The guareschi pyridine scaffold as a valuable platform for the identification of selective PI3K inhibitors

Article abstract of DOI:10.3390/molecules200917275

A novel series of 4-aryl-3-cyano-2-(3-hydroxyphenyl)-6-morpholino-pyridines have been designed as potential phosphatidylinositol-3-kinase (PI3K) inhibitors. The compounds have been synthesized using the Guareschi reaction to prepare the key 4-aryl- 3-cyano-2,6-dihydroxypyridine intermediate. A different selectivity according to the nature of the aryl group has been observed. Compound 9b is a selective inhibitor against the PI3Kα isoform, maintaining a good inhibitory activity. Docking studies were also performed in order to rationalize its profile of selectivity.

Full text of DOI:10.3390/molecules200917275

Molecules 2015, 20, 17275-17287; doi:10.3390/molecules200917275
OPEN ACCESS
molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
The Guareschi Pyridine Scaffold as a Valuable Platform for the
Identification of Selective PI3K Inhibitors
Ubaldina Galli 1,†, Elisa Ciraolo 2,†, Alberto Massarotti 1, Jean Piero Margaria 2,
Giovanni Sorba 1, Emilio Hirsch 2,* and Gian Cesare Tron 1,*
1
Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale “A. Avogadro”,
Largo Donegani 2, Novara 28100, Italy; E-Mails: ubaldina.galli@uniupo.it (U.G.);
alberto.massarotti@uniupo.it (A.M.); giovanni.sorba@uniupo.it (G.S.)
2
Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center,
University of Torino, Via Nizza 52, Torino 10126, Italy; E-Mails: elisa.ciraolo@unito.it (E.C.);
jeanpiero.margaria@unito.it (J.P.M.)
†
These authors contributed equally to this work.
* Authors to whom correspondence should be addressed; E-Mails: emilio.hirsch@unito.it (E.H.);
giancesare.tron@uniupo.it (G.C.T.); Tel.: +39-116-706-425 (E.H.); +39-321-375-857 (G.C.T.);
Fax: +39-116-706-432 (E.H.); +39-321-375-621 (G.C.T.).
Academic Editor: James W. Leahy
Received: 13 July 2015 / Accepted: 14 September 2015 / Published: 18 September 2015
Abstract: A novel series of 4-aryl-3-cyano-2-(3-hydroxyphenyl)-6-morpholino-pyridines
have been designed as potential phosphatidylinositol-3-kinase (PI3K) inhibitors. The
compounds have been synthesized using the Guareschi reaction to prepare the key 4-aryl-
3-cyano-2,6-dihydroxypyridine intermediate. A different selectivity according to the nature
of the aryl group has been observed. Compound 9b is a selective inhibitor against the
PI3Kα isoform, maintaining a good inhibitory activity. Docking studies were also
performed in order to rationalize its profile of selectivity.
Keywords: PI3 kinase; pyridine; Guareschi reaction; isoforms; selectivity

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1. Introduction
Class I phosphatidylinositol-3-kinases (PI3Ks) [1] are lipid kinases able to phosphorylate the
hydroxyl group at the three position of the phosphatidylinositol-4,5-biphosphate (PdtIns(4,5)P2). They
exert a pivotal role on several cellular processes such as proliferation, survival, motility, metabolism,
and differentiation [2].
Class I PI3Ks are usually heterodimers consisting of a catalytic subunit and an adaptor/regulator
subunit. All class I catalytic subunits share substantial homology and are referred to as p110 subunits.
The contribution of each of the four isoforms of class I PI3Ks has been elucidated in detail, as their
tissue localization [3]. For example, in mammals, whereas the expression of PI3Kδ is restricted to the
immune system, PI3Kα and PI3Kβ are ubiquitously expressed, and the p110γ catalytic isoform is
mainly expressed in leukocytes. For these reasons, the identification of PI3K inhibitors with a different
profile of selectivity can be useful for the treatment of different diseases [4].
Over the last decades, pan-PI3K inhibitors [5,6] were extensively investigated for the treatment of
cancer; however, the use of isoform-selective PI3K inhibitors seems to be a better strategy in cancer
therapy in order to reduce the side effects associated with pan-PI3K inhibitors [7,8]. Alterations in the
PI3K pathway, such as PI3Kα mutations, over-expression, or gene amplification, and PTEN
(phosphatase and tensin homologue) phosphatase deletion, have been identified in several types of
cancer (mammary gland, colon, prostate, brain) [5,6]. Moreover, recent evidence demonstrated that
PI3Kα selective inhibitors [7] are more effective against tumors with mutations in the PI3Kα gene.
PI3Kβ-selective inhibitors have been proposed in the treatment of PTEN-deficient tumors [9–11],
while PI3Kδ inhibitors are currently under evaluation in clinical trials for the treatment of some
specific lymphoproliferative diseases including chronic lymphocytic leukemia (CLL), multiple
myeloma, and Hodgkin’s lymphoma [12–15]. In this context, a more specific targeted therapy instead
of the use of pan-PI3K inhibitors could help to maximize the antitumor effects, reducing the potential
side effects (hematological complications, insulin resistance) associated with an indiscriminate
inhibition of all the PI3K isoforms.
The identification of selective PI3K inhibitors is still a topic of research both in industry and
academia and, to date, several potent PI3K inhibitors, able to compete with the ATP binding site, have
been reported [16–19].
The intellectual property of ATP-competitive inhibitors is highly over-crowded, rendering the
identification of novel molecular entities a daunting task for medicinal chemists. One important feature
present in most of the ATP-competitive PI3K inhibitors is the presence of the so-called clamp
motif [20] formed by a morpholine, a hinge-binder typical for lipid kinases, and a meta-substituted
phenol (or one of its bioisosteres) grafted onto a heteroaromatic ring (Figure 1).
The strategy of the clamp motif grafted to a heteroatomatic ring has been utilized by several
research groups. For example, cyanuric chloride was used as the starting material, exploiting the
different reactivity of chlorine atoms in the nucleophilic aromatic substitution to add different
hinge-binders [21].
With this in mind, looking for novel PI3K inhibitors, we focused our attention on the neglected
3-cyano-2,6-dihydroxypyridine scaffold, which can be obtained via Guareschi reaction [22], as a
valuable chemical platform. Indeed, it contains all the chemical functions to build the clamp motif and

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a group pointing towards the rim of the binding pocket. Furthermore, the pyridine ring can increase the
solubility, while the cyano group is an added bonus as it might play an active role in the kinase
inhibition [23] or it can be considered as a handle for further chemical manipulations (Figure 2). As far
as we know, this is the first attempt to use this chemical scaffold in the kinase inhibitor field.
Figure 1. The clamp motif strategy for the identification of novel PI3K inhibitors (in the
case of PI3Kγ, the phenol group interacts with Tyr867, while morpholine interacts
with Val882).
Figure 2. The Guareschi pyridine scaffold can be advantageously used for the design of
novel PI3K inhibitors.
As the amino acid residues located at the entrance to the catalytic site are not conserved in the
different PI3K isoforms [24], we decided to maintain the morpholine and phenol clamp motifs,
exploring the C4-position of the pyridine ring introducing different aromatic groups. It would be
expected that these groups, which protrude outside the ATP-binding pocket, might give additional
contacts with the less conserved amino acid residues, altering the profile of selectivity.
The synthesis, the biological activity, and the PI3K subtype selectivity of the compounds
synthesized are presented herein.
2. Results and Discussion
The 4-aryl-3-cyano-2,6-dihydroxypyridines (3a–h) were synthesized using the improved Guareschi
pyridine synthesis reported by Bobbit and Scola [25]. This methodology consists of the condensation

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of aryl β-keto esters (1a–h) and cyanoacetamide (2) in potassium hydroxide at reflux using methanol
as solvent (Scheme 1).
Aryl β-keto esters 1a–h were prepared from the corresponding commercially available aryl
methyl-ketones 4a–h by deprotonation with sodium hydride and quenching with dimethylcarbonate
(5) [26] (Scheme 2).
Scheme 1. The Guareschi pyridine reaction.
Scheme 2. Synthesis of aryl β-keto esters.
Condensation of these crude dicarbonyl compounds with cyanoacetamide under basic conditions
afforded the corresponding 4-aryl-3-cyano-2,6-dihydroxypyridines (3a–h) (Scheme 1). Despite our
effort to optimize this reaction, the compounds were obtained in modest yields (Table 1).
Table 1. Yields of 4-aryl-3-cyano-2,6-dihydroxypyridines.
Compound Yield (%)
3a
3b
3c
3d
3e
3f
41
15
14
28
9
27
26
10
3g
3h

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This result can be ascribed to the behavior of β-ketoesters which decarboxylate at high
temperatures, and then they underwent ester hydrolysis to β-ketoacids under these basic conditions. In
confirmation of this situation, we recovered aryl methyl-ketones from the reaction mixture.
Unfortunately, under room temperature, the Guareschi reaction did not take place and the use of a
milder reported procedure (1,4-diazabicyclo[2.2.2]octane or DABCO®, r.t.) failed to afford the desired
products [27].
The key intermediates (3a–h) were then converted to the corresponding dichlorides (6a–h) with
phosphorus oxychloride (Scheme 3).
Scheme 3. Synthesis of the dichloride analogues.
The regioselective reaction with morpholine in methanol afforded the derivatives 7a–h (Scheme 4).
A recent paper demonstrated that regioselectivity at the six position can be easily achieved using a
polar solvent like methanol [28].
Scheme 4. Regioselective addition of morpholine at the six position.
Finally, the desired tetrasubstituted pyridines 9a–h were obtained via Suzuki coupling with
3-hydroxyphenylboronic acid (8) (Scheme 5).
Scheme 5. Synthesis of compounds 9a–h.

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All the synthesized compounds were then tested in vitro for their ability to inhibit the kinase activity
of the PI3Kα, PI3Kβ, PI3Kγ, and PI3Kδ isoforms in a luminescent kinase assay (ADP-GloTM kinase
assay) using purified, recombinant human enzymes and ATP. IC50 values were subsequently determined.
As shown in Table 2, the compounds display an activity at low micromolar concentrations against
the four isoforms, changing their profile of selectivity according to the type of aryl group on the
four position of pyridine. In particular, for this series of compounds, the molecule 9b stands over all
the others, showing a remarkable profile of selectivity toward the PI3Kα isoform.
Table 2. IC50 inhibitory profile and standard error (SE).
IC50 Values (µM)
Compound
PI3Kα
PI3Kβ
PI3Kγ
PI3Kδ
9a
9b
9c
9d
9e
9f
0.13 (SE ± 0.03)
0.63 (SE ± 0.13)
1.79 (SE ± 0.47)
0.63 (SE ± 0.15)
0.83 (SE ± 0.15)
>10
1.99 (SE ± 0.79)
>10
1.22 (SE ± 0.47)
>10
>10
>10
>10
2.34 (SE ± 0.54)
6.48 (SE ± 1.85)
>10
2.18 (SE ± 0.51)
1.64 (SE ± 0.29)
2.91 (SE ± 0.56)
4.43 (SE ± 0.69)
1.56 (SE ± 0.27)
2.43 (SE ± 0.41)
1.37 (SE ± 0.37)
1.09 (SE ± 0.19)
0.90 (SE ± 0.11)
1.33 (SE ± 0.19)
0.85 (SE ± 0.14)
0.71 (SE ± 0.13)
9g
9h
1.23 (SE ± 0.14)
0.98 (SE ± 0.12)
>10
>10
Subsequently, compound 9b was analyzed on cell-based assay in order to evaluate its ability to
inhibit the PI3Kα signaling pathway on cells. It is well established that insulin signaling is mostly
regulated by PI3Kα [29]. The activated insulin receptor triggers PI3Kα activity mainly by binding and
phosphorylating adaptor proteins of the IRS (insulin receptor substrate) family. Once activated, PI3Kα
produces the PtdIns(3,4,5)P3 lipid product, which in turn mediates the activation of downstream
effectors such as Akt. Thus, phosphorylation of Akt results as a key event of the PI3Kα activation. In
order to define whether compound 9b was able to inhibit PI3Kα activity and, consequently, the insulin
signaling, NIH3T3 cells were stimulated with insulin in the presence or absence of different
concentrations of compound 9b. A dose response curve and an IC50 value were determined. Compound
9b showed an IC50 value of 2.8 µM (SE ± 0.6), thus demonstrating its ability to inhibit PI3Kα in a
cellular context as well.
Molecular modeling studies were performed in order to investigate and rationalize this interesting
selectivity. A simple search in the Protein Data Bank reveals over 50 releases spanning over all four
PI3K isoforms, with only isoforms α and γ available from human sources. Docking compounds to
rationalize little differences in activity still remains a challenge [30]. However, in our case, compound 9b
shows a relevant difference in activity against PI3Kα and PI3Kγ.
In order to verify the importance of the aryl group at the C4 position to impart isoform selectivity,
analogue 10, where the aryl group has been replaced with a methyl group, was also considered and
docked (Figure 3) (for the synthesis of 10 see supporting information).
Compound 10 is indeed a pan-inhibitor against the different isoforms (PI3Kα = 1.18 μM ± 0.17,
PI3Kβ = 1.55 μM ± 0.30, PI3Kγ = 1.05 μM ± 0.10, and PI3Kδ = 0.42 μM ± 0.05).

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Figure 3. Compounds 9b and 10 were docked on α and γ human PI3Ks.
Both compounds were prepared using Omega2 [31–33], and the docking software FRED [34,35]
was used to predict their binding poses. The docking results for compound 10 (Supporting Information
Table S1, Figure S1) showed a shared binding mode over the considered isoforms α and γ. The oxygen
of morpholine is able to form a hydrogen bond interaction with the -NH of PI3Kγ Val882 (PI3Kα
Val851) in the hinge region, while the phenolic group acts as hydrogen bond donor interacting with the
–OH of Tyr867 in PI3Kγ (Tyr836 in PI3Kα). The methyl and cyano groups protrude toward the
solvent-exposed region.
Poses of compound 9b are consistent with docking results of 10 (Figure 4a,b). In this case, the aryl
group protrudes toward the solvent-exposed region. The second aryl group of 9b fits in a hydrophobic
zone near Cys862 in PI3Kα, while in PI3Kγ a more polar environment is present. This is a
consequence of the presence of Gln893 (Figure 5a,b). In PI3Kα the terminal oxydibenzene ring is
positioned above an electrostatically positive area (Figure 5a), and this would be an attracting
interaction with the electronegative π-cloud of the terminal ring of 9b. In PI3Kγ the area below the
terminal oxydibenzene ring is electrostatically negative and that would make for an unfavorable
interaction (Figure 5b).
Figure 4. Predicted binding pose of compound 9b (purple sticks) in the PI3Kα (a) and
PI3Kγ (b) binding sites (green sticks and white cartoon); aminoacids of hinge region are
shown as yellow sticks.

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Figure 5. Details of surface electrostatic charges in PI3Kα (a) and PI3Kγ (b). The
colors denote the electrostatic charge at the surface of the protein from negative (blue) to
positive (red).
3. Experimental Section
3.1. Molecular Modeling
All molecular modeling studies were performed on a Tesla workstation equipped with two Intel
Xenon X5650 2.67 GHz processors and Ubuntu 12.04 (www.ubuntu.com). All structural images were
prepared using PyMOL [36] with the APBS plugin [37]. Different crystal structures of human PI3K
isoforms with inhibitors have been reported; we select in our study the X-ray structures showing high
resolution (<3 Å) and high chemical similarity of cocrystalized ligand to our compounds. The selected
Protein Data Bank (PDB) id were: human PI3Kα (PDB id: 3ZIM, resolution 2.85 Å) [38], and human
PI3Kγ (PDB id: 3DBS, res. 2.80 Å) [39]. Water molecules and ligands were removed; the binding site
was detected using the original ligand coordinates (Supporting Information Figure S2). Hydrogens
were added to the protein complexes, protonation and tautomer states were set, and finally the
hydrogen bond network was optimized using the MolProbity server. [40]. Ligand structures were built
from a SMILES string and were minimized using Omega2 [31–33]. A conformer library was built with
the program Omega2, which generated an average of 81 conformations per molecule. Default
parameters were used. The docking simulations were performed using FRED [34,35]. Two constraints
were applied due to the presence of hydrogen bond between the original ligands and active pocket
residues (referring PI3Kγ numbering: Val882, backbone amide hydrogen, and Tyr867, phenol
oxygen). Default settings were used.
3.2. Chemistry
Synthetic procedures and spectral data are reported in the Supporting Information.
3.3. In Vitro Enzyme Inhibition
To evaluate the ability of each compound of formula (9a–h) to inhibit the lipid kinase activity of each
PI3K isoform, 30 ng of PI3Kα, β, γ, and δ recombinant protein (purchased from JenaBioscience—Jena,
Germany; PI3Kα #PR-335, PI3Kβ #PR-344, PI3Kγ #PR-343, PI3Kδ #PR-345) were incubated with at
least five different concentrations (from 0.016 to 10 µM) of the compounds (9a–h). The

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phosphorylation reaction was then started by adding 10 μM of ATP, and 10 µg of lipid micelles
containing the appropriate substrate phosphatidylinositol and the phosphatidylserine [41,42].
After 30 min of incubation (1 h for PI3Kβ recombinant protein) at room temperature, the reaction was
stopped, and the amount of ADP metabolite was measured with a luminescent kinase assay, ADP-GloTM
Kinase Assay (purchased from Promega—USA #V9101). The luminescent signal positively correlated
with the formed ADP and, therefore, with the kinase activity. The percentage of kinase activity was
calculated over the control samples, containing only dimethyl sulfoxide (DMSO). To derive the IC50
values for each assayed compound (9a–h), all data were plotted on a dose response curve (Graph Pad
Software) and the IC50 was calculated by using the nonlinear regression fit (equation (log agonist) vs.
response—Sigmoidal dose response). The IC50 was representative of two different experiments performed
in triplicate.
3.4. Cell-Based Assay
NIH3T3 cells were cultured in Eagle's minimal essential medium (DMEM) (GIBCO-Thermo Fisher
Scientific Inc., Waltham, MA, USA) supplemented with 10% Fetal Bovine Serum (FBS) (GIBCO-Thermo
Fisher Scientific Inc.), 100 units/mL penicillin (GIBCO-Thermo Fisher Scientific Inc.), and 100 μg/mL
streptomycin (GIBCO- Thermo Fisher Scientific Inc.). The day before the assay, NIH3T3 cells were
seeded in a 96-well plate at a concentration of 5 × 104 cells/mL and starved O.N. in presence of
DMEM 0.5% FBS. Subsequently, cells were pre-treated for 1.5 h with the inhibitor at different
concentrations (From 0.03 µM to 20 µM). Then cells were stimulated for 5 min with DMEM
containing 1 μM of insulin and proteins were extracted with Laemmli buffer. The P-Akt production is
detected by Western blot analysis and quantified with ChemiDoc™ XRS system. From the absolute
values, a percentage of residual P-Akt is calculated for each inhibitor concentration by using the
control vehicle as 100%. To derive the IC50, all data are plotted on a dose response curve (Graph Pad
software) and the IC50 is calculated by using the non-linear regression fit (equation (log agonist) vs.
response—Sigmoidal dose response) on three different experiments.
4. Conclusions
In this manuscript, we described the use of 4-aryl-3-cyano-2-(3-hydroxyphenyl)-6-morpholino-pyridines
as valuable starting points for the synthesis of PI3K inhibitors. We demonstrated that the modifications
on the C4-position of this pyridine scaffold could impart a different profile of selectivity on the PI3K
isoforms according to the pattern of substitution.
Compound 9b was the most interesting of the series, with an activity profile selective for the
PI3Kα isoform.
Molecular modeling studies tried to rationalize this profile of selectivity, pointing out that the
presence of a polar Gln893 in the PI3Kγ isoform may disrupt the binding of 9b through unfavorable
electrostatic interactions.
Given these interesting results, further medicinal chemistry efforts are in progress to synthesize
more structurally diverse analogues using the Guareschi reaction with the aim to increase the potency
and identify different profiles of selectivity.

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Supplementary Materials
Supplementary materials can be accessed at: http://www.mdpi.com/1420-3049/20/09/17275/s1.
Acknowledgments
A.M. and G.S. gratefully acknowledge OpenEye Scientific Software Inc. (Santa Fe, NM, USA) for
providing an academic license for their software packages. Financial support from the Università del
Piemonte Orientale (Italy) and FIRB 2012 “Infiammazione e cancro: approcci innovativi basati su
nanotecnologie” MIUR Italy is gratefully acknowledged. The work was also supported by AIRC and
Regione Piemonte (E.H.).
Author Contributions
U.G. carried out the synthesis of the compounds and wrote synthetic procedures; E.C. and J.P.M.
evaluated the biological activity; A.M. carried out the molecular docking studies; G.S. and G.C.T.
designed the research; G.C.T. and E.H. wrote the paper. All the authors read and approved the
final manuscript.
Conflicts of Interest
E.H. and G.C.T. are co-founders of Kither Biotech Srl. The other authors declare that they do not
have competing interests.
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Sample Availability: Samples of the compounds 9a–h and 10 are available from the authors.
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