Journal of Biomolecular Structure and Dynamics

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Exploration of the binding of DNA binding ligands

to Staphylococcal DNA through QM/MM docking
and molecular dynamics simulation

Periyasamy Vijayalakshmi , Chandrabose Selvaraj , Sanjeev Kumar Singh ,

Jaganathan Nisha , Kandasamy Saipriya & Pitchai Daisy

To cite this article: Periyasamy Vijayalakshmi , Chandrabose Selvaraj , Sanjeev Kumar

Singh , Jaganathan Nisha , Kandasamy Saipriya & Pitchai Daisy (2013) Exploration of the
binding of DNA binding ligands to Staphylococcal DNA through QM/MM docking and molecular
dynamics simulation, Journal of Biomolecular Structure and Dynamics, 31:6, 561-571, DOI:
10.1080/07391102.2012.706080

To link to this article: https://doi.org/10.1080/07391102.2012.706080

Published online: 13 Aug 2012.

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Journal of Biomolecular Structure and Dynamics, 2013
Vol. 31, No. 6, 561–571, http://dx.doi.org/10.1080/07391102.2012.706080

Exploration of the binding of DNA binding ligands to Staphylococcal DNA through QM/MM
docking and molecular dynamics simulation
Periyasamy Vijayalakshmia,1, Chandrabose Selvarajb,1, Sanjeev Kumar Singhb, Jaganathan Nishaa, Kandasamy Saipriyaa
and Pitchai Daisya*
a
Bioinformatics centre (BIF), PG& Research Department of Biotechnology & Bioinformatics, Holy Cross College (Autonomous),
Tiruchirapalli 620002, Tamil Nadu, India; bComputer Aided Drug Design and Molecular Modeling Lab,Department of Bioinformat-
ics, Alagappa University, Karaikudi 630003, Tamilnadu, India

Communicated by Ramaswamy H. Sarma

(Received 19 December 2011; final version received 5 June 2012)

DNA binding ligands (DBL) were reported to bind the minor groove of bacterial DNA. In the present study, DBL were
analyzed and screened for their Staphylococcus inhibitory activity by inhibiting the Staphylococcal DNA replication.
The orientation and the ligand-receptor interactions of DBL within the DNA-binding pocket were investigated applying
a multi-step docking protocol using Glide and QM/MM docking. The polarization of ligands with QM/MM for DNA-
ligand docking with Staphylococcal DNA minor groove was performed in order to understand their possible interactions.
Molecular dynamics simulation techniques were employed to obtain the dynamic behavior of the DBL with Staphylococ-
cal DNA. Computational docking and simulation represented a promising alternative to bridge the gap, and so that DNA
and gyrase interactions were blocked by DBL. The results revealed the importance of the DBL for strong interactions
with the DNA minor groove region and blocking the bacterial replication.
Keywords: DNA docking; DNA gyrase; QM/MM; DNA binding ligands and Staphylococcus

Introduction dency to infect almost every part of human (Sivaraman,

Venkataraman, & Cole, 2009). Reasons for versatality are
It has been known that Staphylococcus aureus is a
due to a variety of virulence factors (e.g. surface proteins,
notorious bacterium that has the ability to evolve into new
toxins, and immune modulators) produced by the viru-
virulent types and drug-resistant variants (Chambers,
lence bacterium. These virulence factors are organized and
2005). Nosocomial infections of S. aureus have produced
co-ordinated by a network of multiple DNA binding pro-
serious public health issues in recent years (NABI, 2007).
teins. Bacterial DNA gyrase is a DNA binding protein
Humans are natural reservoirs for S. aureus, and it colo-
(Ferrero et al., 1994) and a tetrameric A2B2 protein whose
nizes the anterior nares and skin of approximately 20–
uniqueness is in catalyzing the negative supercoiling of
30% of healthy adults (Franklin & Lowy, 1998; Lindsay
DNA and is essential for DNA replication, transcription,
& Holden, 2006). S. aureus cause a wide range of diseases
and recombination (Mdluli & Ma, 2007).
from soft tissue infections to life-threatening infections
The DNA gyrase supercoiling reaction involves
such as toxic shock syndrome, necrotizing pneumonia,
wrapping DNA around A2B2 complex, cleavage of this
and endocarditis. Loss of skin barrier integrity (e.g. in sur-
DNA in both strands (involving the formation of
gical patients, kidney dialysis patients, trauma and burn
DNA-protein covalent bonds) and a passage of a seg-
patients, etc.) and decreased immunity (e.g. in immune-
ment of DNA through this double stranded break.
compromised individuals, such as cancer and AIDS
Resealing of the break results in the introduction two
patients) are the causes of this infection (Centers for Dis-
negative super coils intimately related to the negative
ease Control and Prevention, 2003a, 2003b; Tejerina
super coiling of covalently closed duplex DNA ring by
et al., 1992). S. aureus is versatile in nature and have ten-

*Corresponding authors. Email: hcctrichyin@mail.hcctni.edu.in (Periyasamy Vijayalakshmi); daisylesslie@gmail.com (Pitchai Daisy)

1
Periyasamy Vijayalakshmi and Chandrabose Selvaraj have equally contributed as first author (equal contribution) for this research
work. All authors read and approved the final manuscript.

Ó 2012 Taylor & Francis

562 P. Vijayalakshmi et al.
DNA gyrase (Liu & Wang, 1978; Maxwell, 1997). DNA
is considerably the most attractive drug target, when
compared to protein targets. As the majority of muta-
tional aberrations in the actual DNA conferring resis-
tance to gyrase inhibitors, there is high possibility of
failure of gyrase inhibitors and hence we concentrated
much on targeting the DNA–DNA gyrase complex.
In our study DNA gyrase–DNA complex of S.
aureus were taken as a target. Drug–DNA interactions
were classified into intercalation and groove binding
based on ligand-binding location (Palchaudhuri & Her-
genrother, 2007). Both the major and minor grooves
of DNA differed in very subtle ways in terms of
hydrogen bonding characteristics, steric disposition,
electrostatic environment, and micro environmental
polarity, which lead to complementary preferences for
the incoming molecules to bind with DNA (Blackburn,
1996). Small molecules were found to bind with both
major and minor groove of the double-helical DNA
regions with a slight preference towards the latter
(Morávek, Neidle, & Schneider, 2002).
The objective of our study is to inhibit the DNA
and also to stop the process of interaction between the
DNA and DNA gyrase. We analyzed the cavity region
that was found in between the DNA and DNA gyrase.
This is the same region where the DNA binding
ligands (DBL) can adopt itself between these two
regions and so here we declare that these base pairs
particularly DG 10, DC 11, and DC 12 are participat-
ing as DBL receptor binding sites. Minor groove bind-
ing agents have long and planar structures that allow
Figure 1. Biological workflow about the importance of DBL: The figure explains the DNA and DNA gyrase interaction, followed
by external DBL interacting with DNA minor groove regions exactly and the reaction completely ejects the gyrase binding towards
the DNA.
them to adopt a crescent shape that fits into the
groove (Sivaraman et al., 2009). Already reported 130
DBL potentiate anti-bacterial activity (functioning spe-
cially to bind with DNA minor groove region) (Munde
et al., 2007). These ligands were designed based on
the natural product Distamycin A (Refer Supplemen-
tary file for core structure) as well as crescent shaped
molecules that bind within the minor groove of DNA
(Kaizerman et al., 2003). These compounds have been
shown to target druggability sites within the bacterial
genome and, as a result, inhibited DNA replication
and RNA transcription (Boger, Fink, & Hedrick, 2000;
Ge et al., 2002). DBL interacts with the minor groove
region of the DNA while the DNA is complexed with
DNA gyrase and alters the conformation so that the
DNA gyrase ejects out from DNA major groove. The
following Figure 1 explains the details of the function
of DBL and its action.
Materials and methods
All computational analyses were carried out on a Red
Hat 5.3 Linux platform running on an IBM-System
K3200 M2 series with Intel Xeon processor and 2 GB of
RAM.
In-silico environmental setup
One hundred and thirty DBL (Kaizerman et al., 2003)
that have not reported in any databases, and which have
the special capacity of binding with minor groove of

DNA were chosen for present work. The 2D structures
of the selected ligands were drawn in marvinsketch pro-
gram (Marvin Draw 5.1.5) and the 2D structures were
converted into 3D structures using ligprep program in
OPLS-AA force field (LigPrep 2.5). The crystal structure
of DNA gyrase in complex with DNA of S. aureus
(PDB ID: 2XCS) was retrieved from the PDB. For deter-
mining the original conformation of DNA–DNA gyrase
complex in molecular modeling environment, we used
macro model for optimization and minimization (Maestro
9.2). Here OPLS-AA force fields were utilized for
obtaining the optimized and minimized conformation of
DNA (Jacobson, Kaminski, Friesner, & Rapp, 2002).
Predicting druggability pockets in DNA
DNA druggability pocket of DNA gyrase–DNA complex
were studied using the SiteMap module of the Schrö-
dinger (Sitemap 2.5). SiteMap provides researchers with
an efficient means to find and better exploit the charac-
teristics of ligand-binding sites in the 3D structural for-
mat. SiteMap can treat entire proteins or DNA to locate
binding sites whose size, functionality, and extent of sol-
vent exposure meet user specifications. DNA druggabili-
ty pocket of DNA gyrase–DNA complex were studied
using the SiteMap module of the Schrödinger. These
sites are very useful for analyzing the interaction of
ligands in the site. The algorithm automatically searches
and identifies potential binding sites from the macromol-
ecules and executes the binding regions for docking
analysis. The charge density was evaluated by the
OPLS-2005 force field on the DNA and the force field
calculates the binding pocket residues that lie within 5 Å
unit area of the macromolecule.
Molecular docking: QM/MM
DBL were docked with predicted DNA gyrase–DNA
druggability pocket through combined approach of glide
and quantum polarized ligand docking (QPLD) and site-
map-predicted sites were used in grid generation step
through receptor-grid generation program from Glide
(version 5.6) (Friesner et al., 2004). A receptor grid was
generated using 1.00 van der Waals (vdW) radius scaling
factor and .25 partial charge cutoff. Initially docking was
performed with glide; conformations obtained from glide
were subjected to QPLD. Because DNA was charged,
obtaining the docking conformations using charge-based
docking algorithm (Jaguar 7.8) found more significant.
The glide outputs of grid file and ligand conformations
were imported in QPLD. The selection of QM level for
charge calculation is a trade off between speed (fast)
which uses the 3-21G basis set, BLYP functional, and
“Quick” SCF accuracy level and accuracy which uses
the 6–31G⁄/LACVP⁄ basis set, B3LYP density
DNA as drug target in S.aureus 563
functional, and “Ultrafine” SCF accuracy level (iacc = 1,
iacscf = 2) (QPLD, 2011). The small molecules (ligands)
were treated quantum mechanically and remainder of the
system (DNA gyrase–DNA complex) was treated as
molecular mechanics. This method applies Glide algo-
rithm to generate the best candidate poses for which
ligand docking polarization was carried out with jaguar.
The final energy evaluation was done with the Glide
Score (Gscore) and a single best pose was generated as
output for a particular ligand with the help of the follow-
ing equation (Sengupta, Verma, & Naik, 2007).
GScore ¼ a vdW þ b Coul þ Lipo þ Hbond þ Metal
þ BuryP þ RotB þ Site
Where, vdW = van der Waal energy; Coul = Coulomb
energy; Lipo = Lipophilic contact term; HBond = Hydro-
gen-bonding term; Metal = Metal-binding term;
BuryP = Penalty for buried polar group; RotB = Penalty
for freezing rotable bonds; Site = Polar interaction at
active site; and the coefficient of vdW and Coul are:
a = .065, b = .0130.
Here the DNA docking was done with both XP and
QPLD, because using the XP docking from glide shows
only one hydrogen bond and less score. QPLD applies
QM/MM methods and reproduce accurate results of
docking and so we applied redocking methods using
QPLD. (The Scores of XP and their interactions are
additionally provided as supplementary information).
Predicting drug-like property
ADME properties were calculated using Qikprop 2.5 tool
of Schrodinger software (QikProp 3.4). It predicted both
physico chemically significant descriptors and pharmac-
okinetically relevant properties. QikProp provided ranges
for comparing a particular molecule’s properties with
those of 95% of known drugs. The principal descriptors
and physiochemical properties with a detailed analysis
included the molecular weight, H-bond donor, H-bond
acceptor, QPlogPw, QPlogKp, ⁄% of Human oral
absorption, QPlogKhsa. It also evaluated the acceptabil-
ity of the analogues based on Lipinski’s rule of 5, which
were essential for rational drug design (Lipinski, Lom-
bardo, Dominy, & Feeney, 2001).
Toxicity prediction
Toxicity prediction by komputer assisted technology
(TOPKAT), an in silico toxicity prediction software
developed by Accelrys Inc. (http://accelrys.com/), pre-
dicted the range of toxicological endpoints, including
mutagenicity, developmental toxicity, and rodent carcino-
564 P. Vijayalakshmi et al.
genicity (Dearden, 2003). The compounds of best inter-
actions and scoring parameters were subjected towards
the carcinogenicity and other toxicity effects. Toxicity
parameters of 10 best candidates were predicted using
TOPKAT, implemented in Accelrys Discovery Studio
2.5. Less toxic compounds can overcome low dosage
response action and so, we predicted the carcinogenic
and toxicity measures of minor groove-binding ligands.
Molecular dynamics study
Simulation studies were carried out for understanding the
behavior of DNA minor groove-binding ligands’ interac-
tion in dynamic movement against Staphylococcal DNA
using an all-atom force field (OPLS-2005). Our purpose
of simulation was to analyze the DBL’ conformational
changes in Staphylococcal DNA and stability of ligand
interactions in a dynamic environment. We computed
simulation studies in SPC model system, constructed for
DNA gyrase – DNA complex and DBL. The water vol-
ume was fit within orthorhombic box (covers the rectan-
gular dimensions of DNA and DBL) along with .15
Na+Cl in system as neutralizing components (Zhang,
Rauge, Eisenberg, & Carloni, 2010). Simulations were
carried out through Desmond molecular dynamics (MD)
package (Kevin et al., 2006). The DNA gyrase – DNA–
DBL complexes were solvated in an orthorhombic simu-
lation box with timescale of 5 ns. Simulation ensemble
properties viz, number of atoms, pressure, area, and
timescale were considered and so NPAT was chosen. For
maintaining the constant volume throughout the simula-
tion, it was ensured that the density and pressure were
correct during these simulations (Ikeguchi, 2004). The
box size was fixed at the end of constant pressure equili-
bration, to ensure the correct atom count (density of
whole system). The distance between the complex and
wall of the box includes the spaces of .9 Å distance.
Temperature scale was maintained at 300 K for whole
simulation using Nose-Hoover thermostats (Kleinerman,
Czaplewski, Liwo, & Scheraga, 2008) and for maintain-
ing stable pressure, Martina-Tobias-Klein barostat
method was used. The equations of motion were inte-
grated using the multistep RESPA integrator with an
inner time step up of 2.0 fs.
MD trajectories analysis
Structural calculations like RMSD were calculated by
build-in function of Desmond – trajectory analysis. The
RMSD between initial and final conformation was uti-
lized from Schrödinger build-in functions. The Trajectory
files which were saved (snapshot) at every successive
1 ps from the start of the simulation, totaling 5000 for
each structure, were used for analysis of time.
Results
Druggability pocket in DNA
The binding site of the DNA has been predicted by site-
map module from Schrödinger and here we consider
both DNA and DNA gyrase for prediction of binding
pockets from specific DNA. This is because the target
chosen for the whole study was specific on DNA inhibi-
tion. Gyrase enzyme interacts with Staphylococcal DNA,
and in between DNA and gyrase there is a cavity region
which have the capacity to adopt itself to bind the DBL.
The cavity of binding pocket was predicted and shown
in Figure 2. The figure shows that the white colored
spheres between the DNA (specifically on the interaction
region of DNA and DNA gyrase (DG 10, DC 11, and
DC 12)) and gyrase protein. The gyrase side chain may
interrupt the binding of DBL in that region, but the pre-
dicted binding sites have much negative region and so
with high possibility of adopting ligands, our DBL have
much possibility of interference with protein–DNA inter-
actions which leads to inhibition of DNA activity. Im
and Py rings distinguish AT from GC base pairs because
of steric factors involving the bulk of the guanine amine,
and the ability of Im to form a hydrogen bond with the
amine (Kopka et al., 1997). In other words, according to
Wahle and Kornberg (1988) DNA on enzyme digestion
by DNase exposes the GC sequences on the outside of
the DNA wrapped around gyrase. This site specificity of
DNA gyrase is partly determined by the bendability of
DNA. Computational prediction of active sites runs
concomitantly with that of Wahle and Kornberg (1988)
where sites on the surface of the DNA were explored by
ligands in order to identify favorable regions on the
DNA surface for selective binding.
DNA–DBL docking interaction
To retain the binding conformation of DNA minor
groove-binding ligands in predicted druggability pocket
of DNA, Drug-DNA docking interactions were per-
formed. The conformational change was necessary for
interactions. So we have retained the possible better con-
formations using the QM/MM docking studies. These
binding pockets match better interaction of DNA minor
groove-binding ligand in its cavity region. White colored
spheres generated by sitemap was replaced by DNA
minor groove-binding ligands, and scoring functions
QPLD were assigned by QM/MM docking algorithm.
(Table 1 and 2) represent the analysis based on glide-
docking score, glide energy values, QPLD score, energy
and their interactions. DNA–ligand docking revealed that
the DC, DG interacts with H, O, N atom of ligands
(Figure 3). Best ligands having the score of more than
9 K/cal were chosen from top ranking poses in QPLD
and interactions were analyzed.
 DNA as drug target in S.aureus 565

Figure 2. Binding pocket present in minor groove region of Staphylococcal DNA (The binding pocket is represented in aquamarine
color and covers the site points of white sphere).

Table 1. Molecular docking results via XP docking and QM/MM (Gscore, glide energy and No. of Hydrogen bonds).

S. Ligand XP Gscore QPLD score Glide energy Glide energy(QPLD) H H bond

No no (kcal/mol) (kcal/mol) (kcal/mol) (kcal/mol) bond (QPLD)
1 86 10.407874 10.799058 84.269630 88.650644 1 5
2 61 8.942278 10.215634 85.964016 91.801783 1 3
3 106 9.126642 9.977846 87.067038 83.544912 1 3
4 125 9.363477 9.973402 91.665741 84.449052 1 2
5 52 9.556905 9.893243 81.351686 75.710021 1 3
6 29 9.771032 9.876834 81.468509 75.748978 1 2
7 83 9.966680 9.869774 84.545154 81.634878 1 2
8 120 9.570983 9.749887 91.777480 84.597231 1 2
9 60 9.511751 9.697479 80.282224 81.971904 1 2
10 88 10.407874 9.488720 84.269630 89.651088 1 4

Assessment of ADME for the selected compounds
To investigate the ADME properties, the best compounds
were analyzed (Table 3). Molecular weight of the 10 dif-
ferent molecules of the study existed in the range
between 630 KDa and 759 KDa out of which, ligand 88,
overrules the defined acceptable range of the molecular
weight. H-bond donors were in the range between 4 and
5, whereas H-bond acceptor of the chosen compounds
found to be in the range 13–15. Predicted water/gas par-
tition coefficient was in the range 20–25 for most of the
compounds. Predicted skin permeability & log Kp
(QPlogKp) negatively ranges between 3 and 5. Predicted
octanol/water coefficient (OPlogPw) was in the range
between 19 and 26 and, predicted human oral absorption
on 0–100% scale was found to be in the intermediate
levels of 40 and 50. Prediction of binding to human
serum albumin (QPlogKhsa) positively ranged between
.2 and .9. The ADME of the ligands are predicted and it
satisfies all the characteristic properties which were
considered the main criterion in the commercialization of
compounds for clinical use in future.
Toxicity prediction of selected compounds
Further to investigate in silico prediction of toxicities of
compounds, TOPKAT (commercially available software
used by pharmaceutical companies and academic institu-
tions in drug discovery and development programs) was
used (Prival, 2001; Richard, 1998). The results of the
toxicity predictions of the DBL using the Ames mutage-
nicity, female rat NTP carcinogenicity, male rat NTP car-
cinogenicity, and skin irritation were summarized
(Table 4). Description of toxicity results by carcinogenic-
ity showed ligands 29, 86, 120 and 125 have less toxic-
ity from the Topkat prediction.
Molecular dynamic behavior of drug–DNA complex
Based on ADME/T and docking score, four best ligands
(2D structure & IUPAC name provided in the supple-
566 P. Vijayalakshmi et al.

Table 2. Interacting atom notifications of H-bond donor and acceptor in QM/MM docking. (For interactions using XP docking
please refer Supplementary information).

Ligand no Interaction behavior H-bond donor H-bond acceptor Distance (Å)

86 DC11(O)–H (Li)O–H DNA(H) 1.793
DC13(H)–O (DNA)H–O (Li)(O) 2.127
DC7(H)–N (DNA)H–N (Li)N 2.291
Li(O)–HOH HOH–O (Li)O 2.350
61 DC11(O)–H (Li)O–H (DNA)H 1.748
Li(O)–HOH HOH–O (Li)O 1.995
106 DC11(O)–H (Li)O–H (DNA)H 1.712
DC11(H)–O (DNA)H–O Li(O) 2.214
Li(O)–HOH HOH–O Li(O) 1.741
125 DC11(O)–H (Li)O–H (DNA)H 1.872
Li(O)–HOH HOH–O Li(O) 1.992
52 DC11(O)–H (Li)O–H (DNA)H 1.938
Li(O)–HOH HOH–O Li(O) 2.219
Li(O)–HOH HOH–O Li(O) 2.277
29 DC10(O)–H (Li)O–H (DNA)H 1.698
83 DC13(H)–O (DNA)H–O Li(O) 2.062
DC11(O)–H (Li)O–H (DNA)H 1.899
120 DC11(O)–H (Li)O–H (DNA)H 1.803
Li(O)–HOH HOH–O Li(O) 1.924
60 DC11(O)–H (Li)O–H (DNA)H 1.700
Li(O)–HOH HOH–O Li(O) 2.012
88 DC11(H)–O (DNA)H–O Li(O) 2.394
DC12(H)–O (DNA)H–O Li(O) 1.873
DG9(O)–H (Li)O–H (DNA)H 2.094

mentary information) were chosen out of these selected
10 ligands for dynamic behavior and whole simulations
were analyzed in trajectories. The DBL in dynamic
movements showed active movement (Energetically most
favorable motion) and good interaction in druggability
pocket. The chosen ligands of ligand 29, 86, 120, and
125 showed good poses (the best geometry of ligands in
the binding site) according to the DNA dynamic changes
and so modification of hydrogen bonds was viable
throughout the simulation. The hydrogen bonds involve-
ment in each nanosecond of simulation was indicated
(Table 5). The RMSD graph plotted in Figure 4 indicated
the result of dynamic behavior of selected ligands from
the initial position to final position throughout the simu-
lation time. In this graph, ligands 29 and 86 remained in
between 0 and 1.0 Å RMSD, remaining two ligands
showed more dynamic movement and hence it reached
up to 1.7 Å. The DBL namely 120 and 125 has not
expressed the hydrogen bond interactions with the com-
plex throughout the dynamic studies. But the dynamic
studies are not only based on the hydrogen bond interac-
tions, the other non-bonded interactions like vander
Waals interactions, polar and non-polar interactions may
or may not arise at the absence of hydrogen bond and
make the equilibrium constant. If these other non-bonded
interactions have not participated in the equilibrium for
the case of DBL 120 and 125, then both will get out of
the box and their RMSD would arise more than 5 Å.
Since the compounds 120 and 125 showed RMSD varia-
tion of 1 Å, there is much possibility of these four DBL
to be equilibrated throughout the dynamics. There may
be microstates, which exist in the equilibrium ensemble
where the hydrogen bonding network changes signifi-
cantly in the large complex, and both members of the
complex (DNA and DBL) are likely to undergo substan-
tial conformational fluctuations. Even though the fluctua-
tions made to discontinuous hydrogen bonds, the force
constant and energy levels maintain the DBL inside the
DNA-binding pocket throughout the simulation. Addi-
tionally in supplementary information we have provided
the interactions for 0–5 ns for selected DBL.
In these total simulations of DBL in Staphylococcal
DNA, the nucleic acid residues of DA-7, DG-10, DC-11,
and DC-13 were present in predicted druggability pocket
of Staphylococcal DNA. When considering the deep
view of dynamic behavior of each ligand.
Ligand 29 showed DC-11 and DG-10 residues of
DNA and their interactions in 1–3 ns and 4–5 ns. Ligand
86 showed hydrogen bond interactions with DC-11 and
DC-13 throughout the whole simulation process, and
additionally DA-7 interacted up to 4 ns. Ligand 120
showed DC-11 from right and left strand of DNA up to
1.2 ns and again hydrogen bonds were forming at 3.2 ns.
Ligand 125 showed interactions with DNA up to 1 ns
and in between 3–4 ns and these results were highly cor-
related with RMSD graph.
 DNA as drug target in S.aureus 567

Figure 3. Molecular interactions of DNA and top ranked DBL (Brown) through H-Bond interactions (Yellow).

Table 3. Drug-like properties calculated by Qikprop simulation.

Ligand No MWa (g/mol) HBb donors HBc acceptors Qplogpwd Qp log kpe % human oral absorbtionf QPlogKhsag
86 705.23 4 13.7 22.986 4.598 50.283 .898
61 640.7 5 15.2 26.642 5.309 41.552 .25
106 651.724 4 14.7 24.903 4.398 53.59 .498
125 635.724 4 13 23.17 4.624 55.058 .781
52 635.121 4 13.7 22.987 4.714 54.055 .453
29 528.969 4 9.5 19.219 3.68 50.217 .279
83 656.758 4 13.7 23.58 4.462 57.251 .67
120 649.751 4 13 23.316 4.569 58.166 .963
60 616.678 4 15.7 24.807 5.354 42.379 .089
88 759.201 4 13.7 22.801 4.457 55.383 .947
a
Molecular weight of the molecule. (Acceptable range 130.0–725.0.)
b
Estimated number of hydrogen bonds that would be donated by the solute to water molecules in an aqueous solution. Values are averages taken over
a number of configurations, so they can be non-integer. (Acceptable range 0.0–6.0.)
c
Estimated number of hydrogen bonds that would be accepted by the solute from water molecules in an aqueous solution. Values are averages taken
over a number of configurations, so they can be non-integer. (Acceptable range 2.0–20.0.)
d
Predicted water/gas partition coefficien. (Acceptable range 4.0–45.0.)
e
Predicted skin permeability, log Kp. (Acceptable range 8.0 to 1.0.)
f
% Human oral absorption (<25% is poor).
g
Prediction of binding to human serum albumin. (Acceptable range 1.5 to 1.5.)

Discussion molecules is a fundamental problem in drug design. The

DNA represents a traditional target for chemotherapeutic problem behind the DNA docking is that most ligand
intervention. Molecular recognition of DNA by small structures do not interact with DNA. Using small
568 P. Vijayalakshmi et al.

Table 4. TOPKAT-predicted properties of the best compounds.

Compound no Rat male NTP prediction Rat female NTP prediction Ames prediction Skin irritancy
29 Non-carcinogen-.077 Non-carcinogen(.000) Non-mutagen(.000) None (.000)
52 Carcinogen -.993 Non-carcinogen(.00) Mutagen(1.000) None (.000)
60 Carcinogen-.884 Non-carcinogen(.00) Mutagen(1.000) None (.000)
61 Carcinogen-.993 Non-carcinogen(.00) Mutagen(1.000) None (.000)
83 Carcinogen-.991 Non-carcinogen(.00) Mutagen(1.000) None (.000)
86 Carcinogen-.991 Non-carcinogen(.00) Mutagen(1.000) None (.000)
88 Carcinogen-.936 Non-carcinogen(.00) Mutagen(1.000) None (.000)
106 Carcinogen-.912 Non-carcinogen(.00) Mutagen(1.000) None (.000)
120 Non-carcinogen-.099 Non-carcinogen(.00) Mutagen(.982) None (.000)
125 Non-carcinogen-.091 Non-carcinogen(.00) Mutagen(.992) None (.000)

Table 5. Interactions of DBL in dynamic environment every ns.

Ligand number 0.0–1.0 ns 1.0–2.0 ns 2.0–3.0 ns 3.0–4.0 ns 4.0–5.0 ns

29 DG-10 DG-10 DG-10 – DG-10
DC-11
86 DC-11 DC-11 DC-11 DC-11 DC-11
DC-13 DC-13 DC-13 DC-13 DC-13
DA-7 DA-7 DA-7 DA-7
120 DC-11 DC-11 – DC-11 –
125 DC-11 – – DC-11 –

molecules toward DNA will be a successful part in drug
designing. Examining structural and energetic features,
the ternary complexes were constructed, by screening of
130 DBL (17).
The present research effort aims at theoretically pre-
dicting the interaction of above-mentioned 130 ligands
by docking with minor groove region of DNA gyrase–
DNA complex of S. aureus through in silco approach
using Schrödinger.
Jacob A et al. has synthesized and reported the
potent DNA minor groove-binding antibacterial com-
pounds that were designed based on the natural product
distamycin A as well as crescent-shaped molecule, that
specifically have tendency to bind within the minor
groove of DNA and these compounds already have the
experimental validations, that these compounds are bind-
ing specific with DNA minor groove regions. The DNA
and DNA gyrase has been reported as crystal structure
complex (PDB 1XCS), here the DNA binds with gyrase
and our study needs to target the inhibition of binding of
DNA and DNA gyrase. Since the DBL compete with the
DNA gyrase-binding site in the DNA it is obvious that
DBL would have targeted the minor groove region deter-
mined for binding of DNA gyrase.
The glide program was employed as primary docking
search engine to dock 130 DBL with that of the DNA
gyrase–DNA complex. According to this study, the
actual conformation of the DNA has been considered for
the DNA and DNA gyrase complex. But to check
whether the DBL binds with DNA or some other regions
in protein, we have minimized the DNA and protein
complex. The distance between the binding pocket and
DNA gyrase is nearly around 2 Å and we have generated
the grid based on site information predicted by sitemap
and followed by XYZ covering axis at 10 Å. Now the
DBL is free to bind anywhere inside the grid (placed in
between the DNA and DNA gyrase), but some protein
amino acids present inside the grid fail to accept the
DBL. However DNA minor groove region accepted the
DBL and its hydrogen bonds capture the DBL. By this
we confirmed the pharmacological behavior of DNA
minor groove binding ligands. Results of docking studies
evaluated the binding mechanism of 130 DNA minor
groove binding ligands with DNA gyrase–DNA complex
and interestingly, involvement of GC content was rich in
these interactions. From the investigation of the docked
results, the more negative value of G-score indicated
good binding affinity of the ligand with the receptor. The
compounds which have the score value of more than 9
were considered as best. The white-colored sphere covers
the 4 Å area of binding pocket and it is a binding cleft,
where the ligand molecule can bind in the specific
region. When ligand molecules replaced the white color
dots in the binding cleft region, the atomic structure
arrangements attained their electronic level and sharing
of acceptor and donor between the DNA and DBL
occurred. In this obtained conformation of DBL, the
numbers of hydrogen bonds formed with DNA were
 DNA as drug target in S.aureus 569

reported as interactions. The spectacular reason behind to be non-carcinogenic. In these models, compounds 52,
using the QPLD for docking was, most of algorithm will 60, 61, 83, 86, 88,106 were predicted to be carcinogenic
not support the DNA docking and so QPLD performs in male rat NTP carcinogenicity model (Table 4). All the
with polarization of ligand charges (QM) and minimiza- compounds were predicted to be non-irritant in the skin
tion of DNA molecules (MM). The partial charges on irritancy model except ligand 88.
the atoms of the ligand were then replaced with charges Simulation provided the ultimate detail concerning
derived from QM calculations on the ligand in the field individual particle motions as a function of time. Thus,
of the receptor for each ligand-receptor complex, and they were used to address specific questions, about the
glide re-docked each of the ligands with updated atom properties of model system, often more easily than
charges, and returned the most energetically favorable experiments on the actual system. Based on ADME/T
pose and so DNA docking was possible in its predicted and scoring parameters, the four interacting complexes
binding pockets. The QPLD results of the selected com- (ligand 29, 86,120,125 with DNA gyrase–DNA) were
pounds were analyzed and most of the compounds cor- chosen for analysis of dynamic behavior through MD
rectly bound to the DNA minor groove region [(DC 11 simulation. Out of the final screened 10 DBL com-
(OH), DC13 (OH), DC7 (HN), and Li (HOH)]. From the pounds, the compound numbered 29, 120, and 125 were
analysis of the computational binding modes of DBL, found to be non-carcinogens so based on this criterion
DC11 was found to be the interaction site of choice for the three ligands were further validated for simulation
most of the DBL ligands. studies. Compound 86 which possesses more hydrogen
The need for early consideration of ADME properties bond interaction, glide score (refer supplementary file for
was also increasingly urgent because of the implementa- calculation of glide score) and which is comparatively
tion of combinatorial chemistry and high-throughput higher than the other ligands was selected for simulation
screening, since this can generate vast numbers of poten- studies even though it is found to be a moderate carcino-
tial lead compounds (Hodgson, 2001). A new paradigm genic.
for toxicity testing that combines the strengths of in vivo,
in vitro, and in silico approaches were being used to aid
prediction of the ADMET profiles of drug candidates in
order to reduce attrition rates at the late drug develop-
ment stage and also to avoid human health risk (Merlot,
2010; Van de Waterbeemd & Gifford, 2003). One
approach to in silico toxicity predictions involved statisti-
cal comparison of the characteristics of chemical interest
and those compounds with known properties in a data-
base. TOPKAT and Qikprop were the widely used sys-
tem of this type.
So, we analyzed 44 physically significant descriptors
and pharmaceutically relevant properties of DNA minor
groove-binding ligands, by taking molecular weight, H-
bond donor, H-bond acceptor, Qplogpw, logkp, and per-
cent of human oral absorption in concern. If a chemical
compound contains certain pharmacological or biological
properties then it can be an active drug. All the proper-
ties were well within acceptable range defined for human
use, thereby indicating their potential as drug-like mole-
cules. The values of DNA minor groove-binding ligands
showed promising effect in terms of ADME properties
and also showed narrow capacity of human intake with
both acceptable ADME and less toxicity. (Table 3).
Toxicity predictions of the DBL using four models
(Ames mutagenicity, female rat NTP carcinogenicity,
male rat NTP carcinogenicity, and skin irritation) were
predicted via TOPKAT. The results indicated that the Figure 4. Comparative MD analysis of the DNA and DBL
compound 29 was non-mutagenic in the Ames mutage- system: the RMSD values of the four systems vs. simulation
time (5 ns) and the RMSD probability of the four systems
nicity prediction model. In the NTP carcinogenicity mod- (DNA–DBL 29, DNA–DBL 86, DNA–DBL 120, and DNA–
els (female rat NTP carcinogenicity and male rat NTP DBL 125), the X-axis represent Time (ps), Y-axis represent
carcinogenicity) most of the compounds were predicted RMSD.
570 P. Vijayalakshmi et al.
When compared with ligand 86, ligand 61 is found
to be more carcinogenic and the glide score also was
comparatively less. Based on this criterion, ligand 61 is
not chosen for further studies.
The MD study also highly supported the predicted
binding sites, and none of the compounds detached from
the system throughout the dynamics. Here we have dis-
cussed about the interactions of DBL with binding pocket
of DNA and throughout the simulations, the DBL show-
ing bound state with DNA. Additionally we have pro-
vided the energy plot for the selected ligands as
supplementary information. This has proved that our sim-
ulations have attained the equilibrium conditions for inter-
action analysis between DNA and DBL in dynamic
environment.
The ligands remained bound to the binding positions
and do not experience considerable deviation in the
minor groove region of DNA, since it conflicts with Fig-
ure 4. RMSD graph (Figure 4) also indicated that all the
complexes were stable and do not show any abnormal
fluctuations during the simulation. MD study was con-
ducted with the aim to find the interaction between
Staphylococcus DNA and ligand molecules. These small
molecules posses greater binding affinity for Staphylo-
coccus DNA, proving to be the best inhibitors for Staph-
ylococcus DNA.
Conclusion
DNA minor groove binders are an important class of
compounds with high therapeutic potential and this class
of compounds provided several FDA approved drugs
and offers a great potential for structure-based drug
design methods. The present comprehensive computa-
tional study with 130 DNA minor groove binders
revealed the strength of their binding capacity to Staphy-
lococcus DNA. The applications of QM/MM force field
for docking interactions performed perfect interactions
with predicted binding pockets and MD simulation also
supported the results. MD studies suggested that the
DBL show a minor deviation upon binding, for which
DNA base pair and system water molecules were highly
co operating as a natural simulation performance. The
current exhaustive study consolidated that these DBL
(29, 86,120 and 125) have the capacity to bind with
Staphylococcus DNA and it can also act against drug
resistant Staphylococcus infection. Out of the above-
mentioned four ligands, ligand 29 was considered as best
in inhibiting Staphylococcal DNA replication.
Therefore, we expect our study might facilitate in
providing novel insight into the mechanism of drug–
DNA interactions. Future studies of pharmacophoric
screening based on these compounds can design new
compounds for DNA inhibition.
Abbreviations
DBL – dna binding ligands
QM – quantum mechanics
MM – molecular mechanics
OPLS – optimized potential for liquid simulation
Acknowledgments
The financial support extended by the BTIS (Biotechnology
information system), DBT (Department of Biotechnology),
Ministry of Science and Technology, Government of India,
India is acknowledged.
Supplementary material
The supplementary material for this paper is available
online at http://dx.doi.10.1080/07391102.2012.706080.
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