Download Enoyl acyl carrier protein reductase inhibitors: a patent review (2006

Review
Enoyl acyl carrier protein
reductase inhibitors: a patent
review (2006 -- 2010)
Introduction
2.
Structure and function of ENR
3.
Specificity for substrate
binding of ENR
Expert Opin. Ther. Patents Downloaded from informahealthcare.com by University of Toronto on 06/24/11
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Xiaoyun Lu, Kun Huang & Qidong You†
1.
4.
Inhibitors of ENR
5.
Conclusions
6.
Expert opinion
†
China Pharmaceutical University, Department of Medicinal Chemistry, Nanjing, China
Introduction: Bacterial enoyl acyl carrier protein reductase (ENR) specificity
reduces the double bond in enoyl thioester substrates in the final enzymatic
step of the elongation cycle of the fatty acid synthase-II pathway. Its function is essential for bacterial organism survival, making it an attractive target
for the development of novel antibiotics. The structural features and therapeutic potential of this enzyme have stimulated the rational design of ENR
inhibitors, and important progress has been achieved to date.
Areas covered: This review describes recent advances made in the search for
ENR inhibitors, as reflected by patent applications filed from 2006 to 2010,
together with an overview of the relevant literature. The first section of this
paper provides a background of the biology of ENR, followed by a description
of its structure and function. The main section describes the substrate specificities for ENR, and the structure-based rational design of patent inhibitors
originating from different companies and academic groups.
Expert opinion: The increase in the number of ENR inhibitors bodes well for
the development of new therapeutics against multidrug-resistant bacteria.
The challenge is now to improve the pharmacokinetic parameters of these
inhibitors and translate them into clinical studies.
Keywords: antibacterial, enoyl ACP reductase (FabI or InhA), FAS, inhibitors, rational design,
substrate binding
Expert Opin. Ther. Patents (2011) 21(7):1007-1022
1.
Introduction
The emergence of bacterial resistance to most of the antibiotics currently in clinical
use becomes a worldwide concern [1]. In particular, methicillin-resistant Staphylococcus aureus (MRSA) [2], penicillin-resistant Streptococcus pneumoniae [3] and
multidrug-resistant tuberculosis (MDR-TB) [4] have become troublesome due
to the ineffectiveness of existing therapeutics. In the case of TB, the WHO estimates
that a third of the world’s population is infected with the latent form of Mycobacterium tuberculosis and that > 0.5 million people worldwide are infected with MDRTB [5]. Novel antibiotics are urgently required to overcome these resistances. As fatty
acid biosynthesis in pathogenic microorganisms is essential for cell viability, the
enzymes involved in the fatty acid biosynthesis pathway have recently attracted
considerable interest, a genomics-driven target for antibacterial drug discovery [6,7].
Fatty acid biosynthesis is conducted through the fatty acid synthase (FAS) system,
which is divided into two distinct forms. FAS-I is made of large multifunctional
enzymes that catalyze all of the reactions of fatty acid chain elongation and the
majority are identified in eukaryote organisms [8]. FAS-II is often identified among
most bacteria strains and the plastids of plants. It is a dissociated system wherein
each reaction of chain initiation and elongation is catalyzed by a unique protein [9,10]. The enzymatic reactions for chain initiation and one cycle of elongation
for a typical FAS-II have been well characterized in Escherichia coli (Figure 1) [11,12].
10.1517/13543776.2011.581227 © 2011 Informa UK, Ltd. ISSN 1354-3776
All rights reserved: reproduction in whole or in part not permitted
1007
Enoyl-ACP reductase inhibitors: a patent review (2006 -- 2010)
Article highlights.
.
.
.
.
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.
Enoyl acyl carrier protein reductase (ENR) remains an
attractive target for the development of novel antibiotics
in the future.
The specificity for substrate binding of ENR
is investigated.
A number of inhibitors of ENR reported from patents
and associated with literatures are described, including
diphenyl ethers, pyrrolidine carboxamides, aryl-eneamides and pyridones.
Diphenyl ethers possess broad spectrum antibacterial
and antiplasmodial activity.
The resolved co-crystal structures of ENR with diverse
inhibitors, especially for the conserved interactions with
the active site, play an important role for structurebased drug design of more potent inhibitors.
This box summarizes key points contained in the article.
The NADH-dependent enoyl acyl carrier protein reductase,
ENR (FabI or InhA), is a key enzyme in the last step of each
cycle of fatty acid elongation, which catalyzes the NADHdependent stereospecific reduction of a, b-unsaturated fatty
acids bound to the acyl carrier protein (ACP) [13-15]. The
essence of ENR for bacterial viability, together with the ideal
selectivity, suggests the ideal that ENR can be used as a particularly promising target for the development of novel antibiotics
against MDR strains. During recent years, numerous research
groups have engaged in developing new types of ENR
inhibitors. Many different types of ENR inhibitors have been
designed, some of which are in preclinical studies [16,17]. Below,
we briefly summarize our current knowledge on ENR and
focus on the patented inhibitors of ENR from 2006 to 2010.
2.
Structure and function of ENR
ENR is present in many important human pathogens, most of
them having multi-resistant E. coli (ecFabI) [18], M. tuberculosis (InhA) [15,19], S. aureus (saFabI) [20], Plasmodium falciparum
(pfENR) [21], Bacillus anthracis (baENR) [22], Francisella tularensis (ftuFabI) [23] and Toxoplasma gondii (TgENR) [24]. Some
organisms also contain other enoyl reductases (FabK [25],
FabL [26] and FabV [27,28]) for catalyzing the reduction reaction, such as Enterococcus faecalis, Pseudomonas aeruginose
and Burkholderia mallei. The structure and active site of
ENR from different species are similar, and we focus on the
ecFabI enzyme but describe InhA and others when they
provide substrate specificity.
Moreover, X-ray structure date of ENR homologues from
different microorganisms are available [15,18,29], which provide
a good starting point for the rational design of novel ENR
inhibitors. ENR are tetrameric a/b proteins with classic Rossmann fold structures that bind the nucleotide cofactor in similar regions of the monomer. A two-helix excursion from this
core structure creates a helical subdomain positioned over the
1008
C-terminal edge of the b-sheet, and there is a deep crevice in
the molecule between the subdomain and the core [9]. The
active site of ENR, the signature active site tyrosine and lysine
residues are situated within this cleft.
The general mechanism of the reduction of ENR has been
extensively studied that is similar for most bacterial strains, for
instance in E. coli as presented in Figure 2. FabI uses NADH
to reduce the C2-C3 carbon-carbon double bond generated
by the prior dehydratase enzymes to complete the synthesis
of the acyl chain. The reduction mechanism involves the
transfer of a hydride to the C3 carbon of the C2-C3 double
bond and the development of an enolate anion on the
C1 carbonyl oxygen, which accepts a proton from hydroxyl
of the tyrosine 156. The resulting enol then undergoes tautomerization to yield the final product. The key lysine 163 plays
the primary role to stabilize the binding of the cofactor
through hydrogen bond interactions with the hydroxyl groups
on the nicotinamide ribose. In InhA, the role of tyrosine
158 and lysine 165 in the catalytic mechanism is similar to
that of ecFabI [30].
3.
Specificity for substrate binding of ENR
ENR from different bacterial species show different substrate
specificities for the enoyl thioester substrates. For example,
ecFabI, saFabI, pfENR and baENR prefer C12-C16 shorter
chain substance, whereas InhA uses C16-C56 longer chain
substrates. The specificity is determined by a loop of the binding region, called the substrate-binding loop, which has been
shown to be flexible [31,32]. Superposition of the crystal structure of ecFabI with InhA demonstrates that there is a significant difference between these two enzymes with respect to
the location of their substrate-binding loops. In InhA, the
loop (residues 194 -- 220) creates a substance-binding crevice
(18 Å) with more depth than loop (residues 192 -- 209) of
ecFabI (10 Å). The intrinsic specificity observed in the
substrate-binding loop is consistent with the size and shape
of the conserved hydrophobic pocket adjacent to the active
site of ENR.
Triclosan (TCN) is known to inhibit the synthesis of fatty
acids in E. coli, S. aureus, M. tuberculosis and other bacteria,
targeting diverse ENR at the acyl substrate-binding pocket
(Figure 3A) [18]. Crystal structure of ecFabI-TCN complex
reveals phenol ring of TCN stacks p--p interaction with the
NAD + nicotinamide ring, while phenolic hydroxyl group
of TCN forms two hydrogen bonds with the active amino
acid Tyr156 and with the 2¢-hydroxyl group of the nicotinamide ribose of the nucleotide. However, in addition to the
ecFabI-TCN complex, another molecule of TCN binds to
the active site of InhA, which has never been observed in
any other ENR-TCN structure [33] (Figure 3B). Obviously,
the presence of two molecules of TCN in the active site of
InhA is attributed to its specificity substrate-binding loop.
These data suggest that the hydrophobic active site of InhA
is much more larger than that of ecFabI and other ENRs.
Expert Opin. Ther. Patents (2011) 21(7)
Lu, Huang & You
Recently, the authors’ research group also reviewed some
predominant examples of InhA direct inhibitors, which may
provide a solid foundation for discovery of new agents for
treatment of TB [34].
FabG
NADH
ENR (FabI and InhA)
FabK
R
R
n
H2O
n
O
FabA
FabZ
S
O
OH
NADP+
S
ACP
ACP
NAD+
NADPH
O
S
FabB
FabF
O
n
ACP
n
FabH
CoA
O
ACP
O
S
FabD
CoA
O
O
Figure 1. The process of type II FAS in Escherichia coli (R = CH3).
R
R
ACP
S
O
O
Diphenyl ethers
The broad spectrum antibacterial activity of TCN, combined
with its unique structural feature, has made it as starting point
for the design of diphenyl ethers with improved activity
against ENR from various species. Alkyl diphenyl ethers
have been designed by structure-based drug design strategies,
replacing chlorine atom on the phenol ring of TCN with various alkyl groups (2PP ~ 14PP), and assayed against InhA
(Figure 4) [35,36]. Tonge et al. have claimed a world patent of
the diphenyl ether derivatives as InhA inhibitors [35]. The analog 5-octyl-2-phenoxyphenol (8PP) showed the best activity
with Ki and IC50 values of 1.1 and 5 nM, respectively. As
the alkyl substituent is lengthened from two to eight carbons,
a corresponding decrease in IC50 values is observed. However,
14PP is much less potent than 8PP with an IC50 value of
150 nM for InhA. The X-ray crystallographic analysis indicated that the substrate-binding hydrophobic pocket is a
major site of interaction for side chains of the alkyl diphenyl
ethers binding to InhA (Figure 5).
Based on 6PP, Ende et al. reported a series of hexyl diaryl
ethers with pyridine ring or nitro-substituted phenyl ring,
and so on (Figure 4) [37]. However, the compounds were not
as good as the lead compounds with IC50 values of 48 nM
to > 100 µM. The SAR analysis of this kind of InhA inhibitor
suggested that the introduction of a bulky substituent at the
phenyl ring or the incorporation nitrogen atom into the
phenyl ring reduces anti-InhA activity.
Recently, Freundlich et al. also reported a series of
5-branched alkyl and aryl substituted TCN derivatives using
structure-based drug design approach (Figure 4) [38]. The
most efficacious inhibitor displayed an IC50 value of 21 nM,
which was 50-fold more potent than TCN. Among these,
the best inhibitor had a MIC value of 13 µM against
H37Rv, and more potent than isoniazid (INH) against two
INH-resistant M. tuberculosis strains. However, the novel
cyclic azole diphenyl ethers proposed by Kini et al. showed
good potency when tested in vitro against H37Rv with MIC
4.1
O
CoA
CoA
S
R
n
O
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Inhibitors of ENR
Considering ENR as a promising target for antibacterial therapy, many new chemical compounds that can selectively
inhibit ENR from different microorganisms, including
important human pathogens such as E. coli, M. tuberculosis
and P. falciparum, and B. anthracis, have been described. In
this section, different patented inhibitors of ENR are listed
and compared; the structure--activity relationships (SARs)
are also discussed. On the other hand, the determination of
the crystal structure of ENR from various species have aided
in the structure-based design of new potent inhibitors.
S
ACP
ACP
4.
Expert Opin. Ther. Patents (2011) 21(7)
1009
Enoyl-ACP reductase inhibitors: a patent review (2006 -- 2010)
S-ACP
O
H
H
R
Substrate
H
H2NOC
Tyr156
H
O
N
H
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NADH
O
O
H
O
O
O
P
N
Lys163
H
H
H
OH
O
O
O
R
H
H
Ser120
O
H
Figure 2. The catalytic reduction mechanism of ec FabI.
values of 2.4 ~ 3.7 µM [39]. It is worth noticing that Mutabilis
also discovered a series of aryloxy-phenol derivatives, some of
which had IC50 values within the nanomolar range against
ecFabI [40].
The studies support this fact that a bulky substituent at the
5 position of phenol ring of TCN could perfectly fit the active
site of an enzyme with a large volume in the cavity, which is
the case of InhA and ftuFabI. This is also consistent with
the fact that no inhibition is reported for the other ENRs
when these variants of TCN are assayed. The ecFabI, pfENR
and baENR are specific for the diphenyl ethers with small volume substituents, such as F, CHO, COOH and short alkyl
chains, and so on (compounds 1 -- 5, Figure 6) [22,23,41,42].
Aryl-ene-amides
GlaxoSmithKline reported a new series of indole-based
derivatives as saFabI and hiFabI inhibitors through highthroughput screening of 305,189 compound collection [43,44].
Preliminary lead compound optimization studies led to the
identification of compounds 6 and 7 (Figure 7) [45], which exhibited excellent in vitro and in vivo potency against S. aureus, while
with less potency against Haemophilus influenzae [46]. Interestingly, the naphthyridinone 7 also showed excellent activity
against E. coli in vitro. Co-crystal structures of both compounds
4.2
1010
bound to ecFabI-NAD+ have been solved (Figure 8). The amide
carbonyl of 7 is engaged in hydrogen bonding interactions with
the hydroxyl of Tyr156 and the 2¢-hydroxyl of the nicotinamide
ribose of the nucleotide. The indole portion occupies the hydrophobic pocket composed of residues Tyr146 and Phe203, and so
on. Furthermore, the pyridine nitrogen and the N-acylhydrogen
of the naphthyridinone are well positioned for hydrogen
bonding interactions with Ala95. The studies demonstrate that
they occupy the enoyl substrate-binding region and cause the
substrate-binding loop ordering, which is similar to that of
TCN bound to ecFabI.
On the basis of above results, a benzofuran analog of
the naphthyridinone (compound 8, Figure 7) was developed
by Affinium Pharmaceuticals [16]. As a result, compound 8
demonstrates potent in vitro activity against a set of clinical isolates of methicillin-susceptible S. aureus (MSSA),
MRSA, methicillin-susceptible Staphylococcus epidermidis and
methicillin-resistant S. epidermidis (MRSE). By introducing
basic functionalities at the naphthyridinone of the molecules,
the results achieved the development of pyridopyrimidinone 9
and naphthyridinone 10 without reduced potency [17,47].
To improve efficacy and desired physicochemical properties,
based on X-ray crystal structure design method, led to the
identification of spiro-naphthyridinone piperidine 11 [48,49]
Expert Opin. Ther. Patents (2011) 21(7)
Lu, Huang & You
A.
B.
Disordered loop
Ordered loop
TCN2
TCN1
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TCN
NAD+
NAD+
Figure 3. Structures of triclosan bound to the A) ec FabI (PDB code: 1QSG) and B) InhA (PDB code: 1P45). The substratebinding loop of ecFabI is ordered and the loop of InhA is disordered.
and pyridodiazepinone 12 [37,50-53], which were identified as
having submicromolar IC50 values against saFabI and ecFabI.
Affinium Pharmaceuticals have claimed patents of the arylene-amides as FabI inhibitors. Furthermore, the in vivo studies
suggested that pyridodiazepine 12 could be a good candidate
for clinical development as an anti-MRSA drug.
pyrrolidine carboxamide classes with good enzyme
inhibitory do not exhibit ideal activity against M. tuberculosis H37Rv with MIC above 125 µM. The results suggest that pyrrolidine carboxamides may exhibit poor
membrane permeability.
Pyridones
Screening programs developed by Kitagawa et al. have also
identified a lead compound 16 (Figure 11) bearing 4-pyridone
basic scaffold as ecFabI inhibitor. Structure optimization studies yielded a set of 4-pyridone derivatives with strong FabIinhibitory activity [55]. The most potent compound 17 showed
good activity against ecFabI and S. aureus with IC50 and MIC
values of 0.3 µM and 0.5 µg/ml, respectively. The preliminary
SAR has revealed that the 1,6-dichlorobenzyl moiety is favorable for both FabI-inhibitory and antibacterial activity. In
addition, the substituents at 1-position perform an important
role for the activity.
More interestingly, the same authors developed other
pyridone derivatives having a phenylimidazole moiety as
FabI and FabK dual inhibitors through iterative medicinal
chemistry and X-ray crystal structure-based design [56,57].
A representative compound 18 showed strong FabI
and FabK inhibitory with IC50 values of 0.38 and
0.0045 µM, respectively, and potent antibacterial activity
against S. pneumoniae with an MIC value of 0.5 µg/ml. These
studies support the point that ENR is probably a valid target
4.4
4.3
Pyrrolidine carboxamides
Pyrrolidine carboxamide 13 was discovered by He et al.
through high-throughput screening of a library of 30,000
compounds against InhA with an IC50 value of 10.05
µM [54]. Due to the importance of the ketopyrrolidine
core, compound 13 was further optimized by replacing
the phenyl ring A and cyclohexyl ring C with other groups
while keeping ketopyrrolidine core B invariable (Figure 9).
Compounds 14 and 15, with symmetric substitutes on the
phenyl ring A, show IC50 values of 0.39 and 0.14 µM
against InhA, respectively. In the crystal structure, the
oxygen of the carbonyl group of ketopyrrolidine is observed
to form hydrogen bonds with the hydroxyl group of
Tyr158 and with 2¢-hydroxyl of the nicotinamide ribose
(Figure 10). The hydrophobic interactions between the large
phenyl ring and the active site of InhA are essential for the
activity. Meanwhile, for compound 15, it is suspected that
hydroxyl group at the phenyl ring enhances the activity
by forming hydrogen bond with the protein and causes
a subtle change in the binding site. Unfortunately,
Expert Opin. Ther. Patents (2011) 21(7)
1011
1012
Expert Opin. Ther. Patents (2011) 21(7)
1
3
4
5
7
13
2000
80
17
11
5
150
IC50 (nM)
5
O
O
Hexyl diaryl ethers
IC50 = 48 nM ~ >100 mM
OH
Alkyl diphenyl ethers
US20060041025
n
OH
Y
Y = N, NH2,
NO2, etc
Cl
OH
O
Triclosan
O
Cl
Cl
Alkyl and aryl diphenyl ethers
IC50 = 21 nM ~ >10 mM
R1
OH
Cl
R2
R1 = Alkyl and Aryl
R2 = Cl and CN
Ar
O
Cyclic azole diphenyl Ethers
MIC = 2.4 – 3.7 mM
Cyclic
azole
Figure 4. The general structures of alkyl diphenyl ether InhA inhibitors. IC50 values are reported against InhA; MIC values are reported against H37Rv.
2PP
4PP
5PP
6PP
8PP
14PP
n
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Enoyl-ACP reductase inhibitors: a patent review (2006 -- 2010)
Lu, Huang & You
Met155
Tyr158
8PP
Leu218
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NAD
Pro193
Figure 5. Structure of 8PP bound to InhA in the presence of NAD+ (PDB code: 2B37).
OH
OH
OH
O
O
Cl
O
F
n
1
2
3
ecKi = 1.1 pM
FtuKi = 1.9 nM
BaIC50 = 0.5 nM
ecKi = 1.5 nM
FtuKi = 289 nM
n = 0 FtuKi = 1.9 nM n =1 FtuKi = 2.1 nM
n = 2 FtuKi = 0.44 nM BaIC50 > 0.8 µM
OH
Cl
OH
O
Cl
O
HOOC
Cl
OHC
Cl
4
5
ecKi = 1.3 µM ecIC50 = 2.25 µM
pfKi = 0.21 µM pfIC50 = 0.56 µM
ecKi = 1.0 µM ecIC50 = 1.83 µM
pfKi = 0.18 µM pfIC50 = 0.38 µM
Figure 6. The representative diphenyl ethers ecFabI, pfENR, baENR and ftuFabI inhibitors.
for the development of broad spectrum antibacterials. However, compound 18 did not show antibacterial activity against
S. aureus despite strong FabI inhibitory activity. It may be
suggested that the 4-pyridone structure with a long hydrophobic side chain was unfavorable for antibacterial activity due to
poor membrane permeability.
INH-NAD analogs
Isoniazid (INH) has been used in TB chemotherapy since its
discovery in 1952. As a pro-drug, INH requires activation
by KatG, a catalase-peroxidase enzyme oxidizing INH to an
acyl radical binding to position 4 of NAD to form an
4.5
active INH-NAD adduct (19, Figure 12) for binding to
InhA [58,59]. The crystal structure of InhA with 19 indicates
that the carbonyl oxygen of isonicotinic acyl group forms
two hydrogen bonds with hydrogens of the amide group of
nicotinamide and the 2¢-hydroxyl of nicotinamide ribose,
with the NAD part maintaining in NADH-binding site, not
in the substrate-binding site.
The disclosure of the mechanism of INH activation
brings a new dimension to design of novel inhibitors to
mimic INH-NAD adduct, which do not require activation
by KatG for combating MDR-TB. It was found that the
benzoylhydrazine-NAD adduct (20) formed via the reaction of
Expert Opin. Ther. Patents (2011) 21(7)
1013
Enoyl-ACP reductase inhibitors: a patent review (2006 -- 2010)
O
O
N
N
N
N
CH3
N
CH3
NH2
N
H
O
7 (WO2001026652)
saFabI IC50 = 0.13 µM
hi FabI IC50 = 0.39 µM
ec FabI IC50 = 0.07 µM
saMIC = 0.06 µg/ml
hi MIC = 16 µg/ml
ec MIC = 8 µg/ml
6
saFabI IC50 = 2.4 µM
hi FabI IC50 = 4.2 µM
sa MIC = 0.5 µg/ml
hi MIC > 64 µg/ml
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N
O
N
O
CH3
N
N
H
O
8
MSSA MIC90 = 0.015 µg/ml
MRSA MIC90 = 0.015 µg/ml
MSSE MIC90 = 0.06 µg/ml
MRSE MIC90 = 0.03 µg/ml
O
O
N
N
S
CH3
N
N
H
O
9 (WO2004052890)
saFabI IC50 = 0.026 µM
ecFabI IC50 = 0.007 µM
Figure 7. Aryl-ene-amide FabI inhibitors.
the activated benzoic acid hydrazide and NAD competes with
INH-NAD for binding to InhA. However, due to poor stability,
three major structures (open keto-amide, cyclized hemiamidal
and oxidized hemiamidal) rather than INH-NAD adducts
exist under biomimetic conditions [60], demonstrating as being
unable to inhibit InhA. Given the above reasons, Pankiewicz
and co-workers redesigned the INH-NAD adduct at position
4 with 4-phenoxy instead of isonicotinoyl residue, affording
phenoxy-NAD (21) [61]. Given the glycosidic bond instability
of INH-NAD adduct, they also replaced the nitrogen of nicotinamide ring with carbon to provide phenoxy-BAD (22) with an
IC50 value of 27 µM against InhA.
Recently, because of the easily cleavage and poor
membrane permeability of diphosphate-linked molecule,
1014
Bernadou and co-workers have developed the truncated
INH-NAD adduct (23) (lacking the ADP moiety) [62].
However, it was indicated that the InhA affinity for the
truncated adducts was lost. To overcome this loss, the
new truncated adducts bearing a lipophilic fragment as
new bi-substrate-type InhA inhibitors were designed based
on mimicking the enoyl substrate and the NADH cofactor [63]. A patent application was filed by Bernadou et al.
[64]. Among them, compound 24 (Figure 12) was shown
to inhibit InhA activity by 41% for only 5 min incubation,
much potent than the truncated adduct 23. The work suggests that the addition of a lipophilic residue is valuable for
the effect on InhA activity and that the alkyl chain makes a
better interaction with the substrate-binding site of InhA.
Expert Opin. Ther. Patents (2011) 21(7)
Lu, Huang & You
O
O
N
N
N
H
CH3
N
N
N
H
O
10 (WO2004052890)
MSSA MIC90 = 0.5 µg/ml
MRSA MIC90 = 0.5 µg/ml
O
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NH
N
O
CH3
N
N
H
O
11 (WO2007067416)
saFabI IC50 = 0.049 µM
ecFabI IC50 = 0.0007 µM
O
NH
N
N
CH3
N
N
H
O
12 (WO2008009122)
saFabI IC50 = 0.13 µM
ecFabI IC50 = 0.33 µM
sa MIC = 0.125 µg/ml
ec MIC = 1 µg/ml
MRSA MIC = 0.125 µg/ml
Figure 7. Aryl-ene-amide FabI inhibitors (continued).
Others
Other classes of ENR inhibitors that have been discovered
include compounds that incorporate rhodamine 25 [21,65,66]
and thiopyridine 27 [67,68] moieties (Figure 13). Rhodamine 25
was designed against pfENR with IC50 value of 0.035 µM
using a combined approach of rational selection, docking
studies, screening and analog search. CG400549 26, developed by CrystalGenomics [65], was highly efficacious against
both MRSA and MSSA, including MDR strains. In all, compounds 25 and 26 bear interesting structural similarities to the
diphenyl ether class.
4.6
5.
Conclusions
aryl-ene-amides, pyridones and INH-NAD analogs, have
been developed in the last few years. The results achieved in
the design of new ENR inhibitors show that, despite differences
in the structure and substrate-binding specificity of ENR
among different species, one compound can inhibit ENR
from different microorganism. Moreover, availability of cocrystal structure ENR with diverse inhibitors, along with the
combination of high-throughput screening and rational drug
design methodology, will undoubtedly aid in the future discovery and development of more and more new ENR inhibitors
that can serve as effective therapeutics against MDR bacteria.
6.
As discussed in this review, many new platforms of ENR
inhibitors, such as diphenyl ethers, pyrrolidine carboxamides,
Expert opinion
Due to the increasing drug resistance in pathogenic
bacteria, there is a critical need for novel broad spectrum
Expert Opin. Ther. Patents (2011) 21(7)
1015
Enoyl-ACP reductase inhibitors: a patent review (2006 -- 2010)
Ala95
Tyr156
Tyr146
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NAD
Compound 7
Phe203
Figure 8. Structure of compound 7 bound to ecFabI in the presence of NAD+ (PDB code: 1FMP).
Cl
H
N
O
O
A
H
N
B
N
N
O
O
C
13
IC50 = 10.05 µM
Cl
14
IC50 = 0.39 µM
O
H
N
OH
N
O
15
IC50 = 0.14 µM
Figure 9. Pyrrolidine carboxamide InhA inhibitors.
agents against bacterial pathogens such as MRSA, MRSE
and MDR-TB. The ENRs are widely expressed with four
isoforms known in bacteria, such as FabI, FabK, FabL
and FabV, and have the highly conserved active site, thus
providing an effective drug target for antimicrobial
1016
development. Moreover, the lack of obvious homologues
for ENR in mammals suggests it might be a good target
for the development of selective antimicrobials.
Several predominant patents of new ENR inhibitors are
described, as well as the role of the 3D-structures of ENR
Expert Opin. Ther. Patents (2011) 21(7)
Lu, Huang & You
Met155
Tyr158
Phe97
Met103
Compound 14
NAD
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IIe215
Figure 10. Structure of compound 14 bound to InhA in the presence of NAD+ (PDB code: 2H7M).
Cl
O
Cl
O
Cl
CF3
N
Cl
N
S
16
17
ecFabI IC50 = 0.3 uM
saMIC = 0.5 ug/ml
ecFabI IC50 = 1.9 µM
saMIC = 64 µg/ml
O
N
O
N
H
N
MeO2S
S
N
H
Cl
N
H
Cl
N
18
ecFabI IC50 = 0.38 µM
spFabK IC50 = 0.0045 µM
sa MIC > 32 µg/ml
sp MIC = 0.5 µg/ml
Figure 11. Pyridone FabI and FabK inhibitors.
Expert Opin. Ther. Patents (2011) 21(7)
1017
Enoyl-ACP reductase inhibitors: a patent review (2006 -- 2010)
N
O
O
O
NH2
HO
OH
O
O
P
P
O
N
Expert Opin. Ther. Patents Downloaded from informahealthcare.com by University of Toronto on 06/24/11
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O
O
N
N
N
O
OH
NH2
O
O
N
OH
HO
N
ADPR
OH
19
INH-NAD adduct
NH2
20
BH-NAD
N
O
O
(CH2)11CH3
O
O
O
OH
NH2
NH
NH2
HO
N
O
O
X
ADPR
21 Phenoxy-NAD (X = N)
22 Phenoxy-BAD (X = C)
HO
OH
23
Truncated adduct
N
24 (WO2009101345)
Lipophilic truncated adduct
Figure 12. INH-NAD analog InhA inhibitors.
from different species in drug design process. Interestingly, it
was found that all of substrate-binding ENR inhibitors had
conserved interactions with the active site, hydrogen bonds
network with the active residue Tyr and the 2-hydroxyl group
of the nicotinamide ribose of the nucleotide and p--p stacking
interaction with the NAD+ nicotinamide ring. However,
deeper investigation concentrated on the binding modes of
InhA inhibitors would be found that enhancing the hydrophobic interaction of inhibitors with protein was very favorable for the activity. Other breakthrough is compounds that
directly inhibit InhA avoiding activation by KatG would
be promising candidates for combating MDR-TB. A further task facing medicinal chemists would be the use of
structure-based drug design that takes advantage of recently
available target structural and inhibitors SAR information.
Our group has developed two types of 3D-QSAR models of
1018
InhA inhibitors based on X-ray crystallography and pharmacophore models [69,70]. We expect to see continued interest
in developing InhA inhibitors for the treatment of MDRTB and, more importantly, for the treatment of extensively
drug-resistant TB.
More importantly, no clinical data for these patented
compounds were reported until now. Attention must always
be paid to clinical development. Some ENR inhibitors that
are described in this review exhibit good affinity of ENR,
but show poor antibacterial activity. Further efforts will
be focused on improving membrane permeability and
bioavailability of the inhibitors.
It is also important to note that other steps in the
FAS-II pathway are candidates for drug development. In particular, the b-ketoacyl-ACP synthase III (FabH) is essential
for organism survival and specific to bacterial. The rapid
Expert Opin. Ther. Patents (2011) 21(7)
Lu, Huang & You
O
O
NH2
O
N
N
S
S
O
S
Expert Opin. Ther. Patents Downloaded from informahealthcare.com by University of Toronto on 06/24/11
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25 (US20080051445)
(EP1834642)
pf FabI IC50 = 0.035 µM
26 CG400549
(WO2007043835)
MRSA MIC90 = 0.5 µg/ml
MSSA MIC90 = 0.5 µg/ml
S
CN
N
S
S
COOH
27 (WO2004064837)
ecFabI IC50 = 4 µM
saMIC = 2 µg/ml
Figure 13. Other classes of ENR inhibitors.
progress in physiology, pharmacology, biochemistry, genomics and proteomics will significantly expedite the investigation of mechanisms in FAS-II homologues in pathogens and
the development of synergistic chemotherapeutic regimes
targeting multiple points in the biosynthesis of fatty acids.
Declaration of interest
The authors state no conflict of interest. This work was
supported by Innovation Program for the Postgraduates in
China Pharmaceutical University, PR China.
Expert Opin. Ther. Patents (2011) 21(7)
1019
Enoyl-ACP reductase inhibitors: a patent review (2006 -- 2010)
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Expert Opin. Ther. Patents (2011) 21(7)
Affiliation
Xiaoyun Lu1,2, Kun Huang1 & Qidong You†1
†
Author for correspondence
1
Guangzhou Institutes of
Biomedicine and Health,
Key Laboratory of Regenerative
Biology and Institute of Chemical Biology,
Chinese Academy of Sciences,
No. 190, Kaiyuan Avenue,
Science Park, Guangzhou,
510530, China
2
China Pharmaceutical University,
Department of Medicinal Chemistry,
24 Tongjiaxiang,
Nanjing 210009, China
E-mail: [email protected]