The isoprenoid derivative N6-benzyladenosine CM223 exerts antitumor effects in glioma patient-derived primary cells through the mevalonate pathway

Article abstract of DOI:10.1111/bph.13824

Background and Purpose: N⁶-Isopentenyladenosine (i6A) is a modified nucleoside exerting in vitro and in vivo antiproliferative effects. We previously demonstrated that the actions of i6A correlate with the expression and activity of farnesyl pyrophosphate synthase (FPPS), a key enzyme involved in the mevalonate (MVA) pathway, which is aberrant in brain cancer. To develop new anti-glioma strategies, we tested related compounds exhibiting greater activity than i6A. Experimental Approach: We designed and synthesized i6A derivatives characterized by the introduction of diverse chemical moieties in the N6 position of adenosine and tested for their efficacy in U87 cells and in primary glioma cultures, derived from patients. NMR-based structural analysis, molecular docking calculations and siRNA mediated knockdown were used to clarify the molecular basis of their action, targeting FPPS protein. Key Results: CM223, the i6A derivative including a benzyl moiety in N6 position of adenine, showed marked activity in selectively targeting glioma cells, but not normal human astrocytes. This was due to induction of intrinsic pathways of apoptosis and inhibition of proliferation, along with blockade of FPPS-dependent protein prenylation, which counteracted oncogenic signalling mediated by EGF receptors. Conclusion and Implications: The biological effects together with structural data on interaction of CM223 with FPPS, provided additional evidence for the correlation of the i6A/CM223 antitumor activity with FPPS modulation. Because the MVA pathway is an important promising target, CM223 and its derivatives should be considered interesting active molecules in antiglioma research.

Full text of DOI:10.1111/bph.13824

The isoprenoid derivative N6-benzyladenosine (CM223) exerts antitumor effect in
glioma patient-derived primary cells through the mevalonate pathway.
Elena Ciaglia,a Manuela Grimaldi,b Mario Abate,a Mario Scrima,b Manuela Rodriquez,b Chiara
Laezza,c Roberta Ranieri,a Simona Pisanti,a Pierangela Ciuffreda,d Clementina Manera,e Patrizia
Gazzerro,b Anna Maria D’Ursi*b and Maurizio Bifulco*a,f.
aDepartment of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Via Salvatore
Allende, 84081 Baronissi Salerno, Italy
bDepartment of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano Salerno, Italy.
cDepartment of Biology and Cellular and Molecular Pathology, University of Naples Federico II, Via Pansini, 80131
Naples, Italy.
dDipartimento di Scienze Biomediche e Cliniche “Luigi Sacco”, Università degli Studi di Milano, Via G.B. Grassi 74,
20157 Milano, Italy.
eDepartment of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy.
fCORPOREA-Fondazione Idis-Città della Scienza, via Coroglio 104 e 57, 80124 Naples, Italy.
Funding: This study was supported by Associazione Italiana Ricerca sul Cancro (AIRC; IG 13312
and IG18999 to M. Bifulco). E. Ciaglia was supported by a fellowship from Fondazione Umberto
Veronesi (FUV 2017, cod.1072).
Conflict-of-interest disclosure: The authors declare no competing financial interests.

Abstract:
Background and Purpose: N6-Isopentenyladenosine (i6A) is a modified nucleoside exerting in
vitro and in vivo antiproliferative effects. We previously demonstrated that the i6A action is
correlated to farnesyl pyrophosphate synthase (FPPS) expression and activity, a key enzyme
involved in the mevalonate (MVA) pathway, which is found aberrant in brain cancer. To develop
new anti-glioma strategies, we looked for other valuable compounds exhibiting improved activity as
compared to i6A.
Experimental Approach: we designed and synthesized i6A derivatives characterized by the
introduction of diverse chemical moieties in the N6 position of adenosine and tested for their
efficacy in U87 and primary derived patient’s glioma cell model. NMR based structural analysis,
molecular docking calculations and siRNA mediated knock-down helped to clarify the molecular
basis of their action, targeting FPPS protein.
Key results: We demonstrated that CM223, the i6A derivative including a benzyl moiety in N6
position of adenine, is endowed with a marked activity in selectively targeting glioma cells but not
normal human astrocytes (NHA). This is achieved by the induction of intrinsic pathways of
apoptosis and inhibition of proliferation along a FPPS-dependent protein prenylation blocking,
which counteract the oncogenic signaling mediated by the epidermal growth factor receptor
(EGFR).
Conclusion and Implications: This biological effect together with structural data on interaction of
CM223 with FPPS, gain additional evidence on the correlation of the i6A/CM223 antitumoral
activity with FPPS modulation. Because the MVA pathway is becoming an important promising
target, CM223 and derivatives should be considered interesting active molecules in antiglioma
pharmacological research.

Introduction.
N6-Isopentenyladenosine (i6A) is a modified nucleoside, formed by an adenosine harboring an
isopentenyl chain derived from dimethylallyl pyrophosphate in the N6 position. It belongs to the
cytokinin family, involved in control of many processes in plants. (Bifulco, Malfitano, Proto,
Santoro, Caruso & Laezza, 2008; Kersten, 1984; Laten & Zahareasdoktor, 1985) In humans, many
biological actions, both in vitro and in vivo, including antitumoral effects, can be attributed to i6A.
(Castiglioni, Casati, Ottria, Ciuffreda & Maier, 2013; Laezza et al., 2014; Laezza et al., 2015;
Pisanti et al., 2014; Woo et al., 2010; Ciaglia et al., 2017)
Interest in the study of this compound has been reinforced by our previous experimental
observations that i6A interferes with the growth of k-ras transformed thyroid cells (KiMol)
xenograft tumors by inhibiting farnesyl pyrophosphate synthase (FPPS) expression and activity
(Laezza et al., 2006). Moreover i6A, exhibited immunomodulatory properties as it selectively
expands and directly targets human natural killer cells through FPPS modulation (Ciaglia et al.,
2013).
FPPS is a key enzyme involved in the mevalonate pathway and in downstream proteins
prenylation; it catalyzes the two steps synthesis of the C15 isoprenoid farnesyl pyrophosphate
(FPP), a crucial precursor for the synthesis of several classes of essential metabolites, such as
sterols, ubiquinones and carotenoids. Therefore, FPPS plays a critical role in many vital cell
reactions such as protein prenylation, synthesis of cell membrane constituents and signal
transduction components. (Sacchettini & Poulter, 1997; Szkopinska & Plochocka, 2005) FPPS is
currently the main biochemical target of bisphosphonates for the treatment of bone-related
disorders, such as osteoporosis diseases, and metastatic bone-related tumors. However, as it is
implicated in many cancer related pathways, and appears deregulated in many tumors, (Thurnher,
Nussbaumer & Gruenbacher, 2012) it draws the interest of the pharmaceutical field in view of the
identification of new specific anticancer compounds. (Fournier, Dauhine, Lundy, Rogers, Ebetino &
Clezardin, 2008; Jahnke et al., 2010) Looking for molecular targets of i6A, using in silico inverse

virtual screening, (Chen & Zhi, 2001; Lauro, Romano, Riccio & Bifulco, 2011; Wang, Chu, Chen
& Lin, 2012) we recently gained additional proofs that FPPS is a valuable molecular target for
i6A.(Scrima et al., 2014) Saturation transfer difference (STD) NMR experiments and enzymatic
assay indicated that i6A is able to bind FPPS active site exerting a moderate inhibition of its
enzymatic activity (vide intra). (Ciaglia et al., 2013; Laezza et al., 2006) Indeed, molecular docking
calculations evidenced that i6A is able to occupy the FPPS active site, with a significant
contribution of the isopentenyl portion of the molecule. (Scrima et al., 2014)
Inspired by these data, in the search of a compound exhibiting improved activity as compared to
i6A, we designed and synthesized i6A derivatives characterized by the introduction of new
substituents in the N6 position of adenosine. (Scheme 1; See Supporting Information): insertion of a
phenyl ring characterized by increasing steric hindrance at 6 position of adenosine (FP11, FP13 and
FP16), insertion, in the same position, of a benzyl ring (CM223) and double bond elimination
(CM224). (Figure 1A). (Ottria, Casati, Baldoli, Maier & Ciuffreda, 2010)
All the compounds were tested for their anti-proliferative activity on U87MG and patients-
derived primary glioma cells. Glioblastoma (GBM) is the most common and highly malignant brain
tumor: recent work highlighted the importance of isoprenoid pathway, regulated by FPPS enzyme,
for glioma development, progression and chemoresistance. (Laezza et al., 2015; Woo et al., 2010).
Very recently it has been highlighted that GBM cells rely on cholesterol uptake for survival. (Villa
et al., 2016) This provides new insights into more effective therapeutic strategies in GBM
treatment, suggesting the repositioning of old class of drugs or the synthesis of new ones that
modulates de novo cholesterol biosynthesis.
In this work we demonstrate that CM223, the i6A derivative including a benzyl moiety in N6
position of adenine, is endowed with a marked cytostatic and cytotoxic activity, higher than the
parent compound i6A. NMR based structural analysis and molecular docking calculations,
evidencing a clear structural interaction of CM223 with FPPS, further delineate the molecular basis
to understand the interaction between i6A analogues and FPPS enzyme and the key events of

antiglioma action of these compounds. In this context the documented antiglioma action of CM223
was mediated primarily by the FPPS-dependent disruption of those lipid moieties which seem to be
critical for the functionality and activity of epidermal growth factor receptor (EGFR) (Warren &
Landgraf, 2006) and its downstream signaling proteins in glioma tumor growth and maintenance.
(Furnari, Cloughesy, Cavenee & Mischel, 2015)
. RESULTS
Chemistry. CM223 and CM224 were prepared and purified as described previously. (Ottria,
Casati, Baldoli, Maier & Ciuffreda, 2010) FP11, FP13 and FP16 were prepared modifying the
synthetic route previously reported (Scheme S1; See Supporting Information). (Hocek, Holy,
Votruba & Dvorakova, 2000) Purity of all compounds (≥ 99%) was verified by HPLC, nuclear
magnetic resonance and mass spectrometry measurements. Structures of the aforementioned
chemicals are presented in Figure 1.
Compounds FP11, FP13 and FP16 were obtained by the synthetic route described in the Scheme
S1 (See Supporting Information).
BIOLOGICAL ASSAYS
Dose - response studies of the effects of i6A and its analogs on DNA synthesis of U87 glioma
cells. The nucleoside i6A and its analogs CM223, CM224, FP11, FP13, FP16 (whose chemical
structures are shown in Figure 1A) were tested to compare their capability to inhibit the growth of
U87MG human glioma cells. To this end U87 were incubated with increasing concentrations of the
indicated compounds. In particular, as i6A had previously shown inhibitory activity in the range
0.3-20 µM, its analogs were tested for antiproliferative activity in the same range for 48h. As
reported in Figure 1B, i6A-exposed glioma cells showed a dose-dependent inhibition of
proliferation compared with untreated cells, as demonstrated by the BrdU incorporation assay.
Interestingly the compound CM223 elicited a more pronounced effect as compared to i6A (P≤

0.05) in the same conditions, whereas CM224, FP11, FP13 and FP16 compounds showed a lack of
activity.
Analysis of the cytostatic and cytotoxic potential for the i6A derivative CM223 on U87 glioma
cells and normal primary astrocytes. The growth inhibitory effect of CM223 was further
investigated at different time points by proliferation and clonogenic assay. i6A – whose anti -
glioma effect has recently reported by our group (Ciaglia et al., 2017) was used as reference.
Specifically the anti-proliferative capacity of increasing concentrations of i6A or CM223 in a 0.3-
20 µM concentration range was assessed in time course (24-72 h) on proliferating U87MG cells by
BrdU incorporation assay (Figure 2A). After 48 h treatment, i6A-exposed glioma cells showed a
dose-dependent inhibition of proliferation compared to untreated cells; in particular, a clear
reduction of proliferative rate became evident at a concentration of about 7.5 µM. Of note, CM223
elicited a more significant reduction of U87MG proliferation as compared to i6A-treated cancer
cells, as a significant response was already achieved at a concentration of 1.2 µM. Of course, this
inhibitory effect on proliferating cells became more evident after 72 h - treatment. Interestingly,
CM223 was able to exert a more significant effect also on the formation of clones (Figure 2B).
Indeed a reduction of number and dimension of clones was registered already in cells treated with
the lowest concentrations of CM223 1 μM and 2.5 μM.
To assess whether the inhibition of cell proliferation by i6A and especially by CM223 was also
associated to the induction of apoptosis, we performed a cytofluorimetric cell death analysis by
Annexin-V and propidium iodide staining. i6A and CM223 exhibited a dose-dependent activity to
induce apoptosis when glioma cells were treated for 48 h (Figure 2C, upper panel). Interestingly
even in this experiment, the percentage of cells in early and late apoptosis after CM223 treatment
was significantly higher as compared to i6A treatment, overall suggesting a better cytostatic and
cytotoxic potential for this i6A derivative. Interestingly CM223 elicited no significant reduction of

normal human astrocyte (NHA) cell viability as compared to cancer cells in the same condition
(Figure 2C, lower panel).
FPPS-CM223 structural interaction: NMR spectroscopy
We have previously demonstrated that i6A interferes with the growth of k-ras transformed
thyroid cells (KiMol) xenograft tumors by inhibiting FPPS expression and activity (Laezza et al.,
2006); moreover the immunomodulatory activity of i6A is proved to occur through FPPS
modulation (Ciaglia et al., 2013). Preliminary NMR data and colorimetric enzymatic assay
evidenced that i6A interacts with FPPS binding site inducing a moderate inhibition of its activity.
Following the screening for the cytostatic and cytotoxic activity of i6A analogs (Figure 1) and to
confirm that activity of these compounds occurs even through FPPS inhibition, we analyzed by
STD NMR experiments (Mayer & Meyer, 1999; Mayer & Meyer, 2001) i6A analogues reported in
Figure 1 for their ability to interact with FPPS protein. (Figure 3A). STD is a powerful NMR
technique that enables the identification of new protein-ligands enabling the determinations of
protein-ligand dissociation constants (KD). NMR sample containing 8.0 μM of FPPS was titrated
with i6A-analogs to have STD build-up at protein-ligand molar ratios: 1:10, 1:20, 1:30, 1:50, 1:70,
and 1:100. For each titration point, STD experiments were carried out using different saturation
1
times (0.50, 1.00, 1.50, 2.00, 3.00, 4.00, and 5.00 s).(Angulo & Nieto, 2011) Standard H
monodimensional and 2D COSY NMR experiments allowed the 1H chemical shift assignment of
i6A-analogs proton signals. (Figure S2-S6; See Supporting Information)
Analysis of STD-NMR experiments for the compounds CM223 and CM224 characterized by
the insertion of the benzyl (CM223) and isopentyl moiety (CM224) indicates a marked interaction
with the enzyme, with an important participation of the adenosine moiety (in particular protons H2-
H8, H4”-H8”, H5”-H7”, H6” and H1’). These effects reached the significant value of 30% CM223
and 20% CM224 respectively. (Figure 3A) The compounds of FP series, containing the aromatic
ring directly linked to the 6-position of adenosine, show less marked interactions. (Supplementary

material, Figure S1) To confirm that i6A analogues (Figure 1A) bind FPPS active site instead of
allosteric binding site, (Jahnke et al., 2010) FPPS-ligand complexes were titrated with increasing
concentrations of 3-carboxymethyl-5,7-dichloro-1H-indole-2-carboxylic acid (allosteric modulator
IC50 = 6.) (Jahnke et al., 2010) and zoledronic acid, high affinity FPPS inhibitor (data not
shown). (Scrima et al., 2014) The quantitative evaluation of STD data confirm that the compound
CM223 interacts with FPPS binding site with a consistent contribution of the N6 substituents.
We calculated the KD for the complex FPPS-CM223 interaction based on the quantitative
measurement of STD effects (Figure 3B). We collected experiments at different protein-ligand
ratios and saturation time conditions, according to the methodology developed by Angulo et al.
(Angulo & Nieto, 2011). Using this procedure, the calculation of protein-ligand affinities is
independent from contingent experimental factors, such as STD saturation time, ligand residence
time in the complex, and the intensity of the signal. (Angulo & Nieto, 2011)
NMR sample containing 8 μM of FPPS was titrated with CM223 to have STD build-up at
protein-ligand molar ratios: 1:10, 1:20, 1:30, 1:50, 1:70, and 1:100. For each titration point, we
recorded STD experiments using different saturation times (0.50, 1.00, 1.50, 2.00, 3.00, 4.00, and
5.00s). The mean KD value calculated for the single protons of CM223 (Figure 3B) is 0.19 mM.
This value, that is 5 fold lower as i6A-FPPS KD value, (Scrima et al., 2014) indicates an
improvement in the binding with FPPS target for CM223 and suggests that the newly introduced
benzyl portion of the molecule may lead to more active FPPS inhibitors.
Interprotonic distances calculated on the basis of STD NMR experiments were imposed as
restraints in molecular docking calculations (AutoDock 4.2 software) (Morris et al., 2009).
Compounds CM223 and FP13, respectively representative of the most and least FPPS binders,
were subjected to molecular docking simulations against 3D FPPS protein model (PDB code:
1ZW5), selected in inverse virtual screening procedure in our previous work (Scrima et al., 2014;
Kavanagh et al., 2006) For an exhaustive exploration of conformational space, iterative docking
calculations consisting of 250 runs were executed, yielding 1500 structures. The resulting binding

poses were clustered together according to positional rmsd (rmsd< 3.5 Å). Docking analysis
revealed a favorable accommodation of i6A analogues in the binding site of FPPS through a large
set of both hydrophobic and polar interactions (Figure 3D). Sugar moiety establishes a network of
H-bonds with Asp118, Asp257 and Lys271.
Adenine core of the molecule is oriented between the three Mg ions co-crystallized with FPPS,
making polar contacts with Lys214, Asp257 and H-bonding with Gln254. In CM223, the benzyl
portion, analogously to isopentenyl moiety of i6A, is placed in the deeper region of the binding site
and engages pi-stacking interactions with Phe113, and Tyr218 of the enzyme. (Scrima et al., 2014)
The increased binding of CM223 (Kd 0.19 mM) as compared to i6A (Kd 1.0 mM) may be due to
these interactions that in CM223 are stabilized by the presence of the aromatic benzyl ring instead
of the isopentenyl chain. Concerning FP13, the difference in the binding mode as compared to i6A
and CM223 is due to the phenyl ring that represents a low flexibility point for this molecule. STD
NMR data, on the contrary show that the weak binding of FP13 with FPPS catalytic pocket is based
on interaction of ribose sugar moiety.
FPPS colorimetric assay. To test whether the interaction of CM223 with FPPS, observed in NMR
data, might result in an enhancement of enzyme inhibition compared to i6A, we performed a
colorimetric assay. (Gao et al., 2010)
The histograms in Figure 3C show FPPS activity after the pre-treatment with CM223 (from 0.1
to 5 mM, 30 min 37 °C) or i6A (from 1.0 to 5 mM, 30 min 37 °C) used for comparison. Enzymatic
activities of FPPS in absence and in presence of high affinity FPPS inhibitor, zoledronic acid (1-2
µM, 30 min 37 °C) are reported as negative and positive controls. As expected, even though far
away from the inhibition efficiency achieved by the bisphosphonate, the curves indicate a trend of
inhibition of FPPS activity by i6A and to a more extent by CM223, with an EC50 value of 5.33
mM and 3.33 mM respectively. This suggest that the modulation of enzyme activity by CM223 is

really improved with respect to the isoprenoid counterpart i6A, even if we cannot rule out the
targeting of other enzymes of the pathway beyond the FPPS.
CM223 acts on U87 glioma cells via FPPS modulation and disruption of lipid dependent-EGF
receptor signaling pathway.
In order to verify that CM223 anti-proliferative and pro- apoptotic effects on U87 glioma cells
were associated with its capacity to interfere with the mevalonate pathway in terms of FPPS
modulation, first we moved to test the ability of CM223 to inhibit post-translational modification of
small GTP-binding proteins, by analyzing the prenylation status of Ras-proximate-1 or Ras-related
protein 1 (Rap1A). Rap1A is a protein prenylated exclusively by GGTase, and its unprenylated
form is recognized by a specific unprenylated anti-Rap1A antibody. U87MG cells were treated with
i6A, CM223 and Zoledronic acid (ZA) for comparison, for 24 h. In control epidermal growth factor
(EGF)-treated U87 cells, Rap1A was in the processed prenylated forms, so not detected in western
blot analysis. As expected, by acting through FPPS modulation, treatment with ZA or i6A and to a
more extent with CM223 inhibited the processing of Rap1A, resulting in increased level of
unprenylated Rap1A form (Figure 4A). Interestingly the transfection of U87MG cells with FPPS
siRNA increased their sensitivity to CM223. Indeed, while FPPS siRNA transfection alone did not
modify the unprenylated Rap1A expression kinetic, probably due to a residual activity of the
enzyme after its knock-down which guarantee the sufficient synthesis of isoprenoid (or other lipid)
moiety, (Wang, Panasiuk & Grainger, 2011) in FPPS siRNA-CM223 co-treatment, the induction of
unprenylated Rap1A expression by CM223 was more evident (Figure 4B), suggesting a more
complete inhibition of FPPS activity achieved by the combination. At the same way a parallel
accumulation of Ras in its unprenylated form, seen as an “up-smearing” on immunoblots, has been
also highlighted. Overall these data point out to FPPS as a possible target of action of CM223. As
lipid environment of plasma membranes and lipids-proteins interaction have been proposed as
molecular platform important for oncogenic signaling processes, (Warren & Landgraf, 2006) then

we moved to test the influence of CM223 on the activity of receptors embedded in the membrane.
Among them, the epidermal growth factor receptor (EGFR, also referred to as ERBB1 or HER1), is
a well-known oncoprotein belonging to HER superfamily of receptor tyrosine kinases together with
ERBB2, ERBB3, and ERBB4. It constitutes the most common genetic alteration associated with
malignant glioma where its over-activation and/or overexpression is responsible for the
deregulation of pleiotropic cellular processes, including cell differentiation, metabolism,
proliferation, and survival. (Furnari, Cloughesy, Cavenee & Mischel, 2015) As expected the
stimulation with EGF induced an early activation of EGF receptor (10 min) by significantly
increasing the EGFR phosphorylation on tyrosine 1068 (Figure 4C). As consequence the rapid
activation of downstream Signal transducer and activator of transcription 3 (STAT3) signaling
pathway was achieved. In this experimental setting the importance of lipid environment in EGFR
physiology was highlighted by the treatment with the membrane impermeable, small cyclic
oligosaccharide methyl--cyclodextrin (MCD). Indeed through the disorganization of lipid rafts
by mean of cholesterol extraction, MCD was able to alter receptor signaling by reducing the
downstream phosphorylation levels of STAT3 in response to EGF (Figure 4C, left panel). The
recovering from cholesterol depletion and the inhibition by MCD was totally reversed after 3h
from its removal even in the absence of added serum, mainly due to lipid synthesis in the cells. As
consequence Simvastatin, an inhibitor of cholesterol synthesis, but to a much extent CM223 did
inhibit the recovery of EGF-induced STAT3 signaling (Figure 4C, right panel), strengthening the
hypothesis that the i6A analogue CM223 significantly interfere with the mevalonate metabolic
pathway.
CM223 selectively inhibits the oncogenic AKT and STAT3 signaling and induces apoptosis,
activating intrinsic caspase cascade in cultured U87 glioma cells.
It is well characterized that Protein kinase B (PKB)/AKT, STAT and Ras-MAPK (ERK)
pathways, which regulate cellular growth, proliferation, and survival, are downstream players of

EGF receptor tyrosine kinase. (Hackel, Zwick, Prenzel & Ullrich, 1999) Then to investigate if
EGFR signaling interference by CM223 significantly affect this downstream cellular pathway, we
treated U87 cells for 24 h with effective increasing concentrations of the nucleoside prior to assay
proteins for western blot analysis. We found that, at all doses tested, CM223 significantly
suppressed AKT and STAT3 activation in cultured U87 glioma cells, reflected by the reduction of
the phosphorylation levels of AKT (Ser 473) and of STAT3 (Tyr 705) (Figure 5A). As regard as
MAPK/ERK pathway, its inhibition, in term of reduction of phosphorylation of activation loop
residues Thr202/Tyr204, is achieved only for the concentration of CM223 ranging from 1 to 5 µM.
On the contrary in response to 10 µM CM223 treatment, we documented a sustained ERK
phosphorylation. In this context several reports (Wei, Yan & Tang, 2011) suggested that ERK
activation can also play an active role in mediating apoptosis, functioning upstream of caspase
activation to initiate the apoptotic signal. In T98G cells activation of ERK was observed in response
to cisplatin and UV light and was shown to strongly promote apoptosis in these GBM cell line.
(Hamdi et al., 2008) To verify this hypothesis and to corroborate the proapoptotic effect of CM223,
we examined the expression of caspases and key proteins that play essential roles in apoptosis
induction. Treatment of 24h with CM223 strongly induced the expression of cleaved caspase-9,
cleaved caspase-7 and -3, as well as cleaved PARP, in a concentration-dependent manner (Figure
5B), without affecting caspase 8 activity, which suggests the CM223 induced execution of the
apoptotic cell intrinsic program. The expression of proapoptotic Bim and antiapoptotic Bcl-2 and
Bcl-XL proteins was further examined to explore the mechanism of CM223-induced apoptosis. The
decreased expression of Bcl-XL, canonical transcriptional target of AKT, well fits with its
inhibition by CM223, as well as the marked increase in the levels of the three major Bim isoforms
(Bim EL, L, S) well correlates with the presence of the cleaved form of PARP and with the
inactivation of AKT and of Bim negative regulator ERK. In keeping with these observations,
phosphorylation of ERK was down-regulated by CM223 treatment which lead to a concomitant
induction of the levels of the pro-apoptotic Bim and to a clear caspase 3 cleavage induction (Figure

5B). Interestingly, in control normal compartment, we were hardly able to detect Bim and caspase 3
cleavage induction as compared to cancer cells in the same condition (Figure 5C). These results
corroborate the inability of CM223 to affect NHA cell viability (Figure 2C) suggesting its
specificity of action for tumor compartment with minimal cytotoxic effects on normal brain.
Analysis of sensitivity of primary glioma patient-derived cells to CM223 treatment.
To test its efficacy in a more physiopathological context ex vivo, we moved to characterize the
sensitivity of two representative glioma patients-derived cell lines (GBM37 and GBM50) to CM223
treatment. As shown, CM223 (10µM) inhibited the phosphorylation of STAT3 in all glioma cells
either when the signaling operated constitutively either when EGFR was activated by EGF stimulus
(50 ng/ml) which, as expected, results in the physiological degradation of the receptor in order to
protect the cell from overstimulation (Figure 6A and Figure 4C) (Sigismund et al. 2013).
Interestingly, the degree of inhibition was more pronounced in primary cells compared to U87
glioma cell line. Accordingly in GBM cells CM223 achieved a 50% growth inhibition (IC50) at
lower concentrations than in U87 cells (Figure 6B), that is 1,2 µM in GBM37 primary cell line and
0.45 µM in those derived from GBM50 tumor versus 1.9 µM in U87 (Figure 6B). Even though by
different mechanisms, CM223 and (EGFR) tyrosine kinase inhibitor Erlotinib share the same target,
so the empirical combinations of these drugs was finally tested in U87 and GBM cell lines. For
Erlotinib the fixed concentration of 0.6 µM was chosen. Interestingly, CM223, was more active
than Erlotinib in reducing proliferation of glioma cells in the same condition (-37% vs -20% in U87;
-35% vs -10% in GBM37; -60% vs -40% in GBM50) which was additionally reduced by drug
combination (-60.6% in U87; -58,8% in GBM37; -72% in GBM50).
Although the extrapolation of in vitro data to the clinical setting should be considered with
caution, these last preliminary results may have implications for the rational development of new
chemotherapeutic regimens, including Erlotinib and CM223 or derivatives for the treatment EGFR-
driven cancers.

DISCUSSION
We have demonstrated that i6A exerts cytotoxic, antiangiogenic and proapoptotic activity in
different cell lines. (Ciaglia et al., 2017; Laezza et al., 2009; Laezza, Malfitano, Di Matola, Ricchi
& Bifulco, 2010; Laezza et al., 2006; Pisanti et al., 2014; Spinola, Colombo, Falvella & Dragani,
2007)
Previous reports by our group highlighted the involvement of FPPS in i6A action in different
physiopathological settings. (Ciaglia et al., 2013; Laezza et al., 2006) More recently we documented
for the first time the antitumor activity of i6A on human glioma cells. (Ciaglia et al., 2017) In our
work, i6A clearly displayed antiglioma action through AMP-activated protein kinase (AMPK)-
dependent internalization and degradation of EGFR; however, we have to take into account that it
might also elicit other effects. Indeed, i6A reduces the growth of xenograft tumors induced by k-ras
transformed thyroid cells (KiMol) by inhibiting farnesyl pyrophosphate synthase (FPPS), a key
enzyme of the isoprenoid biosynthetic pathway and protein prenylation, (Laezza et al., 2006) which
are crucial events for the function and activity of EGFR and its downstream signaling. Moreover
using an inverse virtual screening approach and NMR spectroscopy experiments, we showed that
i6A is able to bind FPPS active site determining a moderate enzyme inhibition. All these evidence,
and in particular the study of the i6A binding in the FPPS site, inspired the design of new analogs
carrying different substituents at the N6 position of the purine ring. As an important contribution of
the isopentenyl moiety was demonstrated in the binding of i6Awith FPPS enzyme, we designed and
synthesized the analogs shown in Figure 1A, including a benzyl ring (CM223) and an isopentyl
moiety (CM224) or a diversely substituted phenyl ring (compounds FP11, FP13 and FP14),
(Ottria, Casati, Baldoli, Maier & Ciuffreda, 2010)
In view of advancing chemotherapeutic administration-targeted drug therapy for glioblastoma,
that is the highest malignant SNC tumor, i6A analogs were studied in cell growth experiments on
U87MG human glioma cells and patients primary derived cells: in these conditions, only CM223
exhibited a marked cytostatic effect significantly higher as compared to that of i6A, whereas the

others showed an irrelevant activity. According to STD-NMR experiments and enzymatic
colorimetric assay CM223 cytostatic activity, analogously to i6A, was related to the modulation of
FPPS. Interaction of CM223 with FPPS active site was regulated by a KD 5 fold lower as i6A and
an EC50 two fold lower than i6A. Interestingly, compounds CM224 and FP13 showing no
significant cytostatic effect, exhibited no-significant STD effects, confirming the relationship
between the antiproliferative activity and the FPPS binding. Interpretation of these data in the light
of SAR considerations, corroborated by molecular modeling calculation, indicates that the increased
binding of CM223 (Kd 0.19 mM) as compared to i6A (Kd 1.0 mM ) is due to the presence of the
aromatic benzyl ring that engages more stable pi-stacking interactions with Phe113, and Tyr218 of
the enzyme. Concerning FP13, the difference in the binding mode as compared to i6A and CM223,
is due to the phenyl ring that represents a low flexibility point for to this molecule.
A more detailed investigation of the CM223 antiproliferative action has evidenced an its marked
anti-clonogenic effect, associated to higher pro-apoptotic action as compared to i6A. Exploration of
the cellular pathway through which CM223 elicited these effects evidenced the ability to suppress
AKT and STAT3 activation, whose signaling is critical for glioma cell proliferation and survival.
The effect of CM223 on MAPK/ERK pathway was concentration dependent, as it appeared
inhibitory at concentration ranging from 1 to 5 µM, but stimulatory at 10 µM. According to several
reports (Hamdi et al., 2008; Wei, Yan & Tang, 2011), these results may be interpreted considering
that ERK activation can also induce apoptosis upstream of caspase activation. Indeed CM223
proved to be responsible of several molecular events coherent with the execution of the apoptotic
cell intrinsic program: induction of cleaved caspase-9, cleaved caspase-7 and -3; induction of PARP
cleavage, without effect on capase 8. Moreover, CM223 increased the levels of the proapoptotic
three major Bim isoforms (Bim EL, L, S) and decreased the expression of antiapoptotic Bcl-XL.
Looking for the putative molecular mechanism, we highlighted that anti-glioma action of CM223 is
related to the modulation of mevalonate pathway and at least in part, to FPPS targeting. The
observation of increased levels of unprenylated form of the small GTPase Rap1A in response to

CM223 (Figure 4B) and the more complete inhibition of FPPS activity achieved by the FPPS
siRNA-CM223 combination (Figure 4C), along NMR interaction data might suggest a direct effect
on FPPS enzyme. However a little discrepancy between the potency of the compound in NMR and
FPPS colorimetric assays, where CM223-FPPS direct interaction was uniquely explored, and that
exibited in a more complex cellular model was documented. Here, the higher efficiency of CM223
in inhibiting the cell growth of tumor cells through the cholesterol depletion (Fig. 4C) suggests that
CM223 does really interfere with the MEV metabolic pathway; however the FPPS might not be the
unique key target of its action and a bystander influence of other key enzymes and intermediate
metabolites of mevalonate and isoprenoid pathway, modulated by CM223, cannot be ruled out. On
the other hand the better efficiency of the compound in culture cells might be due to its conversion
in a more active metabolite inside the cells, as previously documented for i6A that must be
monophosphorylated into 5’-i6A-monophosphate by the adenosine kinase to exert its inhibitory
effects on HUVEC endothelial cells. (Pisanti et al., 2014).
Anyway several reports in literature show the correlation between the FPPS inhibition and the
cytostatic and/or pro-apoptotic effects. Of note it is demonstrated that overactive prenylated Rap1A,
enhanced the proliferative capacity of certain cell types contributing to tumorigenesis. (Frische &
Zwartkruis, 2010; Jeyaraj, Unger & Chotani, 2011) Moreover accumulation of unprenylated Rap1A
due to the inhibition of farnesyl- or geranyl geranyl trasferase in vitro, induced apoptosis in human
plasma cells suggesting that geranylgeranylated proteins, like Rap1A, play a role in signaling
pathways that prevent cell death. (Gordon et al., 2002) Here we showed that the disruption of lipid
moieties by CM223-mediated FPPS inhibition was critical for the functionality and activity of
epidermal growth factor receptor (EGFR) (Warren & Landgraf, 2006) as potently impairs the main
intracellular signaling pathways responsible for the mantainance of neoplastic phenotype.
Prenylation is indeed required for the proper function and localization of several downstream
critical mediators of the EGFR signaling cascade, including the Ras, Rho, and Rab families, which
require farnesyl and geranylgeranyl post-translational modifications for their activity. (Gibbs, Oliff

& Kohl, 1994) Moreover it is well known that the isoprenoid compound dolichol is involved in the
N-linked glycosylation of EGFR, which facilitates its proper conformation and efficient ligand
binding and activation of EGFR. (Carlberg et al., 1996; Ceresa & Bahr, 2006) Accordingly we
highlighted the inability of CM223-treated cells to properly re-establish the endogenous mevalonate
and isoprenoid levels and recover EGFR signaling after washout of MCD (Figure 4C). Consistent
with these mechanism of action, we observed that CM223 is highly efficacious at blocking tumor
cell growth of EGFR-activated primary GBM cells in which the EGF-induced signaling sensitizes
them to CM223 effect. Last, by indirectly targeting EGFR, CM223 has been seen to ameliorate the
response to EGFR-TKI Erlotinib when given in combination (Figure 6B).
In view of the results collected in our experiments and considering the evidence reported in
literature, we may be confident that the antiproliferative and proapoptotic effects of CM223 in
glioma cells, may be in part ascribable to the EGFR signaling perturbation, as consequence of the
modulation of metabolic pathway of the mevalonate and in particular of FPPS key branch point
enzyme
Indeed, we demonstrated by STD-NMR experiments that CM223 binds and inhibits FPPS
activity. Interaction of CM223 with FPPS active site was regulated by a KD 5 fold lower as i6A and
an EC50 two fold lower than i6A. Interestingly compounds CM224 and FP13 showing no
significant cytostatic effect, failed to bind FPPS enzyme in STD-NMR experiment, confirming the
relationship between the antiproliferative activity and the FPPS binding. Interpretation of these data
in a SAR perspective, corroborated by molecular modeling calculation, indicates that the difference
in the binding of CM223 as compared to the compounds of FP series is due to the phenyl ring that
infers rigidity to this molecule portion.
CONCLUSIONS
Taken together our data confirm that i6A and in a much extent its benzyl analog CM223 are
endowed with a promising antitumoral activity on glioblastoma cells. The modification we adopted

on i6A scaffold leads to molecules that can be considered lead compounds in antiglioma
pharmacological research. Indeed the in vitro CM223 efficacy, the lack of cytotoxicity on healthy
brain cells, its additional activity in patients-derived primary GBM cells that more accurately reflect
the physiopathological context, make CM223 an interesting compound for the development of
novel valid chemotherapeutic agents in glioma and other EGFR-driven cancers.
All the biological pathways (vide intra) controlled by i6A (Ciaglia et al., 2013; Laezza et al.,
2006) and CM223 are related to the inhibition of FPPS enzyme, therefore the development of i6A
analogs characterized by increased antitumor activity may take advantage of the FPPS-CM223
structural interaction data.
MATERIALS AND METHODS
General Procedures. Organic solvents were purchased from Sigma-Aldrich (St. Louis, MO, USA).
and dried in the presence of appropriate drying agents and were stored over suitable molecular
1
sieves. Melting points were determined on a Kofler® hot stage apparatus and are uncorrected. H
NMR spectra were recorded with a Bruker Avance-500® spectrometer in δ units with TMS as an
internal standard. Mass spectra were performed with a Hewlett-Packard MS system 5988®. TLC
was performed on silica gel sheets (Silica Gel 60 F254, Merck, Germany). Microwave-assisted
reactions were run in a CEM microwave synthesizer. The system for isocratic flash chromatography
includes a Buchi® Pump Module C-601 (continuous flow of solvents up to 250 ml/min at max 10
bar) and Buchi® prepacked cartridges (silica gel 60, particle size 40-63 µm). The purity was
determined by high performance liquid chromatography (HPLC) Shimadzu system using analytic
C18 Phenomenex column. Purity of all final compounds was 99%.
Reagents and Abs. N6-isopentenyladenosine (i6A), Zoledronic acid monohydrate (Sigma-Aldrich,
St. Louis, MO, USA), methyl--cyclodextrin (MCD), Simvastatin, a synthetic analog of
lovastatin, and erlotinib were purchased from Sigma–Aldrich (St. Louis, MO, USA); Epidermal

growth factor (EGF) was diluted in a buffer containing a stabilizer (5% Trehalose) and added to cell
cultures at the indicated concentration. Human EGF was purchased from Peprotech (London, UK).
(St. Louis, MO, USA).
In transfection procedure Lipofectamine 3000 were from Invitrogen. Optimem were from Gibco
(#51985). For western blot analysis the following antibodies were used: rabbit polyclonal anti-
human β-actin, rabbit polyclonal anti-human ras and rabbit polyclonal anti-human FPPS were
purchased from Abcam (Cambridge, UK), mouse monoclonal anti-human α-Tubulin from Sigma-
Aldrich Inc. (St Luis, MO, USA), rabbit polyclonal anti-human cleaved Caspase-3, rabbit
polyclonal anti-human Rap1A, rabbit polyclonal anti-human Caspase-3, rabbit monoclonal anti
human cleaved caspase-9, rabbit monoclonal anti-human Caspase-9, rabbit monoclonal anti-human
Caspase-7, rabbit monoclonal anti-human cleaved Caspase-7, rabbit monoclonal anti-human
cleaved Caspase-8, rabbit monoclonal anti-human Bim, rabbit monoclonal anti-human Bcl-2, rabbit
monoclonal anti-human Bcl-xL, rabbit polyclonal anti-human phospho-STAT3 (p-STAT3; Tyr705),
rabbit monoclonal anti-human STAT3, rabbit monoclonal anti-human Cleaved PARP (Asp214),
rabbit monoclonal anti-human PARP, rabbit monoclonal anti-human Phospho-p44/42 MAPK (p-
Erk1/2; Thr202/Tyr204), rabbit monoclonal anti-human p44/42 MAPK (Erk1/2), rabbit monoclonal
anti-human Phospho-Akt (p-Akt; Ser473), rabbit monoclonal anti-human Akt,, rabbit monoclonal
anti-human Phospho-EGF Receptor (p-EGFR; Tyr1068) and rabbit monoclonal anti-human
Phospho-EGF Receptor were purchased from Cell Signaling Technology (Danvers, MA).
Secondary HRP-linked goat anti-mouse or goat anti-rabbit IgG, were also purchased from Cell
Signaling Technology (Danvers, MA).
Cells and clinical samples. For experiments on normal human counterpart CloneticsTM Astrocyte
Cell System containing Normal Human Astrocytes (NHA) and an optimized medium for their
growth was used (Lonza; Basel, Switzerland). Normal Human Astrocytes (NHA) are normal human
cells derived from normal fetal human brain tissue and were cultured in recommended medium

CloneticsTM AGM™ BulletKit™ (Lonza; Basel, Switzerland). The human glioma cell lines
U87MG (U87) were obtained from CLS Cell Lines Service GmbH (Eppelheim, Germany) or were
kindly provided by Dr. Daniela Parolaro (University of Insubria, Italy). Small pieces of brain tissue
containing tumor were collected at the time of craniotomy for tumor resection at the Neurosurgery
Service of “G. Rummo" Medical Hospital (Benevento, Italy) and the Neurosurgery Service of “San
Giovanni di Dio Ruggi d'Aragona” Medical Hospital (Salerno, Italy), divided into a portion
immediately processed to generate primary tumor cell lines and a portion stored at –80°C for
subsequent Western blot (WB) analysis. A second sample from each patient was also taken for
clinical diagnosis performed by expert neuropathologists in accordance with the International
Classification of CNS tumors drafted under the auspices of the World Health Organization (WHO).
The tumors were diagnosed as astrocytoma (WHO grade I-III; n=3), glioma (WHO grade II, n=2)
or glioblastoma multiforme (WHO grade IV; n=18). There were not significant differences by
gender, or age between the different groups (Ciaglia et al., 2015). All tissue samples were collected
in accordance with the ethical standards of the Institutional Committee. The patients had been
informed about the establishment of cellular models from their tumors and had given informed
consent in written form. The preparation of adherent primary cultures of brain tumor cells
(designated as GBMn) was conducted as reported elsewhere. (Ciaglia et al., 2015)
Human glioma cell line U87MG was cultured in EMEM (Lonza) supplemented with 10% heat-
inactivated fetal bovine serum (Euroclone), 1% L-glutamine, 1% antibiotic mixture, 1% sodium
pyruvate, 1% non-essential aminoacids (Euroclone).
All cell cultures were maintained at 37°C in humidified 5 % CO2 atmosphere.
Determination of glioma cell proliferation. Glioma cells U87MG or normal human astrocytes
(NHA) (4x103/well), were cultured for 24h into 96-well plates before addition of i6A at the
indicated concentrations and cultured for additional 24, 48 and 72h at 37°C. Cell proliferation was
evaluated by measuring BrdU incorporation into DNA (BrdU colorimetric assay kit; Roche Applied

Science, South San Francisco, CA, USA). Newly synthesized BrdU-DNA was determined on an
ELISA plate reader (ThermoScientific) at 450 nm. All experiments were performed in triplicate,
and the relative cell growth was expressed as a percentage comparison with the untreated control
cells to control for unwanted source of variation.
Apoptosis analysis. Quantitative assessment of apoptosis of U87MG glioma cell line or normal
human astrocytes (NHA) was analyzed by anti-human Annexin V (BioLegend, San Diego, CA,
USA) and PI staining and processed as previously described (Malfitano et al., 2013). Briefly, cells
grown in 100-mm dishes for 24, 48 and 72h in EMEM containing 2% FBS or in recommended
medium AGM™ BulletKit™ (Lonza) were harvested with trypsin and washed in PBS. Following
24h of incubation, immunofluorescence staining was performed. The cells were resuspended in
Annexin V binding buffer (10 mM HEPES/NaOH, pH 7; 140 mM NaCl; and 2.5 mM CaCl2) and
stained with Annexin V-FITC for 20 min at room temperature (RT) and then with PI at RT for
additional 15 min in the dark. The cells were acquired by flow cytometer within 1 h after staining.
At least 10,000 events were collected, and the data were analyzed by Cell- Quest Pro software
(Becton Dickinson, San Jose, CA). Data are expressed as logarithmic values of fluorescence
intensity.
Western blot (WB) analysis. For analysis of protein levels from cells they were grown in p60
tissue culture plates at a density of 2x104 cells/cm2 for 24 h. Tumor cells were then incubated with
vehicle, i6A, CM223 or Zoledronic acid monohydrate in the presence or absence of EGF. After
incubation cells were washed with PBS, harvested and lysed in ice-cold RIPA lysis buffer (50 mM
Tris-HCl, 150 mM NaCl, 0.5% Triton X-100, 0.5% deoxycholic acid, 10 mg/ml leupeptin, 2 mM
phenylmethylsulfonyl fluoride, and 10 mg/ml aprotinin). Tumor pieces were disrupted for protein
extraction by gentle homogenization (Potter-Elvehjem Pestle) in cold RIPA buffer. After removal
of cell debris by centrifugation (14,500 g for 20 min at 4°C), the proteins were estimated. About

30µg of proteins was loaded on 10, 12 or 15% SDS–polyacrylamide gels under reducing conditions
and then transferred to nitrocellulose membranes. The blots were blocked with 5% nonfat dry milk
(Bio-Rad, Richmond, CA, USA) in Tris-buffered saline containing 0.1% Tween-20 (TBST) for 1 h
at room temperature and incubated with the specific antibody. Immunodetection of specific proteins
was carried out with horseradish peroxidase-conjugated donkey anti-mouse or anti-rabbit IgG
(Biorad, Hercules, CA), using the enhanced chemiluminescence (ECL) system (Amersham
Pharmacia Biotech, Piscataway, NJ) according to the manufacturer’s instructions and then exposed
to X-ray film (Amersham Biosciences). Immunoreactive bands were quantified with Quantity One
1-D analysis software (Bio-Rad). To ascertain equal protein loading in Western blots of cell lysates,
membranes were probed with an antibody raised to α-tubulin (Sigma-Aldrich, St. Louis, MO, USA)
or β-actin (Abcam, Cambridge, UK).
siRNA-Mediated Knockdown
FPPS siRNA transfection was carried out according to manufacturer's instructions. First, siRNA
FPPS (Ambion) and negative control siRNA (Silencer Negative Control, Ambion ) were dissolved
in Opti-MEM serum-free media. Both FPPS and scrambled siRNA were delivered into the U87 cell
cultures plated 18 hours before transfection (approximately 80% confluency) via Lipofectamine
3000 (#L3000-001, Invitrogen). The final concentration of FPPS and scrambled siRNA in culture
was 100nM. The cells were incubated with the transfection reagents for 48 hours. Then, cell media
was replaced with serum-free media to induce starvation and treated with 10 µM CM223 for 8
hours. After that EGF was added (final concentration 50ng/mL) for 10 minutes. The cells were then
harvested for analysis of protein knockdown via western blot and tested for cell signaling
experiments.
FPPS gene expression. The plasmid p11, transformed into BL21(DE3)-pLysS cells, was
purchased from SGC-Oxford and contained the T7/Lac promoter and ampicillin resistance. FPPS

was expressed in Escherichia coli as a fusion protein (67−419 residues) with a N-terminal poly-
histidine tail and a mutation (threonin with serine) on residue 266, molecular weight 43kDa. For
expression in E. coli, bacterial clones were grown in 1L of LB (Luria-Bertani) medium containing
50μg/mL ampicillin. Cell growth was monitored spectrophotometrically by measuring OD600 nm
periodically. When growth was performed to an OD600 of 0.7 at 37°C, the 1mM isopropyl-D-
thiogalactoside (IPTG) was added. IPTG was purchased from Sigma- Aldrich (St. Louis, MO).
After 6h of cell growth, cells were pelleted by centrifugation and re-suspended in lysis buffer (50
mL of 5% glycerol, 5 mM imidazole, 500 mM NaCl, 50 mM PBS (pH 7.5)) and sonicated. Protein
was purified with His-Trap HP column at 1 mL/min using an AKTA purifier system, the soluble
extract was applied to a nickel-chelated agarose affinity column that had been equilibrated with the
same buffer. The protein was eluted from the column with elution buffer (5% glycerol, 250 mM
imidazole, 500 mM NaCl, 50 mM PBS (pH 7.5)). Affinity chromatography on a nickel chelated
agarose column permitted a simple one step protein purification. Therefore FPPS was transferred
into Vivaspin 20 concentrator, cutoff 3kDa, to exchange the buffer for NMR studies.
NMR Sample Preparation. All chemicals were purchased from Sigma-Aldrich (St. Louis, MO).
i6A was purchased from Iris Biotech GMBH and zoledronic acid from Sigma-Aldrich (St. Louis,
MO). i6A analogs were synthesize at University of Pisa and University of Milano. STD-NMR and
1
WaterLOGSY experiments were recorded at 25°C on Bruker AV600 MHz spectrometer at a H
1
resonance frequency of 600 MHz equipped with a 5 mm triple resonance H(13C/15N), z-axis
pulsed-field gradient probe head. For characterization purposes, i6A samples consisted of a 5mM
solution in 25 mM d-Tris, pH 7.4, 0.5 mM MgCl2, and 25 mM NaCl with 1% dimethyl sulfoxide-d6
as a co-solvent, and the spectra were referenced to residual solvent. 1H−1D spectra were acquired at
a resolution of 16k complex points in the time domain with 32 accumulations each (sw=6000 Hz,
d1=3s). The FPPS protein at 8 μM concentration was titrated with i6A-analogs to have
protein/ligands molar ratios 1:10, 1:20, 1:30, 1:50, 1:70, and 1:100. For each addition of ligands,

STD build-up experiment was carried out using different saturation times (0.50, 1.00, 1.50, 2.00,
3.00, 4.00, and 5.00s and different relaxation delay 1.50, 2.00, 2.50, 3.00, 4.00, 5.00, and 6.00s).
For each experiment in the frequency list (FQ2LIST), the on-resonance and off-resonance pulse
were 320 and 50000 Hz, respectively. Briefly, two free induction decay (FID) data sets were
collected in an interleaved manner to minimize temporal fluctuations with the protein irradiation
frequency set on-resonance (−0.5 ppm) and off-resonance (40 ppm), respectively (sw = 6000 Hz, 16
steady state scans, 2048 transients, 4k complex points, d1 = 3s). Protein saturation was obtained
using a train of individual 50 ms long, frequency selective Gaussian radio frequency (rf) pulses
separated by an inter pulse delay of 1ms. The FID acquired with off-resonance irradiation generated
the reference spectrum (Ioff), whereas the difference FID (off-resonance on-resonance) yielded the
STD spectrum (ISTD = Ioff - Ion). Spectra were processed with an exponential apodization function
(1Hz line broadening) and zero-filling to 8k complex points before Fourier transformation and
baseline correction with a third order Bernstein polynomial fit. The STD measurements were done
in duplicate, and all data were processed and analyzed using TopSpin software (Bruker v 1.3).
FPPS colorimetric assay. The colorimetric assays were performed in 96-well plates, flat bottom.
200 ng of fresh pure FPPS was assayed in a final volume of 100 µl buffer (50mM Tris pH 7.5,
2mM MgCl2, 1mM DTT, 5 µg/ml BSA) with or without pre-incubation with inhibitors (i6A 1-
10mM, CM223 0.1-5.0mM, zoledronic acid 1-2 µM as positive control) for 30 min. at 37 °C. The
reaction was initiated by the addition of the substrates dimetilallil pirophosphate (DMAPP 50 µM
and IPP 50 µM) and proceeded for 1 hour at 37 °C. 10 µl of 2.5% ammonium molybdate reagent (in
5 N H2SO4) were added and incubated for 10 min to allow the formation of PPi-molybdate
complex, finally the complex was reduced by 10 µl of 0.5 M 2 -mercaptoethanol and 5 µl of
Eikonogen reagent (0.25 g of sodium sulfite and 14.7 g of meta-bisulfite were dissolved in 100 ml
water). Plates were incubated with gentle mixing on a plate shaker for 20 min. The absorbance was
measured at 580 nm employing a microplate reader. The control experiments were carried out with

incubation mixture in the absence of substrate or FPPS for background deduction. To set the
conditions, a standard curve using Na2P2O7 as the source of PPi (Fig. S6) was constructed.
Docking Studies. AutoDock version 4.2(Morris et al., 2009) and AutoDock Vina version 1.0(Trott
& Olson, 2010) in combination with the LGA were used for all docking calculations. The starting
conformations for docking studies of CM223 and FP13 ligands were built with Maestro (version
9.6). (Schr dinger, 2009) Three-dimensional starting model of each compounds for the subsequent
docking calculations, were preliminary optimized by conjugate gradient, (0.05Å convergence
threshold).
3D FPPS protein model was obtained from Protein Data Bank database (PDB code: 1ZW5).
(Kavanagh et al., 2006) Water molecules were removed, and the obtained file was then processed
with Autodock Tools 1.5.6, merging non-polar hydrogens and adding Gasteiger charges.
For both docked ligands, all bonds were considered rotable. For an exhaustive exploration of
conformational space, 6 docking calculations consisting of 250 runs were performed, yielding 1500
structures. An initial population of 450 randomly placed individuals, a maximum number of 5x106
energy evaluations, and a maximum number of 4x106 generations were taken into account. The
mutation and crossover rates used were 0.02 and 0.80, respectively. The local search probability
was 0.26. For all docking calculations, a grid box size of 53 65 57 points (spacing between the grids
points of 0.375Å) was used, centered on the center of the target binding site.
The resulting data, differing by less than 3.5 Å in positional rmsd, were clustered together and
represented by the result with the most favorable free energy of binding. All 3D models were
depicted using Python and VMD. (Humphrey, Dalke & Schulten, 1996).
Nomenclature of Targets and Ligands. Key protein targets and ligands in this article are
hyperlinked to corresponding entries in http://www.guidetopharmacology.org, the common portal
for data from the IUPHAR/BPS Guide to PHARMACOLOGY (Southan et al., 2016), and are

permanently archived in the Concise Guide to PHARMACOLOGY 2015/16 (Alexander et al.,
2015).
Statistical analysis. Statistical analysis was performed in all the experiments shown by using the
GraphPad prism 6.0software for Windows (GraphPad software). For each type of assay or
phenotypic analysis, data obtained from multiple experiments are calculated as mean ± SD and
analyzed for statistical significance using the 2- tailed Student t-test, for independent groups, or
ANOVA followed by Tukey’s post-hoc test for multiple comparisons, when F achieved was P<0.05
and there was no significant variance inhomogeneity. Minimal statistical significance was set at
*P<0.05. Some results were normalized to control for unwanted source of variation. To ensure
reproducibility of the results and minimize bias, the use of authenticated U87MG and NHA at the
same passage and wherever possible, the same manufactures’ kit and reagents were used for
selected experiments. For the control of bias, all data generated during study have been recorded
directly, promptly, accurately, and legibly by a dedicated individual entering the data. The data and
statistical analysis comply with the recommendations on experimental design and analysis in
pharmacology (Curtis et al., 2015)
. AUTHOR INFORMATION
Corresponding Authors
*For M.B.: phone, +39-089-965217; fax, +39-089-969602; Email, maubiful@unisa.it.
*For A.M.D.: phone, +39-089-969748; fax, +39-089-969602; Email, dursi@unisa.it.

. ACKNOWLEDGMENTS
. This study was supported by Associazione Italiana Ricerca sul Cancro (AIRC; IG 18999 and
IG13312 to M. Bifulco,). E. Ciaglia was supported by a fellowship from Fondazione Umberto
Veronesi (FUV 2017, cod.1072).. The authors thank Dr. Francesco Montella and Dr. Ylenia
Senatore (University of Salerno) for their continual support.
ABBREVIATIONS USED
i6A, N6-isopentenyladenosine; FPPS, farnesyl pyrophosphate synthase; CCR2, chemokine receptor
2; CCL2, chemokine ligand 2; CCR5, CC chemokine receptor 5; COSY, correlated spectroscopy;
DMAPP, dimetilallil pirofosfato FEP, free energy perturbation; IPP, isopentenyl pyrophosphate; TI,
thermodynamic integration; LIE, linear interaction energy; NK, natural killer; N-BP, nitrogen-
containing bisphosphonates; NMR, nuclear magnetic resonance; PBS, phosphate buffered saline;
PI, propidium iodide; STD, saturation transfer difference; TLC, thin layer chromatography; tRNA,
tRNA.
Authors contributions: E.C. wrote the paper, designed and conducted biological assays and analyzed
and interpreted data; M.G. conducted FPPS gene expression procedure, NMR studies and analyzed
and interpreted data; M.A. performed biological research, analyzed data and reviewed critically the
paper; M.S. performed Molecular Docking studies; C.L. performed research, R.R., S.P. and P.G.
performed siRNA transfection procedure and established primary derived cells. M.R., C.M. and P.C.
conducted the synthesis of new i6A derivatives and gave substantial contribution to analysis and
interpretation of data; A.M.D. and M.B. supervised the project in its entirety, wrote and reviewed
critically the paper and provided financial support. All authors approved the final version to be
published.

.
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