Several human cyclin-dependent kinase inhibitors, structurally related to roscovitine, as new anti-malarial agents

Article abstract of DOI:10.3390/molecules190915237

In Africa, malaria kills one child each minute. It is also responsible for about one million deaths worldwide each year. Plasmodium falciparum, is the protozoan responsible for the most lethal form of the disease, with resistance developing against the av

Full text of DOI:10.3390/molecules190915237

Molecules 2014, 19, 15237-15257; doi:10.3390/molecules190915237
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molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
Several Human Cyclin-Dependent Kinase Inhibitors, Structurally
Related to Roscovitine, As New Anti-Malarial Agents
Sandrine Houzé 1, Nha-Thu Hoang 2, Olivier Lozach 3, Jacques Le Bras 1, Laurent Meijer 3,4
,
Hervé Galons 4,5 and Luc Demange 2,6,
*
1
Laboratoire de Parasitologie, CNR du Paludisme, AP-HP, Hôpital Bichat & UMR 216 IRD,
Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Pharmaceutiques,
4 avenue de l’Observatoire, Paris 75006, France; E-Mails: sandrine.houze@bch.aphp.fr (S.H.);
jacques.lebras@bch.aphp.fr (J.L.B.)
2
Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (LCBPT),
UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité, UFR Biomédicale des Saints
Pères, 45 rue des Saints-Pères, Paris 75270, France; E-Mail: luc.demange@parisdescartes.fr
Protein Phosphorylation and Human Diseases Group, CNRS, USR 3151, Station biologique,
Roscoff 29680, France; E-Mails: olivier.lozach@sb-roscoff.fr (O.L.); meijer@sb-roscoff.fr (L.M.)
ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff 29680, France;
E-Mail: herve.galons@parisdescartes.fr
3
4
5
6
Laboratoire de Pharmacochimie, INSERM U 1022, Université Paris Descartes, Sorbonne Paris Cité,
UFR des Sciences Pharmaceutiques, 4 avenue de l’Observatoire, Paris 75006, France
Institut de Chimie de Nice (ICN), UMR 7272 CNRS, Université de Nice Sophia-Antipolis,
Parc Valrose, Nice 06108, France
* Author to whom correspondence should be addressed; E-Mail: luc.demange@parisdescartes.fr;
Tel.: +33-(0)4-92-07-65-96; Fax: +33-(0)4-92-07-61-25.
Received: 31 July 2014; in revised form: 8 September 2014 / Accepted: 11 September 2014 /
Published: 23 September 2014
Abstract: In Africa, malaria kills one child each minute. It is also responsible for
about one million deaths worldwide each year. Plasmodium falciparum, is the protozoan
responsible for the most lethal form of the disease, with resistance developing against the
available anti-malarial drugs. Among newly proposed anti-malaria targets, are the
P. falciparum cyclin-dependent kinases (PfCDKs). There are involved in different stages
of the protozoan growth and development but share high sequence homology with human
cyclin-dependent kinases (CDKs). We previously reported the synthesis of CDKs inhibitors
that are structurally-related to (R)-roscovitine, a 2,6,9-trisubstituted purine, and they

Molecules 2014, 19
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showed activity against neuronal diseases and cancers. In this report, we describe the
synthesis and the characterization of new CDK inhibitors, active in reducing the in vitro
growth of P. falciparum (3D7 and 7G8 strains). Six compounds are more potent inhibitors
than roscovitine, and three exhibited IC50 values close to 1 µM for both 3D7 and 7G8
strains. Although, such molecules do inhibit P. falciparum growth, they require further
studies to improve their selectivity for PfCDKs.
Keywords: Plasmodium falciparum; cyclin-dependent kinases CDKs; PfCDKs;
2,6,9-trisubstituted purines; roscovitine; Buchwald-Hartwig amination
1. Introduction
Malaria remains today one of the most devastating infectious diseases in the world. Despite
remarkable progress in the global fight against malaria, this deadly protozoan infection takes an
estimated 700,000 lives per year, mostly African children under five years of age [1].
Among the different species of protozoan parasites responsible for malaria, Plasmodium falciparum,
which is transmitted to humans through the bite of infected Anopheles mosquitoes, is the most lethal [2].
Current treatments effective for malaria include chloroquine, mefloquine and artemisinin, but these
drugs becoming less effective due to the gradual emergence of drug-resistant strains [3]. Artemisinin-based
combination therapies have been adopted as the first-line antimalarial agents of choice against these
resistant Plasmodium parasites. Recently, however, there has been increasing concern regarding the
development of resistance to the artemisinins further emphasizing the need for new antimalarial agents
with different mechanisms of action [4]. As a consequence of the resistance, an alarming resurgence of
malaria has occurred, and the anti-malarial drug space should be urgently extended. New targets, such
as the apicoplast [5], the protozoan proteases [6], or the specific mitochondrial electron transport chain
are currently being investigated [7]. Protein kinases, which regulate protozoan growth and differentiation
during its life cycle, have also emerged to be among the most promising new anti-malarial
targets [8–11]. A short survey of the recent literature highlights the success of targeting P. falciparum
kinases such as thymidinate kinase (KI = 20 µM) [12], cGMP-dependent protein kinase (IC50 = 8 nM) [13],
calcium-dependent kinase 1 (IC50 in the 10–20 nM range) [14,15], and PfRIO-2 kinase, which regulates
the plasmodial ribosome biogenesis [16].
Among the human kinome, the cyclin-dependent kinases (CDKs) constitute a family of 20 ubiquitous
serine/threonine kinases [17–19]. They are mainly involved in cell-cycle regulation [20,21], apoptosis [22]
and gene transcription [23]. Importantly, regulatory proteins called cyclins form dimeric structures
with the CDKs and are therefore responsible for their activation [17]. In humans, CDKs deregulation is
involved in severe pathologies such as cancers (solid tumors and leukemias) [18], neuronal disorders
(including Alzheimer’s and Parkinson’s diseases) [24,25] and type 2 diabetes [26]. Indeed, CDKs
are considered as promising therapeutic targets in a wide range of pathologies including viral
infections (AIDS), renal diseases (glomerulonephritis and polycystic kidney disease), inflammation
and cardio-vascular diseases [27].

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A family of P. falciparum kinases, PfCDKs, which share high sequence homology with human
CDKs, were identified in the 1990s. Thus, PfPK5 (around 60% of sequence identity with human
CDK1 and CDK5) [28], PfPK6 (57% similarity with the catalytic domain of CDK2) [29], and Pfmrk
(46% of sequence identity with CDK7) [30] have been extensively studied and characterized.
Interestingly, CDKs and PfCDKs exhibit similar activation by phosphorylation, catalyzed by CDK
activating kinases [28], and interaction with endogenous inhibitors, such as p21CIP1 [31]. Moreover,
PfCDKs co-incubation with human cyclins leads to their functional activation [32]. Despite these
strong molecular and functional homologies, HsCDKs and PfCDK have structurally diverged to allow
selective targeting the PfCDKs without affecting host CDKs. Indeed, many known CDKs inhibitors
are unable to inhibit PfCDKs [9–12,33–38].
The purine scaffold is widely used for the development of therapeutic agents [39,40], and it has
therefore provided several CDKs inhibitors such as (R)-roscovitine (1) or purvalanol A (2a) and B (2b)
(Figure 1) [41]. Basically, (R)-roscovitine, a 2,6,9-trisubstituted purine, is a very promising molecule
developed by Cyclacel Pharmaceuticals which reached phases 2 and 2b clinical trials against different
types of cancers, and phase 1 clinical trial against glomerulonephritis. Interestingly, the (R)-roscovitine
clinical trials pointed out the low cytotoxicity of this molecule. To summarize, a daily oral dose of
2 g was found as the maximal tolerated dose in human. Pharmacokinetics studies showed a rapid
elimination of this drug with a half-life between 60 and 90 min. In humans, following oral
administration, (R)-roscovitine offers good oral bioavailability and undergoes a rapid passage into the
blood, distribution in tissues, and metabolism. Altogether, these results suggest that oral administration
is possible for extended periods of treatment [41].
Figure 1. Chemical structures of some purine CDK inhibitors.
This molecule binds CDKs in the ATP pocket and is rather selective for CDK1, CDK2, CDK5,
CDK7 and CDK9, but interacts with other kinases although with lower affinity (e.g., casein kinase 1
(CK1), dual specificity, tyrosine phosphorylation regulated kinases (DYRKs), pyridoxal kinase) [42,43].
In this context, our team focused its efforts on the identification of new CDK inhibitors
structurally-related to (R)-roscovitine [44]. Thus, by means of innovative Buchwald-Hartwig aminations
and Suzuki cross-coupling reactions, we developed several series of 2,6,9-trisubstituted purines including
6-aminoaryl, 6-aminoheteroaryl and 6-aminobiaryl moieties [45,46]. Biological characterization of
these molecules revealed “hit” compounds such as DRF053 (3), one of the most potent CK1 inhibitor
(IC50 = 14 nM) and CDK5 inhibitor (IC50 = 80 nM), which antagonizes amyloïd-β production
in the N2A-APP659 cell model, in a dose-dependent manner [44]. In addition, introduction of

Molecules 2014, 19
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6-aminoheteroaryl moieties leads to inhibitors which are 5- to 10-fold more potent than (R)-roscovitine in
cytotoxicity assays on human neuroblastoma SH-SY5Y cells (IC50 ranging from 1.8 µM to 2.1 µM) [45].
In the present paper, we report the synthesis of a new series of 2,6,9-trisubstituted purines
structurally-related to (R)-roscovitine, and bearing amino-heterocyclic motives in the C2 purine ring,
such as 2-aminopyrimidine (4a–d) and 5-aminopyrimidine (5) mimicking the pyrimidine core found in
the anti-cancer drug imatinib (Gleevec®), and an aminopyrazine (6) (Figure 2). In addition, we report
the characterization of new 2,6,9-trisubstituted purines belonging to previously reported series of
HsCDKs inhibitors. All these molecules were evaluated against a panel of human kinases including
CDK1, CDK2, CDK5, glycogen synthase kinase-3 (GSK-3), CK1 and DYRK1A. Finally, these
newly-synthesized molecules and several other compounds belonging to our library of purines were
screened as potential growth inhibitors of P. falciparum.
Figure 2. General structure for the newly-synthesized compounds.
2. Results and Discussion
2.1. Chemical Synthesis
2.1.1. Synthesis of New Purines Series Bearing C2 Amino-Heterocyclic Moities
Compounds 4a–d were synthesized following an efficient three-step procedure outlined in Scheme 1.
Briefly, the commercially available 2-amino-6-chloropurine was regioselectively converted into
2-amino-6-chloro-9-iso-propylpurine (7) in 70% yield using 2-bromopropane at 15–18 °C in DMSO
for 5 days. Then, compound 7 was reacted with 2-bromopyrimidine under the palladium catalysis
Buchwald-Hartwig amination conditions we previously reported (Pd(OAc)2, 10%; BINAP 10%,
KOtBu, 1.5 eq.) to afford 6-chloro-9-isopropyl-N-(pyrimidin-2-yl)-2-aminopurine (8) in 85% yield [47]. A
second amination gave the final compounds 4a–c with 70%–80% yield. Lower amount of catalyst and
ligand (Pd(OAc)2, 4%; BINAP 6%, tBuOK, 1.5 eq.) were required for this second Buchwald-Hartwig
amination to avoid polysubstitution on the purine scaffold [45,48].
We already reported the formation of compounds 5 and 6 as side products from a Buchwald-Hartwig
amination on the 2,6-dichloro-9-isopropylpurine (9), obtained through a region selective N9 alkylation
with the commercially available 2,6-dichloropurine [45].

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Scheme 1. Synthetic route to compounds 4a–d.
We report here the optimization of this catalytic system in order to obtain exclusively this
di-amination product in good yield. As shown in Scheme 2, we used aminopyrazine as a nucleophile
for this optimization, and our study revealed that the use of 8% of Pd(OAc)2 pre-catalyst and 16% of
racemic BINAP ligand gave compound 6 with the highest conversion rate. In contrast to our previous
study on amination with aminopyridines, we do not observe here the formation of a triarylamine
product based upon the aminopyridazine scaffold [47]. Surprisingly, the replacement of the Pd(II)
pre-catalyst by a Pd(0) pre-catalyst (Pd2dba3) leads only to decomposition products. Finally the use of
the Pd(OAc)2 catalytic system allowed the formation of compound 5 in 70% yield (Scheme 2).
Scheme 2. Synthetic route to compounds 5 and 6 and Buchwald-Hartwig diamination optimization.
N
N
N
Cl
N
N
HN
N
Cl
N
HN
N
N
N
N
N
N
N
N
N
N
catalyst
N
2-bromopropane
70 %
N
+
Cl
HN
aminopyrazine, 1.2 eq.
tBuOK 1.5 eq.
N
H
Cl
Cl
N
Toluene
110°C
9
N
6'
6
Catalyst
Pd(OAc)2, 2 %; BINAP 4 %; 1 day : traces (revealed by TLC)
Pd(OAc)2, 3 %; BINAP 6 %; 1 day : traces (revealed by TLC)
Pd(OAc)2, 4 %; BINAP 8 %; 2 days :
Pd(OAc)2, 8 %; BINAP 16 %; 2 days :
Pd2dba3, 5%; BINAP 10 %; 1 day :
25 %
30 %
15 %
45 %
65 %
traces (revealed by TLC)
decomposition
N
N
Cl
HN
N
Pd(OAc)2, 8 %
BINAP 16 %
N
N
N
N
N
N
5-aminopyrimidine, 1.2 eq.
Cl
N
HN
tBuOK 1.5 eq.
Toluene
110°C
70 %
9
N
N
5

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2.1.2. Synthesis of New 6-Aminobiaryl Molecules Structurally-Related to (R)-Roscovitine
To complete our purine library with compounds structurally-related to (R)-roscovitine, we
synthesized compounds 10–13 according to previously reported synthesis routes, whose key steps are
Buchwald-Hartwig aminations and Suzuki cross-coupling reactions (Scheme 3) [44,47].
Scheme 3. Synthesis of new 6-aminobiaryle 10–13.
2.2. Molecular Assays on Mammalian Kinases
All newly synthesized compounds were tested as potential inhibitors on a panel of several
mammalian kinases. The effects on CDK1/cyclin B, CDK2/cyclin A, CDK5/p25, GSK-3αβ, CK1δ/ε
and DYRK1A kinase activity are reported as the IC50 values calculated from dose-response curves.
They are summarized in Table 1. The inhibition was determined covering a range of concentrations of
the compounds by means of a [γ-33P] assay as described in the experimental section.
Globally, compounds 4a–d, with a 2-aminopyrimidine in the C2 position, and compound 6 with a
2-aminopyrazine in the C2 position, are poor kinase inhibitors when compared to (R)-roscovitine (1) or
DRF053 (3). Moreover, we recently reported that 4a–d analogs bearing an aminoalcohol in the purine
C2 position inhibits CDKs with IC50 values ranging from 0.01 µM to 1.00 µM. Altogether, these
results underline the relevance of the C2 aminoalcohol to improve the CDKs ATP-pocket binding,
since the hydroxyl group of the amino-alcohol is engaged in a H-bonding network involving water
molecules. Therefore this hydroxyl group plays a critical role for improved inhibitor binding [49,50].

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Table 1. Newly-synthesized trisubstituted purines effects on several mammalian protein
kinases activity. Purine derivatives were tested at various concentrations as described in the
experimental section; IC50 values are provided in µM were estimated, dose-response curves
and are expressed in µM. All assays were run in triplicates and data points were within less
than a 10% range.
IC50 (µM) a
GSK-3αβ CK1δ/ε DYRK1A
Compounds
CDK1
0.35
0.22
-
CDK2
CDK5
0.2
0.08
1.0
>10
4.3
7.0
0.4
13
1
0.70
N.I.
>10
1.0
2.3
0.01
1.0
-
-
3
-
-
4a
4b
4c
4d
5
3.0
8
12
-
>10
>10
>10
>10
>10
>10
>10
>10
>10
>10
>10
2.8
3.0
9.3
-
1.8
-
8
5.2
0.5
0.5
-
0.2
2.8
-
0.2
6
-
1.1
10
11
12
13
0.01
0.8
0.2
0.2
0.03
0.4
0.1
-
0.2
-
0.04
0.2
-
-
-
0.2
0.5
-
a
IC50 value reported as >10 indicates that the compound display no activity at the highest concentration
tested (10 µM); -: not tested.
The influence of the amino-alcohol stereochemistry on the kinase inhibition appeared to be limited.
Nevertheless, as reported on several series of 2,6,9-trisubstituted purines including (R)-roscovitine
itself, the (R) stereoisomer showed a higher affinity for CDK than the (S) one. This might be
highlighted on CDK5 by comparing 11 (IC50 = 0.4 µM) and 12 (IC50 = 0.1 µM) with their
corresponding (R) stereoisomers (IC50 = 0.08 µM and IC50 = 0.05 µM, respectively [44]).
As expected, compound 10 is a potent CDK5 inhibitor (IC50 = 0.03 µM). This confirms the potency
of the C6 biaryl moiety in term of H-bonding and molecule stacking [44], since its IC50 value is close
to previous results obtained on CDK5 with the 6-aminobiaryl series of inhibitors. For the drug
discovery field, CDK5 is a very promising target. Indeed, this kinase is involved in multiple neuronal
activities (neuronal survival and migration), development of the cerebral cortex, phosphorylation of tau
and production of β-amyloïd, pain signaling and pancreatic secretion of insulin [25,51–53]. To date,
CDK5 specific inhibitors reported by others include complex scaffolds such as pyrazolopyrimidines
(IC50 = 0.03 µM) [54], 2,4-diaminothiazoles (IC50 values included between 0.015 µM and 1 µM) [55]
and cyclohexyl-thiophene moieties (IC50 values included between 0.035 µM and 1 µM) [56].
Compound 11 is a potent inhibitor of CK1, with an IC50 value of 0.04 µM. This kinase is involved
in multiple physiological events, such as circadian rhythm regulation, and its implication in
Alzheimer’s disease was strongly suggested [43,57]. With the significant exception of our previously
reported series or trisubstituted purines including DRF053 [34], known CK1 inhibitors encompass
generally polycyclic complex structures, including natural products such as hymenialdisine
(IC50 = 0.03 µM) [58], a pyrrole-imidazole alkaloid extracted from marine sponges, and original
synthetic molecules [59].

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Interestingly, compounds 5 and 6 retain a marked inhibitory effect on DYRK1A. This activity is
very close to the IC50 (ranging from 0.21 µM to 0.48 µM) that we previously reported for this kinase
with other 2,6,9-trisubstituted purines [45]. Moreover this inhibition is stronger compared to that of
(R)-roscovitine (87% of remaining DYRK1A kinase activity at 1 µM) and of purvalanol A (88% of
remaining DYRK1A kinase activity at 0.1 µM) [43]. This is important because DYRK1A deregulation
is involved in severe neurodegenerative pathologies, such as Down’s syndrome and the cognitive
deficits associated with Alzheimer’s disease [60,61]. Only a few sub-micromolar DYRK1A inhibitors
have been described, such as leucettines (IC50 values around 0.04 µM) [62,63], lamellarin D derivatives
(IC50 = 0.07 µM) [64] or acridone alkaloids from Glycosomis chlorosperma (IC50 = 0.075 µM) [65],
and synthetic original molecules, such as 4,7-disubstituted pyrido[3,2d]pyrimidines [66],
6-arylquinazolin-4-amines [67] and phtalazinone [68]. Nevertheless, these molecules have complex
organic structures requiring multi-steps synthesis and their “hit to lead” optimization might be
difficult. Finally, our results confirm the potency of the purine scaffold as a potent initial scaffold to
develop and optimize new DYRK1A inhibitors.
2.3. Evaluation on P. falciparum
A selection of 15 molecules 4b–c, 10–13 representing the different 2,6,9-trisubstituted purine
series, including newly synthesized products was screened as anti-malarial agents on two different
P. falciparum strains, Pf3D7, a standard drug-sensitive African stain, and Pf7G8, a brazilian
chloroquino-resistant strain (Figure 3). The compound activity was evaluated during the parasitic
erythocytic cycle, by the means of a [3H] hypoxanthine incorporation assay [69]. It is directly
correlated to parasite viability, as described in the experimental section. IC50 values on mammalian
kinases for the P. falciparum screened compounds are summarized in supplementary material, Table A1,
appendix section.
At first, the activity of the fifteen compounds was screened at three different concentrations (10, 50
and 100 µM) on Pf3D7. Chloroquine which is not a kinase inhibitor, but which is the antimalarial
reference drug was used as the positive control. This allowed the selection of the six most active
compounds, which totally inhibit the parasite proliferation during its erythrocytic cycle at a
concentration of 100 µM. Then, in a second assay, these six molecules plus (R)-roscovitine (1) and
purvalanol A (2a) were evaluated in a dose-dependent assay, in order to determine their IC50 values on
the two P. falciparum strains. Chloroquine was again used as a positive control.
As expected, each P. falciparum strain growth is partly inhibited by (R)-roscovitine and purvalanol
A, and the latter exhibited the strongest activities. Nevertheless, previous studies reported that IC50
values for purvalanol A on recombinant PfPK5 and Pfmrk are respectively of 8 µM and 26 µM,
suggesting the likely existence of alternative in vivo molecular targets [32,70].
With the marked exception of compound 20, the screened molecules in the second round of assays
exhibited significant IC50 values ranging from 0.7 µM to 7 µM on both strains (Table 2) and therefore
appeared to be more potent than (R)-roscovitine and purvalanol A [71], and also more potent than
other adenine and adenosine derivatives with a purine ring [72].

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Figure 3. Structures of the 2,6,9-trisubstituted purines screened as P. falciparum growth inhibitors a.
a
Inactive compounds are drawn on a white background; these molecules were not selected for further IC50
measurement. Compounds with IC50 > 6 µM on Pf3D7 are drawn with light grey background. The most
potent P. falciparum growth inhibitors are drawn with dark grey background.
Table 2. IC50 values for Pf3D7 and Pf7G8 for the six mammalian kinase inhibitors and the
three control molecules. These values were estimated by non-linear regression analysis
using an inhibitory sigmoid Emax model. All assays were run in triplicates.
Growth IC50 (µM)
Compounds
Pf3D7
6.53
5.37
7.13
22.21
3.05
1.39
10.48
4.58
Pf7G8
2.06
1.55
1.82
4.66
0.69
0.99
12.56
8.12
0.18
11
12
19
20
21
22
(R)-roscovitine, 1
Purvalanol A, 2a
Chloroquine
0.03

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Interestingly, these six inhibitors appeared to be 3- to 5-fold more potent against Pf7G8 than against
Pf3D7 (e.g., compound 21: Pf3D7 IC50 = 3.05 µM vs. Pf7G8 IC50 = 0.69 µM). Such marked sensitivity
of the chloroquino-resistant strain has been frequently observed, and is generally due to an acute
internalization of the drug into the protozoan. Indeed, protozoans such as P. falciparum are unable to
synthesize purines de novo, and all their purines are provided by the host. To this end, these organisms
have developed very effective and specific systems to take up and internalize purines. Thus, these
uptake pathways might differ from one strain to another, and therefore might be the reason of these
slight differences observed for P. falciparum growth inhibition. However, these differences observed
between P. falciparum growth inhibition according to the chloroquine sensitivity could also depend on
the specific PfCDK inhibited by the tested compounds which remain to be studied.
Compounds 11, 12, 21 and 22 which exhibited sub-micromolar IC50 for the mammalian kinases
appeared to be promising inhibitors of P. falciparum growth with IC50 values around 1–5 µM for both
strains. These results are probably correlated with the similar sequence and structure between mammalian
and protozoan kinases. Nevertheless, further “hit to lead” improvement will be necessary to improve
selectivity towards protozoan growth inhibition. To address this optimization, it might be interesting to
consider molecules 18 and 22 IC50 values. Indeed, for these compounds, the protozoan growth
inhibition potency is directly linked to the purine C2 pyridine core nitrogen position, suggesting a
potential H-bond involving this nitrogen atom and the protozoan cellular target. This is a major
difference with CDK inhibition, as we previously reported very close IC50 values for both of them on
CDK1, CDK2 and CK1 (compound 18: CDK1 : IC50 = 0.41 µM; CDK5: IC50 = 0.73 µM; CK1:
IC50 = 0.10 µM; compound 22 : CDK1: IC50 = 0.59 µM; CDK5: IC50 = 0.60 µM; CK1:
IC50 = 0.08 µM [44]). Starting from this, a specific anti-malaria pharmacophore introduction in another
position of the purine scaffold might pave the way to the design of a more specific and potent “hit”.
3. Experimental Section
3.1. Chemistry
General Procedures
Chemical reagents and solvents were purchased from Sigma-Aldrich (Lyon, France), Fluka (Lyon,
France) and Carlo Erba (Val de Reuil, France). Reactions were monitored by TLC using Merck
(Fontenay sous Bois, France) silica gel 60F-254 thin layer plates. Column chromatographies were
performed on SDS Chromagel 60 ACC 40-63 µM. Melting points were determined on a Reichert
Köfler hot-stage (Depew, NY, USA) and are uncorrected. NMR spectra were recorded on Bruker
13
(Wissembourg, France) Avance 400 MHz (100 MHz for C-NMR) at 300 K. Chemical shifts were
reported as δ values (ppm) indirectly referenced to the solvent signal or to tetramethylsilane (TMS) as
internal standards. Data are reported in the conventional form. Mass spectra were recorded on a ZQ
2000 Waters using a Z-spray (ESI-MS).
General Procedure for N9 alkylation. To a solution of 2,6-dichloro-9H-purine or 2-amino-6-chloro-
9H-purine (1.0 eq.) in DMSO (5.5 mL for 1 mmol of purine) at 15 °C were added K2CO3 (3.0 eq.) and
2-bromopropane (5.0 eq.). After 2–3 days stirring at 15–18 °C, water was added and the solution was

Molecules 2014, 19
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extracted with EtOAc. The organic layer, once combined, was washed with brine, dried (Na2SO4),
concentrated and purified by chromatography on silica gel columns (eluant: cyclohexane/EtOAc 1:9)
to yield white solids (60%–75%).
2-Amino-6-chloro-9-iso-propylpurine (7) and 2,6-dichloro-9-iso-propylpurine (9) have been previously
synthesized [44,72]; 1H-NMR, 13C-NRM and mass spectra are in accordance with previously reported data.
General Procedure for Buchwald-Hartwig Amination. A solution of Pd(OAc)2 and BINAP in dry
toluene was warmed at 45 °C for 5 min. The leaving group-containing purine was then added under N2
bubbling; the mixture was kept at 45 °C for 10 min. and KOtBu was added. After 10 min, the
appropriate nucleophile was added. The mixture was heated at 100 °C under N2 until reaction
completion (3 h to 2 days depending upon the nucleophile used). After cooling to room temperature,
the mixture was filtered through Celite, and concentrated. The residue was dissolved in CH2Cl2 (75 mL)
and washed (1 × 10 mL) with water and brine (2 × 10 mL). The organic layer was dried and
concentrated under vacuum. The residue was purified by chromatography on silica gel using various
amounts of EtOAc/cyclohexane/ethanol as eluants.
We already reported chemical characterization for compounds 5, 6 and 6'; 1H-NMR, 13C-NMR and
mass spectra are in accordance with previously reported data [44].
1
2-Amino(pyrimidin-2-yl)-6-chloro-9-iso-propylpurine (8). H-NMR (400 MHz, CDCl3): δ (ppm) 1.63
(d, 6H, J = 6.8 Hz, (CH3)2-CH), 4.87 (hept, 1H, J = 6.8 Hz, CH(CH3)2), 6.95 (t, 1H, J = 4.8 Hz,
Hpyrimidinyl), 8.00 (s, 1H, H-8purine), 8.31 (s, 1H, NH), 8.62 (d, 2H, J = 4.8 Hz, Hpyrimidinyl).
1
2-Amino(pyrimidin-2-yl)-6-[4-bromophenyl]-9-iso-propylpurine (4a). H-NMR (400 MHz, CDCl3): δ
(ppm) 1.62 (d, 6H, J = 6.8 Hz, (CH3)2-CH), 4.81 (hept, 1H, J = 6.8 Hz, CH(CH3)2), 6.95 (t, 1H, J = 4.8 Hz,
Hpyrimidinyl), 7.01 (m, 2H, J = 7.3 Hz, Hbromophenyl), 7.34 (d, 2H, J = 7.3 Hz, Hbromophenyl), 7.99 (s, 1H,
13
H-8purine), 8.08 (m, 2H), 8.62 (d, 2H, J = 4.8 Hz, Hpyrimidinyl); C-NMR (100 MHz, CDCl3) : δ (ppm)
21.4, 45.3, 114.9, 116.7, 120.4, 121.2, 133.4, 137.6, 147.9, 150.9, 151.3, 157.2, 157.3, 159.5; MS
(ES+) m/z 425.08 [M+H]+.
1
2-Amino(pyrimidin-2-yl)-6-[pyridin-2-yl]-9-iso-propylpurine (4b). H-NMR (400 MHz, CDCl3): δ
(ppm) 1.62 (d, 6H, J = 6.8 Hz, (CH3)2-CH), 4.80 (hept, 1H, J = 4.8 Hz, CH(CH3)2), 6.92 (t, 1H, J = 4.8 Hz,
Hpyrimidinyl), 6.99 (m, 1H, Hpyridyl), 7.54 (m, 1H, Hpyridyl), 7.83 (s, 1H, H-8purine), 8.12 (bs, 2H, NH), 8.32
(m, 1H, Hpyridyl), 8.62 (d, 2H, J = 4.8 Hz, Hpyrimidinyl), 9.29 (m, 1H, Hpyridyl); 13C NMR (100 MHz,
CDCl3) : δ (ppm) 22.4, 22.5, 45.3, 113.7, 114.9, 117.8, 120.4, 133.4, 137.6, 147.9, 149.4, 150.7, 151.2,
157.4, 158.0, 159.4; MS (ES+) m/z 348.08 [M+H]+.
1
2-Amino(pyrimidin-2-yl)-6-[pyridin-3-yl]-9-iso-propylpurine (4c). H-NMR (400 MHz, CDCl3): δ
(ppm) 1.62 (d, 6H, J = 6.8 Hz, (CH3)2-CH), 4.81 (hept, 1H, J = 6.8 Hz, CH(CH3)2), 6.93 (t, 1H, J = 4.8 Hz,
Hpyrimidinyl), 7.30 (m, 1H, Hpyridyl), 7.80 (s, 1H, H-8purine), 8.08 (s, 2H, NH), 8.32 (m, 1H, Hpyridyl), 8.64
(d, 2H, J = 4.8 Hz, Hpyrimidinyl), 8.86 (m, 1H, Hpyridyl), 9.14 (s, 1H, Hpyridyl). 13C-NMR (100 MHz,
CDCl3): δ (ppm) 22.4, 45.3, 113.7, 114.6, 123.2, 126.7, 135.4, 136.4, 141.9, 142.9, 150.7, 151.2,
157.6, 158.1, 159.0; MS (ES+) m/z 348.14 [M+H]+.

Molecules 2014, 19
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1
2-Amino(pyrimidin-2-yl)-6-[pyridin-4-yl]-9-iso-propylpurine (4d). H-NMR (400 MHz, CDCl3): δ
(ppm) 1.61 (d, 6H, J = 6.8 Hz, (CH3)2-CH), 4.82 (hept, 1H, J = 6.8 Hz, CH(CH3)2), 6.93 (t, 1H, J = 4.8 Hz,
Hpyrimidinyl), 7.76 (s, 1H, H-8purine), 7.69 (d, 2H, J = 6.0 Hz, Hpyridyl), 8.00 (s, 2H, NH), 8.32 (d, 1H,
J = 4.8 Hz), 8.64 (d, 2H, J = 4.8 Hz, Hpyrimidinyl), 8.41 (d, 2H, J = 6.0 Hz, Hpyridyl). 13C NMR (100 MHz,
CDCl3): δ (ppm) 22.3, 46.1, 113.4, 115.5, 135.4, 136.4, 141.9, 142.9, 150.7, 151.2, 157.7, 158.1, 159.0.
Chemical Characterizations of Compounds 10–13. These compounds have been obtained following a
previously reported synthesis strategy. See references [43] and [46] for the details of corresponding
experimental procedures and characterizations of intermediates.
1
(R)-2-(1-Hydroxybut-2-ylamino)-6-[6-(3-pyridyl)pyrid-3-ylamino]-9-iso-propylpurine (10). H-NMR
(400 MHz, CDCl3): δ (ppm) 1.00 (t, 3H, J = 7.0 Hz, CH3CH2), 1,50 (d, 6H, J = 6.9 Hz, CH (CH3)2),
1.45–1.7 (m, 2H, CH2CH3), 3.5 (m, 1H, CH2OH), 3.8 (d, 1H, J = 3.1 Hz and J = 10.2 Hz, CH2OH), 3.9
(m, 1H, CHNH), 4.53 (hept, 1H, J = 6.9 Hz, CH(CH3)2), 7.3 (d, 1H, J = 8.0 Hz, Hpyridyl), 7.55 (s, 1H,
H-8purine), 7.7 (d, 1H, J = 8.0 Hz, Hpyridyl), 7.75 (m, 2H, NH), 8.2–8.3 (m, 2H, Hpyridyl), 8.55 (s, 1H,
13
Hpyridyl), 9 (d, 1H, J = 8.0 Hz, Hpyridyl), 9,1 (s, 1H, Hpyridyl). C-NMR (100 MHz, CDCl3) : δ (ppm)
10.8, 22.0, 23.1, 47.8, 55.9, 67.0, 120.8, 124.4, 134.5, 139.7, 140.3, 141.5, 147.9, 149.9, 150.8, 151.9,
157.4, 159.8
(S)-2-(1-Hydroxybut-2-ylamino)-6-[3-(2-pyridyl)phenylamino]-9-iso-propylpurine (11). 1H-NMR
(400 MHz, CDCl3): δ (ppm) 0.98 (t, 3H, J = 7.2 Hz, CH3CH2), 1.49 (d, 6H, J = 6.8 Hz, CH(CH3)2),
1.67–1.78 (m, 2H, CH3CH2), 3.63 (m, 1H, CH2OH), 3.74 (dd, 1H, J = 2.4 Hz and J = 10.6 Hz,
CH2OH), 3.97–4.05 (m, 1H, CHNH), 4.58 (hept, 1H, J = 6.8 Hz, CH(CH3)2), 4.94 (m, 1H, CHNH),
7.10–7.15 (m, 2H, Hpyridyl), 7.38 (t, 1H, J = 7.2 Hz, Hphenyl), 7.50–7.54 (m, 2H, Hphenyl + Hpyridyl),
7.68–7.71 (m, 3H, Hphenyl + Hpyridyl), 7.86 (s, 1H, H-8purine), 8.62 (d, 1H, J = 4.3 Hz, Hpyridyl). 13C-NMR
(100 MHz, CDCl3) : δ (ppm) 10.8, 22.5, 22.6, 24.9, 46.4, 55.9, 66.7, 114.9, 118.6, 120.3, 121.0, 121.4,
122.2, 129.1, 135.1, 136.9, 139.8, 140.1, 149.4, 152.2, 157.3, 159.6.
(S)-2-(1-Hydroxybut-2-ylamino)-6-[3-(3-pyridyl)phenylamino]-9-iso-propylipurine (12). 1H-NMR
(400 MHz, CDCl3): δ (ppm) 0.94 (t, 3H, J = 6.8 Hz, CH3CH2), 1.49 (d, 6H, J = 6.8 Hz, CH(CH3)2),
1.53–1.66 (m, 2H, CH3CH2), 3.61 (m, 1H, CH2OH), 3.78 (m, 1H, CH2OH), 3.88–3.98 (m, 1H,
CHNH), 4.56 (hept, 1H, J = 6.8 Hz, CH(CH3)2), 4.94 (d, 1H, J = 6.1 Hz, CHNH), 7.10–7.15 (m, 2H,
Hpyridyl), 7.29 (m, 1H, Hpyridyl), 7.37 (t, 1H, J = 7.2 Hz, Hpyridyl), 7.53 (s, 1H, H-8purine), 7.62–7.70 (m,
2H, Hphenyl + Hpyridyl), 7.82 (d, 1H, J = 7.6 Hz, Hphenyl), 7.99 (s, 1H, Hphenyl), 8.52 (d, 1H, J = 4.1 Hz,
Hpyridyl), 8.81 (s, 1H, Hpyridyl). 13C NMR (100 MHz, CDCl3) : δ (ppm) 10.8, 22.5, 24.7, 46.6, 56.0, 67.2,
115.1, 118.5, 119.5, 121.6, 123.5, 129.5, 134.5, 135.3, 136.5, 138.5, 139.8, 148.3, 148.5, 152.3, 159.6.
(S)-2-(1-Hydroxybut-2-ylamino)-6-[4-(2-pyridyl)phenylamino]-9-iso-propylpurine (13). 1H-NMR
(400 MHz, CDCl3): δ (ppm) 0.98 (t, 3H, J = 7.2 Hz, CH3CH2), 1.46 (d, 6H, J = 6.8 Hz, CH(CH3)2),
1.52–1.68 (m, 2H, CH3CH2), 3.63 (dd, 1H, J = 6.7 Hz and J‘ = 10.8 Hz, CH2OH), 3.81 (dd, 1H, J = 2.8 Hz
and J = 10.8 Hz, CH2OH), 3.90-3.95 (m, 1H, CHNH), 4.53 (hept., 1H, J = 6.8 Hz, CH(CH3)2), 5.05
(m, 1H, CHNH), 7.10–7.15 (m, 2H, Hpyridyl), 7.51 (s, 1H, H-8purine), 7.60–7.68 (m, 2H, Hpyridyl), 7.80
(d, 2H, J = 8.4 Hz, Hphenyl), 7.90 (d, 2H, J = 8.4 Hz, Hphenyl), 8.59 (m, 1H, Hpyridyl). 13C-NMR

Molecules 2014, 19
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(100 MHz, CDCl3) : δ (ppm) 10.4, 21.8, 24.5, 45.8, 55.4, 65.8, 114.3, 119.5, 119.6, 121.1, 127.0,
132.7, 134.7, 136.4, 140.1, 148.7, 150.5, 151.4, 158.8, 159.7.
3.2. Biology—Protein Kinase Assays
3.2.1. Biochemical Reagents
Sodium orthovanadate, EGTA, EDTA, MOPS, β-glycerophosphate, phenylphosphate, sodium
fluoride, dithiothreitol (DTT), glutathione-agarose, glutathione, bovine serum albumin (BSA),
nitrophenylphosphate, leupeptine, aprotinine, pepstatin, soybean trypsin inhibitor, benzamidine, and
histone H1 (type III-S) were obtained from Sigma Chemicals (Lyon, France). [γ-33P]-ATP was
obtained from Amersham (Pittsburgh, PA, USA). The CK-S peptide (RRKHAAIGpSAYSITA)
(pS stands for phosphorylated serine) was purchased from Millegen (Labege, France), and the GS-1
peptide (YRRAAVPPSPSLSRHSSPHQpSEDEEE) was obtained from GenScript Corporation
(Piscataway, NJ, USA).
3.2.2. Buffers
Buffer A: 10 mM MgCl2, 1 mM EGTA, 1 mM DTT, 25 mM Tris-HCl pH 7.5, 50 µg heparin/mL.
Buffer C: 60 mM β-glycerophosphate, 15 mM p-nitrophenylphosphate, 25 mM MOPS (pH 7.2), 5 mM
EGTA, 15 mM MgCl2, 1 mM DTT, 1 mM sodium vanadate, 1 mM phenylphosphate.
3.2.3. Kinase Preparations and Assays
Kinase activities were assayed in Buffer A or C, at 30 °C, at a final ATP concentration of 15 µM.
Blank values were subtracted and activities expressed in % of the maximal activity, i.e., in the absence
of inhibitors. Controls were performed with appropriate dilutions of DMSO.
CDK1/cyclin B (M phase starfish oocytes, native), CDK2/cyclin A (human, recombinant) and
CDK5/p25 (human, recombinant) were prepared as previously described [73]. Their kinase activity was
assayed in buffer C, with 1 mg histone H1/mL, in the presence of 15 µM [γ-33P] ATP (3000 Ci/mmol;
10 mCi/mL) in a final volume of 30 µL. After 30 min incubation at 30 °C, 25 µL aliquots of
supernatant were spotted onto 2.5 cm × 3 cm pieces of Whatman P81 phosphocellulose paper, and,
20 s later, the filters were washed five times (for at least 5 min each time) in a solution of 10 mL of
phosphoric acid/liter of water. The wet filters were counted in the presence of 1 mL of ACS
(Amersham, Pittsburgh, PA, USA) scintillation fluid.
GSK-3α/β (porcine brain, native) was assayed, as described for CDK1 but in Buffer A and
using a GSK-3 specific substrate (GS-1: YRRAAVPPSPSLSRHSSPHQSpEDEEE) (pS stands for
phosphorylated serine).
CK1δ/ε (porcine brain, native) was assayed in three-fold diluted buffer C, as described for CDK1
but using 25 µM CKS peptide (RRKHAAIGpSAYSITA), a CK1-specific substrate [74].
DYRK1A (human, recombinant, expressed in E. coli as a GST fusion protein) was purified by
affinity chromatography on glutathione-agarose and assayed in buffer A (+0.5 mg BSA/mL) with
using Woodtide (KKISGRLSPIMTEQ) (1.5 µg/assay) as a substrate.

Molecules 2014, 19
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3.3. Biology—In Vitro Drug Susceptibility Assays
Compounds were tested against synchronous ring-stage parasites of Pf3D7 and Pf7G8 strains.
Drugs testing were carried out in 96-well microtiter plates. The chloroquine (CQ) diphosphate was
purchased from Sigma (Lyon, France). The CQ was dissolved and diluted in water to obtain final
concentrations ranging from 12.5 to 3,200 nM. The compounds were dissolved in DMSO and diluted
in RPMI 1640 to obtain final concentrations ranging 0.1 µM to 100 µM. For each assay, each drug
dilution was analyzed in triplicate.
For the in vitro isotopic microtest, 200 µL of the suspension of synchronous parasitized red blood
cells with >90% of the parasites at the ring stage (final parasitaemia, 0.3%; final haematocrit, 4%) per
well were plated in 96-well plates that contained serial CQ or compounds concentrations. Parasite
growth was measured by the incorporation of radiolabeled [3H]hypoxanthine with a specific activity of
14.1 Ci/mmol (Perkin-Elmer, Courtaboeuf, France) (1 µCi per well) to each well at time zero. The
plates were incubated at 37 °C, in an atmosphere of 5% O2, 5% CO2, and 90% N2 for 48 h.
Immediately after incubation, plates were frozen and then thawed to lyse the erythrocytes. Cultures
were harvested onto glass fiber filters and washed using a cell harvester (FilterMAT; Skatron
Instruments, Dalsletta, Norway). The dried fiber filter papers were mixed with 2 mL of scintillation
fluid (OptiScint; Perkin-Elmer, Waltham, UK). The radioactivity was counted using a liquid
scintillation counter (Wallac 1410; Perkin-Elmer, Waltham, UK). The results were recorded as counts
per minute (cpm) per well at each drug concentration. The drug concentration that could inhibit 50% of
the parasite growth (IC50) were estimated by non-linear regression analysis using an inhibitory sigmoid
γ
Emax model (percent) = 100 − [(100 × Cγ)/(Cγ + IC50 )], where C corresponds to the drug concentration
and γ is the sigmoidicity factor. The initial value and the asymptotic result for high concentrations
were fixed to 0% and 100%, respectively [75], available on the web [76].
4. Conclusions
Using a convergent synthesis route which includes as a key step a Buchwald-Hartwig amination, we
report the synthesis of new series of 2,6,9-trisubstituted purines structurally-related to (R)-roscovitine.
The evaluation of these molecules as inhibitors on a mammalian kinases panel revealed that several
compounds (5, 6, 10 and 11) exhibit marked activities against CDK5, CK1 and DYRK1A, a set of
kinases involved in several neuronal pathologies such as Down Syndrome and Alzheimer’s disease.
These molecules might be considered as starting “hits” for further structural optimization.
These newly-synthesized purines were also evaluated as potential inhibitors of P. falciparum
growth in vitro. By means of a two-step screening assay, we identified six molecules which are more
potent against the two P. falciparum clones (Pf3D7 and Pf7G8) than (R)-roscovitine and purvalanol A.
By comparison with chloroquine, these growth inhibitions are still modest, but further structural
optimizations of the purine scaffold are possible. Thus, further studies should allow us to determine
whether potent anti-malarial motives might be introduced into the purine scaffold. Another key point
to address will be the improvement of the compound selectivity, as our strongest P. falciparum growth
inhibitors also appeared among the best mammalian CDK inhibitors we designed.

Molecules 2014, 19
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Altogether, these results open the way to further synthesis of new drugs targeting one of the most
deadly disease in the world, malaria.
Acknowledgments
This research was supported by grants from the “Cancéropole Grand-Ouest” grant (LM), the
“Institut National du Cancer” (INCa «Cancer Détection d’innovations 2006») (LM), the “Association
France-Alzheimer Finistère” (LM), the “Ligue Nationale contre le Cancer (Grand-Ouest)” (LM) and
the Université Paris Descartes “BQR grant” (SH, HG, LD). LM acknowledges the support of the
European Union 7th Framework Program Knowledge-Based Bio- economy (FP7-KBBE)- BlueGenics
2012 grant.
Author Contributions
L.D., N.-T.H. synthesized the molecules; S.H., N.-T.H. performed P. falciparum growth inhibition
experiments; O.L. performed HsCDK inhibition experiments; L.D., S.H., J.L.B., L.M., H.G. designed
experiments and reviewed the manuscript; L.D. wrote the paper; L.D., S.H., L.M., H.G. co-directed
the work.
Appendix
Table A1. IC50 values of the screened compounds on HsCDKs, and comparison with the
Plasmodium faciparum 3D7 and 7G8 strains growth inhibition. Purines were tested at
various concentrations as described in experimental section. IC50 values are reported in
µM. On mammalian kinases, IC50 were estimated from dose-response curves and are
expressed in µM. All assays were run in triplicates and data points were within less than a
10% range. -, not tested. IC50 value reported as >10 means that less than 50% inhibition at
10 µM was observed; N.I. (Not Inhibitor) indicates that the compound did not display any
inhibitory activity. On Pf strains, IC50 were estimated by non-linear regression analysis
using an inhibitory sigmoid Emax model. All assays were run in triplicates.
IC50 on P. falciparum Strains (µM)
IC50 on HsCDKs (µM)
Compounds
Pf3D7
10.48
4.58
N.I.
Pf7G8
12.56
8.12
N.I.
HsCDK1
0.35
0.004
12
HsCDK5
0.20
0.075
>10
4.3
1
2a
4b
4c
10
11
12
13
14
15
16
17
N.I.
N.I.
3.0
N.I.
N.I.
0.01
0.8
0.05
0.4
6.53
5.37
N.I.
2.06
1.55
N.I.
0.2
0.1
0.2
-
N.I.
N.I.
0.05
0.18
0.18
0.18
0.03
0.05
0.10
0.05
N.I.
N.I.
N.I.
N.I.
N.I.
N.I.

Molecules 2014, 19
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Table A1. Cont.
IC50 on P. falciparum Strains (µM)
IC50 on HsCDKs (µM)
Compounds
Pf3D7
N.I.
Pf7G8
N.I.
HsCDK1
0.41
0.5
HsCDK5
0.73
18
19
20
21
22
7.13
1.82
4.66
0.69
0.99
0.27
22.21
3.05
0.7
0.5
0.04
0.6
0.06
1.39
0.6
Conflicts of Interest
All the authors have read the manuscript, concur with its content, and state that its content has
not been submitted elsewhere. The authors declare no competing financial interests and no conflict
of interest.
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