Antiviral screening of
Clerodol derivatives as COV 2 main protease inhibitor in Novel Corona
Virus Disease: In silico approaches
Sindhu. T. J*, Arathi. K. N,
Akhilesh K. J, Anju. Jose, Binsiya K. P, Blessy Thomas, Elizabeth Wilson
Department of Pharmaceutical
Chemistry, Sanjo College of Pharmaceutical Studies, Vellapara, Palakkad.
*Corresponding Author E-mail: sindhutj81@gmail.com
ABSTRACT:
Plant based medicines are
gaining much importance nowadays because of some drawbacks that are associated
with the use of modern medicines. Discovery of new therapeutics is a very
challenging, expensive and time consuming process. With the number of approved
drugs declining steadily combined with increasing costs, a rational approach is
needed to facilitate, expedite and streamline the drug discovery process. In
this regard In silico identification for potential hits has become a
popular approach in computer-aided drug discovery. Here we consider molecular
docking approach in the development of novel antiviral inhibitors for COVID 19.
COV- 2 main protease contain a non-structural protein (PDB ID: 6LU7)
which serve as the potential targets for the studies. Terpenoids can inhibit
the COVID-19 main protease that present in the Corona virus which is an
essential viral enzyme. The COVID-19 main protease of the Corona
virus species is one of the attractive targets in corona associated
diseases. By considering the above observations, an attempt for
molecular docking studies of terpenoids present in Clerodendrum paniculatum
with COVID-19 main protease (PDB ID: 6LU7) by using in silico studies by
molinspiration online tool and evaluated for their antiviral activity. Clerodol
is an important triterpenoid present in Clerodendrum paniculatum leaves
act as a potential inhibitor. Clerodol showed binding energy -5.74 kcal/mol.
Pyrrole derivative of clerodol have highest binding energy -7.4 Kcal/mol. But
all derivatives of Clerodol have binding energies more than the standard. The
compounds showed good activity against Corona virus comparable to that
of standard drug baricitinib. Thus, Clerodendrum paniculatum leaves
appears to be an effective material for development of antiviral drugs against
corona. So that it may serve as a reference for further studies
KEYWORDS: Clerodendrum
paniculatum, Antiviral activity, COV- 2 main protease, COVID-19, Molecular
docking.
INTRODUCTION:
Pandemic
of coronavirus disease 2019 (COVID-19), which is caused by severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global concern for
public health with thousands of fatalities. Plants contain the rich source
of natural products like vitamins, minerals and other immune- modulators used
for human welfare specially to cure disease caused by pathogenic
microorganisms. Clerodendrum paniculatum (Pagoda flower, Krishna
Kireedam) is one of them. Considerable utilisation and progress have been
achieved regarding its biological activities1. Clerodendrum is
a very large and diverse genus and till now five hundred and eighty species of
the genus have been identified and are widely distributed in Asia, Australia,
Africa and America. The whole parts of the plants are used in microbial
infection. Leaf extract is used as antimicrobial, anthelmintic, analgesic,
anticonvulsant, antidiabetic agent and also to increase haemoglobin level in
the blood. Clerodolone, clerodone, clerodol are different isolated compounds
obtained from this plant.2 Slightly warm leaves applied with edible
oil on the painful part of human body gives considerable relief within twelve
hours3.
Morphology:
Shrub about 5-10 ft tall. Bark
grayish brown. Stem and branches hollow, slightly pubescent, obtusely quadrangular,
nodes annulate, slightly hairy. Leaves opposite, larger at the base gradually
becoming smaller towards the apex, ovate-cordate to ovate-suborbicular,
palmately lobed, 4-40 x 3-36cm across, base auriculate or subrotund, margins
lobed or dentate serrate with glands along margins, apex shallow acuminate or
acute, membranous or coriaceous, dark green slightly pubescent above, slightly
paler sub-glabrous with numerous glands beneath, lateral veins 3-7 on either
side of the midrib, veins impressed above and densely pubescent and prominent
beneath, petiole canaliculated, stout, slightly pubescent, about 8-36 cm long.
Inflorescence terminal panicle, 10-40 cm long, wider in the base, peduncle
slightly pubescent, about 1-2 cm long, bracts leaf-like, ovate, apex acute,
bractlets linear. Flowers bisexual, numerous, pedicels filiform 5-15 cm long,
calyx campanulate, 5 toothed, deeply divided nearly to the base, oblong
lanceolate, apex acute, reddish orange, corolla hypocrateriform, 5 lobed, lobes
oblong or obovate, apex acute, pubescent outside, reddish orange, about 0.7 cm
long, corolla tube slender, curvate, glabrous or very slightly hairy outside
about 3mm long, stamens 4 didynamous, exserted, filaments slender, about 2-3 cm
long, reddish, anthers oblong about 2mm long, ovary bicarpellary, ovoid or
globose, 4 lobed, 4 loculed, about 0.2 cm across, style filiform, purple,
stigma shortly 2-fid. Fruit drupaceous, globose, about 1cm in diameter with 4
pyrenes, fleshy, purplish black when ripe, fruiting calyx persistant.4-7
Phytochemical Aspects:
The leaves of the plant
contain saponin, alkyl sterols, some enzymes, and 2, -(3, 4-dehydroxyphenyl)
ethanol1-O-α-2 rhamnopyranosyl (1→3)-β-D-(4-O-caffeoyl)
glycolpyranoside (acetoside)8,9 and a triterpenoid Clerodol. It was also found that the
leaves contain a fixed oil which consists of glycerides of lenoleic, oleic,
stearic and lignoceric acid10.
Figure
No :1Clerodendrum paniculatum
Drug discovery and development11,12:
Drug discovery and development
is an intense, interdisciplinary and endeavour, when a compound is under taken
for discovery. It involves synthesis, characterisation, screening and
evaluation for therapeutic efficiency. A number of researches have been performed
to identify and isolate biologically active compounds from different species of
Clerodendrum. Research report revealed that steroids, terpenoids and flavonoids
are major among them. The aim of the present study was to evaluate, the
antiviral activity by performing molecular docking studies of the chemical
constituents clerodol and its derivatives.
The important chemical
compound clerodol and its derivatives is depicted in Figure No:2and 3.
Figure No:2 Chemical structure
of clerodol
Molecular docking studies:
In the field of molecular
modelling, docking is a method which predicts the orientation of one molecule
to a second when bound to each other to form a stable complex. Preferred
orientation helps to predict the strength of association or binding affinity
between two molecules. The associations with biological molecules such as
proteins, nucleic acids, carbohydrates and lipids play an important role in
signal transduction.13.
Figure No:3 Chemical structure
of clerodol and its derivatives
Molecular
docking is one of the most frequently used methods in structure-based drug
design, due to its ability to predict the binding-conformation of small
molecule ligands to the appropriate target binding site. Characterisation of
the binding behaviour plays an important role in rational design of drugs as
well as to elucidate fundamental biochemical processes. Terpenoids can
inhibit the COVID-19 main protease that present in the Corona virus which
is an essential viral enzyme. By considering the above observations, an attempt
is made here to molecular docking studies of triterpinoids present in Clerodendrum
paniculatum with COVID-19 main protease (PDB ID: 6LU7) by using in
silico studies by molinspiration online tool and evaluated for their antiviral
activity14 - 18.
MATERIALS AND METHODS:
IN-SILICO METHODS:
Softwares and databases used
· AutoDock 4.2
combines
Ø AutodockTools1.5.4
Ø Python Molecule viewer1.5.4
Ø Vision 1.5.4
· Python 2.5
· Accelrys discovery
studio viewer
· Pre ADMET software
· Molinspiration
server
· RCSB protein data
bank
· Online SMILES
translator
All the in-silico
experiments are carried out at Sanjo College of Pharmaceutical Studies,
vellapara, palakkad.
The leads selected were
substituted with various substituents and they were optimized for the
pharmacokinetic parameters by evaluating. The in-vivo absorption
capabilities of the designed molecules were assessed by the means of Lipinski’s
rule of five using molinspiration server.
Docking studies for the lead
molecules:
After the lead has been
optimized, the protein was subjected to docking studies using Auto Dock 4.2 for
evaluating the binding interactions.
Enzyme and ligand preparation:
The X-ray crystal structure of
the enzyme COVID-19 main protease of Corona virus (PDB entry: 6LU7) was
obtained from Protein Data Bank19.
Selection of COV- 2 main
protease From PDB: COVID-19 main protease Corona virus PDB
accession code is 6LU7 Resolution is 2.16
Å Chain A, Sequence Length 306.
Selection of COV- 2 main
protease From PDB: COVID-19 main protease Corona virus PDB
accession code is 6LU7 Resolution is 2.16
Å Chain A, Sequence Length 306. 20-22
Figure No: 4 Corona virus
Figure No: 5 COVID-19 main
protease
RESULTS AND DISCUSSION:
Table No: 1 Drug likeness
scores using molinspiration server.
|
Sl. No |
Compound Code |
mLogP |
MW |
No. of H acceptors |
No. of H donors |
No. of violations |
|
01 |
Clerodol |
8.29 |
426.73 |
1 |
1 |
1 |
|
02 |
Triazole derivative of clerodol |
7.37 |
479.75 |
4 |
1 |
1 |
|
03 |
Pyrimidine derivative of clerodol |
7.44 |
490.78 |
3 |
1 |
1 |
|
04 |
Pyrrole derivative of clerodol |
8.56 |
491.80 |
2 |
2 |
1 |
|
05 |
Pyrazole derivative of clerodol |
7.38 |
478.76 |
3 |
1 |
1 |
|
07 |
Triazine derivative of clerodol |
7.49 |
493.78 |
4 |
1 |
1 |
|
08 |
Baricitinib(std) |
-0.24 |
371.43 |
9 |
1 |
0 |
Table No: 2 Binding energies of
clerodol and its derivatives with COVID-19 main protease
|
Sl. No |
Chemical constituents |
Binding energy (∆G =Kcal/mol) |
No of hydrogen bonds |
|
01 |
Clerodol |
-5.74 |
1 |
|
02 |
Triazole derivative of clerodol |
-7.54 |
- |
|
03 |
Pyrimidine derivative of clerodol |
-7.51 |
- |
|
04 |
Pyrrole derivative of clerodol |
-7.4 |
2 |
|
05 |
Pyrazole derivative of clerodol |
-7.1 |
1 |
|
07 |
Triazine derivative of clerodol |
-6.79 |
- |
|
08 |
Baricitinib(std) |
-6.62 |
- |
Figure No:6 Snapshots and
binding interactions of baricitinib with COVID-19 main protease (Binding
Energy= -6.62 Kcal/mol)
Figure No:7 Snapshots and
binding interactions of Clerodol with COVID-19 main protease (Binding
Energy= -5.74 Kcal/mol)
Figure No:8 Snapshots and
binding interactions of Triazole derivative of clerodol with COVID-19 main
protease (Binding Energy= -7.54 Kcal/mol)
Figure No:9 Snapshots and
binding interactions of Pyrimidine derivative of clerodol with COVID-19 main
protease (Binding Energy= -7.51Kcal/mol)
Figure No:10 Snapshots and
binding interactions of Pyrrole derivative of clerodol with COVID-19 main
protease (Binding Energy= -7.4Kcal/mol)
Figure No:11 Snapshots and
binding interactions of Pyrazole derivative of clerodol with COVID-19 main
protease (Binding Energy= -7.1 Kcal/mol)
Figure No:12 Snapshots and
binding interactions of Triazine derivative of clerodol with COVID-19 main
protease (Binding Energy= -6.79Kcal/mol)
Docking studies:
The results of docking of COVID-19
main protease with chemical constituent clerodol and its derivatives are
reported below. The best docked structure should have the binding energy higher
than that of the standard. The binding sites were represented in the snap shots
and the binding energy was compared with the standard ligand, baricitinib
(-6.62Kcal/mol).The chemical constituent clerodol showed binding energy -5.74
kcal/mol. Pyrrole derivative of clerodol have highest binding energy -7.4
Kcal/mol. But all derivatives of Clerodol have binding energies more than the
standard. The results are mentioned in the table (table No:2) followed by the
snapshots (figure No:4 -12).
CONCLUSION:
Computer aided drug design
helps to minimise the tedious drug discovery process over the traditional
method. In silico ADME study and drug likeness score of the ligands observed
helped to predict a better pharmacokinetic activity and oral bioavailability of
the designed leads. The binding energies obtained from docking study of
COVID-19 main protease confirms that the lead compound inhibit the enzymes
present in Corona virus. Thus the present study depicts that the utilization of
computer aided drug design is an efficient tool in predicting the effectiveness
of a series of compounds under study and thus can result in the design of
potent antiviral agent. Although CADD is an efficient tool in determining the
efficiency of chemical moieties, Isolation of these constituents and its
derivatives may leads us to discover novel medicinal compounds to inhibit
Corona virus. In this study, pyrrole derivative of clerodol have highest
binding energy -7.4 Kcal/mol and two hydrogen bonds. With this point of view
the present article aims at focusing the attention of research scholars on the
unexplored and untouched areas related with Clerodendrum paniculatum.
ACKNOWLEDGEMENT:
The authors are thankful to
Management, Principal and Staff, Sanjo College of Pharmaceutical Studies,
Vellapara, for providing necessary facilities and support to carry out this
work.
REFERENCES:
4. Flora of Tamil Nadu, VOL. II, 1987
5. Hafiz I and Jansen
SR: Antioxidant and Anti-Inflammatory Activity of Pagoda Leaves (Clerodendrum
paniculatum) Ethanolic Extract in White Male Rats (Rattus novergicus).
International Journal of PharmTech Research 2016 9.
6. JOSEPH AJ: In
vitro and in vivo Antiinflammatory Activity of Clerodendrum
paniculatum Leaves. Indian Journal of Pharmaceutical Sciences 2013.
7. Ito R et al.:
Molecular Epidemiological Characteristics of Klebsiella pneumoniae
Associated with Bacteremia among Patients with Pneumonia. Journal of clinical
microbiology 2015 53: 879-86.
8. Leena PN, Aleykutty
NA. Pharmacognostic, Phytochemical studies on the root of Clerodendrum
infortunatum Linn Root. Int J Res Ion Pharm Chem 2013 3(2):182-7.
9. Prof. Ramarao
Nadenda, medicinal chemistry, 2nd edition, pharma med press publications, page
no:50-52, 204
10. Bhaskar das, A review on
biological activities and medicinal properties of clerodendrum infortunatum
Linn, International Journal of Pharmacy and Pharmaceutical Sciences, 2014, Vol
6, Issue 10, 41-43.
11. Prajapati ND, Purohit SS,
Sharma AK, Kumar TA. A Handbook of Medicinal Plants. 1st ed. New Delhi: CRC
Press 2001. p. 154.
12. Khatri N. Studies on
antinociceptive, anti-inflammatory and diuretic activity of methanolic extract
of the aerial part of Cleodendrum infortunatum. J Pharm Sci 2005 5(1-2):63-6.
13. Kapoor LD. Handbook of
Ayurvedic Medicinal Plants.1st ed. New Delhi: CRC Press 2001. p. 124-5.
14. John. M. Beale Jr., John H.
Block, Wilson and Gisvold’s, Textbook of organic and medicinal and
Pharmaceutical chemistry, 12th edition, Pg no. 25, 215.
Jagadeesan ArunkumarSwaminathan Rajarajan
16. Study on
Antiviral Activities, Drug-Likeness and Molecular Docking of Bioactive
Compounds of Punica Granatum L. To Herpes Simplex Virus - 2 (HSV-2), Microb
Pathog, May 2018, 118, 301-309
17. Virupakshaiah
DBM, Chandrakanth Kelmani, Rachanagouda Patil, and Prasad Hegade,
"Computer Aided
18. Docking
Studies on Antiviral Drugs for SARS", World Academy of Science, Engg. and
Tech., 2007, 3
19. http://www.rcsb.pdb.org .
20. Faegheh Farhadi, Antibacterial
activity of flavonoid s and their structure–activityrelationship: An update
review, Phytotherapy Research. 2019 33:13–40
21. Berry
M, Fielding BC, Gamieldien J. Potential Broad Spectrum Inhibitors of the
Coronavirus 3CLpro: A Virtual Screening and Structure-Based Drug Design Study. Viruses.
2015 7(12):6642-60. doi: 10.3390/v7122963. [PubMed: 26694449].
22. Zhao
Q, Weber E, Yang H. Drug targets for rational design against emerging
coronaviruses. Infect Disord Drug Targets. 2013 13(2):116-27. [PubMed:
23895136].
Received on 20.03.2020
Modified on 08.04.2020
Accepted on 19.04.2020 ©Asian Pharma Press All Right Reserved
Asian J. Pharm.
Tech. 2020; 10(2):60-64.
DOI: 10.5958/2231-5713.2020.00012.4