Letters
Journal of Medicinal Chemistry, 2008, Vol. 51, No. 7 2001
Table 1. Inhibition of Pantothenate Synthetase (% Inhibition at 100 µM
and IC50) and Inhibition of Mtb Growth in MABA and LORA Assays
by 1a,b, 2a, 3a-m, 7, and 8
ligands. It seems that polar and nonpolar moieties in the pyrazole
ring result in a decrease in activity as ligand 2c, which is
identical to ligand 1a with the exception of the two extra methyl
groups in the pyrazole ring, showed no inhibition of PS in the
MLSCN/NIH screening program.
% inhibition
at 128 µM
% inhibition
The MICs of 3a-m, 7, and 8 in LORA28 and MABA29 MIC
were found to be larger than 128 µM. The percent of inhibition
at 128 µM in LORA and MABA assays is given in Table 1.
The inhibition ranges from 0% to 84% in the MABA assay
and 62% in the LORA assay and at this high concentration can
be affected by the off-target toxicity of the compounds and their
metabolites. Several possible reasons for the lack of antimicro-
bial activity can be suggested, e.g., poor bacterial wall perme-
ability, metabolic stability, or efflux of the inhibitors.
compd
at 100 µM
IC50 (nM)
MABA
LORA
1a
1b
2a
3a
3b
3c
3d
3e
3f
3g
3h
3i
3j
3k
3l
89
98
18
100
94
98
84
97
100
100
99
79
82
78
17
79
12
43
120 ( 6a,c
150 ( 9a,c
NDa,b,d
46
0
15
0
70
84
73
NDb
70
43
48
56
41
NDb
54
19
34
14
5
53
62
24
NDb
12
NDb
0
97 ( 4c
140 ( 9c
140 ( 9c
160 ( 8c
90 ( 1c
160 ( 1c
130 ( 10c
460 ( 42c
250 ( 8c
210 ( 10c
140 ( 8c
NDb,d
47
2
These studies identified tert-butyl and pyrazole portions of
the PS inhibitors as the two areas containing the key pharma-
cophore elements. On the other hand, the substituents in the
aryl moiety of the pyrazole portion are well tolerated, suggesting
that this part of the scaffold is an auxophore, and thus, it may
be used to fine-tune ADMET profiles of these compounds. More
drastic modifications of the scaffold would be required to
determine the binding pose of the inhibitors and address weak
MIC, and such efforts are currently under way. These findings
are an important step in the development of PS inhibitors and
validation of PS as a therapeutic antimicrobial target and
potential target for NRP-TB.
NDb
46
11
26
14
11
4
3m
7
8
7130 ( 297c
NDb,d
61000 ( 5700c
60
a 1a, 2b, and 2a were also tested within the MLSCN/NIH screening
program. b ND: not done. c No inhibition of the control enzyme was
observed. d Not tested for inhibition of the control enzyme.
Tuberculosis Antimicrobial Acquisition and Coordinating Facil-
ity (TAACF) through a research and development contract with
the U.S. National Institute of Allergy and Infectious Diseases
(NIAID) of the NIH using Rv3602c, EC 6.3.2.1 (PanC).
The new analogues in series 3 exhibited activity ranging from
IC50 of 90 nM to 7.13 µM with the majority of ligands exhibiting
activity better than 250 nM. The increase in potency of the
ligands in series 3 compared to that of intermediates 7 and 8
suggests that the scaffolds of 7 and 8 alone are too small to
exhibit noticeable inhibition and additional substituents in the
pyrazole ring are required to improve activity. The best
activities, IC50 e 100 nM, are achieved for unsubstituted 3a
and naphthalene-substituted ligand 3e. Comparison of 3a with
the other compounds in this series suggests that (i) hydrophobic
substituents on the benzene ring lead to a slightly increased
potency, e.g., 3e (R ) naphthyl) and 1b (R ) 4-FC6H4) vs 3i
Acknowledgment. This research was supported by the
NIAID/NIH Grant R21 AI070997 and the Institute for Tuber-
culosis Research at the University of Illinois at Chicago. PS
inhibition assays were funded by the Division of Acquired
Immunodeficiency Syndrome of the NIAID/NIH. The financial
support for R.U. was provided by the Higher Education
Commission of Pakistan. The authors thank OpenEye Scientific
Software for providing academic license for the modeling
software. We also thank Dr. Alan P. Kozikowski for critical
suggestions.
Supporting Information Available: Representative experimen-
tal procedures, complete synthetic schemes, and 1H NMR, HRMS,
and HPLC data for all target compounds. This material is available
t
(R ) 4-(CO2 Bu)C6H4) and 3 h (R ) 4-(CO2H)C6H4), (ii)
differences in potency resulting from variation of the substitution
pattern on the phenyl ring are not larger than 5-fold. It is unclear
why a small R substituent in 1b (R ) 4-FC6H4) and a large
one in 3k (R ) 4-(CONH(CH2)2Ph)C6H4) result in practically
identical potencies even if their docking poses are very different,
reflecting the fact that 3k (as 3j) is too large to fit into the
binding site without parts of the compound protruding from the
protein. The fact that 3k and 3j exhibit excellent potency
suggests that induced fit effects may play an important role in
accommodating these compounds in the PS binding site.
Unlike modifications in the phenyl that were relatively
insensitive to the size and polarity of the substituents, additional
polar moiety in the linker connecting the pyrazole ring with
the phenyl ring of 3l or in the pyrazole ring of 3m led to a
680-fold decrease in activity of 3m compared to the activity of
3e and marginal inhibition of PS by 3l. The docking of both
ligands shows that the newly introduced moieties in 3l and 3m
are located in the gorge region of the binding site responsible
for accommodation of the phosphate group and sugar ring of
the reaction intermediate. This may indicate that this area is
very sensitive to the nonmatching interactions possibly intro-
duced in 3l and 3m or that the extra moieties have changed the
spatial arrangement of the key pharmacophore elements of the
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