6-Cyano Analogues of Bedaquiline as Less Lipophilic and Potentially Safer Diarylquinolines for Tuberculosis

Article abstract of DOI:10.1021/acsmedchemlett.7b00196

Bedaquiline (1) is a new drug for tuberculosis and the first of the diarylquinoline class. It demonstrates excellent efficacy against TB but induces phospholipidosis at high doses, has a long terminal elimination half-life (due to its high lipophilicity), and exhibits potent hERG channel inhibition, resulting in clinical QTc interval prolongation. A number of structural ring A analogues of bedaquiline have been prepared and evaluated for their anti-M.tb activity (MIC₉₀), with a view to their possible application as less lipophilic second generation compounds. It was previously observed that a range of 6-substituted analogues of 1 demonstrated a positive correlation between potency (MIC₉₀) toward M.tb and drug lipophilicity. Contrary to this trend, we discovered, by virtue of a clogP/M.tb score, that a 6-cyano (CN) substituent provides a substantial reduction in lipophilicity with only modest effects on MIC values, suggesting this substituent as a useful tool in the search for effective and safer analogues of 1.

Full text of DOI:10.1021/acsmedchemlett.7b00196

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Letter
6-Cyano analogues of bedaquiline as less lipophilic
and potentially safer diarylquinolines for tuberculosis
Amy Tong, Peter Choi, Adrian Blaser, Hamish S Sutherland, Sophia Tsang, Jerome
Guillemont, Magili Motte, Christopher B. Cooper, Koen Andries, Walter Van den Broeck,
Scott G. Franzblau, Anna Upton, William A. Denny, Brian D. Palmer, and Daniel Conole
ACS Med. Chem. Lett., Just Accepted Manuscript • DOI: 10.1021/acsmedchemlett.7b00196 • Publication Date (Web): 22 Sep 2017
Downloaded from http://pubs.acs.org on September 24, 2017
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6-Cyano analogues of bedaquiline as less lipophilic and potentially
safer diarylquinolines for tuberculosis
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Amy S.T. Tonga, Peter J. Choia, Adrian Blasera, Hamish S. Sutherland,a Sophia K.Y. Tsang a, Jerome
Guillemontb, Magali Motteb, Christopher B. Cooperc, Koen Andriesd, Walter Van den Broeckd, Scott G.
Franzblaue, Anna M. Uptonc, William A. Dennya,*, Brian D. Palmera, Daniel Conolea,*
aAuckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019,
Auckland 1142, New Zealand; bMedicinal Chemistry Department (Infectious Diseases), Janssen Pharmaceuticals, Campus
de Maigremont, BP315, 27106 Val de Reuil Cedex, France; cGlobal Alliance for TB Drug Development, 40 Wall St, New
York 10005, USA; dInfectious Diseases BVBA, Janssen Pharmaceuticals, Beerse, Belgium ; eInstitute for Tuberculosis Reꢀ
search, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Chicago, Illinois 60612, USA.
KEYWORDS. Bedaquiline, diarylquinoline, tuberculosis, ATP synthase, hERG, lipophilicity
ABSTRACT: Bedaquiline (1) is a new drug for tuberculosis and the first of the diarylquinoline class. It demonstrates excellent
efficacy against TB, but induces phospholipidosis at high doses, has a long terminal elimination halfꢀlife (due to its high lipophiliciꢀ
ty) and exhibits potent hERG channel inhibition, resulting in clinical QTc interval prolongation. A number of structural ring A anaꢀ
logues of bedaquiline have been prepared and evaluated for their antiꢀM.tb activity (MIC90) — with a view to their possible applicaꢀ
tion as less lipophilic second generation compounds. It was previously observed that a range of 6ꢀsubstituted analogues of 1
demonstrated a positive correlation between potency (MIC90) towards M.tb and drug lipophilicity. Contrary to this trend we discovꢀ
ered, by virtue of a clogP/M.tb score, that a 6ꢀcyano (CN) substituent provides a substantial reduction in lipophilicity with only
modest effects on MIC values, suggesting this substituent as a useful tool in the search for effective and safer analogues of 1.
Novel drugs that can reduce the treatment time for tubercuꢀ
losis (TB) are vital, particularly in cases of multiꢀ and extenꢀ
sively drug resistant tuberculosis (MDRꢀTB and XDRꢀTB).1
Ideally, new TB drugs are effective against drugꢀresistant and
drugꢀsensitive TB, well tolerated, suitable for once daily oral
dosing and compatible with antiꢀretroviral therapies for indiꢀ
viduals coꢀinfected with HIV. After several decades without
the approval of a new class of drug for TB, the diarylquinoline
(DARQ) bedaquiline (TMC207, Sirturo, Janssen Pharmaceutiꢀ
cals; 1), was approved by the US Food and Drug Administraꢀ
tion in December 2012 for use in pulmonary multiꢀdrug reꢀ
sistant (MDR) TB. Bedaquiline has a novel mechanism of
action, through inhibition of the mycobacterial ATP synthase
enzyme.2 Improved outcomes were seen when bedaquiline
was added to standard therapy regimens for MDRꢀTB in a
Phase II registration trial.3 Other multidrug trials are in proꢀ
gress, with positive results being reported for a bedaquiꢀ
line/pretomanid/pyrazinamide (BPaZ) combination therapy
phase IIa trial.4,5 Bedaquiline shows inhibition of the hERG
cardiac potassium channel, with the concomitant risk of QTc
prolongation.6 This raises concerns about potential interactions
with other drugs that also prolong the QTc interval (fluoroꢀ
quinolones, clofazimine) in MDRꢀTB patients.7
Figure 1. Structure of bedaquiline (1).
It is also very lipophilic (measured log P 7.25), which may
contribute to its induction of phospholipidosis, seen at high
doses in preclinical models.8 Its high lipophilicity may also
contribute to bedaquiline’s long terminal elimination halfꢀlife9
which may lead to tissue overꢀproportional accumulation at
high doses or with daily dosing. Due to these pharmacokinetic
properties, bedaquiline is currently dosed three times per
week, following a period of once daily loading. Additionally,
due to the possibility of tissue overꢀproportional accumulation,
efficacy has not been thoroughly explored at higher doses.10
These observations suggest that less lipophilic analogues of
bedaquiline would be of potential interest, to reduce the potenꢀ
1
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tial for tissue overꢀproportional accumulation, and hence to uated eight analogues of 1 with differing substituents at the 6ꢀ
1
2
3
4
5
6
7
8
increase suitability for once daily dosing.
position of the methoxyquinoline ring, including compounds
1, 2, 5 and 6 in Table 1 below (mostly as RS,SR diastereomer
mixtures). The authors noted that while substituents generally
improved potency over the unsubstituted parent (2), there
seemed to be little electronic effect, with the IC90s of the 6ꢀ
substituted compounds within a twoꢀfold range compared with
the lead compound (1).11
Bedaquiline emerged from a wholeꢀcell screen of 70,000 liꢀ
brary compounds against the nonꢀpathogenic M.smegmatis
strain of TB,11 where the racemic mixture (comprised of 4
diastereomers) was shown to have useful activity against both
M.smegmatis and M.tuberculosis (M.tb), with the R,S enantiꢀ
omer being the most potent. An SAR study of about 200 anaꢀ
logues of 1 (as mixtures of RR,SS or RS,SR diastereomers)
against M.smegmatis showed a rank order correlation between
M.smegmatis and M.tb, with the latter about 10ꢀfold more
resistant. The SAR study11 showed that the dimethylamiꢀ
noethyl side chain was near optimal for activity, with weaker
bases being less effective. This is consistent with later crystalꢀ
lographic studies12 of 1 bound to its major target (the c subunit
of the ATP synthase Fo moiety), where the dimethylamiꢀ
noethyl unit making a Hꢀbond to Glu65 in the ionꢀbinding site
of the enzyme, anchoring the rest of the molecule to make
multiple additional hydrophobic contacts. The study also evalꢀ
In the present paper we expand the range of 6ꢀsubstituents in
this series, and across a number of modified B and C ring scafꢀ
folds, seeking more polar alternatives to Br that provide anaꢀ
logues of bedaquiline with similar potency of M.tb inhibition.
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The 6ꢀBr compounds in Tables 1 and 2 were primarily synꢀ
thesized following a route described previously,11 from approꢀ
priate benzylquinoline A/B units and 3ꢀ(dimethylamino)ꢀ1ꢀ
phenylpropanꢀ1ꢀone C/D units (Scheme 1). While there have
been two reported asymmetric syntheses of bedaquiline,13,14
these
syntheses
are
Scheme 1. Syntheses of a representative subset of Mannich bases and diarylquinoline analogues
27
36
44
52
55
58
32
X = Br B = Ph C = 3-F (72%)
B
B
X = Br B = 2-F,3-OMe C = 3-F (77%)
X = Br B = 2-F,3-OMe C = 3-OCF3 (67%)
X = Br B = 2-F,3-OMe C = 3-OMe (59%)
X = Br B = 2-F,3-OMe C = 3-Cl (68%)
X = Br B = 2-F,3-OMe C = 3-Me (45%)
X = Br B = 3-F C = 3-OCF3 (20%)
N
(a)
X
X
OH
C
D
N
O
N
O
O
N
104, 117
(c)
C
28
37
45
53
56
59
33
X = CN B = Ph C = 3-F (62%)
X = CN B = 2-F,3-OMe C = 3-F (73%)
O
X = CN B = 2-F,3-OMe C = 3-OCF3 (85%)
X = CN B = 2-F,3-OMe C = 3-OMe (99%)
X = CN B = 2-F,3-OMe C = 3-Cl (40%)
X = CN B = 2-F,3-OMe C = 3-Me (85%)
X = CN B = 3-F C = 3-OCF3 (85%)
134
135
136
C = 3-F (54%)
C = 3-Me (50%)
C = 3-Cl (62%)
(b)
C
137 C = 3-OMe (33%)
138 C = 3-OCF3 (53%)
various
Reagents and conditions: (a) (i) HN(iOPr)2 or TMP, nꢀBuLi, THF, ꢀ40°C, 0.25 h; (ii) 103ꢀ132, THF, ꢀ78°C, 1.5 h; (iii) 133ꢀ139, THF, ꢀ
78°C, 4 h; (b) acetophenone, CH2O, Me2NH.HCl, c.HCl, EtOH, 90°C, 18 h; (c) P(oꢀtol)3, Zn, Zn(CN)2, Pd2(dba)3, DMF, 50°C, 5ꢀ18 h.
lengthy and nonꢀconvergent, calling for stepwise installation
of the B, C and D units, and were not suitable for a medicinal
chemistry SAR program. Our synthetic efforts utilized some
expedient synthetic routes to a range of bedaquiline analogues,
mainly by employing some common intermediates (e.g., funcꢀ
tionalized A/B units where X = Br, I). Tables 1 and 2 report a
vast number of DARQ analogues with combinations of variꢀ
ous A/B and C/D units, most of which and their building
blocks are detailed in the Supporting Information. However,
we highlight in Scheme 1 the key reactions for the preparation
of a subset of the compounds most relevant to this study.
morpholine: 16ꢀ75%). Moreover, the yield appeared to also be
dependent on B–ring substituents, with the 2ꢀF, 3ꢀOMe subꢀ
stituent seemingly preferred over its 3ꢀF and 2,3ꢀdiOMe counꢀ
terparts.
Cyano DARQs (28, 33, 37, 45, 53, 56 and 59) were preꢀ
pared from their corresponding bromides (27, 32, 36, 44, 52,
55 and 58) via a Pdꢀcatalyzed cyanation.15 Cyanation condiꢀ
tions were optimized using various palladium sources and
ligands.
The
purity
of
tris(dibenzylideneacetone)dipalladium(0) was variable from
several commercial sources and was repurified before use.16
The order of addition of reagents was also crucial, with addiꢀ
tion of cyanide source (zinc cyanide) to a preheated mixture
(50 °C) of other reagents critical for high yields and complete
conversion to products.15
The majority of final DARQ compounds (including all 6ꢀBr
in Table 2) were synthesized via condensation of the appropriꢀ
ate A/B unit and C/D unit (Scheme 1). C/D units were preꢀ
pared in one step via Mannich reaction of appropriate acetoꢀ
phenones. The DARQ product was formed in one step as a
racemic mixture of four diastereomers, and the desired RS,SR
diastereomer was isolated by superꢀcritical fluid HPLC at Biꢀ
oDuro LLC (Beijing). A wide range of yields were observed
for the key condensation reaction, even when the Aꢀring subꢀ
stituent remained constant (e.g. X = Br: 20ꢀ77%; A = spiroꢀ
For substituents other than cyano, common intermediates of
A/B units where X = Br, I allowed the introduction of amine
or sulfamide substituents to the 6ꢀposition of the A ring via
Buchwald coupling (107ꢀ110, 121ꢀ127 and 131ꢀ132) or
Ullmann type reaction (113 and 128) respectively (see Supꢀ
porting Information). Other reactions such as Suzuki coupling
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22
Cl
F
Me
7.10
6.53
6.86
7.39
7.31
6.63
7.16
7.09
6.45
6.46
6.20
5.32
5.33
5.66
7.31
7.74
5.08
4.11
5.82
0.71
0.14
0.56
1.02
1.14
0.40
0.80
0.82
-0.38
0.40
0.60
-0.10
-1.03
0.10
0.88
1.04
-0.70
-0.32
-1.23
0.23
0.06
-0.17
-0.15
-0.21
0.23
0.03
-0.02
0.10
0.30
0.01
-0.11
0.00
-0.05
0.54
0.35
0.36
0.45
-0.66
0.71
0.94
1.74
0.23
0.13
0.48
6.1
1.9
6.0
0.21
3.7
>12
6.9
4.3
with the 6ꢀbromo A/B unit afforded a 6ꢀcyclopropyl derivative
(112).
Alternatively, DARQ compounds were directly functionalꢀ
ized at the 6ꢀposition of the Aꢀring. An amino substituent was
accessed via hydrolysis of imine (22), whereas silanes were
reduced to form alkynes (9 and 29) or further down to ethyl
substituents (7). Thioꢀbased DARQ’s were oxidized to sulfoxꢀ
ides (41 and 66) or sulfones (40, 43 and 65) using mꢀ
chloroperoxybenzoic acid (mꢀCPBA) or Nꢀmethylmorpholine
Nꢀoxide (NMO) respectively.
1
2
3
4
5
6
7
8
Et
cyclopropyl
C≡CH
C≡CMe
CH=CH2
CH=NOH
CH=NOMe
CH2NMe2
CH2NH2
CH2OH
CH2COMe
CF3
7.9
3.5
2.2
4.8
1.7
10
9
1.6
>7.0
0.38
0.24
2.2
>6.7
1.9
10
10
11
12
13
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15
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60
As the preparation of bedaquiline (1) has been reported preꢀ
viously, its synthesis has not been described here. The syntheꢀ
ses of compounds 2, 4, 6, 10ꢀ14, 16, 20 and 21 were conductꢀ
ed by Janssen Pharmaceutica (Belgium) previously,17ꢀ19 and so
are not reported in the Supporting Information.
OCF3
CONMe2
COOH
NH2
Nꢀ
cyclobutyl
Nꢀ
6.3
10
6.49
0.80
-0.85
0.48d
23
Table 1 shows the structures and physicochemical and bioꢀ
logical properties of bedaquiline (1) and 25 analogues bearing
a wide variety of different 6ꢀsubstituents. For the majority of
the compounds, MIC90 values were determined for inhibition
of M.tb (strain H37Rv) under aerobic conditions (MABA asꢀ
say20). The majority of the compounds were evaluated as the
RS,SR diastereomers, but a few (23, 25, 26; noted) were availꢀ
able only as the pure R,S enantiomer.
24
25
7.05
7.61
1.10
1.40
-0.85
-0.85
1.7
cyclopentyl
Nꢀpiperidyl
0.67d
6.06
-0.27
-0.50
0.71d
26
aclogP calculated by ChemDraw Ultra v13.0 (CambridgeSoft);
bMIC90 (mg/mL); minimum inhibitory concentration for 90%
inhibition of growth of M.tb strain H37Rv, determined under aerꢀ
obic (MABA)20 conditions. Each value is the mean of at least two
independent determinations; IC50 (µM); Data for R,S enantioꢀ
mer.
Representative examples (as pure R,Sꢀenantiomers) were alꢀ
so evaluated for their ability to inhibit potassium ion through
the hERG potassium ion channel.21,22 While some compounds
showed less potent hERG inhibition, there was no significant
correlation seen between any 6ꢀsubstituent properties and
hERG inhibitory potency.
c
d
Figure 2. Mean Lipophilicity/M.tb activity score of most suitꢀ
able X substituents (c.f. with X = Br).
Mean clogP/Mtb activity score
Table 1: 6-Substituted quinoline analogues of bedaquiline
14
12
10
8
6
4
2
b
c
π
σp
MIC90
hERG IC50
(µM)
1.6
#
X
clogPa
0
(µg/mL)
CN
N(CH2CH2)2O N(CH2)2C(CH2)2O
X substituent of B/C scaffold
1
2
3
Br
H
I
7.25
6.37
7.51
0.86
0.0
1.12
0.23
0.0
0.18
0.09
1.9
0.20
1.6
Table 2: Comparison of different 6-quinoline substituents on modified B/C scaffolds
b
#
B ring substituent
X
clogPa
7.25
6.22
4.86
5.60
6.39
4.20
7.25
MIC90
0.09
0.23
0.69
0.36
4.1d
5d
clog P/ M.tb scorec
C ring substitu-
1
H
1ꢀnaphthyl
Br
Br
CN
27
28
29
30
31
32
3.0
4.8
ꢀ0.04
0.42
C≡CH
H
3ꢀF
NMeSO2Ph
NMeSO2NMe2
Br
3ꢀF
3ꢀOCF3
0.25
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64
65
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71
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73
74
75
CN
5.89
6.22
7.10
6.22
4.87
5.04
6.03
4.23
4.31
6.03
4.11
7.11
5.75
5.92
6.08
6.07
7.46
6.39
7.60
6.00
4.64
4.81
6.79
5.44
5.61
6.58
5.22
5.39
5.48
4.12
4.29
5.28
3.49
3.57
3.45
4.99
3.64
3.97
4.84
6.36
5.01
5.18
5.34
0.47
0.85
0.09
0.10
0.18
0.51d
0.19d
>5d
6.2
1.7
ꢀ0.94
N(CH2CH2)2O
1
2
3
4
5
6
7
8
Cl
Br
CN
17
2.9
2.1
0.41
0.39
6.3
Xe
N(CH2CH2)2S
N(CH2CH2)2SO2
N(CH2CH2)2SO
2ꢀF, 3ꢀOMe
3ꢀF
>5d
SMe
SO2Me
Br
0.13d
2.3d
0.09
0.26
0.77
0.14
0.66
2.3
0.96
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
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45
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47
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50
51
52
53
54
55
56
57
58
59
60
CN
8.0
1.8
21
1.8
ꢀ0.16
6.0
Xe
N(CH2CH2)2O
N(CH2CH2)2NH
Npiperidyl
2ꢀF, 3ꢀOMe
3ꢀOCF3
F
0.21
1.1
OCF3
Br
ꢀ0.51
0.10
0.09
0.87d
0.07
0.13
0.31d
0.04
0.09
1.1d
0.04
0.17
0.66
0.28d
>5d
CN
ꢀ130.0f
1.5
2ꢀF, 3ꢀOMe
2ꢀF, 3ꢀOMe
2ꢀF, 3ꢀOMe
3ꢀOMe
3ꢀCl
Xe
Br
CN
23
4.9
Xe
Br
CN
30
1.1
3ꢀMe
Xe
Br
CN
11
1.9
0.83
0.40
0.40
1.9
Xe
N(CH2CH2)2S
N(CH2CH2)2SO2
N(CH2CH2)2SO
NMeSO2NMe2
2,3ꢀdiOMe
3ꢀF
4.8d
1.13d
0.20
0.34
2.5
0.25
0.09
0.21
0.75
0.68
Br
CN
9.6
0.44
3.0
2,3ꢀdiOMe
2,3ꢀdiOMe
2,3ꢀdiOMe
3ꢀOCF3
N(CH2CH2)2O
Cl
Br
CN
11
1.8
1.7
c
Xe
N(CH2CH2)2O
aclogP calculated by ChemDraw v.13.0 (CambridgeSoft). MIC90 (in µg/mL) for inhibition of M.tb; clog P/M.tb score = clogP(Br)
clogP(Xsub) / MIC90(Xsub) ꢀ MIC90(Br); dData for R,S enantiomer;
ꢀ
b
eX =
N
O ; fThis value was not included as a data point for figure 2, as the
CN analogue was more potent than the Br, producing a negative score.
Calculations show a modest correlation of lower MIC90 with
higher overall lipophilicity (measured as 6ꢀsubstituent π valꢀ
ues) (equation 1) but not with substituent electronic properties.
The latter suggests there is little 6ꢀsubstituent interaction with
the enzyme active site, consistent with the crystal structure of
1 bound to the c subunit of M.phlei.12
against M.tb. We have measured this by calculating the exꢀ
pression [clog P/M.tb score] for each compound (equation 2)
ꢐ
ꢓ
ꢋꢌꢍꢎꢏ ꢑꢒ ꢔꢋꢌꢍꢎꢏꢐꢕꢖꢗꢘꢓ
ꢀꢁꢂꢃꢄ/ꢅ. ꢆꢇ ꢈꢀꢂꢉꢊ = ꢙꢚꢛꢜꢝ ꢕꢖꢗꢘ ꢔꢙꢚꢛꢜꢝ ꢑꢒ
equation 2
ꢐ
ꢓ
ꢐ
ꢓ
Log(MIC90) = ꢀ0.43(±0.14)π + 0.19(±0.11) equation 1
This is the ratio of the difference in overall lipophilicity over
the difference in MIC90 value for each compound, averaged
over all the compounds containing that substituent. The more
positive the value of the ratio for a particular substituent, the
better it fulfills the desired role. Figure 2 shows that, by this
measure, the polar but strongly electronꢀwithdrawing CN subꢀ
stituent is the most preferable of the 6ꢀsubstituents studied,
with the highest average clog P/M.tb score of 13 (albeit rangꢀ
ing widely from 3 to 30). Across the 10 individual Br/CN sets
in Table 2, the CN compounds had an average MIC of 0.25
µM (only twoꢀfold greater than the average 0.12 µM MIC for
the corresponding Br compounds), but with an average clogP
n = 26 R = 0.52 S = 0.51 P = 0.007 F2,25 = 8.8
No correlation was seen between 6ꢀsubstituent properties
and hERG IC50 values.
In Table 2 we extend these studies on the suitability of differꢀ
ent 6ꢀsubstituents to ten sets of compounds containing a varieꢀ
ty of other substituents in the B and C units of the bedaquiline
structure. The aim was to seek more polar 6ꢀsubstituents that
would contribute to lowering overall drug lipophilicity and
potentially hERG inhibition while (in spite of the overall trend
shown by equation 1) not adversely affecting potency (MIC90)
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ACS Medicinal Chemistry Letters
Cooperation of the Netherlands (DGIS), and Irish Aid.
1.5 log units lower than that of their Br counterparts (4.9 verꢀ
sus 6.4). Thus CN is suggested as an accessible and stable 6ꢀ
1
2
3
substituent, able across a range of analogues to substantially
lower lipophilicity with minimal effects on MIC90.
ACKNOWLEDGMENT
4
5
6
7
8
9
Table 2 also reveals preliminary SAR information from varꢀ
iations of B/C units. With X = Br or CN (the preferred 6ꢀ
substituents), a comparison of the MIC90 across different Bꢀ
units suggests that the diꢀsubstituted Bꢀunits (2ꢀF, 3ꢀOMe and
2,3ꢀdiOMe) may be more favorable than the monoꢀsubstituted
ones, showing similar potency as 1. Changing from a bicyclic
naphthalene Cꢀunit to a 3ꢀsubstituted phenyl ring (as well as a
2,3ꢀdiOMe phenyl) were found to be tolerated. A few examꢀ
ples of these B/C scaffolds with a 6ꢀCN substituent afforded
comparable potencies to 1, which warrant further investigation
into other combinations of B/C units with a 6ꢀCN quinoline
scaffold that may further lower both lipophilicity and MIC90.
Our thanks to Frank Ruebsam, Huili Wang, and Zicheng Wu at
BioDuro LLC (Beijing) for the separation of newly synthesized
DARQs into single diasteromers, and for the large scale synthesis
of required DARQ intermediates.
ABBREVIATIONS
DARQ diarylquinoline; DIPEA, diisopropylethylamine; M.tb,
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
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
mycobacterium
tuberculosis;
DMAP,
N,Nꢀdimethylꢀ4ꢀ
aminopyridine; DMDS, dimethyl disulfide; M. smegmatis, myco-
bacterium smegmatis; MABA, Microplate alamar blue assay;
MDRꢀTB, multiꢀdrug resistant tuberculosis; TMP, tetramethylpiꢀ
peridine; XDRꢀTB, extensively drug resistant tuberculosis.
The results of Table 1 suggest that, for a range of 6ꢀ
substituted analogues of 1, there is a positive correlation beꢀ
tween potency (MIC90) towards M.tb and drug lipophilicity, as
has been observed previously. Despite this, in Table 2 we
show that a 6ꢀcyano (CN) substituent provides a substantial
reduction in lipophilicity with only modest effects on MIC90
values, by determining the ratio of the difference in overall
lipophilicity over the difference in MIC90 value for comꢀ
pounds. This is a valuable new substituent to use in the search
for effective but less lipophilic and potentially safer analogues
of 1.
REFERENCES
1. Laurenzi, M.; Ginsberg, A.; Spigelman, M. Challenges associatꢀ
ed with current and future TB treatment. Inf. Dis. Drug Targets, 2007,
7, 105ꢀ119.
2. Koul, A.N.; Dendouga, K.; Vergauwen, B.; Molenberghs, B.;
Vranckx, L.; Willebrords, R.; Ristic, Z.; Lill, H.; Dorange, I.; Guilꢀ
lemont, J.; Bald, D;, Andries, K. Diarylquinolines target subunit c of
mycobacterial ATP synthase. Nat. Chem. Biol. 2007, 3, 323ꢀ324.
3. Diacon, A.H.; Donald, P.R.; Pym, A.; Grobusch, M.; Patientia,
R.F.; Mahanyele, R.; Bantubani, N.; Narasimooloo, T.; De Marez,
RT.; van Heeswijk, R.; Lounis, N.; Meyvisch, K.; Andries, K.;
McNeeley, D.F. Randomized pilot trial of eight weeks of bedaquiline
(TMC207) treatment for multidrugꢀresistant tuberculosis: longꢀterm
outcome, tolerability, and effect on emergence of drug resistance.
Antimicrob. Agents Chemother. 2012, 56, 3271–3276.
4. Media Release, Global Alliance for TB, published 29 January
2015 http://www.tballiance.org/newscenter/viewꢀbrief.php?id=1114
5. Diacon, A.H.; Dawson, R.; von GrooteꢀBidlingmaier, F.; Syꢀ
mons, G.; Venter, A.; Donald, P.R.; van Niekerk, C.; Everitt, D.;
Hutchings, J.; Burger, D.A.; Schall, R.; Mendel, C.M. Bactericidal
activity of pyrazinamide and clofazimine alone and in combinations
with pretomanid and bedaquiline. Am. J. Respir. Crit. Care Med.
2015, 191, 943ꢀ953.
6. Treatment of patients with MDRꢀTB. Briefing document, TMC
207 (bedaquiline). Antiꢀinfective Drugs Advisory Committee, NDA
204ꢀ384 (28 N0vember 2014).
7. Kakkar, A.K.; Dahiya, N. Bedaquiline for the treatment of reꢀ
sistant tuberculosis: Promises and pitfalls. Tuberculosis 2014, 94 (4),
357ꢀ362.
8. Mesens, N.; Verbeeck, J.; Rouan, M.; Vanparys, P. Elucidating
the role of M2 in the preclinical safety profile of TMC207. Abstract
on the 38th Union World Conference on Lung Health, Cape Town,
South Africa, 2007.
9. Svensson, E.M.; Murray, S.; Karlsson, M.O.; Dooley, K.E. Riꢀ
fampicin and rifapentine significantly reduce concentrations of beꢀ
daquiline, a new antiꢀTB drug. J. Antimicrob. Chemother. 2015,
70,1106ꢀ1114.
AUTHOR INFORMATION
Corresponding Author
*William A. Denny
Email: b.denny@auckland.ac.nz.
Address: Auckland Cancer Society Research Centre,
School of Medical Sciences, University of Auckland, Priꢀ
vate Bag 92019, Auckland 1142, New Zealand
Supporting Information.
Scheme 1: Routes and conditions for the synthesis of A/B
intermediates
Scheme 2: Routes and conditions for the synthesis of C/D
intermediates
General chemistry methods
Representative procedures for the syntheses of 6ꢀbromoꢀ, 6ꢀ
cyanoꢀ and 6ꢀmorpholinoꢀ analogues of bedaquiline
Author Contributions
All of the authors contributed to the writing of this manuscript.
10. "Prescribing Information for Bedaquiline" (PDF). Retrieved 20
July
2015
2014.http://www.accessdata.fda.gov/drugsatfda_docs/label/2012/2043
84s000lbl.pdf
11. Guillemont, J.; Meyer, C.; Poncelet, A.; Bourdrez, X.; Anꢀ
dries, K. Diarylquinolines, synthesis pathways and quantitative strucꢀ
ture–activity relationship studies leading to the discovery of TMC207.
Future Med. Chem, 2011, 3, 1345–1360.
Funding sources
This work was supported by the Bill&Melinda Gates Foundation,
the U.S. Agency for International Development (USAID), the
U.K. Department for International Development (DFID), the Diꢀ
rectorate General for International
12. Preiss, L.; Langer, J.D.; Yildiz, O.; EckhardtꢀStrelau, L,; Guilꢀ
lemont, J.; Koul, A.; Meier, T. Structure of the mycobacterial ATP
5
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Page 6 of 6
synthase Fo rotor ring in complex with the antiꢀTB drug bedaquiline.
Sci. Adv. 2015, 1, e1500106.
1
13. Saga, Y.; Motoki, R.; Makino, S.; Shimizu, Y.; Kanai, M.; Shiꢀ
basaki, M. Catalytic asymmetric synthesis of R207910. J. Am.
Chem.Soc. 2010, 132, 7905ꢀ07.
14. Chandrasekhar, S.; Kiran Babu, G.S.; Mohapatra, D.K. Practiꢀ
cal syntheses of (2S)ꢀR207910 and (2R)ꢀR207910. Eur. J. Org. Chem.
2011, 2057ꢀ61.
2
3
4
5
6
15. Ryber, P. Development of a mild and robust method for largeꢀ
scale palladiumꢀcatalysed cyanation of aryl bromides: importance of
the order of addition. Org. Process Res. Dev. 2008, 12, 540ꢀ543.
16. Zalesskiy, S.S.; Ananikov, V.P. Pd2(dba)3 as a precursor of solꢀ
uble metal complexes and nanoparticles: determination of palladium
active species for catalysis and synthesis. Organometallics 2012, 31,
2302ꢀ2309.
17. Andries, K.J.L.M.; Van Gestel, J.F.E. Preparation of aminohyꢀ
droxyaralkylquinolines for the treatment of drug resistant mycobacteꢀ
rial diseases. WO 2005/117875.
7
8
9
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
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
18. Guillemont, J.E.G.; Lancois, D.F.A.; Dorange, I; Andries,
K.J.L.M.; Koul, A. Antibacterial quinoline derivatives and their prepꢀ
aration, and use in the treatment of bacterial infection. WO
2008/068267 A1.
19. Andries, K.J.L.M.; Koul, A.; Guillemont, J.E.G.; Pasquier,
E.T.J.; Lancois, D.F.A. Preparation of aminohydroxyphenylꢀ
butylquinolines as antibacterials. WO 2006/131519 A1.
20. Collins, L.A.; Franzblau, S.G.; Microplate Alamar blue assay
versus BACTEC 460 system for highꢀthroughput screening of comꢀ
pounds against Mycobacterium tuberculosis and Mycobacterium
avium. Antimicrob. Agents Chemother. 1997, 41, 1004ꢀ1009.
21. Recanatini, M.; Poluzzi, E.; Masetti, M.; Cavalli, A.; De Ponti,
F. QT prolongation through hERG K(+) channel blockade: current
knowledge and strategies for the early prediction during drug develꢀ
opment. Med. Res. Rev. 2005, 25, 133ꢀ166.
For Table of Contents Use Only
22. IC50 (µM) for inhibition of the hERG channel; studies conꢀ
ducted by ChanTest Corporation, 14656 NeoParkway, Cleveland, OH
44128 (FASTPatch IC50 screen).
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