et al.
Methyl 1-Methyl-2-[4-(trifluoromethyl)phenyl]-1H-imidazole-
5-carboxylate (67a) (Scheme 2). Reaction of methyl 2-bromo-1-
methyl-1H-imidazole-5-carboxylate30 (66) and 4-(trifluoro-
methyl)phenylboronic acid under the Suzuki coupling condi-
tions described in procedure B for 2 h, followed by column
chromatography using a gradient (0-10% EtOAc:CH2Cl2),
to a solution of 73a (0.200 g, 0.781 mmol) in Et2O (10 mL) at 0 °C.
The mixture was stirred at room temperature for 16 h, cooled to
0 °C, quenched with ice, and then diluted with Et2O (100 mL). The
organic layer was dried and evaporated, and then column chro-
matography of the residue (eluting with CH2Cl2) gave 74a (0.212 g,
85%) as a white solid: mp 68-70 °C. 1H NMR (CDCl3) δ 7.86 (d,
J = 8.4 Hz, 2 H), 7.63 (d, J = 8.4 Hz, 2 H), 6.62 (s, 1 H), 4.50 (s, 2
H), 3.97 (s, 3 H). APCI MS m/z 319, 321 [M þ H]þ.
1
gave 67a (83%) as cream flakes: mp 100-101 °C. H NMR
(CDCl3) δ 7.85 (s, 1 H), 7.78-7.73 (br s, 4 H), 3.98 (s, 3 H), 3.90
(s, 3 H). APCI MS m/z 285 [M þ H]þ.
(6S)-6-({1-Methyl-3-[4-(trifluoromethyl)phenyl]-1H-pyrazol-5-yl}-
methoxy)-2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (31).
Reaction of alcohol 61 with 74a (1.0 equiv) and NaH (1.6 equiv)
in DMF, using procedure A, gave 31 (82%) as a white solid: mp
220-222 °C. 1H NMR[(CD3)2SO] δ 8.02(s, 1 H), 7.96 (d, J = 8.0
Hz, 2 H), 7.73 (d, J = 8.0 Hz, 2 H), 6.86 (s, 1 H), 4.78 (d, J = 12.6
Hz, 1 H), 4.73 (d, J = 12.6 Hz, 1 H), 4.70 (dt, J = 12.1, 2.3 Hz,
1 H), 4.48 (d, J = 11.8 Hz, 1 H), 4.32-4.21 (m, 3 H), 3.81 (s, 3 H).
Anal. (C18H16F3N5O4) C, H, N.
Procedure C. {1-Methyl-2-[4-(trifluoromethyl)phenyl]-1H-
imidazol-5-yl}methanol (68a). LiAlH4 (0.036 g, 0.95 mmol) was
added to a solution of 67a (0.138 g, 0.486 mmol) in anhydrous
THF (10 mL) at 0 °C. The mixture was stirred at 0 °C for 1 h and
then quenched with water and extracted with EtOAc (100 mL).
The organic fraction was dried (MgSO4) and evaporated to give
68a (0.112 g, 90%) as a white solid: mp 158-161 °C. 1H NMR
[(CD3)2SO] δ 7.89 (d, J = 8.2 Hz, 2 H), 7.83 (d, J = 8.2 Hz, 2 H),
6.98 (s, 1 H), 5.13 (t, J=5.3Hz, 1H), 4.51(d,J= 5.3 Hz, 2 H), 3.73
(s, 3 H). APCI MS m/z 257 [M þ H]þ.
See Supporting Information for details of the syntheses of
related compounds 32 and 33 from alkyne 70 and iodobenzenes
71b,c, via the intermediates 72b,c, 73b,c, and 74b,c.
Procedure D. 5-(Chloromethyl)-1-methyl-2-[4-(trifluoromethyl)-
phenyl]-1H-imidazole hydrochloride (69a). A solution of 68a
(0.106 g, 0.414 mmol) in SOCl2 (2 mL) was refluxed for 0.5 h
and then evaporated. The residue was triturated in Et2O to give
crude 69a (0.106 g, 83%) as a white solid, which was used directly
inthe next step. 1H NMR [(CD3)2SO] δ 8.05-7.99 (br s, 1 H), 7.81
(s, 1 H), 5.09 (s, 2 H), 3.84 (s, 3 H).
Procedure H. Ethyl 5-Amino-1-[4-(trifluoromethyl)phenyl]-
1H-pyrazole-4-carboxylate (77a) (Scheme 4). A mixture of ethyl
(2E)-2-cyano-3-ethoxy-2-propenoate (75) (0.935 g, 5.53 mmol),
4-(trifluoromethyl)phenylhydrazine (76a) (0.881 g, 5.00 mmol),
and NaOAc (0.90 g, 11.0 mmol) in AcOH (7.5 mL) and water
(2.5 mL) was stirred at 100 °C under N2 for 15 h. The mixture
was poured onto ice, and the precipitate was filtered and
recrystallized (MeOH/water) to give 77a (1.032 g, 69%) as tan
needles: mp 122-124 °C. 1H NMR [(CD3)2SO] δ 7.90 (d, J = 8.6
Hz, 2 H), 7.81 (d, J = 8.6 Hz, 2 H), 7.77 (s, 1 H), 6.52 (br s, 2 H),
4.23 (q, J = 7.1 Hz, 2 H), 1.28 (t, J = 7.1 Hz, 3 H). APCI MS m/z
300 [M þ H]þ.
(6S)-6-({1-Methyl-2-[4-(trifluoromethyl)phenyl]-1H-imidazol-
5-yl}methoxy)-2-nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine
(26). Reaction of alcohol 61 with 69a (0.96 equiv) and NaH
(3.0 equiv) in DMF, using procedure A, followed by column
chromatography (eluting with 95:5 EtOAc:MeOH containing
2% aq NH3) gave 26 (26%) as a white solid: mp 163-165 °C. 1H
NMR [(CD3)2SO] δ 8.02 (s, 1 H), 7.90 (d, J = 8.4 Hz, 2 H), 7.84
(d, J = 8.4 Hz, 2 H), 7.18 (s, 1 H), 4.78-4.65 (m, 3 H), 4.48 (d,
J = 11.9 Hz, 1 H), 4.29-4.20 (m, 3 H), 3.65 (s, 3 H). Anal.
Procedure I. Ethyl 1-[4-(Trifluoromethyl)phenyl]-1H-pyra-
zole-4-carboxylate (78a). A solution of 77a (0.925 g, 3.09 mmol)
and isoamyl nitrite (0.83 mL, 6.18 mmol) in THF (20 mL) was
refluxed for 14 h. Further isoamyl nitrite (0.83 mL, 6.18 mmol)
was added, and the solution was refluxed for an additional 6 h.
The solvent was then removed under reduced pressure to give a
solid which was recrystallized (EtOH) to give 78a (0.739 g, 84%)
(C18H16F3N5O4 0.5H2O) C, H, N.
3
See Supporting Information for details of the syntheses of
related compounds 27-30 from bromoimidazole 66, via the
intermediates 67b-e, 68b-e and 69b-e.
1
Procedure E. 1-Methyl-5-[(tetrahydro-2H-pyran-2-yloxy)methyl]-
3-[4-(trifluoromethyl)phenyl]-1H-pyrazole (72a) (Scheme 3). A solu-
tion of 2-(2-propynyloxy)tetrahydro-2H-pyran33 (70) (0.758 g,
5.41 mmol), CuI (17 mg, 0.089 mmol), and PdCl2(PPh3)2 (0.158 g,
0.225 mmol) in THF (15 mL) was purged with N2. 1-Iodo-
4-(trifluoromethyl)benzene (71a) (1.30 g, 4.78 mmol) in THF
(10 mL) was added, followed by a solution of methylhydrazine
sulfate (1.95 g, 13.5 mmol) and NaHCO3 (2.27 g, 27.0 mmol) in
water (25 mL). The mixture was flushed with carbon monoxide and
then stirred at room temperature for 2 d under one atmosphere of
carbon monoxide. The resulting mixture was partitioned between
CH2Cl2 and water, the organic fraction was dried and evaporated,
and then column chromatography of the residue (eluting with
CH2Cl2) gave 72a (0.753 g, 46%) as a brown solid: mp 62-64 °C.
1H NMR (CDCl3) δ 7.87 (d, J = 8.1 Hz, 2 H), 7.62 (d, J = 8.1 Hz,
2 H), 6.58 (s, 1 H), 4.76 (d, J = 12.8 Hz, 1 H), 4.70 (t, J = 3.4 Hz, 1
H), 4.57 (d, J = 12.8 Hz, 1 H), 3.96 (s, 3 H), 3.92-3.84 (m, 1 H),
3.61-3.54 (m, 1 H), 1.88-1.69 (m, 2 H), 1.67-1.49 (m, 4 H). APCI
MS m/z 341 [M þ H]þ.
as white flakes: mp 140-141 °C. H NMR (CDCl3) δ 8.47 (s,
1 H), 8.12 (s, 1 H), 7.86 (d, J = 8.5 Hz, 2 H), 7.75 (d, J = 8.5 Hz,
2 H), 4.35 (q, J = 7.1 Hz, 2 H), 1.39 (t, J = 7.1 Hz, 3 H). APCI
MS m/z 285 [M þ H]þ.
Procedure J. {1-[4-(Trifluoromethyl)phenyl]-1H-pyrazol-4-
yl}methanol (79a). A mixture of 78a (0.452 g, 1.59 mmol) and
LiAlH4 (0.120 g, 3.16 mmol) in Et2O (20 mL) was refluxed for
2 h. The resulting mixture was cooled to 0 °C, quenched with ice,
diluted with Et2O (100 mL), and filtered through celite. The
organic layer was dried (MgSO4) and evaporated, and then
column chromatography of the residue (eluting with 1:1 hex-
anes:EtOAc) gave 79a (0.333 g, 86%) as white flakes: mp 80-
81 °C. 1H NMR (CDCl3) δ 7.99 (d, J = 0.5 Hz, 1 H), 7.81 (d, J =
8.5 Hz, 2 H), 7.76 (s, 1 H), 7.71 (d, J= 8.5 Hz, 2 H), 4.71 (d, J=5.5
Hz, 2 H), 1.59 (t, J = 5.5 Hz, 1 H). APCI MS m/z 243 [M þ H]þ.
4-(Bromomethyl)-1-[4-(trifluoromethyl)phenyl]-1H-pyrazole (80a).
Bromination of 79a with PBr3 (1.0 equiv) for 2 h, using procedure
G, gave 80a (89%) as a colorless oil. 1H NMR (CDCl3) δ 8.02 (d,
J = 0.3 Hz, 1 H), 7.80 (d, J = 8.6 Hz, 2 H), 7.77 (s, 1 H), 7.72 (d,
J = 8.6 Hz, 2 H), 4.50 (s, 2 H). APCI MS m/z 305, 307 [M þ H]þ.
(6S)-2-Nitro-6-({1-[4-(trifluoromethyl)phenyl]-1H-pyrazol-4-yl}-
methoxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (34). Reaction
of alcohol 61 with 80a (1.0 equiv) and NaH (1.5 equiv) in DMF,
using procedure A, gave 34 (73%) as a white solid: mp 180-181 °C.
1H NMR [(CD3)2SO] δ 8.64 (s, 1 H), 8.06-8.01 (m, 3 H), 7.86 (d,
J= 8.6 Hz, 2 H), 7.82 (s, 1 H), 4.67-4.58 (m, 3 H), 4.47 (d, J= 11.9
Hz, 1 H), 4.27-4.21 (m, 3 H). Anal. (C17H14F3N5O4) C, H, N.
See Supporting Information for details of the syntheses of
related compounds 35 and 36 from unsaturated ester 75 and
arylhydrazine hydrochlorides 76b,c, via the intermediates 77b,c,
78b,c, 79b,c, and 80b,c.
Procedure F. {1-Methyl-3-[4-(trifluoromethyl)phenyl]-1H-
pyrazol-5-yl}methanol (73a). A solution of 72a (0.657 g, 1.93
mmol) in HCl (4M, 10 mL) and THF (10 mL) was stirred at
80 °C for 16 h. The THF was evaporated, and the residue was
partitioned between EtOAc and aqueous NaHCO3. The organic
layer was dried and evaporated, and the residue was recrystal-
lized (iPr2O) to give 73a (0.371 g, 75%) as a white solid: mp
161-163 °C. 1H NMR [(CD3)2SO] δ 7.97 (d, J = 8.0 Hz, 2 H),
7.73 (d, J = 8.0 Hz, 2 H), 6.74 (s, 1 H), 5.32 (br s, 1 H), 4.54 (br s,
2 H), 3.86 (s, 3 H). APCI MS m/z 257 [M þ H]þ.
Procedure G. 5-(Bromomethyl)-1-methyl-3-[4-(trifluoromethyl)-
phenyl]-1H-pyrazole (74a). PBr3 (0.15 mL, 1.60 mmol) was added

Article
Procedure K. Ethyl 2-Chloro{[4-(trifluoromethyl)phenyl]-
Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2 863
EtOAc to EtOAc) gave 88 (4.031 g, 74%) as a white solid: mp
81-82 °C. 1H NMR [(CD3)2SO] δ 8.02 (s, 1 H), 4.60 (d, J = 12.1
Hz, 1 H), 4.46 (d, J = 12.1 Hz, 1 H), 4.33 (d, J = 2.3 Hz, 2 H),
4.30-4.21 (m, 3 H), 3.52 (t, J = 2.3 Hz, 1 H). Anal. (C9H9N3O4)
C, H, N.
hydrazono}ethanoate (83a) (Scheme 4). 4-(Trifluoromethyl)-
benzenediazonium tetrafluoroborate36 (82a) (5.71 g, 22.0 mmol)
was added to a solution of ethyl 2-chloroacetoacetate (81) (3.29 g,
20.0 mmol) in pyridine (6 mL) and water (6 mL) at -5 °C. The
mixture was stirred at -5 °C for 0.5 h, and the resulting preci-
pitate was filtered and washed with ice cold water. Recrystalliza-
tion from EtOH/water gave 83a (5.318 g, 90%) as orange needles:
mp 140-141 °C. 1H NMR [(CD3)2SO] δ 10.84 (s, 1 H), 7.68 (d,
J = 8.7 Hz, 2 H), 7.51 (d, J = 8.7 Hz, 2 H), 4.31 (t, J = 7.1 Hz, 2
H), 1.31 (q, J = 7.1 Hz, 3 H). APCI MS m/z 293, 295 [M - H]-.
Procedure L. Ethyl 1-[4-(Trifluoromethyl)phenyl]-1H-pyra-
zole-3-carboxylate (84a). A mixture of 83a (1.47 g, 4.99 mmol),
bicyclo[2.2.1]hepta-2,5-diene (2.5 mL, 24.6 mmol) and Et3N
(2.0 mL, 14.3 mmol) in toluene (10 mL) was stirred at 70 °C
for 1 h. The resulting mixture was cooled and filtered, the filter
cake was washed with toluene (10 mL), and the organic fractions
were combined and evaporated. The residue was refluxed in
xylenes (30 mL) for 2 h. Column chromatography of the cooled
reaction mixture, eluting with hexanes, first gave xylenes, and
then further elution with CH2Cl2 gave 84a (1.126 g, 79%) as a
white solid: mp 90-91 °C. 1H NMR (CDCl3) δ 7.99 (d, J = 2.6
Hz, 1 H), 7.90 (d, J = 8.5 Hz, 2 H), 7.76 (d, J = 8.5 Hz, 2 H), 7.03
(d, J = 2.6 Hz, 1 H), 4.45 (q, J = 7.1 Hz, 2 H), 1.43 (t, J = 7.1
Hz, 3 H). APCI MS m/z 285 [M þ H]þ.
Procedure N. (6S)-2-Nitro-6-({3-[4-(trifluoromethyl)phenyl]-
5-isoxazolyl}methoxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine
(40). Triethylamine (0.14 mL, 1.01 mmol) was added to a solution
of alkyne 88 (0.215 g, 0.963 mmol) and N-hydroxy-4-(trifluoro-
methyl)benzenecarboximidoyl chloride21 (89a) (0.240 g, 1.07
mmol) in anhydrous THF (10 mL) at 0 °C, and the mixture
was then stirred at room temperature for 16 h. The solvent was
evaporated, and the residue was partitioned between EtOAc and
water. The organic layer was dried and evaporated, and then
column chromatography of the residue, eluting with EtOAc, gave
1
40 (0.295 g, 75%) as a white solid: mp 204-206 °C. H NMR
[(CD3)2SO] δ 8.10 (d, J = 8.1 Hz, 2 H), 8.04 (s, 1 H), 7.89 (d, J =
8.2 Hz, 2 H), 7.18 (s, 1 H), 4.92 (d, J = 14.4 Hz, 1 H), 4.88 (d, J =
14.4 Hz, 1 H), 4.70 (dt, J = 12.1, 2.3 Hz, 1 H), 4.50 (d, J = 12.1
Hz, 1 H), 4.38-4.23 (m, 3 H). Anal. (C17H13F3N4O5) C, H, N.
See Supporting Information for details of the syntheses of
related compounds 41-45 from alkyne 88 and the known21-24
N-hydroxy-arylcarboximidoyl chlorides 89b-f.
N0-(Chloroacetyl)-4-fluorobenzohydrazide (91) (Scheme 5). A
solution of chloroacetyl chloride (0.62 mL, 7.78 mmol) in
EtOAc (20 mL) was added dropwise to a solution of 4-fluoro-
benzohydrazide (90) (1.00 g, 6.49 mmol) in EtOAc (100 mL)
over 5 min. The mixture was refluxed for 30 min, the solvent was
removed, and the residue was triturated in hexanes to give 91
(1.455 g, 97%) as a white solid: mp 158-160 °C. 1H NMR
[(CD3)2SO] δ 10.52 (br s, 1 H), 10.35 (br s, 1 H), 7.97-7.92 (m,
2 H), 7.38-7.31 (m, 2 H), 4.19 (s, 2 H). APCI MS m/z 229, 231
[M - H]-.
Procedure M. {1-[4-(Trifluoromethyl)phenyl]-1H-pyrazol-3-yl}-
methanol (85a). LiAlH4 (0.140 g, 3.69 mmol) was added to a stirred
solution of 84a (1.023 g, 3.60 mmol) in Et2O (20 mL) at 0 °C, and
the mixture was warmed to room temperature for 1 h, then cooled
to 0 °C and quenched with ice. The resulting mixture was diluted
with Et2O (100 mL) and saturated aqueous sodium potassium
tartrate (100 mL) and filtered through celite. The organic layer was
dried and evaporated, and then column chromatography of the
residue (eluting with 95:5 CH2Cl2:EtOAc) gave 85a (0.760 g, 87%)
as cream flakes: mp 72-74 °C. 1H NMR (CDCl3) δ 7.94 (d, J =
2.5 Hz, 1 H), 7.80 (d, J = 8.6 Hz, 2 H), 7.70 (d, J = 8.6 Hz, 2 H),
6.51 (d, J = 2.5 Hz, 1 H), 4.79 (d, J = 5.8 Hz, 2 H), 2.03 (t, J = 5.8
Hz, 1 H). APCI MS m/z 243 [M þ H]þ.
2-(Chloromethyl)-5-(4-fluorophenyl)-1,3,4-oxadiazole (92). A
mixture of 91 (0.711 g, 3.08 mmol) and POCl3 (10 mL) was
refluxed for 2 h. The solvent was removed under reduced
pressure, and the residue was partitioned between EtOAc and
water. The organic layer was dried and evaporated, and then
column chromatography of the residue using gradient elution
(0-10% EtOAc:CH2Cl2) gave 92 (0.485 g, 74%) as a white
solid: mp 74-76 °C. 1H NMR [(CD3)2SO] δ 8.10-8.04 (m, 2 H),
7.50-7.44 (m, 2 H), 5.13 (s, 2 H). APCI MS m/z 213, 215
[M þ H]þ.
3-(Bromomethyl)-1-[4-(trifluoromethyl)phenyl]-1H-pyrazole (86a).
Bromination of 85a with PBr3 (1.0 equiv) for 17 h, using
procedure G, gave 86a (79%) as a cream solid: mp 81-
83 °C. 1H NMR (CDCl3) δ 7.93 (d, J = 2.5 Hz, 1 H), 7.80 (d,
J = 8.5 Hz, 2 H), 7.71 (d, J = 8.5 Hz, 2 H), 6.57 (d, J = 2.5 Hz,
1 H), 4.56 (s, 2 H). APCI MS m/z 305, 307 [M þ H]þ.
(6S)-6-{[5-(4-Fluorophenyl)-1,3,4-oxadiazol-2-yl]methoxy}-2-
nitro-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (46). Reaction
of alcohol 61 with 92 (1.05 equiv) and NaH in DMF for 30 min,
using procedure A, gave 46 (36%) as a tan solid: mp 170-
171 °C. 1H NMR [(CD3)2SO] δ 8.08-8.02 (m, 3 H), 7.48-7.42
(m, 2 H), 5.02 (s, 2 H), 4.70 (dt, J = 12.2, 2.5 Hz, 1 H), 4.51 (d,
J = 12.2 Hz, 1 H), 4.45-4.42 (m, 1 H), 4.33 (dt, J = 13.8, 2.0 Hz,
1 H), 4.26 (dd, J = 13.8, 3.2 Hz, 1 H). Anal. (C15H12FN5O5) C,
H, N.
(6S)-2-Nitro-6-({1-[4-(trifluoromethyl)phenyl]-1H-pyrazol-3-
yl}methoxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine
(37).
Reaction of alcohol 61 with 86a (1.06 equiv) and NaH (1.5
equiv) in DMF, using procedure A, gave 37 (68%) as a white
solid: mp 161-163 °C. 1H NMR [(CD3)2SO] δ 8.61 (d, J = 2.6
Hz, 1 H), 8.05 (d, J = 8.5 Hz, 2 H), 8.02 (s, 1 H), 7.85 (d, J = 8.6
Hz, 2 H), 6.58 (d, J = 2.6 Hz, 1 H), 4.76-4.70 (m, 2 H), 4.66 (dt,
J = 12.0, 2.4 Hz, 1 H), 4.48 (d, J = 11.9 Hz, 1 H), 4.31-4.20 (m,
3 H). Anal. (C17H14F3N5O4) C, H, N.
See Supporting Information for details of the syntheses of
related compounds 38 and 39 from ester 81 and aryldiazonium
tetrafluoroborates 82b,c, via the intermediates 83b,c, 84b,c, 85b,c,
and 86b,c.
(6S)-2-Nitro-6-(2-propynyloxy)-6,7-dihydro-5H-imidazo[2,1-b]-
[1,3]oxazine (88) (Scheme 5). NaH (60% w/w, 1.40 g, 35.0 mmol)
was added to a solution of alcohol 61 (4.53 g, 24.5 mmol) and
(3-bromo-1-propynyl)(tert-butyl)dimethylsilane19 (87) (6.00 g,
25.7 mmol) in anhydrous DMF (60 mL) at 0 °C. The solution
was stirred at 0 °C for 1 h and then quenched with ice. The product
was extracted with EtOAc, the extract was dried, and the solvent
was evaporated. The oily residue was dissolved in THF (100 mL),
cooled to 0 °C, and TBAF (30 mL, 1 M in THF) was added. The
solution was stirred at 0 °C for 1 h, and then the THF was
evaporated and the residue was partitioned (EtOAc/water). The
organic layer was dried and evaporated, and then column chro-
matography of the residue using gradient elution (1:1 hexanes:
Procedure O. (6S)-2-Nitro-6-({1-[4-(trifluoromethyl)phenyl]-
1H-1,2,3-triazol-4-yl}methoxy)-6,7-dihydro-5H-imidazo[2,1-b]-
[1,3]oxazine (47) (Scheme 5). A mixture of alkyne 88 (0.099 g,
0.44 mmol), 1-azido-4-(trifluoromethyl)benzene (93a) (0.198 g,
1.06 mmol), CuI (5 mg, 0.026 mmol), and Cu(OAc)2 (5 mg,
0.028 mmol) in THF (5 mL) was stirred in a sealed tube at 50 °C
for 16 h. The resulting mixture was partitioned between EtOAc
and water, the organic layer was dried and evaporated, and then
column chromatography of the residue using gradient elution
(1:1 hexanes:EtOAc to EtOAc) gave 47 (0.095 g, 53%) as a
white solid: mp 170-172 °C. 1H NMR [(CD3)2SO] δ 8.95 (s, 1
H), 8.16 (d, J = 8.5 Hz, 2 H), 8.03 (s, 1 H), 7.99 (d, J = 8.5 Hz, 2
H), 4.85 (d, J = 12.6 Hz, 1 H), 4.81 (d, J = 12.6 Hz, 1 H), 4.69
(dt, J = 12.0, 2.2 Hz, 1 H), 4.50 (d, J = 12.0 Hz, 1 H), 4.36-4.22
(m, 3 H). Anal. (C16H13F3N6O4) C, H, N.
See Supporting Information for details of the syntheses of
related compounds 48-52 from alkyne 88 and the known25-28
arylazides 93c-g.

864 Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2
Sutherland et al.
(6S)-2-Nitro-6-[(2-phenyl-2H-1,2,3-triazol-4-yl)methoxy]-6,7-
dihydro-5H-imidazo[2,1-b][1,3]oxazine (53) (Scheme 6). Reac-
tion of alcohol 61 with 4-(bromomethyl)-2-phenyl-2H-1,2,
3-triazole51 (99a) (1.0 equiv) and NaH (2.0 equiv) in DMF for
1 h, using procedure A, gave 53 (94%) as a white solid: mp
152-154 °C. 1H NMR [(CD3)2SO] δ 8.08 (s, 1 H), 8.03 (s, 1 H),
7.99 (dt, J = 7.6, 1.1 Hz, 2 H), 7.56 (td, J = 8.0, 1.9 Hz, 2 H), 7.43
(tt, J = 7.4, 1.1 Hz, 1 H), 4.87 (d, J = 12.7 Hz, 1 H), 4.83 (d, J =
12.7 Hz, 1 H), 4.69 (dt, J = 12.1, 2.5 Hz, 1 H), 4.49 (d, J = 12.0
Hz, 1 H), 4.36-4.22 (m, 3 H). Anal. (C15H14N6O4) C, H, N.
Procedure P. 2-{[4-(Trifluoromethyl)phenyl]hydrazono}pro-
panedial Dioxime (96b). 4-(Trifluoromethyl)phenylhydrazine
(95b) (2.64 g, 15.0 mmol) was added to a solution of 2-oxopro-
panedial dioxime43 (94) (1.74 g, 15.0 mmol) in EtOH (20 mL).
The mixture was stirred at 70 °C for 0.5 h, and then water
(30 mL) was added. The resulting precipitate was filtered and
recrystallized by dissolving in 3:1 toluene:EtOH and refluxing
until all of the EtOH had been removed, to give 96b (1.68 g,
41%) as tan needles: mp 171-173 °C. 1H NMR [(CD3)2CO] δ
12.18 (s, 1 H), 11.26 (s, 1 H), 10.46 (s, 1 H), 8.38 (s, 1 H), 7.85 (s,
1 H), 7.63 (d, J = 8.6 Hz, 2 H), 7.36 (d, J = 8.6 Hz, 2 H). APCI
MS m/z 275 [M þ H]þ.
See Supporting Information for details of the syntheses of
related compounds 55 and 56 from dioxime 94 and arylhydra-
zines 95c,d, via the intermediates 96c,d, 97c,d, 98c,d, and 99c,d.
5-(Bromomethyl)-2-phenyl-2H-tetraazole (103a) (Scheme 6).
N-Bromosuccinimide (0.184 g, 1.03 mmol) was added to a
solution of (2-phenyl-2H-tetraazol-5-yl)methanol52 (102a)
(0.122 g, 0.692 mmol) and PPh3 (0.272 g, 1.04 mmol) in CH2Cl2
(10 mL) at -40 °C. The mixture was stirred at -40 °C for 2 h and
then quenched with aqueous K2CO3 and warmed to room
temperature. The resulting mixture was extracted with CH2Cl2,
the extract was dried, and the solvent was removed. Chroma-
tography of the residue (eluting with CH2Cl2) gave 103a
(0.123 g, 74%) as a white solid: mp 70-71 °C. 1H NMR
(CDCl3) δ 8.14-8.09 (m, 2 H), 7.60-7.48 (m, 3 H), 4.72 (s,
2 H). APCI MS m/z 239, 241 [M þ H]þ.
(6S)-2-Nitro-6-[(2-phenyl-2H-tetraazol-5-yl)methoxy]-6,7-di-
hydro-5H-imidazo[2,1-b][1,3]oxazine (57). Reaction of alcohol
61 with 103a (1.0 equiv) and NaH (1.4 equiv for 1 h, then extra
1.4 equiv for an additional 1 h) in DMF, using procedure A, gave
57 (81%) as a white solid: mp 169-172 °C. 1H NMR [(CD3)2SO]
δ 8.10-8.05 (m, 2 H), 8.03 (s, 1 H), 7.59-7.50 (m, 3 H), 5.08 (d,
J = 13.2 Hz, 1 H), 5.05 (d, J = 13.2 Hz, 1 H), 4.72 (dt, J = 12.1,
2.6 Hz, 1 H), 4.51 (d, J = 12.1 Hz, 1 H), 4.46-4.42 (m, 1 H), 4.33
(dt, J = 13.7, 2.1 Hz, 1 H), 4.27 (dd, J = 13.6, 3.3 Hz, 1 H). Anal.
(C14H13N7O4) H, N. C: calcd, 48.98; found, 49.72. HPLC purity
100%.
Procedure Q. 2-[4-(Trifluoromethyl)phenyl]-2H-1,2,3-tria-
zole-4-carbaldehyde (97b). A solution of 96b (1.66 g, 6.05 mmol)
in Ac2O (15 mL) was stirred at room temperature for 30 min.
The reaction solution was diluted with water (60 mL), stirred for
a further 30 min, and then the resulting precipitate was collected
by filtration. This solid was partitioned between EtOAc and
water, and the organic fraction was dried and the solvent was
removed under reduced pressure. The resulting crude acetyl
oxime was treated with Cs2CO3 (2.17 g, 6.66 mmol) in THF
(70 mL), stirring at room temperature for 30 min, and the
resulting mixture was filtered and the solvent was removed.
The residue was dissolved in Et2O, washed with water, and
dried. Removal of the solvent gave a solid which was refluxed
with paraformaldehyde (0.38 g, 11.9 mmol) in HCl (2M, 50 mL)
for 2 h. The crude product was extracted with Et2O and washed
with water. The organic layer was dried and evaporated, and
then column chromatography of the residue (eluting with 1:1
hexanes:CH2Cl2) gave 97b (0.739 g, 51%) as a pale-yellow solid:
mp 80-81 °C. 1H NMR (CDCl3) δ 10.24 (s, 1 H), 8.30 (s, 1 H),
8.29 (d, J = 8.5 Hz, 2 H), 7.81 (d, J = 8.5 Hz, 2 H). APCI MS m/
z 240 [M - H]-.
Procedure R. {2-[4-(Trifluoromethyl)phenyl]-2H-1,2,3-triazol-
4-yl}methanol (98b). NaBH4 (0.21 g, 5.55 mmol) was added to a
solution of 97b (0.663 g, 2.75 mmol) in MeOH (15 mL). The
mixture was stirred at room temperature for 30 min, and then
the solvent was evaporated. The residue was dissolved in Et2O
and washed with water. The organic layer was dried and
evaporated, and then column chromatography of the residue
(eluting with 9:1 CH2Cl2:EtOAc) gave 98b (0.557 g, 83%) as a
white solid: mp 103-105 °C. 1H NMR (CDCl3) δ 8.19 (d, J =
8.6 Hz, 2 H), 7.84 (s, 1 H), 7.74 (d, J = 8.6 Hz, 2 H), 4.90 (d,
J = 6.0 Hz, 2 H), 1.96 (t, J = 6.0 Hz, 1 H). APCI MS m/z 242
[M - H]-.
Procedure S. Methyl 2-[4-(Trifluoromethyl)phenyl]-2H-tetra-
azole-5-carboxylate (101b). Sodium (0.19 g, 8.26 mmol) was
reacted with absolute ethanol (15 mL) and then 2-{[4-(trifluoro-
methyl)phenyl]hydrazono}ethanoic acid45 (100b) (0.978 g,
4.21 mmol) and 2-azido-1,3,5-tribromobenzene47 (1.50 g,
4.22 mmol) were added. The mixture was refluxed for 5 h under
nitrogen and then poured onto ice. The tribromoaniline was
filtered off, and the filtrate was acidified to pH 1. The resulting
precipitate was filtered and then dissolved in MeOH (40 mL).
A solution of diazomethane in ether was added, and the mixture
was stirred until gas evolution ceased. Removal of the solvent
gave the crude product, which was chromatographed using
gradient elution (3:1 CH2Cl2:hexanes to CH2Cl2), to give 101b
(0.127 g, 11%) as a white solid: mp 130-131 °C. 1H NMR
(CDCl3) δ 8.37 (d, J = 8.4 Hz, 2 H), 7.88 (d, J = 8.4 Hz, 2 H),
4.12 (s, 3 H). APCI MS m/z 273 [M þ H]þ.
{2-[4-(Trifluoromethyl)phenyl]-2H-tetraazol-5-yl}methanol (102b).
Reduction of 101b with LiAlH4 (2.0 equiv) in Et2O at 0 °C for 1 h,
using procedure M, followed by column chromatography
(eluting with 3:1 CH2Cl2:EtOAc), gave 102b (77%) as a white
solid: mp 61-62 °C. 1H NMR (CDCl3) δ 8.29 (d, J = 8.5 Hz,
2 H), 7.84 (d, J = 8.5 Hz, 2 H), 5.08 (d, J = 6.4 Hz, 2 H), 2.28 (t,
J = 6.4 Hz, 1 H). APCI MS m/z 245 [M þ H]þ.
5-(Bromomethyl)-2-[4-(trifluoromethyl)phenyl]-2H-tetraazole
(103b). Bromination of 102b with PBr3, using procedure G, gave
103b (32%) as a white solid, which was used directly in the next
1
step: mp 60-61 °C. H NMR (CDCl3) δ 8.29 (d, J = 8.5 Hz,
2 H), 7.85 (d, J = 8.5 Hz, 2 H), 4.72 (s, 2 H).
(6S)-2-Nitro-6-({2-[4-(trifluoromethyl)phenyl]-2H-tetraazol-5-yl}-
methoxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine (58). Reaction
of alcohol 61 with 103b (1.0 equiv) and NaH (1.5 equiv) in DMF,
using procedure A, gave 58 (70%) as a white solid: mp 151-
153 °C. 1H NMR [(CD3)2SO] δ 8.32 (d, J = 8.5 Hz, 2 H), 8.06 (d,
J = 8.5 Hz, 2 H), 8.03 (s, 1 H), 5.11 (d, J = 13.3 Hz, 1 H), 5.07 (d,
J = 13.3 Hz, 1 H), 4.72 (dt, J = 12.1, 2.5 Hz, 1 H), 4.52 (d, J =
12.1 Hz, 1 H), 4.47-4.43 (m, 1 H), 4.34 (dt, J = 13.6, 2.1 Hz, 1 H),
4.27 (dd, J = 13.7, 3.2 Hz, 1 H). Anal. (C15H12F3N7O4) C, H, N.
See Supporting Information for details of the syntheses of
related compounds 59 and 60 from 2-(2-arylhydrazono)acetic
acids 100c,d, via the intermediates 101c,d, 102c,d, and 103c,d.
Solubility Determinations. Method A. The solid compound
sample was mixed with water (enough to make a 2 mM solution)
in an Eppendorf tube, and the suspension was sonicated for 15
min and then centrifuged at 13000 rpm for 6 min. An aliquot of
4-(Bromomethyl)-2-[4-(trifluoromethyl)phenyl]-2H-1,2,3-tria-
zole (99b). Bromination of 98b with PBr3 (1.0 equiv) for 15 h,
using procedure G, gave 99b (76%) as a white solid, which was
used directly in the next step: mp 70-72 °C. 1H NMR (CDCl3) δ
8.18 (d, J = 8.5 Hz, 2 H), 7.87 (s, 1 H), 7.75 (d, J = 8.5 Hz, 2 H),
4.60 (s, 2 H).
(6S)-2-Nitro-6-({2-[4-(trifluoromethyl)phenyl]-2H-1,2,3-triazol-
4-yl}methoxy)-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine
(54).
Reaction of alcohol 61 with 99b (1.0 equiv) and NaH in DMF
for 1 h, using procedure A, gave 54 (84%) as a white solid: mp
209-210 °C. 1H NMR [(CD3)2SO] δ 8.20 (d, J = 8.6 Hz, 2 H),
8.18 (s, 1 H), 8.03 (s, 1 H), 7.94 (d, J = 8.6 Hz, 2 H), 4.89 (d, J =
12.8 Hz, 1 H), 4.86 (d, J= 12.8 Hz, 1 H), 4.70 (dt, J=12.0, 2.5Hz,
1 H), 4.50 (d, J = 12.0 Hz, 1 H), 4.37-4.22 (m, 3 H). Anal.
(C16H13F3N6O4) C, H, N.

Article
Journal of Medicinal Chemistry, 2010, Vol. 53, No. 2 865
the clear supernatant was diluted 2-fold with water, and then
HPLC was conducted. The solubility was calculated by compar-
ing the peak area obtained with that from a standard solution of
the compound in DMSO (after allowing for varying dilution
factors and injection volumes).
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Denny, W. A. Synthesis and structure-activity studies of biphenyl
analogues of the tuberculosis drug (6S)-2-nitro-6-{[4-(trifluoro-
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Denny, W. A. Intermediates in the reductionof the antituberculosis
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Method B. Aliquots of the compound DMSO stocks (10 mM)
were transferred to pH 7.4 buffer, Hank’s balanced salt solution
containing 25 mM HEPES (HBSS), to give target concentra-
tions of 250 μM in compound and 2.5% DMSO. After equili-
bration at room temperature overnight, the solutions were
filtered and the compound concentration was determined by
fast gradient HPLC without further dilution of the samples.
UV/vis/MS detection was used with reference to 1, 5, 10, 50, 100,
and 250 μM analytical standards, prepared from a 500 μM
intermediate stock solution, made by diluting 10 μL of the
10 mM sample stocks into 190 μL of 50:50 (v/v) CH3CN/water.
Aliquots of this stock solution (0.4, 2, 4, 20, 40, and 100 μL) were
transferred in duplicate into a 96-well plate, with the volumes
made up to a total of 200 μL by CH3CN/water, and the plate was
then heat sealed with a foil sheet. Prior to sample filtration,
filters were primed with 600 μL of sample to resolve potential
adsorption problems. Duplicate determinations were made in
all cases, with the average being reported.
The study was conducted by Admetryx, 4717 Campus Drive,
Kalamazoo, MI 49008.
Minimum Inhibitory Concentration Assays (MABA and
LORA). These were carried out according to the published
protocols.49,50
Microsomal Stability Assays. These were conducted by MDS
Pharma Services, 22011 30th Drive SE, Bothell, WA 98021,
using a published protocol.6 The percentage of compound
remaining after 1 h incubation was calculated as:
%remaining ¼ 100 ꢀ ðmean PART60=meanPART0
Þ
where PAR ¼ analyte=IS peak area ratio
In Vivo Acute TB Infection Assay. Each compound was
administered orally to a group of 7 M. tb-infected BALB/c mice
at a standard dose of 100 mg/kg, daily for 5 days a week for
3 weeks, beginning on day 11 postinfection, in accordance with
published protocols.6,50 The results are recorded as the ratio of
the average reduction in colony forming units (CFUs) in the
compound-treated mice /the average CFU reduction in the mice
treated with 1. In this assay, 1 itself caused up to 2.5-3 log
reductions in CFUs.
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Acknowledgment. We thank the Global Alliance for
Tuberculosis Drug Development for financial support through
a collaborative research agreement.
Supporting Information Available: Additional experimental
procedures and characterizations for compounds in Table 1;
combustion analytical data. This material is available free of
charge via the Internet at http://pubs.acs.org.
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