Conformational mimetics of the α-methyl chalcone TUB091 binding tubulin: Design, synthesis and antiproliferative activity

Article abstract of DOI:10.1016/j.ejmech.2018.02.019

Based on the conformation of the α-methyl chalcone TUB091 in its complex with tubulin, a series of conformational mimetics have been designed and synthesized where the methyl group of the chalcone has been fused to phenyl ring B resulting in 1,2,3,4-tetrahydronaphthalen-2-yl aryl ketones. Among the synthesized compounds, the 5-amino-6-methoxy derivative, with a similar substitution pattern to that of TUB091, showed antiproliferative activity around 20 nM against tumor and endothelial cells. Tubulin binding experiments confirmed its binding to tubulin at the colchicine site with a Kb of 2.4 × 10⁶ M^?1 resulting in the inhibition of the in vitro assembly of purified tubulin. Moreover, based on the recently reported complex of combretastatin A4 (CA4) with tubulin, a comparative analysis of the binding mode of CA4 and the α-methyl chalcone to tubulin has been performed.

Full text of DOI:10.1016/j.ejmech.2018.02.019

Accepted Manuscript
Conformational mimetics of the α-methyl chalcone TUB091 binding tubulin: Design,
synthesis and antiproliferative activity
Oskía Bueno, Gloria Tobajas, Ernesto Quesada, Juan Estévez-Gallego, Sam
Noppen, María-José Camarasa, José-Fernando Díaz, Sandra Liekens, Eva-María
Priego, María-Jesús Pérez-Pérez
PII:
S0223-5234(18)30141-7
10.1016/j.ejmech.2018.02.019
EJMECH 10196
DOI:
Reference:
To appear in: European Journal of Medicinal Chemistry
Received Date: 21 November 2017
Revised Date: 5 February 2018
Accepted Date: 6 February 2018
Please cite this article as: Oskí. Bueno, G. Tobajas, E. Quesada, J. Estévez-Gallego, S. Noppen,
Marí.-José. Camarasa, José.-Fernando. Díaz, S. Liekens, Eva.-Marí. Priego, Marí.-Jesú. Pérez-
Pérez, Conformational mimetics of the α-methyl chalcone TUB091 binding tubulin: Design, synthesis
and antiproliferative activity, European Journal of Medicinal Chemistry (2018), doi: 10.1016/
j.ejmech.2018.02.019.
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ACCEPTED MANUSCRIPT
Conformational mimetics of the α-methyl chalcone TUB091
binding tubulin: Design, synthesis and antiproliferative
activity
Oskía Bueno, a Gloria Tobajas, a Ernesto Quesada, a Juan Estévez-Gallego,b Sam
Noppen,c María-José Camarasa,a José-Fernando Díaz,b Sandra Liekens,c Eva-María
Priegoa* and María-Jesús Pérez-Péreza*
a Instituto de Química Médica (IQM, CSIC), Juan de la Cierva 3, E-28006 Madrid, Spain
bCentro de Investigaciones Biológicas (CIB, CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
c Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
* Corresponding author: Dr. María-Jesús Pérez-Pérez
Instituto de Química Médica (CSIC)
c/ Juan de la Cierva 3
E-28006 Madrid (Spain)
Phone number: 34 91 258 75 16
Fax number: 34 91 5644853
e-mail: mjperez@iqm.csic.es
Dr. Eva-Maria Priego
Instituto de Química Médica (CSIC)
c/ Juan de la Cierva 3
E-28006 Madrid (Spain)
Phone number: 34 91
Fax number: 34 91 5644853
e-mail: empriego@iqm.csic.es
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Highlights
•
•
•
•
Novel 1,2,3,4-tetrahydronaphthalen-2-yl aryl ketones have been synthesized.
These derivatives are proposed to mimic the conformation of α-methyl chalcones.
The most potent derivative has antiproliferative activity around 20 nM.
The binding mode of CA4 and the α-methyl chalcone to tubulin has been compared.
Abbreviations : CA1 : combretastatin A1; CA2: combretastatin A2; CA4: combretastatin A4;
CA4P: combretastatin A4 phosphate; R-PT: (R)-(+)-ethyl 5-amino 2-methyl-1,2-dihydro-3-
phenylpyrido[3,4-b]pyrazin-7-yl carbamate; VDAs : vascular disrupting agents
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Abstract
Based on the conformation of the α-methyl chalcone TUB091 in its complex with tubulin, a series
of conformational mimetics have been designed and synthesized where the methyl group of the
chalcone has been fused to phenyl ring B resulting in 1,2,3,4-tetrahydronaphthalen-2-yl aryl
ketones. Among the synthesized compounds, the 5-amino-6-methoxy derivative, with a similar
substitution pattern to that of TUB091, showed antiproliferative activity around 20 nM against
tumor and endothelial cells. Tubulin binding experiments confirmed its binding to tubulin at the
colchicine site with a Kb of 2.4 x 106 M-1 resulting in the inhibition of the in vitro assembly of
purified tubulin. Moreover, based on the recently reported complex of combretastatin A4 (CA4)
with tubulin, a comparative analysis of the binding mode of CA4 and the α-methyl chalcone to
tubulin has been performed.
Keywords: tubulin; chalcones; antiproliferative activity; molecular modeling
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1. – Introduction
Combretastatins are a group of naturally occurring cis stilbenes isolated from the bark of
Combretum caffrum. Several members of this family of compounds, including combretastatin A4
(CA4, 1) [1, 2], combretastatin A1 (CA1, 2) [1] and to a lesser extend combretastatin A2 (CA2, 3)
[3], have been deeply investigated due to their capacity to inhibit tubulin polymerization by binding
at the colchicine site (Figure 1). These compounds show antimitotic properties against cancer cells
but in addition they are able to disrupt vascular irrigation in the tumor environment, thus CA4
represents the prototype compound of the so called vascular disrupting agents (VDAs) acting on
tubulin [4-6]. Despite the interesting properties of these compounds, combretastatins suffer from
two significant drawbacks: poor aqueous solubility and easy isomerization towards the trans
stilbenes, that are significantly less active [7]. The low solubility issue has been addressed through
the synthesis of prodrugs, of which the phosphate of CA-4 (fosbretabulin, 4) [8] or the diphosphate
of CA-1 (OXi4503, 5) [9] are being tested in clinical trials. Concerning the stability of the cis
stilbene, many efforts have been performed to fix the cis conformation by incorporation of the
stilbene into a restricted bridge or by replacing it by other linkers, as recently reviewed [10-13].
Among skeletons abundantly present in compounds inhibiting tubulin polymerization of natural
or synthetic origen, chalcones and chalconoides occupy an important position [14]. In 2009, a series
of chalcones (compounds 6-8) (Figure 1) were described as CA4 surrogates, among which the α-
methyl chalcone 7 showed antiproliferative activity at the nM or subnM range [15, 16]. Moreover,
based on docking studies, it was proposed that the chalcones adopt an orientation similar to that of
podophyllotoxin (9), so that the α-phenyl chalcone 8 could be seen as a podophyllotoxin mimetic
[16]. More recently, other α-methyl chalcones with an indole as ring B, have been described as
potent antiproliferative agents, also binding at the colchicine domain of tubulin [17]. We have also
reported the α-methyl chalcone TUB091 (10), whose A ring corresponds to that of CA-2, as a
potent tubulin depolymerizing agent, inhibiting cancer and endothelial cell growth at IC50 values of
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1-10 nM [18]. In addition, the Lys-Pro prodrug of TUB091 (11), that strongly enhanced the
aqueous solubility, showed potent antitumor activity in melanoma and cancer xenograft models as
well as antimetastatic activity [18]. The active conformation of these chalcones when binding at the
colchicine site is the s-trans conformer, as initially propose by Ducki [16] and unequivocally
confirmed by the resolution of the complex of the hydroxyl derivative TUB092 (12) with tubulin
[18].
Despite their interesting biological properties, chalcones are Michael acceptors due to their αβ-
unsaturated ketone structure and this feature may compromise their pharmacological development
[19, 20]. Moreover, we [18] and others [21] have described that chalcones are prone to
photoisomerization while the biological activity is due to one isomer, in our case the E-isomer. We
have now used the conformation of the E-isomer of the α-methyl chalcone 12 bound to tubulin to
design a conformational constrained mimetic through the incorporation of a tetrahydronaphthalene
scaffold as ring B. With the incorporation of such a scaffold and the conformational restrictions that
this implies, it is intended to surmount some of the general drawbacks associated to chalcones, such
as possible isomerization to the Z-isomer or potential Michael additions.
Moreover, since the X-Ray structure of CA-4 binding to tubulin has been recently determined
[22], we have compared the binding mode of chalcone 12 with that of CA4, to determine which
common residues are crucial in the interaction of these ligands.
2.- Results and discussion
2.1. Structural information and conformational mimetic proposal.
As already mentioned, the X-Ray structure of the T2R-TTL-TUB092 complex has recently been
solved at 2.4 Å resolution (PDB ID: 5JVD) [18], where the ligand 12 was soaked into crystals
formed by a protein complex composed of two bovine brain αβ-tubulin heterodimers, the rat
stathmin-like protein RB3 and chicken tubulin tyrosine ligase (T2R-TTL). The binding site is
formed by residues of strands S8 and S9, loop T7 and helices H7 and H8 of the β-tubulin, while
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loop T5 of the α-tubulin is also involved. Detailed interactions between the ligand and the protein
have been reported [18], and some of the key interactions have been taken into consideration for the
design of the new compounds. Thus, the carbonyl group of the chalcone is at hydrogen-bond
distance to the backbone amide of Aspβ251, while the OH at ring B establishes an hydrogen bond
interaction with the main-chain of Thr179 (Figure 2). It is expected that the NH2 of its analogue
(11) establishes a similar interaction with this residue. Rings A and B of chalcone 12 are stacked
between the side chains of Cys241 and Leu255, and between Asn258 and Lys352, respectively.
Regarding the bioactive conformation of the ligand, chalcone 12 binds as the s-trans conformer of
the double bond, and rings A and B are not coplanar. Indeed, the deviation of ring B with respect to
the plane containing ring A is approximately 45º. By analyzing this binding mode, it was
hypothesized that a similar conformation might be accomplished by bridging the methyl group at
position α of the chalcone and position 2 of ring B. This closing should be performed by using a
saturated ring to accomplish the deviation from the plane above mentioned (Figure 3). Thus,
compound 13 was constructed in its two enantiomeric forms and the geometries of both isomers
were optimized with MOPAC2012 [23]. This was followed by a manual superposition of the
geometry-optimized structures with the conformation of 12 in its complex with tubulin. As shown
in Figure 4, the 3D structure of the R-enantiomer of 13 very nicely overlaps with that of the
chalcone 12. Thus, the synthesis of a series of 1,2,3,4-tetrahydronaphthalen-2-yl arylketones was
addressed.
2.2. Chemistry
The 6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (14) was chosen as the starting
material. This acid was converted to the aldehyde 15 by treatment BH3·Me2S followed by Dess-
Martin oxidation of the intermediate alcohol (Scheme 1). Reaction of the 6-bromo-4-
methoxybezo[d][1,3]dioxole in the presence of n-BuLi with the aldehyde 15 did not lead to the
expected alcohol, and only the debrominated derivative 4-methoxy[d][1,3]dioxole was detected. As
an alternative pathway, a Friedel-Crafts acylation between the acid chloride 16, prepared by
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treatment of the acid 14 with SOCl2 in toluene at reflux, and 4-methoxy[d][1,3]dioxole (17) [24]
was assayed (Scheme 1). When the reaction was performed using AlCl3 as catalyst at rt or heating
at 60 ºC, no acylation products were detected. By using ZnCl2 and performing the reaction at 60 ºC
in anhydrous 1,2-dichloroethane, two new isomeric compounds were obtained (18 and 19, in low
yield) whose structures were determined by NMR experiments. Confirmation of the correct
assignment of compound 19 was performed based on NOESY experiments where a correlation peak
is observed between the OCH3 signal of ring A (δ 3.90 ppm) and an aromatic proton of this same
ring (δ 6.82 ppm) (see spectra in the Supplementary data). In order to avoid the formation of
regioisomers, the symmetrical 1,2,3-trimethoxybencene (20) was used as the arene (Scheme 2). In
this case, the Friedel-Crafts acylation between 20 and the acid chloride 16 afforded two compounds,
that were characterized as 21 (24% yield) and 22 (7% yield) (Scheme 2). In the 1H NMR spectrum
of 22, a phenolic OH was detected at 12.46 ppm, suggesting that this OH could be involved in an
internal hydrogen bond with the carbonyl through a pseudo 6-membered ring. Thus, the phenolic
OH should be at position 2 in ring A. This demethylation reaction vicinal to the ketone during
Friedel-Crafts acylations has been described by other authors [25-27]. By changing the catalyst, the
reaction could be selectively directed towards each of these two compounds. Thus, when the
reaction between 16 and 20 was performed in the presence of TfOH [28], compound 21 was
isolated in 64% yield. On the other hand, by employing BF3·OEt2 [29] and extending the reaction
time to 16 h, the phenolic derivative 22 was obtained as the major compound in 46% yield. When
the arene used was 1,2-dimethoxybencene (23), and using TfOH as the catalyst, the ketone 24 was
obtained as the only regioisomer in 76% yield, containing the methoxy groups at positions 3 and 4,
according to previous reports [30, 31].
Compounds 21 and 24 were nitrated by treatment with HNO3 in Ac2O at -40 ºC for 20-30 min
(Scheme 3). As expected, a mixture of the corresponding 5- and 7-NO2 derivatives was obtained. It
should be highlighted that the control of the temperature is crucial to avoid double nitration [32].
The assignment of the nitration position in 25 and 26 was performed based on NMR experiments
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(COSY, HBMC and HSQC). Catalytic hydrogenation of 25 in the presence of Pt/S afforded the 7-
amino derivative 27 in 50% yield. Interestingly, when these reaction conditions were applied to the
5-nitro isomer 26, no reduction was observed, probably due to steric hindrance. Alternatively,
treatment of 26 with Fe in the presence of HCl in a mixture EtOH/H2O [33] afforded the 5-amino
derivative 28 in moderate yield. In the case of compound 24, the nitration reaction led to a mixture
of the 5- and 7-NO2 isomers that could not be separated by chromatography. Thus, the mixture was
reduced by treatment with Fe in acidic media. In this way, the 7-amino and 5-amino derivatives
31and 32 were isolated in 16 and 10% overall yield for the two steps. Indeed, the different behavior
of the 5- and 7-NO2 isomers when subjected to catalytic hydrogenation may be exploited to
selectively reduce the 7-isomer in a mixture.
2.3 Biological Evaluation.
2.3.1 Antiproliferative activity
The synthesized compounds were evaluated for their antiproliferative activity (Table 1) in four
different cell lines: three tumor cell lines (L1210, CEM and HeLa) and one endothelial cell line
(HMEC-1). Data are expressed as the 50% inhibitory concentration (IC50), defined as the
concentration at which the compounds reduced cell proliferation by 50%. Colchicine and CA4P
were included as reference compounds. The IC50 values of the chalcone 10 [18] are also included
for comparative purposes.
It is interesting to highlight the strict structural requirements in this series of tetrahydronaphthalene
derivatives for antiproliferative activity. The most potent compound is the 5-NH2-6-OMe derivative
(28) with IC50 values around 20-50 nM in all the cell lines tested. Its regioisomer, the 7-NH2-6-OMe
derivative (27) is between 10-15 fold less active, with IC50 values similar to those of the 6-OMe
derivative 21, all of them in the subµM range. The substitution pattern on ring A is also crucial for
activity. Thus, the 2,3,4-trimethoxy derivatives (21, 26, 27 and 28) are the ones that provide better
antiproliferative activity. If the OCH3 at position 2 is absent (as in 32 compared to 28) or if the
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substituent at position 2 is an OH instead of an OCH3 (compare 22 versus 21), the antiproliferative
activity is significantly reduced.
2.3.2 Tubulin binding and assembly inhibition
In order to determine if the antiproliferative activity of the here reported compounds was related to
their capacity to destabilize tubulin, representative compounds were tested in a tubulin
polymerization assay including podophyllotoxin and the chalcone 10 for comparative purposes. As
shown in Figure 5, compound 28 display at the tested concentration a destabilizing effect similar to
those of podophyllotoxin and the chalcone 10. For compound 21, a similar effect was observed
although some aggregation seemed to occur at the end of the reaction. Compound 26 showed a
weaker effect on tubulin polymerization, while compound 24 was inactive in this assay. These data
are in agreement with the antiprolifertiave activity in cell culture.
In addition, for compound 28, , a competition experiment with R-PT was performed, as previously
described [34], to determine to its capacity to bind at the colchicine site and its binding potency.
The Kb for R-PT was 3.2 x 106 M-1[35], while the Kb value determined for 28 was 2.4 ± 0.1 x106
M-1. This Kb, as well as all other data for these compounds, corresponds to the racemic mixtures.
2.3.3 Inhibition of mitotic spindle formation and cell cycle experiments
Tubulin-binding agents typically interfere with DNA division during mitosis. Immunofluorescence
assays in HeLa cells were performed for compound 28 at two different concentrations (0.3 and 0.1
µM). As shown in Figure 6, highly aberrant multipolar spindles were observed in cells treated with
compound 28 compared to control cells.
In addition, we assessed the effect of compound 28 on cell cycle progression of HeLa cells. As
shown in Figure 7, control cells show a typical pattern of cells in G1, S and G2/M phase of the cell
cycle. In contrast, compound 28, at concentrations of 0.1 µM and higher caused almost a complete
blockage of cells in G2/M phase, indicating that that the compound halts cell mitosis.
2.4. Docking studies
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Using the crystalline complex of the chalcone 12 binding tubulin (PDB ID: 5JVD) and Autdock 4.2
[36], docking studies of the R isomer of 28 were performed. The best solution obtained was
subjected to molecular dynamic simulations. As shown in Figure 8, the tetrahydronaphthalene
derivative is bound almost in the same location as the chalcone 12, with the trimethoxyphenyl ring
located towards the β-subunit and surrounded by residues Tyrβ202, Glyβ237, Valβ238, Thrβ239,
Cysβ241, Leuβ242, Alaβ250, Aspβ251, Leuβ252, Lysβ254, Leuβ255, Ileβ318 and Ileβ358.
However, there is no hydrogen bond between the ketone of 28 and the NH of Aspβ251. The
tetrahydronaphthalene ring is located close to the αβ-interface, so that not only residues from the β-
subunit but also residues from loop 5 of α-tubulin are involved. It should be stressed that the NH2 of
28 is in hydrogen bond distance (1.8 Å) to the backbone carbonyl of Thrα179, mimicking the
interaction of the OH of chalcone 12 with this same residue.
2.5. Comparison of the complexes CA-4 and chalcone TUB092 with tubulin
Next, we compared the binding mode of CA-4 (PDB id: 5LJD) [22] and chalcone 12 (PDB id:
5JVD) [18] with tubulin. Thus, superimposition of the tubulin-CA4 complex onto the tubulin-12
structure revealed that rings B from both compounds occupy the same space in the binding site
(Figure 9A). In fact, the hydrogen bond between the OH group in B-ring and the backbone carbonyl
of Thrα179 is present in both complexes. However, the 1,3-benzodioxole ring of chalcone 12 is
located deeper in the binding site compared with the 3,4,5-methoxybencene ring of CA-4. As a
consequence, the side chain of Ile318 in the 12-tubulin structure changes its position to
accommodate the dioxole ring and allow the interaction with Cys241 and Gly237.
Overall, from the comparison of CA-4- and 12-tubulin complexes, no significant differences in the
binding site were observed. Only very few and punctual differences were found, such as polar
interactions (hydrogen bonds), rearrangements in the side chain of some residues (Ile 318) and
energy contribution of the residues involved in the interaction, as shown in Figure 9B.
Taking together, the α-methyl chalcone 12 can be considered as a synthetic mimetic of the natural
product CA-4.
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3. Conclusions
Chalcones are interesting chemical entities from a medicinal chemistry perspective with a wide
variety of applications although their ease of isomerization and Michael-acceptor potential may
hamper some of these applications. We have used the bioactive conformation of the α-
methylchalcone TUB092 in its complex with αβ tubulin to search for conformational mimetics that
surmount the above refereed limitations. Thus, tetrahydronaphthalene derivatives were proposed as
restricted ring B mimetics, and their synthesis was performed. From the synthesized compounds,
compound 28 showed potent antiproliferative activity with IC50 values around 20 nM, and complete
blockage of cells in G2/M phase at a concentration of 0.1 µM or higher. Its binding to tubulin (Kb)
at the colchicine site was also determined by displacement of R-PT, thus confirming that our
working hypothesis was correct. Moreover, a comparison of the complexes of combretastatin A4
and chalcone 12 with tubulin, both recently published, led to the conclusion that the α-methyl
chalcone binds to tubulin using almost the same interactions as CA4, thus indicating that the
chalcone could be considered a good mimetic of the natural combretastatin.
4. Experimental
4.1. Synthesis
Melting points were obtained on a Mettler Toledo M170 apparatus and are uncorrected. The
elemental analysis was performed with a Heraeus CHN-O-RAPID instrument. Analyses indicated
by the symbols of the elements or functions were within ± 0.4 % of the theoretical values. For the
tested compounds, satisfactory elemental analysis or HPLC purity greater than 95% was obtained.
For compounds 18 and 31, HPLC purity is indicated and the compounds were not submitted to
biological evaluation. Electrospray mass spectra were measured on a quadruple mass spectrometer
1
equipped with an electrospray source (Hewlett-Packard, LC/MS HP 1100). H and 13C NMR
spectra were recorded on a Varian INNOVA-300 operating at 299 MHz (1H) and 75 MHz (13C),
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respectively, a Varian INNOVA-400 operating at 399 MHZ (1H) and 99 MHz (13C), respectively,
and a VARIAN SYSTEM-500 operating a 499 and 125 MHz, respectively.
Analytical TLC was performed on silica gel 60 F254 (Merck) precoated plates (0.2 mm). Spots were
detected under UV light (254 nm) and/or charring with ninhydrin or phosphomolybdic acid.
Separations on silica gel were performed by preparative centrifugal circular thin-layer
chromatography (CCTLC) on a ChromatotronR (Kiesegel 60 PF254 gipshaltig (Merck)), with layer
thickness of 1 and 2 mm and flow rate of 4 or 8 mL/min, respectively. Flash column
chromatography (HPFC) was performed in a Biotage Horizon instrument.
HPLC analysis was performed in Agilent 1120 compact LC, column ACE 5 C18-300 (15 cm x 4.6
mm), UV detection, and flow rate 1ml/min, using as mobile phase A H2O (containing 0.1% TFA)
and as mobile phase B acetonitrile.
Microwave reactions were performed using the Biotage Initiator 2.0 single-mode cavity instrument
from Biotage (Uppsala). Experiments were carried out in sealed microwave process vials utilizing
the standard absorbance level (400 W maximum power). The temperature was measured with an IR
sensor on the outside of the reaction vessel.
(±)-6-Methoxy-1,2,3,4-tetrahydronaphthalene-2-carbaldehyde (15)
To a solution of 6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (14) (150 mg, 0.73
mmol) in anhydrous THF (6.5 mL), 2 M BH3·Me2S in THF (0.5 mL, 0.89 mmol) was added at rt
under argon. After stirring at rt for 1h, ethyl acetate was added and the solution was successively
washed with saturated aqueous NaHCO3, water and brine. The combined organic layers were dried
over Na2SO4, filtered and evaporated to dryness to provide a yellow oil which was used in the next
step without further purification. To a solution of this alcohol in CH2Cl2 (7.2 mL) Dess−Martin
periodinane (370 mg, 0.88 mmol) was added at rt. The mixture was stirred for 2h at rt, washed with
saturated aqueous NaHCO3 and extracted with ethyl acetate. The combined organic layers were
dried over Na2SO4, filtered and evaporated under reduced pressure. The crude residue was purified
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1
by CCTLC (dichloromethane/methanol, 10:0.5) to yield 68 mg (49%) of 15 as colorless oil. H
NMR (DMSO-d6, 400 MHz) δ: 1.68 (m, 1H, H-3), 2.08 (m, 1H, H-3), 2.70–2.84 (m, 5H, H-1, H-4,
H-2), 3.69 (s, 3H, OCH3), 6.64 (d, J = 2.7 Hz, 1H, Ar), 6.69 (dd, J = 8.4, 2.8 Hz, 1H, Ar), 7.03 (d, J
= 8.4 Hz, 1H, Ar), 9.70 (s, 1H, COH).
(±)-6-Methoxy-1,2,3,4-tetrahydronaphthalene-2-carbonyl chloride (16)
To a solution of 6-methoxy-1,2,3,4-tetrahydronaphthalene-2-carboxylic acid (14) (260 mg, 1.26
mmol) in anhydrous toluene (12 mL), distillate thionyl chloride (1.48 mL, 12.6 mmol) was added at
room temperature under argon. The solution was heated at reflux for 3h, cooled to room
temperature and concentrated under reduced pressure to provide a tan solid. The acid halide was
used in the next step without further purification.
4-Methoxybenzo[d][1,3]dioxole (17)[24]
To a mixture of 3-methoxybenzene-1,2-diol (500 mg, 3.56 mmol) and K2CO3 (785 mg, 4.28 mmol)
in anhydrous DMF (18 mL) bromochloromethane (374 µL, 5.35 mmol) was added. The mixture
was heated at 100 °C for 4 h. The solution was allowed to reach room temperature and volatiles
were evaporated under reduced pressure. The residue was diluted with dichloromethane and
neutralized with 1N HCl. The aqueous phase was further extracted with dichloromethane (3 x 20
mL). The combined organic layers were washed with brine, dried over Na2SO4, filtered and
evaporated to dryness. The crude was purified by flash chromatography (hexane/ethyl acetate, 10:1)
to yield 255 mg (47%) of 17 as colorless oil. 1H NMR (DMSO-d6, 400 MHz) δ: 3.81 (s, 3H, OCH3),
5.96 (s, 2H, OCH2O), 6.58 (d, J = 7.8 Hz, 1H, Ar), 6.63 (d, J = 8.1 Hz, 1H, Ar), 6.79 (t, J = 8.2 Hz,
1H, Ar).
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(±)-(6-Methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)(4-methoxybenzo[d][1,3]dioxol-5-
yl)methanone (18) and (±)-(6-Methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)(7-
methoxybenzo[d][1,3]dioxol-4-yl)methanone (19)
To a solution of 4-methoxybenzo[d][1,3]dioxole (17) (18 mg, 0.12 mmol) in anhydrous 1,2-
dichloroethane (1.0 mL), ZnCl2 (16 mg, 0.12 mmol) was added under argon, followed by the
addition of 16 (55 mg, 0.24 mmol). The resultant mixture was stirred at 60 ºC for 4h, quenched with
ice water and extracted with dichloromethane (3 x 15 mL). The combined organic layers were dried
over Na2SO4, filtered and evaporated to dryness. The crude was purified by CCTLC (hexane/ethyl
acetate, 2:1) to yield 7 mg of 18 (68% purity), as a white amorphous solid and 6 mg (16% isolated
yield) of 19 as a white amorphous solid.
Experimental data for 18: MS (ES, positive mode): m/z 341 (M+H)+. Analytical HPLC (gradient
10% to 100% phase B in 10 min): TR: 9.36; area: 68 %. 1H NMR (DMSO-d6, 500 MHz) δ: 1.59 (m,
1H, H-3), 2.03 (m, 1H, H-3), 2.71–2.86 (m, 4H, H-1, H-4), 3.49 (m, 1H, H-2), 3.69 (s, 3H, OCH3),
3.98 (s, 3H, OCH3), 6.12 (m, 2H, OCH2O), 6.64 (d, J = 2.7 Hz, 1H, Ar), 6.67 (dd, J = 8.3, 2.7 Hz,
2H, Ar), 6.74 (d, J = 8.2 Hz, 1H, Ar), 7.00 (d, J = 8.4 Hz, 1H, Ar), 7.14 (d, J = 8.2 Hz, 1H, Ar).
Experimental data for 19: MS (ES, positive mode): m/z 341 (M+H)+. Analytical HPLC (gradient
10% to 100% phase B in 10 min): TR: 9.16; area: 98 %. (gradient 60 to 80% phase B in 10 min): TR:
1
3.62; area: 98 %. H NMR (DMSO-d6, 500 MHz) δ: 1.63 (m, 1H, H-3), 2.06 (m, 1H, H-3), 2.70 –
2.91 (m, 4H, H-1, H-4), 3.54 (m, 1H, H-2), 3.70 (s, 3H, OCH3), 3.90 (s, 3H, OCH3), 6.13 (m, 2H,
OCH2O), 6.66 (d, J = 2.7 Hz, 1H, Ar), 6.68 (dd, J = 8.3, 2.8 Hz, 1H, Ar), 6.82 (d, J = 9.1 Hz, 1H,
Ar), 7.01 (d, J = 8.3 Hz, 1H, Ar), 7.39 (d, J = 9.0 Hz, 1H, Ar). 13C NMR (DMSO-d6, 125 MHz) δ:
25.6 (C-3), 28.7 (C-4), 30.1 (C-1), 44.5 (C-2), 55.0 (OCH3), 56.4 (OCH3), 102.1 (OCH2O), 108.1,
112.1, 113.1, 113.2, 122.8, 127.3, 129.8, 135.1, 136.8, 147.2, 148.6, 157.3 (Ar), 198.3 (CO).
(±)-(6-Methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)(2,3,4-trimethoxyphenyl)
methanone (21)
14

ACCEPTED MANUSCRIPT
To a solution of 1,2,3-trimethoxybenzene (20) (346 mg, 2.06 mmol) in anhydrous 1,2-
dichloroethane (8.2 mL), 16 (692 mg, 3.09 mmol) was added under argon, followed by the addition
of TfOH (183 µL, 2.06 mmol). The resultant mixture was stirred at 60 ºC for 1h. The mixture was
quenched by the addition of saturated aqueous solution of NaHCO3 and ice water and extracted
with dichloromethane (3 x 20 mL). The combined organic layers were washed with brine, dried
over Na2SO4, filtered and evaporated to dryness. The crude was purified by flash chromatography
(hexane/ethyl acetate, 2:1) to yield 355 mg (64%) of 21 as a white solid. Mp 66-67 ºC. MS (ES,
1
positive mode): m/z 357 (M+H)+. H NMR (DMSO-d6, 500 MHz) δ: 1.61 (m, 1H, H-3), 2.03 (m,
1H, H-3), 2.71 – 2.86 (m, 4H, H-1, H-4), 3.51 (m, 1H, H-2), 3.69 (s, 3H, OCH3), 3.77 (s, 3H,
OCH3), 3.85 (s, 3H, OCH3), 3.86 (s, 3H, OCH3), 6.65 (d, J = 2.7 Hz, 1H, Ar), 6.67 (dd, J = 8.3, 2.7
Hz, 1H, Ar), 6.91 (d, J = 8.8 Hz, 1H, Ar), 7.00 (d, J = 8.3 Hz, 1H, Ar), 7.33 (d, J = 8.8 Hz, 1H, Ar).
13C NMR (DMSO-d6,100 MHz) δ: 25.7 (C-3), 28.6 (C-4), 30.4 (C-1), 45.4 (C-2), 54.9 (OCH3), 56.1
(OCH3), 60.4 (OCH3), 61.6 (OCH3), 107.8, 112.1, 113.1, 124.8, 125.3, 127.3, 129.8, 136.8, 141.5,
152.5, 156.6, 157.2 (Ar), 203.2 (CO). Anal. calc. for (C21H24O5): C, 70.77; H, 6.79. Found: C,
70.38; H, 6.84.
(±)-(2-Hydroxy-3,4-dimethoxyphenyl)(6-methoxy-1,2,3,4-tetrahydronaphthalen-2-
yl)methanone (22)
To a solution of 1,2,3-trimethoxybenzene (20) (82 mg, 0.49 mmol) in anhydrous 1,2-dichloroethane
(2 mL), BF3.OEt2 (62 µL, 0.49 mmol) was added under argon, followed by the addition of 20 (163
mg, 0.73 mmol). The resultant mixture was stirred at 60 ºC overnight. The mixture was quenched
by the addition of ice water and extracted with dichloromethane (3 x 20 mL). The combined organic
layers were washed with brine, dried over Na2SO4, filtered and evaporated to dryness. The crude
was purified by flash chromatography (hexane/ethyl acetate, 2:1) to yield 76 mg (46%) of 22 as a
1
white solid. Mp 78-80 ºC. MS (ES, positive mode): m/z 343 (M+H)+. H NMR (DMSO-d6, 500
MHz) δ: 1.73 (m, 1H, H-3), 2.03 (m, 1H, H-3), 2.77 – 2.86 (m, 3H, H-1, H-4), 2.92 (m, 1H, H-1),
15

ACCEPTED MANUSCRIPT
3.71 (s, 6H, OCH3), 3.82 (m, 1H, H-2), 3.89 (s, 3H, OCH3), 6.66 – 6.72 (m, 3H, Ar), 7.02 (d, J =
7.9 Hz, 1H, Ar), 7.84 (d, J = 9.1 Hz, 1H, Ar), 12.46 (br s, 1H, OH). 13C NMR (DMSO-d6,125 MHz)
δ: 26.4 (C-3), 28.4 (C-4), 31.0 (C-1), 41.3 (C-2), 55.0 (OCH3), 56.1 (OCH3), 59.9 (OCH3), 103.8,
112.1, 113.1, 113.7, 127.0, 127.2, 129.7, 135.9, 136.8, 156.3, 157.3, 158.3 (Ar), 208.1 (CO). Anal.
calc. for (C20H22O5): C, 70.16; H, 6.48. Found: C, 69.78; H, 6.62.
(±)-(3,4-Dimethoxyphenyl)(6-methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)methanone (24)
To a solution of 1,2-dimethoxybenzene (23) (95 µL, 0.74 mmol) in anhydrous 1,2-dichloroethane (3
mL), TfOH (65 µL, 0.74 mmol) was added under argon, followed by the addition of 16 (228 mg,
1.02 mmol). The resultant mixture was stirred at 60 ºC for 2h. The mixture was quenched by the
addition of saturated aqueous solution NaHCO3 and ice water and extracted with dichloromethane
(3 x 15 mL). The combined organic layers were dried over Na2SO4, filtered and evaporated to
dryness. The crude was purified by flash chromatography (hexane/ethyl acetate, 2:1) to yield 184
mg (76%) of 24 as a white solid. Mp 98-100 ºC. MS (ES, positive mode): m/z 327 (M+H)+. 1H
NMR (DMSO-d6, 500 MHz) δ: 1.67 (m, 1H, H-3), 2.01 (m, 1H, H-3), 2.74 – 2.86 (m, 3H, H-1, H-
4), 2.92 (m, 1H, H-1/ H-4), 3.71 (s, 3H, OCH3), 3.78 (m, 1H, H-2), 3.82 (s, 3H, OCH3), 3.85 (s, 3H,
OCH3), 6.67 (s, 1H, Ar), 6.68 (d, J = 8.1 Hz, 1H, Ar), 7.01 (d, J = 8.0 Hz, 1H, Ar), 7.08 (d, J = 8.5
Hz, 1H, Ar), 7.49 (s, 1H, Ar), 7.72 (d, J = 8.5 Hz, 1H, Ar). 13C NMR (DMSO-d6, 125 MHz) δ: 26.4
(C-3), 28.5 (C-4), 31.0 (C-1), 40.8 (C-2), 55.0 (OCH3), 55.5 (OCH3), 55.8 (OCH3), 110.5, 111.0,
112.0, 113.1, 122.9, 127.3, 128.6, 129.7, 136.9, 148.7, 153.0, 157.3 (Ar), 201.1 (CO). Anal. calc.
for (C20H22NO4): C, 73.60; H, 6.79. Found: C, 73.21; H, 6.64.
(±)-(6-Methoxy-7-nitro-1,2,3,4-tetrahydronaphthalen-2-yl)(2,3,4-trimethoxyphenyl)
methanone
(25)
and
(±)-(6-Methoxy-5-nitro-1,2,3,4-tetrahydronaphthalen-2-yl)(2,3,4-
trimethoxyphenyl)methanone (26)
To a solution of 21 (233 mg, 0.65 mmol) in acetic anhydride (2 mL) at -40 °C, 65% HNO3 (100 µL)
was slowly added. The reaction was allowed to reach -14 ºC and stirred 20 min at this temperature.
The reaction mixture was diluted with ethyl acetate and ice water was added. The crude product
16

ACCEPTED MANUSCRIPT
was washed with brine and extracted with ethyl acetate (3 x 15 mL). The combined organic layers
were dried over Na2SO4, filtered and evaporated to dryness. The crude was purified by CCTLC
(dichloromethane/ethyl acetate, 10:0.2) to yield 121 mg (46%) of 25 as a yellow solid and 100 mg
(38%) of 26 as a yellow solid.
1
Experimental data for 25: Mp 120-122 ºC. MS (ES, positive mode): m/z 401 (M+H)+. H NMR
(DMSO-d6, 400 MHz) δ: 1.67 (m, 1H, H-3), 2.06 (m, 1H, H-3), 2.79 – 2.95 (m, 4H, H-1, H-4), 3.58
(m, 1H, H-2), 3.77 (s, 3H, OCH3), 3.87 (s, 6H, OCH3), 3.89 (s, 3H, OCH3), 6.91 (d, J = 8.8 Hz, 1H,
Ar), 7.08 (s, 1H, Ar), 7.35 (d, J = 8.8 Hz, 1H, Ar), 7.68 (s, 1H, Ar). 13C NMR (DMSO-d6, 100 MHz)
δ: 25.0 (C-3), 28.5 (C-4), 29.7 (C-1), 44.5 (C-2), 56.1 (OCH3), 56.5 (OCH3), 60.4 (OCH3), 61.6
(OCH3), 107.8, 113.8, 124.8, 125.0, 125.1, 128.0, 137.1, 141.5, 143.6, 150.0, 152.5, 156.7 (Ar),
202.6 (CO). Anal. calc. for (C21H23NO7·0.5H2O): C, 61.46; H, 5.89; N, 3.41. Found: C, 61.61; H,
5.91; N, 3.56.
1
Experimental data for 26: Mp 93-95 ºC. MS (ES, positive mode): m/z 401 (M+H)+. H NMR
(DMSO-d6, 400 MHz) δ: 1.64 (m, 1H, H-3), 2.06 (m, 1H, H-3), 2.53 – 2.72 (m, 2H, H-4), 2.77 –
2.98 (m, 2H, H-1), 3.55 (m, 1H, H-2), 3.77 (s, 3H, OCH3), 3.83 (s, 3H, OCH3), 3.86 (s, 3H, OCH3),
3.87 (s, 3H, OCH3), 6.91 (d, J = 8.8 Hz, 1H, Ar), 7.12 (d, J = 8.6 Hz, 1H, Ar), 7.33 (d, J = 8.6 Hz,
13
1H, Ar), 7.35 (d, J = 8.8 Hz, 1H, Ar). C NMR (DMSO-d6, 100 MHz) δ: 23.1 (C-4), 24.4 (C-3),
30.2 (C-1), 44.2 (C-2), 56.1 (OCH3), 56.5 (OCH3), 60.4 (OCH3), 61.6 (OCH3), 107.8, 111.1, 124.8,
124.9, 127.7, 129.0, 131.7, 140.6, 141.5, 148.1, 152.6, 156.8 (Ar), 202.5 (CO). Anal. calc. for
(C21H23NO7): C, 62.84; H, 5.78; N, 3.49. Found: C, 62.80; H, 5.96; N, 3.58.
(±)-(7-Amino-6-methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)(2,3,4-
trimethoxyphenyl)methanone (27)
Compound 25 (30 mg, 0.07 mmol) was dissolved in ethyl acetate (12 mL) in a pressure vessel and
then 5% Pt/S (catalytic amount) was added. The mixture was hydrogenated at 30 psi for 3 h at 30
ºC. Then, the reaction mixture was filtered and the solvent was evaporated. The crude was purified
by flash chromatography (dichloromethane/ethyl acetate, 10:0.5) to yield 14 mg (54%) of 27 as
17

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colorless oil. MS (ES, positive mode): m/z 372 (M+H)+. 1H NMR (DMSO-d6, 500 MHz) δ: 1.55 (m,
1H, H-3), 2.00 (m, 1H, H-3), 2.61 – 2.72 (m, 4H, H-1, H-4), 3.45 (m, 1H, H-2), 3.70 (s, 3H, OCH3),
3.77 (s, 3H, OCH3), 3.84 (s, 3H, OCH3), 3.86 (s, 3H, OCH3), 4.43 (br s, 2H, NH2), 6.34 (s, 1H, Ar),
6.48 (s, 1H, Ar), 6.90 (d, J = 8.8 Hz, 1H, Ar), 7.32 (d, J = 8.8 Hz, 1H, Ar). Anal. calc. for
(C21H25NO5·H2O): C, 64.77; H, 6.99; N, 3.60. Found: C, 64.66; H, 7.23; N, 3.89.
(±)-(5-Amino-6-methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)(2,3,4-
trimethoxyphenyl)methanone (28)
Iron powder (125 mg, 2.2 mmol) and 37% HCl (1 drop) were added to a solution of 26 (90 mg, 0.22
mmol) in EtOH (2.2 mL) and water (1 mL). The mixture was heated at reflux for 1h. Ethyl acetate
(10 mL) was added to the mixture, washed with water and extracted with ethyl acetate (3 x 15 mL).
The combined organic layers were dried over Na2SO4, filtered and evaporated to dryness. The crude
was purified by CCTLC (dichloromethane/ethyl acetate, 10:1) to yield 34 mg (40%) of 28 as a
white solid. Mp 133-135 ºC. MS (ES, positive mode): m/z 372 (M+H)+. 1H NMR (DMSO-d6, 500
MHz) δ: 1.59 (m, 1H, H-3), 2.09 (m, 1H, H-3), 2.43 (m, 1H, H-4), 2.59 (m, 1H, H-4), 2.67 – 2.79
(m, 2H, H-1), 3.41 (m, 1H, H-2), 3.72 (s, 3H, OCH3), 3.77 (s, 3H, OCH3), 3.84 (s, 3H, OCH3), 3.86
(s, 3H, OCH3), 4.35 (br s, 2H, NH2), 6.34 (d, J = 8.1 Hz, 1H, Ar), 6.62 (d, J = 8.1 Hz, 1H, Ar), 6.91
(d, J = 8.8 Hz, 1H, Ar), 7.33 (d, J = 8.8 Hz, 1H, Ar). 13C NMR (DMSO-d6, 125 MHz) δ: 23.9 (C-4),
25.7 (C-3), 31.6 (C-1), 45.2 (C-2), 55.6 (OCH3), 56.1 (OCH3), 60.4 (OCH3), 61.6 (OCH3), 107.8,
108.4, 116.2, 120.0, 124.8, 125.4, 127.9, 134.4, 141.5, 144.2, 152.5, 156.6 (Ar), 203.5 (CO). Anal.
calc. for (C21H25NO5·H2O): C, 64.77; H, 6.99; N, 3.60. Found: C, 64.39; H, 6.85; N, 4.00.
(±)-(7-Amino-6-methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)(3,4-dimethoxyphenyl)
methanone
(31)
and
(±)-(5-Amino-6-methoxy-1,2,3,4-tetrahydronaphthalen-2-yl)(3,4-
dimethoxyphenyl)methanone (32)
To a solution of 24 (170 mg, 0.49 mmol) in acetic anhydride (2 mL) at -40 °C, 65% HNO3 (100 µL)
was slowly added. The reaction was allowed to reach -10 ºC and stirred for 20 min at this
temperature. The reaction mixture was diluted with ethyl acetate and ice water was added. The
18

ACCEPTED MANUSCRIPT
aqueous layer was extracted with ethyl acetate (3x15 mL). The combined organic layers were
washed with brine, dried over Na2SO4, filtered and evaporated to dryness. The residue was purified
by CCTLC (dichloromethane/ethyl acetate, 10:0.1) to yield 95 mg of a mixture of the 5/7 nitro
isomers. Analytic HPLC (gradient 15-95% acetonitrile in 10 min): TR: 7.48; area: 60 % and TR:
7.78; area: 40 %. MS (ES, positive mode): m/z 372 (M+H)+. The mixture of the two isomers was
dissolved in EtOH (2.7 mL) and water (1 mL), and iron powder (140 mg, 2.5 mmol) and HCl 37%
(2 drops) were added to the solution. The mixture was heated to reflux for 3h. Ethyl acetate (6 mL)
was added to the mixture, washed with water and extracted with ethyl acetate (3 x 15 mL). The
combined organic layers were dried over Na2SO4, filtered and evaporated to dryness. The crude was
purified by CCTLC (dichloromethane/ethyl acetate, 10:2) to yield 27 mg (16%, area 75%) of 31 as
a colorless oil and 17 mg (10%) of 32 as a white solid.
Experimental data for 31: Analytical HPLC (gradient from 10% to 100% of mobile phase B in 10
1
min): TR: 5.96; area: 75%. MS (ES, positive mode): m/z 342 (M+H)+. H NMR (DMSO-d6, 400
MHz) δ: 1.62 (m, 1H, H-3), 1.97 (m, 1H, H-3), 2.61 – 2.85 (m, 4H, H-1, H-4), 3.71 (s, 3H, OCH3),
3.75 (m, 1H, H-2), 3.82 (s, 3H, OCH3), 3.85 (s, 3H, OCH3), 4.43 (br s, 2H, NH2), 6.35 (s, 1H, Ar),
6.51 (s, 1H, Ar), 7.07 (d, J = 8.4 Hz, 1H, Ar), 7.48 (d, J = 2.0 Hz, 1H, Ar), 7.71 (dd, J = 8.5, 2.0 Hz,
1H, Ar).
1
Experimental data for 32: Mp 125-127 ºC. MS (ES, positive mode): m/z 342 (M+H)+. H NMR
(DMSO-d6, 400 MHz) δ: 1.66 (m, 1H, H-3), 2.07 (m, 1H, H-3), 2.52 – 2.70 (m, 2H, H-1, H-4), 2.71
– 2.81 (m, 2H, H-1, H-4), 3.68 (m, 1H, H-2), 3.73 (s, 3H, OCH3), 3.82 (s, 3H, OCH3), 3.85 (s, 3H,
OCH3), 4.37 (br s, 2H, NH2), 6.35 (d, J = 8.2 Hz, 1H, Ar), 6.64 (d, J = 8.2 Hz, 1H, Ar), 7.07 (d, J =
8.4 Hz, 1H, Ar), 7.49 (d, J = 2.0 Hz, 1H, Ar), 7.71 (dd, J = 8.5, 2.0 Hz, 1H, Ar). 13C NMR (DMSO-
d6, 125 MHz) δ: 23.8 (C-4), 26.3 (C-3), 32.2 (C-1), 40.6 (C-2), 55.6 (OCH3), 55.7 (OCH3), 108.4,
110.4, 111.0, 116.2, 120.1, 122.8, 127.9, 128.7, 134.4, 144.2, 148.7, 153.0 (Ar), 201.4 (CO). Anal.
calc. for (C20H23NO4·H2O): C, 66.84; H, 7.01; N, 3.90. Found: C, 66.94; H, 6.94; N, 4.29.
19

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4.2 Biological Methods
4.2.1. Cell proliferation.
Human microvascular endothelial (HMEC-1) cells were seeded in 48-well plates at 20,000
cells/well. After 24 h, 5-fold dilutions of the compounds were added. The cells were allowed to
proliferate 4 days in the presence of the compounds, trypsinized, and counted by means of a Coulter
counter (Analis, Belgium). Human cervical carcinoma (HeLa) cells were seeded in 48-well plates at
10,000 cells/well. After 24h, different concentrations of the compounds were added. After 3 days of
incubation, the cells were trypsinized and counted in a Coulter counter. Suspension cells (human T-
cell leukemia Cem and mouse B-cell leukemia L1210 cells) were seeded in 96-well plates at 60,000
cells/well in the presence of different concentrations of the compounds, allowed to proliferate for 96
h, and counted in a Coulter counter. The 50% inhibitory concentration (IC50) was defined as the
compound concentration required to reduce cell proliferation by 50%.
4.2.2. Tubulin binding
Calf brain tubulin was purified as described [37]. Aliquots of frozen tubulin (10 mg) were clarified
by exclusion chromatography in Sephadex G-25 and equilibrated in GAB buffer (10 mM sodium
phospahte, 1 mM EGTA (ethylene glycol-bis(β-aminoethyl ether)-N,N,N',N'-tetraacetic acid), 25%
v/v Glycerol, 0.1 mM GTP pH= 7.0) to a final concentration of 25 µM of soluble protein. Protein
concentrations were determined by spectrophotometric absorbance at λ=295 nm (ε= 107000 M-1
cm-1).
4.2.2.1. Tubulin assembly time-course.
100 µL of Tubulin prepared as described was vacuum-degassed and dispensed in a 96-well
microplate and 30 uM of the tested compounds were added. Assembly at 37 °C was
spectrophotometrically monitorized in a Varioskan Flash (Thermo Fisher Scientific) at λ = 350 nm
up to 6000 s. Negative controls (DMSO) and positive controls (podophyllotoxin) for polymerization
inhibition were included to validate the analysis. Figures represent normalized absorbance at 350
nm.
20

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4.2.2.2. Tubulin binding constant
(R)-(+)-ethyl 5-amino 2-methyl-1,2-dihydro-3-phenylpyrido[3,4-b]pyrazin-7-yl carbamate (R-PT)
was a kind gift of Prof. G.A. Rener, Organic Chemistry Research Department, Southern Research
Institute, Birmingham, Alabama (Temple 1989).The binding constant of 28 to tubulin was
determined by competition with a well characterized colchicine binding site ligand (R-PT) as
described.[38, 39] For that purpose, the fluorescence emission of a previous mixed sample of 0.2
µM of R-PT and 0.2 µM of tubulin was evaluated in presence of increasing concentrations of
studied ligand in a black 96-well plate (0; 0.05; 0.2; 0.5; 2; 5; 10; 30; 50; 70 µM). The samples were
incubated 30 minutes at 25 ºC in a Varioskan plate reader (Thermo Scientific Waltham,
Massachusetts, USA) before the fuorescence emission intensity at 456 nm (excitation 374 nm) was
measured. The data were analyzed and the binding constants determined using Equigra V5.0 [40]
4.2.3. Immunocytochemistry.
HeLa cells were seeded overnight on poly-L-Lysine coated 8-well Millicell slides (Millipore). Next,
0.1% DMSO (control cells) or compound 28 (0.3 and 0.1 µM) were added for 24 h. The cells were
fixed, permeabilized and incubated with a monoclonal anti-β-tubulin antibody (2 µg/ml, Sigma-
Aldrich). After washing, cells were incubated with goat anti-mouse Alexa Fluor 555 antibody (4
µg/ml; Molecular Probes, Invitrogen). Nuclei were stained with 2 µg/ml Hoechst33342 (Sigma-
Aldrich). Fluorescence microscopy was done using an Axiovert 200 M inverted microscope (Zeiss,
Göttingen, Germany).
4.2.4. Cell cycle analysis.
HeLa cells were seeded in 6-well plates at 125,000 cells/well in DMEM with 10 % FBS. After 24 h,
the cells were exposed to different concentrations of the compound. After 24 h, the DNA of the
cells was stained with propidium iodide using the CycleTEST PLUS DNA Reagent Kit (BD
Biosciences, San Jose, CA). The DNA content of the stained cells was assessed by flow cytometry
on a FACSCalibur flow cytometer and analyzed with CellQuest software (BD Biosciences) within
21

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3h after staining. Cell debris and clumps were excluded from the analysis by appropriate dot plot
gating. Percentages of sub-G1, G1, S, and G2/M cells were estimated using appropriate region
markers.
4.3. Computational methods.
4.3.1. Docking of compound 28
3D structure of compound 28 was generated through conversion from their SMILES strings to 3D
pdb format using CORINA (Molecular Networks GmbH, Germany and Altamira, LLC, USA). The
geometry of 28 were first optimized using the semiempirical quantum chemistry program
MOPAC2012 (AM1 method) [23]. Partial atomic charges were then obtained using the RESP [41]
methodology with the 6-31G(d) basis set as implemented in the ab initio quantum chemistry
program Gaussian09 [42].
Compound 28 was used as ligand for the automated docking experiments using TUB092-tubulin
complex (PDB ID: 5JVD) [18]. The Lamarkian genetic algorithm implemented in AutoDock 4.2
[36] as used to generate the docked conformations within the putative binding cavity by randomly
changing the overall orientation of the molecule as well as the torsion angles of all rotatable bonds.
Default settings were used except for the number of runs, population size, and maximum number of
energy evaluations, which were fixed at 250, 100 and 250.000, respectively. Rapid intra- and
intermolecular energy evaluations of each configuration was achieved by having the receptor´s
atomic affinity potentials for aliphatic and aromatic carbon, oxygen, nitrogen and hydrogen atoms
pre-calculated in a three-dimensional grid with a spacing of 0.375 Å. A distance-dependent
dielectric function was used in the computation of electrostatic interactions.
4.3.2. Molecular dynamics simulations
The MD simulations were carried out using the AMBER 12 suite of programs [43]. The bonded and
non-bonded parameters for 28, GTP4-, GDP3- and Mg2+ were assigned, by analogy or through
22

ACCEPTED MANUSCRIPT
interpolation from those already present in the AMBER database, in a way consistent with the
general AMBER force field (GAFF) for organic molecules [44].
The molecular system consisting of bovine α,β-tubulin, 28, GDP3-, GTP4- and 2 Mg2+ ions was
neutralized by the addition of 36 Na+ ions [45] and immersed in a truncated octahedron of ~29500
TIP3P water molecules [46]. Periodic boundary conditions were applied and electrostatic
interactions were treated using the smooth particle mesh Ewald (PME) method [47] with a grid
spacing of 1 Å. The cutoff distance for the non–bonded interactions was 9 Å. The SHAKE
algorithm [48] was applied to all bonds and an integration step of 2.0 fs was used throughout.
Solvent molecules and counterions were relaxed by energy minimization and allowed to redistribute
around the positionally restrained solute (25kcal·mol–1·Å–2) during 50 ps of MD at constant
temperature (300 K) and pressure (1 atm). These initial harmonic restraints were gradually reduced
in a series of progressive energy minimizations until they were completely removed. The resulting
systems were heated again from 100 to 300 K during 20 ps and allowed to equilibrate in the absence
of any restraints for 10.0 ns during which system coordinates were collected every 2 ps for further
analysis.
Three–dimensional complexes structures and trajectories were visually inspected using the
computer graphics program PyMOL (The PyMOL Molecular Graphics System, Version 1.5.0.5.
Schrödinger, LLC). Interatomic distances and angles, as well as root–mean–square deviations
(rmsd) from a given structure, were monitored using the Ptraj module in AMBER.
Acknowledgements
This project has been supported by MINECO (SAF2012-39760-C02-01) and MINECO/FEDER
(SAF2015-64629-C2-1-R), and to M.-J.P.-P., E.-M.P. E. Q. and M. J. C. and MINECO/FEDER
BFU2016-75319-R to J.F.D. The authors acknowledge networking contribution by the COST
Action CM1407 “Challenging organic syntheses inspired by nature - from natural products
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chemistry to drug discovery” (to M-J. P.-P. S.L. and J.-F.D.) We also would like to acknowledge
Eef Meyen and Lizette Van Berckelaer for excellent technical assistance.
Conflict of interests
The authors declare no conflict of interests
Appendix A. Supplementary data
The following is the supplementary data related to this article
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