Synthesis and structure-activity relationships of novel benzoxaboroles as a new class of antimalarial agents

Article abstract of DOI:10.1016/j.bmcl.2010.12.034

A series of boron-containing benzoxaborole compounds was designed and synthesized for a structure-activity relationship investigation surrounding 7-(HOOCCH₂CH₂)-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (1) with the goal of discovering

Full text of DOI:10.1016/j.bmcl.2010.12.034

Bioorganic & Medicinal Chemistry Letters 21 (2011) 644–651
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and structure–activity relationships of novel benzoxaboroles
as a new class of antimalarial agents
Yong-Kang Zhang a, , Jacob J. Plattner a, Yvonne R. Freund a, Eric E. Easom a, Yasheen Zhou a, Jiri Gut b,
⇑
Philip J. Rosenthal b, David Waterson c, Francisco-Javier Gamo d, Inigo Angulo-Barturen d, Min Ge e, Zhiya Li e,
Lingchao Li e, Yong Jian e, Han Cui e, Hailong Wang e, Jian Yang e
a Anacor Pharmaceuticals, Inc., 1020 E. Meadow Circle, Palo Alto, CA 94303, USA
b Department of Medicine, University of California, 1001 Potrero Avenue, Building 30, San Francisco, CA 94110, USA
c Medicines for Malaria Venture, International Center Cointrin, Block G, 20 Route de Pré-Bois, POB 1826, CH-1215 Geneva, Switzerland
d Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, 28760 Tres Cantos, Spain
e Acesys Pharmatech, Inc., Science and Technology Building 24B, 5 Xing Mo Fan Road, Nanjing 21009, China
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of boron-containing benzoxaborole compounds was designed and synthesized for a structure–
activity relationship investigation surrounding 7-(HOOCCH2CH2)-1,3-dihydro-1-hydroxy-2,1-benzoxabo-
role (1) with the goal of discovering a new antimalarial treatment. Compound 1 demonstrates the best
potency (IC50 = 26 nM) against Plasmodium falciparum and has good drug-like properties, with low molec-
Received 20 October 2010
Revised 2 December 2010
Accepted 6 December 2010
Available online 10 December 2010
ular weight (206.00), low ClogP (0.86) and high water solubility (750 lg/mL at pH 7).
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
Benzoxaborole
Boron-containing compound
Structure–activity relationship
Antimalarial agent
Plasmodium falciparum
Malaria is a parasitic infection that is responsible for an
estimated 250 million clinical cases and nearly 1 million deaths
worldwide each year, 85% of which occur in children under the
age of five. The most important causative parasite Plasmodium fal-
ciparum is transmitted to humans by mosquitoes and is responsi-
ble for a majority of the serious morbidity and mortality of the
disease. While there are a number of effective therapeutics
available, resistance to even the newest medications is appearing
and is a significant concern. There is an urgent need to discover
new medications that counter resistance and that are safe and easy
for use in the most vulnerable populations.1
Previously we have reported benzoxaboroles with selective
activity against fungi,2 bacteria,3 inflammation4 and parasites,5
including the trypanosome, Trypanosoma brucei and the filarial
worm,Brugia malayi. As an extension of this work, we have screened
our boron-containing compound collection in a whole cell assay
against the malaria parasite P. falciparum. This screening campaign
series of analogs of 1 that were designed to asses the structural fea-
tures required for potent antimalarial activity. We examined a num-
ber of changes to structure 1, including length of the side-chain on
the oxaborole nucleus, the attaching positions of the side-chain,
the side-chain functional groups and modifications to the benzoxab-
orole scaffold. Herein we report the synthesis and the SAR for in vitro
potency for compounds 1–20.
The chemistry for the synthesis of compound 1 is shown in
Scheme 1. The acid 21 was converted to cyano compound 22 by
amide formation followed by dehydration reaction. Bromination
on the methyl of 22 and further substitution with acetate anion
gave compound 23 that was catalytically boronylated to replace
the bromo atom providing 24. Hydrolysis of the acetate group of
24 followed by acidification generated the cyano boron compound
25 that was treated with Raney nickel in aqueous formic acid to
give the aldehyde 26. Final acid compound 1 was obtained by
reacting 26 with 2,2-dimethyl-1,3-dioxane-4,6-dione in the
presence of HCOOH and triethylamine.
identified a number of potent hits under 1 lM, including 7-(2-car-
boxyethyl)-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (1 in Fig. 1)
with an IC50 of 26 nM. In order to explore the SAR for this new class
of boron-containing anti-malarial compounds, we synthesized a
Compound 2 was synthesized by the methods in Scheme 2.
Reduction of the cyano group of 23 gave the aldehyde 27 that
was converted to 28 via the Wittig reaction. Hydrogenation of 28
followed by treatment with acid generated the alcohol 29 that
was oxidized to the aldehyde 30. Further oxidation of 30 gave
the acid 31 that was alkylated to the ester 32. The bromo atom
⇑
Corresponding author.
E-mail address: yzhang@anacor.com (Y.-K. Zhang).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.12.034

Y.-K. Zhang et al. / Bioorg. Med. Chem. Lett. 21 (2011) 644–651
645
of 37 followed by acidification provided the cyclic boron com-
pound 38 that was hydrolyzed to give the final acid compound 4.
Scheme 5 illustrates the chemistry for the synthesis of 5 and 6.
The amino group in 39 was converted to bromo in 40 of which the
methyl group was bromonated to give 41. This compound was
transformed to the 7-amino boron compound 45 by substitution
of the bromo with acetate, boronylation of 42, hydrolysis and acid-
ification of 43 and then reduction of 44. Subsequent alkylation of
the amino of 45 and then hydrolysis of the ester in 46 resulted in
5. Methylation of 46 followed by hydrolysis of 47 provided the
analog 6.
The synthesis of the ketone boron compound 7 is shown in
Scheme 6. Wittig reaction with 27’s aldehyde group gave com-
pound 48 that was reduced to provide 49. Further boronylation
of 49 followed by hydrolysis and acidification of 50 generated
the final compound 7.
Scheme 7 shows the chemistry for the synthesis of compounds
8–14. Methylation of acid 1 gave ester 8 that was converted to
amide 9 by treatment with NH4OH. Also from acid 1, compounds
10 and 11 were prepared by the corresponding amide formation
reactions. Dehydration of 9 gave the cyano compound 12 which
was transformed to amine 13 by reduction and to tetrazole 14 by
reacting with sodium azide.
Acids 15–17, the three regio-isomers of 1, were synthesized by
the methods same as that shown in Scheme 1 with the variation of
the cyano substitution patterns of the starting materials.
Synthesis of the six-membered ring compound 18 is illustrated
in Scheme 8. Hydrolysis of the acetate group in 23 gave the alcohol
51 that was oxidized to the aldehyde 52. Wittig reaction with 52
generated the methoxy vinyl compound 53 that was hydrolyzed
to provide the one-carbon-extended aldehyde 54. Further reduc-
tion of 54 followed by alcohol protection of 55, catalytical borony-
lation of 56, and hydrolysis and acidification of 57 provided the
cyclic boron compound 58. The cyano group in 58 was reduced
to the aldehyde of 59 that went a Wittig reaction to give 60. The
final compound 18 was achieved by double bond reduction of 60
followed by ester hydrolysis and acidification of 61.
COOH
(CH2)n
COOH
Y
X
OH
OH
OH
B
B
B
O
O
O
1
: n=2
: n=3;
: n=4.
4
5
6
: Y=O;
7
:
X=C(O)Me;
2
3
: Y=NH;
8: X=COOMe;
9: X=C(O)NH2;
: Y=NMe.
10
: X=C(O)NMe2;
OH
7
11: X=C(O)NHSO2-c-Pr;
12: X=CN;
6
HOOC
B
O
13
: X=CH2NH2;
5
14: X=CN4H (tetrazole).
4
15
: at 6-position;
16: at 5-position;
17: at 4-position.
COOH
OH
COOH
COOH
OH
B
OH
B
B
O
O
O
18
19
20
Figure 1. Chemical structures of the benzoxaborole compounds synthesized6
during a structure–activity relationship investigation for the discovery of a new
class of antimalarial agents by variations of the side-chain length (1–3), one of the
side-chain CH2 with hetero atoms such as O or N (4–6), the side chain functional
group (7–14), the position of attachment of the side chain on the benzoxaborole
scaffold (15–17), the oxaborole ring size (18) and additional substitution changes
on the
a-carbon next to the carboxylic group (19) and to oxaborole 3-position
carbon (20).
The dimethyl-substituted compound 19 was synthesized by the
method shown in Scheme 9. Substitution of the benzyl bromo in 62
by the anion generated from ethyl isobutyrate and LiN(i-Pr)2 gave
63 that was reduced to the aldehyde 64. Further boronylation of 64
gave 65 that was reduced and acidified to generate 66. Hydrolysis
and acidification of 66 finally yielded 19.
CN
CN
COOH
Br
Br
a
Br
b
OAc
21
22
23
c
Scheme 10 illustrated the methodologies for the synthesis of
compound 20. Esterification and bromination converted 21 to 67
of which the bromo atom was replaced with hydroxyl group form-
ing 68. Further oxidation of the alcohol in 68, aldehyde protection
of 69, dimethyl formation from 70 to 71, boronylation and acidifi-
cation of 71 generated compound 72 that was reacted with 2,2-di-
methyl-1,3-dioxane-4,6-dione to give the final acid compound 20.
The experimental procedures for the preparation of compounds
1–20 is described in the reference section.6
The in vitro inhibitory activity of compounds 1–20 against the
malaria parasite P. falciparum was tested and their IC50 values are
summarized in Table 1. Compounds 1–3 (see Fig. 1) were designed
and synthesized for testing the effect of side-chain length. Com-
pound 1 with two carbon space (C2) between the carboxylic acid
group and the benzene ring was 24-fold more potent than com-
pound 2 with C3 space. Additional 3-fold potency loss resulted
when the space was increased to C4 of compound 3. The effect of
side-chain atom variation is observed among compounds 1 and
4–6. Replacement of the side-chain next-to-benzene CH2 of 1 with
O-atom of 4, NH of 5 and NMe of 6 gives IC50 values of 0.46, 0.95
CN
CN
O
B
CHO
OH
OH
B
e
f
O
B
d
1
O
O
OAc
26
25
24
Scheme 1. Synthesis of compound 1. Reagents and conditions: (a) (1) i-PrOC(O)Cl,
TEA, DCM, 0 °C, 10 min, (2) NH4OH, 0 °C, 2 min, (3) (CNCl)3, rt, 16 h; (b) (1) NBS, Bz2O2,
CCl4, reflux, 16 h, N2, (2) KOAc, DMF, 80 °C, 1 h; (c) Pin2B2, Pd(dppf)Cl2, KOAc, 1,4-
dioxane, reflux, 16 h, N2; (d) (1) NaOH, MeOH, rt, 2 h, (2) HCl, H2O, THF, rt, 50 min; (e)
Raney Ni, HCOOH, H2O, 100 °C, 1 h; (f) 2,2-dimethyl-1,3-dioxane-4,6-dione, HCOOH,
TEA, reflux, 15 h.
in 32 was replaced with (pinacolato)boron group by a catalytical
boronylation to give 33 which was hydrolyzed and then acidified
to generate the final acid boron compound 2.
Scheme 3 illustrates the synthesis of the long side-chain com-
pound 3 starting from the aldehyde 26 by a Wittig reaction to
provide 34 that was reduced by the hydrogenation reaction.
Synthesis of compound 4 is shown in Scheme 4. The phenol
group of 35 was alkylated to introduce the side-chain of 36 that
was catalytically boronylated to generate 37. Aldehyde reduction
and >5 lM, respectively. The potency was sensitive to the
side-chain electron change from CH2 to O to NH, and the steric var-
iation of the chain from NH to NMe.

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Y.-K. Zhang et al. / Bioorg. Med. Chem. Lett. 21 (2011) 644–651
OTHP
CHO
OH
CN
Br
a
b
Br
c
Br
Br
OAc
OAc
OAc
OAc
27
23
28
29
h
d
2
H
O
O
O
O
O
OH
O
e
f
g
O
B
Br
Br
Br
O
OAc
OAc
OAc
OAc
30
31
32
33
Scheme 2. Synthesis of compound 2. Reagents and conditions: (a) Raney Ni, HCO2H, H2O, 100 °C, 1 h; (b) Ph3P@CHCH2CH2OTHP, THF, À78 °C to rt, 20 h; (c) (1) H2, Pd/C,
EtOAc, rt, 1 h, (2) 2 N HCl, EA, MeOH, H2O, 40 °C, 0.5 h; (d) (COCl)2, DMSO, DCM, À78 °C, 15 min, then TEA, rt, 2 h; (e) 2-methylbut-2-ene, NaClO2, NaH2PO4, t-BuOH, rt, 1.5 h;
(f) MeI, K2CO3, DMF, rt, 1 h; (g) Pin2B2, KOAc, Pd(dppf)Cl2, KOAc, 1,4-dioxane, N2, 85 °C, 16 h; (h) (1) NaOH, MeOH, rt, 2 h, (2) HCl, H2O, THF, rt, 1 h.
NO2
NO2
O
OH
NO2
O
OH
NO2
NH2
Br
Br
Br
Br
a
b
c
CHO
OH
B
a
b
39
40
OH
41
42
OH
OAc
O
O
B
B
d
O
O
26
O
O
NO2
NO2
NH2
3
OH
OH
34
B
g
B
B
e
O
f
NH
OH
O
O
Scheme 3. Synthesis of compound 3. Reagents and conditions: (a) Ph3PCH2CH2CH2
COOH bromide, NaH, DMSO, rt, 4 h; (b) H2, Pd/C, EtOAc, rt, 1 h.
OAc
B
O
45
O
44
6
43
46
O
i
Compounds 7–14 were synthesized to examine the effect of
side-chain terminal functional group variation. Ketone compound
7 showed weak activity with 2.72
had 0.32 M IC50. The primary amide 9 with 1.30
h
N
OH
B
l
M IC50 and the methyl ester 8
j
l
l
M IC50 was
5
O
50-fold less potent than the acid 1 whereas addition of the di-
methyl to the amide nitrogen resulted in an inactive compound
47
10 with IC50 >5
cyclopropylsulfonyl group increased the potency by 3-fold from
1.30 M of 9 to 0.46 M of 11, which has the acidic C(O)NHSO2
group. Replacement of the carboxylic group in 1 by the cyano
group in 12 resulted in an IC50 of 1.02 M, a 39-fold potency de-
lM. Modification on the amide nitrogen with a
Scheme 5. Synthesis of compounds 5 and 6. Reagents and conditions: (a) (1)
NaNO2, 40% aq HBr, 0 °C, 1 h, (2) CuBr, 100 °C, 1 h; (b) NBS, CCl4, AIBN, reflux, 16 h;
(c) NaOAc, DMF, 70 °C 16 h; (d) Pin2B2, Pd(dppf)Cl2, KOAc, 1,4-dioxane, 95 °C, 20 h;
(e) NaOH, MeOH, rt, 24 h, then 5 N HCl, THF, 40 °C, 16 h; (f) H2, Pd/C, rt, 2.5 h; (g)
ethyl 2-bromoacetate, K2CO3, DMA, rt, 16 h; (h) LiOH, THF/MeOH/H2O, rt, 2 h; (i)
DMF,CH3I, K2CO3, DMF, rt, 2 h; (j) LiOH, THF/MeOH/H2O, rt, 2 h.
l
l
l
crease. Transformation of the cyano group to the aminomethyl of
13 and tetrazole of 14 improved the potency by 2- and 6-fold,
respectively. The tetrazole compound 14 was the most potent
among 7–14 from side chain terminal modification.
The effect of the side-chain substitution position change on
antimalarial activity is clearly demonstrated among compounds 1
and 15–17 in a potency sequence of 7-position of 1 (26 nM) > 6-po-
sition of 15 (0.12
17 (>5 M). Expanding the ring size, that is, six-membered of 18,
decreased the activity to IC50 >5 M. Dimethyl substitution on
lM) > 5-position of 16 (2.89 lM) > 4-position of
l
l
the side chain carbon next to COOH in 19 or on the 3-position of
CN
CN
CN
OH
Br
O
O
O
B
O
a
b
OH
d
c
Br
B
4
O
CHO
O
CHO
CHO
35
36
37
38
Scheme 4. Synthesis of compound 4. Reagents and conditions: (a) BrCH2CN, K2CO3, DMF, rt 20 h; (b) Pin2B2, Pd(dppf)Cl2, KOAc, 1,2-DME, 90 °C 16 h; (c) NaBH4, EtOH, rt, 1 h,
then HCl; (d) HCl (g), MeOH, H2O, rt, 1 h.

Y.-K. Zhang et al. / Bioorg. Med. Chem. Lett. 21 (2011) 644–651
COOEt
647
O
O
COOEt
O
COOEt
Br
O
B
OH
O
B
Br
Br
X
B
c
a
O
Br
d
Br
a
O
d
b
c
O
27
7
64
CN
CHO
62
65
66
63
OAc
: X=CN
OAc
OAc
48
49
50
b
e
64: X=CHO
Scheme 6. Synthesis of compound 7. Reagents and conditions: (a) Ph3P@CHCOCH3,
PhMe, 90 °C, 1 h; (b) H2, 10% Pd/C, EA, rt, 1 h; (c) Pin2B2, Pd(dppf)Cl2, KOAc, 1,4-
dioxane, 103 °C, 16 h; (d) NaOH, MeOH, rt, 1 h, then HCl, THF.
19
Scheme 9. Synthesis of compound 19. Reagents and conditions: (a) LiN(i-Pr)2, ethyl
isobutyrate, À20 °C, 45 min; (b) Raney Ni, HCO2H, H2O, 100 °C, 1 h; (c) Pin2B2,
Pd(dppf)Cl2, KOAc, 1,4-dioxane, N2, 103 °C, 16 h; (d) NaBH4, EtOH, 0 °C to rt, 1 h,
then HCl; (e) LiOH, THF/MeOH/H2O, rt, 16 h, then HCl.
O
OH
O
O
O
NH2
CN
OH
OH
Br
OH
Br
a
OH
b
OH
e
CHO
B
B
B
B
O
Br
Br
O
a
O
b
O
c
21
20
1
COOMe
COOMe
8
COOMe
9
12
69
d
68
67
d
c
f
g
O
S
O
N
N
N
NH
H
N
O
O
O
O
O
N
O
NH2
HCl
OH
CHO
OH
B
Br
Br
g
f
e
OH
OH
O
OH
OH
B
B
B
B
COOMe
O
O
O
O
70
71
72
10
11
13
14
Scheme 10. Synthesis of compound 20. Reagents and conditions: (a) (1) SOCl2,
MeOH, reflux, 3 h, (2) NBS, Bz2O2, CCl4, 80–85 °C, 5 h; (b) CaCO3, H2O, 1,4-dioxane,
100 °C, 5 h; (c) silica gel, PCC, DCM, 0–5 °C, 3 h; (d) HOCH2CH2OH, p-TsOH, toluene,
reflux, 5 h; (e) MeMgBr, THF, À10 °C to rt, 16 h; (f) n-BuLi, THF, À78 °C, 0.5 h, then
B(OMe)3, À78 °C to rt, 16 h, and finally HCl, H2O, rt, 1 h; (g) 2,2-dimethyl-1,3-
dioxane-4,6-dione, HCOOH, Et3N, 100 °C, 12 h.
Scheme 7. Synthesis of compounds 8–14. Reagents and conditions: (a) MeI, K2CO3,
DMF, rt, 1 h; (b) NH4OH, MeOH, 50 °C, 16 h; (c) Me2NH HCl, EDC HCl, DIPEA, HOAt,
THF, DCM, rt, 3 h; (d) (1) CDI, THF, reflux, 1 h, (2) cyclopropanesulfonamide, DBU, rt,
16 h; (e) (CNCl)3, DMF, rt, 16 h; (f) H2, Ni, NH4OH, MeOH, rt, 1 h; (g) NaN3, NH4Cl,
DMF, 95 °C, 3 days.
Table 1
CN
CN
CN
CN
In vitro IC50 results of benzoxaborole compounds 1–20 against the malaria parasite
Plasmodium falciparuma
Br
Br
Br
Br
Br
a
b
d
c
23
Compound
IC50
(
lM)
Compound
IC50 (lM)
CHO
1b
2
3
4
5
6
7
8
9
0.026
0.62
2.01
0.46
0.95
>5
2.72
0.32
1.30
>5
11
12
13
14
15
16
17
18
19
20
0.46
1.02
0.52
0.16
0.12
2.89
>5
>5
>5
>5
54
OH
52
CHO
51
53
OMe
e
CN
O
B
CN OH
B
CN
CN
h
g
O
Br
O
f
10
57
56
58
55
OAc
OAc
a
OH
Experimental procedure for the in vitro assay is described in the references and
notes section.7
i
COOEt
b
COOEt
Cytotoxicities of compound 1: human Jurkat cell IC50 = 60.5
lM and human
HeLa cell IC50 >100
l
M.8
CHO OH
B
OH
OH
B
B
j
O
k
l
O
O
18
the oxaborole ring in 20 is expected to improve the pharmacoki-
netic profile of 1 by decreasing the possible glucuronidation of
the carboxylic acid or by minimizing the oxidative metabolism of
boron through steric hindrance of the dimethyl groups, but these
59
60
61
Scheme 8. Synthesis of compound 18. Reagents and conditions: (a) LiOH, THF/
MeOH/H2O, rt 1 h; (b) PCC, DCM, rt, 2 h; (c) Ph3PCH2OMe chloride, t-BuOK, DMSO,
0 °C to rt, 16 h; (d) 6 N HCl, THF, reflux 1 h; (e) NaBH4, MeOH, rt, 1 h; (f) CH3COCl,
Et3N, DCM, 0 °C, 2 h; (g) Pin2B2, Pd(dppf)Cl2, KOAc, 1,4-dioxane, N2, reflux, 2 h; (h)
NaOH, MeOH, H2O, then HCl, THF; (i) Raney Ni, HCO2H, H2O, 100 °C, 1 h; (j)
Ph3PCH2COOCH2CH3 bromide, NaH, THF, 0 °C to rt, 16 h; (k) H2, Pd/C, EtOAc, rt, 2 h;
(l) NaOH, MeOH, H2O, rt, 16 h, then HCl.
substitutions resulted in loss of antimalarial activity (>5 lM).
In summary, this series of compounds is distinguished from our
earlier benzoxaborole analogs2–5 by the presence of a carboxy-
substituted side chain, which appears to be associated with
potent antimalarial activity. The structure–activity relationship

648
Y.-K. Zhang et al. / Bioorg. Med. Chem. Lett. 21 (2011) 644–651
washed with water (3 Â 20 mL) and petroleum ether (3 Â 20 mL) to provide 25
(7.6 g, yield 62%). 1H NMR of 25 (500 MHz, DMSO-d6): d 5.05 (s, 2H), 7.63–7.68
(t, 1H), 7.73–7.81 (m, 2H) ppm. To Raney Ni (0.849 g, 14.5 mmol, 2.3 equiv) in
formic acid (10 mL) and water (2 mL) was added 25 (1 g, 6.29 mmol) at rt. The
reaction was stirred at 100 °C for 1 h, cooled and then filtered. The solvent was
removed to give a solid that was purified by silica gel column chromatography
eluted with CH2Cl2 to give 26 as a solid (0.714 g, yield 70%). 1H NMR of 26
(500 MHz, CDCl3): d 10.03 (s, 1H), 8.08 (s, 1H), 7.86 (t, 1H), 7.63–7.71 (m, 2H),
5.20 (s, 2H) ppm. To a mixture of HCOOH (116.2 g, 10.0 equiv) and TEA (102.2 g,
4.0 equiv) were added 26 (40.9 g, 252.5 mmol) and 2,2-dimethyl-1,3-dioxane-
4,6-dione (43.7 g, 1.2 equiv). The resulting mixture was refluxed for 15 h and
cooled to rt. Hydrochloric acid (2 N, 320 mL) was added into the mixture that
was then extracted with ethyl acetate twice (2 Â 250 mL). The combined
organic layer was washed with 2 N HCl (160 mL) and rotary evaporated to give
the crude product that was recrystallized from DMF and 2 N HCl (34:204 mL)
investigation yielded two additional compounds with
IC50 6 0.16 M against P. falciparum, compound 14 containing tetra-
zole at the terminal side-chain (0.16 M) and compound 15 contain-
ing the side-chain at the 6-position (0.12 M). Compound 1
demonstratedthebestpotency(26 nM)amongthisseriesofbenzox-
aborole scaffolds. It showed low cytotoxicities against human cells
l
l
l
(Jurkat IC50 = 60.5
has good drug-like properties with low molecular weight (206.00),
low ClogP (0.86) and high water solubility (750 g/mL at pH 7). Fur-
lM and HeLa IC50 >100 lM). This compound also
l
ther study of this compound is in progress and results will be docu-
mented in future publications.
providing compound
1 as a white solid (15.6 g, yield 30%). An additional
References and notes
recrystallization from DMF and 2 N HCl (16:96 mL) was performed to give high
purity product (12.9 g). 1H NMR (500 MHz, DMSO-d6): d 12.02 (s, 1H), 8.95 (s,
1H), 7.37 (t, 1H), 7.13–7.22 (m, 2H), 4.96 (s, 2H), 3.00 (t, 2H), 2.54 (t, 2H) ppm.
HPLC purity: 99.50% at 220 nm and 99.51% at 266 nm. MS: m/z = 205 (MÀ1,
ESIÀ).
1. (a) Enserink, M. Science 2010, 328, 844; (b) Kappe, S. H. I.; Vaughan, A. M.;
Boddey, J. A.; Cowman, A. F. Science 2010, 328, 862; (c) Mackinnon, M. J.; Marsh,
K. Science 2010, 328, 866; (d) Enserink, M. Science 2010, 328, 842; (e) Rottmann,
M.; McNamara, C.; Yeung, B. K.; Lee, M. C.; Zou, B.; Russell, B.; Seitz, P.; Plouffe,
D. M.; Dharia, N. V.; Tan, J.; Cohen, S. B.; Spencer, K. R.; Gonzalez-Paez, G. E.;
Lakshminarayana, S. B.; Goh, A.; Suwanarusk, R.; Jegla, T.; Schmitt, E. K.; Beck, H.
P.; Brun, R.; Nosten, F.; Renia, L.; Dartois, V.; Keller, T. H.; Fidock, D. A.; Winzeler,
E. A.; Diagana, T. T. Science 2010, 329, 1175; (f) Medicines for Malaria Venture
2009 annual report, www.mmv.org.
Synthesis of 4-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)butanoic acid (2):
To a mixture of Raney nickel (0.533 g, 9 mmol, 2.3 equiv) in formic acid (10 mL)
and water (2 mL) was added 23 (1 g, 3.9 mmol, 1.0 equiv) at rt. The reaction
mixture was stirred at 100 °C for 1 h, cooled to rt and then filtered. The filtrate
was concentrated in vacuum to give a solid residue that was purified by silica
gel column chromatography eluted with EA/PE (1:4, v/v) to give 27 as a solid
(600 mg, yield 60%).
A mixture of Ph3PCH2CH2CH2OTHP bromide (3.77 g,
2. Baker, S. J.; Zhang, Y.-K.; Akama, T.; Lau, A.; Zhou, H.; Hernandez, V.; Mao, W.;
Alley, M. R. K.; Sanders, V.; Plattner, J. J. J. Med. Chem. 2006, 49, 4447.
3. (a) Rock, F. L.; Mao, W.; Yaremchuk, A.; Tukalo, M.; Crépin, T.; Zhou, H.; Zhang,
Y.-K.; Hernandez, V.; Akama, T.; Baker, S. J.; Plattner, J. J.; Shapiro, L.; Martinis, S.
A.; Benkovic, S. J.; Cusack, S.; Alley, M. R. K. Science 2007, 316, 1759; (b) Baker, S.
J.; Akama, T.; Zhang, Y.-K.; Sauro, V.; Pandit, C.; Singh, R.; Kully, M.; Khan, J.;
Plattner, J. J.; Benkovic, S. J.; Lee, V.; Maples, K. R. Bioorg. Med. Chem. Lett. 2006,
16, 5963.
4. (a) Zhang, Y.-K.; Plattner, J. J.; Akama, T.; Baker, S. J.; Hernandez, V.; Sanders, V.;
Freund, Y.; Kimura, R.; Bu, W.; Hold, K. M.; Lu, X. S. Bioorg. Med. Chem. Lett. 2010,
20, 2270; (b) Akama, T.; Baker, S. J.; Zhang, Y.-K.; Hernandez, V.; Zhou, H.;
Sanders, V.; Freund, Y.; Kimura, R.; Maples, K. R.; Plattner, J. J. Bioorg. Med. Chem.
Lett. 2009, 19, 2129.
7.78 mmol, 2.0 equiv) in THF (19.5 mL) was treated n-BuLi (2.644 mL,
6.61 mmol, 2.5 M in hexanes) at À78 °C, and then stirred for 1 h. Compound
27 (1 g, 3.89 mmol, 1.0 equiv) was then added, followed by removal of the
cooling bath. After 20 h, the reaction mixture was diluted with ethyl acetate, and
then washed with water, brine, dried over anhydrous sodium sulfate and
evaporated. The crude residue was purified by column chromatography eluted
with 5% EA/DCM to give 28 (1.25 g, yield 87%). To a solution of 28 (3.1 g,
8.09 mmol, 1 equiv) in EA (40 mL) was added Pd/C (310 mg, 10 wt %). The
reaction flask was vacuumed and backfilled with hydrogen for three times. The
reaction was stirred at rt for 1 h, filtered and evaporated. The residue was
dissolved in a mixed solvents of EA, MeOH and 2 N HCl (8/15/8 mL), and then
stirred at 40 °C for 0.5 h. The reaction was extracted with EA. The organic phase
was washed with brine, dried over anhydrous sodium sulfate and evaporated to
give a crude residue. The residue was purified by column chromatography
eluted with EA/PE (30%) to give 29 (1.54 g, yield 63.4%). To a stirred solution of
5. Ding, D.; Zhao, Y.; Meng, Q.; Xie, D.; Nare, B.; Chen, D.; Bacchi, C. J.; Yarlett, N.;
Zhang, Y.-K.; Hernandez, V.; Xia, Y.; Freund, Y.; Abdulla, M.; Ang, K. H.; Ratnam,
J.; McKerrow, J. H.; Jacobs, R. T.; Zhou, H.; Plattner, J. J. ACS Med. Chem. Lett. 2010,
1, 165.
oxalyl chloride (480
lL, 5.6 mmol, 1.4 equiv) in DCM (28 mL) was added DMSO
(513
l
L, 7.2 mmol, 1.8 equiv) dropwise at À78 °C. After gas evolution was
6. Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)propanoic acid
(1): To 2-bromo-3-methylbenzoic acid (21, 159 g, 739 mmol) in
dichloromethane (1000 mL) was added triethylamine (TEA, 119.7 mL,
813 mmol, 1.1 equiv) followed by iso-butyl chloroformate (101.5 mL,
813 mmol, 1.1 equiv) in dichloromethane (DCM, 200 mL) at 0 °C over 10 min.
Concentrated ammonia water (323 mL) was then added at 0 °C over 2 min. The
reaction mixture was poured into water (200 mL), cooled to rt and filtered. The
solid was washed with water (2 Â 300 mL), 0.5 N HCl (2 Â 150 mL) and dried to
give the amide as a solid (120 g, yield 76%). To the solution of the amide
obtained (50 g, 233.6 mmol) in DMF (300 mL) was added 2,4,6-trichloro-1,3,5-
triazine (64.6 g, 350.4 mmol, 1.5 equiv) dropwise at 0 °C and the reaction was
stirred at rt overnight. To the reaction was added 600 mL of water and the
reaction was stirred for 30 min. All insoluble was removed by filtration and the
solid was triturated with ethyl acetate (EA, 3 Â 100 mL) for 40 min and filtered.
The filtrate was washed with saturated sodium carbonate (3 Â 200 mL),
saturated sodium chloride (200 mL) and dried over anhydrous sodium sulfate.
The solvent was removed under reduced pressure to give 22 as a solid (42 g,
yield 87.3%). To a solution of 22 (20 g, 102.2 mmol, 1 equiv) in CCl4 (200 mL) was
added NBS (18.2 g, 102.0 mmol, 1.0 equiv), Bz2O2 (0.15 g, 0.6 mmol,
0.006 equiv). The reaction was refluxed overnight under N2, cooled and
filtered. The filtrate was crystallized at 0 °C to provide the brominated
intermediate (15 g, yield 53.6%). To a solution of the brominated intermediate
(90 g, 327.3 mmol) in DMF (760 ml) was added KOAc (38.6 g, 393.1 mmol,
1.2 equiv). The reaction mixture was stirred at 80 °C for 1 h, cooled and water
(1 L) was added. The mixture was extracted with EA (1 L). The organic layer was
washed with 0.5 N HCl (3 Â 200 mL), 2% NaHCO3 (200 mL) and dried over
anhydrous sodium sulfate. The solvent was removed to give 23 as a yellow solid
(77.3 g, yield 92.9%). 1H NMR of 23 (500 MHz, CDCl3): d 2.16 (s, 3H), 5.21 (s, 2H),
7.43–7.46 (t, 1H,), 7.63 (m, 2H) ppm. To a solution of 23 (20 g, 78.8 mmol) in 1,4-
dioxane (400 mL) was added bis(pinacolato)diboron (30 g, 118.1 mmol,
1.5 equiv) and KOAc (33.2 g, 338.1 mmol, 4.3 equiv). After being de-gassed
and backfilled with nitrogen, Pd(dppf)Cl2 (3.2 g, 3.935 mmol, 0.05 equiv) was
added. The reaction was refluxed overnight under nitrogen, cooled and filtered.
The filtrate was concentrated and the residue was purified by silica gel column
chromatography eluted with petroleum ether (PE)/EA = 5:1 to give 24 as red oil
(29 g, crude yield 100% with 80% purity). 1H NMR of 24 (500 MHz, DMSO-d6): d
1.42 (s, 12H), 2.20 (s, 3H), 5.25 (s, 2H), 7.44–7.49 (t, 1H), 7.57–7.64 (m, 2H) ppm.
To a solution of 24 (29 g) in MeOH (100 mL) was added a solution of NaOH in
MeOH (7.0 g/130 mL, 175.8 mmol, 2.3 equiv) and the reaction was stirred for 2 h
at rt. The reaction mixture was concentrated under vacuum and the residue was
dissolved in THF (150 mL) and 2 N HCl (138 mL, 69 mmol, 0.9 equiv). The
reaction was stirred at rt for 50 min, concentrated and filtered. The solid was
subsided, 29 (1.2 g, 4 mmol, 1.0 equiv) in DCM (5 mL) was added. After 15 min,
the white suspension was treated dropwise with TEA (2.8 mL, 20 mmol,
5.0 equiv) and the cooling bath was removed and stirring was continued for
2 h. The reaction was diluted with DCM and then washed with water, brine,
dried over anhydrous sodium sulfate, and evaporated to give a crude residue.
The residue was purified by column chromatography eluted with EA/PE (20%) to
give 30 (0.981 mg, yield 82%). To a solution of 30 (1.2 g, 4 mmol) in tert-butyl
alcohol (28.5 mL) was added 2-methyl-2-butene (3 mL) and a solution of NaClO2
(723.5 mg, 8 mmol, 2 equiv) and NaH2PO4 (1.872 g, 12 mmol, 3 equiv) in water
(12 mL) at rt. The reaction was stirred at rt for 90 min, quenched with 1 N HCl
and extracted with EA. The organic phase was washed with brine, dried over
anhydrous sodium sulfate, filtered and concentrated in vacuum. The crude was
titrated with PE for 10 min and then filtered to give 31 (1.1 g, yield 87%). To a
solution of 31 (1 g, 3.2 mmol, 1 equiv) in DMF (16 mL) was added potassium
carbonate (0.877 g, 6.35 mmol, 2 equiv). The reaction was stirred at rt for
20 min. To the mixture was added iodomethane (987 lL, 16 mmol, 5 equiv), and
the reaction was stirred at rt for 1 h. The reaction was quenched with water and
extracted with EA. The organic phase was washed with 0.5 N HCl, saturated
Na2CO3, and brine, dried over anhydrous Na2SO4 and filtered. The organic phase
was evaporated to give a crude residue. The residue was purified by column
chromatography eluted with EA/PE (20%) to give 32 (0.9 g, yield 89%). To a
solution of 32 (300 mg, 0.91 mmol, 1 equiv) in 1,4-dioxane (4.55 mL) was added
bis(pinacolato)diboron (277 mg, 1.09 mmol, 1.17 equiv), KOAc (384.24 mg,
4.08 mmol, 4.3 equiv). The flask was vacuumed and bubbled with nitrogen for
15 min. To the reaction mixture was added Pd(dppf)Cl2 (74 mg, 0.09 mmol,
0.1 equiv), then vacuumed and backfilled with nitrogen. The reaction was stirred
at 85 °C overnight, cooled, and filtered. The filtrate was evaporated to give a
crude residue that was purified by column chromatography eluted with EA/PE
(10%) to give 33 (350 mg, yield 100%). To a solution of 33 (342 mg, 0.9 mmol) in
methanol was added NaOH (118 mg, 2.97 mmol, 3.3 equiv) at 0 °C, then stirred
at rt for 2 h. The reaction mixture was concentrated under vacuum at 35 °C. The
residue was dissolved in HCl/THF (2 N, 1.5 mL) and the reaction was stirred at rt
for 1 h. The mixture was extracted with EA. The organic phase was washed with
brine, dried over anhydrous sodium sulfate, and evaporated to give a crude
residue that was purified by column chromatography eluted with EA/PE (30%) to
give the desired final compound 2. 1H NMR (500 MHz, DMSO-d6): d 12.00 (br s,
1H), 8.89 (br s, 1H), 7.39–7.36 (m, 1H), 7.20 (d, 1H), 7.10 (d, 1H), 4.96 (s, 2H),
2.80–2.76 (m, 2H), 2.20–2.16 (m, 2H) and 1.84–1.77 (m, 2H) ppm; MS: m/z = 219
(MÀ1, ESIÀ).
Synthesis of 5-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)pentanoic acid
(3): To
a solution of Ph3PCH2CH2CH2COOH bromide (5.3 g, 12.35 mmol,

Y.-K. Zhang et al. / Bioorg. Med. Chem. Lett. 21 (2011) 644–651
649
4 equiv) in DMSO (16 mL) was added a suspension of NaH (1.18 g of 50% oil
dispersion) in DMSO (19.7 mL). After being stirred for 20 min at rt, a solution of
26 (500 mg, 3.09 mmol) in DMSO (6.4 mL) was added in one portion. The
reaction was stirred at rt for 4 h, quenched with saturated NH4Cl, adjusted to pH
1–2 with 1 N HCl and extracted with EA. The organic phase was washed with
brine and dried over anhydrous Na2SO4. The residue after rotary evaporation
was purified by column chromatography eluted with EA/PE (50%) to give 34 as a
solid (120 mg, yield 16%). TLC analysis (silica gel plate, EA/PE = 1:1): Rf = 0.3. To a
solution of 34 (120 mg, 0.517 mmol) in EA (2.6 mL) was added Pd/C (120 mg).
The reaction was stirred under hydrogen at rt for 1 h. The reaction was filtered
and the residue after rotary evaporation was purified by preparative TLC (EA/
PE = 1:1) to give 3 (30 mg, yield 25%). 1H NMR (300 MHz, DMSO-d6): d 11.90 (s,
1H), 8.85 (s, 1H), 7.37 (t, 1H), 7.19 (d, 1H), 7.09 (d, 1H), 4.95 (s, 2H), 2.79 (t, 2H),
2.19 (t, 2H), 1.48–1.60 (m, 4H) ppm. Mass: m/z = 235 (M+1, ESI+).
Synthesis of 2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yloxy)acetic acid
(4): The mixture of 35 (20.3 g, 101 mmol), BrCH2CN (15.75 g, 131 mmol,
1.3 equiv) and K2CO3 (20.9 g, 151 mmol, 1.5 equiv) in DMF (50 mL) was stirred
at rt for 20 h and water was added. The mixture was extracted with EA, dried
over anhydrous Na2SO4, filtered and rotary evaporated to give a crude solid that
was recrystallized from DCM/hexane providing 36 as light brown solid (13.2 g,
yield 54%). Compound 36 (13.2 g, 55.0 mmol) was catalytically boronylated with
pin2B2 (27.9 g, 110.0 mmol, 2 equiv), Pd(dppf)Cl2 (2.9 g, 0.075 equiv) and KOAc
(16.2 g, 165 mmol, 3 equiv) under N2 in 1,2-DME at 90 °C for 16 h. Normal
work-up gave 37 as a yellow solid (10.92 g, yield 69%). Compound 37 (1.02 g,
4 mmol) in MeOH (10 mL) was reduced with NaBH4 (0.18 g, 4.8 mmol,
1.2 equiv) at 0 °C for 1 h. Then DCM (5 mL) and HCl (2 N) were added to
pH = 3 and the mixture was stirred at 0 °C for 1 h. Normal work-up provided
crude 38 that was purified by silica gel column chromatography (2% MeOH/
DCM) giving 38 as a white solid (0.26 g, yield 34%). Gas of HCl was bubbled
through a solution of 38 (0.132 g, 0.67 mmol) in MeOH/H2O (8:2, 25 mL) at 0 °C
for 5 min and the mixture was stirred at 0 °C for 10 min and at rt for 1 h.
Removal of MeOH and then the pH was adjusted to 6 resulting in white
precipitates which was collected and washed with ether to give the final
compound 4 (0.105 g, yield 76%). 1H NMR (400 MHz, DMSO-d6): 7.38 (t, 1H),
6.98 (d, 1H), 6.77 (d, 1H), 4.90 (s, 2H), 4.13 (s, 2H) ppm. HPLC purity: 92.8% at
220 nm and 95.5% at 282 nm. MS: m/z = 207 (MÀ1, ESIÀ).
The mixture was purified by preparative TLC (EA/PE = 1:1) to give the desired
final compound 5 as a solid (11 mg, yield 42.3%). 1H NMR (300 MHz, DMSO-d6):
d 8.99 (s, 1H), 7.19 (s, 1H), 6.53 (d, 1H), 6.23 (s, 1H), 5.72 (s, 1H), 4.83 (s, 2H), 3.75
(s, 2H) ppm. MS: m/z = 205.8 (MÀ1, ESIÀ).
Synthesis of 2-((1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl) (methyl)amino)
acetic acid (6): To the mixture of 46 (100 mg, 0.435 mmol) and K2CO3 (176 mg,
1.27 mmol) in DMF (2.1 mL) was added CH3I (302 mg, 2.12 mmol). The reaction
was stirred for 2 h, diluted with water and extracted with EA. The organic layer
was washed with 0.5 N HCl, brine, dried over Na2SO4 and concentrated. The
residue was purified by preparative TLC (EA/PE = 1:1) to give 47 (39 mg, yield 37%)
as a solid. 1H NMR (500 Hz, DMSO-d6): d 9.03 (s, 1H), 7.28 (t, 1H), 6.70 (d, 1H), 6.57
(d, 1H), 4.87 (s, 2H), 4.46 (s, 2H), 4.05 (q, 2H), 2.95 (s, 3H), 1.15 (t, 3H) ppm. Mass:
m/z = 250 (MÀ1, ESIÀ). The mixture of 47 (60 mg, 0.24 mmol) and LiOHÁH2O
(20.2 mg, 0.255 mmol) in THF/MeOH/H2O = 3:2:1 (0.936 mL) was stirred for 2 h.
The mixture was purified by preparative TLC (EA/PE = 1:1) to give 6 (17 mg, yield
34.9%) as a solid. 1H NMR (300 Hz, DMSO-d6): d 9.05 (s, 1H), 7.26 (t, 1H), 6.67 (d,
1H), 6.56 (d, 1H), 4.86 (s, 2H), 4.39 (s, 2H), 2.96 (s, 3H) ppm. Mass: m/z = 220 (MÀ1,
ESIÀ).
Synthesis of 4-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)butan-2-one (7):
Toasolution of27 (1 g, 3.9 mmol)intoluene(30 mL)wasadded theWittigreagent
Ph3P@CHC(O)CH3 (1.48 g, 5 mmol, 1.3 equiv). The reaction was stirred at 90 °C for
1 h. The residue after rotary evaporation was purified by column chromatography
to give the desired product 48 (0.5 g, 43.5% yield). TLC analysis (silica gel plate, EA/
PE = 1:9): Rf = 0.2. To a solution of 48 (2.1 g, 7.06 mmol) in EA (35 mL) under
nitrogen was added Pd/C (600 mg). The reaction vessel was vacuumed and
backfilled with H2 for three times. The reaction was stirred at rt for 1 h, filtered and
evaporated. The residue was purified by column chromatography to give 49 (1.1 g,
53% yield). 1H NMR (300 MHz, DMSO-d6): d 7.30 (m, 3H), 5.11 (s, 2H), 2.91 (t, 2H),
2.76 (t, 2H), 2.10 (s, 3H), 2.08 (s, 3H) ppm. To a solution of 49 (500 mg, 1.67 mmol)
in 1,4-dioxane (8.4 mL) was added KOAc (709 mg, 7.22 mmol, 4.3 equiv),
bis(pinacolato)diboron (640 mg, 2.52 mmol, 1.5 equiv) and Pd(dppf)Cl2
(137 mg, 0.167 mmol, 0.1 equiv). The reaction vessel was vacuumed, backfilled
by N2 for three times and stirred at 103 °C overnight. The reaction was filtered and
evaporated. The residue was purified by column chromatography to give 50
(600 mg, 100% yield). Toa solution of 50 (580 mg, 1.67 mmol) inMeOH (5 mL) was
added NaOH (154 mg, 3.86 mmol, 2.3 equiv). The reaction was stirred at rt for 1 h
and then rotary evaporated. THF (2.5 mL) and 2 N HCl (2.4 mL) were added. The
reaction was stirred at rt for 0.5 h and then extracted with EA. The organic phase
was washed with brine and dried over anhydrous Na2SO4. The residue after rotary
evaporation was purified by column chromatography (EA/PE = 1:1) to give the
final compound 7 as a slight yellow solid (50 mg, yield 15%). 1H NMR (300 MHz,
DMSO-d6): d 8.92 (s, 1H), 7.36 (t, 1H), 7.20 (d, 1H), 7.12 (d, 1H), 4.95 (s, 2H), 2.9 (t,
2H), 2.76 (t, 2H), 2.08 (s, 3H) ppm; HPLC purity: 99.6% at 220 nm and 100% at
254 nm; MS: m/z = 227.2 (M+23, ESI+).
Synthesis of 2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-ylamino)acetic acid
(5): The suspension of 39 (30.4 g, 0.2 mol) in water (250 mL) and HBr (100 mL,
40% aq) was refluxed for 10 min and then was cooled to 0 °C. A solution of
NaNO2 (13.8 g, 0.2 mol) in water (80 ml) was added dropwise at <5 °C. The
dizaonium solution was stirred for a further 30 min at 0–5 °C and then added
slowly to a stirring mixture of CuBr (28.7 g, 0.2 mol) in HBr (80 mL) and water
(150 mL) at rt. The mixture was stirred at rt for 30 min and then on a steam-bath
for 1 h. The mixture was washed with saturated NaHCO3, brine, dried over
MgSO4 and concentrated. The residue was purified by column chromatography
with petroleum ether as eluent to give 40 as a pale yellow solid (25.9 g, yield
60%). The mixture of 40 (14.3 g, 0.066 mol), NBS (17.7 g, 0.099 mol) and AIBN
(0.3 g, 1.8 mmol) in CCl4 (250 ml) was refluxed overnight. The mixture was
filtered and the filtrate was concentrated to give 41 as a red liquid (21 g). The
mixture of 41 (21 g) and NaOAc (16.4 g, 0.2 mol) in DMF (300 mL) was stirred at
70 °C overnight, and then diluted with water and extracted with EA. The organic
layer was washed with brine, dried over Na2SO4 and concentrated under
vacuum. The residue was purified by column chromatography with PE/EA (20:1,
v/v) as eluent to give 42 as a white solid (7.7 g, 42% over two steps). To the
solution of 42 (16.5 g, 0.06 mol) in 1,4-dioxane (250 mL) was bubbled with
nitrogen for 20 min. Potassium acetate (20.6 g, 0.21 mol), Pd (dppf)Cl2 (3.92 g,
4.8 mmol) and bis(pinacolato)diboron (22.9 g, 0.09 mol) were added and the
reaction mixture was stirred under N2 at 95 °C for 20 h. The reaction mixture
was then cooled and evaporated. The residue was partitioned between EtOAc
and water. The organic layer was washed with brine, dried over Na2SO4 and
concentrated. The residue was purified by column chromatography with PE/EA
(20:1, v/v) as eluent to give 43 as a yellow oil (9.9 g, 51%). MS: m/z = 322 (M+1,
ESI+). To the solution of 43 (9.9 g, 0.03 mol) in methanol (300 mL) was added
NaOH (5 N, 12 mL, 0.06 mol). The reaction mixture was stirred and refluxed
under nitrogen for 24 h. It was then concentrated under vacuum and the residue
was dissolved in THF (100 mL). HCl (5 N, 60 mL, 0.3 mol) was added and the
reaction mixture was stirred and heated at 40 °C for 16 h. It was cooled, diluted
with EtOAc and poured into brine. The organic layer was washed with brine,
dried over Na2SO4 and concentrated. The residue was recrystallized from the
mixed solvents of EA and PE to give 44 as a yellow solid (3.8 g, yield 71%). 1H
NMR (300 MHz, DMSO-d6): d 8.99 (s, 1H), 8.01 (d, 1H), 7.81 (m, 2H), 5.05 (s, 2H)
ppm. MS: m/z = 180 (M+1, ESI+). To the solution of 44 (0.92 g, 5.1 mmol) in
MeOH (50 mL) was added Pd/C (0.5 g) and the hydrogenation was conducted at
one atmosphere and rt for 2.5 h to provide the desired product 45 as a solid
(0.68 g, yield 88%). 1H NMR (300 MHz, DMSO-d6): d 8.78 (s, 1H), 7.10 (t, 1H),
6.47 (d, 1H), 6.39 (d, 1H), 5.32(s, 2H), 4.82(s, 2H) ppm. MS: m/z = 150 (M+1,
ESI+). To a mixture of 45 (800 mg, 5.37 mmol) and K2CO3 (2.23 g, 0.0161 mol) in
N,N-dimethylacetamide (17.9 mL) was added ethyl bromoacetate (0.623 mg,
3.76 mmol). The reaction was stirred overnight at rt. It was diluted with water
and extracted with EA. The organic layer was washed with 2 N HCl, brine, dried
over anhydrous Na2SO4 and concentrated. The residue was purified by column
chromatography eluted with EA/DCM (10%) to give the desired product 46 as a
solid (380 mg, yield 30%). 1H NMR (300 MHz, DMSO-d6): d 8.98 (s, 1H), 7.20 (t,
1H), 6.60 (d, 1H), 6.25 (d, 1H), 5.63 (s, 1H), 4.86 (s, 2H), 4.14 (q, 2H), 3.80 (s, 2H),
1.20 (t, 3H) ppm. The mixture of 46 (30 mg, 0.127 mmol) and LiOHÁH2O
(10.7 mg, 0.255 mmol) in THF/MeOH/H2O = 3:2:1 (0.51 mL) was stirred for 2 h.
Synthesis
of
methyl
3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)
propanoate (8): To a solution of 1 (300 mg, 1.45 mmol) in DMF (7 mL) was
added K2CO3 (501 mg, 3.625 mmol, 2.5 equiv). The reaction was stirred at rt for
10 minandthenCH3I(907 lL, 14.56 mmol, 10 equiv) was added. Thereaction was
stirred at rt for 1 h and quenched with 1 N HCl and extracted with t-butyl methyl
ether (TBME). The organic phase was washed with saturated NaHCO3, then brine,
dried over anhydrous Na2SO4 and filtered. The residue after rotary evaporation
was purified by column chromatography (EA/PE = 1:2) to give the desired product
as white solid (220 mg, yield 69%). 1H NMR (300 MHz, DMSO-d6): d 9.00 (s, 1H),
7.40 (t, 1H), 7.21 (d, 1H), 7.15 (d, 1H), 4.96 (s, 2H), 3.81 (s, 3H), 3.00 (t, 2H), 2.65 (t,
2H) ppm. Mass: m/z = 221.1 (M+1, ESI+).
Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)propanamide (9):
To a solution of 8 (1 g, 4.5 mmol, 1 equiv) in MeOH (22 mL) was added NH4OH
(20 mL, 337.5 mmol, 75 equiv). The reaction was stirred at 50 °C overnight and
evaporated. EA (100 mL) was added and the organic phase was washed with 0.1 N
HCl, then brine, dried over anhydrous Na2SO4 and filtered. The residue after rotary
evaporation was stirred in Et2O and filtered to give the amide compound 9 as
white solid (700 mg, yield 82%). 1H NMR (300 MHz, DMSO-d6): d 8.98 (s, 1H), 7.38
(t, 1H), 7.24 (br s, 1H), 7.21 (d, 1H), 7.14 (d, 1H), 6.76 (br s, 1H), 4.95 (s, 2H), 2.98 (t,
2H), 2.37 (t, 2H) ppm. Mass: m/z = 206.5 (M+1, ESI+).
Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)-N,N-dimethyl-
propanamide (10): To a mixture of 1 (100 mg, 0.485 mmol) in THF (2.4 mL) and
DCM (2.4 mL) were added DIPEA (344.8 mg, 2.66 mmol, 5.5 equiv),
EDCÁHCl (200 mg, 1 mmol, 2 equiv), HOAt (79 mg, 0.58 mmol, 1.2 equiv) and
dimethylamine hydrochloride (180 mg, 2.2 mmol, 4.5 equiv). The reaction
mixture was stirred at room temperature for 3 h, evaporated, and then EA
(20 mL) was added. The organic phase was washed with 1 N HCl, brine and dried
over anhydrous Na2SO4. The residue after rotary evaporation was purified by
preparative TLC (EA/PE = 1:1) to give 10 (56 mg, yield 50%). 1H NMR (300 MHz,
DMSO-d6): d 8.94 (s, 1H), 7.37 (t, 1H), 7.21 (m, 1H), 7.14 (d, 1H), 4.95 (s, 2H), 2.95 (t,
2H), 2.93 (s, 3H), 2.81 (s, 3H), 2.49 (t, 2H). Mass: m/z = 234 (M+1, ESI+).
Synthesis of N-(cyclopropylsulfonyl)-3-(1-hydroxy-1,3-dihydrobenzo[c] [1,2]oxab-
orol-7-yl) propanamide (11): The mixture of 1 (0.377 g, 1.83 mmol) and CDI
(0.892 g, 5.5 mmol, 3 equiv) in THF (15 mL) was refluxed for 1 h. After being
cooled down to rt, the solution was transferred with a syringe into a solution of
cyclopropanesulfonamide (0.667 g, 5.5 mmol, 3 equiv) in THF (5 mL), followed by
addition of DBU (0.56 g, 3.66 mmol, 2 equiv). The resulting mixture was stirred
overnight, quenched with 1 N HCl and extracted with EtOAc (100 mL). The organic
layer was concentrated and the residue was purified by preparative HPLC
(column: Luna 300 Â 50.0 mm, 10
l; liquid phase: [A—H2O; B—CH3CN + 0.1% TFA]
B%: 18–48%, 25 min) and freeze-dried to afford the compound 11 (270 mg, yield
48.2%). 1H NMR (400 MHz, DMSO-d6): d 11.57 (s, 1H), 8.97 (s, 1H), 7.39–7.34 (m,

650
Y.-K. Zhang et al. / Bioorg. Med. Chem. Lett. 21 (2011) 644–651
1H), 7.21 (d, 1H), 7.14–7.12 (d, 1H), 4.95 (s, 2H), 3.01 (t, 2H), 2.92–2.89 (m, 1H),
2.59 (t, 2H), 1.05–1.03 (m, 4H) ppm. HPLC purity: 99.58% at 220 nm and 100% at
254 nm.
EA = 3:1): Rf = 0.7. To the solution of 57 (1 g) in MeOH (20 mL) was added NaOH
(0.254 g, 2 equiv) in one portion at 0 °C. The reaction solution was stirred at rt for
1 h. MeOH was rotary evaporated to give a residue that was mixed with HCl (6 N,
1.1 mL). The reaction was stirred overnight, quenched with NaOH (1 N, 10 mL),
washed with EA. The aqueous phase was acidified with HCl (1 N) to pH 1–2 and
extracted with EA. The combined organic layer was washed with brine, dried over
Na2SO4, and evaporated to give 58 (540 mg, yield 51%) as a white solid. 1H NMR
(300 MHz, DMSO-d6): d 8.84 (s, 1H), 7.67 (d, 1H), 7.54 (m, 2H), 4.07 (t, 2H), 2.94 (t,
2H). MS: m/z = 174 (M+1, ESI+). To the solution of 58 (540 mg, 3.12 mmol) in
HCOOH/water (5.4:0.54 mL) was added Raney Ni. The reaction was stirred at
100 °C for 1 h, cooled to rt, quenched with water and extracted with EA. The
organic phase was washed with water, brine, dried over Na2SO4, and
concentrated. The residue was purified by silica gel column (PE/EA = 3:1) to give
59 (460 mg, 85%) as a white solid. 1H NMR (300 MHz, DMSO-d6): d 10.69 (s, 1H),
9.01 (s, 1H), 7.74 (q, 1H), 7.54 (m, 2H), 4.09 (t, 2H), 2.96 (t, 1H) ppm. MS: m/z = 177
(M+1, ESI+). To the solution of Ph3PCH2COOCH2CH3 bromide in THF (6 mL) was
added NaH (60%, 68 mg, 3 equiv). The reaction was stirred under N2 for 1 h at rt.
Compound 59 (100 mg, 1 equiv) in THF (2 mL) was added in one portion at 0 °C.
The mixture was stirred overnight, quenched with water (10 mL) and HCl (1 N
10 mL), extracted with EA. The organic phase was washed with brine, dried over
Na2SO4 and concentrated. The residue was purified by silica gel column (PE/
EA = 10:1–3:1) to give 60 (140 mg, yield 98%) as a white solid. 1H NMR (300 MHz,
DMSO-d6): d 8.73 (s, 1H), 8.70 (d, 1H), 7.70 (d, 1H), 7.42 (t, 1H), 7.26 (d, 1H), 6.45 (d,
1H) 4.30 (q, 2H), 4.03 (t, 2H), 2.89 (t, 2H), 1.20 (t, 3H) ppm. MS: m/z = 255 (M+23,
ESI+). The mixture of 60 (60 mg, 0.24 mmol) and Pd/C (10% 10 mg) in MeOH
(20 mL) was stirred under H2 for 2 h. The reaction solution was filtered and
concentrated to give 61 as oil (54 mg, yield 90%). TLC (PE/EA = 3:1): Rf = 0.5. 1H
NMR (300 MHz, DMSO-d6): d 8.40 (s, 1H), 7.26 (t, 1H), 7.04 (m, 2H), 4.00 (m, 4H),
3.15 (t, 2H), 2.83 (t, 2H) 2.56 (t, 2H), 1.15 (t, 3H). MS: m/z = 249 (M+1, ESI+). To the
solution of 61 (50 mg) in MeOH/H2O (10/1 mL) was added NaOH (50 mg, 6 equiv)
in one portion. The mixture was stirred overnight at rt, quenched with NaOH (1 N,
5 mL) and washed with EA. The aqueous phase was acidified with 1 N HCl to pH 1–
2, extracted with EA. The organic layer was washed with brine, dried over Na2SO4
and concentrated. Theresiduewas purifiedbysilicagel columntogivethe product
18 (17 mg, yield 38% over 2 steps) as a white solid. 1H NMR (300 MHz, DMSO-d6): d
8.41 (s, 1H), 7.25 (t, 1H), 7.05 (m, 2H), 3.98 (t, 2H), 3.07 (t, 2H), 2.82 (t, 2H), 2.48 (t,
2H) ppm. MS: m/z = 243 (M+23, ESI+) and 463 (2 M+23).
Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)propanenitrile
(12): To a solution of 9 (700 mg, 3.414 mmol) in DMF (17 mL) was added
(CNCl)3 (945 mg, 5.1 mmol, 1.5 equiv). The reaction was stirred at rt overnight,
quenched with water and extracted with EA. The organic phase was washed with
brine, dried over anhydrous Na2SO4 and filtered. The residue after rotary
evaporation was purified by column chromatography to give the cyano
compound 12 as white solid (370 mg, yield 58%). 1H NMR (300 MHz, DMSO-d6):
d 9.07 (s, 1H), 7.41 (t, 1H), 7.27 (d, 1H), 7.21 (d, 1H), 4.98 (s, 2H), 3.06 (t, 2H), 2.80 (t,
2H) ppm. MS: m/z = 186 (MÀ1, ESIÀ).
Synthesis of 7-(3-aminopropyl)benzo[c][1,2]oxaborol-1(3H)-ol HCl salt (13): To a
solution of 12 (70 mg, 0.37 mmol) in MeOH (2 mL) was added Raney Ni (21 mg)
and NH4OH (140 lL). The reaction flask was vacuumed and backfilled with H2 for
three times. The reaction was stirred at rt for 1 h. The reaction was filtered and
evaporated. The residue was purified by preparative TLC and treated with HCl to
give 13 as HCl salt (19 mg, yield 27%). 1H NMR (300 MHz, DMSO-d6): d 9.00 (s, 1H),
7.86(br s, 3H), 7.41 (t, 1H), 7.24(d, 1H), 7.14 (d, 1H), 4.98(s, 2H), 2.84–2.73 (m, 4H),
1.85 (t, 2H) ppm. Mass: m/z = 193 (MÀ1, ESIÀ).
Synthesis of 7-(2-(1H-tetrazol-5-yl)ethyl)benzo[c][1,2]oxaborol-1(3H)-ol (14): To a
solution of 12 (130 mg, 0.695 mmol) in DMF (3.5 mL) were added NaN3 (76.8 mg,
1.18 mmol, 1.7 equiv) and NH4Cl (63.13 mg, 1.18 mmol, 1.7 equiv). The reaction
was stirred at 95 °C for 3 days, quenched with 0.5 N HCl and extracted with ethyl
acetate. The organic phase was washed with brine and dried over anhydrous
Na2SO4. The residue after rotary evaporation was purified by preparative TLC plate
(EA/PE = 1:2) to give the tetrazole compound 14 (20 mg, yield 12.5%). 1H NMR
(300 MHz, DMSO-d6): d 15.9 (br s, 1H), 8.96 (s, 1H), 7.36–7.24 (m, 1H), 7.20 (d, 1H),
7.04 (d, 1H), 4.97 (s, 2H), 3.40 (m, 4H) ppm. Mass: m/z = 231 (M+1, ESI+) and 229
(MÀ1, ESIÀ).
Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-6-yl) propanoic acid
(15): This compound was synthesized starting with 3-bromo-4-methylbenzo-
nitrile by the method similar to that used for the synthesis of 1. Compound 15 was
obtained as white solid. 1H NMR (300 MHz, DMSO-d6): d 12.08 (s, 1H), 9.09 (s, 1H),
7.56 (s, 1H), 7.32 (m, 2H), 4.94 (s, 2H), 2.86 (t, 2H), 2.53 (t, 2H) ppm. MS: m/z = 205
(MÀ1, ESIÀ). HPLC purity: 95.64% at 220 nm and 95.78% at 254 nm.
Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-5-yl) propanoic acid
(16): This compound was synthesized starting with 4-bromo-3-methylbenzo-
nitrile by the method similar to that used for the synthesis of 1. Compound 16 was
obtained as a white solid. 1H NMR (300 MHz, DMSO-d6): d 12.13 (s, 1H), 9.10 (s,
1H), 7.64 (d, 1H), 7.22 (m, 2H), 4.97 (s, 2H), 2.87 (t, 2H), 2.58 (t, 2H) ppm. Mass: m/
z = 205 (MÀ1, ESIÀ).
Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-7-yl)-2,2-dimethyl
propanoic acid (19): To a solution of i-Pr2NH (3.44 mL, 24.55 mmol, 2.25 equiv)
in THF (15 mL) was added n-BuLi (7.84 mL, 19.6 mmol, 1.8 equiv) dropwise at
À78 °Cunder N2. Thereactionwas stirredat À20 °Cfor20 min. Tothereaction was
added, a solution of ethyl isobutyrate (2.2 mL, 16.36 mmol, 1.5 equiv) in THF
(2 mL) over 10 min. The reaction was stirred for 45 min, and then the solution of
62 (3 g, 10.9 mmol, 1 equiv) in THF (12 mL) was added. The reaction was stirred at
À20 °C for 45 min, quenched with saturated NH4Cl and extracted with EA. The
organic layer was washed with brine and dried over anhydrous Na2SO4. The
residue after rotary evaporation was purified by column chromatography to give
63 (3.2 g, yield 97.5%). A mixture of Raney Ni (4 g), 63 (4 g, 12.9 mmol) in HCOOH
and water (20/2 mL) was stirred at 100 °C for 1 h. The reaction was cooled and
filtered. The residue after rotary evaporation was purified by column
chromatography to give 64 as a solid (3.2 g, yield 80%). 1H NMR (300 MHz,
DMSO-d6): d 10.32 (s, 1H), 7.71 (m, 1H), 7.75 (m, 2H), 4.09 (q, 2H), 3.16 (s, 2H),
1.01–1.23 (m, 9H). To a solution of 64 (2 g, 6.4 mmol) in 1,4-dioxane (32 mL) was
added KOAc (2.7 g, 27.5 mmol, 4.3 equiv), pin2B2 (2.44 g, 9.6 mmol, 1.5 equiv) and
Pd(dppf)Cl2 (522 mg, 0.64 mmol, 0.1 equiv). The reaction was vacuumed and
backfilled by N2 for three times. The reaction was stirred at 103 °C overnight,
filtered and evaporated. The residue was purified by column chromatography
eluted with EA/PE (1:3) to give 65 (2.4 g, yield 100%). To a solution of 65 (2.3 g,
6.4 mmol) in EtOH (32 mL) was added NaBH4 (0.241 g, 6.4 mmol, 1 equiv) at 0 °C.
The reaction was stirred at rt for 1 h, quenched with 0.5 N HCl and extracted with
EA. The organic phase was washed with brine and dried over anhydrous Na2SO4.
The residue after rotary evaporation was purified by column chromatography
eluted with EA/PE (1:2) to give 66 (900 mg, yield 56%). 1H NMR (300 MHz, DMSO-
d6): d 8.93 (s, 1H), 7.38 (t, 1H), 7.21 (d, 1H), 6.97 (d, 1H), 4.95 (s, 2H), 4.02 (m, 2H),
3.06 (s, 2H), 1.01–1.23 (m, 9H) ppm. MS: m/z = 264 (M+1, ESI+). To a mixture of 66
(350 mg, 1.335 mmol) in THF/MeOH/water = 3:2:1 (6.6 mL) was added LiOH
(224 mg, 5.34 mmol, 4 equiv). The reaction was stirred at rt overnight and then
evaporated. The residue was acidified with 0.5 N HCl and extracted with EA. The
organic layer was washed with brine and dried over anhydrous Na2SO4. The
residueafterrotaryevaporationwas purifiedby preparativeTLCtogivetheacid 19
(22 mg, yield 7%). 1H NMR (300 MHz, DMSO-d6): d 12.19 (s, 1H), 8.92 (s, 1H), 7.36
(t, 1H), 7.23 (d, 1H), 7.08 (d, 1H), 4.96 (s, 2H), 3.06 (s, 2H), 1.05 (s, 6H) ppm. MS: m/
z = 233 (MÀ1, ESIÀ).
Synthesis of 3-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-4-yl) propanoic acid
(17): This compound was prepared starting with 3-bromo-2-methylbenzonitrile
by the method similar to that described for 1. 1H NMR (300 MHz, DMSO-d6): d
12.10 (s, 1H), 9.08 (s, 1H), 7.57(d, 1H), 7.29 (m, 2H), 5.03 (s, 2H), 2.76(t, 2H), 2.53 (t,
2H) ppm. Mass: m/z = 205 (MÀ1, ESIÀ). Purity: 96.72% at 220 nm.
Synthesis of 3-(1-hydroxy-3,4-dihydro-1H-benzo[c][1,2]oxaborinin-8-yl) propanoic
acid (18): To the solution of 23 (26.0 g, 0.103 mol) in THF/MeOH/H2O
(55:50:100 mL) was added LiOHÁH2O (17.3 g, 0.411 mol, 4 equiv). The mixture
was stirred for 1 h and concentrated. DCM was added. The organic layer was
washed with 1 N HCl, saturated NaHCO3, brine, dried over anhydrous Na2SO4,
filtered and concentrated. The residue was washed with PE to give the product 51
(16.2 g, yield 80%). To the mixture of 51 (14.2 g, 67 mmol) and silica gel (14.2 g) in
DCM (268 mL) was added PCC (21.6 g, 0.1005 mol, 1.5 equiv). The mixture was
stirred for 2 h. The reaction mixture was filtered and the filtrate was concentrated.
The residue was purified by silica gel chromatography to give the desired product
52 (11.8 g, 84.2%) as a solid. To the solution of 52 in DMSO (75 mL) were added
Ph3PCH2OMe chloride (29.4 g, 3.6 equiv) in DMSO (75 ml) and t-BuOK (9 g,
3.4 equiv) in one portion. The mixture was stirred for 1 h at rt and 52 (5 g, 1 equiv)
in DMSO (50 mL) was added in one portion at 0 °C, and then stirred overnight. The
reaction solution was poured into water, extracted with EA, washed with brine,
dried over Na2SO4, filtered and evaporated. The residue was purified by silica gel
column to give 53 (4.1 g, yield 72%) as a yellow solid. TLC (silica gel plate, PE/
EA = 10:1): Rf = 0.45. To the solution of 53 (2 g, 8.37 mmol) in THF (42 mL) was
added HCl (6 N, 14 mL) at rt and the reaction was refluxed for 1 h. The reaction was
cooled, poured into water, extracted with EA, washed withwater, brine, dried over
anhydrous Na2SO4 and evaporated to give 54 (2.54 g) as crude oil. TLC (silica gel
plate, PE/EA = 10:1): Rf = 0.2. To the solution of 54 (2.54 g) in methanol (20 mL)
was added NaBH4 (319 mg, 1 equiv) in portions for 10 min. The solution was
stirred for 1 hand water(50 mL) was added for 10 min. The solution was extracted
with EA, washed with water, dried over Na2SO4 and evaporated to give 55 (2.41 g)
ascrude oil. TLC(silicagel plate, PE/EA = 3:1): Rf = 0.3. Tothesolutionof 55(2.41 g)
and Et3N (1.2 g, 1.1 equiv) in DCM (35 mL) was added acetyl chloride (0.84 g,
1 equiv) dropwiseat0 °C. Thereaction wasstirred at0 °Cfor2 hand water(50 mL)
was added to the reaction solution. The solution was extracted with EA and the
organic layer was washed with brine, dried over anhydrous Na2SO4 and
evaporated. The residue was purified by silica gel column (PE/EA = 10:1) to give
the product 56 (2.2 g, 98% of three steps). 1H NMR (300 MHz, CDCl3): d 7.57 (d, 1H),
7.48 (d, 1H), 7.37 (t, 1H), 4.32 (t, 2H), 3.15 (t, 2H), 2.03 (s, 1H) ppm. To the mixture
of 56 (1 g), pin2B2 (1.04 g, 1.1 equiv) and KOAc (0.73 g, 2 equiv) in 1,4-dioxane
(20 mL) was added Pd(dppf)Cl2 (100 mg, 5% equiv) under N2. The reaction was
refluxed for 2 h. The reaction solution was cooled to rt, poured into water (50 mL)
and extracted with EA. The organic phase was washed with water, brine, dried
over anhydrous Na2SO4 and concentrated. The residue was purified by silica gel
column (PE/EA = 10:1) to give 57 (0.9 g) as a colorless oil. TLC (silica gel plate, PE/
Synthesis of 3-(1-hydroxy-3,3-dimethyl-1,3-dihydrobenzo[c][1,2] oxaborol-7-
yl)propanoic acid (20): To
a solution of 21 (150 g, 697.5 mmol) in MeOH
(1350 mL) was added SOCl2 (165.0 g, 2.0 equiv) dropwise at 5–10 °C. The
mixture was refluxed for 3 h and then MeOH was removed. EA was added to
extract the product and the EA layer was washed by water, Na2CO3/H2O, separated
and concentrated to givethe methylesteras orangeoil (158.7 g, yield 99.5%). HPLC
purity is 96%. To a 2 L 3-necked flask were added the methyl ester obtained
(158.7 g), CCl4 (1440 mL), NBS (128.7 g, 1.05 equiv) and BPO (8.4 g, 0.05 equiv).
The mixture was heated to 80–85 °C, stirred for 5 h, cooled to rt and filtrated. After
removal of solvent, EA was added into the residue, washed with 2 N Na2S2O3,
concentrated to give 67 as orange oil (229.5 g, yield 100%). CaCO3 (166.3 g,
2.4 equiv) was added into the solution of 67 (229.5 g) in a mixed solvent of THF
(1380 mL) and H2O (1380 mL). The mixture was stirred at 100 °C for 5.0 h, cooled

Y.-K. Zhang et al. / Bioorg. Med. Chem. Lett. 21 (2011) 644–651
651
to rt, filtered, extracted with EA, concentrated to give the crude 68 as orange oil
(199.0 g) that was purified by a short silica gel column to give 68 with 100% HPLC
purity as yellow solid (89.4 g, yield 52.6%). Silica gel (152.5 g) was added into the
solution of 68 (152.5 g) in DCM (2280 mL). PCC (201.0 g, 1.5 equiv) was added in
portions at 0–10 °C and the mixture was stirred for 3 h. The solvent was removed
to give the crude 69 (163.0 g) that was purified by a short silica gel column to give
69 as black oil (142.7 g, yield 94.4%). Pyridinium p-toluenesulfonate (PPTS, 14.7 g,
0.1 equiv) was added into the solution of 69 (142.7 g) in toluene (2.8 L) and
ethylene glycol (72.9 g, 2.0 equiv). The mixture was stirred at 130 °C for 5.0 h,
cooled to 40 °C and concentrated. The residue was purified by a short silica gel
column to give 70 as yellow oil (160.1 g, yield 95.0%). To a solution of 70 (5 g,
17.48 mmol) in dry THF (90 mL) was added CH3MgI (25 mL, 4 mol/L) dropwise at
À10 °C. The mixture was stirred overnight warming to rt, quenched by NaHCO3
and extracted with EA. The combined organic layers were washed with brine,
dried over anhydrous Na2SO4, filtered and concentrated. The residue was purified
by silica gel chromatography (PE/EA = 4:1) to give 71 (4.2 g, yield 84%) as a solid.
1H NMR (300 MHz, CDCl3): d 7.72 (d, 1H), 7.53 (d, 1H), 7.33 (t, 1H), 6.23 (s, 1H),
4.18–4.05 (m, 4H), 2.81 (s, 1H), 1.78 (s, 6H). MS: m/z = 287 and 289 (M+1, ESI+). To
a solution of 71 (4.2 g, 14.634 mmol) in dry THF (70 mL) was added n-BuLi
(12.3 mL, 2.5 M, 2.1 equiv) dropwise at À78 °C under N2 and stirred for 30 min.
Trimethyl borate (3.2 mL, 2 equiv) was added at À78 °C. The mixture was stirred
overnight warming to rt, quenched with water and acidified with 1 N HCl to pH 2–
3. The reaction mixture was stirred for 1 h and extracted with EA. The combined
organic layers were washed with brine, dried over anhydrous Na2SO4, filtered and
concentrated. The residue was purified by silica gel chromatography (PE/EA = 3:1)
to give 72 (176 mg, yield 6.8%) as a solid. 1H NMR (300 MHz, DMSO-d6): d 10.36 (s,
1H), 9.08 (s, 1H), 7.78–7.86 (m, 2H), 7.68 (t, 1H), 1.51 (s, 6H) ppm. MS: m/z = 191
(M+H). A mixture of 72 (176 mg, 0.9263 mmol), 2,2-dimethyl-1,3-dioxane-4,6-
dione (147 mg, 1.019 mmol, 1.1 equiv) in HCOOH/TEA (1.9 mL, v/v = 5:2) was
heated to 110 °C for 12 h. The mixture was cooled to rt and powered into ice-
water. The mixed solution was acidified with 1 N HCl to pH 1 and extracted with
EA. The combined organic layers were washed with brine, dried over Na2SO4,
filtered and concentrated. The crude product was purified by preparative TLC (PE/
EA = 2:1) to give 20 (23.5 mg, yield 10.8%) as a white solid. 1H NMR (500 MHz,
DMSO-d6): d 12.00 (s, 1H), 8.80 (s, 1H), 7.35 (t, 1H), 7.20 (d, 1H), 7.12(d, 1H), 2.98 (t,
2H), 2.54 (t, 2H), 1.44 (s, 6H) ppm. MS: m/z = 235 (M+1, ESI+) and 233 (MÀ1, ESIÀ).
HPLC purity: 95.0% at 220 nm and 98.6% at 266 nm.
7. Method for determining IC50 for growth inhibition of erythrocytic-stage P. falciparum
by benzoxaboroles 1–20: Erythrocytic-stage W2 strain P. falciparum parasites
were cultured in human erythrocytes and RPMI-1640 culture media with either
10% human serum or 0.5% Albumax serum substitute. Parasites were
synchronized to ring stage by treatments with 5%
with serial dilutions from to 10 mM stock concentrations were used to
determine IC50 values in 96 well microplate cultures in 200 L of media/well, 2%
D-sorbitol. Benzoxaboroles
5
l
hematocrit, 1% parasitemia, under atmosphere 3% O2, 5% CO2 balance N2. At the
completion of 48 h incubations, cultures were fixed with 2% formaldehyde, After
48 h of fixation,
5 lL aliquots were transferred to another 96 well plate
containing 150 L/well of staining solution: PBS, 100 mM NH4Cl, 0.1% Triton X-
l
100, and 1 nM YOYO-1. Parasites per erythrocyte were then determined by flow
cytometry from plots of forward scatter against fluorescence (excitation 488 nm,
emission 520 nm) using FacSort flow cytometer (Beckton Dickinson) equipped
with AMS Loader (Cytek Development). All values were normalized to percent
control activity, and IC50’s were calculated using the Prism 3.0 program (GRAPHPAD
Software). Goodness of fit was assessed by R2 values, with the expectation that
meaningful dose-response curves should yield R2 values >0.95.
8. Cytotoxicity was determined against human Jurkat and HeLa cells. For each cell
line, IC50’s were measured using a 12-point concentration curve, in triplicate and
viability was determined using 3-(4,5-dimethylthiazol-2-yl)-2,5diphenyl-
tetrazolium bromide (MTT) after 72 h exposure to compounds.