ISSN: 2455-944X Int. J. Curr. Res. Biol. Med. (2020).

5(1): 1-9

INTERNATIONAL JOURNAL OF CURRENT RESEARCH IN

BIOLOGY AND MEDICINE
ISSN: 2455-944X
www.darshanpublishers.com
Volume 5, Issue 1 - 2020
Original Research Article
DOI: http://dx.doi.org/10.22192/ijcrbm.2020.05.01.001

In-Silico Evaluation of Anti-Viral Potential of Siddha herbal

Formulation Moringa oleifera (Murungai) against 3-CLpro
Enzyme target in the treatment of SARS Co-V-2 (COVID-19)

M. K. Sathesh Kumar*1, P. Sharmila2, P. Jayapriya3, T. Lakshmikantham4,

R. Meenakumari5
1&2
P.G Scholar, Department of Maruthuvam, National Institute of Siddha, Tambaram Sanatorium,
Chennai-6000047, Tamil Nadu, India
3
P.G Scholar, Department of Kuzhandai Maruthuvam, National Institute of Siddha, Tambaram Sanatorium,
Chennai-6000047,Tamil Nadu, India
4
Head of the Department, Department of Maruthuvam, National Institute of Siddha Tambaram Sanatorium,
Chennai-6000 047,Tamil Nadu, India.
5
Director, Professor and Head of the Department, Department of Gunapadam, National Institute of Siddha,
Chennai- 6000047, Tamil Nadu, India.
Corresponding Address: M. K. Sathesh Kumar, P.G. Scholar, Department of Maruthuvam,
National Institute of Siddha, Tambaram Sanatorium, Chennai 6000 047, Tamil Nadu, India.

Abstract
Infections becomes a regular part of the human life, as it is hypothesizes that ever since from the birth humans are constantly
exposed to the wide spectrum of microbial infestation. One such recent infectious paradigm caused by severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) is novel corona virus disease (COVID-19). Due to limitation prevails in availing the
allopathic drugs there is a constant drive for the researchers to strive for alternate therapeutic strategy for controlling the
pandemic spread of COVID-19. Herbs like Moringa oleifera traditionally used for treating various diseases and disorders since
centuries. The main aim of the present investigation is to explore the anti-viral potential of the phytocomponents such as
Ascorbic acid, Moringine, Beta-Sitosterol, Nicotinic acid, Zeatin, Alpha tocopherol, Quercetin, Chlorogenic acid and Kaemferol
present in the herb Moringa oleifera against the enzyme target 3-chymotrypsin-like protease (3CLpro)by using AutoDock
prediction. Results of molecular docking analysis strongly suggested that out of nine phyto components leads such as Beta-
Sitosterol, Zeatin, Alpha tocopherol, Quercetin and Chlorogenic acid present in the herb Moringa oleifera revels significant
binding against the target protein 3CLpro thereby it was concluded that these compounds may exerts promising inhibiting against
3CLpro enzyme and hereby halt the formation of 16 non-structural proteins (nsp1-nsp16) that are highly essential for viral
replication and there by prevents the viral survival in the host environment.

Keywords: COVID-19, SARS-CoV-2, 3CLpro, Moringa oleifera, Phytocomponents, Docking

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1. Introduction binding affinity predictive tool [10]. Virtual screening

is nowadays a method of choice to search large
Coronaviruses infect the upper gastrointestinal and databases of compounds and to select compounds for
respiratory tract of the mammals (including humans) in vitro testing. Virtual screening approaches can be
and the birds. These viruses cause many diseases in divided into ligand-based and structure-based. When
animals and human beings but we are limited in this the 3D structure of a target is known from
article with SARS-CoV-2, leading to COVID-19 experimental or computational studies, high-
disease. The whole clinical picture of COVID-19 is throughput docking is a method of choice. The
not completely known. The occurrence of the illness alternative method is pharmacophore-based virtual
ranged from mild to severe. SARS-CoV-2 propagate screening.
through RNA replication using RNA-dependent RNA
polymerases enzyme. This virus can mutate slowly, 2. Materials and Methods
posing a challenge for its treatment and control. The
symptoms of COVID-19 may arise within 2 to 14 days 2.1. Protein-ligand docking
after the infection [1].
Computational molecular investigation was performed
The 3CLpro cleaves the polyprotein at 11 distinct sites using Auto Dock version 4 which predicts interaction
to generate various non-structural proteins that are binding affinity between selected therapeutic lead with
important for viral replication [2]. 3CLpro plays a that of the protein target COVID-19 main protease (3-
critical role in the replication of virus particles and chymotrypsin-like protease (3CL pro)) -PDB- 6LU7.
unlike structural/accessory protein-encoding genes, it
is located at the 3′ end which exhibits excessive 2.2. Protein preparation
variability. Therefore, it is a potential target for anti-
coronaviruses inhibitors screening [3]. Structure-based Three dimensional (3D) structure of COVID-19 main
activity analyses and high-throughput studies have protease (3-chymotrypsin-like protease 3CL pro with
identified potential inhibitors for SARS-CoV and protein data bank (PDB)-6LU7 (Figure 1) retrieved
MERS-CoV 3CLpro [4]. from Research Collaboratory for Structural
Bioinformatics (RCSB) [11].
In the past few decades, natural products have been an
important source of potential drug hits and leads [5]. 2.3. Ligand model preparation
However, development efforts in NP drug discovery
have demonstrated a certain downturn in recent years Structures of the phyto components such as
[6]. Despite this decline, the vast chemical space of Moringine, Beta-Sitosterol, Nicotinic acid, Zeatin,
natural products continues to provide abundant Alpha tocopherol, Quercetin, Chlorogenic acid and
structural diversity for discovering novel lead Kaemferol subjected to docking investigation were
compounds with low molecular weight. Less than 10% outlined using ChemDraw sketch software and
of the world’s biodiversity has been explored to find converted from two dimension (2D) to3D structures.
potential biologically active compounds [7] Figure 2 summarizing 2D and 3D structure of
approved ligand subjected to molecular docking
Herbs like Moringa oleifera traditionally used for the Investigation against COVID-19 main protease (3-
management of infective and degenerative disorders. chymotrypsin-like protease 3CL pro with protein data
This unique herb posses several structurally versatile bank (PDB)-6LU7.
components like Moringine, Beta-Sitosterol, Nicotinic
acid, Zeatin, Alpha tocopherol, Quercetin, 2.4. Docking simulations
Chlorogenicacid and Kaemferol. Each of these leads is
already well explored for its efficacy against several Molecular docking analysis were performed using
diseases and disorders. licensed version of Auto Dock 4, which predicts
interactions between FDA approved drug molecules
Molecular docking is frequently used in the process of with that of the selected protein target (Novel
computer aided drug design (CADD). It can be applied coronavirus 3-chymotrypsin-like protease (3CL pro).
in different stages of the drug design process in order 3D structure of main protease that is 3- chymotrypsin-
to predict the binding mode of already known ligands like protease (3CL pro) with protein data bank (PDB)-
[8]; identify novel and potent ligands [9] and as a 6LU7 retrieved from Research Collaboratory for
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Structural Bioinformatics (RCSB). 3D componential 3. Results

structure of lead molecules and protein were docked
using AutoDock analytical tool version 4. Docking Docking score implicates the binding affinity between
simulations were performed using the programmed the lead and target higher the negativity in the value
algorithm inbuilt with pre automation in the software. that showcase the level of potency of the drug.
Initial position, orientation, and torsions of the ligand Development and advancement in the field of
molecules were set randomly. All rotatable torsions computational analysis increased the precision level in
were released during docking. Each docking identifying the potential drug molecule and deriving
experiment was derived from 2 different runs that its mechanism of action at target site. Selective
were set to terminate after a maximum of 250000 alterations in the functional groups greatly minimize
energy evaluations. The population size was set to the non-specific binding and impedes the adverse
150. During the search, a translational step of 0.2 Å, event at clinical level. Total of 9 bioactive lead
and quaternion and torsion steps of 5 were applied compounds were retrieved from the herb Moringa
[12],[13]. oleifera. Out of nine compounds’ the lead molecules
such as Beta-Sitosterol and Zeatin has maximum of 6
interactions with the core active amino acid residues
present on the target. Followed by this the compounds
such as Alpha tocopherol, Quercetin and Chlorogenic
acid ranked second and with the maximum of 5 and 4
interactions with the active site of the target enzyme
3CLpro.Interaction analysis represented in Figure 3
and 4, Data’s were tabulated in Table 2 and 3.

Figure 1: 3D crystalline structure of the target protein COVID-19 main protease (3-chymotrypsin-like protease
(3CL pro) – PDB 6LU7

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Figure 2: 2D and 3D Structure of Selected Ligands

Table 1: Ligand Properties of the Compounds Selected for Docking Analysis

Molar weight Molecular H Bond H Bond Rotatable

Compound
g/mol Formula Donor Acceptor bonds

Ascorbic acid
176.12 g/mol C6H8O6 4 6 2
Moringine 311.36 g/mol C14H17NO5S 3 7 4
Beta-Sitosterol 414.7g/mol C29H50O 1 1 6
Nicotinic acid 123.11 g/mol C6H5NO2 1 3 1
Zeatin 219.24 g/mola C10H13N5O 3 5 4
Alpha tocopherol 472.7 g/mol C31H52O3 0 3 14
Quercetin 302.23 g/mol C15H10O7 5 7 1
Chlorogenic acid 354.31 g/mol 6 9 5
C16H18O9
Kaemferol 286.24 g/mol 4 6 1
C15H10O6

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Table 2: Summary of the molecular docking studies of compounds against COVID-19 main protease (3-
chymotrypsin-like protease (3CL pro) – PDB 6LU7

Binding Free Inhibition Electrostatic Total

Intermolecular
Compounds energy constant Ki µM energy Interaction
energy Kcal/mol
Kcal/mol (*mM)(**nM) Kcal/mol Surface
Ascorbic acid
-4.56 456.88 -0.10 -3.52 427.78

Moringine -5.26 138.91 -1.74 -5.89 328.99

Beta-Sitosterol -9.53 103.78** -0.05 -10.89 940.19
Nicotinic acid -3.74 1.83* -0.02 -4.03 311.39
Zeatin -5.70 66.31 -0.01 -5.13 574.30
Alpha tocopherol -9.11 208.38** -0.21 -11.63 917.63
Quercetin -6.80 10.38 -0.17 -6.85 611.20
Chlorogenic acid -6.61 14.37 -0.08 -7.90 741.79
Kaemferol -7.29 4.54 -0.11 -7.67 603.66

Table 3: Amino acid Residue Interaction of Lead against COVID-19 main protease (3-chymotrypsin-like
protease (3CL pro) – PDB 6LU7

Molecule Interactions Amino Acid Residue- Binding

Ascorbic 142 144 145 163 165 189
acid 3 ASN SER CYS HIS MET GLN
140 141 142 163 166 172
Moringine 3 PHE LEU ASN HIS GLU HIS
Beta- 27 142 144 145 165 166 168 189
Sitosterol 6 LEU 41HIS ASN SER CYS MET GLU PRO GLN
Nicotinic 140 142 144 145 163 166
acid 3 PHE ASN SER CYS HIS GLU
41 140 141 144 145 163 165 166 172 189
Zeatin 6 HIS PHE LEU SER CYS HIS MET GLU HIS GLN
Alpha 41 59 54 140 144 145 163 165 166 189
tocopherol 5 HIS MET TYR PHE SER CYS HIS MET GLU GLN
140 144 145 163 165 166 189 192
Quercetin 5 PHE SER CYS HIS MET GLU GLN GLN
Chlorogenic 49 142 145 163 165 168 189 192
acid 4 MET ASN CYS HIS MET PRO GLN GLN
41 49 54 165 168 189 192
Kaemferol 2 HIS MET TYR MET PRO GLN GLN

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Figure 3: Representing best docking pose of lead molecules against COVID-19 main protease (3-chymotrypsin-like
protease (3CL pro)) -PDB- 6LU7

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Figure 4: Representing interaction analysis plot of FDA approved lead molecules against COVID-19 main protease
(3-chymotrypsin-like protease (3CL pro)) -PDB- 6LU7

4. Discussion human history in terms of substances related to herbal

medicines, potions, oils, remedies, and foods. Many of
The use of in silico approaches as chemoinformatics, these substances have been discovered by trial and
molecular modeling, and artificial intelligence (AI) error, and through the years they have become
has significantly increased in the last decades [14]. standard products in human lives [15].
Indeed, in silico approaches now enable the virtual
screening of millions of compounds in an affordable Molecular docking consists of three main connected
time, thus reducing the initial costs of hit identification goals: pose prediction, virtual screening and binding
and improving chances of finding the desired drug affinity estimation [16]. A successful docking
candidates. methodology must be able to correctly predict the
native ligand pose within the receptor binding site (i.e.
A natural product (NP) is generally defined as a to find the experimental ligand geometry within a
chemical compound or substance that is produced by certain tolerance limit) and the associated physical–
living organisms. NPs can be classified by many chemical molecular interactions. Furthermore, when
criteria and characteristics, such as source, biological investigating large compound libraries, the method
function, biosynthetic pathway, physical and chemical must be able to successfully distinguish binding from
properties, etc. Nowadays, NPs find a broad spectrum non-binding molecules and to correctly rank these
of applications related to human life, including an ligands among the best compounds in the database
important role in medicine. Notably, the use of natural [17].
products as medicines has been described throughout

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How to cite this article:

M. K. Sathesh Kumar, P. Sharmila, P. Jayapriya, T. Lakshmikantham, R. Meenakumari. (2020). In-Silico
Evaluation of Anti-Viral Potential of Siddha herbal Formulation Moringa oleifera (Murungai) against 3-
CLpro Enzyme target in the treatment of SARS Co-V-2 (COVID-19). Int. J. Curr. Res. Biol. Med. 5(1): 1-9.
DOI: http://dx.doi.org/10.22192/ijcrbm.2020.05.01.001