Structural insights into a novel anticancer sulfonamide chalcone

Article abstract of DOI:10.1039/c7nj03523c

Natural products have stood out due to their wide range of biological activities. Among the various naturally occurring classes, we can highlight chalcones, sulfonamides and hybrid compounds formed by both. Although many pharmacological activities of these classes of compounds are known, new ones have arisen lately and require detailed structural and biological analyses. Herein, we report the synthesis and structural elucidation of a novel sulfonamide chalcone 2,5-dichloro-N-{3-[(2E)-3-(4-nitrophenyl)prop-2-enoyl]phenyl}benzenesulfonamide (BSC) by Single Crystal X-ray Diffraction and spectroscopy analysis (Infrared, NMR and Mass Spectroscopy). Topology was determined through Hirshfeld surface analysis and the electrostatic potential map, while the energy of frontier molecular orbitals was used to evaluate the stability of BSC. Additionally, the cytotoxicity of the title compound was evaluated through the MTT colorimetric method. We show that the BSC compound has a planar conformation in its chalcone portion, which is further corroborated by the low angle between the aromatic rings (5.23°). In addition, intermolecular interactions of type C-H?O and N-H?O make up a dimeric supramolecular arrangement. An inverse virtual screening approach allowed identifying potential biological applications for BSC, which indicated that BSC might interact with the binding sites of RARα and RARβ. Consequently, BSC was experimentally evaluated against three cancer cell lines, and was shown to hold potent anticancer activity. In addition, a cytotoxic effect was observed for all strains, which was more pronounced for HCT-116, a colon cancer cell line.

Full text of DOI:10.1039/c7nj03523c

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PAPER
Jason B. Benedict et al.
The role of atropisomers on the photo-reactivity and fatigue of
diarylethene-based metal–organic frameworks
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DOI: 10.1039/C7NJ03523C
New Journal of Chemistry
ARTICLE
Structural Insights on a Novel Anticancer Sulfonamide Chalcone
Jean M. F. Custodioa,b, Lidiane J. Michelinia, Mirian Rita C. de Castroa, Wesley F. Vazb, Bruno J.
Nevesc, Pedro V. L. Cravoc,d, Francisco S. Barretoe, Manoel O. M. Filhoe, Caridad N. Pereza and
Hamilton B. Napolitanob,c
Received 00th January 20xx,
Accepted 00th January 20xx
Natural products have stood out due to their wide range of biological activities. Among the various naturally occurring
classes, we can highlight chalcones, sulfonamides and hybrid compounds formed by both. Although many pharmacological
activities of these classes of compounds are known, new ones have arisen lately and require detailed structural and biological
analyses. Herein, we report the synthesis and structural elucidation of a novel sulfonamide chalcone2,5-dichloro-N-{3-[(2E)-
3-(4-nitrophenyl)prop-2-enoyl]phenyl}benzenesulfonamide (BSC) by Single Crystal X-ray Diffraction and spectroscopy
analysis (Infrared, NMR and Mass Spectroscopy). Topology was determined through Hirshfeld surfaces analysis and
electrostatic potential map, while the energy of frontier molecular orbitals evaluated the stability of BSC. Additionally, the
cytotoxicity of the title compound was evaluated through the MTT colorimetric method. We show that the BSC compound
has a planar conformation in its chalcone portion, which is further corroborated by the low angle between the aromatic
rings (5.23°). In addition, intermolecular interactions of type C-H⋯O and N-H⋯O make up a dimeric supramolecular
arrangement. An inverse virtual screening approach allowed identifying potential biological applications for BSC, which
indicated that BSC might interact with binding sites of the RARα and RARβ. Consequently, BSC was experimentally evaluated
against three cancer cell lines, and was shown to hold potent anticancer activity. In addition, a cytotoxic effect was observed
for all strains, which was more pronounced for HCT-116, a colon cancer cell line.
DOI: 10.1039/x0xx00000x
www.rsc.org/
of replaceable hydrogens that allow generating a large number
of derivatives, ease of synthesis, and a variety of promising
biological activities4. These privileged structures have been
widely studied as anti-inflammatory5, anti-oxidant6, anti-
Introduction
Natural products (NPs) have traditionally formed the backbone
of modern drug discovery programs1. Recently it was shown
that 28% of all approved drugs are either NPs (15%) or NP-
inspired compounds (13%)2. In other words, the exploration of
NPs offers a remarkable opportunity to identify interesting
chemical scaffolds for drug discovery by providing chemically
diverse compounds. To expand on their success, and explore
areas of chemical space not covered by biosynthesis, there has
been a movement to develop synthetic compounds that have
complexity comparable to that of NPs. This strategy can provide
prototypes that represent the best of both chemical spaces:
structurally diverse molecules with physicochemical properties
analogous to those of NPs, accessed as rapidly as the other
synthetic compounds3.
obesity7, anti-protozoal8, hypnotic9, anti-histaminic10, anti-
spasmodic11, anticancer12, anti-gout13, etc.
Moreover, sulfonamide (-SO2NHR-, or their closely related
variants, such as thiosulfonyl, sulfonate, sulfamate) constitutes
an important moiety of synthetic drugs, with several types of
pharmacological agents possessing antibacterial14, antimalarial
15, diuretic16, hypoglycemic17, anticonvulsant18,19, antirheumatic
20,21
,
and antiretroviral22 activity, among others. More
specifically, chalcones that have chlorine and nitro linkers
exhibit appreciable antitumor activities as suppressors of the
p53 protein23–25. Therefore, for this work chlorine and nitro
substituents were chosen from the aromatic rings. It is
interesting to note that the chemical space of approved drugs is
composed of a small number of privileged building blocks,
recurrently found in potent drug molecules, and the
sulfonamide moiety is one of them.
Among the most promising NPs, chalcones (1,3-diphenyl-2-
propen-1-ones) have gained attention due to the large number
Based on this perspective, molecules that contain
sulfonamide and chalcone moieties could lead to the new
hybrid architectures with improved biological profiles. Under
this premise, the aim of this study was the synthesis and
structural elucidate in terms of lengths and bond angles, intra
and intermolecular interactions and supramolecular
arrangements of the hybrid molecule 2,5-dichloro-N-{3-[(2E)-3-
(4-nitrophenyl)prop-2-enoyl]phenyl}benzenesulfonamide (BSC)
This journal is © The Royal Society of Chemistry 20xx
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Journal Name
Further, their biological activities were assessed by 20), 130.50 (C-4 e C-5), 130.34 (C-18), 130.27 (C-1V7ie),w1A2rti7cl.e6O4nl(inCe-
integration of an in silico target fishing approach and biological 19), 126.76 (C-6), 125.86 (C-11), 125.27 D(CO-I8: )1,0.1102349.3/C97N(CJ0-235e23CC-
assays.
3), 124.24 (C-14), 118.85 (C-12). IV: 3218 (N-H), 1710 (C=O),
1342 (S=O), 1661 (Ar-CO-C=C-Ar), 1591-1472 (C-CAr), 1163 (Ar-
Cl). M (m/z): 477.99376.
Experimental and computational procedures
Crystallographic characterization. X-ray diffraction data of BSC
were collected at room temperature using the Bruker APEX II
CCD diffratometer with graphite-monochromated MoKα
radiation (λ=0.71073 Å). The data were processed in the Bruker
software SAINT26 and the structure was solved and refined by
direct and least square methods, respectively, throughout
SHELX201427 software. All the hydrogen atoms were placed in
calculated positions and refined with fixed individual
displacement parameters [Uiso(H) = 1.2 Ueq or 1.5 Ueq]
Materials and Method
Synthesis. Acetophenone sulfonamide (
using a 50 mL round bottom flask. 2,5-dichlorobenzenesulfonyl
chloride ( , 1.0 mmol) was simultaneously added to 3-
aminoacetophenone ( , 1.0 mmol) using triethylamine (C6H15N)
3) was synthesized
1
2
as catalyst and dichloromethane (CH2Cl2, 15 mL). The reaction
was kept under stirring and reflux for 4 hours. Subsequently, the
precipitate could dry and recrystallized in ethanol. Yield: 50%.
Boiling point: 165-167 °C. ¹H RMN (DMSO-d6, 500 MHz)
(500MHz – DMSO-D ): (N-H) δ= 2.67 (s, 1H), (COCH )= 2.49 (s,
3H) , H3’ = 6.54 (ddd, 1H J=7, 0, 1.2 Hz), H4’=7,20 (ddd, 1H,
:
according to the riding model (C–H bond lengths of 0.97
Å and
6
3
0.96 for aromatic and methyl groups, respectively). The
Å
’
structural information (molecular representation, tables and
figures) was obtained throughout the WinGX28, Ortep28 and
Mercury29 programs. The possible interactions and hydrogen
bonds were checked by PARST30 and PLATON31 software and
analyzed from Hirshfeld surface.
J=1.10, 0.60, 7.0 Hz), H5’=6.75 (ddd, 1H, J=0.50, 1.2, 7.0 Hz),
H6’=7,56 (ddd, 1H, J =1.20, 7.0, 1.5 Hz), H9’=7.40 (ddd, 1H, J=
0.40, 1.10, 7.25 Hz), H10’= 7.24 (dd, 1H, J=1.5, 6.9, Hz), H12’=
8.0 (dd, 1H, J=1.5, 6.9 Hz). IV (cm-1): 3081 (N-H),1649 (C=O),
1578 (N-H), 1496(C=O),1360 (S=O),1249 (C-N), 1179 (S=O) e 821
(C-CL). EM (m/z): 341.97685.
Hirshfeld surface. Hirshfeld surface (HS) analysis was used to
investigate the intermolecular interactions in the crystal
packing of the BSC molecule and the associated 2D fingerprint
Equimolar amounts of
3 (1.0 mmol) and p-nitro-
benzaldehyde ( , 2.0 mmol) were dissolved in ethanol (10 mL)
4
and concentrated potassium hydroxide (KOH) in the proportion
of 50% m/m. The reactions were stirred at room temperature
and accompanied by thin layer chromatography (Scheme 1).
After the reaction was complete, ice-cold distilled water was
added and then neutralized with dilute hydrochloric acid (HCl).
plots were generated using the software Crystal Explorer 3.1.32
33,34
Spackman and coworkers
have demonstrated how useful
the Hirshfeld surfaces are and two-dimensional fingerprints
derived from them characterize crystal packing, and allow
understanding the spatial molecular relationships into crystal.
The resulting precipitate (5) was filtered and purified by slow
35
HS were developed to partition the space in molecular
recrystallization from acetone and isopropyl alcohol (3: 1), after
drying. Yield: 62%. Boiling point: 231-234 °C. 1H (DMSO-d6, 500
MHz): δ 8.26 (d, J=8.90 Hz, H-2 e H-3, 2H), 8.11 (d, J=8.90 Hz, H-
4 e H-5, 2H), 8.02 (d, J=2.54 Hz, H-18, 1H), 7.95 (ddd, J=1.06 Hz,
1.70 Hz e 7.84 Hz, H-11), 7.76 (d, J=15.87 Hz, H-8, 1H), 7.75-7.74
(m, H-12, 1H), 7.71 (dd, J=2.54 Hz e 8.48 Hz, H-21, 1H), 7.67 (d,
J=8.48 Hz, H-19, 1H), 7.49 (dd, J=7.84 Hz e 8.27 Hz, H-13, 1H),
7.41 (ddd, J=1,06 Hz, 2.33 Hz e 8.27 Hz, H-14, 1H). 13C (DMSO-
d6, 500 MHz): δ 188.92 (C-9), 148.57 (C-1), 141.98 (C-7), 138.62
(C-10), 136.77 (C-15), 135.00 (C-16), 134.70 (C-21), 132.15 (C-
crystals for electron density integration purposes, this surface
defines a region of space where the molecule electron density
exceeds that of all neighboring molecules that is defined by W(
r)
= 0.5, where W is a weight function, for a molecule in a crystal,
36
derived from the atomic electron densities ρi(r) :
ꢃ∈ꢄꢅꢆꢇꢈꢉꢆꢇ ꢂꢃ ꢁ
ꢀ ꢁ =
(1)
ꢃ∈ꢈꢊꢋꢌꢍꢎꢆ ꢂꢃ ꢁ
where the numerator is a sum of the atoms in the molecule of
interest and the denominator is an analogous sum of the crystal
34. The analysis of the curvature can indicate the presence and
nature of close contacts. Additionally, further information is
gathered by mapping properties such as the electrostatic
potential onto these surfaces35. Consequently, for this analysis,
the normalized contact distances (dnorm) are defined in terms of
the distances from the HS to the nearest nucleus inside the
surface (di) and outside the surface, (de) and the van der Waals
radii of the atoms. dnorm is given by
ꢏꢃ − ꢑꢒꢓꢔ
ꢏꢇ − ꢑꢒꢓꢔ
ꢇ
ꢃ
ꢏꢐꢅꢊꢄ
=
+
(2)
ꢑꢒꢓꢔ
ꢑꢒꢓꢔ
ꢇ
ꢃ
where ꢑꢒꢓꢔ and ꢑꢒꢓꢔ are the van der Waals radii 37. HS uses
ꢇ
ꢃ
colors to represent the interactions with distances that are
closer, equal or longer to the sum of the van der Waals radii
2 | J. Name., 2012, 00, 1-3
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graphically representing them by red, white and blue areas, proteases) pHs. Subsequently, full-atom protein structure
View Article Online
47
respectively.
minimization using the OPLS-2005 force fDieOldI: 1w0a.1s03c9a/rCr7ieNdJ0o3u52t3C
.
The prepared proteins were then subjected to the grid-
Optimization and assignments. The starting geometry used in generation protocol using two different binding site detection
the calculations was taken directly from the X-ray data and was strategies. In the first strategy, grids were generated using a
fully optimized without constraint using density functional molecular probe for detection of pockets around the proteins
theory (DFT) as implemented in the Gaussian 09 package of that could potentially be allosteric binding sites. In the second
programs38. The functional M06-2X39 was employed throughout strategy, co-crystallized ligands were considered geometric
the calculations, alongside the extended Gaussian basis set 6- centers of the grids. Grid information is available in Table S1.
311+G(d,p). The harmonic frequencies were calculated at the After grid generation, molecular docking studies were
same level of theory to confirm that the optimized geometry performed using the high-resolution protocol from FRED and
was found in a local minimum. These calculations showed that HYBRID programs, both available on OEDocking suite
there are no imaginary frequencies for the optimized structure; v.3.2.048,49, and the ChemGauss4 score function. Finally, a
the absence of imaginary frequencies confirms that the consensus score was created by averaging the predicted values
optimized structure is truly in a local minimum. The assignments from the individual docking programs, providing better
of the vibrational frequencies were carried out by potential predictive ability as compared to the individual scores.
energy distribution (PED) analysis using VEDA 4 software and
were supported by the animation option of Gaussview 40
.
Evaluation of cytotoxicity. Cytotoxicity analysis of the 2,5-
dichloro-N-{3-[(2E)-3-(4-nitrophenyl)prop-2-enoyl]phenyl}ben
Structure-based pharmacophoric screening. PharmMapper is a zenesulfonamide (BSC) was performed using the MTT method,
web server for prediction of potential biological activities colorimetric analysis, based on the conversion of the
against any given small molecule using a structure-based tetrazolium 3- (4,5-dimethyl-2-thiazole) -2,5-diphenyl-2-H -
pharmacophore mapping approach. This automatically predicts bromide salt (MTT) in formazan blue, from mitochondrial
the best mapping poses for a given query molecule against all enzymes present only in metabolically active cells.
the pharmacophore models in PharmTargetDB and lists the
The tumor cells used, SF-295 (human glioblastoma), PC-3
(prostate cancer) and HCT-116 (colon cancer) were donated by
41,42
best-fitted biological targets with their respective scores
.
Briefly, the 3D structure of BSC in Mol2 format was submitted the National Cancer Institute (USA) and cultured in RPMI 1640
to PharmMapper. During the procedure, the maximum medium supplemented with 10% of fetal bovine serum
conformations were set up to 300, and the number of reserved antibiotics Streptomycin and penicillin at 1%, incubated at 37°
matched targets was 300. Other parameters were kept as C and an atmosphere containing 5% of CO2. The tested
default.
compound was diluted into sterile and pure DMSO at 5 mg.mL-
1. For IC50 determination, the samples were tested at increasing
ChEMBL analysis. Substructure searching of the chalcone concentrations (0,39 to 52,37 μM) in serial dilutions.
scaffold (1,3-diphenyl-2-propen-1-one) was performed in the
Cells were plated at 0.1 x 106 cells/ml for SF-295 and PC-3
ChEMBL database using the Sketch tool. This chemical searching and 0.7 x 105 cells/ml for HCT-116 lineage. The plates were
yielded 1,416 compounds that are active (IC50, Ki, or Kd ≤ 10 µM) incubated for 72 hours at 5% CO2 and 37° C. At the end of this,
against at least one of 263 found biological targets. Further, we they were centrifuged and the supernatant removed. Then, 150
note that 22 of these biological targets also were available on μL of the MTT solution (tetrazolium salt) was added and the
PharmMapper list (see Supplementary Table S2), increasing the plates were incubated for 3h. The absorbance was read after
reliability of our predictions. Therefore, only targets found in dissolution of the precipitate with 150 μL of pure DMSO in a
both approaches (ChEMBL and PharmMapper) were carried on plate spectrophotometer at 595 nm. Doxorubicin was used as
for further analyses.
positive control at concentrations from 0,06 to 8,62 μM.
Molecular docking. The structure of BSC was imported into the
Maestro workspace v.9.3 and prepared using LigPrep 2.5
(Schrödinger, LCC, New York, 2012). Subsequently, 1000
conformations were generated using OMEGA v.2.5.143, while
AM1-BCC charges44 were added using QUACPAC v.1.6.3. In
parallel, 3D structures of selected targets were imported from
the Protein Data Bank (PDB) database45 and pre-processed
using Protein Preparation Wizard available on the Maestro
workspace (Schrödinger LLC). During protein preparation,
hydrogen atoms were first added to the proteins, and bond
orders and formal charges were adjusted. Missing side chains
and loops were predicted using Prime v.3.1 (Schrödinger LLC).
The protonation states of polar amino acids were predicted by
PROPKA v.3.1 (Schrödinger LLC) 46 at neutral and acid (only for
Results
Solid state characterization
The analyzed structure is a hybrid compound 2,5-dichloro-N-{3-
[(2E)-3-(4-nitrophenyl)prop-2-enoyl]phenyl}benzenesulfonami
de (BSC) derived from sulfonamide chalcone. Its molecular
structure is composed by a nitrophenyl group connected at the
chalcone moiety and a sulfonamide group at the meta position
of the aromatic chalcone ring. The sulfonamide group possesses
two chloro atoms at meta and orto positions. Additionally, this
molecule has an E conformation in relation the double bond C7–
C8 in conjugation to carbonyl group. This sulfonamide chalcone
crystallized in the monoclinic space group C2/c with a single
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DOI: 10.1039/C7NJ03523C
Figure 1: Ortep representation with ellipsoids at 60% of probability and
numbering scheme of BSC. Hydrogen atoms are represented by spheres with
arbitrary radii.
Figure 2: Intermolecular interactions of BSC. Dimers formed by interactions
C15-H15•••O3•••N2-HN1 and C7-H7•••O5 (a), C12-H12•••O1 (b) and C2-
H2•••O4 (c) are shown. In addition, the 1D chain formed is shownin(d), while
the stacking of layers is shown in (e).
independent molecule in the asymmetric unit and consequently
eight molecules in unit cell. Although the residual electronic
density indicated the presence of solvent, its refinement was
not successful and we chose to treat it as void. The unit cell
metrics are: a = 22.2982(18) Å, b = 8.5917(8) Å and c =
26.0739(14) Å, α = γ = 90° and β = 112.116(5) °. The main
crystallographic parameters are shown at Table 1, followed by
Ortep representation of BSC in Figure 1. The nitro group has a
positional disorder, in which the second conformation has a
39.71% occupancy factor and was handed separately of the
first one conformation. In this way, the whole discussion is
based on the dominant conformation.
In total, there are three non-classical H-bonds (C7-H7···O5,
C2-H2···O4, C12-H12···O1) and one bifurcated (C15-
H15···O3···N2-HN1) in which two donors compete for the same
receptor, as can be seen in Figure 2 (quantitative data are
tabulated in Table 3).
The crystal packing of BSC is stabilized by dimers, as seen in
Figures 2 a-c. The interactions C15-H15···O3···N2-HN1 join two
BSC molecules in a ꢕꢖꢗ(6) ring motif, while C7-H7···O5 gives rise
to a ꢕꢖꢖ 20 ring motif involving carbonyl and amine groups,
both forming a H-bonded dimer (dimer 1, Figure 2a). A series of
ꢕꢖꢖ 26 ring motifs are present in the dimers involving nitro
(dimer 2, Figure 2b) and sulfone (dimer 3, Figure 2c) groups.
In the first place, the quasi planarity of the chalcone portion
is confirmed by the angle of 5.23° formed between the planes
of its aromatic rings, whereas the sulfonamide moiety is almost
perpendicular to it (85.72°). Besides the interplanar angles, the
Hydrogen bonded dimers are linked in a chain by a C-H⋯O
interaction, involving the nitrobenzene aromatic ring (Figure
2d). These chains form a layer associated by interactions around
sulfone and nitro groups. The crystal packing is obtained by
stacking these dimeric chains, intercalating chalcone moieties
and sulfonamides aromatic rings. Solvent accessible voids with
13.2% of unit cell volume were observed, which is compatible
with an acetone solvent, as seen in Figure S1.
The intermolecular interactions of BSC (donor and acceptor
regions) were quantitively analyzed by normalized Hirshfeld
surface dnorm. Since Hirshfeld surfaces are calculated from
electronic density, this was made before squeeze routine. This
surface shows the intermolecular interactions, where hot colors
indicate the presence of higher intensities and cold colors
indicate the presence of lower intensity. The signals from the
first dimer interactions (Figure 3a), showed different intensities
for N2-HN1···O3 (I), C15-H15···O3 (II) and N7-H7···O5 (III)
interactions. The higher intensity on the interaction involving
the amino group indicates a greater force in this region,
matching the higher energy of hydrogen bonds. When then
compared to the other dimers stabilized by the C12-H12···O1
(IV) and C2-H2···O4 (V) interactions, and inferred that dimer 1
has greater effectiveness in the crystalline packing of BSC.
chalcone moiety flatness is confirmed by the dihedral angles
4, corresponding to rotations around single bonds C4-C7, C8-
C9 and C9-C10, respectively (Table 2). On other hand, planarity
deviations are noted near to nitro ( 1), sulfone ( 6) and
dichlorobenzene groups 7). The olefin portion has
t2
-
t
t
t
(
t
a
synperiplanar conformation regarding the amino group, while
the Cl2 atom has a synclinal conformation regarding to the
plane formed by atoms N2, S1 and C16. A search made in the
Mogul software revealed that the dihedral angle t6 is unusual,
since out of 898 hits analysed, only 16 (1.78%) had similar
values.
Empirical Formula
Formula Weight
C21H14Cl2SN2O5
477.30 g/mol
Temperature
296 K
Wavelenght
0.7103 Å
Crystal system, space group, Z
Unit cell dimension
Monoclinic, C2/c
a = 22.2982(18) Å, α = 90°
b = 8.5917(8) Å, β = 112.116(5)°
c = 26.0739(14) Å, γ = 90°
4627.7 (6) Å3
Volume
Z, calculated density
Absorption coefficient
F (000)
8, 1.370 mg/m3
0.405 mm-1
1952
Reflections collected / unique
Refinement method
Goodness-of-fit on F2
Final R índices [I > 2σ(I)]
R indices (all data)
26695 / 4793 [R(int) = 0.0330]
Full-matrix least-squares on F²
1.067
Involved atoms
O1-N1-C1-C2
C3-C4-C7-C8
C7-C8-C9-C10
C8-C9-C10-C15
C15-C14-N2-S1
C14-N2-S1-C16
Angle
t1
t2
t3
t4
Value (°)
5.4(3)
1.6(6)
174.2(3)
177.1(3)
178.2(2)
-69.7(3)
R1 = 0.0579, wR2 = 0.1490
R1 = 0.0923, wR2 = 0.1699
t5
t6
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Table 3: Hydrogen bonds involved in crystal packing of BSC
N
1
2
3
4
5
D-H···A
dD-H(Å)
0.897
0.878
0.963
0.955
0.826
dH···A(Å)
2.568
2.694
2.707
2.506
dD···A (Å)
3.430
3.488
3.272
3.288
∡D-H···A (°)
161.49
151.05
118.08
139.04
Symmetry code
C7-H7···O5
C2-H2···O4
C12-H12···O1
C15-H15···O3
N2-HN1···O3
-x,1-y,-z
1/2-x,1/2-y,-z
1/2-x,-1/2-y,-z
-x,1-y,-z
2.105
2.890
158.64
-x,1-y,-z
for the C=O vibration results at 1644 cm-1, while in experimental
IR the value is 1713 cm-1.
Assignments
Table 4 shows the main IR intensities, the experimental and
calculated vibrational frequencies for the optimized geometry
and the proposed vibrational assignments for BSC, while the
spectrum (experimental and theoretical, overlapped) is
presented in Figure 4.
For the sake of clarity, will be discussed only the values for
the main absorbing groups. To correct the systematic
overestimation of the vibrational frequencies of the DFT
methods was applied a scaling factor of 0.94050.
The calculated N–H stretching vibration for BSC is one band
at about 3367 cm-1 and for βN-H is 1410 cm-1. In the IR spectra,
these values are 3220 cm-1 and 1521 cm-1, respectively. Still, the
C–N stretching modes vibrations is observed at 1344 cm-1 in the
IR experimental spectrum and at 1218 cm-1 in theoretical.
Whereas the theoretical wavenumbers of C–Cl stretching
vibration is 582 cm-1 and the calculated value is 544 cm-1.
The assignment of thiocarbonyl group in our DFT
calculations appears in 977 cm-1, while in the IR spectra this
value is 962 cm-1. In its turn, the SO2 asymmetric and symmetric
stretches are calculated at 1252 cm-1 and 1078 cm-1,
respectively. In experimental IR, these bands appear at 1249
cm-1 and 1163 cm-1, respectively. Likewise, the vibrational
spectral modes of S–N vibration was calculated at 797 cm-1 and
the experimental value was obtained at 900 cm-1.
The DFT results for
3074 cm-1 and experimental values were in the range of 3046–
3071 cm-1. Concerning to the experimental values of
(C-
n(CH)aromatic are in the range of 3029 to
n
C)aromatic stretches absorptions were found in 1612 cm-1 and
1473 cm-1, while DFT results are 1597.75 cm-1 and 1326.98 cm-
1
.
The carbonyl stretching vibrations occur at 1581 cm-1 in DFT
and 1661 cm-1 in IR spectra, while the calculated wavenumber
The NO2 stretching vibrations give two strong bands
(asymmetric and symmetric), in BSC, 1519 cm-1 and 1342 cm-1
are, respectively, the values in the IR spectrum, while 1500 cm-
1
and 1325 cm-1 are, respectively, the theoretical values. To
conclude, the bands at 847 cm-1 and 846 cm-1 in this paper are
assigned to the
rNO2 mode in theoretical calculations and
experimental IR, respectively.
Figure 3: dnorm Hirshfeld surface of BSC showing intermolecular interactions
involved in crystal packing.
Figure 4: Experimental (KBr) (black) and theoretical (red) IR spectra of BSC
This journal is © The Royal Society of Chemistry 20xx
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Journal Name
Table 4: Vibrational assignments and wave numbers (cm-1)
calculated, with M06-2X/6-311+G(d,p), to C21H14 Cl2 N2O5S
View Article Online
DOI: 10.1039/C7NJ03523C
Unscaled IR
freq.
Scaled IR
freq.a
IR
Intensityb
observedc
3029.59
to
3074.48
1597.75
to
3222.97 to
3242.00
4.70 to
13.90
3046 to
3071
n (CH)aromatic
n (C-
C)aromatic
1669.74 to
1411.68
22.77 to
169.97
1612 to
1473
1326.98
1581.46
1644.93
3367.35
1410.28
1218.74
544.79
977.30
1252.60
1078.07
797.06
n C=C
n C=O
n N-H
β N-H
n C–NH
n C–Cl
n C–S
1682.41
1749.93
3582.29
1500.30
1296.53
579.57
1039.68
1332.55
1146.88
847.94
191.61
116.83
44.28
186.36
81.82
21.16
96.01
103.68
134.42
78.45
1661
1713
3220
1521
1344
582
Figure 5: Molecular electrostatic potential map of BSC
ꢙꢚꢎꢛ = ꢙꢜꢝꢞꢟ − ꢙꢠꢟꢞꢟ
(3)
(4)
− ꢙꢠꢟꢞꢟ − ꢙꢜꢝꢞꢟ
962
ꢡ =
n
asym SO2
1249
1163
900
2
n
sym SO2
−2
ꢘ =
(5)
n S–N
ꢙꢠꢟꢞꢟ − ꢙꢜꢝꢞꢟ
n
asym NO2
1596.31
1500.53
233.64
1519
n
sym NO2
1410.49
901.42
1325.40
847.33
289.52
124.47
1342
846
with values of 5.92 eV, 2.96 eV and 0.34 eV, respectively. These
high values indicate a high chemical stability and high first
excitation energies for the compound.
r NO2
Molecular electrostatic potential map and frontier molecular
orbitals
Potential biological activities for BSC
The molecular electrostatic potential (MEP) map on a
surface can be a positive or negative quantity. It is positive if the
positive charges (nuclei) dominate over the negative charge
(electrons). The MEP is generally visualized through the
mapping of its values onto the molecular surface reflecting the
molecular boundary. The MEP is a very powerful tool to
describe molecular sites of electrophilic attack, nucleophilic
reactions and hydrogen bonding interaction. In addition, MEP is
Potential biological activities of BSC were predicted using
two different approaches as described in the methods. Initially,
the top 300 potential protein targets of BSC were predicted
using PharmMapper server. In parallel, 263 potential targets
also were identified by substructure search in ChEMBL
database. Finally, to improve the specificity, a total of 22
potentially interacting targets identified in both sets of results
were selected for further investigation (Table S2).
To further characterize the binding modes and interaction
scores of BSC with predicted protein targets, molecular docking
studies were performed using FRED and HYBRID programs.
FRED performs an exhaustive search, by systematically
searching rotations and translations of each conformer of the
ligand within the active site, filtering the possible poses for
shape complementarity and pharmacophoric features before
selecting and optimizing poses using the Chemgauss4 scoring
function. Like FRED, HYBRID performs a systematic, exhaustive,
non-stochastic examination of poses within the protein binding
site. However, HYBRID reduces this search space based on
shape and chemical complementarity to known bound ligands.
very used to describe drug-receptor and enzyme-substrate
51
interactions, because it is a force that acts on long distance
.
As MEP is an observable reflection of the wavefunction, it can
be determined experimentally by diffraction or by
computational methods. Figure 5 shows the MEP surface
calculated, showing regions that are well distinguished, using
M06-2X/6-311+G(d,p) level of theory for the BSC in gas-phase.
The negative MEP (red color in Figure 5) corresponds to the
areas of high electron density; which are in the site of O atoms
in SO2, C=O and NO2 groups. The positive MEP (blue color in
Figure 5) corresponds to the areas of high depleted electron
density; which are the site of H3 bounded C3 and HN1 bounded
N1.
In addition, Figure 6 displays a graphical representation of
the HOMO (Highest Occupied Molecular Orbital) and LUMO
(Lowest Unnocupied Molecular Orbital) frontier molecular
orbitals calculated under a M06-2X/6-311+G(d,p) level of
theory. The HOMO (E = - 8.58 eV) orbital that presents
p*-
bonding symmetry, is located mainly at the aromatic ring
substituted with a benzenesulfonamide group. Figure 6(b)
shows that the LUMO (E = -2.66 eV) molecular orbital presents
p
-antibonding symmetry, located along to C=O, C=C and
nitrobenzene ring. The gap energy (EGap), hardness ( ) and
softness (
) values were calculated using the equations 52
h
ꢘ
6 | J. Name., 2012, 00, 1-3
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The scores of docking analysis are shown in Tables S2 and 5.
From the consensus docking scores, we suggest that the BSC can
act as an anticancer agent by interacting with nuclear retinoic
acid receptors alpha (RARα, score = -16.08) and beta (RARβ,
score = -17.45). Due to these excellent docking scores, we
suggest that BSC may be investigated as a potential anticancer
agent. The proposed biological activity is based on following
observations: (i) chalcone derivates are known RARs agonists
with IC50s in the nanomolar range 53–55; (ii) the RARs interact
with many different coactivator and corepressor proteins to
regulate transcription 56; and (iii) the binding of retinoids to
View Article Online
DOI: 10.1039/C7NJ03523C
Figure 7: Intermolecular interactions of RARα (a) and RARβ (b) with BSC
is expected for the chalcone backbone, since the aromatic rings
and the carbonyl, nitro, and olefin groups form a conjugate
RARs induce apoptosis in various human cancer cells 56
.
Figure 7 illustrates the binding of BSC into the active sites of
RARs identified as their potential targets. Like in all retinoid
complexes (see co-crystalized ligands in Supplementary Figure
S1), the nitro moiety of the ligand is anchored by a network of
hydrogen bonds with a water molecule, and the sidechains of
Arg276 and Ser287. In addition, this structural analysis shows
that the predicted binding modes allow several hydrophobic
interactions between the phenyl rings of the ligand with
residues Phe228, Ile236, Leu398, Leu 414, Leu306, Cys265,
Ile271, Leu269, Phe302, and Ile273.
system. In addition, intermolecular interactions of type C-H
⋯O
and N-H O form a dimeric supramolecular arrangement, as
⋯
confirmed from Hirshfeld surface analysis and molecular
potential maps for BSC. Regarding molecular stability of BSC,
the calculated gap energy (EGap=5.92 eV), hardness (
h=2.96 eV)
and softness ( =0.34 eV) indicates a high chemical stability and
ꢘ
high first excitation energies for analyzed compound. The
results of inverse virtual screening approach and experimental
testing allowed identifying potential biological applications for
BSC. Based on this approach, we found that BSC might interact
with binding sites of the RARα and RARβ.
Experimental validation
To evaluate the predicted anticancer activity of BSC, we
investigated its inhibitory effects on a three cancer cells.
Doxorubicin was used as positive control. Inhibitory percentage
was 92.47 (± 0,32), 99.97 (± 2.21) and 97.73 (± 1.37 for PC-3,
HCT-116, and SF-295, respectively). Results showed that BSC
exhibited remarkable inhibitory effect on cell growth with IC50s
of 10.84 (8.39-14.01)ꢀμM, 5,39 (4.24-6.86)ꢀμM, and 13.16
(11.78-14.69)ꢀμM in PC-3, HCT-116, and SF-295, respectively.
Conflicts of interest
There are no conflicts to declare.
Acknowledgements
The authors would like to thank Brazilian funding agencies
CNPq, CAPES, and FAPEG for financial support and fellowships.
Also, the authors are grateful to OpenEye Scientific Software
Inc. (https://www.eyesopen.com/) for providing academic
license of their softwares and to Raquel Ferreira Naves for RMN
analysis. Single crystal X-ray diffraction data were collected at
Physics Institute of the Federal University of Goiás. Pedro Cravo
and Hamilton B. Napolitano are research fellowes of the
Conselho Nacional de Desenvolvimento Científico e Tecnológico
(CNPq) of Brazil.
Conclusions
The main results showed that the BSC compound has a planar
conformation in its chalcone portion, corroborated by the low
angle formed between the aromatic rings (5.23°). This planarity
Predicted
biological target
(organism)
PharmMapper
fit score
FRED
score
HYBRID Consensus
score
score
Notes and references
1
2
3
4
5
6
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