N-substituted benzenesulfonamide compounds: DNA binding properties and molecular docking studies

Article abstract of DOI:10.1080/07391102.2021.1897683

Benzenesulfonamide-based imine compounds 5–8 were prepared and screened for their binding properties to the FSdsDNA. The structures of synthesized compounds were elucidated by the spectroscopic and analytical methods. Compounds 5–8 were screened for their

Full text of DOI:10.1080/07391102.2021.1897683

Journal of Biomolecular Structure and Dynamics
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N-substituted benzenesulfonamide compounds:
DNA binding properties and molecular docking
studies
Seyit Ali Güngör, Mehmet Tümer, Muhammet Köse & Sultan Erkan
To cite this article: Seyit Ali Güngör, Mehmet Tümer, Muhammet Köse & Sultan Erkan (2021):
N-substituted benzenesulfonamide compounds: DNA binding properties and molecular docking
studies, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2021.1897683
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JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
https://doi.org/10.1080/07391102.2021.1897683
N-substituted benzenesulfonamide compounds: DNA binding properties
and molecular docking studies
a
a
a
and Sultan Erkanb
€
€
€
€
Seyit Ali Gungor
, Mehmet Tumer
, Muhammet Kose
a
b
€ €
Chemistry Department, K.Maras Sutcu Imam University, K.Maras, Turkey; Department of Chemistry and Chemical Processing Technologies,
Sivas Cumhuriyet University Yıldızeli Vocational School, Sivas, Turkey
Communicated by Ramaswamy H. Sarma
ABSTRACT
ARTICLE HISTORY
Received 2 December 2020
Accepted 25 February 2021
Benzenesulfonamide-based imine compounds 5–8 were prepared and screened for their binding prop-
erties to the FSdsDNA. The structures of synthesized compounds were elucidated by the spectroscopic
and analytical methods. Compounds 5–8 were screened for their interactions with the FSdsDNA.
Compound 8 showed the highest binding affinity to the FSdsDNA with intrinsic binding constant of
3.10 ꢀ 104 Mꢁ1. The compounds caused the quenching of the DNA–EB emission indicating displace-
ment of EB (ethidium bromide) from the FSdsDNA. Finally, the binding interactions between the DNA
and binder molecules 5–8 were examined by the molecular docking studies. The compounds locate
approximately same region of the minor groove of DNA via hydrogen bonding contacts between the
sulfonamide oxygen atoms and the DG10/DG16 nucleotides of DNA.
KEYWORDS
Sulfonamide; propargyl;
imine; DNA;
molecular docking
1. Introduction
Investigation of the interactions between DNA or other
biomolecules and small molecules is the key to design new
drugs for the treatment of several diseases (Boer et al., 2009;
Horiuchi, 2002). Small molecules can bind to DNA via cova-
lent or non-covalent interactions (Mokaberi et al., 2020). DNA
molecules have several type of binding sites and the inter-
action between drug molecules and DNA can cause DNA
damage in cancer cells. The type of interactions depends
mainly on the size, conformation and the functional groups
in the binding molecules. The interactions between the cer-
tain molecule and DNA can be investigated by experimental
(UV–vis absorption and emission) and docking studies
(Tumer et al., 2017). The change in the absorption wave-
lengths and intensities of the DNA binding agents can give a
clue about the possible binding mode. The hyperchromic
and hypochromic shifts, for example, in the absorption bands
are indicative of changes in minor or major distortions in
DNA conformation. The hyperchromic shift is usually attrib-
uted to the breakage of the secondary structure of DNA via
binding agent.
Schiff bases are one of the most easily synthesized com-
pounds and they are usually obtained from the condensation
reaction of the aromatic or aliphatic primary amines and the
carbonyl compounds (especially aromatic aldehydes) (Basak
& Ray, 2020; Golcu et al., 2005; Wang et al., 2020). Schiff
bases are organic in nature and contain heteroatoms such as
nitrogen, oxygen or sulphur in their nature. For this reason,
these compounds have important biological properties. For
example, Schiff bases have found numerous applications
Before penicillin was commercially available and used, many
sulfonamide-derived drugs with good solubility in water
were used by humans. But, the sulfonamide-based drugs
used in the early times have caused many health problems.
Sulfonamides have a functional group that forms the basis of
several drug groups called sulfa drugs. Several organic mole-
cules containing a sulfonamide group have been prepared
and their structures have been characterized. The chemical,
physical and biological properties (antibacterial, antifungal,
diuretic, anticarbonicanhydrase, antithyroid, hypoglycemic,
antitumour, etc.) of these compounds have also been investi-
gated (Davenport, 2012; Drews, 2000; Durgun et al., 2016;
ꢀ ꢀ
Jaiswal et al., 2004; Kratky et al., 2012). Original antibacterial
sulfonamides are synthetic (non-antibiotic) and they contain
the sulfonamide group (Henry, 1943). Since the sulfonamide-
based compounds have different biological properties, the
biological properties of such compounds have been exten-
sively studied. For example, sulfonamide compounds are
often used for the prevention and treatment of bacterial
infections in humans. The interactions with DNA of sulfona-
mides have been studied since for a long time. In many
studies, it has been determined that the substituted groups
on the ring of sulfonamides affect the interactions with DNA
ꢀ
ꢀ
(Dixit et al., 2011; Garcıa-Gimenez et al., 2013; Rajendiran &
Thulasidhasan, 2015). It was determined that the Cu(II) com-
plexes of sulfonamides interact more strongly with DNA than
ꢀ
ꢀ
free ligand (Garcıa-Gimenez et al., 2013).
€ €
Chemistry Department, K.Maras Sutcu Imam University, K.Maras
CONTACT M. Tumer
46100, Turkey
mtumer@ksu.edu.tr; S.A. Gungor
sagungor@ksu.edu.tr
Supplemental data for this article can be accessed online at https://doi.org/10.1080/07391102.2021.1897683
ß 2021 Informa UK Limited, trading as Taylor & Francis Group

2
S. A. GÜNGÖR ET AL.
Scheme 1. Synthesis reactions of the sulfonamide-based compounds.
such as microbiological, insecticidal, anticancer, antiviral and
dye compound (Marchetti et al., 2015, 2019; Pahontu et al.,
2015; Tajudeen & Kannappan, 2016). On the other hand,
Schiff bases are also suitable for applications such as chemo-
2. Methods and material
Physical measurements, preparation and characterization
data for the starting compounds [carbonyls (1, 2) and N-sub-
stituted benzenesulfonamides (3, 4)] were provided in the
Supplementary File. The X-ray crystallographic data collection
and refinement details, molecular docking and DNA binding
procedures have also been given in the Supplementary File.
ꢁ
sensors and gas sensors (Dogan et al., 2020; Formica et al.,
2018; Wei et al., 2019; Xing et al., 2018).
In the current work, two sulfonamide amine derivatives (3
and 4) and four sulfonamide-based imine compounds 5–8
were prepared and characterized their structures using the
spectroscopic and analytical techniques. Molecular structures
of compounds 3, 5–7 were identified by the X-ray diffraction
studies. To review the keto-enol tautomeric forms of com-
pounds 5–8, their electronic properties have studied in the
polar and a polar solvents. The synthesized sulfonamide-
based Schiff base compounds were screened for their bind-
ing affinities towards FSdsDNA (fish sperm double strand
DNA) by using spectrophotometric techniques. Finally, the
binding modes of the compounds with DNA were investi-
gated by molecular docking studies.
2.1. Preparation of the sulfonamide-based Schiff base
compounds 5–8
The N-substituted benzenesulfonamides 3 or 4 (1 mmol)
were dissolved in methanol (15 mL). The carbonyl com-
pounds 1 or 2 (1 mmol) dissolved in MeOH (15 mL) were
added to the sulfonamide solution. The mixture was refluxed
for 5–6 h and cooled to room temperature. The precipitates
were filtered and dried in a vacuum desiccator. The obtained
compounds were recrystallized from methanol.

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
3
Figure 1. (a) Molecular structure of 3 with thermal ellipsoid 30% probability. (b) Packing diagram of 3 viewing down the a axis showing 2D hydrogen
bond network.
5: C22H17ClN2O4S. Yield: 88%, Color: Light orange, Mp: 79.25, 79.09, 56.15. IR (ꢀ, cmꢁ1): 3274 ꢀ(ꢁOH), 3237 ꢀ(ꢁNH),
156–158 ꢂC. Elemental analysis; found (Calculated) %: C, 2116 ꢀ(–CꢃC–), 1615 ꢀ(–C 5 N–), 1333 and 1155 ꢀ(–SO2).
58.34 (59.93); H, 3.90 (3.89); N, 6.36 (6.35); S 7.52 (7.27). 1H Mass ESI-MS (m/z): Calculated 440.06, found 440.10
NMR (d6-DMSO, ppm): d 13.57 (s, 1H), 10.47 (s, 1H), 8.80 (s, [C22H17ClN2O4S]þ.
1H), 7.76 (d, 2H), 7.65 (d, 2H), 7.51 (d, 1H), 7.30 (d, 2H), 7.14
6: C22H17ClN2O4S. Yield: 84%, Color: Dark orange, Mp:
(d, 2H), 6.58 (d, 1H), 6.54 (s, 1H), 4.86 (s, 2H), 3.63 (s, 1H). 13C 131–133 ꢂC. Elemental analysis; found (Calculated) %: C,
NMR: d 163.14, 162.46, 161.82, 144.69, 138.64, 138.34, 136.17, 58.48 (59.93); H, 3.94 (3.89); N, 6.31 (6.35); S 7.41 (7.27). 1H
134.43, 129.95, 129.09, 122.56, 121.97, 113.93, 107.78, 102.26, NMR (d6-DMSO, ppm): d 12.43 (s, 1H), 10.49 (s, 1H), 8.83 (s,

4
S. A. GÜNGÖR ET AL.
Table 1. Crystallographic data for the compounds.
Identification code
3
5
6
7
Empirical formula
Crystal size
Crystal colour
Formula weight
Crystal system
Space group
Unit cell a (Å)
b (Å)
C12H11ClN2O2S
0.17 ꢀ 0.12 ꢀ 0.09
Colorless
282.74
Orthorhombic
P212121
4.9961(3)
14.7657(12)
17.9014(12)
90
C22H17ClN2O4S
0.14 ꢀ 0.10 ꢀ 0.07
Yellow
C22H17ClN2O4S
0.17 ꢀ 0.11 ꢀ 0.07
Yellow
440.88
Triclinic
P-1
6.239(2)
8.2368(10)
20.167(3)
91.669(10)
90.94(2)
102.68(2)
1010.4(4)
2
C23H20N2O4S
0.18 ꢀ 0.12 ꢀ 0.08
Yellow
440.88
420.47
Monoclinic Monoclinic
P 1 21/c1
23.3986(16)
11.1632(7)
16.0504(11)
90
96.863(6)
90
4162.4(5)
Monoclinic
P 1 21/c 1
11.9692(3)
11.1727(3)
16.1300(4)
90
95.627(2)
90
2146.64(10)
c (Å)
a (ꢂ)
b (ꢂ)
90
90
c (ꢂ)
Volume (Å3)
1320.60(16)
4
0.442
3138
Z
8
4
Abs. coeff. (mmꢁ1
Refl. collected
)
0.316
14412
0.325
7508
0.182
8911
Completeness to theta
99.1%
98.9 %
99.6%
99.8%
Ind. Refl. [Rint
]
2344 [0.0187]
0.0488, 0.0899
0.0770, 0.10227
1990864
8284[0.0326]
0.0659, 0.1272
0.1423, 0.1605
1990865
4552 [0.0685]
0.0788, 0.1815
0.2112, 0.2828
1990866
4883 [0.0183]
0.0512, 0.1242
0.0769, 0.1432
1990867
R1, wR2 [I > 2r(I)]
R1, wR2 (all data)
CCDC
1H), 7.77 (d, 2H), 7.65 (d, 2H), 7.32 (d, 2H), 7.27 (s, 1H), 7.16 The carbonyl compounds 1 and 2 that were used to synthe-
(d, 2H), 7.09 (d,1H), 6.90 (d, 1H), 4.76 (s, 2H), 3.57 (s, 1H). 13C size the sulfonamide-based Schiff base compounds 5–8 have
€
€
NMR: d 162.47, 155.24, 150.20, 145.00, 138.65, 138.36, 136.63, previously obtained and characterized by our group (Gungor
129.97, 129.09, 122.82, 121.82, 121.67, 119.68, 117.84, 117.45,
79.82, 78.73, 56.61. IR (ꢀ, cmꢁ1): 3292 ꢀ(ꢁOH), 3260 ꢀ(ꢁNH),
2110 ꢀ(–CꢃC–), 1620 ꢀ(–C 5 N–), 1338 and 1158 ꢀ(–SO2).
Mass ESI-MS (m/z): Calculated 440.06, found 440.25
[C22H17ClN2O4S]þ.
et al., 2020). These compounds have prepared from the reac-
tion of the 4-hydroxy and 5-hydroxy salicylaldehyde carbonyl
€
€
compounds and 3-bromopropyne in acetonitrile (Gungor
et al., 2020). From the reaction of the N-(4-aminophenyl)-4-
benzenesulfonamide derivatives (3, 4) and the carbonyl com-
pounds (1, 2) in the ethanol solution, we have prepared the
sulfonamide-based Schiff base compounds (5–8). The organic
compounds have been characterized by using the elemental
7: C23H20N2O4S. Yield: 86%, Color: Light orange, Mp:
172–175 ꢂC. Elemental analysis; found (Calculated) %: C,
63.71 (65.70); H, 4.89 (4.79); N, 6.93 (6.66); S 7.67 (7.62). 1H
NMR (d6-DMSO, ppm): d 13.60 (s, 1H), 10.33 (s, 1H), 8.79 (s,
1H), 7.66 (d, 2H), 7.50 (d, 1H), 7.35 (d, 2H), 7.28 (d, 2H), 7.15
(d, 2H), 6.58 (d, 1H), 6.54 (s, 1H), 4.86 (s, 2H), 3.64 (s, 1H),
2.33 (s, 3H). 13C NMR: d 163.13, 162.26, 161.77, 144.23,
143.79, 137.01, 136.72, 134.38, 130.19, 127.19, 122.46, 121.39,
113.93, 107.76, 102.25, 79.26, 79.12, 56.15, 21.42. IR (ꢀ, cmꢁ1):
3303 ꢀ(ꢁOH), 3282 ꢀ(ꢁNH), 2122 ꢀ(–CꢃC–), 1614 ꢀ(–C 5 N–),
1335 and 1156 ꢀ(–SO2). Mass ESI-MS (m/z): Calculated 420.11,
found 422.18 [C23H20N2O4S þ 2H]þ.
1
analyses, mass (LC–MS), H(13C) NMR, UV–vis, photolumines-
cence and FTIR methods. The single crystals of compounds
3, 5–7 were grown and their solid structures were further
determined by the X-ray crystallography.
The 1H(13C) NMR spectra of compounds 3–8 were
recorded in d6-DMSO solvent. The 1H(13C) NMR spectra of
the compounds are provided in the Supplementary
1
Documents. In the H NMR spectra of compounds 3 and 4,
the signals at 9.56 and 9.40 ppm come from the amide pro-
ton (–NH–C ¼ O). The multiplets in the 7.61–6.37 ppm range
may be assigned to the aromatic ring hydrogen atoms
(Ar–H). The hydrogen atoms of the primary –NH2 groups on
the p-phenylene diamine ring have been shown at 5.02 and
4.94 ppm as broad band. In compound 4, the singlet at
2.34 ppm can be attributed to the hydrogen atoms of the
–CH3 group. The 13C NMR spectra of compounds 3 and 4
show that the aromatic ring carbon atoms are in the
147.27–114.42 ppm range. The methyl group carbon atom of
compound 4 is shown at 21.41 ppm.
The sulfonamide-based Schiff base compounds 5–8
showed broad peaks due to the phenolic OH in the
12.43–13.60 ppm range. The hydrogen atoms of the amide
groups of the imine compounds were observed in the
10.33–10.49 ppm range. The singlets of the hydrogen atoms
8: C23H20N2O4S. Yield: 83%, Color: Orange, Mp:
143–145 ꢂC. Elemental analysis; found (Calculated) %: C,
63.93 (65.70); H, 4.94 (4.79); N, 7.07 (6.66); S 7.63 (7.62). 1H
NMR (d6-DMSO, ppm): d 12.46 (s, 1H), 10.36 (s, 1H), 8.83 (s,
1H), 7.67 (d, 2H), 7.36 (d, 2H), 7.30 (d, 2H), 7.26 (d, 1H), 7.16
(d, 2H), 7.08 (dd, 1H), 6.90 (d, 1H), 4.75 (s, 2H), 3.57 (s, 1H),
2.34 (s, 3H). 13C NMR: d 183.95, 162.26, 155.24, 150.19,
144.54, 143.82, 137.15, 137.01, 130.21, 127.19, 122.72, 121.60,
121.24, 119.69, 117.82, 117.46, 79.83, 78.72, 56.61, 21.42. IR
(ꢀ, cmꢁ1): 3303 ꢀ(ꢁOH), 3261 ꢀ(ꢁNH), 2105 ꢀ(–CꢃC–), 1621
ꢀ(–C 5 N–), 1332 and 1151 ꢀ(–SO2). Mass ESI-MS (m/z):
Calculated 420.11, found 421.80 [C23H20N2O4S þ H]þ.
3. Results and discussions
In this work, two N-substituted benzenesulfonamide-based belonging to the imine group (–CH ¼ N–) were shown in the
starting materials 3 and 4 have been obtained from the reac- 8.79–8.83 ppm range. The aromatic ring protons (Ar–H) of
tion of the 4-chloro (or 4-methyl) benzenesulfonyl chloride the imine compounds 5–8 were observed in the
and p-phenylenediamine at low temperature (Scheme 1). 6.54–7.77 ppm range as multiplet. The aliphatic hydrogen

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
5
Figure 2. Asymmetric unit of 5–7 with thermal ellipsoid 30% probability. Two independent molecules in 5 are labelled as molecule A and B.

6
S. A. GÜNGÖR ET AL.
Table 2. Selected bond lengths (Å) and angles (ꢂ) for compounds 5–7.
atoms of the –OCH2– group in the imine compounds 5–8
have been determined in the 4.75–4.86 ppm range.
Hydrogen atoms of the acetyl group (–CꢃCH) attached to
the salicylidene ring of the imine compounds have been
shown in the 3.57–3.64 ppm range. In the spectra of com-
pounds 7 and 8, the singlets at 2.33 and 2.34 ppm belong to
the hydrogen atoms of the –CH3 group on the N-benzene-
sulfonamide rings.
5
6
7
S(1)–O(1)
S(1)–O(2)
1.427(3)
1.430(3)
1.420(4)
1.439(4)
1.4249(18)
1.4319(16)
S(1)–N(1)
1.619(3)
1.626(5)
1.6224(17)
S(1)–C(6)
1.755(4)
1.748(6)
1.764(2)
N(2)–C(13)
O(3)–C(15)
1.306(4)
1.299(4)
1.281(6)
1.371(6)
1.310(3)
1.296(2)
C(21)–C(22)
1.132(6)
1.128(8)
1.150(5)
S(1A)–O(1A)
1.427(2)
–
–
In the 13C NMR spectrum of compound 1, the signals in
the 164.19–115.75 ppm are due to the aromatic ring carbon
atoms (Ar–C). The oxygen atoms attached to the carbon
atoms attached to the ortho- and para-positions of the aro-
matic ring shifted the chemical shift values of the carbon
atoms to the lower regions. In the 13CNMR spectra of
compounds 5–8, the signals in the 164.55–162.26 ppm range
are assigned to the carbon atoms of the azomethine
groups. The aromatic ring carbons were observed in the
S(1A)–O(2A)
S(1A)–N(1A)
S(1A)–C(6A)
1.426(2)
1.609(3)
1.758(4)
1.293(4)
1.321(4)
1.149(6)
118.31(17)
110.58(16)
108.03(18)
105.31(16)
108.53(17)
105.33(16)
178.4(7)
109.45(16)
107.74(17)
120.22(16)
105.15(15)
107.54(16)
105.89(15)
178.6(5)
–
–
–
–
–
–
–
–
–
–
–
–
N(2A)–C(13A)
O(3A)–C(15A)
C(21A)–C(22A)
O(1)–S(1)–O(2)
O(1)–S(1)–N(1)
O(1)–S(1)–C(6)
O(2)–S(1)–N(1)
O(2)–S(1)–C(6)
N(1)–S(1)–C(6)
C(20)–C(21)–C(22)
O(1A)–S(1A)–N(1A)
O(1A)–S(1A)–C(6A)
O(2A)–S(1A)–O(1A)
O(2A)–S(1A)–N(1A)
O(2A)–S(1A)–C(6A)
N(1A)–S(1A)–C(6A)
C(20A)–C(21A)–C(22A)
120.1(3)
105.1(2)
107.9(3)
108.4(3)
108.2(3)
106.4(3)
177.1(7)
119.78(11)
108.60(10)
108.05(11)
104.41(10)
107.94(11)
107.48(10)
178.5(5)
155.24–102.25 ppm
range.
The
signals
in
the
–
–
–
–
–
–
–
–
–
–
–
–
–
–
79.83–78.72 ppm range can be attributed to the terminal
acetylene carbon atoms (–CꢃCH) of the propargyl group on
the salicylidene rings. The carbon atoms of the ꢁ OCH2ꢁ
group on the salicylidene rings were seen in the
56.15–56.61 ppm range. In the spectra of compounds 7 and
Figure 3. (a) 1D hydrogen bond chain in 5. (b) p–p stacking interactions in 5.

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
7
Figure 4. (a) Packing diagram of 6 viewing down the a axis showing. The p–p stacking interactions are shown as dashed lines. (b) Packing diagram of 7 viewing
down the bc axis showing hydrogen bond chain.
Table 3. The electronic spectral data for compounds 3–8 in the solution and solid state.
(kmax
)
Compounds
Solution (MeOH) k (E)
Solid state
235, 290
250, 290
260, 340, 425
205, 295, 360
235, 275, 345, 425
265, 365
3
4
5
6
7
8
240(0.31 ꢀ 105), 290(0.05 ꢀ 105)
240(0.18 ꢀ 105), 295(0.02 ꢀ 105)
240(0.11 ꢀ 105), 340(0.07 ꢀ 105), 430(0.03 ꢀ 105)
225(0.24 ꢀ 105), 280(0.16 ꢀ 105), 320(0.11 ꢀ 105), 360(0.11 ꢀ 105)
230(0.13 ꢀ 105), 340(0.10 ꢀ 105), 430(0.03 ꢀ 105)
235(0.23 ꢀ 105), 285(0.10 ꢀ 105), 325(0.11 ꢀ 105), 370(0.10 ꢀ 105)
8, the signal at 21.42 ppm may be assigned to the methyl (Das et al., 2015; Mondal et al., 2015; Yildiz et al., 2010). The
group carbon atom of the sulfonamide fragment.
free amine group (–NH2) and sulphony oxygen atoms are
involved in intermolecular hydrogen bonds [–NH2ꢄꢄꢄꢄꢄO2S–
and NHꢄꢄꢄꢄꢄN) forming a 2D hydrogen bond network along
the ab axis (Figure 1(b)). The sulfonamide NH group also
makes hydrogen bond with sulfony oxygen atom of an adja-
cent molecule forming a hydrogen bond chain. These 2D
hydrogen bond sheets are further connected by hydrogen
bond chains producing a 3D hydrogen bond supramolecu-
lar structure.
3.1. Molecular structure of compound 3
Perspective view of compound 3 is shown in Figure 1(a). The
structure of compound 3 was solved in orthorhombic and
space group P212121. The compound contains two aromatic
units, para-aminophenyl and para-chlorophenyl, connected
by a –SO2NH (sulfonamide) functional bridge. The molecule
is in U shape and two phenyl rings are inclined at 42.05(39)ꢂ.
The S1–O1 and S1–O2 bond distances are 1.424(3) Å which
is in the range of expected S ¼ O double distances. S1–N1
3.2. Molecular structures of compounds 5–7
and S1–C6 bond lengths of 1.614(4) and 1.754(5) Å, respect- Molecular structures of compounds 5–7 were investigated by
ively, are comparable to those similar structures reported single crystal X-ray diffraction studies. The structures of 5

8
S. A. GÜNGÖR ET AL.
Figure 5. UV–vis spectra of compounds 5 and 7 in MeOH and solid state.
and 7 were solved in monoclinic unit cell and P121/c1 space shorter C15A–O3A bond distances are 1.293(4) and 1.321(4)
group (Table 1). Compound 6 crystallizes in triclinic unit cell Å, respectively, indicating the enol-imine tautomeric form for
and P-1 space group. The structure of the three sulfonamide molecule B. For both independent molecules, the S–O distan-
Schiff bases 5–7 contain a central phenyl ring linked to two ces are consistent with S ¼ O double bonding. The O–S–O
outer phenyl and phenol rings by sulfonamide (–SO2NH–) bond angles for molecules A and B are 118.31(17)ꢂ and
and azo-methine (–CH ¼ N–) bridges.
120.22(16)ꢂ, respectively, this values are considerably devi-
The asymmetric unit of 5 has two independent molecules ated from the value for ideal tetrahedral geometry due to
labelled as molecule A and B (Figure 2). The two independ- the Thorpe–Ingold effect (Yildiz et al., 2010). The propargyl
ent molecules differ in the azomethine bond (–C13–N2 and (–O–CH2–CꢃCH) and chloro-benzene ring are aligned oppos-
–C13A–N2A) and phenolic (C15–O3 and C15A–O3A) bond ite direction with respect to the almost planar phenyl–phe-
distances and dihedral angles between the phenyl rings. In nol rings. The phenyl (C7/C12) and phenol (C14/C19) rings in
molecule A, the C13–N2 bond distance of 1.306(4) Å is rela- molecule A are almost co-planar with the twist angle of
tively longer than usual C ¼ N imine bond distance while 5.49(21)ꢂ. However, in molecule B, the phenyl (C7A/C12A)
C15–O3 distance of 1.299(4) Å is close to C ¼ O double bond and phenol (C14A/C19A) rings are considerably twisted from
distance suggesting the keto-amine tautomeric form for mol- planarity with the dihedral angle of 36.76(14)ꢂ. Molecules A
ecule A (Table 2). However, in molecule B, C13A–N2A and and B show intra-molecular NHꢄꢄꢄꢄꢄO and OHꢄꢄꢄꢄꢄN hydrogen

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
9
Figure 6. Emission spectra of compound 5–8 in MeOH (kex: 340 nm for compound 5, kex: 320 nm for compound 6, kex: 345 nm for compound 7 and kex: 330 nm
for compound 8).
Figure 7. UV–vis spectra of compound 7 in different solvents.
bonds, respectively. In the structure of 5, the NH group of are 1.281(6) and 1.371(6) Å, respectively, showing the charac-
sulfonamide makes hydrogen bond with the phenolic oxy- teristic C ¼ N (double bond) and C–O (single bond) distances.
gen atom of an adjacent molecule forming a 1D hydrogen The geometry around sulphur atom of the sulfonamide is
bond chain along the b axis (Figure 3(a)). The hydrogen distorted tetrahedral and the O–S–O bond angle is 120.1(3)ꢂ.
bond chains are further linked by –CꢃC–HꢄꢄꢄꢄꢄO interactions As seen in compound 5, the propargyl (–O–CH2–CꢃCH) and
forming 2D supramolecular structures. The almost co-planar chloro-benzene ring are located the opposite directions. In
phenyl and phenol rings in molecule A led the formation of the molecule, the phenyl (C7/C12) and phenol (C14/C19)
the p–p stacking interactions with the same section of an rings are slightly inclined with the dihedral angle of
adjacent molecule forming centro-symmetric p–p stacked 4.214(28)ꢂ. The molecule shows an expected intra-molecular
dimers (Figure 3(b)). However, the similar stacking interac- phenol-imine (O3–HꢄꢄꢄꢄꢄN2). The molecules of 6 are arranged
tions were not observed for molecules with enol-imine tauto- in head-to-tail columns via p–p stacking interactions. The sul-
meric form.
fonamide (–SO2NH–) groups do not involve hydrogen bond-
Compound 7 exists in the enol-imine tautomeric form in ing interactions between the neighbouring molecules. The
the solid state (Figure 2). The C13–N2 and C15–O1 distances NHꢄꢄꢄꢄCpropargyl contacts support the p–p stacking

10
S. A. GÜNGÖR ET AL.
Figure 8. UV–vis spectral change of 5 upon incremental addition of FSdsDNA.
Table 4. Intrinsic binding (Kb) and quenching Ksv constants for com-
pounds 5–8.
interactions. The head-to-tail columns are further linked by
halogen bond type interactions (ClꢄꢄꢄꢄꢄCl distance is 3.417 Å
(Figure 4(a)).
Compounds
Kb (Mꢁ1
)
Ksv (Mꢁ1
)
5
6
7
8
2.10 ꢀ 104
2.40 ꢀ 104
3.90 ꢀ 104
3.10 ꢀ 104
2.88 ꢀ 104
2.00 ꢀ 104
1.00 ꢀ 104
1.58 ꢀ 104
The structure of compound 7 (Figure 2) is similar to that
compound 5 differing in the substitute group on the phenyl
ring (C1/C6). The X-ray crystallographic data showed that the
compound crystallizes in the keto-amine tautomeric form in
the solid state. The C13–N2 distance of 1.310(3) Å is longer
than characteristic C ¼ N bond distance. On the other hand,
C15–O1 distance (1.296(2) Å) is shorter than that of usual
Ph–O bond distance confirming the keto-amine form. The
structural parameters for the sulfonamide (–SO2NH–) group
(geometry around sulphur atom and S–O bond distances) of
compound 7 are similar to that of compound 5. The phenyl
(C7/C12) and phenol (C14/C19) rings are slightly twisted
from planarity with the dihedral angle of 10.05(13)ꢂ. In the
three or four bands in the range 225–430 and 205–425 nm.
When the spectral and reflectance values obtained from in
the methanol solution medium and solid state of the com-
pounds are compared; it was determined that the absorb-
ance values in the methanol solvent medium shifted to
longer wavelengths due to the solvent effect (hydrogen
bonding between solute and solvent). As different from the
UV–vis spectra of 6 and 8 both in MeOH and solid state,
compounds 5 and 7 showed an absorption band with lower
structure of 7, there is N2–HꢄꢄꢄꢄꢄO3 intramolecular hydrogen absorbance values in the range of 400–450 nm. The appear-
bond. The molecules of 7 form one dimensional head-to-tail ance of this band may be due to the tautomeric transform-
€
hydrogen bond chains (–SO2NHꢄꢄꢄꢄꢄOphenol) along the bc axis ation from enol-imine to keto-amine form (Gozel et al., 2014;
€
(Figure 4(b)). The hydrogen bond chains are further linked Kose et al., 2013). The X-ray crystallographic data also con-
by the p–p stacking interactions. The phenyl (C7/C12) and
phenol (C14/C19) rings are stacked with the same section of
an adjacent molecule forming centro-symmetric dimers.
firmed that compounds 5 and 7 favour the keto-amine
tautomeric form in the solid state.
The emission spectral properties of the N-(4-amino-
phenyl)-4-chloro-benzene sulfonamide (3), N-(4-amino-
phenyl)-4-methylbenzenesulfonamide
(4)
and
their
3.3. Photophysical properties
condensation products 5–8 have been investigated in the
methanol solution (1.0 ꢀ 10ꢁ3 M). The inner filter effect in
the fluorescence intensities were eliminated using absorption
of the exciting light and reabsorption of emitted light
(Rashidipour et al., 2016). The emission spectra of com-
pounds 5–8 are given in Figure 6. The starting sulfonamide
compounds 3 and 4 in the solution show the emission
The UV–vis absorption properties of compounds 3–8 were
investigated in the CH3OH and solid state. The obtained
spectral data are given in Table 3. The UV–vis spectra of
compounds 5 and 7 are given in Figure 5 and rest of the
spectra are provided in the Supplementary File. Compounds
3 and 4 in the solid state and CH3OH solution have two
absorption bands in the range 235–290 and 240–295 nm, bands at 408 and 407 nm, respectively. On the other hand,
ꢅ
respectively. These bands may be assigned to the p–p and the emission spectra of compounds 5–8 in the methanol
n–p transitions. On the other hand, compounds 5–8 have solution have shifted to higher wavelengths in the
ꢅ

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
11
Figure 9. Effect of addition of 5 (a) the emission intensity of the FSdsDNA-bound ethidium bromide (75 mM) at different concentrations (0–65 mM) in 2 mM Tris-HCl
buffer (pH 7.1) (kex: 526 nm for EB–DNA), (b) Stern–Volmer plot of fluorescence titrations of the complexes with FSdsDNA.
475–517 nm range. Compounds 5 and 7 are the most shift- often referred to the damage in the DNA double-helix struc-
ing to long wavelengths. In the structure of these com- ture due to the electrostatic binding or to partial uncoiling
pounds, the propargyl group is in the 4-position relative to of the helix structure of DNA (Anjomshoa et al., 2014;
the carbonyl group and attracts electrons from the ring. Vijayalakshmi et al., 2000). This increase showed a linear
curve (1 ꢀ 10ꢁ5 and 5 ꢀ 10ꢁ5 M DNA concentration range).
Another important point is that these molecules exhibit
tautomeric properties by the movement of p-electrons.
Stokes shift is the difference between absorption and emis-
sion maxima and occurs due to structural relaxation in the
excited state. In short, it reflects the difference between the
equilibrium geometries of the fundamental and excited
states. Compounds with the highest Stokes shift are the sulfa
derivatives 5 and 7.
Compounds 5–8 have the potential to show tautomer
properties in different solvents. In order to further investigate
the effect of the solvent on the tautomeric transformation of
compounds 5 and 7, the electronic spectral properties were
studied in DMF, methanol, chloroform and toluene. The spec-
tra obtained for compound 7 are given in Figure 7.
Moreover, the interactions between the binder molecules
5–8 and DNA resulted in hyperchromism with no change in
the position of bands.
Based on the absorbance values obtained from the
UV–vis spectroscopic titration, the intrinsic DNA binding con-
stant, Kb, was calculated according to the equation reported
in literature (Tumer et al., 2017). The Kb binding constants of
compounds 5–8 are given in Table 4. The sulfonamide-based
compounds showed similar binding constants and these are
close to the binding affinity of the intercalating agent, eth-
idium bromide (Kb ¼ 1.23 0.07 ꢀ 105 Mꢁ1) (Psomas, 2008).
The order of the binding efficiency of compounds
is 8 > 6 > 5 > 7.
Compounds
5 and 7 have one absorption band at
According to the UV–vis titration experiments, Kb values
were found to be around 104 Mꢁ1, which shows the non-
intercalative binding (Kamshad et al., 2019). The affinity of
intercalating agents is very high with Kb around 105 to
106 Mꢁ1. Moreover, only the molecules with planar aromatic
rings involve in intercalation between DNA base pairs. Non-
planar nature of the compounds also shows the non-interca-
lative binding with DNA (Howe-Grant et al., 1976; Sehlstedt
et al., 1994).
400–450 nm range in MeOH and DMF which are polar sol-
vents. This relatively weak absorption bands may be due to
the keto-amine tautomeric formation in these solutions.
However, this band was not observed in toluene and chloro-
form confirming the solvent dependent tautomeric trans-
formation for compounds 5 and 7.
3.4. DNA binding studies
To further examine the interaction between the sulfona-
mide-based compounds 5–8 and FSdsDNA, competitive
binding experiments with DNA was carried out. Ethidium
bromide, a standard DNA inter chelating agent, shows very
weak emission in the range of 560–680 nm when excited
340 nm. However, the emission intensity of EB increases sig-
nificantly upon interaction with DNA (Bera et al., 2008; Qais
et al., 2017). The gradual addition of compounds 5–8 to the
EB–DNA complex cause a decrease in the emission band
(quenching effect) (Figure 9). The quenching of the emission
band of the EB–DNA complex can be assigned to the non-
To examine the interaction between the synthesized com-
pounds (5–8) and FSdsDNA, UV–vis spectral changes of the
compounds were monitored upon addition of DNA. The
spectral change of compound 5 upon addition of DNA is
shown in Figure 8 and rest of the spectra are provided in
the Supplementary Documents. The compounds showed
three absorption bands in the range of 210–500 nm due to
ꢅ
ꢅ
the p–p and n–p electronic transitions. The addition DNA
to the solution of 5–8 increased the intensity of the all three
absorption bands (hyperchromic effect). However, the most
ꢅ
obvious increase was observed for p–p transition in the displacement based quenching due to the enhanced energy
range of 210–260 nm. The gradual increase was observed in transfer, either from excited ethidium to an acceptor or from
the absorption band of p–p transition by the incremental a donor to an excited ethidium acceptor (Arabzadeh et al.,
ꢅ
addition of the DNA solution. The hyperchromism has been 2002; Bathaie et al., 2007; Pasternack et al., 1991). The

12
S. A. GÜNGÖR ET AL.
Figure 10. Competition between compounds 5–8 with ethidium bromide for the binding sites of FSdsDNA (Scatchard plot). In curves nos. 50 mM (᭹), 100 mM (᭿),
150 mM (᭜), respectively, 5, 6 and 8 at room temperature were added.
fluorescence quenching data were analysed by the
Table 5. Binding parameters for compounds 5–8 on the fluorescence of EBr
Stern–Volmer equation and the quenching constants (Ksv)
were calculated. The compounds showed very similar
quenching efficiencies and the substitute groups (chloro or
methyl) on benzene sulfonamide unit and positions of the
propargyl arm did not have considerable effect on the DNA
binding properties of the molecules.
In order to further investigate the binding mode of the
compounds with DNA, the Scatchard plots of the binding of
EtBr to DNA in the absence and presence of compounds 5–8
were obtained by fluorometric data (Figure 10 and Table 5).
The X-ray crystallographic data showed that compounds 5–8
lack planar aromatic rings. Therefore, the compounds are not
good candidates for intercalation between DNA base pairs.
The changes in both K and n revealed the non-competitive
inhibitory manner of the ligand in Et-DNA interaction
(Arabzadeh et al., 2002; Bathaie et al., 2007).
in the presence of CT-DNA.
Compound
rf
K
n
5
0.83
0.166
2.5
0.83
0.166
2.5
0.83
0.166
2.5
0.156
0.1329
0.1426
0.1431
0.1386
0.124
0.068
0.071
0.083
0.9311
0.8145
0.9017
0.8621
0.8396
0.8124
0.4154
0.48.13
0.5636
6
8
the drug candidate. The preferred place of the examined
5–8 compounds on fish sperm DNA (PDB ID: 423 D)
(Jamshidvand et al., 2018) and their binding energies, type
of interaction and nucleotides in the binding sites resulting
from their interaction with DNA are given in Table 6. The
molecular docking and the binding site of compounds 5–8
interacting with DNA are shown in Figure 11. According to
the results of the docking, the compounds considered as
drug candidates settled in the groove of DNA. The inter-
action energy obtained with molecular docking were quite
consistent with experimental binding constants. The docked
models suggest that the synthesized compounds 5–8 inter-
act with the minor groove of DNA with binding energy of
3.5. Molecular docking studies
Molecular docking studies are a technological perspective of
today’s drug discovery. It is also an important technique in
illuminating the type of interaction of the drug candidate
with the selected target protein. Knowing the physics of
interaction of drug candidates with DNA today can convey
striking information in the application and development of ꢁ8.45, ꢁ8.55, ꢁ8.76 and ꢁ8.69 kcal/mol, respectively. The

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
13
Table 6. Molecular docking result data of compound 5–8 with 423 D.
p–p
Compounds
Binding energy (kcal/mol)
Bases around molecules
H-bond
interaction
5
ꢁ8.45
DG7, DT8, DC9, DG10, DG11,
DG16, DA17, DC18, DG19
DG7 (2.6 Å), DG10 (2.0 Å, 2.2
Å), DG16 (3.0 Å), DA17
(2.1 Å), DC18 (1.8 Å)
Yes
6
7
ꢁ8.55
ꢁ8.76
DG7, DT8, DC9, DG10, DG11,
DG16, DA17, DC18, DG19
DG10 (1.8 Å, 2.1 Å, 2.7 Å),
DG16 (1.9 Å, 2.1 Å), DA17
(2.3 Å), DC18 (1.9 Å)
DG7 (2.7 Å), DG10 (1.8 Å, 2.7
Å, 3.0 Å), DG16 (1.8 Å, 3.0
Å), DA17 (2.6 Å), DC18
(2.1 Å, 2.6 Å)
Yes
Yes
DC6, DG7, DT8, DC9, DG10,
DG11, DG16, DA17,
DC18, DG19
8
ꢁ8.69
DG7, DT8, DC9, DG10, DG11,
DG16, DA17, DC18, DG19
DG7 (2.9 Å), DG10 (1.8 Å, 2.8
Å), DG16 (1.9 Å, 2.4 Å, 2.9
Å), DA17 (2.2 Å), DC18
(2.1 Å)
Yes
Figure 11. Molecular docking pose showing the potential interactions of compound 5–8 with 423 D.
binding energy of compounds 5–8 with DNA are consistent DNA. The sulfonamide oxygen atoms involved in strong
with experimental values (Dehghani Sani et al., 2018;
Shakibapour et al., 2019). However, binding energy of the
compounds are higher than those intercalation agents
reported in literature which also suggests non-intercalative
binding of compounds with DNA.
hydrogen bond interactions with the DG10 and DG16
nucleotides of DNA. Alkyne groups in all compounds makes
hydrophobic interactions with the DG7 nucleotide. Moreover,
the compounds also make p–p stacking interactions with the
DNA bases.
According to the free binding energies, compound 7
showed the best interaction with DNA. In addition, com-
pound 7 appear to be fixed on DNA by forming H-bond and
hydrophobic interactions. The number of interactions of
compound 7 is higher than the number of interactions of
other compounds. The backbone of all four compounds
locates approximately same region of the minor groove of
4. Conclusions
In the course of this work, four new sulfonamide-based
Schiff base compounds 5–8 were prepared and characterized
by common analytical and spectroscopic methods. The com-
pounds favours either enol-imine or keto-amine tautomeric

14
S. A. GÜNGÖR ET AL.
Journal of Biological Macromolecules, 42(1), 14–21. https://doi.org/10.
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form in the solid state. The absorption spectra of the com-
pounds have also shown that these compounds can also
exist in the both tautomeric form in solution depending on
the solvent polarity. The compounds were screened for their
binding affinity to the FSdsDNA and results showed that
compounds have high binding affinity to the DNA compared
to the ethidium bromine (a DNA intercalating agent). Finally,
the interaction modes were investigated by molecular dock-
ing studies.
The experimental results from DNA binding studies as
well as the molecular modeling, compounds 5–8 were able
to interact with DNA via non-intercalative way with relatively
high binding constants. These sulfonamide-based Schiff base
compounds have potential to inhibit tumor growth.
Moreover, this work will provide useful information to further
understand the binding mechanism of small organic mol-
ecule with DNA and to design more efficient drug candidates
targeting DNA.
_
_
Disclosure statement
ꢁ
€
Dogan, S., Tumay, S. O., Mutlu Balci, C., YeS¸Ilot, S., & BeS¸lI, S. (2020).
Synthesis of new cyclotriphosphazene derivatives bearing Schiff bases
and their thermal and absorbance properties. Turkish Journal of
Chemistry, 44(1), 31–47. https://doi.org/10.3906/kim-1905-60
Drews, J. (2000). Drug discovery: A historical perspective. Science (New
York, N.Y.), 287(5460), 1960–1964. https://doi.org/10.1126/science.287.
5460.1960
No potential conflict of interest was reported by the authors.
Funding
Authors thank to the research unit of Kahramanmaras Sutcu Imam
University for financial support of this work (Project number: 2019/
1-17D).
Durgun, M., Turkmen, H., Ceruso, M., & Supuran, C. T. (2016). Synthesis
of 4-sulfamoylphenyl-benzylamine derivatives with inhibitory activity
against human carbonic anhydrase isoforms I, II, IX and XII. Bioorganic
& Medicinal Chemistry, 24(5), 982–988. https://doi.org/10.1016/j.bmc.
2016.01.020
Formica, M., Favi, G., Fusi, V., Giorgi, L., Mantellini, F., & Micheloni, M.
(2018). Synthesis and study of three hydroxypyrazole-based ligands: A
ratiometric fluorescent sensor for Zn(II). Journal of Luminescence, 195,
193–200. https://doi.org/10.1016/j.jlumin.2017.11.018
ORCID
€
€
€
Seyit Ali Gungor
Mehmet Tumer
Muhammet Kose
Sultan Erkan
http://orcid.org/0000-0002-3233-4529
http://orcid.org/0000-0002-1882-429X
http://orcid.org/0000-0002-4597-0858
http://orcid.org/0000-0001-6744-929X
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
~
Garcıa-Gimenez, J. L., Hernandez-Gil, J., Martınez-Ruız, A., Castineiras, A.,
€
ꢀ
ꢀ
ꢀ
~
Liu-Gonzalez, M., Pallardo, F. V., Borras, J., & Alzuet Pina, G. (2013).
DNA binding, nuclease activity, DNA photocleavage and cytotoxic
properties of Cu(II) complexes of N-substituted sulfonamides. Journal
of Inorganic Biochemistry, 121, 167–178. https://doi.org/10.1016/j.
jinorgbio.2013.01.003
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