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Cell-Based Medicinal Chemistry Optimization of High-Throughput

Screening (HTS) Hits for Orally Active Antimalarials. Part 1:
Challenges in Potency and Absorption, Distribution, Metabolism,
Excretion/Pharmacokinetics (ADME/PK)
Miniperspectives Series on Phenotypic Screening for Antiinfective Targets
Arnab K. Chatterjee*
Calibr, 11119 North Torrey Pines Road, Suite 100, San Diego, California 92037, United States
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ABSTRACT: Malaria represents a significant health issue, and

novel and effective drugs are needed to address parasite
Publication Date (Web): September 13, 2013 | doi: 10.1021/jm400314m

resistance that has emerged to the current drug arsenal.

Antimalarial drug discovery has historically benefited from a
whole-cell (phenotypic) screening approach to identify lead
molecules. This approach has been utilized by several groups
to optimize weakly active antimalarial pharmacophores, such as
the quinolone scaffold, to yield potent and highly efficacious
compounds that are now poised to enter clinical trials. More
recently, GNF/Novartis, GSK, and others have employed the
same approach in high-throughput screening (HTS) of large
compound libraries to find novel scaffolds that have also been
optimized to clinical candidates by GNF/Novartis. This
perspective outlines some of the inherent challenges in cell-based medicinal chemistry optimization, including optimization of
oral exposure and hERG activity.

After thousands of years, malaria is still one of the major
Atovaquone 1 (Figure 1) is an important napthoquinone
infectious diseases, affecting millions of people, especially those antimalarial drug that is used in combination therapy with the
in underdeveloped countries.1 In the absence of effective dihydrofolate reductase inhibitor proguanil (Malarone, GSK).
antimalarial vaccines,2 low molecular weight antimalarial drugs After atovaquone was discovered in the early 1990s, it was
are important treatments against the disease. Quinine, found to be a potent inhibitor of the mitochondrial electron
chloroquine, mefloquine, and artemisinin derivatives have transport chain via inhibition of the cytochrome bc1 complex.
Atovaquone is a ubiquinone competitive inhibitor of bc1 and
played an important role in the fight against malaria. However,
serves as an excellent lead that has been investigated by several
widespread drug resistance has made these drugs less effective,
groups. The majority of the optimization of pyridone and
with artemisinin derivatives being the only exception. quinolone-based compounds has been carried out based on
Artemisinin-based combination therapies (ACT) recommen- phenotypic cell-based chemical optimization, with these starting
ded by the WHO will likely delay the emergence of clinical points having deep roots in the literature as phenotypic hits.
resistance against artemisinins, but reports of increased parasite For example, endochin (2),5−7 3 (ICI-56,780),8,9 and clopidol
clearance times have emerged recently.3 Therefore, it is (4)10 were discovered as having antimalarial activity several
important to discover antimalarials with novel mechanisms of decades ago (Figure 1). For example, 3 was shown to have
action that are effective against multidrug resistant parasite activity against blood- and liver-stage infections (including
strains. Several historical pharmacophores (including quino- dormant liver hypnozoites) by Ryley and Peters in the early
lones) have recently been optimized to provide potent 1970s.8 All these compounds have significant drawbacks
compounds. Additionally, scaffolds from recent large-scale including high resistance frequencies, poor physiochemical
HTS campaigns have been utilized to generate several novel
antimalarial pharmacophores from GNF/Novartis and others.4 Special Issue: Miniperspectives Series on Phenotypic Screening for
This miniperspective outlines the optimization of these Antiinfective Targets
pharmacophores, highlighting the challenges and opportunities Received: March 1, 2013
faced in cell-based optimization. Published: August 8, 2013

© 2013 American Chemical Society 7741 | J. Med. Chem. 2013, 56, 7741−7749
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Figure 1. Quinone and pyridone antimalarials.

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Figure 2. Early optimization of endochin.

Publication Date (Web): September 13, 2013 | doi: 10.1021/jm400314m

properties, and low in vivo potency. Recent work from multiple

groups has focused on making very potent hybrid compounds
of atovaquone, clopidol, endochin, and 3 to address these
shortcomings and is discussed further in this miniperspective.
Interestingly, much of the medicinal chemistry optimization has
been based on whole cell screening data. So while biochemical
assays and in silico molecular modeling have been applied in
some of this work, most of the compounds reported have been Figure 3. Optimization of quinolones.
optimized based on whole-cell potency while minimizing their
toxicity to normal cells. For example, Riscoe and co-workers EC50 against Plasmodium. falciparum of 26 nM and was
have demonstrated excellent optimization results in a series of equipotent against the atovaquone-resistant strain TM90-C2B,
quinolones derived from endochin 2. Figure 2 outlines some of with an EC50 = 15.3 nM. In addition, this compound has
the important compounds from this work, including a moderate aqueous solubility (between 5 and 10 μM at neutral
trifluoromethyl-substituted endochin 5 with good potency pH), good in vitro permeability (Pe = 48.3 × 10−6 cm/s) in an
(EC50 = 32 nM) and limited cross-resistance to atovaquone artificial permeability assay (PAMPA), and good to moderate
resistant parasites (strain Tm90-C2B with an EC50 = 66 nM). liver microsomal stability (mouse half-life = 21.3 min and
While many compounds from this series do not possess good human half-life =128.3 min) that are consistent with potential
murine liver microsomal stability, limiting their use in patients, use of this compound as an oral medication. Subsequent data
recent work from the Roscoe group has shown a modest on the oral efficacy of such compounds have not been reported
improvement in metabolic stability by modification of the yet. This team has also replaced the carboxylate group of
quinolone aromatic ring. For example, 6 (ELQ-121) has a quinolone 3 to provide 2,4-disubstituted aryl analogue 8
microsomal t1/2 of ∼15 min (Figure 2).11 While this is a modest (Figure 3) whose in vitro EC50 against W2 parasites
improvement over endochin 2 (t1/2 ∼ 2 min), clearly more SAR (atovaquone sensitive) is 28 nM and in close agreement
on the aromatic portion of the quinolone is warranted. It is (EC50 = 31 nM) to atovaquone-resistant parasite line TM90-
likely that improvement in log P/log D in this series can further C2B.13 No further details of in vivo efficacy or pharmacoki-
improve metabolic stability and will likely be reported in due netics have been reported on this series of compounds.
course. While several recent compounds were reported in the Kip Guy and co-workers at St. Jude Children’s Research
patent literature in 2012, no peer-reviewed articles have been Hospital along with several collaborators have also done
published to further demonstrate the optimization of this extensive work on quinolone esters related to 3, and the
scaffold with improved oral efficacy in rodent models of resulting leads are exemplified by compounds 9 and 10 in
Plasmodium infection. Figure 4. Initial optimization indicated that meta-substituted
The groups at the University of South Florida (Dennis Kyle, aromatic rings, such as are present in 9, lead to moderate
Roman Manetsch, and co-workers) have also done extensive potency on the parasite (EC50 = 100−130 nM) while balancing
work in the last several years on the optimization from excellent aqueous solubility (>100 μM) and good in vitro
endochin 2, and their SAR studies have identified similar permeability (172 cm−6/s) (Figure 4). Activity against
patterns to those reported by Riscoe and co-workers. Figure 3 atovaquone resistant parasites was in a similar range (EC50 =
highlights some of the SAR, including the introduction of a 210 nM).14 A recent disclosure has reported improved potency
phenyl ring at the 6-position of the quinolone (while removing in analogue 10 (EC50 = 80 nM) with slightly lower aqueous
the long alkyl groups present in 2, 5, and 6) and addition of solubility (20 μM) by addition of a fluorine atom. This
chloro and methoxy groups at the distal aromatic group in their substitution also affords good oral exposure (Cmax = 38 μM and
first-generation compound 7.12 Compound 7 had an in vitro AUCinf = 130 μM·h after a 50 mg/kg oral dose).15 When tested
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Figure 4. Optimization of quinoline esters.

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Figure 5. Optimized clopidol analogues.

in oral PK studies, this compound series shows less than preclinical candidates 13 (GW844520) and 14 (GW308678)
(Figure 5).19 Introduction of an appropriately substituted
Publication Date (Web): September 13, 2013 | doi: 10.1021/jm400314m

proportional exposure when the dose is raised 4-fold from 50 to

200 mg/kg. For example, compound 9 results in only a 1.7-fold phenoxyphenyl group improves the in vitro activity to EC50 ∼5
increase in Cmax and a 2.2-fold increase in Cmax when the dose is nM and the ED50 in a suppressive animal model of infection
increased 4-fold.15 This might be due to low solubility but from 40 mg/kg for clopidol to 0.2 mg/kg from compounds 13
appears to be consistent across the entire compound series and 14. The SAR patterns are quite analogous to the SAR for
regardless of intrinsic aqueous solubility. This nonlinear and atovaquone, with a hydrophobic group proximal to the
less than proportional oral exposure could limit the multiples of carbonyl functionality. In addition, these compounds are
efficacious exposure needed to determine compound safety in equipotent or more potent against an FCR3 strain of parasites
toxicity studies and make human dose calculation difficult. that are resistant to atovaquone. While these compounds also
Compound 10 was only able to suppress parasitemia by 57% in act through the cytochrome bc1 complex (at the “Qo” binding
a rodent model of malaria (dosed at 30 mg/kg po for three days site), the lack of cross-resistance and lower resistance frequency
starting three days postinfection) and would require further compared to atovaquone indicates that these compounds have
improvement to be considered a viable preclinical candidate. potential utility in man. From a medicinal chemistry
Some recent work from O’Neill and co-workers at the perspective, the increase in potency is truly remarkable, with
University of Liverpool has also demonstrated potent inhibitors a >500-fold improvement in the EC50 against P. falciparum in
in the quinilone chemotype. For example, compound 11 has a vitro and about 100-fold improvement with respect to the ED50
reported EC50 of 0.46 nM. The improved potency is attributed against Plasmodium yoelii in mice, showing that the relatively
by the authors to more favorable interactions with the Qo weak hit clopidol could be rapidly optimized to viable lead
binding site in the bc1 complex.16 These compounds likely structures. A trifluoromethoxy analogue of lead compounds 13
require optimization of physiochemical properties such as and 14, compound 15 (GW932121) was advanced to first in
solubility (clogP = 4.3) and must also be characterized for man studies, however, rat toxicology data on a phosphate
cross-resistance to atovaquone. This group also optimized the prodrug resulted in termination.20 Further optimization of this
scaffold (originally found in the course of HTS) for activity quinolones toward a preclinical candidate in described below.
against the bc1 complex while also inhibiting NADH:ubiqui- Acridones (the tricyclic version of pyridones) have also been
none oxidoreductase (Plasmodium falciparum NDH2 employed used to incorporate other interesting pharmacophores and have
in the HTS), allowing excellent in vivo efficacy in mice and been an area of investigation in the Riscoe laboratories.21
activity against liver-stage parasites in vitro to be demon- Starting from xanthones, replacement of the xanthone oxygen
strated.17 The lead compound from this optimization (12) with a nitrogen atom was investigated to provide another area
exhibits in vitro potencies in the 30−50 nM range (EC50) and for modification to improve potency/cross-resistance to
ED50 ∼ 2 mg/kg in a Plasmodium. berghei mouse model. This atovaquone. Recently, Riscoe and co-workers have combined
compound has a good oral pharmacokinetic profile (t1/2 = 10.6 the heme-targeting functionality of the acridone (due to π-
h) that could be useful for single-dose treatment, and further stacking with porphyrin) with a basic amine side chain that
development of these compounds is highly anticipated, concentrates compounds in the food vacuole of the parasite
particularly in the area of improved solubility (clogP = 5.0 (common to quinoline drugs chloroquine and mefloquine). In
for 12). addition, the Riscoe acridone 16 (T3.5)22 incorporates a
Since the discovery of atovaquone, chemists at GSK have chemosensitizing substituent on the acridone nitrogen to aid in
conducted pioneering work on pyridones, and much of the overcoming chloroquine resistance (caused by gene mutations
recent studies have centered on optimization of clopidol in the chloroquine resistant transporter termed PfCRT)
(plasmodium EC50 ∼ 20 μM), leading to potent compounds (Figure 6). Acridone/pyridone hybrid structures from Kyle,
including one very recent report.18 Another such example from Manetsch, and co-workers at the University of South Florida
Yeates and co-workers reported replacement of one of the have also demonstrated some interesting activities, especially
chloro group on the pyridine ring of clopidol to provide compound 17, where one of the aromatic rings is saturated
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particularly interesting that the SAR of this scaffold does

diverge somewhat from atovaquone itself, which may explain
the differences in the resistance profile of these compounds and
their interactions with the cytochrome bc1 complex. While 18
is less potent in vivo than atovaquone, laboratory generation of
parasites resistant to 18 has not been successful to date. These
results suggest that clinical resistance to 18 may be lower than
that of atovaquone, where lab-evolved resistance and clinical
Figure 6. Novel acridones/quinolines.
resistance are well precedented. As 18 progresses through pre-
IND studies it will be interesting to see the clinical effects of the
(Figure 6).23 Compound 17 has shown in vitro potency in the
extensive SAR and SPR studies performed to date on this
30−60 nM range against P. falciparum as well as having
privileged antimalarial template.

equivalent activity on the atovaquone resistant TM90-C2B
strain. Compound 17 has poor aqueous solubility at pH = 7.4
(2−3 μM), moderate in vitro permeability in the PAMPA assay, WHOLE-PARASITE HTS
and good stability in mouse liver microsomes (half-life >3 h).23 As we began the Novartis/GNF antimalarial medicinal
While no in vivo PK data has been described thus far, these data chemistry program in 2007 based on target-based optimization,
clearly indicate that these compounds (particularly those that we observed a significant disconnect between enzymatic and
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have aryl substitutions on the pyridone ring) warrant further cellular potency with human kinase inhibitor scaffolds that also
investigation. inhibited P. falciparum calcium-dependent kinase cdpk1.25 This
The tremendous amount of work by these groups based on observation led us to ask a more general question that
Publication Date (Web): September 13, 2013 | doi: 10.1021/jm400314m

the quinolone scaffolds has culminated in the discovery and eventually moved us away from our original goal to work on P.
selection of a preclinical candidate 18 (ELQ300) for advanced falciparum kinase inhibitors: Can cellular potency, namely
formulation and preclinical safety studies.24 18 is potent in vitro antimalarial activity, be derived from a repurposed human
on P. falciparum (EC50 ∼ 1−15 nM on P. falciparum strains kinase pharmacophore? Eliminating the kinase pharmacophore
including clinical isolates) and efficacious at low doses in vivo early in hit-to-lead optimization would also reduce molecular
on liver and blood stages of infection (ED90 ∼ 0.15 mg/kg) weight, improve ligand efficiency, and potentially reduce off-
(Figure 7). The exposure at the efficacious dose is quite low in target toxicity. Figure 8 outlines one such example reported that
has been reported in work from our laboratories.26 Compound
19, originally designed as a pan-kinase Bcr-Abl inhibitor,
displays moderate activity against the chloroquine sensitive 3D7
strain of P. falciparum (EC50 ∼ 200 nM). The primary issues
with this compound series included potent human kinase
activity as well as reduced potency against multidrug resistance
strains (such as W2). A scan of aqueous solubility-enhancing
groups quickly identified a methylpiperidinylpiperidine group
with similar 3D7 potency but improved potency on W2. Small
Figure 7. Novel quinoline preclinical candidate.
changes on the distal phenyl ring were also tolerated, resulting
in equipotent compounds, and led to a complete loss of human
mice (1.1 ug/mL·h), indicating that reaching sufficient kinase activity as measured in a Ba/F3 cell line panel of
multiples of exposures in toxicity studies should be attainable. receptor tyrosine kinases. From this observation, we concluded
However, while 18 has a remarkably clean in vitro ADMET that the pharmacophore responsible for kinase activity might
profile (Cyp P450 inhibition, hERG inhibition, human target not be essential for antimalarial activity, and thus removing this
panel, mutagenicity), the scaffold does have low solubility (<1 moiety from the scaffold could yield the minimum
μM at pH 6.8) due to high crystallinity (mp >300 °C). The low pharmacophore. As expected, the loss of activity on human
intrinsic solubility has not hampered the oral exposure of the kinases also resulted in a better safety profile for the series on
compounds at this point but may be a concern as the various mammalian cell lines (CC50 > 10 μM). Optimization of
compound progresses toward clinical trials. the substituent on both aromatic rings led to 20, displaying an
The work around the quinolones scaffold illustrates the EC50 = 58 nM against the 3D7 strain of P. falciparum and an
excellent whole-cell potency-based medicinal chemistry opti- EC50 = 211 nM vs the multidrug resistant W2 strain. This
mization. While these pharmacophores have been known in the represents a ∼4-fold improvement in potency from the starting
literature for quite some time, effective optimization has only point, a nearly 2-fold reduction in molecular weight (which
recently been reported to generate preclinical candidates. It is provided an orally bioavailable compound), and removal of

Figure 8. Benzamide optimization from a kinase template.

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Figure 9. Optimization of imidazolopyrimidine kinase library hit.

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Publication Date (Web): September 13, 2013 | doi: 10.1021/jm400314m

Figure 10. Enantiospecific potency of spiroindolone hit.

potential off-target effects due to human kinase inhibition. compared to those of the hit compound 21. In addition, a
When compound 20 was screened against 15 different P. potential hERG channel blocker pharmacophore was intro-
falciparum wild-type and drug-resistant strains, the in vitro duced by incorporation of a basic lipophilic group. Because we
EC50s were between 100 and 300 nM. On the basis of were unable to improve physiochemical properties and in vitro
comparison to known antimalarials, we predicted this series potency, we decided to focus on other scaffolds.
would lack the in vitro potency required for in vivo efficacy and
did not progress the series further. Despite this, we concluded
that hit compounds that are human kinase inhibitors can be
useful starting points for lead optimization, providing that the Natural product derived antimalarials represent the mainstay of
intrinsic kinase activity can be separated from cellular activity antimalarial chemotherapies that were primarily optimized by
early on and that positive SAR could be obtained from cell- whole-cell screening approaches, including quinine and
based optimizations. artemisinin. On the basis of this premise, the Novartis natural
The imidazolopyrimidines represent another class of product library of ∼10K compounds, containing both pure
antimalarial hits previous optimized from a human kinase natural products and natural product-like synthetic compounds,
program (Figure 9). The hit compound 21 possessed moderate was screened. Hit compound 23 was identified as a racemic
activities on the 3D7 parasite strain (EC50 = 420 nM) and did mixture of unknown configuration (Figure 9) and displayed
not exhibit significant activity against a panel of 40 mammalian moderate potency on both on the drug susceptible NF54 and
kinases, which suggested that it was not a pan-kinase chloroquine-resistant K1 P. falciparum strains (EC50 ∼ 90
inhibitor.27 The primary liability of 21 is low aqueous solubility nM).28 This compound was unique compared to many other
(36 μM at pH 6.8), which is likely driven by the high clogD natural product hits in that most of the hits were complex high
(7.4) of the compound. We initially sought to address this by molecular weight structures with many rotatable bonds, making
the introduction of hydrophilic or ionizable functionality into them less interesting structures for this indication where cheap
the series. An SAR study of the optimal site(s) on the molecule oral compounds are needed. Compound 23 is a fully synthetic
to introduce hydrophilic groups that did not have a large molecule inspired by the privileged tetrahydrobetacarboline
negative effect on potency led us to the C2 pyrimidine position. moiety.29 The compound displayed moderate aqueous
We generated a focused library which identified the N- solubility (75 μM at pH 6.8) and good oral exposure, as a 25
methylpiperazine derivative 22, which displayed an EC50 of mg/kg oral dose in mice resulted in a high Cmax (1.4 μM), good
34 nM against the P. falciparum strain 3D7. Compound 22 was oral bioavailability (F = 59%), and an oral t1/2 of nearly 4 h.
also evaluated against a panel of 15 drug resistant strains of P. Compound 23 also has a favorable safety profile for a screening
falciparum. EC50 values across all strains were lower than 140 hit when evaluated against a panel of mammalian cell lines, in
nM and many of which were below 100 nM, suggesting that the hERG inhibition assays, against cytochrome P450 isoforms, and
compound might be a good lead to address drug resistance. in a human off-target panel (IC50 >10−30 μM), making it an
The incorporation of the basic functionality on the central ring attractive hit compound. On the basis of the favorable
that is in close proximity to the presumed kinase binding physicochemical properties and in vivo PK of 23, it was
pharmacophore also resulted in a clean human kinase profile. evaluated in the P. berghei mouse model where compound is
This was done through testing the compound on a larger panel administered 24 h after infection. Remarkably, a single oral dose
of 190 kinases in both biochemical and cellular assay formats. of 100 mg/kg resulted in a 96% reduction in parasitemia
Unfortunately, despite the greater than 10-fold improvement in measured two days after treatment. Given this exciting profile,
potency and the addition of an ionizable group, both the chiral separation followed by X-ray crystal structure determi-
aqueous solubility and the clogD of 22 were not improved nation unambiguously defined the configuration of both
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stereocenters. Interestingly, only one enantiomer is active with mg/kg) reduced parasitemia by 99.6% and has the potential to
the (1R,3S) enantiomer 24 responsible for biological activity. be used as a single-dose cure in man.
Enantiomer 25 (1S,3R) is inactive against the parasite at >5000 The imidazolopiperazines represent the latest scaffold
nM EC50. Even more interesting was the discovery that the optimized from the whole-cell screen, which resulted in the
active enantiomer had significantly different ADME properties identification of a new chemotype with promising blood- and
with regard to metabolic stability in microsomes (Figure 10). liver-stage activity. Imidazolopiperazine hits 28−30 represented
Transitioning to the six-member spirocycle 26 (primarily due an attractive series displaying favorable potency on both drug-
to an improvement in potency relative to the seven-member susceptible and -resistant strains while maintaining good
congener), the more active enantiomer was also the more selectivity in Huh7 cells (Table 1). Potency was retained
rapidly metabolized (t1/2 = 1.8 min). In contrast, the 1S,3R upon resynthesis, adding confidence to the HTS data set. These
enantiomer of 26 had a t1/2 = 103 min in mouse microsomes three hit compounds, along with ∼5K other HTS hits from a
(structure not shown). This significant difference in potency 1+ million compound screen at Novartis/GNF, have been
and microsomal stability between enantiomers led the team to deposited in the EBI public database.31 Data from other large
improve metabolic stability in the active 1S,3R series using MS/ screens have also been made available in this database and have
MS based metabolite ID as a guiding tool for optimization. been used as a source of additional potential hit compounds for
The phenyl ring of indole 26 is metabolically susceptible optimization.32−35
(Figure 10). Small halogen substituents were introduced to Compound 28 displayed excellent aqueous solubility (>175
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hinder oxidation at these sites. By systematic substitutions of μM at pH 6.8) and did not inhibit a panel of cytochrome P450
the indole moiety of the spiroindolones, it was discovered that isoforms (IC50 >10 μM). The SAR from the screening
blocking the C7 position had the most marked effect on collection indicated some flexibility in the amino acid
increasing the half-life determined in the presence of liver substitutions off the piperazine nitrogen. Early issues associated
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microsomes. Fortuitously, an added halogen at C6 also with the scaffold included metabolic instability and a moderate
provides a 3−10-fold gain in potency. The 6,7-disubstituted hERG binding signal (IC50 = 19 μM). Figure 12 outlines the
derivatives display the most additive effects, providing current early optimization results based on ∼100 initial analogues
phase 2 clinical candidate 27 (NITD609, Figure 11).30 The made. Compound 31 (GNF776) was identified as our lead
molecule. Potency was improved 15-fold, exposure was
improved significantly (AUC, Cmax and high bioavailability),
and efficacy in mice was achieved (ED90 ∼20 mg/kg).
However, hERG binding activity also increased to an IC50 ∼
4 μM.
Early toxicity profiling identified a potential hERG liability
which we associated with the primary amine of the glycine
moiety. A hERG liability has also been observed for other
antimalarial scaffolds, including quinolines and more recently in
aminopyridines.36 A significant effort was spent on under-
Figure 11. Optimization of metabolic stability of spiroindolones. standing the SAR of hERG activity and differentiating it from in
vitro potency. As the terminal amine was required for favorable
solubility and PK properties, we found that glycine turned out
improvements in the metabolic stability and potency of 27 to be the optimal substituent in terms of lower hERG activity.
translated remarkably well to in vivo efficacy in the P. berghei The key was to incorporate the improved hERG inhibition
infected mouse model. Orally administered 27 displayed a long properties of the glycine group in 28 (presumably due to less
half-life (T1/2 = 10 h in mice) and excellent oral bioavailability lipophilicity in the vicinity of the primary amine) with
(F =100%). The 10-fold improvement in potency and reduced improved PK of the dimethylglycine analogues (31).37 The
clearance led to demonstration that a single oral dose of 27 (30 breakthrough result was in the incorporation of the dimethyl

Table 1. Imidazolopiperazines in EBI Public Database

compd powder Huh7 CC50

ID HTS 3D7 EC50 (μM) HTS W2 EC50 (μM) HTS Huh7 CC50 (μM) powder 3D7 EC50 (μM) powder W2 EC50 (μM) (μM)
28 0.063 0.097 >10 0.46 0.473 >100
29 0.235 0.271 >10 0.119 0.122 >79
30 0.116 0.119 >10 0.030 0.029 42.82

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Figure 12. Hit to lead optimization of an imidazolopiperazine scaffold.

Figure 13. Lead optimization summary for imidazolopiperazine.

groups into the piperazine rings from the amino acid group of optimization of an HTS hit.39 We anticipate several more
31 as shown in Figure 13. Our primary motivation for making reports of cell-based optimization of HTS hits to yield novel
this substitution was data suggesting chemical instability of the drug candidates that can also provide new insight into parasite
benzylic methylene functionality and was confirmed by biology.
independent synthesis as being an inactive degradation product.
Subsequent substitution of the benzylic carbon of the
piperazine present in 32 led to identification of compound
Corresponding Author
33 (GNF179) that significantly improves oral exposure and *Phone: +1 858 242-1016. E-mail:
potency against parasites raised to resistance of the parent HTS Notes
hit 28.38 This result might have importance because the in vivo The authors declare no competing financial interest.
activity of substituted piperazine derivatives such as 33 are quite Biography
remarkable. Compound 33 displays an ED90 of ∼1 mg/kg (a Arnab K. Chatterjee was born in Calcutta, India, in 1975. After
20× improvement from 31) that is superior to any of the completing a Bachelor of Arts in Chemistry from Northwestern
compounds discussed in this perspective. A close analogue of University in 1997, he proceeded on to Caltech in 1998 in the
33 is now progressing as a clinical candidate for both blood- laboratory of Professor Robert H. Grubbs. His doctoral research
stage and liver-stage infections according to cell-based focused on understanding the selectivity patterns of olefin cross-

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Journal of Medicinal Chemistry Perspective

metathesis reactions using catalytic ruthenium alkylidenes. Upon K. Lead Optimization of 3-Carboxyl-4(1H)-Quinolones to Deliver
completion of his doctoral research in September 2002, Arnab joined Orally Bioavailable Antimalarials. J. Med. Chem. 2012, 55, 4205−4219.
the Genomics Institute of the Novartis Research Foundation. His work (16) Cowley, R.; Leung, S.; Fisher, N.; Al-Helal, M.; Berry, N. G.;
over the last 10+ years has been focused on optimization in several Lawrenson, A. S.; Sharma, R.; Shone, A. E.; Ward, S. A.; Biagini, G. A.;
O’Neill, P. M. The development of quinolone esters as novel
medicinal chemistry projects ranging a variety of therapeutic areas
antimalarial agents targeting the Plasmodium falciparum bc1 protein
(neuroscience, oncology, respiratory disease, and infectious diseases). complex. MedChemComm 2012, 3, 39−44.
He is currently at the newly formed nonprofit California Institute for (17) Biagini, G. A.; Fisher, N.; Shone, A. E.; Mubaraki, M. A.;
Biomedical Research (Calibr) where he leads the chemistry efforts. Srivastava, A.; Hill, A.; Antoine, T.; Warman, A. J.; Davies, J.;

Pidathala, C.; Amewu, R. K.; Leung, S. C.; Sharma, R.; Gibbons, P.;
Hong, D. W.; Pacorel, B.; Lawrenson, A. S.; Charoensutthivarakul, S.;
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