seminar

1. In silico validation of the
efficacy of phytochemicals
from Passiflora edulis Sims
against SARS-CoV-2.
 PRESENTED BY: SNEYA VALANCIYA FERNANDES , THE OXFORD COLLEGE OF
SCIENCE DEPARTMENT OF ZOOLOGY AND GENETICS.
 UNDER THE GUIDANCE : DR DHANYA B PILLAI AND SHEFIN B (GREEN
CLONES NATURAL PVT.LTD, KOCHI KERALA)
 DR DEEPA GOPINATH, ASSOCIATE PROFESSOR OF THE OXFORD COLLEGE
OF SCIENCE.

2. Background of study
 In the present scenario , the greatest health hazard affecting the
world is of corona virus, a deadly disease that affects almost all
countries in the world .
 As of 5th September 2020, there were 26,468,031 confirmed cases,
871,166 confirmed deaths affecting 216 countries .
 SARS-CoV-2 , is a positive- sense , single stranded RNA virus.
 on basis of literature survey, the plant species Passiflora edulis Sims
was selected for the present study to evaluate its anti SARS-CoV-2
activity .

3. Hypothesis
 In vitro screening coupled with in silico screening is
the best option to validate drug activity of herbal
medicine and identification of lead molecules for
further experiments leading to drug discovery (Rates
et al, 2001).
 In order to rapidly discover lead compounds for
clinical use and the whole world is looking forward
and engaged in research studies to find out newer
therapeutic drugs or vaccines against SARS-CoV-2.
There is only one way the world can exit this
pandemic and that is through scientific research.

4. Objectives
 Identification of potential target protein from SARS CoV-2.
 To retrieve the phytochemicals from Passiflora edulis Sims.
 To identify hit molecules.
 To analyse the various properties of hit molecules
 H-bonding pattern
 Molecular properties
 Bio activity
 Drug likeness property
 ADME properties.
 To find the best lead molecule against target protein.

5. Materials and methods
Collection and preparation of phytochemicals:
 Information about 206 phytochemicals isolated from
Passiflora edulis were available in various literatures .
 Canonical smiles, molecular weight, molecular
formula and 3D structure (sdf) of 130 phytochemicals
retrieved from PubChem.
 130 molecules 3D structure were prepared in pdb
format.

6. Selection & preparation of
Target protein
 Mpro is a key enzyme of corona viruses and has a pivotal
role in mediating viral replication and transcription , making
it an attractive drug target for SARS-Cov-2.
 Mpro represent a non structural protein that cuts two
replicase polyproteins resulting in matured proteins that are
required to mediate viral replication and transcription.
 The potent multifunctional protein Mpro (Main protease)
from SARS CoV-2 (PDB ID:6LU7) was selected as the target
molecule. Three dimensional (3D) structures of the target
protein was obtained from RCSB PDB.
 By inhibition of Mpro through the study , we can stop virus
replication.
 Interaction of the proteins with ligand molecules and
cofactors were analyzed using the tool PDBsum.

7. In silico screening
 A total of 130 molecules from Passiflora edulis Sims
were screened against the target protein SARS-CoV-2
Mpro protein via virtual screening.

8. Results
 From Passiflora edulis Sims, a total of 130 phytochemicals were docked
into the active site of the target protein, Main protease, SARS-CoV-2
Mpro.
 After docking process, molecules that showed free energy of binding,
ΔGbind ≤-6 kcal/mol were considered as hit molecules.
 The top ranked five molecules that possess free energy of binding <-
8Kcal/mol were selected for further analysis.
Post Docking Analysis
H bond analysis
Docked Complex
Molecular property and Drug likeness
Bioactive properties of different drug
classes
ADME
Water solubility
Pharmacokinetic properties
Drug likeness properties

9. Results – Hydrogen Bond interaction
study
Ligand Name
Free
energy of
binding
(kcal/mol)
H bond
Type
H Bond Residue H.Bond Length Hydrophobic residues
Prulaurasin -9.0
OHN Gln110 3.19
Asn151, Ile106, Val104, Phe294, Thr292
OHN Gln110 3.15
OHO Thr111 3.17
OHO Gln107 3.28
OHO Pro108 2.82
OHO Pro108 2.02
OHO GLu240 3.26
OHO Glu240 3.01
Phytofluene -8.1 No Hbonds
Ile249, Pro293, Phe294, Asn151, Arg105, Val104,
Ile106, Gln107, Gln110, Pro108, Pro132, Thr198,
Glu240, Val202, His246,
Tannic acid -8.0
NHO His246 3.15
Asn151, Phe294, Ile152, Asp153, Thr292, Pro108,
Asp245, Gln107, Val 202, Glu240, Val104
NHO His246 3.20
OHO Thr111 2.92
OHO Asp295 2.83
NHO Gln110 2.96
Vanillic acid -8.0 NHO Gln110 3.04 Asn151, Ile152, Asp153, Phe294, Thr111, Ile106,
Longifloroside A -8.0
OHO Thr11 2.87
Pro293, Gln110, Cal297, Thr292, Phe294, Pro252,
Ile249, Ile106, Cal104, Asn151, Asp153, Ile152
NHO Thr11 3.05
OHO Thr11 3.02

10. Docked complex images of top ranked
molecules with its target Mpro
Prulaurasin with SARS CoV-2 Mpro: a. Discovery Studio view and b.
LigPlot view;

11. Phytofluene with SARS CoV-2 Mpro: a. Discovery Studio view and b. LigPlot
view

12. Tannic acid with SARS CoV-2 Mpro: a. Discovery Studio view and b.
LigPlot view

13. Vanillic acid with SARS CoV-2 Mpro: a. Discovery Studio view and b.
LigPlot view;

14. Longifloroside A with SARS CoV-2 Mpro: a. Discovery Studio view and b.
LigPlot view

15. Molecular property Analysis
Name of
phytochemical
MiLogP
TPSA
nAtoms
MolecularWeight
nON
nOHNH
nViolations
nrotb
Drug-likenessscore
Prulaurasin -0.66 123.17 21
295.29
7 4 0 4 0.98
Phytofluene 10.08 0.00 40 542.94 0 0 2 19 0.20
Tannic acid 7.06 777.98 122 1701.21 46 25 4 31 --
Vanillic acid 1.19 66.76 12 168.15 4 2 0 2 -0.18
Longifloroside A 0.52 156.54 38 534.56 11 5 2 10 0.58

16. Bioactivity property prediction
Name of
phytochemicals
GPCR
Ligand
Ion channel
modulator
Kinase
Inhibitor
Nuclear
Receptor
Ligand
Protease
Inhibitor
Enzyme
Inhibitor
Prulaurasin 0.26 0.03 -0.03 -0.07 0.21 0.60
Phytofluene 0.07 0.12 -0.06 0.29 -0.06 0.17
Tannic acid -4.06 -4.07 -4.08 -4.08 -4.04 -4.05
Vanillic acid -0.85 -0.42 -0.99 -0.61 -1.12 -0.35
Longifloroside A 0.34 0.11 -0.10 -0.07 -0.09 0.48

17. ADME Analysis
Name of
Molecule
ESOLLogS
ESOLSolubility
(mg/ml)
ESOLSolubility
(mol/l)
ESOLClass
AliLogS
AliSolubility
(mg/ml)
AliClass
Water Solubility
Prulaurasin -1.17 1.99E+01 6.75E-02
Very
soluble
-1.4 1.17E+01 Very soluble
Phytofluene -11.65 1.20E-09 2.22E-12 Insoluble -15.53 1.60E-13 Insoluble
Tannic acid -12.61 4.16E-10 2.45E-13 Insoluble -22.32 8.10E-20 Insoluble
Vanillic acid -2.02 1.60E+00 9.52E-03 Soluble -2.44 6.15E-01 Soluble
Longifloroside A -3.13 3.95E-01 7.39E-04 Soluble -3.5 1.68E-01 Soluble

18. ADME - Pharmacokinetic
properties
Molecule
Pharmacokinetic properties DruglikenessGIabsorption
BBBpermeant
Pgpsubstrate
CYP1A2inhibitor
CYP2C19inhibitor
CYP2C9inhibitor
CYP2D6inhibitor
CYP3A4inhibitor
Lipinski#violations
Ghose#violations
Veber#violations
Egan#violations
Muegge#violations
BioavailabilityScore
Prulaurasin High No No No No No No No 0 1 0 0 0 0.55
Phytofluene Low No Yes No No No No No 2 4 1 1 3 0.17
Tannic acid Low No Yes No No No No No 3 3 2 1 7 0.17
Vanillic acid High No No No No No No No 0 0 0 0 1 0.85
Longifloroside A Low No Yes No No No No No 2 3 1 1 2 0.17

19. Discussion
 The compound prulaurasin exhibited free energy of binding (ΔGbind -
9Kcal/mol) against the target protein with 8 hydrogen bonds together
with five amino acids involved in hydrophobic interactions.
 Among the top 5 molecules selected for further evaluation(ΔGbind <-8.0),
two compounds totally passed all of the Lipinski's rule and thus no
violations. The compound, tannic acid showed four violations with
lipinski's rule of five whereas phytofluene and longifloroside A showed two
violations each.
 Analysis revealed that prulaurasin exhibited the best drug likeness
compared to all the other molecules studied.

20.  Analysis against six drug target classes revealed that among the five
molecules studied, vanillic acid and tannic acid were found to be
inactive against all the drug classes, whereas prulaurasin,
phytofluene and longifloriside A were found to be inactive
some targets only.
 Prulaurasin and vanillic acid possess the best pharmacological
activities as well as druglikeness properties .
 Interestingly, among the top leads, only prulaurasin was found to be
very soluble in water whereas phytofluene and tannic acid were
appeared to be insoluble . Vanillic acid and longifloroside were
found be soluble moderately.

21. Conclusion
 Prulaurasin > longifloroside A > phytofluene.
 However, the considering all the criteria selected for
the study, the compound prulaurasin is selected as
the best lead molecule from the plant through the
study.
 Thus, prulaurasin can be considered for further in
vitro/in vivo studies against SARS-CoV-2 virus to
confirm the results of in silico studies and thus can be
validated experimentally.

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