Hindawi

BioMed Research International

Volume 2020, Article ID 6237160, 15 pages
https://doi.org/10.1155/2020/6237160

Research Article
Phytochemicals from Selective Plants Have Promising
Potential against SARS-CoV-2: Investigation and Corroboration
through Molecular Docking, MD Simulations, and
Quantum Computations

Kafila Kousar,1 Arshia Majeed,2 Farkhanda Yasmin,3 Waqar Hussain ,4,5

and Nouman Rasool 5
1
Department of Healthcare Biotechnology, Atta ur Rahman School of Applied Biosciences,
National University of Science and Technology Islamabad, Pakistan
2
Medicare Health Services, Lahore, Pakistan
3
Department of Biotechnology, Khawaja Fareed University of Science and Technology, Rahim Yar Khan, Pakistan
4
National Center of Artificial Intelligence, Punjab University College of Information Technology, University of the Punjab,
Lahore, Pakistan
5
Center for Professional and Applied Studies, Lahore, Pakistan

Correspondence should be addressed to Nouman Rasool; [email protected]

Received 6 June 2020; Revised 4 August 2020; Accepted 12 August 2020; Published 13 October 2020

Academic Editor: Antonello Merlino

Copyright © 2020 Kafila Kousar et al. This is an open access article distributed under the Creative Commons Attribution License,
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Coronaviruses have been reported previously due to their association with the severe acute respiratory syndrome (SARS). After
SARS, these viruses were known to be causing Middle East respiratory syndrome (MERS) and caused 35% evanescence amid
victims pursuing remedial care. Nowadays, beta coronaviruses, members of Coronaviridae, family order Nidovirales, have
become subjects of great importance due to their latest pandemic originating from Wuhan, China. The virus named as human-
SARS-like coronavirus-2 contains four structural as well as sixteen nonstructural proteins encoded by single-stranded
ribonucleic acid of positive polarity. As there is no vaccine available to treat the infection caused by these viruses, there is a dire
need for taking necessary steps against this virus. Herein, we have targeted two nonstructural proteins of SARS-CoV-2, namely,
methyltransferase (nsp16) and helicase (nsp13), respectively, due to their substantial activity in viral pathogenesis. A total of
2035 compounds were analyzed for their pharmacokinetics and pharmacological properties. The screened 108 compounds were
docked against both targeted proteins and were compared with previously reported known compounds. Compounds with high
binding affinity were analyzed for their reactivity through DFT analysis, and binding was analyzed using molecular dynamics
simulations. Through the analyses performed in this study, it is concluded that EryvarinM, Silydianin, Osajin, and Raddeanine
can be considered potential inhibitors for MTase, while TomentodiplaconeB, Osajin, Sesquiterpene Glycoside, Rhamnetin, and
Silydianin for helicase after these compounds are validated thoroughly using in vitro and in vivo protocols.

1. Introduction agents for SARS-CoV, so the use of face mask, hand washing,
and careful disposal of medical equipment and other
Coronaviruses have become a source of multiple systematic materials infected with nasal secretions are preliminary pre-
infections in various animals [1]. These viruses have previ- ventive measures which must be followed to avoid the spread
ously caused respiratory tract infections in humans, includ- of the pandemic virus [3]. The initial clinical manifestations
ing severe acute respiratory syndrome and the Middle East in the SARS-CoV infected patients observed were fever,
respiratory syndrome [2]. As there are no specific therapeutic cough, headache, myalgia, diarrhoea, dyspnea, leucopenia,
2 BioMed Research International

lymphopenia, thrombocytopenia, hypoxaemia, pulmonary They provide an operative platform, where scientists can ana-
infiltration, and disturbed hepatic and renal function leading lyze a wide range of biological phenomena, different pathways,
to death in some individuals [4]. and molecular interactions. These methods are primarily cost-
The genome of SARS-CoV is 30 kb encoding 27 proteins effective and consist of authentic methods which predict the
and has 14 ORFs. These proteins are further classified as results with the highest accuracy [21, 22].
structural proteins and nonstructural proteins. The structural The present study aims at the in silico analysis of two
proteins like nucleocapsid protein (N), pike surface glycopro- nonstructural proteins of novel coronavirus (SARS-CoV-2),
tein (S), a small envelope protein (E), and matrix protein (M) i.e., helicase (nsp13) and methyltransferase (nsp16). The
are known to play a role in binding to host receptors. The study is performed opting standard protocols of computer-
genome of the virus encodes 16 nonstructural proteins like aided drug discovery, as previously mentioned in a series of
Helicase (nsp13), RNA-dependent RNA polymerase publication [23–35]. The analyses performed included
(nsp12), Papain-like protease (nsp3), main protease (nsp5) ADMET analysis of phytochemicals, molecular docking of
also known as 3C-like protease (3CLpro), and 2 ′ O methyl- phytochemicals with targeted proteins of a novel coronavi-
transferase (nsp16). The nonstructural proteins are likely to rus, binding analysis through molecular dynamics (MD)
be involved in transcription, replication, and pathogenesis simulations, and reactivity analysis through density func-
and play a vital role in the life cycle of the pathogen [5–9]. tional theory (DFT) calculations.
Owing to the critical role of nonstructural proteins of the
virus in virulence, these proteins are potential targets for 2. Materials and Methods
antiviral drugs [9].
Helicase of coronavirus is a member of superfamily-I Herein, the MTase and helicase of the novel coronavirus were
helicase comprising of seven conserved regions. This protein targeted for the identification of candidate inhibitors; thus, a
winds down partially duplex ribonucleic acid in a 5 ′ to 3 ′ series of analyses were performed, and the flowchart is shown
way to make it open [10]. The helicase (nps13) of SARS- in Figure 1.
CoV belongs to superfamily 1 (SF1) of the six helicase super-
families; the division is based upon various specified regions. 2.1. Obtaining the Phytochemicals. The datasets comprising
This enzyme can open up both ribo- and deoxyribonucleic of a wide range of phytochemicals (2035) were collected by
acid duplexes in 5 ′ to 3 ′ direction [11]. The associated using two different databases [36, 37] and also have been
NTPase action can target all-natural nucleotides and deoxy- reported previously in [35] (Table S1). The set comprised
nucleotides as substrates [12]. It is also reported that SARS- of a variety of phytochemical groups, i.e., 322 alkaloids, 113
CoV-nsp12 can improve the helicase action of SARS-nsp13 terpenoids, 105 aurones, 101 chalcones, 378 flavonoids, 211
by cumulative action on nucleic acid (dsRNA or dsDNA) lignans, 255 carboxylic acids, 301 polyphenols, and 249
unwinding by 2-folds [13]. quinones [35]. The 3D structures for the phytochemicals
There are almost a dozen conserved motifs in SF1 heli- were obtained from PubChem (https://pubchem.ncbi.nlm
cases, those involved in direct binding with nucleic acid tri- .nih.gov/). The pharmacological and pharmacokinetic
phosphates and nucleic acids. Two motifs known as Walker properties based on parameters of ADMET (Absorption,
A and B are common in all of members of this super family. Distribution, Metabolism, Excretion and Toxicity) were
By investigating the structure of the enzyme, it is revealed evaluated with the help of the SwissADME web server [38]
that the two RecA-like domains (1A and 2A) constitute the and PreADMET server [39], as reported in [23, 26, 28, 29,
catalytic site of SF1 helicases. This enzyme is known to be 31]. SwissADME server was utilized for the determination
engaged in synthesis of viral RNA and also manipulates the of ADME properties of the phytochemicals, while
DNA of host [13–15]. 2 ′ -O-MTase (2’O methyltransferase) PreADMET was utilized to assess the druglikeness features
of coronaviruses is highly conserved and is known to play and toxicity level of the drug. The structural file (.SDF) of
an indispensable role in viral replication and evasion from the 2035 phytochemicals was utilized for the prediction
innate immunity [16]. It is also reported that the methyl- purposes.
transferases are vital for viral replication in cell cultures.
Another protein nsp10 is also crucial for the proper function- 2.2. Homology Modelling. The crystal structure of MTase was
ing of MTase activity in the host cells for proliferation [17, available at RCSB with PDB ID: 6W61; however, helicase
18]. Due to the conserved nature of this enzyme and its role structure was unavailable. For protein structure prediction
in virulence, this enzyme is an ideal target for potential anti- and homology modelling, the polypeptide sequence of
viral agents and vaccines against SARS-CoV-2, SARS-CoV, SARS-CoV-2 (GenBank ID: QHD43415.1) was used, com-
MERS-CoV, or other RNA and DNA viruses [19]. prising 7096 residues. For mapping helicase sequence, multi-
Phytochemicals have been known from ancient times for ple sequence alignment was performed between targeted
their immense potential and beneficial properties against sev- sequence and SARS-CoV sequence (UniProt Acc ID:
eral infectious diseases and health-related complications [20]. P0C6X7). Later on, homology modelling was performed.
The phytochemicals constitute magnificent potentials, specifi- PSI-BLAST method was performed for template structure
cally antiviral properties, and can be used in treating viral which was homologous to the helicase. Thus, it was observed
infections. With time, in silico approaches are gaining much that the sequence of helicase showed 96.08% similarity with
attention around the world for their advanced strategies and 6YJT. The Modeller 9.18 was used to perform the homology
effective techniques related to the field of medical sciences. modelling with help of 6YJT structure [40]. Opting
BioMed Research International 3

Protein structure
Phytochemicals retrival and Binding analysis Reactivity
collection and initial prediction through MD analysis through
screening through through simulations DFT
ADMET homology
modelling

Figure 1: Flowchart of methodology.

homology modelling, 100 models were predicted and evalu- Table 1: Grid box dimensions for receptors (Å3).
ated based on Discrete Optimized Protein Energy (DOPE)
Receptor Grid box dimensions
score. The structure quality assessment was performed by
the Ramachandran Plot using RAMPAGE tool [41]. For MTase 26 × 20 × 18
identifying pocket, POVME 2.0 was used [42]. Helicase 20 × 18 × 18

2.3. Molecular Docking and Binding Analysis. The possible

inhibitory effects of these naturally occurring compounds and for all simulations, standard pH of 7.0 was considered.
were evaluated by the docking method against the targeted This set of constraints was selected due to keeping the simu-
both proteins. AutoDock Tools and AutoDock Vina were lations similar to the human biological system. The duration
used for molecular docking of proteins and ligands [43–45]. for both equilibrations was 1 ns whereas the force field used
Binding energies were estimated, and interactions were ana- in both equilibrations was Particle Mesh Ewald (PME) with
lyzed. Using binding affinities, K i values were also calculated a cubic interpolation implementation [48]. The hydrogen
by equation (1) bonds were readjusted with the help of Linear Constraint
Solver (LINCS) technique while performing equilibrations
ΔG [49]. The final production MD simulation was performed
Ki = , ð1Þ for 50 ns, keeping the method same as equilibrations [50].
eR x T
2.4. Reactivity Studies through DFT. Density functional the-
where ΔG represents binding energy, T depicts the tempera- ory (DFT) analysis was performed to study the reactivity of
ture which is 298.15 k, and R depicts gas constant with value ligands with MTase and helicase. For analysis, HOMO (high-
1.9872036 kcal/mol. To find out the binding affinity of inhib- est occupied molecular orbital) and LUMO (lowest unoccu-
itors with targeted proteins, docking was performed. A grid pied molecular orbital) energies were computed. The ΔE
box was generated with the help of AutoDock Tools, and (band energy gap) calculation was performed using the
sizes of x, y, and z were determined. Grid box dimensions expression ELUMO − EHOMO . These descriptors are based on
are provided in Table 1. Binding affinity values of these quantum mechanics and its computations and were per-
ligands were determined to evaluate how well they interact formed using the program named ORCA [51]. B3LYP
with the protein of interest. The docking was performed with exchange-correlation functional was employed for calcula-
6 different exhaustiveness heuristics which were E = 4, E = 8, tions, which is a hybrid exchange-correlation functional.
E = 16, E = 32, E = 64, and E = 128. However, no deviation Generally, the hybrid exchange-correlation is a combination
was observed in the values of binding affinity after E = 8. of Hartree-Fock exact exchange functional and any other
The output files obtained from docking were used for struc- density functional. However, the targeted correlation, i.e.,
tural analysis in the Discovery Studio 2.5 [46]; thus, 2D and B3LYP, is defined as:
3D structural images for binding were generated.
Constant temperature MD simulations were performed LDA


EB3LYP
xc = ELDA
x + a0 EHF
x − Ex + ax EGGA
x − ELDA
x
to study the stability in the binding of phytochemicals with
ð2Þ
MTase and helicase using Groningen Machine for Chemical + ELDA
c + ac EGGA
c − ELDA
c ,
Simulations (GROMACS) v 5.0 [47]. Only those complexes
were analyzed, where phytochemicals showed high binding where a0 = 0:20,ax = 0:72, and ac = 0:81. EGGA
x is the general-
affinity. For all those protein-ligand complexes, the opti- ized gradient approximation for the Becke 88 functional
mized potential for liquid simulation (OPLS-AA) was while the EGGA
c reflects the correlation functional of Lee-
applied, and the system was solvated with spc216 water mol- Yang-Parr. With this hybrid functional, local density approx-
ecules. This solvated system was neutralized by adding coun- imation is added in the form of ELDA
c [52].
ter ions of Na+ and Cl-. At the next step, this system was
subjected to energy minimization with the steepest descent 3. Results and Discussion
method, keeping step limit as 50000. Later on, constant
Number Volume and Temperature (NVT) and constant Human CoVs are zoonotic pathogens, originating from ani-
Number Pressure and Temperature (NPT) equilibrations mals, infecting humans leading to respiratory complications.
were performed with 1 atm pressure and at 300 K. Explicit All HCoVs provide substantial evidence of its origin from
water molecules were also added in the phosphoserine sites, bats [53]. Phylogenetically related CoVs in bats and humans
4 BioMed Research International

Figure 2: Predicted 3D model for helicase. Red depicts α-helices; β-purple depicts the strands while green depicts random coil.

180

0
Ψ

–180
–180 0 180

Figure 3: Ramachandran plot for predicted helicase model.

BioMed Research International 5

Table 2: Results of molecular docking of Remdesivir, Prulifloxacin, and Nelfinavir with MTase of SARS-CoV-2.

Sr. no Compound name Binding affinity (kcal/mol) K i value (μM) Interactions with MTase of SARS-CoV-2

1 Nelfinavir -8.2 1.138

2 Prulifloxacin -7.6 2.648

3 Remdesivir -7.0 7.299

suggest host switches. SARS-CoV switched hosts from herein, another set of phytochemicals has been used to target
Rhinolophid bats to palm civets and human [54]. The evolu- MTase and helicase.
tionary studies also showed that bats also host MERS-like The criteria for evaluating the compounds based on their
virus suggesting bats as MERS-CoV source; infecting ADMET profiles was “Violations from Lipinski’s rule = Zero;
humans had evidence that camels might also be its likely Soluble = High/Very High; Absorption in Gastrointestinal
source [55]. These viruses can transmit to humans, directly (GI) tract = Efficient or Moderate; Blood-brain barrier
or indirectly [56]. (BBB) permeability = No; and Toxicity/carcinogenicity =0”
Currently, there is no suitable vaccine available which can [58]. Through the screening criteria for their ADMET prop-
be used to cure infections caused by the novel coronavirus erties, 108 phytochemicals out of 2035 qualified for perform-
currently named as COVID-19. It is highly needed to design ing the further analysis (Table S2). These selected
a drug or a vaccine to treat this virus as well as to reduce the phytochemicals were prepared for molecular docking with
viral deportment so that its spread could be limited. Repur- our targeted proteins.
posing of drugs is a remarkable approach to opt antiviral
compounds as COVID-19 drug candidates [57]. Recently, a 3.1. Structure Evaluation for Helicase. The structure of heli-
study has been reported targeting the main protease of case was modelled using homology modelling due to unavail-
SARS-CoV-2, using a set of phytochemicals [30]. However, ability of X-ray crystallographic structure. As the predicted
6 BioMed Research International

Table 3: Results of molecular docking of Remdesivir, Prulifloxacin, and Nelfinavir with helicase of SARS-CoV-2.

Sr. no Compound name Binding affinity (kcal/mol) K i value (μM) Interactions with helicase of SARS-CoV-2

1 Prulifloxacin -8.1 1.138

2 Remdesivir -6.8 10.234

3 Nelfinavir -6.2 28.205

model with the lowest DOPE score was used further, it was residues in helicase model, it was observed that 98.0% resi-
observed to be -24913.17, and the predicted model is shown dues were in the favoured region, and 1.9% residues were in
in Figure 2. the allowed region while only 0.1% residues were in outlier
For quality assessment of the structure, the region (Figure 3).
Ramachandran plot was generated for the predicted model
using RAMPAGE tool [41]. As per the analysis of possible 3.2. Molecular Docking and Binding Stability. Initially,
conformations of φ and ψ angles for individual amino acid Remdesivir, Prulifloxacin, and Nelfinavir were docked with
BioMed Research International 7

Table 4: Results of molecular docking of MTase of SARS-CoV-2.

Sr. no Compound name Binding affinity (kcal/mol) K i value (μM) Interactions with MTase of SARS-CoV-2

1 EryvarinM -8.6 0.489

2 Silydianin -8.5 0.579

3 Osajin -8.2 0.961

8 BioMed Research International

Table 4: Continued.

Sr. no Compound name Binding affinity (kcal/mol) K i value (μM) Interactions with MTase of SARS-CoV-2

4 Raddeanine -8.2 0.961

H-Bonds
Donor

Acceptor

Figure 4: 3D interaction model for EryvarinM docked with MTase.

MTase and helicase, and the binding affinities of these com- A recent paper reported an inhibitor effect of Remdesivir (a
pounds were used as a threshold for screening phytochemi- new antiviral drug) on the growth of SARS-CoV-2 in vitro,
cals (Tables 2 and 3). Based on the results, it was observed and an early clinical trial conducted in SARS-CoV-2 Chinese
that threshold for screening phytochemicals for MTase was patients [61]. When Remdesivir interacted with MTase and
-8.2 kcal/mol, and for helicase, it was -8.1 kcal/mol. Using helicase, it showed -7.0 kcal/mol and -6.8 kcal/mol binding
these thresholds, phytochemicals were screened and further affinity, respectively. Recent studies proposed a few drugs
analyzed for stability and reactivity. that target COVID-19 and suggested these compounds could
Herein, we selected Nelfinavir, Prulifloxacin, and be used to treat COVID-19 [62]. Prulifloxacin gave -7.6 kcal/-
Remdesivir from three different drug repurposing studies mol with MTase and -8.1 kcal/mol with helicase. Nelfinavir, a
and docked them as controls in the present study [59, 60]. repurposed drug, is previously known for its selectively
BioMed Research International 9

Table 5: Results of molecular docking of helicase of SARS-CoV-2.

Sr. Binding affinity K i value

Compound name Interactions with helicase of SARS-CoV-2
no (kcal/mol) (μM)

1 TomentodiplaconeB -8.4 0.685

2 Osajin -8.2 0.961

Sesquiterpene
3 -8.2 0.961
Glycoside
10 BioMed Research International

Table 5: Continued.

Sr. Binding affinity K i value

Compound name Interactions with helicase of SARS-CoV-2
no (kcal/mol) (μM)

4 Rhamnetin -8.1 1.138

5 Silydianin -8.1 1.138

inhibitory properties against HIV protease. This enzyme EryvarinM docked with MTase with a binding affinity of
performs the posttranslational treatment of HIV propep- -8.6 kcal/mol with a K i value of 0.489 μM while forming a
tides. Undeveloped, noninfectious viral particles form in conventional hydrogen bond with ASN6841, ASP6873,
the cells containing this drug [63]. When Nelfinavir was ASN6899, CYS6913, and LYS6968. Formation of pi-cation and
docked against MTase, it showed binding affinity of pi-anion was observed with LYS6844 and ASP6897. Further-
-8.2 kcal/mol, while for helicase, it gave binding affinity value more, along with these interactions, pi-alkyl interactions with
of -6.2 kcal/mol. MET6929 and LEU6898 were observed (Figure 4).
Silydianin docked with binding affinity -8.5 kcal/mol and
3.2.1. Results of Molecular Docking of MTase of SARS-CoV-2. K i value of 0.579 μM while interacting with GLY6911,
All 108 compounds, initially screened through ADMET, ASP6928, CYS6913, and ASN6899, by forming conventional
were docked with MTase of SARS-CoV-2, and the threshold hydrogen bonds. Furthermore, it formed a carbon-
used for screening phytochemicals was -8.2 kcal/mol. Thus, hydrogen bond and pi-acceptor-acceptor interactions with
by applying the threshold, it was observed that only four MET6929 and ASP6897, while pi-alkyl and alkyl interactions
compounds passed the threshold which were EryvarinM, with LEU6898, PHE6947, and LYS6944 were observed.
Silydianin, Osajin, and Raddeanine and showed similar or Osajin and Raddeanine docked with binding affinity
better results than those of Remdesivir, Prulifloxacin, and -8.2 kcal/mol and K i value of 0.961 μM. Osajin formed a con-
Nelfinavir (Table 4). ventional hydrogen bond with ASP6928; while Raddeanine
BioMed Research International 11

H-Bonds
Donor

Acceptor

Figure 5: 3D interaction model for TomentodiplaconeB docked with helicase.

Table 6: Average RMSD values for all complexes.

formed conventional hydrogen bonds with ASP6912, CYS6913,
LEU6898, and ASN6841, however various other interactions Complex Average RMSD (Å)
were observed as shown in Table 4.
MTase-EryvarinM 1.95
3.2.2. Results of Molecular Docking of Helicase of SARS-CoV- MTase-Silydianin 2.05
2. After analyzing the ligand interactions with the binding MTase-Osajin 2.99
pocket of MTase, selected phytochemicals were auto docked MTase-Raddeanine 3.12
with helicase of SARS-CoV-2. All 108 compounds, initially Helicase-TomentodiplaconeB 2.11
screened through ADMET, were docked with helicase of Helicase-Osajin 2.32
SARS-CoV-2, and the threshold used for screening phyto- Helicase-Sesquiterpene Glycoside 2.46
chemicals was -8.1 kcal/mol. Thus, by applying the threshold,
Helicase-Rhamnetin 2.76
it was observed that only five compounds passed the thresh-
old which was TomentodiplaconeB, Osajin, Sesquiterpene Helicase-Silydianin 3.31
Glycoside, Rhamnetin, and Silydianin and showed similar
or better results than those of Remdesivir, Prulifloxacin,
and Nelfinavir (Table 5). and SER310; pi-cation and anion with ASP534 and ARG560;
TomentodiplaconeB formed carbon-hydrogen bond with carbon-hydrogen bond and pi-sigma interactions with
ARG129, amide pi-stacked with GLU128, and alkyl and pi- PRO408; and amide pi-stacked with ALA407 as well as pi-
alkyl interactions with PRO23, 234, and 238, LEU132, VAL6, alkyl with PRO406 and ARG409. Silydianin formed conven-
PHE24, and ARG1. As in result, the binding affinity was tional hydrogen bonds with ARG129 and ASN9. Furthermore,
-8.4 kcal/mol while Ki was 0.685 μM (Figure 5). it formed pi-alkyl and alkyl interactions with PHE133,
Both, Sesquiterpene Glycoside and Osajin docked with a LEU132, VAL6, and PHE24.
binding affinity of -8.2 kcal/mol and K i of 0.961 μM. Sesqui-
terpene Glycoside formed conventional hydrogen bonds with
ARG21 and ARG129, ASN9, and GLU136; donor interactions 3.2.3. Stability in Complexes Analyzed through MD
with ARG22; carbon-hydrogen bond with PHE133; and pi- Simulations. After analyzing the interactions of ligands with
alkyl interactions with LEU132, VAL6, and PRO234. Osajin targeted receptors, the MD simulations were performed to
formed conventional hydrogen bonds with ARG21 and analyze the stability in complexes and binding of ligands with
ARG129 and alkyl and pi-alkyl interactions with LEU132 and the proteins. These MD simulations helped in estimating the
VAL6. stability of binding of screened ligands with SARS-CoV-2
Both, Rhamnetin and Silydianin docked with a binding proteins. The radius of gyrations (Rg ) was plotted to analyze
affinity of -8.1 kcal/mol and K i of 1.138 μM. Rhamnetin the stability in complexes, while the root means square devi-
formed conventional hydrogen bonds with ASP179, ARG178, ation (RMSD) values were also observed for whole
12 BioMed Research International

Rg graph for helicase complexes at 300 K

3.50

3.00

2.50

2.00

1.50

1.00

0.50

0.00
0 5000 10000 15000 20000 25000 30000 35000 40000 45000 50000
TomentodiplaconeB Rhamnetin
Osajin Silydianin
Sesquiterpene glycoside
(a)
Rg graph for MTase complexes at 300 K
3.00

2.50

2.00

1.50

1.00

0.50

0.00
0 5000 10000 15000 20000 25000 30000 35000 40000 45000 50000
EryvarinM Osajin
Silydianin Raddeanine
(b)

Figure 6: MD simulations based Rg graphs of complexes for strongly binding phytochemicals: (a) complexes of helicase; (b) complexes of
MTase.

simulations. Average RMSD values are reported in Table 6, of gyration. These values depict high stability, compactness,
while graphs of the radius of gyration are shown in Figure 3. and stable folding of protein tertiary structure, as well as
According to the results shown in Table 6, the RMSD stability in protein-ligand complexes. The changes and fluc-
values were observed to have mere changes, while looking tuations were observed in all complexes and not in any spe-
in complexes of same receptors; however, these values were cific complex. The complexes with less binding affinity
very low, i.e., less than 3.50 Å. Furthermore, the graphs showed a decrease in stability and compactness, as these
shown in Figure 6 depicted fewer fluctuations in the radius compounds were not bound strongly. These trends and
BioMed Research International 13

Table 7: Reactivity of phytochemicals with helicase and MTase depicted by band energy gaps.

Complexes ELUMO (kcal/mol) EHOMO (kcal/mol) Band energy gap (ΔE) (kcal/mol)
MTase-EryvarinM -0.274 -0.391 0.112
MTase-Silydianin -0.236 -0.351 0.115
MTase-Osajin -0.271 -0.400 0.129
MTase-Raddeanine -0.242 -0.375 0.133
Helicase-TomentodiplaconeB -0.280 -0.395 0.116
Helicase-Osajin -0.218 -0.335 0.117
Helicase-Sesquiterpene Glycoside -0.198 -0.321 0.123
Helicase-Rhamnetin -0.303 -0.428 0.125
Helicase-Silydianin -0.118 -0.246 0.128

results are also in accordance with various previously International Concern on 30 January 2020. However, still,
reported results [33, 60]. there exists no remedy, drug, or vaccine for the treatment
of COVID-19. This study provides insights into the mecha-
3.3. Reactivity Studies for Phytochemicals and Targeted nism of selective phytochemicals, when docked against two
Proteins’ Complexes. Reactivity of bound phytochemicals main targets of a novel coronavirus, MTase and helicase, by
with helicase and MTase was analyzed through density func- showing their pharmacological properties, binding and its
tional theory- (DFT-) based computations, which works on stability, and the reactivity. Through analysis, it is concluded
the principles of quantum mechanics and its descriptors. that phytochemicals such as EryvarinM, Raddeanine,
The result showed that the phytochemicals with the broad TomentodiplaconeB, Osajin, Sesquiterpene Glycoside,
range of chemical diversity exhibited good binding interac- Rhamnetin, and Silydianin can be considered as candidate
tions with both the proteins. EryvarinM, Silydianin, Osajin, inhibitors for targeted proteins and as drugs, after their
and Raddeanine, which mainly exhibited best docking results in vitro and in vivo examinations.
for MTase, were further selected for reactivity analysis, while
for helicase, TomentodiplaconeB, Osajin, Sesquiterpene
Glycoside, Rhamnetin, and Silydianin were selected. For
Data Availability
studying reactivity, band energy gap was computed using The data used to support the findings of this study are
molecular orbital energy descriptors, and the results are included within the supplementary information files.
shown in Table 7.
Lower band energy gaps show high reactivity; thus, these
results exhibited in Table 7 exhibited high reactivity of phy- Conflicts of Interest
tochemicals with targeted receptors. The band energy gap
The authors declare that there is no conflict of interest
values for these phytochemicals ranged from 0.112 kcal/mol
to 0.133 kcal/mol and 0.116 kcal/mol to 0.128 kcal/mol, for regarding the publication of this paper.
MTase and helicase, respectively, showing narrow energy
gaps and proving their high reactivity properties. B3LYP Supplementary Materials
function from DFT was applied to analyze the molecular
orbital energies, and it is well established in the literature Table S1: list of 2035 phytochemicals and their plants.
that the lower band energy gap depicts higher reactivity of Table S2: ADMET of Screened 108 Phytochemicals.
compounds. The reason is that band energy gaps are com- (Supplementary Materials)
puted through molecular descriptors, and these descriptors
are responsible for the charges transferred in a chemical References
reaction [64]. These energies can characterize the electro-
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