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HIGH-THROUGHPUT SCREENING AND DYNAMIC STUDIES OF SELECTED

COMPOUNDS AGAINST SARS-COV-2

Article in International Journal of Applied Pharmaceutics · January 2022

DOI: 10.22159/ijap.2022v14i1.43105

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 International Journal of Applied Pharmaceutics

ISSN- 0975-7058 Vol 14, Issue 1, 2022

Original Article
HIGH-THROUGHPUT SCREENING AND DYNAMIC STUDIES OF SELECTED COMPOUNDS
AGAINST SARS-COV-2

RATUL BHOWMIK1, RANAJIT NATH2, SAMEER SHARMA3*, RATNA ROY4, RIYA BISWAS5
1Medicinal Chemistry and Molecular Modelling Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education a nd
Research, Jamia Hamdard, New Delhi, India, 2Department of Pharmaceutics, NSHM Knowledge Campus, Kolkata-Group of Institutions,
Kolkata, West Bengal, India, 3*Department of Bioinformatics, BioNome Private Limited, Bengaluru, India, 4Department of Pharmacology,
NSHM Knowledge Campus, Kolkata Group of Institutions, Kolkata, West Bengal, India, 5Department of Pharmaceutical Technology,
Jadavpur University, Kolkata, West Bengal, India
Email: sameer21.97@gmail.com
Received: 11 Sep 2021, Revised and Accepted: 19 Oct 2021
ABSTRACT
Objective: This study was aimed to analyze the inhibitory effect of the drugs used in nanocarrier as well as nanoparticles formulation based drug
delivery system selected from PubChem database literature against 3CLpro (3C-like protease) receptor of SARS-CoV-2 (severe acute respiratory
syndrome coronavirus 2) by implementing several in silico analysis techniques.
Methods: This paper detailed a molecular docking-based virtual screening of 5240 compounds previously utilized in nanoparticle and nanocarrier
drug delivery systems utilizing AutoDock Vina software on 3CL protease to discover potential inhibitors using a molecular docking technique.
Results: According to the results of the screening, the top two compounds, PubChem Id 58823276 and PubChem Id 60838 exhibited a high affinity
for the 3CL protease binding region. Their binding affinities were-9.6 and-8.5 kJ/mol, indicating that they were tightly bound to the target receptor,
respectively. These results outperformed those obtained using the co-crystallized native ligand, which exhibited a binding affinity of-7.4 kJ/mol.
PubChem Id 60838, the main hit compound in terms of both binding affinity and ADMET analysis, displayed subst antial deformability after MD
simulation. As a result of the VS and molecular docking techniques, novel 3CL protease inhibitors from the PubChem database were discovered
using the Lipinski rule of five and functional molecular contacts with the target protein, as evidenced by the findings of this work.
Conclusion: The findings suggest that the compounds discovered may represent attractive opportunities for the development of COVID -19 3CLpro
inhibitors and that they need further evaluation and investigation.
Keywords: Molecular docking, Phytocompounds, Dynamic simulation, Drug discovery
© 2022 The Authors. Published by Innovare Academic Sciences Pvt Ltd. This is an open-access article under the CC BY license (https://creativecommons.org/licenses/by/4.0/)
DOI: https://dx.doi.org/10.22159/ijap.2022v14i1.43105. Journal homepage: https://innovareacademics.in/journals/index.php/ijap

INTRODUCTION for regulating numerous major activities of the virus and contains a
highly retained catalytic domain from the SARS virus, is the second
According to scientific discovery, COVID-19 may have three phases. in silico docking model. Several of its functions include virus
Certain medications are probably more effective when used replication, making it a good approach for pharmaceutical research.
independently of the other phases. The three stages are the viral A database of identified bioactive chemicals was tested against the
early infection stage, the pulmonary stage, and the hyper- SARS-CoV-2 3CL protease inhibitors' catalytic region [4].
inflammation stage. The world is currently experiencing a COVID-19
pandemic (caused by SARS-CoV-2) for which no effective antiviral When it comes to medication activity, molecular recognition is
drugs or immunizations have been developed. There are currently regarded as the most important factor. The phrase "drug action"
no target-specific drugs available for SARS-CoV-2, hence strategies refers to the pharmacological activity displayed by drug molecules
such as repurposing existing treatments are being investigated when binding to the targeted protein and creating a stable protein-
rapidly [1]. As COVID-19 therapies, the drugs lopinavir and ritonavir, ligand complex. SBVS, also known as structure-based virtual
as well as chloroquine phosphate (commonly known as Aralen), screening, aims to exploit and explore the molecular recognition
arbidol, remdesivir, and dexamethasone (also known as Decadron), between the target protein and the chosen ligand molecules to select
have all been given. The virus contains four non-structural proteins: specific molecules that show good binding affinity with the active
papain-like (PLpro) and 3-chymotrypsin-like (3CLpro) proteases, sites of the targeted biological receptor allowing 3D structures to be
RNA polymerase, and helicase. Both proteases (PLpro and 3CLpro) inferred. The docking approach is based on identifying the optimal
are involved in the transcription and replication stages of the virus. conformation or pose of the ligand with the receptor's specific active
Because it is most closely related to viral replication, the 3CLpro region. The dock score binding affinity indicates the binding
type is regarded as the most important of the four types [2]. The relationship between the ligand molecules and the targeted protein.
primary protease 3CLpro of COVID19 exhibits 96 percent structural Based on calculated binding interactions, docking scores may also be
similarities to the SARS-CoV protease, according to a study. The used to predict the biological activity of ligand molecules. VS is a
3CLpro enzyme is the major enzyme required for the proteolysis computational method that is frequently used to evaluate
process. It destroys the viral polyprotein, separating it into prospective drug candidates in a computer-simulated environment.
functional components that can be used independently. Because of In the area of novel drug discovery, virtual screening-based drug
its crucial function in the virus life cycle, 3CLpro is an excellent discovery is acknowledged as an effective strategy. It's being used to
target for the development of effective antiviral medications against identify unique or prospective leads for more optimization and
a range of Coronaviruses [3]. advancement as alternatives to therapeutically accessible medicines
As there is a crystal structure for the SARS-CoV-2 3CL Protease at by identifying various molecular scaffolds that work on a target
the present, we used molecular docking to bind the virus using the protein of interest [5]. From the previous decads, various types of
SARS 3CL protease (PDB: 7dpv) as a Protein. 7-O-methyl- drugs frequently used in nanoparticles, as well as nanocarrier drug
dihydromyricetin, on the other hand, has a covalent interaction with delivery systems, were identified for performing virtual screening
the SARS-CoV-2 3CL Protease. The 3CL protease, which is important methodology. The purpose of this study was to use a target-based
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Int J App Pharm, Vol 14, Issue 1, 2022, 251-260

virtual screening approach to identify potential COVID-19 3CL ADMET analysis

protease inhibitors amongst compounds previously used in
nanoparticle and nanocarrier drug delivery systems from the The initially screened ligands obtained with the help of dock scores were
PubChem database, accompanied by a molecular docking process to then subjected to ADMET analysis. SwissADME and Pre-ADMET web
determine novel inhibitors that could be used as potential leads for servers were used to predict drug-likeness and ADMET properties of our
treating coronavirus-related infections. ligand molecules [11, 12]. Lipinski’s rule was used to check whether the
initially screened ligand molecules were suitable for docking. Ligand
MATERIALS AND METHODS violating any two rules of Lipinski’s was considered unsuitable for
further screening. Other than Lipinski’s rule, physicochemical analysis, as
Computer environment well as Drug-likeliness properties of all the ligand molecules, were also
VSDK (Virtual Screening by Docking) may be done and executed on taken into consideration for the drug screening process. The toxicity
any version of Microsoft Windows or the LINUX platform. A high- study was examined with the help of the Pre-ADMET webserver. When it
speed computer machine with multiple operating systems was utilized comes to PAINS (for pan assay interference compounds, which are also
to do virtual screening (windows, Linux). It also had a Java known as frequent hitters or promiscuous compounds), these are
environment, a strong internet connection, and a stable power supply. molecules with substructures that exhibit a potent reaction in assays
regardless of the protein target while also appearing to give selective and
Collection of dataset and preparation of ligand library optimizable hits. The most frequent PAINS are easily distinguished by
the way they are constructed. Bioactivity screening was carried out using
An intensive literature review was used to choose various types of drugs molinspiration software [13].
frequently used in nanoparticles, as well as nanocarrier drug delivery
systems from the PubChem database [6]. The structures of all the Boiled-egg analysis
identified compounds were downloaded in SDF format. Using the python
script, prepare ligand4. py, the substructures were then translated to For predicting blood-brain barrier permeability as well as
pdbqt format. These structures were utilized to build a virtual library gastrointestinal absorption of our selected phytochemicals, BOILED
that would later be used for molecular docking and ADMET evaluation. EGG was used. According to BOILED-Egg plot analysis, compounds
found in the yellow region were considered to be having higher
Selection and preparation of receptor blood-brain barrier permeability, whereas compounds found in the
white region of the plot were considered to be having higher
The chosen receptor molecule SARS-CoV-2 3CL protease (PDB-Id: 7dpv)
gastrointestinal absorption properties [14]. The BOILED-Egg plot
was downloaded in PDB format from the protein data bank database [7].
analysis was performed using the SwissADME web server [15].
After that, the protein molecule was imported into the AutoDock Tools
program. To begin, the co-crystallized ligand was extracted to verify the Molecular dynamics simulations
protein. Following that, the protein was prepared by removing water
molecules, eliminating unnecessary chains or heteroatoms, mending The molecule with the best binding affinity along with satisfactory
missing atoms, adding hydrogen atoms, computing charges (Kollman ADMET properties was further subjected to a molecular dynamics
charges), and lastly, converting it to pdbqt format. simulation study. Molecular Dynamics Simulation is a computer-
based simulation approach used to analyze the physical motions of
Preparation of grid site atoms or molecules. MD simulations can identify a few critical
hydrogen bond interactions. MD simulations assist in protein
After the preparation of protein, a grid box was generated with the co-
docking and virtual screening advances. The iMODS server was
crystallized ligand in the middle. During the docking process, AutoDock
utilized in this work to simulate molecular dynamics. The iMODS
4.2 was used; the center grid parameters were set to 23.2636, 18.7239,
and 14.9490 for the x-, y-, and z-axes, in that order, and the Dimensions service aids in the exploration of normal mode analysis and
parameters were set to 22.9145, 27.3923, and 30.4039 for the x-, y-, and generates accessible information about routes that may involve
z-axes in angstrom, in that order, with a spacing of 0.375 and located at macromolecules or homologous structures.
the center of the active site. The grid box dimensions were stored as For the hit chemical receptor complex, molecular dynamics simulations
config. txt files for docking with Autodock Vina. The generated protein were also run using the Desmond program. Individually, the complex
pdbqt file was used to extract the co-crystallized ligand. was solvated in an explicit water box of size 10 with a single-point
Virtual screening and molecular docking charge (SPC) water model TIP3P with periodic boundary condition
(PBC). The protein and ligand were modeled using the OPLS3e force
The initial stage was to construct a database of tiny molecules by field, and Na and Cl-ions were added to make the total charge of the
selecting a library, removing counter ions, adding hydrogen, resolving system neutral. Following that, the system was energy reduced for 2000
valency issues, protonation at physiological pH, calculating 2D steps before a 50 ns production run. Following minimization, the
characteristics, converting 2D molecules to 3D, and minimizing energy. complex was subjected to run at the NPT ensemble. Using the Nose-
The second stage was to identify our target receptor using NMR or X-ray, Hoover thermostatic algorithm and the Martina-Tobias-Klein approach,
with a resolution value of less than 2 A°. The final step was to locate the the system was gently heated to maintain a temperature of 300 K and
binding location of our desired receptor. The fourth step was to run the pressure. To simulate long-range electrostatic interactions, the Particle-
docking technique to estimate the optimal ligand confirmation at the Mesh Ewald (PME) approach was used with a grid spacing of 0.8. The
selected receptor's binding region. The docking score or binding affinity Desmond package's Simulation Interaction Diagram tool was used to
was utilized to estimate and assess the interaction energy between our investigate the precise interactions between the ligand and protein. The
ligand and the target receptor. The sixth and last stage was to filter the data was examined in terms of protein and ligand RMSD and root mean
docked molecules further based on ADME characteristics. square fluctuation (RMSF).
The AutoDock Vina was used to conduct the virtual screening
RESULTS
process [8]. Protein was converted from pdb to pdbqt, and a Config.
txt file was produced with all the information needed for VS utilizing Molecular docking analysis
ADT; other options were deemed default. The prepared protein was
then docked against our prepared library set of ligands using A total of 5240 compounds were identified from an intense
AutoDock Vina. Perl Script was used for docking of our multiple literature survey from the PubChem database which had been
ligands. The results were displayed in terms of binding affinity. The previously used as drugs in nanoparticle or nanocarrier drug
binding affinity represents the binding energy. The binding energy delivery systems. These compounds were then docked with the
exhibits the extent of binding of the ligand molecule. For each targeted receptor SARS-CoV-2 3CL protease. The native ligand of the
docking experiment, a total of ten independent runs were retrieved receptor SARS-CoV-2 3CL protease was also separately
performed. Each conformation was chosen based on its lowest docked with the receptor to compare the binding affinity of the
binding energy. Furthermore, the best type of configuration would native ligand with the hit compounds. The native ligand was
be the one that would bind with its target. The docking results were observed to exhibit a docking score of-7.4 kJ/mol. Among the 5240
analyzed using Discovery Studio Biovia 2021 [9, 10]. docked compounds,-8.5 kJ/mol was set as a cut-off score to initially

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screen the ligands based on binding affinity. A total of 17 compounds kJ/mol (table 1, table 2). These 17 compounds were further
were screened and identified, which had a docking score of-8.5 subjected to ADME analysis.

Table 1: This table represents the structures, ids, and names of the initially screened 17 compounds

S. No. PubChem Id Structure Name

1 58823276 NH
Benzoporphyrin
NH

2 86280045 N Phthalocyanine
N HN
N N
NH N

3 3663 HO OH
OH Hypericin
HO

O
OH

OH
CH3
H3C O

4 373075 Hydramycin
O
H3C

O O OH

HO
O
HO

5 16678941 NH CH3 Lumacaftor

NO
F
O O
F
O
OH
6 65064 Epigallocatechin Gallate
HO OH

HO

HO O
O
HO OH
O
HO HO

7 5280805 Rutin
OH
HO
OH
HO O OH
OH HO
HO O
O O
O O OH
HO
CH3

8 11676786 N
3-(2-Cyanopropan-2-yl)-N-(4-methyl-3-((3-methyl-
4-oxo-3,4-dihydroquinazolin-6-
H3C CH3
yl)amino)phenyl)benzamide

HN

CH3 O
HN CH3
N

N
9 42890 Idarubicin
O
OH

OH
O CH3
HO
O O

O NH2

H3C OH

10 60838 Irinotecan
N

O N CH3

O
O
N
N

HO
O
CH3

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S. No. PubChem Id Structure Name

11 104903 N N
Tirilazad
O N
N
H3C CH3
N

N
H3C

12 2259 OH
aurintricarboxylic acid
O OH
OH
O

HO OH
O
13 119373 Elacridar
CH3
CH3 O
O

O
N

NH
O
NH O H3C

14 443831 Carminomycin
O
OH

HO
OH
O CH3
HO
O O

O NH2

H3C OH

15 5701999 Hespiridin
HO OH

HO O
O
HO O O CH3
O
HO O HO
O OH
HO CH3

16 57417192 Natamycin
HO
O OH OH

HO O O
HO
O
H2N
O
O
HO O
CH3
CH3

17 90813259 (7-Amino-4-chloronaphthalen-1-yl) 3',6'-

O

O CH3
diacetyloxy-3-oxospiro[2-benzofuran-1,9'-
xanthene]-5-carboxylate
O
O
O
O

H3C O

O NH2
O

Cl

ADME and boiled-egg analysis Compound 3 represents PubChem Id 1167686, Compound 4

represents PubChem Id 60838, Compound 5 represents PubChem Id
The second step of the virtual screening methodology was based on 104903, and Compound 6 represents PubChem Id 119373 (fig. 1).
ADME analysis. The compounds having a docking score of-8.5 kJ/mol
and above were subjected to ADME analysis mainly based on Bioactivity analysis
Lipinski’s rule, GI absorption property, and PAINS analysis.
Compounds not complying with Lipinski’s rules were ruled out. The compounds screened based on ADME analysis were further
subjected to bioactivity screening. The bioactivity screening was
Compounds that have low GI absorption properties as well as
performed on the Molinspiration webserver. The smiles of the
exhibiting alerts in PAINS analysis were also ruled out for further
secondarily screened 6 compounds were load on the Molinspiration
screening. The ADME-based screening helped to identify 6 compounds webserver to check receptor specificity towards GPCR ligand, Ion
from the initially screened 17 compounds (table 2). The initially Channel Modulator, Kinase Inhibitor, Nuclear Receptor Ligand,
screened 6 compounds are Pubchem Ids 58823276, 16678941, Protease Inhibitor, and Enzyme Inhibitor (table 3). The compounds
1167686, 60838, 104903, and 119373. The screened 6 compounds showing specificity towards Enzyme Inhibitor activity were
were also subjected to Boiled-Egg analysis to visualize the intensity of identified. This is because SARS-CoV-2 3CL protease is an enzyme.
GI absorption property. Besides this, the Boiled-Egg plot demonstrated So, to act against it, the hit compounds should have enzyme
that all the screened 6 compounds showed good gastrointestinal inhibitory activity. The bioactivity screening identified 2 hit
retention properties (fig. 1). Compound 1 represents PubChem Id compounds, PubChem Ids 58823276, and 60838 from the previously
58823276, Compound 2 represents PubChem Id 16678941, screened 5 compounds.

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Table 2: Primary screening of the docked compounds based on dock score and ADME analysis. Yellow color highlighted compounds
represent the screened compounds
Pubchem Dock Pains BBB GI P-gp LogS Lipinski's Rule
Id score permeability Absorption substrate
58823276 -9.6 0 alert yes high no -5.48 Yes; 0 violation
86280045 -9.5 0 alert no high yes -7.88 No; 2 violations: MW>500, MLOGP>4.15
3663 -9.1 1 alert: ene_one_D no low no -6.99 No; 2 violations: MW>500, NHorOH>5
373075 -9.1 1 alert: quinone_A no high no -3.22 Yes; 0 violation
16678941 -8.8 0 alert no high yes -5.45 Yes; 0 violation
65064 -8.8 1 alert: catechol_A no low no -3.56 No; 2 violations: NorO>10, NHorOH>5
5280805 -8.7 1 alert: catechol_A no low yes -3.3 No; 3 violations: MW>500, NorO>10,
NHorOH>5
11676786 -8.5 0 alert no high no -5.38 Yes; 0 violation
42890 -8.5 1 alert: quinone_A no low yes -4.1 Yes; 0 violation
60838 -8.5 0 alert no high yes -5.71 Yes; 1 violation: MW>500
104903 -9.6 0 alert yes high yes -7.13 Yes; 1 violation: MW>500
2259 -9.3 0 alert no low no -5.14 Yes; 0 violation
119373 -8.5 0 alert no high no -6.7 Yes; 1 violation: MW>500
443831 -8.5 1 alert: quinone_A no low yes -4.01 No; 3 violations: MW>500, NorO>10,
NHorOH>5
5701999 -8.5 0 alert no low yes -3.28 No; 3 violations: MW>500, NorO>10,
NHorOH>5
57417192 -8.6 0 alert no low no -2.92 No; 3 violations: MW>500, NorO>10,
NHorOH>5
90813259 -9.1 0 alert no low no -7.7 No; 2 violations: MW>500, MLOGP>4.15

Fig. 1: This fig. represents secondarily screened 6 ligand molecules based on ADME properties. The white part of the BOILED-EGG Model
represents the physicochemical space of molecules with the highest probability of being absorbed by the GI (gastrointestinal tract), while
the yellow part represents the physicochemical space of molecules with the highest probability of permeating to the brain

Table 3: Secondary screening of the compounds based on bioactivity. Yellow color highlighted compounds represent the screened
compounds

Pubchem GPCR Ion channel Kinase Nuclear receptor Protease Enzyme

Id ligand modulator inhibitor ligand inhibitor inhibitor
58823276 0.18 0.31 0.39 -0.01 -0.03 0.23
16678941 0.21 -0.23 0.12 0.16 0.1 0.06
11676786 -0.11 -0.23 0.32 -0.35 -0.23 -0.03
60838 0.33 -0.45 -0.1 -0.15 0.02 0.54
104903 0.01 -0.81 -0.71 -0.02 0.03 -0.12
119373 0.03 -0.51 -0.1 -0.41 -0.1 -0.11

Toxicity analysis analysis further subjected to a Molecular Dynamics Simulation Study. Here
The final step of the screening was toxicity prediction. The toxicity compound PubChem Id 60838 showed a better toxicity profile than
prediction was performed on the Pre-ADMET webserver. The compound PubChem Id 58823276. Thus PubChem Id 60838 was
compound with the least toxicity was identified as a hit and was thus identified as the main hit compound.

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Fig. 2: Biovia discovery studio structural analysis of compound pubchem Id 60838 (sky blue) with receptor SARS-CoV-2 3CL Protease
(violet) along with the native ligand (red)

Fig. 3: Biovia discovery studio structural analysis of compound Pubchem Id 58823276 (sky blue) with receptor SARS-CoV-2 3CL Protease
(violet) along with the native ligand (red)

Table 4: Final screening of the compounds based on toxicity. The yellow color highlighted compound represents the final hit compound

PubChem Id 58823276 60838

algae_at 0.0705416 0.00447712
Ames_test mutagen non-mutagen
Carcino_Mouse positive positive
Carcino_Rat positive negative
daphnia_at 0.0529423 0.0110542
hERG_inhibition medium_risk medium_risk
medaka_at 0.00639048 0.000377343
minnow_at 0.0164685 0.00146839
TA100_10RLI positive negative
TA100_NA negative negative
TA1535_10RLI negative negative
TA1535_NA negative negative

Molecular dynamics simulation study receptor SARS-CoV-2 3CLpro was considered for MD simulation.
Normal mode analysis mobility allows us to analyze the large-scale
Pubchem Id 60838 compound was identified as the best hit and was B-factor and mobility as well as the stability of the molecules. The
subjected to molecular dynamics simulation analysis (fig. 4). Here IMOD server exposed the internal coordinate’s analysis depending
the docked complex of the compound Pubchem Id 60838 with on the protein-ligand structural interactions.

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Fig. 4: iMODs normal mode analysis (NMA) of the hit compound PubChem Id 60838 with the targeted receptor

IMODs also measure the B-factor and structural deformity and variances than an individual variance. The elastic network map also
calculate the eigenvalue. Image 1 represents the docked complex of produced satisfactory results.
our protein and ligand. Image 2 of the fig. represents the
deformability graph. The deformity graph illustrated peaks in the For MD Simulation using the Desmond program for our hit compound-
graph, which represent regions in the protein with deformability. receptor complex, the protein RMSD fluctuated between 2-18 ns but
then showed a stable trajectory up to 50 ns. The ligand RMSD exhibited
Image 3 represents the B-Factor graph. The main-chain
fluctuations from 0-12ns but then demonstrated a stable trajectory up to
deformability, also known as the B-Factor, is a measure of a
50 ns (fig. 5). Regarding the Protein RMSF analysis, the highest
molecule's ability to deform at each of its residues. Image 4
fluctuation was observed at 4.2 Å. Overall, the Protein and Ligand RMSF
represents the eigenvalue of the complex. The motion stiffness is
trajectories were found to be stable (fig. 6, fig. 7). Other than these, the
represented by the eigenvalue associated with each normal mode. amino acid interactions of our protein-ligand complex were also
Its value is proportional to the amount of energy required to distort analyzed. The notable hydrogen interactions were observed at PRO52,
the structure. The simpler the deformation, the lower the ARG188. The notable hydrophobic interactions were observed at ARG40,
eigenvalue. Our docked complex demonstrated an eigenvalue of ILE43, TYR54, LEU57, LEU58, HIS80, MET82, ARG188. Water bridges
1.4141084e-04. Image 5 represents the variance plot. The variance were observed in ARG40, ASP48, MET49, ASN51, PRO52, TYR54,
plot demonstrates individual variances in red color, whereas MET82, ASP187, ARG188, GLN199. Among these residues, only TYR54
cumulative variance in green color. Image 6 represents the and HIS80 exhibited strong interactions throughout the entire
covariance map. This map demonstrates the correlation motion simulation process (fig. 8, fig. 9, fig. 10). Other than this, other ligand
between a pair of residues in red color, uncorrelated motion in white properties of the hit compound such as radius of gyration, molecular
color, and anti-correlated motion in blue color. Image 7 represents surface area, intramolecular hydrogen bonds, solvent accessible surface
the elastic map of our docked complex. Each dot in the graph area, and polar surface area were monitored throughout the 50 ns
represents one spring inside the atoms' pair. The dots are colored simulation process (fig. 11). The radius of gyration, molecular surface
dependent on stiffness, with darker grey dots indicating stiffer area, and polar surface area plots of the hit compound demonstrated
springs and lighter grey dots indicating softer springs. From the stable trajectories throughout the entire 50 ns simulation study. The
molecular dynamics study, it was evident that our complex showed a solvent-accessible surface area plot showed slight fluctuations up to 15
good amount of deformability. Furthermore, it also showed a ns but still showed a stable trajectory throughout the rest of the
moderately low eigenvalue, suggesting that it could be deformed simulation process. Furthermore, the intramolecular hydrogen bond plot
easily. The variance map exhibited a higher degree of cumulative of the hit compounds demonstrated zero hydrogen bonds.

Fig. 5: Protein-ligand RMSD plot

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Fig. 6: Protein RMSF plot

Fig. 7: Ligand RMSF plot

Fig. 8: Protein-Ligand contacts plot detailing amino acid interactions concerning interaction fraction

Fig. 9: Ligand-protein contact detailing best prominent amino acid interactions during the simulation process

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Fig. 10: Protein-ligand contacts plot detailing amino acid interactions concerning the time

Fig. 11: Root mean square deviation, radius of gyration, intramolecular hydrogen bonds, molecular surface area, solvent accessible
surface area, polar surface area plots of the hit compound

DISCUSSION and crucial functional features, 3CLpro has been validated as a viable
target for the development of medicines to treat SARS, MARS, and
SARS CoV-2 3CLpro, the main target chosen in this study, is a COVID-19 [16].
multifunctional protein involved in viral RNA transcription and
replication. It also includes proteinases, which are responsible for There are currently no officially recognized or authorized targeted
polyprotein cleavage. By interacting with the 40s ribosomal subunit, treatment agents or medications to treat the viral infection caused
it also suppresses host translation. The 3C like protease (3CLpro) by SARS-CoV-2. Effective treatment techniques are still few, and the
hydrolyzes polyproteins to create functional proteins. It is required current standard of care is supportive care. Antiviral therapeutics
for coronavirus replication and is seen as an important therapeutic that target critical proteins involved in the SARS-CoV life cycle would
target for coronavirus disorders, particularly coronavirus disease be ideal. Antiviral treatments (such as remdesivir, favipiravir, and
2019. (COVID-19). During coronavirus replication, the 3CLpro lopinavir/ritonavir) have been proposed for the treatment of COVID-
cysteine protease hydrolyzes the polyproteins pp1a and pp1b to 19, but their efficacy has not been fully demonstrated, and toxicity
create functional proteins. Because of its highly conserved sequence issues must be examined and handled systematically and

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comprehensively. Small-molecule medications approved for other 2. Jamalipour Soufi G, Iravani S. Potential inhibitors of SARS-CoV-
human diseases may limit the virus-host interaction of novel CoVs, 2: recent advances. J Drug Target. 2021;29(4):349-64. doi:
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officinale (Ginger), Allium sativum (Garlic), and
findings and evaluate the impact of the chemicals on COVID-19 using
Murrayakoenigii (Curry. Zingiber officinale (Ginger), Allium
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ACKNOWLEDGMENT Pharm. 2021;13(5):280-6.
15. Daina A, Zoete V. A BOILED-egg to predict gastrointestinal
We thank BioNome for providing excellent insight regarding absorption and brain penetration of small molecules. Chem
Bioinformatics Skills. Med Chem. 2016;11(11):1117-21. doi: 10.1002/
cmdc.201600182, PMID 27218427.
FUNDING
16. Kwatra B, Roy R, Bhowmik R, Sengupta S. Drug repurposing: in
Nil silico modeling of COVID-19. Res J Life Sci Bioinformatics
Pharm Chem Sci. 2021;7(2):19-40.
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All authors have contributed equally. pathophysiology, drug development and future perspectives of
SARS-CoV-2. Front Cell Dev Biol. 2020;8(1124):580202. doi:
CONFLICT OF INTERESTS 10.3389/fcell.2020.580202, PMID 33240881.
18. Shaji J, Shaikh M. Drug-resistant tuberculosis: recent approach
Declared none in polymer-based nanomedicine. Int J Pharm Pharm Sci.
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