In Silico Screening of Some Naturally Occurring Bioactive Compounds Predicts Potential

Inhibitors against SARS-COV-2 (COVID-19) Protease*

Ashok Kumar Mishra1 and Satya Prakash Tewari

Department of Physics, Dr.Shakuntala Misra National Rehabilitation University, Lucknow,

Uttar Pradesh, India-226017

1
Corresponding Author: [email protected]; [email protected] (A.K. Mishra)

• This research is dedicated to the peoples who have lost the lives, been struggling for the
lives, been working hard to save the lives as well as been frightened for the lives while
fighting against the pandemic COVID-19 i.e. the all CORONA WARRIORS.

1
 Abstract
SARS-COV-2 identified as COVID-19 in Wuhan city of China in the month of December, 2019 has
now been declared as pandemic by World Health Organization whose transmission chain and cure both
have emerged as a tough problem for the medical fraternity. The reports pertaining to the treatment of
this pandemic are still lacking. We firmly believe that Nature itself provides a simple solution for any
complicated problem created in it which motivated us to carry out In Silico investigations on some
bioactive natural compounds reportedly found in the fruits and leaves of Anthocephalus Cadamba which
is a miraculous plant found on the earth aiming to predict the potential inhibitors against aforesaid virus.
Having modeled the ground state ligand structure of the such nine natural compounds applying density
functional theory at B3LYP/631+G (d, p) level we have performed their molecular docking with SARS-
COV-2 protease to calculate the binding affinity as well as to screen the binding at S-protein site during
ligand-protein interactions. Out of these nine studied naturally occurring compounds; Oleanic Acid has
been appeared to be potential inhibitor for COVID-19 followed by Ursolic Acid,
IsoVallesiachotamine,Vallesiachotamine,Cadambine,Vincosamide-N-Oxide, Isodihydroamino-
cadambine, Pentyle Ester of Chlorogenic Acid and D-Myo-Inositol. Hence these bioactive natural
compounds or their structural analogs may be explored as anti-COVID19 drug agent which will be
possessing the peculiar feature of cost-less synthesis and less or no side effect due to their natural
occurrence. The solubility and solvent-effect related to the phytochemicals may be the point of concern.
The In-vivo investigations on these proposed natural compounds or on their structural analogs are
invited for designing and developing the potential medicine/vaccine for the treatment of COVID-19
pandemic.
Keywords: COVID-19 inhibitors; anti- SARS-COV-2 bioactive natural compounds; Molecular-
Docking; DFT; Phytochemicals; Molecular -modeling

2
Introduction
The novel corona virus disease (COVID-19) identified in Wuhan City of China [1] spread across the
earth as pandemic putting the whole world on high alert [2–5] led to 823626 total cases and 40598 deaths all
over the world till 01 April 2020 [6]. Available evidence indicates that this virus is transmitted through the
respiratory droplets (such as coughing) and by fomites that can propagate through air at distances of 1 meter [7-
9] and no evidence is available about its airborne transmission in the current study [10] which establishes the
principle of maintaining the distance of more than 1 meter termed as ‘social distancing’/’physical distancing’
along with hand-hygiene for the prevention of COVID-19. A recent study based on the mathematical modeling
conducted by Indian Council of Medical Research (ICMR) has suggested the proper quarantine and isolation as
the preventive measures for stopping the outbreak of COVID-19 through community transmission [11]. It
appears that in view of this, country- wide lock-down has been declared in India since the midnight of the 23 rd
March, 2020 in continuation to pre-lock down action of evacuating the possible places expected for people’s
gathering as well as the social awareness drive already started from the very beginning of February, 2020 which
we welcome.
Appreciable contribution in the development of diagnostics, therapeutics and vaccines for this novel
corona virus has been indicated [11] and based on some clinical investigations, an anti-malarial drug namely
chloroquine phosphate has been reported to be having a certain curative effect on the COVID-19 [12]. ICMR
has also recommended an anti-malarial drug namely Hydroxy-chloroquine for those individuals which are
asymptomatic healthcare workers involved in the care of suspected or confirmed cases of COVID-19 and
asymptomatic household contacts of laboratory confirmed cases [13]. The possibility of high risk-factor
associated with these suggested drugs has not been ruled out which projected it to be a trial measure. No
specific therapy and medicine for the treatment of COVID-19 has ever been reported to the best of our
knowledge which inspired us to think on the natural products relying on the concept of particle-antiparticle
theory of Nature implying that if there is a novel corona virus then there must be its anti-virus material in the
Nature itself and we have obtained motivating results in the present research carried out with the help of
available computational facility at our home during lock-down period.
We have selected total eleven bioactive natural compounds embedded spontaneously in Anthocephalus
Cadamba which has been reported to be a miraculous tree having crucial significance in Hindu Mythology
containing the largest number of phytochemicals and secondary metabolites having pharmacological and
biological properties, however, the solubility and solvent-effect to be the point of concern [14]. The four bio
molecules contained in the leaves of the said tree namely 7-hydroxy-6-methoxy coumarian (C10H8O4), Methyl
ester of chlorogenic acid (C17H20O9) , Pentyle Ester of Chlorogenic Acid (C21H28O9), D-Myo-Inositol
(C7H14O6); 07 biomolecules contained in fruits of the said tree namely Oleanic Acid (C30H48O3), Ursolic Acid

3
(C30H48O3), Vallesiachotamine (C21H22N2O3), Iso-Vallesiachotamine (C21H22N2O3), Cadambine (C27H32N2O10),
Vincosamide-N-Oxide (C26H31N2O9), Isodihydroamino-cadambine (C26H33N3O7) already reported to be isolated
and characterized in Central Drug Research Institute, Lucknow, India [15-16] and the electronic properties of
the few of them have already been studied by us computationally [17-21]; were screened as ligands to interact
with the targeted SARS-COV-2 protease. The first two of the aforsaid compounds responded negatively but rest
nine compounds exhibited the positive results which have been presented in this paper. We expect that the
present study will offer a new dimension in developing the drug/vaccine for the COVID-19.
Methodology
The In silico optimized ligand-structure of the aforementioned eleven bioactive natural compounds were
obtained as per reported approach of density functional theory at B3LYP/631+G (d, p) level [22-23]
implemented through Gaussian 09 program-package [24]. We have used main protease of SARS-COV-2
retrieved from the RCSB protein data bank having PDB ID: 6Y84 [25] and PDB ID: 6LU7 [26] as potential
target protein for the binding of these ligands obtained using molecular docking approach implemented through
Autodock 4.2 program package [27-29]. The binding of these natural bioactive ligands with the PDB ID: 6CRV
which is SARS Spike Glycoprotein for corona virus SARS-COV emerged in 2002 as a highly transmissible [30]
has also been obtained with the help of same docking approach in order to investigate the consistency of the
performance of these compounds with the class of viral protein. The binding of these compounds with the PDB
ID: 6VXX which is the SARS-COV-2 spike glycoprotein for COVID-19 [31] has also been examined to
illustrate the potential of these compounds to deactivate this novel corona virus at the receptor end.
Results and Discussion
The In silico optimized molecular structure of 09 bioactive natural compounds modeled using DFT-B3LY/6-
31+G (d,p) level of theory which exhibited the property of inhibitor against main protease of COVID-19, have
been displayed in figure 1. The binding affinity for all displayed molecules as ligand with the target protease of
the SARS-Cov-2 virus (PDB ID: 6Y84 and 6LU7) as well as with the SARS Spike Glycoprotein for corona
virus (PDB ID: 6CRV) have been depicted in table 1 to table 9. We observe a complete cycle for the binding of
all these compounds with the said protease in maximum ten cluster run and the final free energy of binding is
significant for all the ligand-protein interactions. The insignificant result for the binding of molecule no.8
(pentyl ester of chlorogenic acid) with 6LU7 and 6CRV receptors have been obtained where the same molecule
exhibits a significant final free energy of binding with 6Y84 protease of COVID-19 as obvious from the table 8.
The significant binding of these natural compounds with the said protease results in the conformational changes
in the main protease of SARS-COV-2 as displayed in figure 2 to figure 10. It is, therefore, predicted that the
naturally occurring bio molecules displayed in figure 1 may be explored as potential inhibitors for the COVID-

4
19 protease. The docking results of these molecules are presented in decreasing order of the binding affinity i.e.
the binding affinity with the target protein is largest for molecule 1followe by molecule 2,3,4,5,6,7,8 and 9.

1.Oleanic Acid (C30H48O3) 2.Ursolic Acid (C30H48O3) 3. Iso-Vallesiachotamine (C21H22N2O3)

4. Vallesiachotamine (C 21 H 22 N 2 O 3 ) 5. Cadambine(C 27 H 32 N 2 O 10 ) 6.Vincosamide-N-Oxide (C 26 H 31 N 2 O 9 )

7. Isodihydroamino-Cadambine(C26H33N3O7) 8.Pentyle Ester of Chlorogenic Acid (C21H28O9) 9.D-Myo-Inositol (C7H14O6)

Figure 1: The optimized molecular structure of Nine Bioactive Natural Compounds *reported to be found in fruits (molecule no 1to 7)
and leaves (molecule no 8 to 9) of Anthocephalus cadamba [* 14-16]. Blue balls: N-atoms , black balls: C-atoms, white balls: H-atoms

The significantly negative value of the final free energy of binding obtained through the molecular docking of
these compounds with the SARS-COV-2 protease reveals that these molecules may be explored as potential
inhibitor against COVID-19. Since these compounds are naturally occurring, hence they do not cost for their
synthesis and bears less or nil side-effect which enables them to be explored as user-friendly drug. The
solubility and the effect of the solvent which are usually associated with the phytochrmicals may be the point of

5
attention while using these compounds as drug candidate. The other chemical structure may also be derived
from these bioactive natural compounds to further design potential drug agent for COVID-19.

Table 1: Binding affinity of Oleanic Acid (C30H48O3) with the target proteins

Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein

Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -11.28 kcal/mol 5.38nM -6.11 kcal/mol 33.45μM -5.90 kcal/mol 47.30μM
2 -9.78 kcal/mol 67.90nM -5.83 kcal/mol 52.86μM -5.73 kcal/mol 63.60μM
3 -9.60 kcal/mol 91.21nM -5.70 kcal/mol 66.07μM -5.41 kcal/mol 107.78μM
4 -9.10 kcal/mol 213.24nM -5.59 kcal/mol 79.53μM -4.91 kcal/mol 249.99μM
5 --------- --------- -5.57 kcal/mol 82.47μM -4.39 kcal/mol 607.04μM
6 --------- --------- -5.44 kcal/mol 102.54μM -4.28 kcal/mol 723.95μM
7 --------- --------- -5.08 kcal/mol 189.25μM -4.25 kcal/mol 768.82μM
8 --------- --------- -4.89 kcal/mol 258.48μM --------- ---------
9 --------- --------- -4.77 kcal/mol 318.64μM --------- ---------
10 --------- --------- --------- --------- --------- ---------

(a) 6Y84 (b) 6LU7 (c) 6CRV

Figure 2: Conformational changes observed due the binding of ligand-1 (Oleanic Acid) with the COVID-19 protease and S-protein receptor

Table 2: Binding affinity of Ursolic Acid (C30H48O3) with the target proteins

Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein

Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Binding Inhibition Free Energy of Inhibition Free Energy of Inhibition
Constant Binding Constant Binding Constant
1 -10.94 kcal/mol 9.63nM -6.40 kcal/mol 20.38μM -6.96 kcal/mol 7.88μM
2 -10.30 kcal/mol 28.35nM -6.34 kcal/mol 22.70μM -6.81 kcal/mol 10.26μM
3 -9.74 kcal/mol 72.73nM -6.00 kcal/mol 40.32μM -6.76 kcal/mol 11.17μM
4 -9.72 kcal/mol 74.54nM -5.89 kcal/mol 47.97μM -6.61 kcal/mol 14.24μM
5 -9.36 kcal/mol 137.19nM -5.34 kcal/mol 122.36μM -6.30 kcal/mol 24.24μM
6 -8.90 kcal/mol 299.83nM -4.96 kcal/mol 232.96μM -6.19 kcal/mol 29.17μM
7 --------- --------- --------- --------- -6.14 kcal/mol 31.59μM
8 --------- --------- --------- --------- -6.08 kcal/mol 34.90μM
9 --------- --------- --------- --------- -5.91 kcal/mol 46.80μM
10 --------- --------- --------- --------- -5.86 kcal/mol 50.93μM

6
 (a)6Y84 (b) 6LU7 (c) 6CRV
Figure 3: Conformational changes observed due the binding of ligand-2 (Ursolic Acid) with the COVID-19 protease and S-protein receptor

Table 3: Binding affinity of Iso-Vallesiachotamine (C21H22N2O3) with the target proteins

Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein

Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -9.55 kcal/mol 99.42nM -6.00 kcal/mol 39.82μM -5.16 kcal/mol 165.89μM
2 -7.93 kcal/mol 1.53μM -5.71 kcal/mol 65.58μM -5.00 kcal/mol 214.52μM
3 -7.63 kcal/mol 2.54μM -5.70 kcal/mol 66.53μM -4.94 kcal/mol 237.57μM
4 -7.61 kcal/mol 2.63μM -5.35 kcal/mol 20.56μM -4.81 kcal/mol 296.22μM
5 -7.45 kcal/mol 3.43μM -5.11 kcal/mol 178.30μM -4.75 kcal/mol 332.16μM
6 -6.51 kcal/mol 16.94μM -4.86 kcal/mol 275.30μM -4.70 kcal/mol 357.55μM
7 --------- --------- --------- --------- -4.68 kcal/mol 370.48μM
8 --------- --------- --------- --------- -4.45 kcal/mol 548.28μM
9 --------- --------- --------- --------- -4.36 kcal/mol 640.89μM
10 --------- --------- --------- --------- -4.03 kcal/mol 1.11mM

(a) 6Y84 (b) 6LU7 (c) 6CRV

Figure 4: Conformational changes observed due the binding of ligand-3 (Iso-Vallesiachotamine) with the COVID-19 protease and S-protein
receptor
Table 4: Binding affinity of Vallesiachotamine(C21H22N2O3) with the target proteins

Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein

Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -9.50 kcal/mol 109.66nM -4.98 kcal/mol 224.33μM -6.35 kcal/mol 22.14μM
2 -9.32 kcal/mol 148.51nM -4.80 kcal/mol 302.86μM -6.04 kcal/mol 37.63μM
3 -8.77 kcal/mol 371.00nM -4.43 kcal/mol 564.68μM -5.52 kcal/mol 89.42μM
4 -8.33 kcal/mol 784.52nM -4.31 kcal/mol 693.59μM -5.05 kcal/mol 197.72μM
5 -6.91 kcal/mol 8.64μM -4.30 kcal/mol 699.66μM -4.88 kcal/mol 262.69μM

7
 6 -6.87 kcal/mol 9.28μM -4.28 kcal/mol 723.92μM -4.77 kcal/mol 320.94μM
7 -6.62 kcal/mol 13.94μM -3.94 kcal/mol 1.30mM -4.36 kcal/mol 633.00μM
8 --------- --------- -3.73 kcal/mol 1.84mM -4.25 kcal/mol 769.77μM
9 --------- --------- -2.84 kcal/mol 8.22mM -4.02 kcal/mol 1.12mM
10 --------- --------- --------- --------- -3.90 kcal/mol 1.39mM

(a)6Y84 (b) 6LU7 (c) 6CRV

Figure 5: Conformational changes observed due the binding of ligand-4 (Vallesiachotamine) with the COVID-19 protease and S-protein receptor

Table 5: Binding affinity of Cadambine(C27H32N2O10) with the target proteins

SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein

Cluster (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Rank Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -8.85 kcal/mol 323.97nM -6.93 kcal/mol 13.86μM -5.35 kcal/mol 118.85μM
2 -7.57 kcal/mol 2.81μM -4.80 kcal/mol 301.24μM -4.83 kcal/mol 287.35μM
3 -7.46 kcal/mol 3.39μM -4.44 kcal/mol 553.34μM -4.65 kcal/mol 391.37μM
4 -7.18 kcal/mol 5.45μM -4.26 kcal/mol 756.51μM -4.56 kcal/mol 451.55μM
5 -6.79 kcal/mol 10.57μM -4.24 kcal/mol 779.20μM -4.33 kcal/mol 673.01μM
6 -6.22 kcal/mol 27.54μM -4.05 kcal/mol 1.07mM -4.24 kcal/mol 783.98μM
7 -6.15 kcal/mol 30.85μM -4.03 kcal/mol 1.11mM -3.78 kcal/mol 1.71mM
8 -5.85 kcal/mol 51.89μM -3.72 kcal/mol 1.88mM -3.50 kcal/mol 2.70mM
9 -5.72 kcal/mol 64.44μM -3.33 kcal/mol 3.60mM -3.06 kcal/mol 5.75mM
10 -5.45 kcal/mol 100.34μM -3.31 kcal/mol 3.77mM -2.88 kcal/mol 7.78mM

(a)6Y84 (b) 6LU7 (c) 6CRV

Figure 6: Conformational changes observed due the binding of ligand-5 (Cadambine) with the COVID-19 protease and S-protein receptor
Table 6: Binding affinity of Vincosamide-N-Oxide (C 26 H 31 N 2 O 9 ) with the target proteins
Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein
Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -8.81 kcal/mol 348.65nM -5.81 kcal/mol 55.52μM -4.59 kcal/mol 434.05μM
2 -8.77 kcal/mol 370.30nM -4.78 kcal/mol 312.98μM -4.47 kcal/mol 532.26μM
3 -8.41 kcal/mol 686.48nM -4.49 kcal/mol 511.38μM -4.28 kcal/mol 730.11μM
8
 4 -8.08 kcal/mol 1.19μM -3.93 kcal/mol 1.31mM -4.05 kcal/mol 1.07mM
5 -7.92 kcal/mol 1.58μM -3.89 kcal/mol 1.40mM -4.00 kcal/mol 1.17mM
6 -7.70 kcal/mol 2.26μM -3.75 kcal/mol 1.79mM -3.49 kcal/mol 2.78M
7 -7.22 kcal/mol 5.08μM -3.48 kcal/mol 2.83mM -3.44 kcal/mol 3.02mM
8 -6.26 kcal/mol 25.76μM -3.41 kcal/mol 3.15mM -3.38 kcal/mol 3.31mM
9 -5.08 kcal/mol 187.55μM -3.33 kcal/mol 3.64mM -3.29 kcal/mol 3.91mM
10 --------- --------- -3.03 kcal/mol 5.96mM -3.04 kcal/mol 5.93mM

(a)6Y84 (b) 6LU7 (c) 6CRV

Figure 7: Conformational changes observed due the binding of ligand-6 (Vincosamide-N-Oxide) with the COVID-19 protease and S-protein
receptor
Table 7: Binding affinity of Isodihydroamino-cadambine(C 26 H 33 N 3 O 7 )with the target proteins
Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein
Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -8.57 kcal/mol 520.33nM -4.85 kcal/mol 277.88μM -4.10 kcal/mol 922.19μM
2 -7.88 kcal/mol 1.67μM -4.10 kcal/mol 990.69μM -3.90 kcal/mol 1.39mM
3 -6.49 kcal/mol 17.43μM -4.08 kcal/mol 1.02mM -3.53 kcal/mol 2.60mM
4 -5.27 kcal/mol 137.23μM -3.09 kcal/mol 5.42mM -3.44 kcal/mol 2.99mM
5 -5.11 kcal/mol 181.03μM -2.92 kcal/mol 7.26mM -3.31 kcal/mol 3.73mM
6 -4.76 kcal/mol 324.79μM -2.58 kcal/mol 12.88mM -3.00 kcal/mol 6.28mM
7 -4.21 kcal/mol 816.29μM -2.53 kcal/mol 14.04mM -2.97 kcal/mol 6.63mM
8 -3.90 kcal/mol 1.39mM -2.51 kcal/mol 14.54mM -2.88 kcal/mol 7.71mM
9 --------- --------- -1.04 kcal/mol 172.81mM -2.84 kcal/mol 8.27mM
10 --------- --------- --------- --------- -2.69 kcal/mol 10.75mM

(a) 6Y84 (b) 6LU7 (c) 6CRV

Figure 8: Conformational changes observed due the binding of ligand-7 (Isodihydroamino-cadambine) with the COVID-19 protease and S-protein
receptor

9
Table 8: Binding affinity of Pentyle ester of chlorogenic acid (C 21 H 28 O 9 ) with the target proteins
Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein
Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -5.61 kcal/mol 77.71μM -1.95 kcal/mol 37.57mM -2.35 kcal/mol 19.10mM
2 -5.10 kcal/mol 182.54μM -1.52 kcal/mol 76.24mM -1.77 kcal/mol 50.49mM
3 -5.06 kcal/mol 194.58μM -1.46 kcal/mol 85.21mM -1.66 kcal/mol 60.43mM
4 -5.05 kcal/mol 198.85μM -1.03 kcal/mol 176.88mM -1.64 kcal/mol 62.51mM
5 -4.18 kcal/mol 869.07μM -0.86 kcal/mol 233.66mM -1.37 kcal/mol 99.72mM
6 -3.40 kcal/mol 3.21mM -0.61 kcal/mol 356.69mM -1.23 kcal/mol 126.32mM
7 -3.30 kcal/mol 3.80mM -0.42 kcal/mol 490.95mM -1.03 kcal/mol 176.85mM
8 -3.15 kcal/mol 4.87mM -0.37 kcal/mol 531.76mM -0.20 kcal/mol 713.11mM
9 -3.03 kcal/mol 6.04mM -0.06 kcal/mol 903.01mM -0.10 kcal/mol 840.36mM
10 -2.86 kcal/mol 8.01mM +0.05 kcal/mol ------------ -0.00 kcal/mol 991.66mM

(a) 6Y84 (b) 6LU7 (c) 6CRV

Figure 9: Conformational changes observed due the binding of ligand-8 (Pentyle Ester of Chlorogenic Acid) with the COVID-19 protease and S-
protein receptor
Table 9: Binding affinity of D-Myo-Inositol (C 7 H 14 O 6 ) with the target proteins
Cluster SARS-COV-2 protease SARS-COV-2 protease SARS-COV Spike Glycoprotein
Rank (PDB ID: 6Y84) (PDB ID: 6LU7) (PDB ID: 6CRV)
Free Energy of Inhibition Free Energy of Inhibition Free Energy of Inhibition
Binding Constant Binding Constant Binding Constant
1 -5.51 kcal/mol 90.67μM -2.22 kcal/mol 23.63mM -3.11 kcal/mol 5.22mM
2 -5.06 kcal/mol 195.69μM -2.05 kcal/mol 31.17mM -2.77 kcal/mol 9.34mM
3 -4.30 kcal/mol 702.05μM -1.86 kcal/mol 43.37mM -2.64 kcal/mol 11.57mM
4 -3.56 kcal/mol 2.47μM -1.74 kcal/mol 53.02mM -2.53 kcal/mol 13.88mM
5 -3.04 kcal/mol 5.86mM -1.72 kcal/mol 54.66mM -2.32 kcal/mol 20.09mM
6 -3.00 kcal/mol 6.30mM -1.53 kcal/mol 75.47mM -2.30 kcal/mol 20.46mM
7 -2.93 kcal/mol 7.09mM -1.38 kcal/mol 98.07mM -2.11 kcal/mol 28.50mM
8 --------- --------- -1.10 kcal/mol 154.91mM -1.98 kcal/mol 35.50mM
9 --------- --------- -1.07 kcal/mol 164.03mM -1.94 kcal/mol 37.54mM
10 --------- --------- --------- --------- -1.56 kcal/mol 71.41mM

10
 (a)6Y84 (b) 6LU7 (c) 6CRV
Figure 10: Conformational changes observed due the binding of ligand-9 (D-Myo-Inositol) with the COVID-19 protease and S-protein receptor

The significantly negative value of free energy of binding of these molecules with PDB ID: 6VXX (SARS-
COV-2 spike glycoprotein for COVID-19) in ligand-protein interaction as depicted in table 10 and 11 reveals
that these molecules or their structural-derivatives may stop the replication of the virus at the receiver end in the
human body. The results regarding binding affinity of the some of these compounds and corresponding
conformational changes occurred in the target protein are presented in figure 11and 12.
Table 10: Binding affinity in SARS-COV-2 spike glycoprotein interaction
Oleanic Acid (C30H48O3)-6VXX interaction Ursolic Acid(C30H48O3) -6VXX interaction
Cluster Free Energy of Binding Inhibition Constant Free Energy of Binding Inhibition Constant
Rank
1 -6.76 kcal/mol 11.05μM -7.15 kcal/mol 5.73μM
2 -6.54 kcal/mol 16.17μM -7.07 kcal/mol 6.53μM
3 -6.41 kcal/mol 19.85μM -6.74 kcal/mol 11.56μM
4 -6.41 kcal/mol 19.90μM -6.72 kcal/mol 11.78μM
5 -6.12 kcal/mol 32.71μM -6.48 kcal/mol 17.64μM
6 -6.04 kcal/mol 37.45μM -6.39 kcal/mol 20.63μM
7 -5.80 kcal/mol 56.45μM -6.29 kcal/mol 24.67μM
8 -5.70 kcal/mol 66.58μM -6.22 kcal/mol 27.76μM
9 -5.45 kcal/mol 101.12μM -6.20 kcal/mol 28.40 μM
10 -5.81 kcal/mol 55.41μM

Figure 11 (a) Ligand [Oleanic Acid] - Protein [6VXX] interaction (b) Ligand [Ursolic Acid ] - Protein [6VXX] interaction

11
Table 11: Binding affinity in SARS-COV-2 spike glycoprotein interaction
Iso-Vallesiachotamine (C21H22N2O3)-6VXX interaction Isodihydroamino-cadambine (C26H33N3O7) -6VXX
interaction
Cluster Free Energy of Binding Inhibition Constant Free Energy of Binding Inhibition Constant
Rank
1 -5.18 kcal/mol 160.30μM -5.36 kcal/mol 118.39μM
2 -5.12 kcal/mol 177.97μM -3.88 kcal/mol 1.44mM
3 -5.01 kcal/mol 211.92μM -3.56 kcal/mol 2.46mM
4 -4.76 kcal/mol 322.60μM -3.48 kcal/mol 2.80mM
5 -4.72 kcal/mol 344.73μM -3.35 kcal/mol 3.49mM
6 -4.55 kcal/mol 462.95μM -3.22 kcal/mol 4.39mM
7 -4.32 kcal/mol 676.74μM -2.88 kcal/mol 7.78mM
8 -4.25 kcal/mol 762.33μM -2.65 kcal/mol 11.39mM
9 -3.58 kcal/mol 2.37mM -2.62 kcal/mol 12.08mM
10 -3.40 kcal/mol 3.20mM -2.53 kcal/mol 14.00mM

Figure 12 (a) Ligand [Iso-Vallesiachotamine] - Protein [6VXX] interaction (b) Ligand [Isodihydroamino-cadambine] - Protein
[6VXX] interaction

Similar types of significant binding affinity have been obtained in all the SARS-COV-2 spike glycoprotein –
ligand (studied compounds) interactions whose results are available on demand but not depicted due to space
limitations.

Concluding Remarks
We have carried out a schematic In Silico investigation applying density functional theory and molecular
docking approach on the nine naturally occurring bioactive compounds listed in figure 1 spontaneously found in
the leaves and fruits of Anthocephalus cadamba. On the basis of the binding affinity, we have found these
compounds as potential inhibitors against the COVID-19 having final free energy of binding in the order of
molecule 1>2>3>4>5>6>7>8>9. These molecules have also emerged as potential inhibitors against the SARS-
12
COV-2 spike glycoprotein for COVID-19 in our investigation. These compounds may be explored as drug
candidate and their molecular structure may be exploited to develop a vaccine for COVID-19. In-vivo study is
invited on these compounds for developing user friendly drug for COVID-19. The further study on derived
structures of these compounds is going on in our laboratory.
Acknowledgements
Authors are thankful to Professor Neeraj Misra, Department of Physics University of Lucknow, India for
permitting us to use his computational facility. Thanks are due to Dr. D.P. Mishra, former Research fellow,
Central Drug Research Institute, Lucknow, India for immense help regarding the information about bioactive
natural products.

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