New imino-methoxy derivatives: design, synthesis, characterization, antimicrobial activity, DNA interaction and molecular docking studies

Article abstract of DOI:10.1080/07391102.2021.1955741

Four new diarylmethylamine imine compounds (5a-5d) were prepared in order to examine their DNA binding properties, antimicrobial activity and molecular docking. The compounds were characterized by the common spectroscopic and analytic methods. Furthermore

Full text of DOI:10.1080/07391102.2021.1955741

Journal of Biomolecular Structure and Dynamics
ISSN: (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/tbsd20
New imino-methoxy derivatives: design, synthesis,
characterization, antimicrobial activity, DNA
interaction and molecular docking studies
Sultan Onur, Mustafa Çeşme, Muhammet Köse & Ferhan Tümer
To cite this article: Sultan Onur, Mustafa Çeşme, Muhammet Köse & Ferhan Tümer (2021):
New imino-methoxy derivatives: design, synthesis, characterization, antimicrobial activity, DNA
interaction and molecular docking studies, Journal of Biomolecular Structure and Dynamics, DOI:
10.1080/07391102.2021.1955741
To link to this article: https://doi.org/10.1080/07391102.2021.1955741
View supplementary material
Published online: 06 Aug 2021.
Submit your article to this journal
Article views: 9
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at
https://www.tandfonline.com/action/journalInformation?journalCode=tbsd20

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
https://doi.org/10.1080/07391102.2021.1955741
New imino-methoxy derivatives: design, synthesis, characterization,
antimicrobial activity, DNA interaction and molecular docking studies
€
€
and Ferhan Tumer
Sultan Onur , Mustafa C¸es¸me , Muhammet Kose
_
€ €
Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras¸ Sutc¸u Imam University, Kahramanmaras¸, Turkey
Communicated by Ramaswamy H. Sarma
ABSTRACT
ARTICLE HISTORY
Received 26 March 2021
Accepted 10 July 2021
Four new diarylmethylamine imine compounds (5a-5d) were prepared in order to examine their DNA
binding properties, antimicrobial activity and molecular docking. The compounds were characterized by
the common spectroscopic and analytic methods. Furthermore, solid-state structure of compounds 5a
and 5c were determined by single-crystal X-ray diffraction studies. The compounds were then investi-
gated for their DNA binding properties employing UV absorption, fluorescence spectroscopy under the
physiological pH condition Tris-HCl buffer at pH 7.4. The compounds 5a-5d showed moderate binding
KEYWORDS
Imino-methoxy; diarylme-
thylamine; X-ray structure;
DNA binding;
constants with Kb values of 3.56 0.3ꢀ 104, 2.18 0.2ꢀ 105, 1.44 0.3ꢀ 105 and 2.56 0.3ꢀ 104 Mꢁ1
,
molecular docking
respectively. The molecular dockings were performed to investigate the ligand-DNA interactions. The in-
silico DNA-compound interaction studies showed that the compounds interact with DNA in groove bind-
ing mode. Antimicrobial activity studies of imine compounds were tested against E. coli as bacteria,
S. typhimurium, S. aureus, B. cereus, B. subtilis, and C. albicans as fungi. While all compounds show moder-
ate activity against bacteria, no activity against fungi has been investigated.
1. Introduction
The fact that the complexes formed by the ligands con-
taining atoms such as oxygen, nitrogen and sulfur in their
structures display different activities (antitumor, antiviral,
antifungal, antibacterial) and being used in the industrial
field increased the interest in this field (Lakshmi et al., 2012;
McCord & Fridovich, 1969; Riley et al., 1997). When Schiff,
some metal complexes are used as a binding agent or react-
ive monomer, the metal-containing polymers have been syn-
thesized and used in numerous applications with this
polymer (Yang et al., 2013).
Deoxyribonucleic acid (DNA) is one of the biopolymers
that contain genetic instructions used in the development
and functioning of all known living organisms and are also
essential for all known life forms (Dahm, 2005). DNA has two
primary functions; transcription and replication. The tran-
scription process of DNA refers to the conversion of genetic
information from DNA to RNA to synthesize proteins in the
body, including hormones, enzymes, and receptors. In other
words, it is the transfer of genetic information from DNA to
RNA. On the other hand, DNA replication is a biological pro-
cess that occurs in all organisms and forms the basis of her-
edity by copying DNA (J. H. Shi et al., 2015a). Transcription
and replication are essential for cell survival, proliferation
and the systematic functioning of all physiological processes.
Medicinal chemists mainly focus on DNA interactions with
drugs or ligands (novel compounds and drug candidates),
commonly called small molecules. Generally, small molecules
bind to DNA through three dominant non-covalent modes
Diarylmethylamine derivatives are molecules that attract atten-
tion in organic chemistry due to their pharmaceutical and dis-
tinctive chemical properties. Diarylmethylamine units are
commonly found in a variety of biologically active compounds
such as anticancer, anti-tuberculosis, antimalarial, antiviral,
potent and selective non-steroidal aromatase inhibitors (NSAIs)
and anti-HCV (Hepatitis C Virus) agents (Ameen & Snape, 2013;
Ashton et al., 1984; Cardellicchio et al., 2010; Di Santo et al.,
2005; Gemma et al., 2007; Plobeck et al., 2000; Roy & Panda,
2020; Thomas et al., 2001). Imine compounds constitute the
class of compounds that are intensively researched due to their
photochromic and thermochromic properties, tautomeric bal-
ance, analytical applications, as well as their biological and
pharmacological properties. Due to the convenience of the syn-
thesis stage and the ability of the ligands to flex easily, the fact
that they are suitable ligands for the determination and coord-
ination of many metal ions has caused these compounds to
gain significant importance (Soliman & Linert, 2007). Since car-
bon and nitrogen (C ¼ N) in Schiff bases prevent double bond
rotation, the orientation of the connected groups creates iso-
meric structures. Since the C¼ N bond is freer than the C ¼ C
bond, it is possible for the stereoisomers to transform into one
another (Allan et al., 1992). Schiff bases (Ph-CH ¼ N-Ph, Ph-
CH ¼ N-R) containing only imine groups as functional groups
are the best Schiff bases that contain groups such as -OH, -NH2,
€
-SH, -OCH3 in ortho-position (Goppert-Mayer, 1931).
_
€ €
€
CONTACT Ferhan Tumer
ftumer@ksu.edu.tr
Department of Chemistry, Faculty of Art and Sciences, Kahramanmaras¸ Sutc¸u Imam University,
Kahramanmaras¸, Turkey.
Supplemental data for this article can be accessed online at https://doi.org/10.1080/07391102.2021.1955741.
ß 2021 Informa UK Limited, trading as Taylor & Francis Group

2
S. ONUR ET AL.
Scheme 1. General synthesis procedure of compounds.
called intercalative binding, groove binding, and electrostatic and have been used as received except otherwise noted.
€
€
interactions (Adı mcı lar et al., 2021; Gungor et al., 2019). Fish sperm DNA (74782), Tris-HCl (RES3098T-B7), Ethidium
bromide (EtBr) and Sodium chloride (ꢂ99.5%) were supplied
Consequently, synthetic or natural small molecules or cur-
from Sigma Aldrich, USA. Elemental analyses (C, H, N) were
performed using a Costech ECS 4010 (CHN). The NMR spectra
data (1H and 13C NMR) were recorded on a Bruker Avance III
HD 400 MHz Spectrometer and TMS was used as an internal
standard. Absorption measurements were performed using a
double-beam spectrophotometer (Perkin Elmer, Lambda 45,
USA) equipped with 1.0 cm quartz cells. Fluorescence spectra
were collected on a Perkin Elmer LS55 photoluminescence
spectrophotometer analyzer. Infrared spectra were recorded
on a Perkin-Elmer FT-IR spectrometer (Spectrum 400) kitted
with an ATR apparatus. Thermo Scientific Orion Star A215
was utilized for the measurement of pH values.
rently commercially available drug compounds can be used
as drugs to inhibit or activate DNA function to ameliorate or
manage the disease. For this reason, the examination of the
intermolecular relationship between small molecules/drugs
and DNA using spectroscopic and theoretical methods has
increasingly become an area of interest for many researchers
(Dong et al., 2018; J.-H. H. Shi et al., 2018; J. H. Shi et al.,
2018; J. H. Shi et al., 2015a; Wang et al., 2020).
In our previous work, we reported the synthesis and antibac-
terial properties of a series of diarylmethylamine imine com-
pounds (Onur et al., 2020). In continuation of our interest in the
synthesis and biological properties of these compounds, four
new imine compounds with hydroxyl and methoxy substitute
groups (Scheme 1) were prepared and their DNA binding prop-
erties were investigated. In addition, biological and molecular
2.2. Synthesis of the compounds
docking studies have evaluated the suitability of these deriva- 2.2.1. General procedure for the preparation of oxime 2
tives for applications in biological systems.
and diarylmethylamine 3
DNA binding of newly synthesized compounds was inves- The synthesis of oxime 2 and diarylmethylamine 3 was car-
tigated using fluorescence quenching and UV-Vis spectros- ried out using a literature method (Onur et al., 2020).
copy. The atomic details of these ligand-DNA interactions
were investigated by the molecular placement method.
Results based on in silico dna-ligand interaction studies show
2.2.2. General method for the synthesis of imine com-
pounds (5a-d)
that all ligands are corrugated binders, and that H-bond
Compound 5a-5d was obtained according to our previous
interactions play a fundamental role in the stability of these
report (Onur et al., 2020). To a stirring solution of (4-methoxy-
ligand-DNA complexes. This study demonstrates the mode of
phenyl)(phenyl)methanamine (4 g; 20.27 mmol) CH2Cl2 (40 mL)
binding interaction, binding affinity, the main forces of inter-
under nitrogen atmosphere, potassium carbonate (4 g;
action of ligands with FS-DNA, and details of the structure of
29 mmol) was added followed by addition of salicylaldehyde
the ligand-FS-DNA complex. The interaction of FS-DNA with
derivatives (20.27 mmol). After stirring for 10–15 min, sodium
ligands is important in pharmaceutical drug discovery. Based
sulfate (4 g; 28 mmol) were added and resulting mixture were
on molecular docking studies in silico, the binding score of
stirred at room temperature for 24 h. The progress of the reac-
DNA interaction of compounds is highly satisfactory.
tion was followed by TLC. The mixture was filtered. After
removing the solvent, the oily residue was obtained and this
2. Experimental
was filtered over silica gel using ethyl acetate/hexane (1: 9) as
eluent. Solvent was removed on a rotary evaporator and
resulting solid was re-crystallized from ethanol.
2.1. Materials and measurements
All chemicals and solvents were of reagent-grade quality and
5a: Yield 4.6 g (71%), color: yellow. melting point:
obtained from commercial suppliers (Sigma Aldrich or Merck) 123–125 ꢃC. FTIR: (mmax, cmꢁ1): 3443, 3049, 2833, 1620, 1503,

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
3
1460, 1246, 1174, 1078, 1037, 971, 822, 751 cmꢁ1 1H NMR refrigerated for up to 72h at 4ꢃC. The FS-DNA concentration
.
(400 MHz, CDCl3, d ppm): 1H NMR (400 MHz, CDCl3) d 14.21 was calculated in all experiments using the 260nm absorption
(s, 1H), 8.47 (s, 1H), 7.34 (m, 7H), 6.90 (m, 5H), 5.62 (s, 1H), band and a molar absorption coefficient of 6600 L molꢁ1.cmꢁ1
3.94 (s, 3H), 3.80 (s, 3H). 13C NMR (101 MHz, CDCl3) d 164.77, (Lakshmipraba et al., 2015). The relevant calculations were
158.90, 151.59, 148.47, 142.81, 134.77, 128.70, 128.58, 127.35, made based on this concentration. The purity of the stock FS-
127.31, 123.19, 118.73, 118.21, 114.22, 114.10, 77.44, 77.12, DNA solution was verified by the UV absorption rate (A260/
76.81, 75.82, 56.12, 55.30. Anal. Calcd for C22H21NO3: C, 76.06; A280 > 1.8) as a result of measurements taken at 260 and
H, 6.09; N, 4.03. Found C, 76.15; H, 5.98; N, 4.10.
280nm to determine that FS-DNA did not contain protein
5b:Yield 3.65 g (58%), color: light yellow. melting impurity (Isika et al., 2020). Similarly, the ligand stock solutions
point:114–116 ꢃC. FTIR: (mmax, cmꢁ1): 3431, 3006, 2958, 2839, were prepared in DMSO and then diluted with Tris-HCl buffer
1621, 1510, 1443, 1386, 1292, 1166, 1033, 960, 833, to the appropriate concentrations. The EtBr used in photolumi-
732 cmꢁ1. 1H NMR (400 MHz, CDCl3) d 14.10 (s, 1H), 8.36 (s, nescence experiments was prepared in ethanol at a concentra-
1H), 7.40 ꢁ 7.34 (m, 4H), 7.30 ꢁ 7.24 (m, 3H), 7.16 (d, tion of 3.0ꢀ 10ꢁ3 mol. Lꢁ1 and used right away in the
J ¼ 8.4 Hz, 1H), 6.91 (d, J ¼ 7.0 Hz, 1H), 6.51 (d, J ¼ 2.0 Hz, 1H), experiments. All experiments were performed in triplicate.
6.45 (dd, J ¼ 8.5, 2.3 Hz, 1H), 5.59 (s, 1H), 3.84 (s, 3H), 3.81 (s,
3H). 13C NMR (101 MHz, CDCl3) d 164.22, 163.84, 163.58,
158.88, 142.98, 134.92, 132.90, 128.68, 128.65, 127.42, 127.28,
114.08, 112.68, 106.51, 101.17, 77.39, 77.08, 76.76, 75.35,
55.40, 55.30. Anal.Calcd for C22H21NO3: C, 76.06; H, 6.09; N,
2.4.1. UV-visible spectroscopy studies
For the analyzing of the interaction between FS-DNA and
compounds, absorption spectra were measured in the
200–700 nm wavelength range. Spectra obtained by adding
specific amounts of FS-DNA by titration method were
recorded for each ligand solution. All measurements were
4.03. Found C, 76.45; H, 5.72; N, 4.08.
5c:Yield 4.24 g (66%), color: orange. melting point:112–114 ꢃC.
FTIR: (mmax, cmꢁ1): 3385, 3272, 3016, 2836, 1629, 1607, 1510,
achieved in triplicate and the falcon tubes were gently
1462, 1386, 1307, 1235, 1204, 1178, 1030, 866, 818, 740 cmꢁ1. 1H
shaken and incubated for 15 min before taking measure-
ments of the corresponding spectrum of the mixture for
each sample. The intrinsic binding constant Kb was obtained
NMR (400 MHz, CDCl3) d 8.38 (s, 1H), 7.41ꢁ 7.34 (m, 5H), 7.27 (d,
J¼ 8.5 Hz, 2H), 7.02 (dd, J¼ 7.7, 1.6 Hz, 1H), 6.93 (d, J¼ 8.8 Hz,
2H), 6.83 (dd, J¼ 7.9, 1.6 Hz, 1H), 6.75 (t, J¼ 7.8 Hz, 1H), 5.70 (s,
from the plot of [DNA]/(ea ꢁ ef) versus [DNA] graphic, where
[DNA] is the concentration of DNA. The absorption coeffi-
cient ea, ef, eb correspond to Aobs/Ligand], the extinction
coefficient for the free compounds (5a-d), and the extinction
coefficient of the ligand compounds in the bound form,
respectively (Isika et al., 2020). The observed values were
appointed to Eq. (1), with a slope equal to 1/(eb-ef) and the
intercept equal to 1/[Kb(eb-ef)]. Kb was obtained from the
ratio of the slope to the intercept (Isika et al., 2020).
1H), 3.83 (s, 3H). 13C NMR (101 MHz, CDCl3) d 164.58, 159.10,
151.84, 145.63, 142.06, 133.92, 128.82, 128.75, 127.60, 127.41,
122.38, 118.08, 117.43, 116.90, 114.24, 77.40, 77.28, 77.08, 76.76,
74.42, 55.33. Anal.Calcd for C21H19NO3: C, 75.66; H, 5.74; N, 4.20.
Found C, 76.30; H, 5.20; N, 4.23.
5d:Yield
3.98 g
(62%),
color:
orange.
melting
point:128–130 ꢃC, FTIR: (mmax, cmꢁ1): 3401, 3024, 2903, 1627,
1578, 1462, 1364, 1253, 1220, 1169, 1118, 1021, 970, 890, 834,
1
750. 697 cmꢁ1. H NMR (400 MHz, CDCl3, d ppm) d 8.02 (s, 1H),
½DNAꢄ=ðea ꢁ efÞ ¼ ½DNAꢄ=ðeb ꢁ efÞ þ 1=½Kbðeb ꢁ efÞꢄ
(1)
7.39 ꢁ 7.25 (m, 5H), 7.23 (d, J¼ 8.7 Hz, 2H), 6.92 (d, J¼ 8.6 Hz, 1H),
6.88 (d, J¼ 8.5 Hz, 2H), 6.43 (d, J¼ 2.1 Hz, 1H), 6.29 (dd, J¼ 8.6,
1.8 Hz, 1H), 5.62 (s, 1H), 3.78 (s, 3H). 13C NMR (100 MHz, CDCl3, d
ppm): 169.08, 163.32, 163.15, 159.07, 141.71, 134.26, 133.55,
128.83, 128.73, 127.63, 127.37, 114.25, 111.42, 107.96, 104.25,
77.37, 77.06, 76.74, 72.27, 55.30. Anal.Calcd for C21H19NO3: C,
75.66; H, 5.74; N, 4.20. Found C, 76.36; H, 5.24; N, 4.18.
2.4.2. Fluorescence spectroscopy studies
Fluorescence quenching experiments were conducted to inves-
tigate the interactions of DNA with the compounds. To investi-
gate the binding properties of compounds with DNA, the
FS-DNA solution was carefully mixed with the DNA:EtBr (10:1)
concentration ratio of ethidium bromide (EtBr), prepared just
before the experiment at 25ꢃC, 15 min before the measure-
ments. The intercalation mode docking of EtBr molecules to the
double helix structure of DNA causes a significant increase in
EtBr fluorescence intensity. Then, various concentrations of lig-
and solutions were added to this mixture, allowing the final mix-
ture to incubate for 15 min. The fluorescence spectra of the
resulting final solutions were shown in the range of 500–700 nm
with an excitation wavelength of 520 nm. Fluorescent quenching
efficiency was evaluated according to the following equation
(Stern–Volmer equation, Eq. (2)) (Isika et al., 2020).
2.3. X-ray structures solution and refinement for
the compounds
Single crystals X-ray crystallographic data were collected on
a Bruker APEX 2 CCD diffractometer. The crystals were kept
at 293(2) K during data collection. Using Olex2 (Dolomanov
et al., 2009), the structures were solved with the SHELXT
(Sheldrick, 2015) structure solution program using Intrinsic
Phasing and refined with the SHELXL (Sheldrick, 2015) refine-
ment package using least-squares minimization.
2.4. DNA interaction study
½ ꢄ
I0=I ¼ Ksv Q þ 1
(2)
The FS-DNA stock solution was made in a Tris-HCl buffer with where I0 and I are the intensities of the emission in the pres-
a pH of 7.4 and a concentration of 50mM, then kept ence and absence of the quencher, Ksv is the quenching

4
S. ONUR ET AL.
binding constant, and [Q] is the concentration of the ligand (þ), Gram negative (-) bacteria and yeast strains and the
(quencher). The slopes of the obtained plots of I0/I versus [Q]
value was determined.
were used to calculate the Ksv values (Isika et al., 2020).
3. Results and discussion
2.5. Molecular docking studies
3.1. Characterization of 5a-d
The synthesized compounds, 5a-d, were sketched in drawing
BIOVIA Draw 2019 software, and their energies were mini-
mized by Chem3D 20. The molecular docking analysis was
conducted on the ligands against 1BNA as a model system
by using the Autodock vina tool PyRx docking software (aca-
demic licensed version 0.9.8) (Dallakyan & Olson, 2015). The
free DNA’s high-resolution (1.90 Å) structure was downloaded
from the PDB database (PDB code: 1BNA) (http://www.rcsb.
org/pdb). In the next step, 1BNA was enclosed in a box with
number of grid points in x ꢀ y ꢀ z (30 ꢀ 25 ꢀ 47) directions,
In the FT-IR spectra recorded for characterization of synthesized
imine compounds, stretching peaks at 3443, 3431, 3401 and
3385 cmꢁ1 are due to the phenolic hydroxyl group (mOH). The
characteristic signals of imine groups (-C ¼ N-) are the bands
observed at 1623, 1619, 1628 and 1627 cmꢁ1. The absence of
signals belonging to the carbonyl group in the starting salicylal-
dehyde derivatives in the spectrum of the result products also
confirmed the formation of imine compounds.
1
The H–13C NMR spectra of the compounds were examined
and the spectral data obtained were given in the experimental
and docking was performed using
a cubic box with
part and in the supplementary documents (Figures S1–S4). In
15 ꢀ 21 ꢀ 10 dimensions. In this analysis, flexible-ligand:rigid-
receptor docking was performed, and accurate docking
conditions were selected. The docked complexes (5a-DNA,
5 b-DNA, 5c-DNA and 5d-DNA) were assessed on the lowest
binding energy (kcal/mol) values. The graphical representa-
tions and related results of all the docking complexes were
carried out and monitored using Discovery Studio 2020.
1
the H NMR spectra of synthesized compounds, especially the
expected ortho and meta interactions in the salicylaldehyde
1
ring can be seen very clearly. When the H NMR spectra of the
new imine compounds were examined, singlets for 5a-5d
observed at 8.47, 8.36, 8.38 and 8.02ppm respectively are the
proton signals of the characteristic azomethine group
(-CH ¼ N-). Singlets observed at 5.62, 5.59, 5.70 and 5.62 ppm
in the spectra of all ligands for 5a-5d are dibenzylic proton sig-
nals adjacent to the imine group, respectively. The methoxy
groups in the structure of imine compounds resonated as sing-
let at 3.94, 3.80, 3.84, 3.81, 3.83 and 3.78 ppm, respectively. In
the 13C NMR spectra characteristic imine carbons resonated at
164.77, 164.22, 164.58 and 163.15 ppm, respectively. The other
carbon atoms of 5a-d compounds resonated between 169.08
2.6. Preparation and cultivation of bacterial strains
The imine compounds were evaluated in vitro antibacterial
and antifungal activity against the Staphylococcus aureus,
Bacillus cereus as the gram (þ); Escherichia coli and
Salmonella typhimurium as the gram (-); and Candida albi-
cans as the fungi. Antibiotics (Gentamicin and amikacin)
were used as positive control groups. The susceptibility of a
microorganism to antimicrobial agents and antibiotics was
determined by assay plates incubated at 37 ꢃC for 18–24 h
for bacteria and 25 ꢃC for three days for yeasts. In the anti-
microbial activity studies, Malt Extract Agar (MEA) for the
1
and 55.30ppm. The H–13C NMR spectra of the ligands appear
to be in complete agreement with the proposed structures.
Single crystals of compounds 5a and 5c were able to
grow from the slow evaporation of the ethanol solutions of
the compounds. X-ray crystallographic data are listed in
Table 1. The structures of both compounds were solved in
monoclinic unit cell P21/n space group. The thermal ellipsoid
plots of the compounds are shown in Figure 1. The C15-N1
bond distances in 5a and 5c are 1.2722(18) and 1.282(2) Å,
respectively, showing characteristic C ¼ N double bond dis-
tances. X-ray crystallographic data showed that both com-
pounds are in phenol-imine tautomeric form in the
crystalline state.
In the structures of the compounds, there is a phenol-
imine (O2-HꢅꢅꢅꢅꢅN1) intramolecular hydrogen bond. In the
structure of 5a, two molecules are stacked via antiparallel
p-p interactions between phenol rings (C16-C21) Figure 2.
Crystal packing of 5a are further stabilized by C-Hꢅꢅꢅꢅꢅ p and
C-HꢅꢅꢅꢅꢅO interactions. Compound SA36 contains a second
hydroxy group (O3) located at the meta position with respect
to the imine bond (C15 ¼ N1). In the structure of 5c, mole-
cules form dimers by hydrogen bonding between phenolic
oxygen atoms (O3-HꢅꢅꢅꢅꢅO2) under symmetry operation of
1 ꢁ x, ꢁy, 1 ꢁ z. The dimers are further linked by weaker
C10-HꢅꢅꢅꢅꢅO1 interactions forming a supramolecular chain
€
yeast strain and Mueller Hinton Agar (MHA) for bacteria were
used as a stock medium. Bacteria standardized with 0.5
McFarland standard was inoculated to sterile prepared petri
dishes and incubated for 1 h at 37 1 ꢃC (Balouiri et al.,
2016). DMSO was used as control. Amikacin (AK: 30 mg) and
Gentamicin (CN: 10 mg) were used as standards. The anti-
microbial activity of the imine compounds was determined
using Kirby-Bauer Disk Diffusion Method (Balouiri et al., 2016;
C.L.S.I., 2012). The imine compounds (12.50 mg/mL) were dis-
solved in 10% DMSO and impregnated with disks at a con-
centration of 25 mL to discs made of blank sterile Whatman
papers of 6 mm diameter. Prepared discs were placed on the
cultivation of bacteria in the MHA. Discs were placed on
planted cultures of bacteria in MHA and yeast strains in MEA.
Discs were incubated at 37 1 ꢃC for 24 2 h to determine
inhibition zones (Bauer et al., 1966; Bradshaw, 1992; Lennette
et al., 1974; Power & McCuen, 1988). The study was per-
formed in three replicates and the mean values were given.
The samples (5a-d) were 12.5 mg/mL, 1.25 mg/mL and
0.125 mg/mL dissolved in 10% DMSO to determine the min-
imum inhibitory concentration (MIC) against Gram positive along the c axis. Packing plot of 5c is depicted in Figure 3.

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
5
Table 1. Crystal data information and structure refinement for 5a and 5c compounds.
Identification code
5a
5c
Empirical formula
Formula weight
Temperature/K
C22H21NO3
347.40
293(2)
C21H19NO3
333.37
293(2)
Crystal system
Space group
Monoclinic
P21/n
Monoclinic
P21/n
a/Å
b/Å
12.4651(4)
9.7941(3)
15.8493(6)
90
108.862(4)
90
1831.05(11)
4
1.260
13.6519(4)
9.1288(3)
14.4256(4)
90
92.715(3)
90
1795.78(9)
4
1.233
c/Å
a/ꢃ
b/ꢃ
c/ꢃ
Volume/Å3
Z
qcalcg/cm3
l/mmꢁ1
0.084
0.083
F(000)
736.0
704.0
Crystal size/mm3
Reflections collected
Ind. Ref. [Rint]
Data/restraints/parameters
Goodness-of-fit on F2
Final R indexes [I> ¼2r (I)]
Final R indexes [all data]
CCDC
0.17 ꢀ 0.12 ꢀ 0.09
0.17 ꢀ 0.12 ꢀ 0.09
6769
24334
4099 [Rint ¼ 0.0191]
4099/0/239
1.063
R1 ¼ 0.0461, wR2 ¼ 0.1104
R1 ¼ 0.0714, wR2 ¼ 0.1229
2049019
4421 [Rint ¼ 0.0325]
4421/0/230
1.060
R1 ¼ 0.0543, wR2 ¼ 0.1412
R1 ¼ 0.1015, wR2 ¼ 0.1652
2049020
Figure 1. Thermal ellipsoid (50% probability) plots for compounds 5a and 5c.
the conformation of the DNA. However, in the case of the
groove binding mode between DNA and compounds, the
hypochromic effect can be recognized largely unchanged by
the location of the absorption band; this can be attributed
to the fact that the electronic states of the chromophore are
superimposed on the DNA grooves of the complex with
nitrogenous bases. (Shah et al., 2013; Xu et al., 2009).
To examine the interaction between FS-DNA and 5a-d
compounds, UV-vis absorption spectra were measured in the
presence and absence of various DNA concentrations. The
UV-vis spectra of compounds 5a-d in the absence and
3.2. Compound-DNA interaction study
3.2.1. Absorption spectroscopy studies
One of the most commonly used research techniques is elec-
tronic absorption spectroscopy, which is widely used to
study DNA’s interactions with small compounds. By a major-
ity, the mechanism by which small molecules are bound to
DNA by the intercalative binding mode has been enlight-
ened, resulting in the hypochromic and bathochromic of the
resultant absorption bands (Sirajuddin et al., 2013). Once
electrostatic interaction occurs between DNA and com-
pounds, a hyperchromic effect can be seen, with changes in

6
S. ONUR ET AL.
Figure 2. The p-p and CHꢅꢅꢅꢅꢅp interactions in 5c.
Figure 3. Packing diagram of 5c showing hydrogen bond interactions.
presence of FS-DNA are given in Figure 4. In the absence of When these values are compared with the classical intercal-
DNA, 5a showed three different absorbance peaks at 245, ation agent Ethidium bromide, which is known to interact with
275, and 415 nm respectively. As the absorption in the DNA (although the EtBr-DNA (Kb¼1,4ꢀ 106) complex is signifi-
245 nm band increased with the addition of different DNA cantly lower than binding) it can be said that it falls within the
concentration, the absorption at 275 nm decreased and a range of groove binding (J. H. Shi et al., 2015a) constant from
partial red shift was observed. In compound 5 b, the absorp- binding modes when DNA interacts with a small molecule.
The absorption spectra of FS-DNA and its (5a-5d) DNA-
Compound complexes formed by synthetic compounds are
presented in Figure 5(a)–(d). When this figure is examined, it
can be found that FS-DNA has a maximum absorption nearly
at 260 nm, which is attributed to the chromophoric groups
in the purine (adenine and guanine) and pyrimidine (cytosine
and thymine) bases located within the sugar-phosphate
backbone in the structure of DNA and responsible for elec-
tronic transitions (Dong et al., 2018; J.-H. H. Shi et al., 2018; J.
tion of the bands at 245, 300, 375 nm increased with the
addition of DNA, while a slight blue shift was observed in
the wavelength of the band at 300 nm. The maximum
absorption peak at 265 nm seen in compound 5c started to
become more pronounced with the gradual increase in DNA,
and no shift was observed in the band seen at 360 nm.
When the spectrum of the 5d compound is examined, the
maximum absorption peaks at 240, 300 and 360 nm have
increased steadily with the addition of DNA.
Based on changes in the absorption bands, the binding H. Shi et al., 2015b). By gradually adding synthetic com-
constant (Kb) for the ligand-DNA was calculated using the pounds at fixed concentrations (5a-5d) onto [DNA] at con-
equation (Eq.1). The intrinsic binding constant (Kb) was found stant concentration, the UV absorbance of Fs-DNA showed a
to be 3.56 0.3 ꢀ 104 Mꢁ1 for 5a, 2.18 0.2ꢀ 105 Mꢁ1 for 5b, hypochromic effect with a negligible (around 1 nm) shift in
1.44 0.3 ꢀ 105 Mꢁ1 for 5c and 2.56 0.3 ꢀ 104 Mꢁ1 for 5d. wavelength. With this spectral change, it was concluded that

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
7
Figure 4. Absorption spectra of 20 lmol/L 5a (a), 20 lmol/L 5 b (b), 20 lmol/L 5c (c) and 20 lmol/L 5d (d) in the presence of FS-DNA at different concentrations (a:
0.0, b: 1.94, c:3.89 d: 5.84, e: 7.78, f: 9.73, g: 11.68, h: 13.63, i: 15.58, and j: 17.52 lmol/L in Tris-HCl buffer (0.1 mol/L, pH 7.4)). The inset showing the plot of [DNA/
(ea-ef)] versus [DNA]. The corresponding solution of DNA was used as the reference solution.
the binding interaction of FS-DNA with synthetic compounds fluorescence intensity of EtBr, it also causes poor fluores-
mainly might be an interaction in the groove binding mode,
which is more acceptable (J.-H. H. Shi et al., 2018; J. H. Shi et
al., 2018). To put it another way, when small molecules inter-
act with DNA in the groove-binding mode, the position of
the absorption band is almost unchanged, while the hypo-
chromic effect can be observed, which can be explained by
the overlapping of electronic positions of the chromophore
with nitrogenous bases in the DNA-compound complex (J. H.
Shi et al., 2018; J. H. Shi et al., 2015b).
cence emission in solution due to the transition of hydro-
gen into solution as a result of non-radiative degradation
from the amino groups of EtBr (Jamshidvand et al., 2018).
Hereby, these compounds can be used to replace EtBr by
changing DNA conformation. As a consequence, the fluor-
escence is quenched as DNA-bound EtBr molecules are
converted into their free forms in solution.
The fluorescence spectra of 5a-5d in the absence and
presence of FS-DNA were shown in Figure 6. As 5a-5d com-
pounds are gradually titrated into the EtBr-DNA complex, the
maximum emission of the solution is reduced. This data has
been validated by the interaction of the ligands with FS-
DNA, which causes the formation of non-fluorescent com-
plexes in both compounds and quenches the endogenous
fluorescence. According to the Eq.2, the KSV values of the
compounds have been calculated to be 3.88 0.2 ꢀ 103,
4.41 0.2 ꢀ 103, 5.26 0.3 ꢀ 103, 5.64 0.3 ꢀ 103 Mꢁ1 for 5a-
5d respectively. KSV values calculated from the Stern-Volmer
equation are lower than the values of agents such as acrid-
ine orange, ethidium bromide, and methylene blue, which
are well known to bind intercalation mode with DNA and
find a wide place in the literature (Nafisi et al., 2007).
Therefore, in the interaction of fluorescence DNA with com-
petitive EtBr, it cannot be said for compounds to interact
with DNA by intercalation and replace with EtBr (Sha et al.,
2017). As can be seen from the fluorescence spectra, the
3.2.2. Fluorescence quenching studies
Fluorescence quenching experiments were performed to
further investigate the interaction mode of 5a-5d with
DNA. EtBr, a strong intercalation agent known to interact
with DNA, was chosen as a fluorescence indicator to
research this interaction. Due to its robust location
between adjacent DNA base pairs, EtBr has a poor fluores-
cence in the absence of DNA, but displays strong fluores-
cence at 597 nm when excited at 280 nm in the presence
of DNA (intercalation). As a result, variations in this charac-
teristic peak can be used to investigate the interaction of
the compounds with FS-DNA. It has been determined in a
previous study in the literature that by adding a second
molecule, the increased fluorescence of DNA-EtBr can be
quenched by a rivalry between EtBr and the second mol-
ecule to bind to DNA (Isika et al., 2020). While the addition
of DNA solutions causes
a
large increase in the decrease in the fluorescence intensity of EtBr-DNA with the

8
S. ONUR ET AL.
Figure 5. UV absorption spectra of FS-DNA (50 lmol/L) in the absence and presence of synthetic compounds (5a-5d) a:5a, b:5b, c:5c, d:5d. The concentration of
synthetic compounds from 0 to 6 were 0: 0.0, 1: 1.94, 2:3.89 3: 5.84, 4: 7.78, 5: 9.73, 6: 11.68 lmol/L in Tris-HCl buffer (0.1 mol/L, pH 7.4)). The corresponding solu-
tions of 5a-5d compounds was used as the reference solution.
addition of the compound is an indication that these com-
pounds may be partially intercalated. However, this inter-
action is not very stable as in the EtBr-DNA system in line
with the obtained KSV values and fluorescence intensity of
magnitude (Gan et al., 2020). The fact that the compounds
have a partial intercalation mode is supported by molecular
docking studies, which will be validated in the follow-
ing sections.
In molecular docking studies, docked compound confor-
mations were analyzed in terms of energy, hydrogen bond-
ing and interactions between DNA and molecules. According
to the docking complex models with compounds and DNA,
all compounds that bind to the major groove of DNA are
also partially intercalated to the sugar-phosphate backbones.
The binding energies were found to be ꢁ7.8, ꢁ7.7, ꢁ8.1 and
ꢁ7.3 kcal/mol according to the best pose conformations for
the 5a-5d, respectively. These scores relate to the set of min-
imum binding energy and maximum docking cluster. In add-
ition, docking studies have shown that hydrogen and pi
bond interactions are primarily prominent for the perman-
ence of ligand-DNA structures. The optimal conformation
poses of the ligand-DNA complexes based on their maximum
binding energies for the four compounds are depicted in a
3D in Figure 7. These results are consistent with the spectro-
scopic results. When the 2D plot depiction of the interaction
between DNA with 5a-d compounds is examined (Figure 8),
for all compounds, DNA appears to have H bond interactions
with both A and B chains of DNA. Considering the nucleotide
bonding and molecular structures of 5a-5d it is seen that the
conventional H and carbon H-bonds formed occur between
all nucleotides of DNA and oxygen in the methoxy groups of
the compounds. This suggests that the compounds have a
3.3. Molecular docking studies
Studying the binding interaction mechanisms of biological
macromolecules with small molecules has sparked a surge
in molecular docking studies. Molecular docking is a valu-
able tool in rational drug design because it predicts the
most stable structure and binding mode of the receptor-
ligand complex structure, allowing interaction information
to be identified appropriately and investigated during the
production of new drugs. In critical stages of drug design
and production, this method is often used as a virtual
search tool (Isika et al., 2020). The preferred position of
ligands on DNA may determine via molecular dock-
ing studies.

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
9
Figure 6. Quenching fluorescence spectra of FS-DNA bound to the EtBr system with the addition of ligands 20 lmol/L 5a (a), 20 lmol/L 5 b (b), 20 lmol/L 5c (c)
and 20 lmol/L 5d (d) Inset: I0/I versus [DNA](mM).
Figure 7. Molecular docked structure of 5a (a), 5 b (b), 5c (c) and 5d (d) complexed with DNA.
location between the opposite nucleotides in the DNA chains except 5d, while the pi alkyl bond was observed in the oxy-
and bind in a partial intercalation mode, as indicated in gen and hydrogen atoms in the methoxy groups of the com-
fluorescence quenching studies. Besides, in all compounds pounds, this situation was Pi-Pi T-shaped for 5d.

10
S. ONUR ET AL.
Figure 8. 2D plot of interaction between the 5a (a), 5 b (b), 5c (c) and 5d (d) with the dodecamer duplex sequence, d(CGCGAATTCGCG)2 (PDB ID: 1BNA).
Table 2. Detailed residues with compound interactions-bonding types and distances of 5a, 5b, 5c and 5d with DNA complexes.
Score (kcal/mol)
Interactions
Distance (Aꢃ)
Bonding Types
From
To
5A-DNA
ꢁ7.8
A:DA6:H3—:5 A:O21
B:DG22:H3—:5 A:O7
:5A:H7–B:DC23:O2
:5A:H15–B:DT20:O2
A:DA6–:5 A:C20
2.06101
2.60655
2.84868
2.86155
5.32569
5.46209
2.11154
2.78114
2.52057
5.26969
2.20032
2.15337
1.82145
2.41086
2.84588
2.69746
5.25542
2.33093
2.58835
2.84181
5.71177
Conventional H Bond
Conventional H Bond
Carbon H- Bond
Carbon H- Bond
Pi-Alkyl
A:DA6:H3
B:DG22:H3
:5A:H7
:5A:H15
A:DA6
B:DG22
A:DA6:H3
:5B:H8
:5B:H15
A:DA6
:5C:H14
A:DA6:H3
B:DG22:H3
:5C:H13
:5C:H13
A:DG4:H22
A:DA6
:5A:O21
:5A:O7
B:DC23:O2
B:DT20:O2
:5A:C20
:5A:C8
:5B:O21
B:DC23:O2
B:DT20:O2
:5B:C22
B:DC23:O4’
:5C:O21
:5C:O13
B:DT20:O2
B:DC21:O4’
:5C
B:DG22–:5 A:C8
Pi-Alkyl
5B-DNA
5C-DNA
ꢁ7.7
ꢁ8.1
A:DA6:H3–:5B:O21
:5B:H8–B:DC23:O2
:5B:H15–B:DT20:O2
A:DA6–:5B:C22
:5C:H 14–B:DC23:O4’
A:DA6:H3–:5 C:O21
B:DG22:H3–:5 C:O13
:5C:H13–B:DT20:O2
:5C:H13–B:DC21:O4’
A:DG4:H22–:5 C
Conventional H Bond
Carbon H Bond
Carbon H Bond
Pi-Alkyl
Conventional H Bond
Conventional H Bond
Conventional H Bond
Carbon H- Bond
Carbon H- Bond
Pi-Donor H Bond
Pi-Alkyl
A:DA6–:5 C:C22
:5C:C22
5D-DNA
ꢁ7.3
A:DA6:H3–:5D:O21
:5D:H5–B:DG22:O4’
A:DG4:H22–:5D
Conventional H Bond
Carbon H- Bond
Pi-Donor H Bond
Pi-Pi T-shaped
A:DA6:H3
:5D:H5
A:DG4:H22
:5D:O21
B:DG22:O4’
:5D
:5D–B:DC21
:5D
B:DC21

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
11
Table 3. Antimicrobial activity values of the bacteria and fungi (mm)a.
Gram (ꢁ)
Gram (þ)
Fungi
Compound
Escherichia coli
Salmonella typhimurium
Staphylococcus aureus
Bacillus cereus
Candida albicans
5a
5b
5c
5d
8
8
8
10
16
12
8
10
10
10
10
18
18
10
10
8
12
22
16
–
–
–
–
–
–
10
10
12
18
18
Amikacin
Gentamicin
–: Zone was not shown.
aCompounds (20 lL) in DMSO/H2O (1:9) were pipetted into the hollow agar at 12.5 mg/mL concentration.
4. Conclusion
New imino-methoxy derivatives have been successfully syn-
thesized in this study. Fluorescence quenching and UV–Vis
spectroscopy were used to investigate how these com-
pounds bound to DNA. In addition, the molecular docking
approach was used to examine the atomic specifics of these
ligand-DNA interactions. The findings of the in-silico DNA-
compound interaction studies indicate that compounds are
groove binders, with hydrogen and pi bond interactions
playing a key role in the ligand-DNA complexes stability. The
current study demonstrates the mode of binding interaction,
binding affinity, key ligand–FS-DNA interaction powers, and
structure of the ligand–FS-DNA complex.
Figure 9. Antibacterial activity of the compounds showing inhibition zones
in (mm).
In addition, there has been a significant change in the
conformation of the molecules in their ability to bind along
the major groove, and this conformational change is closely
related to the structure of the DNA major groove. Besides,
this situation can be evaluated as an important indicator of
the formation of a complex structure between DNA and
compounds. Data shows, bond types and bond lengths
formed between nucleotides and ligands for compound-DNA
complexes resulting from the docking process are summar-
ized in Table 2.
Acknowledgements
The authors are thankful to the Scientific Research Projects Unit of
€
€
Kahramanmaras¸ Sutcu Imam University (Project code: BAP-2017/6-34 M),
(Turkey). Furthermore, we would like to thank the Research Council of
the Turkish Council of Higher Education (YOK 100/2000) for awarding a
postgraduate scholarship (to SO).
€
Disclosure statement
The authors declare no conflicts of interest.
ORCID
3.4. Antimicrobial activity
Sultan Onur
Mustafa C¸e¸sme
Muhammet Kose
http://orcid.org/0000-0003-4305-9638
http://orcid.org/0000-0002-2020-5965
http://orcid.org/0000-0002-4597-0858
http://orcid.org/0000-0003-2222-2133
In in vitro antimicrobial activity studies, we used Escherichia
coli and Salmonella typhimurium as gram negative and
Staphylococcus aureus, Bacillus aureus and Bacillus cereus as
gram positive; Candida albicans as fungi. Amikacin and gen-
tamicin antibiotics were used as positive control group.
Antimicrobial activities of the ligands (5a-d) used in the
study were investigated against Gram (þ), Gram (-) bacteria
strains and Candida albicans fungi by disk diffusion method.
The results were compared with the standard antibiotics
amikacin and gentamicin. The observed antimicrobial activ-
ities of the ligands are shown in Table 3. According to the
findings, 5a ligand against Staphylococcus aureus and
Bacillus cereus strains, 5b ligand against Salmonella typhimu-
rium, Staphylococcus aureus and Bacillus cereus strains, 5d
ligand against Salmonella typhimurium and Bacillus cereus
strains showed moderate level of activity against Salmonella
typhimurius and Bacillus strains. Antimicrobial activity of the
complexes are shown in Figure 9 and summarized in
Table 3.
€
€
Ferhan Tumer
Credit authorship contribution statement
Sultan Onur: Investigation. Mustafa C¸es¸me: Data curation, Software,
Writing—review & editing Investigation. Muhammet Kose: Data curation,
Software, Writing—review & editing. Ferhan Tumer: Supervision, Project
administration, Writing—Original draft.
€
€
References
_
€
€
€
Adımcılar, V., C¸es¸me, M., S¸enel, P., Danıs¸, I., Unal, D., & Golcu, A. (2021).
Comparative study of cytotoxic activities, DNA binding and molecular
docking interactions of anticancer agent epirubicin and its novel cop-
per complex. Journal of Molecular Structure, 1232, 130072. https://doi.
org/10.1016/j.molstruc.2021.130072
Allan, J. R., Gardner, A. R., McCloy, B., & Smith, W. E. (1992). Structural
and thermal studies of the chloro complexes of cobalt, nickel and
copper with 2,6-diaminopyridine and an assessment of their

12
S. ONUR ET AL.
suitability as anti-static additives for polyethylene. Thermochimica Jamshidvand, A., Sahihi, M., Mirkhani, V., Moghadam, M.,
Acta, 208(C), 125–131. https://doi.org/10.1016/0040-6031(92)80158-S
Mohammadpoor-Baltork, I., Tangestaninejad, S., Amiri Rudbari, H.,
Kargar, H., Keshavarzi, R., & Gharaghani, S. (2018). Studies on DNA
binding properties of new Schiff base ligands using spectroscopic,
electrochemical and computational methods: Influence of substitu-
tions on DNA-binding. Journal of Molecular Liquids, 253, 61–71.
https://doi.org/10.1016/j.molliq.2018.01.029
Ameen, D., & Snape, T. J. (2013). Chiral 1,1-diaryl compounds as import-
ant pharmacophores. In MedChemComm (Vol. 4, No. 6, pp. 893–907).
The Royal Society of Chemistry. https://doi.org/10.1039/c3md00088e
Ashton, M. J., Ashford, A., Loveless, A. H., Riddell, D., Salmon, J., &
Stevenson, G. V. (1984). Heterocyclic analogues of chlorcyclizine with
potent hypolipidemic activity. Journal of Medicinal Chemistry, 27(10), Lakshmi, B., Shivananda, K. N., Prakash, G. A., Isloor, A. M., & Mahendra,
1245–1253. https://doi.org/10.1021/jm00376a002
K. N. (2012). Synthesis and characterization of schiff base metal com-
plexes and reactivity studies with malemide epoxy resin. Bulletin of
the Korean Chemical Society, 33(2), 473–482. https://doi.org/10.5012/
bkcs.2012.33.2.473
Balouiri, M., Sadiki, M., & Ibnsouda, S. K. (2016). Methods for in vitro eval-
uating antimicrobial activity: A review. Journal of Pharmaceutical
Analysis, 6(2), 71–79. https://doi.org/10.1016/j.jpha.2015.11.005
Bauer, A. W., Kirby, W. M., Sherris, J. C., & Turck, M. (1966). Antibiotic sus- Lakshmipraba, J., Arunachalam, S., Solomon, R. V., Venuvanalingam, P.,
ceptibility testing by a standardized single disk method. American
Journal of Clinical Pathology, 45(4), 493–496. https://doi.org/10.1093/
ajcp/45.4_ts.493
Bradshaw, L. J. (1992). Laboratory microbiology. Acta Crystallographica
Section A: Foundations and Advances 4, 435.
Riyasdeen, A., Dhivya, R., & Akbarsha, M. A. (2015). Surfactant-
copper(II) Schiff base complexes: Synthesis, structural investigation,
DNA interaction, docking studies, and cytotoxic activity. Journal of
Biomolecular Structure & Dynamics, 33(4), 877–891. https://doi.org/10.
1080/07391102.2014.918523
C.L.S.I. (2012). Performance standards for antimicrobial disk susceptibility
tests approved standard. In CLSI document M02-A11 (Vol. 950, 7th
ed.). Clinical and Laboratory Standards Institute.
Lennette, E. H., Spaulding, E. H., & Truant, J. P. (1974). Manual of clinical
microbiology (7th ed., 970p). ASM Press. https://doi.org/10.4269/ajtmh.
1971.20.3.tm0200030508a
Cardellicchio, C., Capozzi, M. A. M., & Naso, F. (2010). The Betti base: The
awakening of a sleeping beauty. In Tetrahedron asymmetry. (Vol. 21,
No. 5, pp. 507–517). Pergamon. https://doi.org/10.1016/j.tetasy.2010.
03.020
Dahm, R. (2005). Friedrich Miescher and the discovery of DNA.
Developmental Biology, 278(2), 274–288. https://doi.org/10.1016/j.
ydbio.2004.11.028
McCord, J. M., & Fridovich, I. (1969). Superoxide dismutase. An enzymic
function for erythrocuprein (hemocuprein). Journal of Biological
Chemistry, 244(22), 6049–6055. https://europepmc.org/article/med/
5389100 https://doi.org/10.1016/S0021-9258(18)63504-5
Nafisi, S., Saboury, A. A., Keramat, N., Neault, J. F., & Tajmir-Riahi, H. A.
(2007). Stability and structural features of DNA intercalation with eth-
idium bromide, acridine orange and methylene blue. Journal of
Molecular Structure, 827(1–3), 35–43. https://doi.org/10.1016/j.molstruc.
2006.05.004
Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by
docking with PyRx. In J. E. Hempel, C. H. Williams, & C. C. Hong (Eds.),
€
€
Methods in molecular biology (Vol. 1263, No. January, pp. 243–250). Onur, S., Kose, M., Koc¸er, F., & Tumer, F. (2020). Synthesis, characteriza-
Springer. https://doi.org/10.1007/978-1-4939-2269-7_19
Di Santo, R., Tafi, A., Costi, R., Botta, M., Artico, M., Corelli, F., Forte, M.,
Caporuscio, F., Angiolella, L., & Palamara, A. T. (2005). Antifungal
tion and antibacterial effect of diarylmethylamine-based imines.
Journal of Molecular Structure, 1214, 128150. https://doi.org/10.1016/j.
molstruc.2020.128150
agents. 11. N-substituted derivatives of 1-[(aryl)(4-aryl-1H-pyrrol-3- Plobeck, N., Delorme, D., Wei, Z. Y., Yang, H., Zhou, F., Schwarz, P.,
yl)methyl]-1H-imidazole: Synthesis, anti-Candida activity, and QSAR
studies. Journal of Medicinal Chemistry, 48(16), 5140–5153. https://doi.
org/10.1021/jm048997u
Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K., &
Puschmann, H. (2009). OLEX2: A complete structure solution, refine-
ment and analysis program. Journal of Applied Crystallography, 42(2),
339–341. https://doi.org/10.1107/S0021889808042726
Gawell, L., Gagnon, H., Pelcman, B., Schmidt, R., Yue, S. Y., Walpole, C.,
Brown, W., Zhou, E., Labarre, M., Payza, K., St-Onge, S., Kamassah, A.,
Morin, P. E., … Roberts, E. (2000). New diarylmethylpiperazines as
potent and selective nonpeptidic delta opioid receptor agonists with
increased In vitro metabolic stability. Journal of Medicinal Chemistry,
43(21), 3878–3894. https://doi.org/10.1021/jm000228x
Power, D. A., & McCuen, P. J. (1988). Manual of BBL products and labora-
tory procedures. In Becton Dickinson Microbiology Systems (6th ed.,
pp. 67–72). Becton, Dickinson and Company.
Dong, X.-M. M., Lou, Y.-Y. Y., Zhou, K.-L. L., & Shi, J.-H. H. (2018).
Exploration of association of telmisartan with calf thymus DNA using
a series of spectroscopic methodologies and theoretical calculation. Riley, D. P., Lennon, P. J., Neumann, W. L., & Weiss, R. H. (1997). Toward
Journal of Molecular Liquids, 266, 1–9. https://doi.org/10.1016/j.molliq.
2018.06.057
the rational design of superoxide dismutase mimics: Mechanistic stud-
ies for the elucidation of substituent effects on the catalytic activity
of macrocyclic manganese(II) complexes. Journal of the American
Chemical Society, 119(28), 6522–6528. https://doi.org/10.1021/
ja964271e
Gan, C., Huang, X., Zhan, J., Liu, X., Huang, Y., & Cui, J. (2020). Study on
the interactions between B-norcholesteryl benzimidazole compounds
with ct-DNA. Spectrochimica Acta Part A: Molecular and Biomolecular
Spectroscopy, 227, 117525. https://doi.org/10.1016/j.saa.2019.117525
Gemma, S., Campiani, G., Butini, S., Kukreja, G., Joshi, B. P., Persico, M.,
Catalanotti, B., Novellino, E., Fattorusso, E., Nacci, V., Savini, L.,
Roy, D., & Panda, G. (2020). Benzhydryl amines: Synthesis and their bio-
logical perspective. ACS Omega, 5(1), 19–30. https://doi.org/10.1021/
acsomega.9b03090
Taramelli, D., Basilico, N., Morace, G., Yardley, V., & Fattorusso, C. Sha, Y., Chen, X., Niu, B., & Chen, Q. (2017). The interaction mode of
(2007). Design and synthesis of potent antimalarial agents based on
clotrimazole scaffold: Exploring an innovative pharmacophore. Journal
of Medicinal Chemistry, 50(4), 595–598. https://doi.org/10.1021/
groove binding between quercetin and calf thymus DNA based on
spectrometry and simulation. Chemistry Biodiversity, 14(10),
e1700133. https://doi.org/10.1002/cbdv.201700133
&
jm061429p
Goppert-Mayer,
Shah, A., Nosheen, E., Munir, S., Badshah, A., Qureshi, R., Rehman, Z. U.,
Muhammad, N., & Hussain, H. (2013). Characterization and DNA bind-
ing studies of unexplored imidazolidines by electronic absorption
spectroscopy and cyclic voltammetry. Journal of Photochemistry and
Photobiology B: Biology, 120, 90–97. https://doi.org/10.1016/j.jphoto-
biol.2012.12.015
€
€
M.
(1931).
Uber
Elementarakte
mit
zwei
€
Quantensprungen. Annalen Der Physik, 401(3), 273–294. https://doi.
org/10.1002/andp.19314010303
€
€
€
€
€
Gungor, O., C¸es¸me, M., C¸ınar, M. E., & Golcu, A. (2019). The new metal-
based compound from anticancer drug cytarabine: Spectral, electro-
chemical, DNA-binding, antiproliferative effect and in silico studies. Sheldrick, G. M. (2015). SHELXT - integrated space-group and crystal-
Journal of Molecular Structure, 1193, 532–543. https://doi.org/10.1016/
j.molstruc.2019.05.014
Isika, D., C¸es¸me, M., Osonga, F. J., & Sadik, O. A. (2020). Novel quercetin
structure determination. Acta Crystallographica. Section A, Foundations
and Advances, 71(Pt 1), 3–8. https://doi.org/10.1107/
S2053273314026370
and apigenin-acetamide derivatives: Design, synthesis, characteriza- Shi, J. H., Chen, J., Wang, J., & Zhu, Y. Y. (2015a). Binding interaction
tion, biological evaluation and molecular docking studies. RSC
Advances, 10(42), 25046–25058. https://doi.org/10.1039/D0RA04559D
between sorafenib and calf thymus DNA: Spectroscopic methodology,
viscosity measurement and molecular docking. Spectrochimica Acta

JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS
13
Part A: Molecular and Biomolecular Spectroscopy, 136(PB), 443–450.
https://doi.org/10.1016/j.saa.2014.09.056
No. 3, pp. 175–189). Springer Wien. https://doi.org/10.1007/s00706-
007-0585-6
Shi, J. H., Liu, T. T., Jiang, M., Chen, J.,
& Wang, Q. (2015b).
Thomas, J. B., Herault, X. M., Rothman, R. B., Atkinson, R. N., Burgess,
J. P., Mascarella, S. W., Dersch, C. M., Xu, H., Flippen-Anderson, J. L.,
George, C. F., & Carroll, F. I. (2001). Factors influencing agonist
potency and selectivity for the opioid delta receptor are revealed in
structure-activity relationship studies of the 4-[(N-substituted-4-piperi-
Characterization of interaction of calf thymus DNA with gefitinib:
Spectroscopic methods and molecular docking. Journal of
Photochemistry and Photobiology B: Biology, 147, 47–55. https://doi.
org/10.1016/j.jphotobiol.2015.03.005
Shi, J. H., Zhou, K. L., Lou, Y. Y., & Pan, D. Q. (2018). Multi-spectroscopic
and molecular docking studies on the interaction of darunavir, a HIV
protease inhibitor with calf thymus DNA. Spectrochimica Acta Part A:
Molecular and Biomolecular Spectroscopy, 193, 14–22. https://doi.org/
10.1016/j.saa.2017.11.061
dinyl)arylamino]-N,N-diethylbenzamides.
Chemistry, 44(6), 972–987. https://doi.org/10.1021/jm000427g
Wang, B. L., Kou, S. B., Lin, Z. Y., & Shi, J. H. (2020). Investigation on the
binding behavior between BSA and lenvatinib with the help of vari-
ous spectroscopic and in silico methods. Journal of Molecular
Structure, 1204, 127521. https://doi.org/10.1016/j.molstruc.2019.127521
Journal
of
Medicinal
Shi, J.-H. H., Lou, Y.-Y. Y., Zhou, K.-L. L.,
& Pan, D.-Q. Q. (2018).
Exploration of intermolecular interaction of calf thymus DNA with sul-
fosulfuron using multi-spectroscopic and molecular docking techni-
ques. Spectrochimica Acta Part A: Molecular and Biomolecular
Spectroscopy, 204, 209–216. https://doi.org/10.1016/j.saa.2018.06.054
Sirajuddin, M., Ali, S., & Badshah, A. (2013). Drug-DNA interactions and their
study by UV-Visible, fluorescence spectroscopies and cyclic voltametry.
Journal of Photochemistry and Photobiology B: Biology, 124(October 2015),
1–19. https://doi.org/10.1016/j.jphotobiol.2013.03.013
Xu, X., Wang, D., Sun, X., Zeng, S., Li, L.,
& Sun, D. (2009).
Thermodynamic and spectrographic studies on the interactions of ct-
DNA with 5-fluorouracil and tegafur. Thermochimica Acta, 493(1–2),
30–36. https://doi.org/10.1016/j.tca.2009.03.017
Yang, L., Zhu, W., Fang, M., Zhang, Q., & Li, C. (2013). A new carbazole-
based Schiff-base as fluorescent chemosensor for selective detection
of Fe3þ and Cu2þ. Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy, 109, 186–192. https://doi.org/10.1016/j.saa.
2013.02.043
Soliman, A. A., & Linert, W. (2007). Structural features of ONS-donor sali-
cylidene Schiff base complexes. In Monatshefte fur Chemie (Vol. 138,