Stilbene Drug Candidate Against Covid - 19

Stilbene – A Natural Drug Candidate against COVID -19.
STILBENE – A NATURAL DRUG CANDIDATE

AGAINST COVID – 19
GUIDED BY: SUBMITTED BY:

PROF SUMARANI.G.O VEENA SEKHAR LAL
ASSISTANT PROFESSOR REG NO: MCT17BT032
DEPARTMENT OF BIOTECHNOLOGY AND

BIOCHEMICAL ENGINEERING
MOHANDAS COLLEGE OF ENGINEERING AND TECHNOLOGY ANAD,

NEDUMANGAD, THIRUVANANTHAPURAM, KERALA
BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 1

A P J ABDUL KALAM TECHNOLOGICAL UNIVERSITY 2020

MOHANDAS COLLEGE OF ENGINEERING AND TECHNOLOGY ANAD,
NEDUMANGAD, THIRUVANANTHAPURAM
DEPARTMENT OF BIOTECHNOLOGY AND BIOCHEMICAL

ENGINEERING
CERTIFICATE
Certified that this is a bonafide report of the seminar work done by
VEENA SEKHAR LAL
during the year 2020 in partial fulfillment of the requirement for the
award of the Degree of Bachelor of Technology in Biotechnology
and Biochemical Engineering by A.P.J Abdul Kalam Technological
University.
PROJECT SUPERVISOR HEAD OF DEPARTMENT
PROF.SUMARANI.G.O DR. SHALINI. A. NAIR
ASSISTANT PROFESSOR PROFESSOR

ACKNOWLEDGEMENT
This seminar would have been incomplete without the support of certain people. I
consider it as my privilege to express my gratitude and respect to all those who guided
and supported me in the completion of this seminar.
First, I would like to thank our Director, Dr. Ashalatha Thampuran and our Principal,
Dr. S. Sheela , MCET, Thiruvananthapuram for the wholehearted support given to me

for my seminar.
I acknowledge Sumarani.G.O, Assistant Professor, Department of Biotechnology and

Biochemical Engineering who guided me and helped me to complete my seminar
successfully.
I am indebted to Dr. Shalini.A.Nair, Professor and Head of Department of

Biotechnology and Biochemical Engineering for her never-ending encouragement.
I express my sincere gratitude to Shiji Jameson, Staff Advisor and Seminar

Cordinator, Department of Biotechnology and Biochemical Engineering for providing
necessary facilities and for her sincere cooperation
I express my profound gratitude to all the teaching staff of Department of

Biotechnology and Biochemical Engineering for their constant guidance and support
Last but not the least I wish to record the moral and emotional support provided by my
parents and friends in completing this seminar
Above all I thank God Almighty for his grace without which it would have been
impossible to complete this work in time.

ABSTRACT
COVID -19 is a devastating global pandemic around the world caused by severe acute
respiratory syndrome coronavirus 2 (SARS- CoV-2). There are no specific treatments for
COVID -19 as yet, though a number are under evaluation, including experimental antivirals.
Quest for new drugs especially from natural plant sources is an area of vast potential. This study
aimed to reprocess stilbenoid analogs against SARS- CoV- 2 spike protein and human ACE2
receptor complex for their affinity and stability using molecular dynamics simulation and
binding free energy analysis based on molecular docking. Compounds were examined for their
affinity using molecular docking, it was observed that fifty nanoseconds molecular dynamic
simulation in aqueous solution revealed highly stable bound conformation of resveratrol to the
viral protein: ACE2 receptor complex. Net free energy of binding using MM-PBSA also
affirmed the stability of the resveratrol-protein complex. Based on the results, Stilbene-based
compounds in general and resveratrol, in particular, can be promising anti-COVID-19 drug
candidates acting through disruption of the spike protein. The findings in this study are
promising and call for further in vitro and in vivo testing of stilbenoid, especially resveratrol
against the COVID-19.
Keywords: Covid-19, Stilbenoid, Molecular dynamics simulation, Molecular docking,
MM- PBSA

TABLE OF CONTENTS
CHAPTER TITLE PAGE NO
1. INTRODUCTION ............................... 7-8
2. LITERATURE REVIEW… ................. 9 - 10
3. MATERIALS AND METHODS….11-13
4. RESULTS AND DISCUSSION ........... 14 - 19
5. CONCLUSION ........................................ 20
6. REFERENCES… .................................... 21 – 24

LIST OF FIGURES
1. FIGURE 1……………….PAGE NO. 7


1. INTRODUCTION
Novel Coronavirus (COVID-19) that emerged in late 2019, is a pandemic that has become a
global challenge and has affected hundreds of thousands of people worldwide. COVID-19
belongs to the beta coronavirus genus. Coronaviruses are the RNA viruses carrying the largest
positive sense genome of 22–26 kilobases (kb) encoding four structural proteins including spike
(S), Nucleocapsid (N), Membrane (M) and Envelop (E). COVID-19 like SARS coronavirus
enters the bronchial epithelial cells through its spike protein using the Angiotensin-Converting
Enzyme – 2 (ACE2) as a receptor on the host cells. However, COVID-19 is a much more
invasive and contagious than SARS with much higher infection and fatality One of the major
reasons for more widespread and abrupt damage caused by COVID-19 is its novelty and high
rate of recombination. Stilbenoids are natural phenolic compounds produced by several plants.
Stilbenoids are categorized as phytoalexins because they are synthesized by the plants in
response to ultraviolet radiation, injuries, or bacterial and fungal toxins. Over the last few years,
stilbene- based compounds have been extensively studied because of their diverse biological
roles in humans. Resveratrol is the most popular and most studied stilbenoid to date. The reason
for this extensive study is the number of biological activities resveratrol carries, such as
antioxidative, antitumoral, antiviral, anti-inflammatory and life span extension. It is abundantly
found in grapes’ skins.
FIGURE 1: SARS – CoV2 STRUCTURE

Other stilbenoids structurally related to resveratrol also carry biological activities. Piceatannol
(trans-30, 40, 3, 5-tetrahydroxystilbene) for example, is a metabolite of resveratrol commonly

found in grapes, berries, rhubarb, and white tea, it is reported to have anticancer and antioxidant
activities. Another dimethyl ether analog of resveratrol is pterostilbene (trans-3, 5-dimethoxy-40
-hydroxystilbene). Pterostilbene possesses many pharmacological similarities with resveratrol
including antiaging, antidiabetic and anti-inflammatory effects. Pinosylvin (3, 5-dihydroxytrans-
stilbene) found in the leaves and woods of several pinus species trees is also a related stilbenoid.
It is known to have effects on many important cellular processes namely apoptosis, cell
proliferation and antioxidant activity. Keeping in view the diverse biological activities,
especially the antimicrobial activity of stilbenoids, the current study aimed to identify the
compounds of stilbene family as potential drug candidates against the coronavirus infections in
the future.
FIGURE 2: STRUCTURE OF STILBENOID

2. LITERATURE REVIEW
At the current time, Coronavirus is becoming very deadly in several countries. Coronavirus
primarily targets the human respiratory system. The Severe Acute Respiratory Syndrome
Coronavirus 2 (SARSCoV-2), previously named as 2019 novel Coronavirus (2019-nCoV), is a
positive-sense, single-strand RNA virus. ‘SARS-CoV E’ protein’ is a short, integral membrane
protein comprised of 76–109 amino acids and its size range from 8.4 to 12 kDa. SARS-CoV-2 is
a (+) SS RNA virus that encodes many structural and non-structural proteins. The Mpro is a non-
structural protein that cuts two replicase polyproteins resulting in matured proteins that are
required to mediate viral replication and transcription. In this way, by inhibition of the Mpro, we
can stop virus replication while inhibition of ACE2 catalytic pocket by small molecules could
change the conformation of ACE2 in such a way that it could block SARS-CoV-2 entry inside
host cells through ACE2.Resveratrol is an antioxidant nutraceutical plant polyphenol which has
been extensively researched for its health benefits. It has been reported that resveratrol acts as a
pro-oxidant in presence of copper 10 which is another widely researched nutraceutical.
Resveratrol can reduce copper (II) to copper (I) thereby generating highly unstable free radicals. .
Resveratrol and pterostilbene showed antiviral activity in African green monkey kidney cells and
in human primary bronchial epithelial cells cultured in an air-liquid interface system.
Mechanistic analyses demonstrated that both compounds actively interfere with the post-entry
steps of virus replication cycle and their antiviral activity is long-lasting. In most cases,
resveratrol was found to directly interfere with viral replication. Next to the direct effect on virus
replication, resveratrol was also reported to exhibit anti-inflammatory and antioxidant properties
thereby having the potential to mitigate virus-induced disease pathogenesis. Computational
Docking is performed to obtain a population of possible orientations and conformations for the
ligand at the binding site using Ligplot+, it is a computer program that generates schematic 2-D
representations of protein-ligand complexes from standard Protein Data Bank file input. The
LIGPLOT is used to generate images for the PDBsum resource that summarizes molecular
structure. Backbone atoms’ free energy for the ‘SARS-CoV2 E’ protein was calculated using the
‘GROMACS 5.1’ from 20 ns to 200 ns with 20 ns interval. Molecular dynamics (MD)
simulations, a computer model of the molecular system is prepared from nuclear magnetic

resonance (NMR), crystallographic, or homology-modeling data. In brief, it contributes forces

arising from interactions between bonded and non-bonded atoms. In order to improve molecular
mechanics Poisson–Boltzmann surface area (MMPBSA) binding free energy calculations for
membrane protein–ligand systems, we can optimize a new heterogeneous dielectric implicit
membrane model, with respect to free energy simulations in explicit membrane and explicit
water, and implemented it into the Amber software suite. Based on these findings, Resveratrol
and its structural analogs might be an advantageous treatment option for SARS-CoV-2 infected
individuals.

3. MATERIALS AND METHODS
3.1 LIGAND STRUCTURE PREPARATION

Four stilbenoids with the strong evidence of biological activities were chosen for this study.
Chemical structures of the stilbenoids were obtained from the chemical database of Chemspider
(Royal Society of Chemistry) (http://www.chemspider.com/). Respective Chemspider IDs of the
compounds are as follows; trans-resveratrol 392875, pterostilbene 4445042, resveratrol 445154,
cis-resveratrol 1265933, Pinosylvin 4444110, Piceatannol 581006. Chem office 2004 was used
to generate two-dimensional structures of selected compounds. The geometry of generated
structures was optimized by using UCSF Chimera 1.14.
3.2 PROTEIN PREPARATION

The three-dimensional (3D) structure of S-protein: ACE2 receptor complex (PDB ID: 6VW1)
was retrieved from RCSB PDB(https://www.rcsb.org/structure/6VW1). Co-crystallized ligands,
as well as crystallographic water molecules, were excluded from the 3D coordinate file of the
receptor.
3.3 MOLECULAR DOCKING

For the inhibition mechanism of optimized compounds at the molecular level, a docking study
using Autodock/vina was carried out at the interface of viral spike protein and human ACE2
receptor. In addition to stilbenoids, we have also used chloroquine as a positive control
compound, as chloroquine has been recently reported as a repositioned drug to treat patients
infected with COVID-19. Preparatory steps, namely, pdbqt files generation for receptor and
ligand as well as grid box setting at the active site was accomplished by using the GUI program
of Auto Dock Tool. The grid size was set at 40 x 40 x 40 xyz points with a grid spacing of 0.375
Å. pdbqt files name along with grid box properties were written into a configuration file, conf
file. Both the protein and ligand were treated as rigid entities, during docking. The results <1.0 Å
were clustered in positional RMSD and characterized with the most favorable free energy of

binding. For further study, the pose with the lowest binding affinity has been extracted, for each
studied compound, and aligned with the complex. Using different visualization tools, Visual
Molecular Dynamics (VMD), LigPlot + and Chimera pattern of binding were explored.
3.4 MOLECULAR DYNAMIC SIMULATION

To get a better understanding of the dynamics of the prioritized complexes, a molecular dynamic
simulation was practiced for 50-ns. During the first phase, a set of libraries and parameters were
developed for the protein-receptor complex and ligand molecules via antechamber module of
Amber18. Using the Leap module of the Amber, solvation of the system was carried out in 8.0 Å
TIP3P solvation box, the ff14SB force field was then incorporated to figure out the
intermolecular and intramolecular interactions. To neutralize the charge, Na+ was added to the
systems as an opposing ion. Energy optimization was accomplished via 2000 steps minimization
of hydrogen atoms, 1000 steps minimization of system solvation box energy with the restraint of
200 kcal/mol – Å2 on the rest of the system,1000 steps minimization of the entire set of system
atoms with the restraint of 5 kcal/mol –Å2 exercised on system carbon alpha atoms, and 300
steps minimization on non-heavy atoms of the system with the restraint of 100 kcal/mol –Å2 on
the remaining components of the system. The system was then heated to 300 K through the NVT
ensemble supported via Langevin dynamics and SHAKE algorithm to limit hydrogen bonds. An
equilibration for 100-ps was attained while sustaining pressure on the system via NPT ensemble
letting restraint on Ca atoms of 5 kcal/mol – Å2. During the third phase, trajectories of 50-ns
were constructed. A threshold distance of 8.0 Å was introduced to separate nonbounded
interactions. The stability of the system was examined by the analytical computation of structural
parameters using the CPPTRAJ module.VMD1.9.3 was then implied to visualize and analyze
these trajectories.

FIGURE 3: 3 D REPRESENTAION OF THE COMPLEX INSIDE THE TIP 3P WATER

BOX.
3.5 MMPBSA BINDING FREE ENERGIES ESTIMATION

MMPBSA.py module of AMBER18 was taken into practice to calculate the solvation free
energy and interaction energy for the receptor, ligand, and receptor-ligand complexes. Net
binding free energy of the system was calculated as the average of the above-mentioned energies
via the MM-PBSA method and its complement MM-GBSA of the AMBER to trace the
difference between bound and unbound states of solvated conformations of a molecule. This
equation can be used to calculate the binding free energy mathematically,
Poisson Boltzmann (PB) or Generalized Born (GB) equation was used to calculate the solvation
energy for all states of the system which revealed the electrostatic contribution of the solvation
state.

4. RESULTS AND DISCUSSION
4.1 MOLECULAR DOCKING

To illustrate the inhibition potential and effectiveness of stilbene-based compounds against novel
coronavirus viral Sprotein:ACE2 receptor complex, molecular docking studies using
Autodock/vina was performed. All the compounds, including chloroquine, showed good binding
with the protein complex. The highest-ranked bound conformations of all compounds made up a
cluster at the S-protein: ACE2 receptor interface, indicating that all the studied compounds
exhibited similar binding mode against the protein (Figure 4).
FIGURE 4: (A) PREDICTED CONFORMATIONS OF ALL COMPOUNDS INTO THE

POCKET.
(B) IMPORTANT INTERACTING RESIDUES OF THE BINDING POCKET OF S-
PROTEIN: ACE2 RECEPTOR INTERFACE
Asn33, His34, Glu37, Asp38, Lys353, Ala387, Gln388, Pro389, Phe390, Arg393, Lys403,
Tyr453, Tyr495, Gly496, Phe497, Ser494, and Tyr505 were found to be the key interacting
residues, including residues reported being crucial for binding of viral S-protein with its human
host ACE2 receptor. Nearly all of the selected small molecules, also chloroquine (positive
control), analyzed exhibited several hydrophobic and some hydrophilic interactions with main
residues of interface. Analysis of docked complexes revealed that all compounds bind tightly to

the pocket of Sprotein: ACE2 complex through multiple strong hydrogen bond interactions.
Lys353, Gly496, Lys403, ASN33, and Pro389 were involved in ionic interactions with
electronegative atoms of compounds. Besides, hydrophobic contacts were also observed. Among
all the studied compounds, based on binding affinity, piceatannol and resveratrol were selected
as the top-ranked compounds (Figure 5).
FIGURE 5: BINDING AFFINITIES

Complexes of aforesaid compounds were extracted for additional analysis using LigPlot + and
VMD. The two-dimensional interaction maps of selected conformations highlighted the network
of hydrophobic as well as hydrogen bond interactions for two ligand-interface (Figure 6 (A,B)).
For the resveratrol-interface complex, two hydrogen bonds with two key residues, Lys 353 of viral
spike protein (3.34 Å)and Gly496 of ACE2 receptor (2.80 Å) were observed. The H bond involving
Lys 353 is very important for the stability of docked conformation, as it has been reported as a
more critical residue being highly selective towards receptor-binding domain (RBD). Piceatannol
interacted via seven H-bonds, one ionic as well as ten hydrophobic interactions (Figure 7(A)). In
the case of resveratrol number of electrostatic complementarity, hydrogen bonding and
hydrophobic interactions with the electronegative as well as carbonyl groups were observed
(Figure 7(B)), making these compounds an ideal target for further optimization using MD
simulation.

FIGURE 6: DOCKED POSES: 2 D DEPICTION OF HYDROGEN BOND AND

HYDROPHOBIC INTERACTIONS USING LIGPLOT+.
(A) PICEATANNOL- INTERFACE (B) RESVERATROL- INTERFACE.
FIGURE 7: DOCKED POSES: 3D DEPICTION OF HYDROGEN BOND, IONIC AND

HYDRPHOBIC INTERACTIONS USING VMD.
(A) PICEATANNOL- INTERFACE (B) RESVERATROL- INTERFACE.

4.2 MOLECULAR DYNAMIC SIMULATION
To check the stability of the top two stilbene-based compounds docked with viral s-protein and
hACE2 receptor complex and to further optimize the complexes, molecular dynamic simulations
were carried out. The trajectories generated for simulation run were analyzed using RMSD,
RMSF, and MM-PBSA binding free energies calculations. For each selected ligand-protein
complex, the stability of backbone carbon-alpha atoms was computed using RMSD and RMSF.
The RMSD value of the resveratrol-protein complex was least compared to the other complex.
The system attained equilibrium after 1 ns and remained the same throughout the 50 ns
simulation time with an average RMSD value of 1.78 Å (Figure 8). When pdbs obtained at
different nanoseconds were analyzed using VMD, it was observed that the minor fluctuations
noted at different intervals were due to ligand adjustment at the active site. Additionally, to
check the mobility of protein residues and to check the conformational changes upon the binding
of compounds, the average RMSF for backbone atoms for each system was calculated. It was
observed after analyzing the RMSF graph that the resveratrol-protein complex showed fewer
fluctuations as compared to the other studied system. The estimated average RMSF value for
resveratrol-protein was 1.19 Å (Figure 9). Analysis of the RMSF graph revealed unusual stability
of interacting residues. Based on these analyses, we can conclude that although piceatannol
exhibited better docking affinity as compared to complex having resveratrol, but simulation
results deviate from the docking results and proved resveratrol-protein as the most stable and
suitable complex for further analysis.
FIGURE 8: ROOT MEAN SQUARE DEVIATION OF THE BACKBONE ATOMS OF

THE DOCKED COMPLEX.
FIGURE 9: ROOT MEAN SQUARE FLUCTUATION OF THE BACKBONE ATOMS

OF THE DOCKED COMPLEX.
4.3 MM – PBGBSA BINDING FREE ENERGIES ESTIMATION

To elucidate intermolecular chemical interactions role in resveratrol-protein complex stability, an
endpoint MMPBGBSA assay was performed on the generated trajectories. This was significant
not only to validate the findings of docking but also to guide us on the key role of chemical
moiety responsible for docked complex stability. The detailed contribution of binding free
energies in both MM-GBSA and MMPBSA is listed in Tables 3 and 4, respectively. Both
techniques illustrated very low net binding energies that are in line with the docking results.
These low energies are an affirmation of high complex stability. The total binding energy in case
of the MM-GBSA method is lower for the complex i.e. -23.8889 kcal/mol compared to the MM-
PBSA that is -20.2657 kcal/mol. The contribution of gas-phase energy to the total net energy of
the system is significantly high in both techniques as opposed to the system’s net solvation
energy revealing to complex stability mainly because of the best conformation of the receptor
with respect to the ligand. The net gas phase energy for both methods (MMGBSA and
MMPBSA) was same i.e.-32.4924 kcal/mol . To this energy the eloquent role was found from
van dar Waals (-30.5754 kcal/mol in both MM-GBSA and MM-PBSA). The role of electrostatic
energy in binding was found minor(-1.9170 kcal/mol). The total solvation energy in MM-GBSA
is 8.6035 kcal/mol that is lower than its counterpart in MMPBSA (12.2267 kcal/mol).
Additionally, the net binding energy of both approaches was decomposed into specific amino

acids, in particular, those that were seen in binding with the inhibitor. The binding free energy of
the receptor residues that are hotspots in interaction with the inhibitor are as follows: Asn33
(MM-GBSA -1.23 kcal/mol and MMPBSA 2.01 kcal/mol), His34 (MM-GBSA -0.37 kcal/mol
and MMPBSA -0.01 kcal/mol), Lys353 (MM-GBSA -0.37 kcal/mol and MMPBSA -0.11
kcal/mol), Phe390 (MM-GBSA -0.58 kcal/mol and MMPBSA -0.45 kcal/mol), and Gly496
(MM-GBSA -1.23 kcal/mol and MMPBSA 2.01 kcal/mol).
The present study computationally probed four stilbene based natural compounds for the
prediction of their potential to act as an inhibitor of complex formed between spike (S1) protein
from novel coronavirus and human angiotensin converting enzyme 2 (ACE2). Recently reported
crystallographic structure of the SARS-CoV-2 S-protein: human ACE2 complex signifies its
worth as a suitable target to design potent structure-based therapeutics that will be helpful in the
disruption of novel coronavirus viral S-protein-ACE2 interface. Considering that the COVID-19
outbreak has now become a global challenge, discovering, designing, and repurposing already
well-characterized synthetic as well as natural drugs would be of great benefit to control and
eradicate this pandemic. Keeping this in mind, we computationally tested the capability of
stilbenoids to bind S-protein: ACE2 receptor interface, which probably in-turns will serve to
disrupt the host-recognition and infection pathway of SARS-CoV-2. Molecular docking results
showed a good binding affinity for all the compounds but piceatannol and resveratrol with the
highest affinity for the S1: ACE2 complex were analyzed further. Molecular dynamics
simulation studies and free energy calculations revealed that resveratrol is most stable under
maximum orientations once bound to the above-mentioned protein-receptor complex.
Resveratrol can, therefore, act as an inhibitor of the ACE2 receptor and prevent the S1: ACE2
complex formation and entry of the virus into host cells.

5. CONCLUSION
Investigation of the most favorable docked conformations of studied compounds revealed the
involvement of several important residues of pocket, including the residues of S-protein: ACE2
receptor interface. These residues, involved in hydrogen bonding, ionic as well as hydrophobic
interactions, were characterized as important factors for improving the inhibitor’s activity and
stability. All the studied compounds showed good binding with the selected target, but the level
of selectivity of protein for resveratrol over other stilbenoids was found to be remarkably
significant. MD trajectories analysis and MMBPSA results revealed that resveratrol showed
strong binding with key residues making it available for immediate in vivo and in vitro testing.
Taken together, our results point towards the significance of developing drugs against COVID-
19 using stilbene based natural compounds, especially resveratrol. This is a very promising
finding keeping in view the pre-reported biological roles of resveratrol and structurally related
stilbenoids. Expedited experimental research in this connection is warranted by the extensive
research and reported biological safety of these natural compounds.

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Stilbene Drug Candidate Against Covid - 19

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Stilbene – A Natural Drug Candidate against COVID -19.

STILBENE – A NATURAL DRUG CANDIDATE

GUIDED BY: SUBMITTED BY:

DEPARTMENT OF BIOTECHNOLOGY AND

MOHANDAS COLLEGE OF ENGINEERING AND TECHNOLOGY ANAD,

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 1

A P J ABDUL KALAM TECHNOLOGICAL UNIVERSITY 2020

DEPARTMENT OF BIOTECHNOLOGY AND BIOCHEMICAL

Certified that this is a bonafide report of the seminar work done by

VEENA SEKHAR LAL

PROJECT SUPERVISOR HEAD OF DEPARTMENT

PROF.SUMARANI.G.O DR. SHALINI. A. NAIR

ASSISTANT PROFESSOR PROFESSOR

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 2

Dr. S. Sheela , MCET, Thiruvananthapuram for the wholehearted support given to me

I acknowledge Sumarani.G.O, Assistant Professor, Department of Biotechnology and

I am indebted to Dr. Shalini.A.Nair, Professor and Head of Department of

I express my sincere gratitude to Shiji Jameson, Staff Advisor and Seminar

I express my profound gratitude to all the teaching staff of Department of

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 3

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 4

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 5

1. FIGURE 1……………….PAGE NO. 7

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 6

FIGURE 1: SARS – CoV2 STRUCTURE

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 7

FIGURE 2: STRUCTURE OF STILBENOID

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 8

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 9

resonance (NMR), crystallographic, or homology-modeling data. In brief, it contributes forces

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 10

3. MATERIALS AND METHODS

3.1 LIGAND STRUCTURE PREPARATION

3.2 PROTEIN PREPARATION

3.3 MOLECULAR DOCKING

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 11

3.4 MOLECULAR DYNAMIC SIMULATION

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 12

FIGURE 3: 3 D REPRESENTAION OF THE COMPLEX INSIDE THE TIP 3P WATER

3.5 MMPBSA BINDING FREE ENERGIES ESTIMATION

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 13

4. RESULTS AND DISCUSSION

4.1 MOLECULAR DOCKING

FIGURE 4: (A) PREDICTED CONFORMATIONS OF ALL COMPOUNDS INTO THE

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 14

FIGURE 5: BINDING AFFINITIES

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 15

FIGURE 6: DOCKED POSES: 2 D DEPICTION OF HYDROGEN BOND AND

FIGURE 7: DOCKED POSES: 3D DEPICTION OF HYDROGEN BOND, IONIC AND

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 16

4.2 MOLECULAR DYNAMIC SIMULATION

FIGURE 8: ROOT MEAN SQUARE DEVIATION OF THE BACKBONE ATOMS OF

FIGURE 9: ROOT MEAN SQUARE FLUCTUATION OF THE BACKBONE ATOMS

4.3 MM – PBGBSA BINDING FREE ENERGIES ESTIMATION

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 18

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 19

BIOTECHNOLOGY AND BIOCHEMICAL ENGINEERING 20

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[4] Bhakkiyalakshmi.E., Sireesh.D, Sakthivadivel.M, Sivasubramanian.S ,Gunasekaran.P &

[7] Case.D.A, Ben-Shalom.I.Y, Brozell.S.R, Cerutti.D.S, Cheatham. III T.E, Cruzeiro.V.W.D,