IN-SILICO SCREENING OF POTENTIAL PHYTOCOMPOUNDS AGAINST STAPHYLOCOCCUS AUREUS AND AN IN-VITRO ANTIBACTERIAL EVALUATION

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Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4128
IJPSR (2023), Volume 14, Issue 8 (Research Article)
Received on 28 December 2022; received in revised form, 26 March 2023; accepted 30 May 2023; published 01 August 2023
IN-SILICO SCREENING OF POTENTIAL PHYTOCOMPOUNDS AGAINST
STAPHYLOCOCCUS AUREUS AND AN IN-VITRO ANTIBACTERIAL EVALUATION
Vidya and Sathish Kumar *
Department of Biotechnology, Kongunadu Arts and Science College, Coimbatore - 641029, Tamil Nadu,
India.
ABSTRACT: Staphylococcus aureusis a Gram-positive facultative pathogenic
bacterium responsible for a wide range of infections ranging from skin to life-
threatening infections. Antibiotic resistance of Staphylococcus aureus is an emerging
global concern. Thus, developing viable antibiotics are in high demand. This study
identified novel lead compounds from traditionally used medicinal plants via in-
silico molecular docking and in-vitro antibacterial analysis. Thus, we have derived
literature-evident phytocompounds from numerous traditional medicinal plants such
as Boerhavia diffusa, Clerodendrum infortunatum, Sida rhombifolia, Tephrosia
purpurea, Scoparia dulcis, Breynia retusa, Euphorbia heterophylla, Hemigraphis
alternata, Hedyotis corymbose, Imperata cylindrica and their structures were
retrieved from PubChem. Lipinski’s rule in ADMET (Absorption, Distribution,
Metabolism, Excretion and Toxicity) profiles were used to screen derived
phytocompounds, followed by in-silico docking to the target protein. Clumping
factor A (ClfA)-fibrinogen, a key virulence factor in S. aureus, was taken as a target
protein. ClfA is a cell-wall-anchored protein that causes bacterial adherence to the
blood plasma protein fibrinogen, which causes a variety of infections. Thus, an
appealing strategy is to discover a novel lead compound with antiadhesive properties
to prevent cell adherence. After performing molecular docking, Eupalitin 3-o-
galactoside, a natural compound derived from Boerhavia diffusa, exhibited strong
binding affinity with the least glide score of -8.56 kcal/mol. Antibacterial
investigations were carried out using different solvent extractions of plants with
phytocompounds that exhibited a significant glide score. Leaf extract of Boerhavia
diffusa, Clerodendrum infortunatum and Sida rhombifolia shows the strongest
activity against Staphylococcus aureus.
INTRODUCTION: Staphylococcus aureus is a
Gram-positive spherical bacterium belonging to the
Staphylococcaceae family. It is one of the most
harmful bacteria, causing diseases ranging from
minor skin infections like folliculitis and impetigo
to life-threatening infections including bloodstream
infection, endocarditis, and pneumonia 1.
QUICK RESPONSE CODE
DOI:
10.13040/IJPSR.0975-8232.14(8).4128-41
This article can be accessed online on
www.ijpsr.com
DOI link: http://doi.org/10.13040/IJPSR.0975-8232.14(8).4128-41
S. aureus can create a broad spectrum of virulence
factors connected to the cell wall and play a major
role in invading microbes into the host tissue. It can
also release exotoxins, which promote
staphylococcal infections. The adherence of
bacteria to host extracellular matrix proteins such
as fibrinogen, fibronectin, and collagen triggers the
molecular pathogenesis of infections 2.
Antibiotics have been used to treat bacterial
illnesses since the early 20th century. Antibiotic
exploitation is assumed to be responsible for
antibiotic-resistant strains' widespread growth.
Most bacteria are now resistant to multiple
treatments, making this scenario difficult to treat.
Keywords:
Staphylococcus aureus, Antibiotic
resistance, Multidrug Resistance,
ClfA-Fibrinogen, Phytocompounds,
ADME, Molecular docking,
Antibacterial
Correspondence to Author:
Dr. R. Sathishkumar
Assistant professor,
Department of Biotechnology,
Kongunadu Arts and Science College,
Coimbatore - 641029, Tamil Nadu,
India.
E-mail: rsathishkumar_bt@kongunaducollege.ac.in

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4129
Multidrug-resistant bacteria cause a massive range
of bacterial diseases, with Staphylococcus aureus
being one of the most threatening MDR strains.
The emergence of resistant strains poses a
persistent hazard to human health, which is now a
serious challenge 3. To combat multidrug resistance
strain, a variety of techniques have been
implemented. Currently, antibiotics such as
ceftaroloine, ceftobiprole, co-trimoxazole,
cephalosporin, dalfopristin, tedizolid and linezolid
are available but they are not employed in clinical
procedures because of their high cost and safety
concerns 4; therefore, there is a compelling need for
the development of novel drugs. The conventional
drug development method is complex and time-
consuming so computer-assisted docking can be
utilized to find new lead molecules. Molecular
docking is a time-saving method for docking a
large number of molecules to a target protein 5.
In the current scenario, virtual screening is
employed to develop an efficient therapeutic
compound in which structure-based virtual
screening will be carried out where screening is
based on receptor structure 6. In this study plant,
phytocompounds were used as ligands since plants
produce a vast range of secondary metabolites with
diverse pharmaceutical properties like
antimicrobial, anti-fungal, anti-inflammatory, and
antitumor activity and are mostly preferred due to
their fewer no side effects 7. Developing drugs
from herbal plant samples would be cost-effective
and biocompatible 8.
And as target protein ClfA- fibrinogen was utilized.
Clumping factor A (ClfA) is a cell adhesion protein
anchored to the surface of Staphylococcus aureus
that allows bacteria to adhere to fibrinogen in host
tissue, thus it is known to be a fibrinogen binding
protein. Fibrinogen is a glycoprotein found in the
blood that consists of a polypeptide chain (2α, 2β
and 2γ chains) 9. A- region of ClfA binds to
fibrinogen by interacting C-terminal of two γ-
chains of fibrinogen. ClfA protects S. aureus
against macrophage phagocytosis, as a result,
bacteria become more virulent 10.
Therefore, we have considered ClfA- fibrinogen as
a potential target protein and phytocompounds
from medicinal plants such as Boerhavia diffusa,
Clerodendrum infortunatum and Sida rhombifolia,
Scoparia dulcis, Breynia retusa, Euphorbia
heterophylla, Hemigraphis alternata, Imperata
cylindrica, Hedyotis corymbosa and Tephrosia
purpurea were used as ligand. Boerhavia diffusais
a well-known Ayurvedic plant and the aerial part of
B. diffusa are reported to have notable antioxidant
and antibacterial activity 11. The entire plant,
including the roots, leaves, and stem of
Clerodendrum infortunatum, exhibits a variety of
biological functions. According to studies, leaf
extracts of C. infortunatum poses significant
antibacterial and antifungal activities than root and
stem 12. Similarly, the aerial part of Sida
rhombifolia is rich source of phytoconstituents and
is known to have antibacterial properties 13.
Therefore, the current study focuses on in-silico
analyses to determine the phytocompound with
the best binding efficiency against the target
protein and in-vitro antibacterial screening was
used to determine the plant extract with optimum
antibacterial activity against Staphylococcus
aureus.
METHODS:
In-silico Studies: Molecular docking is an efficient
and expanding method for developing prospective
lead drugs. Molecular docking involves various
computational procedures, including preparing
receptors and ligands, docking and post-docking
analyses, etc. 14. The computational software
maestro Schrodinger version 9.0.211 was utilized
for ADME profiling, LigPrep, Protein preparation,
Glide grid generation, and G scoring function.
Structure Retrieval: This study aimed to evaluate
the antibacterial activity of phytocompounds from
different natural plants. After conducting a
literature survey, GC-MS identified 125
phytocompounds from 10 different plants
considered ligands. The PubChem database
(http://pubchem.ncbi.nlm.nih.gov) was used to
derive the chemical structures of phytocompounds
15. The three-dimensional structure of the protein to
be targeted, ClfA- Fibrinogen was retrieved from
the PDB- Protein Data Bank database
(http://www.rcsb.org/pdb). The target protein's
active site region was determined using the LigSite
online tool
(http://projrct.biotec.tudresden.de/pocket/), which
predicts the amino acids with binding pockets 16.

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4130
ADME Profiling of Phytocompounds: To assess
the drug-likeness of particular ligands, the ADME
properties, which include Absorption, Distribution,
Metabolism, Excretion, and Toxicity of
phytocompound were analyzed. The Schrodinger
program's QikProp module version 4.4 was used to
predict the ADME properties including,
the number of rotatable bonds, molecular weight,
number of donor hydrogen bonds, number of
acceptor hydrogen bonds and octanal water
partition coefficient logP, etc as per Lipinski rule of
five 17 and the Pass online way2drug online tool
(http://way2drug.com/PassOnline/predict.php)was
used to further analyze the biological properties of
the ligand 18.
Ligand and Receptor Preparation: Before
molecular docking, ligands were prepared using the
LigPrep module, optimized by bond ordering and
angles. In contrast, GLIDE's Protein preparation
wizard was used to prepare proteins. In which
water molecules were removed from the structure
for preparation, hydrogen bonds were optimized
and energy was minimized, further structure-based
virtual screening was performed 19.
Molecular Docking: Identification of new
therapeutic compounds is a critical step in the in-
silico investigation and is accomplished through
molecular docking, where structure-based virtual
screening was performed for each screened
phytocompound against ClfA-Fibrinogen. The
glide module of the Schrodinger program was used
to simulate receptor-ligand interaction and binding
affinities.
Effective ligands against the target protein will be
identified due to molecular docking based on the
least glide score value and by the formation of
hydrogen bonds and hydrophobic interactions 20.
The PyMol visualization tool was further used to
see the hydrogen bond interaction between the
ligand and the target protein, where the interaction
between the amino acid residues and the hydrogen
bonds with bond length can be evaluated 21.
In-vitro Studies:
Sample Collection and Authentication: The three
different plant species Boerhavia diffusa,
Clerodendrum infortunatum and Sida rhombifolia
were chosen for in-vitro antibacterial screening
among the remaining ten plants as a result of in-
silico studies. Those plants were harvested within
the Kanyakumari district of Tamil Nadu and the
Botanical Survey of India (BSI) in Coimbatore,
Tamil Nadu, identified those plants as Boerhavia
diffusa (BSI/SRC/5/23/2022/Tech/520),
Clerodendrum infortunatum
(BSI/SRC/5/23/2022/Tech/518) and Sida
rhombifolia (BSI/SRC/5/23/2022/Tech/519).
Sample Preparation: Leaves, stem, root and
flowers of Boerhavia diffusa, Clerodendrum
infortunatum and Sida rhombifolia were washed,
dried and crushed into fine powder. 50 grams of
powdered samples were subjected to Soxhlet
extraction using hexane, ethyl acetate and methanol
at 40°C for roughly 6-8 hours 22. After extraction
excess solvents were evaporated using rotary
evaporator under lower pressure. Final extracts
were collected and kept for future use in an airtight
container.
Anti-Bacterial Screening: The Agar well
diffusion method was used to determine the
antibacterial activity of various extracts 23.
Staphylococcus aureus culture was purchased from
MTCC (MTCC-96). 100 µl of bacterial culture
were swabbed into MHA plates, followed by 6 mm
wells that were created using a sterile cork borer.
50 µl of crude extract from each sample and 50 µl
of neomycin sulphate as a positive control were
introduced to the wells. Organic solvents hexane,
ethyl acetate, and methanol were used as the
negative control. Plates were further kept for
overnight incubation at 37 °C.
After the incubation period, the sensitivity of the
test plates was assessed using a zone of inhibition,
with the diameter of the zone surrounding the well
determined in millimeters.
RESULT:
Structure Retrieval and Active Site Prediction:
3D Structure of the target protein ClfA-Fibrinogen
was retrieved from Protein Data Bank with a PDB
ID of 2VR3 (Fig. 1), and its active site pockets
ASN 525, ILE 384, GLU 526, ALA 528 was
discovered via the LigSite online tool.

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4131
FIG. 1: 3D STRUCTURE OF TARGET PROTEIN 2VR3
ADME Screening Using QIKPROP Module:
The bioavailability of selected phytocompounds
was predicted using ADME profiling, which is a
crucial step in the discovery of potential lead
compounds. Out of 125 phytocompounds, only 24
compounds satisfy the Lipinski rule of five and are
considered to be drug-likeness. Parameters like
lipophilicity, permeability in octanol/ water
partition coefficient and brain/ blood barrier along
with these, properties like Number of rotatable
bonds, Number of metabolic reactions, Molecular
weight, Hydrogen bond donor, Hydrogen bond
acceptor and Skin permeability were evaluated.
The compounds that satisfied the Lipinski rule of
five were tabulated in Table 1 and the
pharmacological properties of ADME-cleared
compounds were validated using PASSonline
Way2Drugand are reported in Table 2.
TABLE 1: ANALYSIS OF ADME PROPERTIES FOR THE PLANT COMPOUNDS USING QIKPROP
Molecule Name
No. of
rotatable
bonds
Molecular
weight
Dipole
moment
SASA
Donor
Hydrogen
bonds
Acceptor
Hydrogen
bonds
QPlogP for
Octanol/gas
Normal Range
0-15
130.0-725.0
1.0-12.5
300.0-1000.0
0.0-6.0
2.0-20.0
8.0-35.0
3,4-Dihydroxy-benzyl
alcohol
7
356.683
2.689
618.238
3
3.2
17.553
4-(2-methoxy phenyl)
piperidine
1
191.272
2.518
440.293
1
2.25
9.851
5-Benzyloxypyrimidine-
2-carboxylic acid
4
230.223
9.473
475.807
1
4.75
13.762
Acacetin
3
284.268
6.881
517.54
1
3.75
13.963
Apigenin
3
270.241
6.07
537.139
2
3.75
13.963
Benzofuran 2,3, dihydro
2
199.224
7.011
385.618
2
5.25
12.53
Boeravinone B
3
312.278
4.885
516.43
2
5.45
16.195
Caffeic acid
5
180.16
7.175
392.531
3
3.5
12.706
Desulphosingrin
11
279.307
6.977
491.931
5
11.2
20.811
Ellagic acid
4
302.197
4.916
446.65
4
8
18.761
Epicatechin
5
290.272
2.921
509.455
5
5.45
19.681
Eupalitin 3-O-
galactoside
11
492.435
8.321
695.424
5
13.75
29.318
Ferulic acid
5
194.187
6.295
420.153
2
3.5
11.367
Furon-2-ylmethanol
3
216.279
2.385
455.662
1
2.2
10.219
Gallic acid monohydrate
4
170.121
5.716
342.782
4
4.25
13.283
Kaempferol
4
286.24
5.622
501.402
3
4.5
16.695
Malic acid
7
350.633
2.463
633.865
0
4.85
14.129
Purpurin
3
256.214
3.14
445.607
1
4.25
12.061
Quercetin
5
302.24
3.533
512.235
4
5.25
18.32
Semiglabrin
1
392.407
8.159
572.912
0
6
17.46
Succinic acid
5
262.452
3.975
587.602
0
4
11.448
Ursolic acid
2
456.707
6.246
694.702
2
3.7
21.246
Vasicinol
2
204.228
5.644
422.555
2
3.95
12.316
Vasicinone
1
202.212
1.481
412.623
1
5.7
11.374
Molecule Name
QPlog
P
Water
/Gas
QPlogP
Octanol
/Water
QPlog BB
for brain
/Blood
No. of
Metabolic
reactions
QPlogKp
for
skin
permeability
Human
Oral
absorpti
on
Rule
of
Five
Rule
of
Three
Normal Range
4.0-
45.0
-2.0-6.5
-3.0-1.2
1.0-8.0
-8.0 to -1.0
1,2 (or)3
L, M, H
Max
4
Max
3

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4132
TABLE 2: 2D STRUCTURE OF ADME CLEARED PHYTOCOMPOUNDS WITH PHARMACOLOGICAL
PREDICTION
S. no.
Phytocompound with PubChem ID
2D structure
Pass prediction
1
3'4-dihydroxy-benzyl alcohol
(101663520)
2
4-(2-methoxy phenyl) piperidine
3
5- Benzyloxypyrimidine (561874)
4
Acacetin (5280442)
3,4-Dihydroxy-benzyl
alcohol
17.553
7.834
-0.519
3
-2.169
3
0
0
4-(2-methoxy phenyl)
piperidine
9.851
5.453
0.656
3
-3.498
3
0
0
5-Benzyloxypyrimidine-2-
carboxylic acid
13.762
9.154
-1.033
4
-2.84
3
0
0
Acacetin
13.963
8.351
-0.976
3
-3.002
3
0
0
Apigenin
13.963
8.351
-0.976
3
-3.002
3
0
0
Benzofuran 2,3, dihydro
12.53
10.124
-0.679
1
-3.441
3
0
0
Boeravinone B
16.195
11.412
-1.073
3
-3.386
3
0
0
Caffeic acid
12.706
9.871
-1.569
2
-4.524
2
0
1
Desulphosingrin
20.811
18.74
-2.122
6
-4.733
2
0
0
Ellagic acid
18.761
16.688
-2.333
4
-6.753
2
0
1
Epicatechin
19.681
15.562
-1.845
7
-4.686
2
0
1
Eupalitin 3-O-galactoside
29.318
22.69
-2.488
8
-4.47
1
2
1
Ferulic acid
11.367
1.378
-1.189
2
-3.697
2
0
0
Furon-2-ylmethanol
10.219
3.179
0.087
5
-1.206
5
0
0
Gallic acid monohydrate
13.283
-0.567
-1.669
3
-5.486
3
0
1
Kaempferol
16.695
1.06
-1.803
4
-4.533
4
0
0
Malic acid
14.129
4.506
-0.182
2
-1.51
2
0
0
Purpurin
12.061
1.025
-1.39
3
-4.32
3
0
0
Quercetin
18.32
0.387
-2.309
5
-5.422
5
0
1
Semiglabrin
17.46
3.368
-0.144
1
-1.889
1
0
0
Succinic acid
11.448
3.446
-0.332
2
-2.15
2
0
0
Ursolic acid
21.246
6.142
-0.455
3
-3.152
3
1
1
Vasicinol
12.316
1.187
-0.559
3
-3.045
3
0
0
Vasicinone
11.374
0.646
-0.413
1
-2.833
1
0
0

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4133
5
Apigenin (5280443)
6
Benzofuran 2,3 dihydro (20209882)
7
Boeravinone B (14018348)
8
Caffeic acid (689043)
9
Desulphosinigrin (9601716)
10
Ellagic acid (5281855)
11
Epicatechin (72276)
12
Eupalitin 3-O- galactoside
(44259727)

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4134
13
Ferulic acid (445858)
14
Furon- 2yl methanol (49962474)
15
Gallic acid monohydrate (24721416)
16
Kaempferol (5280863)
17
Malic acid (522155)
18
Purpurin (6683)
19
Quercetin (5280343)
20
Semiglabrin (156341)

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4135
21
Succinic acid (520988)
22
Ursolic acid (64945)
23
Vasicinol (442934)
24
Vasicinone (442935)
Molecular Docking Studies: Molecular docking
investigation predicts the interaction of bioactive
compounds against the target protein in
Staphylococcus aureus. Molecular docking was
carried out using the Glide module of maestro
Schrodingerr software.
The docking result interprets the active site and
binding efficiency of phytocompounds against the
target protein 2VR3. Phytoconstituents from
Boerhavia diffusa, Clerodendrum infortunatum and
Sida rhombifolia were found to be potential lead
compounds against 2VR3.
Each phytocompounds were allowed to dock with
the target protein and the binding efficiency that is
the formation of hydrogen bonds was visualized
using the PyMol visualization tool. The bioactive
compound Eupalitin 3-O- galactoside showed
efficient binding interaction against the target
protein with theleast Glide score is -8.56 Kcal/mol
and the residues interacted were GLN 253 (O-H),
GLN 253 (H-O), GLN 253 (H-O), HIS 252 (H-O),
GLU 526 (H-O), GLU 526 (O-H), ASN 525 (O-H),
ARG 506 (O-H) and ILE 384 (O-H) and with a
bond length of 2.6Å, 2.0Å, 2.5Å, 2.1Å, 1.8Å, 1.8Å,
1.9Å and 2.3Å, respectively. Additionally, the
compound quercetin and vasicinone from the plants
Clerodendrum infortunatum and Sida rhombifolia
also hada better binding ability with a G. score of -
8.35 and -5.29 Kcal/mol respectively.
Apart from these phytocompounds from other
plants such as Tephrosia purpurea, Scoparia
dulcis, Breynia retusa and Euphorbia
Herterophylla also had significant binding
properties with the target protein. The
phytocompound Ursolic acid from the plant
Boerhavia diffusa has shown poor binding
interaction with the target protein with a G score of
-1.92 Kcal/mol.
The binding interactions with the glide score value
was reported in Table 3. Fig. 2 represents the
binding efficiency of Eupalitin 3-O-galactoside
with the target protein 2VR3. Therefore, the
molecular docking studies reveal that
phytocompounds from Boerhavia diffusa,
Clerodendrum infortunatum and Sida rhombifolia
have significant inhibition against 2VR3 and
further in-vitro antibacterial studies were carried
out to investigate its antibacterial activity.

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4136
TABLE 3: MOLECULAR DOCKING OF PHYTOCOMPOUNDS AGAINST TARGET PROTEIN CLFA-
FIBRINOGEN
S. no.
Name of the Ligand
(Pubchem ID
Residues Interaction
Bond Length
(Å)
No. of Hydrogen
Bonds
G-Score
(Kcal/mol)
Boerhavia diffusa
1
Eupalitin 3-O- galactoside
(44259727)
GLN 253 (O-H)
GLN 253 (H-O)
HIS 252 (H-O)
GLU 526 (H-O)
GLU 526 (O-H)
ASN 525 (O-H)
ARG 506 (O-H)
ILE 384 (O-H)
2.6
2.0
2.5
2.1
1.8
1.8
1.9
2.3
8
-8.56
2
Kaempferol (5280863)
ASP 385 (H-O)
ILE 384 (O-H)
ILE 384 (H-O)
ASN 525 (O-H)
ASP 340 (H-O)
ILE 339 (O-H)
2.0
2.3
2.0
2.1
1.8
1.8
6
-8.37
3
Gallic acid monohydrate
(24721416)
ILE 384 (H-O)
SER 447 (H-O)
SER 447 (H-O)
HIS 252 (O-H)
1.8
2.1
2.0
2.1
4
-7.53
4
Boeravinone B (14018348)
TRP 523 (O-H)
ASP 524 (H-O)
1.8
1.8
2
-7.14
5
3'4-dihydroxy-benzyl alcohol
(101663520)
GLU 526 (H-O)
ILE 384 (O-H)
2.0
2.2
2
-5.43
6
Ferulic acid (445858)
ALA 528 (H-O)
ILE 389 (O-H)
ILE 389 (O-H)
ASN 525 (H-O)
2.2
2.0
2.4
2.0
4
-5.07
7
Malic acid (522155)
ILE 384 (O-H)
2.1
1
-4.68
8
Succinic acid (520988)
ALA 254 (O-H)
GLU 526 (O-H)
ASN 525 (O-H)
ILE 384 (O-H)
ASN 525 (O-H)
2.2
2.5
2.2
2.2
2.1
5
-4.61
9
Ursolic acid (64945)
ARG 395 (O-H)
2.1
1
-1.92
Clerodendrum infortunatum
10
Quercetin (5280343)
ASN 525 (O-H)
ILE 384 (O-H)
ILE 384 (H-O)
ILE 339 (H-O)
GLY 287 (H-O)
2.1
2.4
2.3
1.9
2.1
5
-8.35
11
Ellagic acid (5281855)
ALA 528 (O-H)
GLU 382 (H-O)
TRP 523 (O-H)
ASP 524 (H-O)
ASN 525 (O-H)
2.8
2.5
2.2
2.0
2.7
5
-7.53
12
Desulphosinigrin (9601716)
PRO 251 (H-O)
ILE 339 (H-O)
ASN 284 (O-H)
HIS 252 (O-H)
ILE 384 (H-O)
1.8
2.2
2.3
2.6
2.1
5
-7.52
13
Acacetin (5280442)
ASN 525 (O-H)
ASN 525 (O-H)
ASN 524 (H-O)
GLU 526 (H-O)
2.2
2.7
2.0
2.0
4
-6.28
14
Apigenin (5280443)
ALA 528 (H-O)
GLU 526 (H-O)
2.7
2.0
5
-5.96

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4137
ASP 524 (H-O)
ASN 525 (O-H)
ASN 525 (O-H)
2.0
2.5
2.7
15
Caffeic acid (689043)
ILE 339 (H-O)
GLY 287 (H-O)
ILE 384 (H-O)
1.9
2.6
1.9
3
-5.77
Sida rhombifolia
16
Vasicinone (442935)
ALA 254 (O-H)
PRO 251 (H-O)
ILE 384 (H-O)
2.2
1.9
3.4
3
-5.29
17
Vasicinol (442934)
ALA 258 (H-O)
ILE 339 (H-O)
2.4
1.9
2
-5.25
Tephrosia purpurea
18
Purpurin (6683)
ILE 384 (H-O)
ILE 339 (H-O)
2.1
2.0
2
-6.92
19
Semiglabrin (156341)
ILE 384 (O-H)
ALA 254 (O-H)
ILE 339 (O-O)
2.4
2.3
2.8
3
-5.86
Scoparia dulcis
20
5- Benzyloxypyrimidine
(561874)
ILE 384 (N-H)
ILE 384 (O-H)
ASN525 (O-H)
ASN 525 (O-H)
2.6
2.2
2.3
2.0
4
-4.84
21
Benzofuran 2,3 dihydro
(20209882
TYR 338 (O-H)
LEU 295 (H-O)
LYS 293 (H-O)
GLY 532 (O-H)
2.2
2.4
2.6
2.3
4
-4.66
Breynia retusa
22
Epicatechin (72276)
ILE 339 (H-O)
PRO 251 (H-O)
GLU 526 (H-O)
GLU 526 (O-H)
TRP 523 (O-H)
2.2
1.9
1.8
1.9
2.5
5
-5.75
Euphorbia Herterophylla
23
Furon- 2yl methanol (49962474)
ASN 525 (O-H)
GLU 526 (O-H)
GLU 526 (H-O)
ASN 525 (O-H)
2.7
2.4
1.9
2.0
4
-5.23
FIG. 2: MOLECULAR INTERACTION OF EUPALITIN 3-O- GALACTOSIDE WITH THE TARGET PROTEIN (A)
AND DOCKED COMPLEX (B). Note: The deep teal color represents the target protein and the deep salmon color indicates
the Eupalitin 3-O-galactoside. Blue dots represent the hydrogen bond interaction of Eupalitin 3-O-galactoside with the active
site region of the target protein.
Antibacterial Screening: As a result of in-silico
studies, we conclude that phytocompounds from
Boerhavia diffusa have shown significant binding
interaction with the target protein, followed by the
plants Clerodendrum infortunatum and Sida
rhombifolia. Thus, the antibacterial activity of these

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4138
pants was performed using the agar well diffusion
method. Fig. 3 depicts the antibacterial activity of
different plant extracts in which crude ethyl acetate
leaf extract of all three plants showed efficient
antibacterial activity. The zone of inhibition was
used to determine the sensitivity of test plates. The
maximum zone of inhibition was 24 mm observed
in ethyl acetate leaf extract of Boerhavia diffusa
and a minimum zone of inhibition was 10 mm
observed for hexane root extract as illustrated in
Table 4. Neomycin sulphate was used as a positive
control and exhibited good antibacterial activity.
Whereas all the negative controls hexane, ethyl
acetate and methanol revealed no activity against
Staphylococcus aureus.
FIG. 3: ANTIBACTERIAL ACTIVITY OF PLANTS EXTRACTS AGAINST STAPHYLOCOCCUS AUREUS. Note:
Agar well diffusion method was used to evaluate the Antibacterial activity of leaf, stem, root, and flower extracts against
Staphylococcus aureus. (a) represents the activity of the plant Clerodendrum infortunatum, followed by Boerhavia diffusa (b),
and Sida rhombifolia (c)
TABLE 4: DIAMETER OF ZONE OF INHIBITION OF DIFFERENT PLANT EXTRACTS AGAINST
STAPHYLOCOCCUS AUREUS
S. no.
Sample (100 µL)
Zone of Inhibition (mm)
Leaf
Stem
Root
Flower
Negative Control
Antibiotic (NS)
1
Boerhavia diffusa
M
18
18
-
18
-
23
EA
24
18
-
18
-
H
20
20
10
18
-
2
Clerodendrum
infortunatum
M
-
-
-
-
-
22
EA
23
-
-
-
-
H
-
-
-
-
-
3
Sida rhombifolia
M
16
17
10
21
-
23
EA
21
17
10
21
-
H
16
17
10
21
-
Note: (M): Methanol, (EA): Ethyl acetate, (H): Hexane, (NS): Neomycin sulphate. For each extract’s average zone of inhibition ,
the diameter was calculated from the triplicates.
DISCUSSION: Antibiotic resistance is a massive
issue. Overuse or abuse of antibiotics leads bacteria
to become more resistant to the inhibitory effects of
antibiotics 24. Every year 700,000 people die due to
diseases caused by multidrug-resistant bacteria 25.
Staphylococcus aureus is one of the multidrug-
resistant bacteria and is resistant to penicillin and
methicillin. The lack of treatment options for
MRSA infections is also a major global concern 26.
Thus, the current research mainly focuses on
developing efficient drug molecules against
Staphylococcus aureus from traditional medicinal
plants. Here we used bioinformatics tools such as
molecular docking to find efficient lead molecules
and further validation was done using in-vitro
antibacterial evaluation. S. aureus infections are
usually caused by the adhesion of multiple surface-
anchored virulence proteins, which interact with
the host tissue 27. Studies have revealed that ClfA is
important in developing staphylococcal infections
28. Additionally, ClfA is responsible for infective
endocarditis, which is initiated by platelet
aggregation in the host 29. It was reported that the
extracellular matrix protein ClfA found in
Staphylococcus aureus protects the bacterium from
phagocytosis, rendering them more virulent 10.
Thus, targeting ClfA could be a promising way to
identify the effective lead molecule. Hence, in this
work, ClfA-Fibrinogen is considered the target
protein. The literature identified that

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4139
phytocompounds from different plants were
considered ligands since phytochemicals have a
wide range of biological activities 30. These
bioactive compounds were evaluated for ADME
characteristics, and their drug-likeness was
determined using the Lipinski rule of five (RO5) 31.
This study used structure-based virtual screening to
estimate phytocompound interaction and binding
affinities with the target protein by which efficient
drug molecules will be identified based on scoring
function and glide energy 32.
As a result of docking studies, phytocompounds
from the plants Boerhavia diffusa, Clerodendrum
infortunatum, and Sida rhombifolia have shown
excellent glide scores. And all these three plants are
known for their biological properties. Docking
studies revealed that the compound eupalitin 3-O-
galactoside from the plant Boerhavia diffusa had
remarkable binding interaction with the target
protein. A study reported that the Boerhavia diffusa
contains phytoconstituents with a wide range of
therapeutic benefits, including antioxidant and
anticancer properties. Methanolic extracts are
found to have strong antioxidant activity 33.
According to reports, it was revealed that roots and
aerial parts of B. diffusa contain methylated
eupalitin in both free and glycoside forms 34.
It has anti-inflammatory and immunosuppressive
properties as a consequence of the high content of
polyphenols in it. Additionally, Eupalitin was
found to have improved cancer chemopreventive
properties. it induces ROS levels which leads to
apoptosis in prostate cancer 35. In-silico studies
have revealed that the anti-inflammatory compound
eupalitin-3-O-galactoside has a dual effect on
cancer, one by inhibiting the target protein aldose
reductase enzyme (ALR2) and other by suppressing
cancer-mediating pathways 36. This suggests that
eupalitin 3-O- galactoside can be used to develop
efficient drug molecule against S. aureus. To
confirm the in-silico studies we have evaluated
invitro antibacterial activity of Boerhavia diffusa
along with the other two plants whose bioactive
compounds also showed efficient interaction with
the target protein. In a study, various solvents were
used to conduct an antibacterial study on the roots,
stems and leaves of B. diffusa. where There was no
indication of antibiotic resistance in the aqueous or
chloroform extracts. The root extract shows a
maximum level of inhibition. At 200 µg of extract
concentration, the greatest inhibition of bacterial
growth was discovered with a zone of roughly 8
mm37. In this study, crude ethyl acetate leaf extract
showed significant activity with a maximum zone
of inhibition of 24mm, followed by stem and
flower extract.
Another study observed that a low polar ethanolic
extract of B. diffusa had a higher concentration of
phytochemicals than an aqueous extract. Since,
phytocompounds are more soluble in less polar
solvents. In addition, leaf extracts of B. diffusa
were found to have effective antibacterial efficacy
against S. aureus38. This supports our outcome that
the mid-polar solvent, ethyl acetate leaf extract of
B. diffusa has efficient antibacterial activity.
Ethanolic and chloroform extracts of
Clerodendrum infortunatum were studied to have
efficient inhibitory efficacy against S. aureus when
compared to the common drugs tetracycline and
fluconazole 39. Similarly, in our study, when
compared to the standard antibiotic neomycin
sulphate, the ethyl acetate leaf extract of C.
infortunatum demonstrated effective inhibitory
activity against S. aureus.
A study reported that the ethyl acetate and
chloroform extracts had the strongest antibacterial
activity against S. aureus, whereas the petroleum
ether extract had the weakest. Furthermore, their
findings indicate active compounds in plant
extracts are more likely to be found in mid-polar
solvents 40. Likewise, in our study, when compared
to other solvent extracts, the mid-polar ethyl acetate
leaf extract demonstrated significant inhibition,
thereby validating our result. Studies shows that,
aerial part of Sida rhombifolia has been effective
against a wide range of gram-positive and gram-
negative bacteria41. Altogether, the in-silico
molecular docking studies demonstrated the
binding interaction of phytocompound against the
target protein. From findings, it was identified that
the bioactive compound eupalitin 3-O- galactoside
can be usedto develop potential inhibitors against S,
aureus by targeting ClfA- Fibrinogen protein. From
in-vitro antibacterial studies, it was found that the
leaf extracts of all three plants Boerhavia diffusa,
Clerodendrum infortunatum and Sida rhombifolia
have shown efficient antibacterial activity against
the growth of Staphylococcus aureus.

Vidya and Kumar, IJPSR, 2023; Vol. 14(8): 4128-4141. E-ISSN: 0975-8232; P-ISSN: 2320-5148
International Journal of Pharmaceutical Sciences and Research 4140
CONCLUSION: The present study clearly
indicates that phytocompounds from the plants
Boerhavia diffusa, Clerodendrum infortunatum,
and Sida rhombifolia are found to be potential
inhibitors of the ClfA-fibrinogen protein. The
phytocompound Eupalitin 3-O- galactoside from
Boerhavia diffusa effectively binds to target protein
2VR3 with a least G score of -8.56 Kcal/mol. Our
in-vitro research revealed that the crude ethyl
acetate extract of Boerhavia diffusa exhibited
significant antibacterial activity with a zone of
inhibition of 24mm. Future studies will concentrate
on the molecular dynamic study to understand the
stability and structural behaviour of the identified
compound. Further exploration into concentration-
based antibacterial analyses and their mode of
action on Staphylococcus aureus needs to be done.
Declarations:
Ethics Approval and Consent to Participate:
This article does not contain any authors' studies
involving animals and human participants.
Consent for Publications: Not applicable
Availability of Data and Materials: The Data
used and/or analyzed in the present study will be
available from the corresponding author upon
reasonable request.
Funding: No funding was received for conducting
this study.
Author Contribution: Vidya S. L- Performed the
in-silico and in-vitro studies and drafted the
manuscript. R. Sathishkumar- Designed the study,
edited the manuscript and guided throughout the
study. The final manuscript was read and approved
by all authors
ACKNOWLEDGMENT: The authors are grateful
to the Kongunadu Arts and Science College
administration for supplying all software required
to complete this project.
CONFLICTS OF INTEREST: The authors
declared that they have no competing interest in the
studies.
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How to cite this article:
Vidya SL and Kumar R: In-silico screening of potential phytocompounds against Staphylococcus aureus and an in-vitro antibacterial
evaluation. Int J Pharm Sci & Res 2023; 14(8): 4128-41. doi: 10.13040/IJPSR.0975-8232.14(8).4128-41.