Characterization of clioquinol and analogues as novel inhibitors of methionine
aminopeptidases from Mycobacterium tuberculosis
Omonike Olaleyea,b,*, Tirumalai R. Raghunandd,f, Shridhar Bhata, Curtis Chonga,g, Peihua Gue,
Jiangbing Zhoue, Ying Zhange, William R. Bishaid, Jun O. Liua,c,**
aDepartment of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
bDepartment of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
cDepartment of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
dCenter for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
eDepartment of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
Mycobacterium tuberculosis (Mtb)
Methionine aminopeptidase (MetAP)
s u m m a r y
Mycobacterium tuberculosis, the causative agent of tuberculosis claims about five thousand lives daily
world-wide, while one-third of the world is infected with dormant tuberculosis. The increased emer-
gence of multi- and extensively drug-resistant strains of M. tuberculosis (Mtb) has heightened the need
for novel antimycobacterial agents. Here, we report the discovery of 7-bromo-5-chloroquinolin-8-ol
(CLBQ14)-a congener of clioquinol (CQ) as a potent and selective inhibitor of two methionine amino-
peptidases (MetAP) from M. tuberculosis: MtMetAP1a and MtMetAP1c. MetAP is a metalloprotease that
removes the N-terminal methionine during protein synthesis. N-terminal methionine excision (NME) is
a universally conserved process required for the post-translational modification of a significant part of
the proteome. The essential role of MetAP in microbes makes it a promising target for the development
of new therapeutics. Using a target-based approach in a high-throughput screen, we identified CLBQ14 as
a novel MtMetAP inhibitor with higher specificity for both MtMetAP1s relative to their human coun-
terparts. We also found that CLBQ14 is potent against replicating and aged non-growing Mtb at low micro
molar concentrations. Furthermore, we observed that the antimycobacterial activity of this pharmaco-
phore correlates well with in vitro enzymatic inhibitory activity. Together, these results revealed a new
mode of action of clioquinol and its congeners and validated the therapeutic potential of this pharma-
cophore for TB chemotherapy.
Published by Elsevier Ltd.
The lethal synergy of Mycobacterium tuberculosis (Mtb) with
Human Immunodeficiency Virus (HIV) has heightened the need for
the development of new antimycobacterials. Particularly, the
therapeutic management of HIV patients co-infected with Mtb
poses great challenges because of drugedrug interactions and
toxicity.1Moreover, the rise of multi- and extensively drug-
resistant strains of (Mtb) as well as dormant tuberculosis (TB)
calls for novel anti-tuberculosis agents with new mechanisms of
action.2In an attempt to identify novel inhibitors of TB and validate
new targets, we have focused on methionine aminopeptidases
(MetAP) that have been shown to be required for the viability of
some organisms3e5including Mtb.18
MetAP is a metalloprotease that removes the N-terminal
methionine from proteins and peptides.3NME is an essential
process in both prokaryotes and eukaryotes.4,5This universally
conserved process is important for localization, stability and post-
translational modifications of a significant number of proteins.4In
prokaryotes, protein synthesis is initiated by formyl-methionyl-
tRNA. The formyl group is removed by peptide deformylase
(PDF), a prerequisite step for the action of MetAP.4In the past,
drug discovery efforts have focused significantly on PDF. However,
resistant mutants appear to limit the use of the PDF inhibitors,
especially because the mutations in transformylase gene renders
* Corresponding author. Present address: College of Pharmacy and Health
Sciences, Texas Southern University, Houston, TX 77004, USA. Tel.: þ1713 313 1883;
fax: þ1 713 313 4219.
** Corresponding author. Department of Pharmacology and Molecular Sciences,
Johns Hopkins School of Medicine, Baltimore, MD 21205, USA. Tel.: þ1 410 955
4619; fax: þ1 410 955 4620.
E-mail addresses: email@example.com (O. Olaleye), firstname.lastname@example.org (J.O. Liu).
fPresent address: Center for Cellular and Molecular Biology, Hyderabad, India.
gPresent address: Dana Farber Cancer Institute, Harvard Medical School, Boston,
MA 02215-5450, USA.
Contents lists available at SciVerse ScienceDirect
journal homepage: http://intl.elsevierhealth.com/journals/tube
1472-9792/$ e see front matter Published by Elsevier Ltd.
Tuberculosis 91 (2011) S61eS65
deformylation non- essential.6Recent attention has been turned
to MetAPs as antibacterial targets,2,4,5as it has been shown that
deletion of MetAP from Escherichia coli, and Salmonella typhimu-
eukaryotes.3e5Inhibitors of MetAP enzymes have been developed
as potential therapeutic agents for treating diseases such as
cancer, rheumatoid arthritis, as well as malarial and fungal
More recently, using a chemical genomics approach we
successfully identified and characterized inhibitors of the two
MtMetAPs from Mtb: MtMetAP1a and MtMetAP1c.18Other groups
have also characterized these mycobacterial enzymes and their
revealed the potential usefulness of these enzymes as anti-
mycobacterial targets.18e25Particularly, one study suggests that
both MetAPs from Mtb might play different roles at different
growth phases in the excision of N-terminal methionine from
There are two classes of MetAPs: MetAP1 and MetAP2.3
Eukaryotes possess both classes while prokaryotes have homo-
logs of either MetAP1 (eubacteria) or MetAP2 (archeabacteria).
M. tuberculosis possesses two MetAPs as mentioned above:
MtMetAP1a and MtMetAP1c which share 33% sequence iden-
tity.18,23,24Both MtMetAPs have less than 48% similarity to human
MetAP1 (hMetAP1) and less than 30% similarity to human MetAP2
(hMetAP2).24Moreover, the X-ray crystallography of MtMetAP1c
revealed the existence of a highly conserved proline rich N-
terminal extensionwhich is absent in MtMetAP1a.24A recent study
showed the indispensability of this N-terminal extension in Mtb.25
We could take advantage of the differences in enzyme structure to
design selective inhibitors. Hence, selectively targeting the myco-
bacterial MetAPs may be a viable strategy for the development of
new and effective antimycobacterial agents.
Herein, we report the discovery of clioquinol (CQ) and its
analogues as novel inhibitors of MtMetAP enzymes which accounts
for their inhibition of Mtb growth. Clioquinol’s anti-TB activity has
been previously reported42,43; however the mechanism of action
was unknown. Weunexpectedly
chloroquinolin-8-ol (CLBQ14), the bromine analogue of CQ in
a high-throughput screen for inhibitors of MtMetAP1c. CQ is
a derivative of 8-hydroxyquinoline that was used to treat infec-
tions.26,27However, it was withdrawn from the clinic because of
untoward effects of subacute myelo-optic neuropathy (SMON)
experienced in Japan in the 1950’s.28e30More recently, CQ and its
derivatives are being studied as therapeutics for neurodegenerative
diseases, cancer, and infectious diseases.31e40As mentioned above,
this pharmacophore has been identified by other groups in drug
screens and activity assays for drug sensitive, drug resistant and
dormant M. tuberculosis.41e43However, its mode of action has
remained elusive. In this study, we assessed the effect of CLBQ14,
CQ and two additional analogues on the activity of both MtMetAPs.
We also determined the specificity of the CLBQ14 and CQ for the
mycobacterial enzymes in comparison to the human isoforms of
MetAP. Furthermore, we determined the activityof the inhibitors in
Mtb. The results suggest that CLBQ14 is a new potent and selective
inhibitor of the MetAPs from Mtb.
2. Materials and methods
The M. tuberculosis culture medium, Middlebrook 7H9, was
purchased from Becton Dickinson (Sparks, MD). The compounds
were provided by ASDI (Newark, DE). We prepared all stock solu-
tions in Dimethylsulfoxide (DMSO).
2.2. High-throughput screening
In a high-throughput screening assay as described previously,18
we identified 7-bromo-5-chloroquinolin-8-ol. Briefly, we screened
about 175,000 compounds against MtMetAP1c at concentrations of
30 mM in 384-well plates, using the chromogenic substrate Met-
Pro-pNA.45The compounds were dissolved in DMSO. The initial
screen was conducted using a titertek instrument (Titertek
Instruments, Inc., Alabama, USA) with liquid handling capabilities
coupled to a spectrophotometer. The total reaction volume was
50 mL and each reaction contained 40 mM Hepes buffer (pH 7.5),
100 mM NaCl, 100 mg/mL BSA, 0.1 U/mL ProAP, 1.5 mM CoCl2,
600 mM substrate (Met-Pro-pNA), and 252 nM MtMetAP1c. The
enzyme was pre-incubated with compounds for 20 min at room
temperaturefollowed byaddition of 600mM substrate. The reaction
was incubated at room temperature for 30 min and monitored at
405 nm on a spectrophotometer. The Compounds that showed
greater than 30e40% inhibition were chosen as “hits”.
2.3. Determination of IC50of 7-bromo-5-chloroquinolin-8-ol
(CLBQ14) and its analogues
We obtained CQ and two additional analogues and determined
the concentration needed for 50% enzyme inhibition in 96-well
plates at final concentrations ranging from 100 mM to 300 nM.
The total reaction volume as described18was 50 mL and each
reaction contained each MetAP1 respectively and 40 mM Hepes
buffer (p.H 7.5), 100 mM NaCl, 100 mg/mL BSA, 0.1 U/mL BcProAP,
1.5 mM CoCl2, 600 mM substrate (Met-Pro-pNA). The enzyme was
pre-incubated with compounds for 20 min at room temperature
followed by addition of substrate. The reaction was incubated at
room temperature for 30 min and monitored at 405 nm on
a spectrophotometer. The background hydrolysis was subtracted
and the data was fitted to a four-parameter logistic (variable slope)
equation using GraphPad prism software.
2.4. Determination of minimum inhibitory concentration in
replicating M. tuberculosis
The MetAP inhibitors were serially diluted in DMSO and added
to 7H9 broth and OADC (without Tween 80) to give final
concentrations of 50, to 0.05 mg/mL. A culture of M. tuberculosis
H37Rv was grown till O.D. ¼ 1.0, and diluted to 1/100. Then each
tube containing a compound was inoculated with 0.1 mL of culture
to give a total assay volume of 5 mL. The controls were DMSO,
Isoniazid (a positive control) and a blank (drug free media). The
15-ml conical assay tubes containing mycobacteria were incubated
at 37?C and 5% CO2. M .tuberculosis growth was monitored for two
2.5. Activity of inhibitors on aged non-growing M. tuberculosis
We determined the activity of 7-bromo-5-chloroquinolin-8-ol
in aged non-growing M. tuberculosis at concentrations ranging
from 0.5 to 100 mM for three weeks using a persister model as
described.44Briefly, a 2 month old M. tuberculosis H37Ra culture
grown in 7H9 medium (Difco) with 10% albumin-dextrose-catalase
(ADC) and 0.05% Tween 80 was resuspended in acid 7H9 medium
(pH5.5) without ADC. The bacterial cell suspension was used as
inocula for assaying the activity of the compounds for persister
bacilli. The inhibitor was diluted from the stock solution (10 mM in
DMSO) to 10 mM (final) followed by incubation with the bacilli in
200 ml in acid pH5.57H9 mediumwithout ADC in 96-well plates for
3 days without shaking under 1% oxygen in a hypoxic chamber. The
assay was done in duplicate. Rifampin (5 mg/ml) was used as
O. Olaleye et al. / Tuberculosis 91 (2011) S61eS65
a positive control. After 3 day drug exposure, the viability of the
bacilli was determined by adding 20 ml of 1 mg/ml XTT (2,3-bis-(2-
and incubated at 37?C up to 7 days when the plates were read at
3.1. Effects of 7-bromo-5-chloroquinolin-8-ol (CLBQ14) and its
analogues on MetAP activity
In our high-throughput screening efforts to identify inhibitors
of MetAPs from M. tuberculosis, we discovered CLBQ14, a deriva-
tive of clioquinol, as a hit. Clioquinol is a compound in the
hydroxyquinoline class that was used to treat some infections in
the past26,27and is now under evaluation for the treatment of
Alzheimer’s disease, cancer and other disorders.31e40We deter-
mined the effects of CLBQ14, CQ and two additional analogues on
MtMetAPs. We found that all four compounds inhibited both
MtMetAPs with IC50values in the low micro molar concentration,
with CLBQ14 being the most potent and CQ being the least potent
amongst the analogues tested (Table 1). In addition, all four
inhibitors displayed little or insignificant specificity for either
MtMetAP1a or MtMetAP1c. These results revealed a new mode of
action for CQ. More importantly, this is the first report indicating
that MetAP is a target of clioquinol and its analogues. All three
analogues, CLBQ14-1, CLBQ14-2 and CLBQ14 are more potent
than CQ, with IC50 values ranging from 3.76 mM to 5.44 mM
3.2. Selectivity of CLBQ14 and CQ for M. tuberculosis MetAPs over
Next, we determined the selectivity of CLBQ14 and CQ for
MtMetAPs over the human MetAPs (HsMetAP1 and HsMetAP2).
Both CLBQ14 and CQ were specific for the mycobacterial enzymes
compared to the human MetAPs (Table 1). Of the two, CLBQ14
exhibited greater than 19 folds selectivity for both MtMetAPs over
human MetAPs (Table 1). CQ showed less than 10 folds selectivity
for the mycobacterial enzymes relative to their human counter-
parts (Table 1). The selectivity of both CLBQ14 and CQ for MtMetAPs
over their human counterparts raised the possibility to selectively
target the mycobacterial enzymes with a sufficiently wide thera-
peutic window with new analogues.
3.3. Effects of MtMetAP1 inhibitors on M. tuberculosis growth
We determined the Minimum Inhibitory Concentrations (M.I.C.)
of CLBQ14 and CQ in M. tuberculosis (Table 2). In the replicating
M. tuberculosis culture, CLBQ was more potent than CQ with a two-
in Mtb is in agreement with their relative activity against the two
MtMetAP enzymes in vitro. Moreover, we observed an increase in
potency in the aged non-growing M. tuberculosis for CLBQ14 with
concentration that killed the viable bacilli and prevented redox dye
XTT color development at 0.65e1.62 mg/mL (Table 2). These results
suggest that CLBQ14 and CQ might be promising leads for TB ther-
of the effects of the 8-hydroxyquinolines in M. tuberculosis.41e43
Effects of 7-bromo-5-chloroquinolin-8-ol (CLBQ14) and its analogues on MetAP enzyme activity.
Inhibitor ID Chemical structure IC50(mM)
4.30 3.76ND ND
5.44 4.92 105.29112.20
N.D., not determined.
O. Olaleye et al. / Tuberculosis 91 (2011) S61eS65
The availability of pure, active and well-characterized MtMe-
tAP1a and MtMetAP1c enabled us to identify novel inhibitors of
MetAP from M. tuberculosis using a high-throughput screening
approach. We screened a structurallydiversesmall molecule library
of over 175,000 compounds and identified CLBQ14, a structural
relative of CQ as a potent and selective inhibitor of MtMetAP1a and
MtMetAP1c. We have been able to characterize the effect of CLBQ14
and three of its analogues on both bacterial and human MetAPs.
CLBQ14 displayed higher specificity for the mycobacterial MetAPs
than their human counterparts (Table 1). More importantly, we
found that these class of compounds were active as inhibitors of
M. tuberculosis (Table 2). CLBQ14 showed potent activity in aged
non-growing M. tuberculosis (Table 2), validating the potential of
this pharmacophore as a therapeutic agent for TB chemotherapy.
Despite the reported adverse effects of clioquinol,28e30this
pharmacophore has attracted much attention recently in studies
aimed at discovering novel therapeutics for neurodegenerative
diseases, cancer, and other disorders.31e40More recently, this class
of compounds were also identified in drug screens for drug sensi-
tive, drug resistant and dormant M. tuberculosis by other
reports.41e43However, their exact mode of action was unknown.
Our results show that the clioquinol pharmacophore has activity
against a novel target in mycobacterial: MtMetAPs. Moreover, we
observed that the bromine analogue of clioquinol-CLBQ14 is
slightly more potent and highly specific for the two mycobacterial
MetAPs relative to the two human MetAPs (Table 1). Particularly,
this selectivity suggests that CLBQ14 might not have the same
adverse effects experienced with CQ in the past,28e30potentially
alleviating some of the concerns with CQ.
We recently reported the identification of the 2,3-dichloro-1,4-
naphthoquinone pharmacophore as potent inhibitors of the two
MetAPs from Mtb.18Like the 2,3-dichloro-1,4-naphthoquinones,
the 8-hydroxyquinolines have been used to treat bacterial infec-
tions in the past. Similarly, we observed correlations from our
in vitro MetAP assay with the Mtb activity. However, unlike the 2,3-
dichloro-1,4-naphthoquiones, the hydroxyquinolines show signif-
icantly high specificity for the mycobacterial enzymes compared to
the human MetAP isoforms. These results suggest that the
hydroxyquinolines could be further optimized for MtMetAP1
inhibition and anti-tuberculosis effects. Moreover, this report
suggests that CLBQ14 shows more promise with selective toxicity.
In comparison to the 2,3-dichloro-1,4-naphthoquinones, the
CLBQ14 structural class is more active against both replicating and
aged non-growing Mtb. The observation that our in vitro enzymatic
studies translate and correlate proportionally to the activity in
replicating Mtb (Table 2) suggest that MtMetAPs are likely to be
relevant targets of both CQ and CLBQ in vivo. Furthermore, it is
important to note that the M.I.C. values from replicating
M. tuberculosis correlated well with that of dormant tuberculosis
for the 2,3-dichloro-1,4-naphthoquinones which we have validated
genetically.18Similarly, the increase in potency of CLBQ14 shows
promise for use of this novel mode of action for therapeutic treat-
ment of dormant TB (Table 2). Our identification of a new mode of
action for CQ and discovery of CLBQ as a potent and selective
MtMetAP1 inhibitor makes this pharmacophore and target
a promising combination for further optimization.
Although there have been recent reports on the identification of
MetAP inhibitors from Mtb,18,19,21this is the first report to show
a potent and selective inhibitor with potent antimycobacterial
activity in Mtb as well as dormant Mtb. Moreover, these inhibitors
could be used as tools in the future to understand the physiologic
role of MetAP in NME, an essential process in all organisms. Further
SAR and crystal structure studies will aid the rational design and
synthesis of morepotentinhibitors. Because MetAP is a novel target
and its activity is a requirement for N-terminal processing of some
proteins, its inhibitors have the potential to treat dormant TB, and
limit the development of MDR-TB and XDR-TB. In addition, potent
and selective MtMetAP inhibitors have the prospects of shortening
the duration of TB therapy if evaluated in conjunction with current
treatment options as well as reduce the drug to drug interactions
presently encountered by TB-HIV co-infected patients.
This paper was published as part of the Special Topic issue from
the TB symposium on the Emerging Directions of TB Research,
sponsored by University of Texas Medical Branch, Galveston, TX.
We thank Drs. Xiaochen Chen, Xiaoyi Hu, Keechung Han and
Norman Morrison for helpful discussions. We thank ASDI Inc. for
the provision of the chemical compounds.
AI37856, AI43846, and AI30036. O.O was supported by the
UNCF*Merck Graduate Science Research Dissertation Fellowship
and National Aeronautics Space Administration (NASA)-Harriett
Jenkins Pre-doctoral Fellowship.
This work was supported in part by NIH AI36973,
There are no conflicts of interest.
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