Article  
Molecular docking, prediction of drug-likeness properties, and  
toxicity risk assessment of compounds from Cinnamomum  
zeylanicum as inhibitors of Dengue DEN2 NS2B/NS3.  
Neni Frimayanti1* , Armon Fernando1, Rizka I’zaa Rahmah1, Benni Iskandar1  
1Department of Pharmacy, Sekolah Tinggi Ilmu Farmasi Riau, Jalan Kamboja, Simpang Baru, Pekanbaru,  
28293 Indonesia  
Abstract  
Dengue hemorrhagic fever (DHF) is a serious mosquito-borne disease caused by the dengue virus, most  
often transmitted by the bite of female Aedes aegypti mosquitoes. In Indonesia, the number of DHF cases  
has steadily increased since the disease was first reported, underscoring the urgent need for effective  
treatments. This study used in silico methods to explore the potential of three bioactive compounds from  
Cinnamomum zeylanicum i.e. cinnamaldehyde, α-terpineol, and chavicol as inhibitors of the dengue virus  
NS2B/NS3 protease and evaluated their drug-likeness and potential toxicity. The compounds sourced  
from the NADI database were compared with panduratin A as a positive control. Molecular docking was  
performed using the Molecular Operating Environment (MOE) 2023.0901 software, and drug-likeness  
and toxicity predictions were performed using SwissADME and Protox-II. Among the tested compounds,  
α-terpineol exhibited the strongest potential to inhibit NS2B/NS3, while all three met the standard drug-  
likeness criteria. Notably, α-terpineol demonstrated the most favorable safety profile compared to  
cinnamaldehyde, chavicol, and panduratin A  
Keywords: Cinnamomum zeylanicum; Dengue DEN2 NS2B/NS3; Docking; Drug-likeness; Toxicity  
Graphical Abstract  
*
Corresponding author  
Received April 30th 2025; Accepted August 18th 2025; Available online November 04th 2025  
Copyright © 2025 by Authors, Published by Chempublish Journal. This is an open access article under the CC BY License  
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Introduction  
immunomodulatory effects  
[3]. It has  
against various  
pathogens in  
demonstrated  
bacterial and  
efficacy  
fungal  
Dengue hemorrhagic fever (DHF) is an  
infectious disease caused by a virus that is  
transmitted by a vector. Dengue infection is  
caused by the dengue virus. This virus  
belongs to the arbovirus group (arthropod-  
borne virus) within the genus Flavivirus and  
family Flaviviridae. The dengue virus has four  
serotypes: dengue virus 1, 2, 3, and 4 (DENV-  
1, DENV-2, DENV-3, and DENV-4). The most  
common serotype of dengue virus that  
causes infection in the human body is DENV-  
2. Replication of DENV-2 requires a complex  
experimental models, making it a promising  
lead for the development of anti-infective  
drugs [3]. Phenolic compounds, including  
those  
found  
in  
cinnamon,  
have  
demonstrated antiviral activity against the  
dengue virus (DENV) through multiple  
mechanisms  
targeting  
viral  
particles,  
proteins, and host pathways [4]. Natural  
compounds and their analogs, such as  
alkaloids, phenols, and terpenoids, have  
shown potential in inhibiting DENV entry and  
of  
non-structural  
proteins,  
specifically  
replication  
[5].  
Cinnamon  
and  
its  
protein non-structural 3 (NS3) and its  
cofactor (NS2B), known as NS2B/NS3 serine  
protease. NS3 is responsible for proteolytic  
processes of viral proteins, whereas NS2B  
acts as a cofactor for the replication of DENV-  
2. It is likely that this protease could be a  
potential target for dengue drugs by  
blocking the interaction between the NS3  
protease and its cofactor protein NS2B [1].  
constituents, particularly cinnamaldehyde,  
exert antibacterial effects by damaging cell  
membranes, inhibiting ATPases, cell division,  
and biofilm formation, and disrupting  
quorum sensing [6]. These findings support  
the  
exploration  
of  
cinnamon-derived  
compounds as potential therapeutic agents  
for various microbial infections. Thus, in this  
research three of these compounds (i.e  
cinnamaldehyde, α-terpineol, and chavicol)  
are investigated as potential ligands in  
molecular docking studies to assess their  
inhibitory activity against the Dengue virus  
serotype 2 (DEN2) NS2B/NS3 protease.  
Dengue fever remains a global health  
concern, with an alarming increase in the  
number of dengue cases reported each year.  
The DEN2 NS2B/NS3 protease is a pivotal  
target in the development of antiviral agents,  
making it a promising target for drug  
discovery [2]. Currently, no specific antiviral  
drug has been approved for this disease. In  
this study, compounds were obtained from  
a database, that is NADI database which is a  
Recent studies have explored the potential  
of phytochemicals as inhibitors of dengue  
virus (DENV) NS2B/NS3 protease, a crucial  
target for antiviral drug development. In  
silico  
approaches,  
including  
molecular  
natural  
database contained of 77 compounds found  
in Cinnamomum zeylanicum, commonly  
product  
collection.  
The  
NADI  
docking, ADMET analysis, and molecular  
dynamics simulations, have been employed  
to screen and evaluate natural compounds  
known as cinnamon. Among these 77  
compounds, three were selected for the  
molecular docking studies: cinnamaldehyde,  
α-terpineol, and chavicol.  
against  
this  
enzyme  
[7-9].  
These  
investigations identified several promising  
phytochemicals with high binding affinities  
and favorable pharmacokinetic profiles.  
Notable compounds include erycristagallin,  
osajin, papraineA, and aloe-emodin [7], as  
Cinnamaldehyde, the primary compound in  
cinnamon essential oils, exhibits diverse  
well  
as  
3′,4′-methylenedioxy-7,8-(2″,2″-  
pharmacological  
antimicrobial,  
activities,  
antioxidant,  
including  
and  
dimethylpyrano)-flavone and limonianin [8].  
Additionally, compounds CID-440015 and  
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Chempublish Journal, 9(2) 2025,183-195  
CID-7424 have shown potential as novel anti-  
dengue agents [8]. These studies highlight  
the promise of natural products in the  
development of effective therapies against  
dengue fever, addressing the current lack of  
approved antiviral treatments for this  
globally significant disease.  
protein was carried out using Discovery  
Studio Visualizer (DSV, BIOVIA) by removing  
water  
chloride ions. The structure was then  
energy-minimized in MOE using the  
molecules,  
bound  
ligands,  
and  
CHARMM27 force field with an RMS gradient  
of 0.01 kcal/mol/Å. The binding site was  
identified using MOE’s Site Finder module,  
with Site 13comprising residues His51,  
Lys74, Asp75, Gly151, Asn152, Gly153, and  
Val154selected as the docking target and  
defined as a dummy atom.  
Molecular docking is  
technique that offers a unique perspective  
on the interactions between isolated  
compounds from Cinnamomum zeylanicum  
and DEN2 NS2B/NS3 protease [10].  
a
computational  
In MOE 2023.0901, docking simulations were  
performed using the London dG scoring  
function for initial posture generation and  
the Triangle Matcher placement approach.  
Force-field-based minimization was used for  
refinement, and the GBVI/WSA dG scoring  
algorithm was used for final rescoring. The  
best 10 poses with the lowest binding free  
energy (ΔG, kcal/mol) were selected for  
additional examination from 50 poses  
created for each ligand. The MOE Ligand  
Interaction Analysis tool was used to analyze  
and visualize proteinligand interactions,  
such as hydrogen bonds, hydrophobic  
contacts, and van der Waals interactions,  
using DSV.  
Simultaneously, evaluating the drug-likeness  
properties of these compounds is a crucial  
step in identifying those that not only  
interact favorably with the target, but also  
possess the necessary characteristics for  
successful drug development[11]. Predicting  
drug-likeness streamlines the selection  
process by highlighting the candidates with  
optimal  
pharmacokinetic  
and  
also  
pharmaceutical attributes.  
Materials and Methods  
Molecular Docking  
The molecular structures of the three  
compounds and panduratin A, which was  
used as a positive control, were sketched  
using ChemDraw 2015. Subsequently, the  
3D structures of these ligands were  
energetically optimized using the MOE  
2023.0901 software with the MMFF94x force  
field and a gradient of 0.0001. A ligand  
database in the *mdb format was generated  
ADMET Profiling and Toxicity Prediction  
To acquire ADME profiling and toxicity  
predictions, the process involved retrieving  
the SMILES formula for the chemical  
structures of compounds cinnamaldehyde,  
α-terpineol, and chavicol. These structures  
were obtained from the PubChem website  
by  
SwissADME (accessible  
http://www.swissadme.ch/index.php)  
visiting  
the  
following  
link:  
by  
incorporating  
all  
the  
molecular  
structures. Table 1 lists the molecular  
structures of the positive controls and  
molecular structures of all the ligands. The  
three-dimensional crystal structure of the  
dengue virus NS2B/NS3 protease (PDB ID:  
2FOM) was retrieved from the Protein Data  
Bank (www.rcsb.org). Pre-processing of the  
at  
was  
used for further analyses. Additionally, in  
silico toxicity data were obtained through  
the Protox II website by navigating to the  
Facetox predictions were performed.  
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Table 1: Molecular structure of ligands and positive control  
No  
Molecular name  
Molecular structure  
Cinnamaldehyde  
(E)-3-phenylprop-2-enal  
Molecular formula: C9H8O  
Molecular weight: 132.16 g/mol  
Compound 1  
α -Terpineol  
2-(4-methylcyclohex-3-en-1-yl) propan-2-ol  
Molecular formula: C10H18O  
Molecular weight: 154.25 g/mol  
compound 2  
compound 3  
Chavicol  
4-allylphenol  
Molecular formula: C9H10O  
Molecular weight: 134.17 g/mol  
Panduratin A  
(2,6-dihydroxy-4-methoxyphenyl) ((1R,2R,3S)-4-  
methyl-3-(3-methylbut-2-en-1-yl)-1,2,3,6-  
tetrahydro-[1,1'-biphenyl]-2-yl) methanone  
Molecular formula: C26H30O4  
Positive control  
Molecular weight : 406.5 g/mol  
Result and Discussion  
green dashed lines. Additionally, Panduratin  
A engage in hydrophobic interactions with  
Arg54, represented by a blue ring, and with  
Asp75 through Van Der Waals interactions,  
marked by a red ring. Spatial arrangement of  
panduratin A is presented in Figure 1.  
Molecular Docking  
The molecular docking results for three of  
these compounds are presented in Table 2.  
Figure 1 shows the spatial arrangement of  
panduratin A as a positive control. Based on  
the docking results, Panduratin A used as a  
positive control, exhibited a binding free  
energy of -6.55 kcal/mol with an RMSD value  
of 1.65 Å. It can interact with 10 amino acid  
residues at the active site of the receptor.  
These residues included His51, Arg54,  
Asp75, Tyr161, Val72, Gly151, Leu128,  
In the docking results of compound 1 (Table  
2), it was observed that the binding free  
energy is -4.51 kcal/mol, with an RMSD value  
of 1.01 Å. Compound 1 binds to 11 amino  
acid residues at the active site of the  
receptor. These residues included Leu128,  
Tyr161, His51, Tyr150, Asn152, Phe130,  
Gly151, Gly153, Ser135, Ser131, and Pro132.  
Visualization of the docking results for  
compound 1 revealed interactions with  
various amino acid residues, including  
hydrogen bond interactions with Leu128's  
phenyl group, where the phenyl group acts  
as a hydrogen bond acceptor, marked by  
Asn152,  
Gly153,  
and  
Ser135.  
The  
visualization of the docking results indicated  
that Panduratin A formed a hydrogen bond  
interaction with the phenyl group of His51,  
where the phenyl group serves as the  
hydrogen bond acceptor, as denoted by the  
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Chempublish Journal, 9(2) 2025,183-195  
green dashed lines. Additional interactions  
were observed between Tyr161, His51,  
Tyr150, Asn152, Phe130, Gly151, Gly153,  
Ser135, Ser131, and Pro132. It is worth  
noting that compound 1 shares only five  
amino acid residues in common with the  
positive control (binding factor) in the  
docking results, specifically in interactions  
with Tyr161, Asn152, Gly151, Gly153, and  
Ser135. Spatial arrangement of compound 1  
is presented in Figure 1.  
Table 2. Docking results  
Binding free  
energy  
(kcal/mol)  
Hydrophobic  
interaction  
van der  
Waals  
The others  
interaction  
Binding  
Factor  
Compound  
RMSD  
1.6514  
H bond  
His 51  
Tyr 161, Val  
72, Gly 151,  
Leu 128, Asn  
152, Gly 153,  
Ser 135  
Positive  
control  
Panduratin  
A
-6.5575  
Arg54  
Asp75  
10  
Tyr 161, His  
51, Tyr 150,  
Asn 152, Phe  
130, Gly 151,  
Gly 153, Ser  
135, Ser 131,  
Pro 132  
compound 1  
-4.5104  
1.0129  
Leu 128  
-
-
5
Tyr 161, Gly  
153, Asn 152,  
Leu 128, Tyr  
150, Phe 130,  
Ser 135, Ser  
131, Gly 151,  
Pro 132  
Tyr 161, His  
51, Tyr 150,  
Asn 152, Gly  
151, Gly 153,  
Ser 135, Ser  
131, Pro 132  
Compound 2  
Compound 3  
-4.9748  
-4.7247  
1.1528  
1.0358  
His 51  
-
-
-
-
7
5
Leu 128,  
Phe 130  
Note: compound 1 is cynamaldehyde; compound 2 is α -Terpineol; compound 3 is chavicol  
Compound 2 was obtained the binding free  
energy of -4.97 kcal/mol and an RMSD of  
1.15 Å. Compound 2 can bind to 11 amino  
acid residues in the active site of the  
receptor, including His51, Tyr161, Gly153,  
Asn152, Leu128, Tyr150, Phe130, Ser135,  
Ser131, Gly151, and Pro132. Visualization of  
the docking results for compound 2 revealed  
interactions with the catalytic triad amino  
bonding on the benzene group, where the  
benzene group acts as a hydrogen bond  
donor, indicated by green dashed lines. It  
also interacts with other bonds in the amino  
acid residues Tyr161, Gly153, Asn152,  
Leu128, Tyr150, Phe130, Ser135, Ser131,  
Gly151, and Pro132.The docking results for  
compound 2 share seven amino acid  
residues in common with the positive  
control (binding factor), which were found in  
acid  
residue  
His51  
through  
hydrogen  
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Chempublish Journal, 9(2) 2025,183-195  
amino  
acid  
residues  
His51  
through  
the most favorable binding free energy  
hydrogen bonding and other interactions  
with amino acid residues Tyr161, Gly153,  
Asn152, Leu128, Ser135, and Gly151. Figure  
1 is presented the spatial arrangement of  
compound 2 with protein.  
(−4.97  
kcal/mol),  
compared  
to  
cinnamaldehyde and chavicol, suggesting  
enhanced stability of the ligandprotein  
complex.  
Hydrogen bonding patterns play a critical  
role in stabilizing the ligand orientation  
within the active site. α-Terpineol formed  
hydrogen bonds with the catalytic residue  
His51, a key interaction also observed with  
the positive control, contributing to its  
superior binding performance. In contrast,  
cinnamaldehyde and chavicol, although  
forming hydrogen bonds (e.g., with Leu128  
or Phe130), lacked interactions with His51,  
which may explain their relatively lower  
binding affinities.  
Compound 3 showed a binding free energy  
of -4.72 kcal/mol and an RMSD of 1.03 Å.  
Compound 3 can bind to 11 amino acid  
residues in the active site of the receptor,  
including Leu128, Phe130, Tyr161, His51,  
Tyr150, Asn152, Gly151, Gly153, Ser135,  
Ser131, and Pro132. Visualization of the  
docking results for compound 3 (Figure 1)  
revealed the amino acid residues involved in  
hydrogen bonding interactions. Specifically,  
Leu128 forms a hydrogen bond with the  
phenol group, which acts as a hydrogen  
bond acceptor, as indicated by the green  
dashed lines. Additionally, the amino acid  
residue Phe130 is involved in a hydrogen  
bond interaction with the hydroxyl group,  
where the hydroxyl group acts as a hydrogen  
bond donor, indicated by blue dashed lines  
with an arrow pointing towards amino acid  
The  
structural  
differences  
among  
the  
compounds also influenced their activity. α-  
Terpineol’s cyclic terpene backbone and  
hydroxyl group enable both hydrophobic  
contacts with non-polar residues (e.g.,  
Tyr161, Leu128) and polar interactions  
through  
Cinnamaldehyde,  
hydrogen  
with  
bonding.  
conjugated  
residue  
Phe130.  
Compound  
3
also  
its  
interacted with other bonds in the amino  
acid residues Tyr161, His51, Tyr150, Asn152,  
Gly151, Gly153, Ser135, Ser131, and Pro132.  
The docking results for compound 3 share  
only five amino acid residues with the  
positive control (binding factor), which are  
involved in other interactions, including  
amino acid residues Tyr161, Asn152, Gly151,  
Gly153, and Ser135.  
aldehyde group, offers planarity and π–π  
stacking potential; however, the absence of  
strong polar anchoring in the catalytic triad  
may limit its binding strength. Chavicol,  
which features an allylphenol structure,  
allows  
hydroxyl  
hydrophobic  
hydrogen  
group  
bonding  
but  
through  
exhibits weaker  
than α-  
its  
complementarity  
terpineol.  
The activity of the tested compounds against  
dengue NS2B/NS3 protease, as shown in  
Table 1 and Figure 1, can be attributed to a  
The docking results obtained in this study  
are consistent with previously reported  
findings for cinnamon-derived compounds.  
Cinnamaldehyde has been shown to exert  
antiviral effects against influenza A and  
herpes simplex viruses in vitro, with  
combination  
of  
molecular  
interaction  
parameters and inherent chemical structure  
features. Binding free energy is a primary  
determinant, with more negative values  
indicating a stronger binding affinity. Among  
the tested compounds, α-terpineol exhibited  
proposed  
mechanisms  
involving  
the  
inhibition of viral envelope fusion and  
suppression of replication [12]. In vivo  
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Chempublish Journal, 9(2) 2025,183-195  
studies have further demonstrated its anti-  
enveloped viruses, such as herpes simplex  
virus type 1 [14]. Although fewer antiviral  
studies are available for chavicol, phenolic  
derivatives with similar allyl side chains have  
demonstrated antibacterial, antifungal, and  
moderate antiviral activities  
inflammatory  
and  
immunomodulatory  
effects, which could indirectly contribute to  
its antiviral efficacy [13]. Similarly, α-  
terpineol  
possesses  
antimicrobial  
and  
antifungal properties and, in some cases,  
has displayed inhibitory effects against  
(a)  
(b)  
(d)  
(c)  
Figure 1: Spatial arrangement of (a) panduratin A (b) compound 1 (c) compound 2 (d)  
compound 3  
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When comparing docking affinities, the  
binding free energies of α-terpineol and  
cinnamaldehyde against dengue NS2B/NS3  
in our study are in line with previous  
computational investigations on terpenoid  
and phenylpropanoid derivatives, which  
reported similar interaction patterns with  
catalytic residues such as His51 and Asp75  
[15]. These findings suggest that the antiviral  
potential of cinnamon-derived compounds  
observed in vitro and in vivo may be partially  
explained by their ability to interact with key  
active site residues of viral proteases, as  
indicated by our in silico results.  
Superimposition  
depicted  
the  
conformational pose of the compound  
structure that best aligns with the positive  
control [16]. Based on the superimposition  
results  
(cinnamaldehyde), 2 (α-terpineol), and 3  
(chavicol) with the positive control  
(Figure  
2)  
of  
compounds  
1
(panduratin A), compound 2 (α-terpineol)  
was found to bind more effectively to the  
active site, forming a complex and sharing  
similar interactions with the positive control.  
Based on these findings, compound 2 (α-  
terpineol) could be categorized as a potential  
inhibitor of dengue NS2B/NS3  
(a)  
(b)  
(c)  
Figure 2. Superimposisition of panduratin A (green) with (a) compound 1 (b) compound 2 and  
(c) compound 3  
ADMET profiling and toxicity prediction  
(406.51 g/mol) respectively, fall within the  
acceptable range as they have molecular  
weights below the Lipinski rule's threshold of  
<500 g/mol [17]. Molecular weight is known  
to influence the ability of a compound to  
passively diffuse through cell membranes. If  
a compound has a molecular weight (MW) of  
>500 g/mol, its ability to diffuse through cell  
membranes becomes more challenging[18].  
Molecular weight also affects intestinal  
absorption, blood-brain barrier penetration,  
elimination rate, and interactions with target  
receptors [19].  
The findings from the SwissADME analysis  
for the three compounds isolated from  
Cinnamomum  
zeylanicum,  
specifically  
cinnamaldehyde, α-terpineol, and chavicol  
along with the panduratin A as positive  
control,  
have  
yielded  
drug-likeness  
parameters, as detailed in Table 3.  
The  
molecular  
weights  
obtained  
for  
compounds 1 (132.16 g/mol), 2 (154.25  
g/mol), 3 (134.18 g/mol), and panduratin A  
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Table 3. Drug-likeness  
Topological  
Hydrogen  
Bond  
Donor  
Hydrogen  
Polar  
Surface  
Area (TSPA  
Å)  
MW  
Compound  
Bond  
Acceptor  
(HBA)  
Log P  
Rotabl  
e Bond  
Drug-  
Likeness  
(g/mol)  
(HBD)  
Yes  
Score: 0.55  
Yes  
Score: 0.55  
Yes  
Score: 0.55  
Yes  
Score: 0.55  
-
Cinnamaldehyde  
α-Terpineol  
Chavicol  
132.16  
154.25  
134.18  
1.97  
2.58  
2.33  
0
1
1
1
1
1
17.07  
20.23  
20.23  
2
1
2
Panduratin A  
406.51  
< 5009  
4.77  
< 59  
2
4
66.76  
6
Parameter  
< 59  
< 109  
≤ 14010  
< 1010  
Based on the obtained Log P values for  
compounds 1 (1.97), 2 (2.58), 3 (2.33), and  
panduratin A (4.77), they met the Lipinski  
rule criterion with Log P values below of five  
[20]. Log P is a parameter that describes a  
required in the absorption process. If the  
number of hydrogen bond donors is >5 and  
the number of acceptors >10, the energy  
required for the absorption process is  
higher. The higher the number of hydrogen  
bond donors and acceptors, the higher the  
energy required for absorption process to  
occur [20].  
compound's  
ability  
to  
dissolve  
in  
octanol/water (biological membrane). As the  
Log P value increases, the compound  
becomes more hydrophobic. Compounds  
that are excessively hydrophobic tend to  
have higher toxicity because they remain  
trapped in lipid bilayers and are distributed  
extensively within the body, reducing target-  
The Topological Polar Surface Area (TPSA)  
has a value of ≤140 Å and the number of  
rotatable bonds (rotable bonds) has a value  
of <10[21]. TPSA is defined as the sum of the  
surface areas of polar atoms (mainly oxygen  
or nitrogen, including bound hydrogen) in a  
binding  
selectivity.  
Conversely,  
if  
a
compound's Log P value is more negative,  
crossing the lipid bilayers may be difficult  
[20].  
molecule.  
This  
parameter  
has  
been  
successfully applied to predict human  
intestinal absorption, single-layer CaCo-2 cell  
The Compounds 1, 2, 3, and panduratin A  
had hydrogen bond donor values of 0, 1, 1,  
and 2, respectively, while their hydrogen  
bond acceptor values were 1, 1, 1, and 4. It  
can be said that the hydrogen bond donor  
and acceptor values are good as they meet  
the Lipinski rule of having hydrogen bond  
donor values less than 5 and hydrogen bond  
acceptor values is less than 10 [17].  
hydrogen-bond donor and acceptor values  
are parameters used to describe the  
hydrogen-bond capacity of a compound  
permeability,  
and  
blood-brain  
barrier  
penetration [22]. Based on the results  
obtained, the TPSA values of compounds 1,  
2, 3, and A indicated good absorption with  
TPSA values ≤140 Å.  
The numbers of rotatable bonds for  
compounds 1, 2, 3, and pandurtatin A were  
2, 1, 2, and 6, respectively, which were all  
within the acceptable range. Lipinski's rule of  
five limits the number of rotatable bonds to  
no more than ten (rotatable bonds <10) for  
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Chempublish Journal, 9(2) 2025,183-195  
drug candidates [21]. Rotatable bonds are  
defined as the number of single bonds,  
excluding bonds in rings that can rotate  
freely around themselves.  
Table 4: Prediction toxicity level  
Compound  
LD50  
Toxicity Level11  
Hepatotoxicity  
Cinnamaldehyde  
α-Terpineol  
1850 mg/kg  
2830 mg/kg  
870 mg/kg  
2000 mg/kg  
Class IV  
Class V  
Class IV  
Class V  
Inactive  
Inactive  
Inactive  
Inactive  
Chavicol  
Panduratin A  
Generally, toxicity of compounds could be  
classified into six classes. Class 1 with LD50  
5, class II consist of compounds with LD50  
value ranging from 5 to 50, class III consist of  
compounds with LD50 value ranging from 50  
to 300. Compounds falling into class IV have  
liver. Compounds that can significantly  
induce hepatotoxicity may lead to liver  
damage, and are a major reason why drugs  
may not be marketed [25]. In the drug  
discovery process, drug-induced liver injury  
(DILI) is the most serious concern, as it often  
LD50 values from 300 to 2000.  
Class V  
leads  
to  
the  
termination  
of  
drug  
comprises compounds with LD50 between  
2000 to 5000. Finally, class VI includes  
development programs [26]. Based on the  
prediction results in this study, as presented  
in Table 4, it was found that none of the  
tested compounds exhibited hepatotoxicity,  
compounds  
with  
LD50  
>
5000  
[23].  
Compounds 1, 2, 3 and the positive control  
(panduratin A) have LD50 values of 1850  
and  
Therefore,  
they  
were  
it can  
considered inactive.  
be concluded that  
mg/kg,  
2830,  
870,  
and  
2000  
mg/kg,  
respectively. In this context, LD50 values  
within the range of 300 < LD50 5000 mg/kg  
indicate relatively low toxicity, falling into  
toxicity classes IV and V, which are  
panduratin A, compound 1, compound 2,  
and compound 3 are safe to use and do not  
cause harm to the live.  
Conclusion  
considered safe [23].  
Toxicity prediction  
suggests that the smaller the numerical  
value, the more toxic the compound is  
predicted to be; conversely, the larger the  
numerical value, the safer the compound  
[24].  
Docking of three isolates from cinnamon  
(Cinnamomum zeylanicum) predicted that  
compound 2 (α-terpineol) has the potential  
to inhibit dengue NS2B/NS3. Compound 2  
-terpineol) has binding free energy more  
negative  
than  
compounds  
1
The results of the Protox-I I analysis are  
displayed in Table 4, illustrating the toxicity  
levels observed in rodents for the three  
isolated compounds from Cinnamomum  
zeylanicum, cinnamaldehyde, α-terpineol,  
and chavicol along with the panduratin A as  
positive control. Hepatotoxicity indicated the  
level of damage caused by compounds in the  
(cinnamaldehyde) and 3 (chavicol). However,  
it was not more negative than Panduratin as  
the positive control. Based on the drug-  
likeness  
compounds exhibited good drug-likeness  
parameters according to Lipinski and  
Veber's rules. In terms of safety, compound  
property  
predictions,  
all  
test  
192  
Frimayanti et al.  
Chempublish Journal, 9(2) 2025,183-195  
2 -terpineol) was safer than compounds 1  
27(3):  
1157-1169.  
(cinnamaldehyde),  
3
(chavicol),  
and  
[3]. Guo, J.; Yan, S.; Jiang, X.; Su, Z.; Zhang,  
F.; Xie, J.; Hao, E.; Yao, C. Advances in  
panduratin A, as it had an LD50 value of 2830  
mg/kg, classifying it as practically non-toxic  
(toxicity class V). Thus, compound 2 -  
terpineol) has potency become new inhibitor  
for dengue DEN2 NS2B/NS3.  
pharmacological  
mechanism  
cinnamaldehyde.  
Pharmacology.  
effects  
action  
Frontier  
and  
of  
of  
in  
2024;  
15:1365949.  
Acknowledgement  
[4]. Loaiza-Cano, V.; Monsalve-Escudero  
Financial support from Sekolah Tinggi Ilmu  
Farmasi Riau through grant penelitian  
kompetitif 2024 is greatly acknowledged and  
appreciated.  
L.M;  
Filho,  
C.D.S.M.B.;.Martinez-  
Gutierrez, M.; de Sousa, DP. Antiviral  
Role of Phenolic Compounds against  
Dengue Virus: A Review. Biomolecules.  
2020;  
11(1):11.  
Author Contributions  
[5]. Komarudin, AG.; Adharis, A.; Sasmono,  
R.T. Natural Compounds and Their  
Analogs as Antivirals Against Dengue  
All authors have read and agreed to the  
published  
version  
of  
the  
manuscript.  
Conceptualization, research design, and  
methodology: N.F, A. F, Validation: N.F, A.F,  
B.I. All authors have read and agreed to the  
published version of the manuscript.  
Virus:  
A
Review”.  
Phytotherapy  
Research.  
2025;  
39(2):888-921.  
[6]. Vasconcelos, NG.; Croda, J.; Simionatto,  
S.  
cinnamon and its constituents: A  
review. Microbial Pathogenesis.  
2018;120:198-203.  
Antibacterial  
mechanisms  
of  
Conflict of Interest  
The authors declare no conflict of interest.  
[7]. Rasool, N.; Ashraf, A.A.; Waseem, M.;  
References  
[1]. Sutriyawan, A.; Aba, M.; and Habibi, J.  
Hussain,  
W.;  
&
Mahmood,  
S.  
Determinan  
Epidemiologi  
Demam  
Computational exploration of antiviral  
activity of phytochemicals against  
NS2B/NS3 proteases from dengue  
virus. Turkish Journal of Biochemistry  
2018; 44: 261 - 277.  
Berdarah Dengue (DBD) Di Daerah  
Perkotaan: Studi Retrospektif’. Journal  
of Nursing and Public Health 2020; 8(2):  
19.  
[8]. Bari, M.A.; Ahmed, S.; Perveen, F.F.;  
Akter, M.; Ahmed, N.; Hossain, J.;  
Nasrulla, M.; Akter, K.; & Islam, M.N.  
Novel Antiviral Phytochemicals Against  
Dengue Virus 2 NS2BNS3 Protease: An  
[2]. Frimayanti, N.; IKhtarudin, I.; Septama,  
A. W.; Susanty,  
A.; Isroq, N.D.  
Synthesis, In Silico and Structural  
Insight  
Compounds  
of  
Flavonol  
as New  
Derivative  
Competitive  
In  
Silico  
Drug  
Development  
2024.  
Dengue NS2B/NS3 Protease Inhibitor.  
Journal Research in Pharmacy 2023;  
Approach. ChemistrySelect  
193  
Frimayanti et al.  
Chempublish Journal, 9(2) 2025,183-195  
and Underlying Mechanisms Against  
Human  
Viral  
Infections.  
Recent  
[9]. Purohit, P.; Sahoo, S.; Panda, M.;  
Sahoo, P.S.; Meher, B.R. Targeting the  
DENV NS2B-NS3 protease with active  
antiviral phytocompounds: structure-  
based virtual screening, molecular  
advances in anti-infective drug discovery  
2025.  
[14]. Orosco FL, Quimque MTJ. “Antiviral  
potential of terpenoids against major  
docking  
simulation studies. Journal of Molecular  
Modeling. 2022. 28(365).  
and  
molecular  
dynamics  
viral  
challenges, and opportunities. Journal  
of Advanced Biotechnology and  
infections:  
Recent  
advances,  
Experimental Therapeutics. 2024; 7(1):  
221-238.  
[10]. Frimayanti,  
N.;  
Lukman,  
A.;  
and  
Nathania, L. Studi molecular docking  
senyawa 1, 5-benzothiazepine sebagai  
inhibitor dengue DEN-2 NS2B/NS3  
serine protease. Chempublish Journal  
2021; 6(1): 54-62.  
[15]. Frimayanti, N.; Septama, AW.; Teruna,  
[11]. Adawara, S. N.; Shallangwa, G. A.;  
serine protease. Journal of Pharmacy &  
Pharmacognosy Research. 2025; 13 (1),  
193-202.  
Mamza,  
P.  
A.;  
and  
Ibrahim,  
A.  
Molecular  
docking  
and QSAR  
theoretical model for prediction of  
phthalazinone derivatives as new class  
of potent dengue virus inhibitors.”  
Beni-Suef University Journal of Basic and  
Applied Sciences 2020; 9(1): 1-17.  
[16]. Frimayanti,  
N.;  
Yaeghoobi,  
M.;  
Ikhtiarudin, I.; Rizki, D.; and Putri, W.  
Insight on the In silico Study and  
Biological Activity Assay Molecular  
Docking”. Chiang Mai University. Chiang  
Mai Journal of Natural Sciences 2021;  
[12]. Wani, A.R., Yadav, K., Khursheed, A., &  
Rather,  
M.A.  
An  
updated  
and  
20(1):  
111.  
comprehensive review of the antiviral  
potential of essential oils and their  
chemical constituents with special  
focus on their mechanism of action  
[17]. Lipinski, C. A.; Lombardo, F.; Dominy, B.  
W.; and Feeney, P. J. Experimental and  
computational approaches to estimate  
solubility and permeability in drug  
discovery and development settings.  
Advanced Drug Delivery Reviews. 2001;  
46(1): 3-26.  
against  
coronaviruses. Microbial Pathogenesis  
2020; 152: 104620.  
various  
influenza  
and  
[13]. Ghosh, S.; Jana, K.; Parua, P.; Seth, A.;  
Bishal, A.; Debnath, B., Kumar Rout, S.;  
Halder, J.; Rai, V.K.; Dash, P.; Das, C.;  
Kar, B.; Ghosh, G.; & Rath, G. Antiviral  
Bioactive Compounds: Their Activities  
[18]. Erbel, P.; Schiering, N.; D’Arcy, A.;  
Renatus, M.; Kroemer, M.; Lim, S. P.;  
Yin, Z.; Keller, T.H.; Vasudevan, S.G.;  
194  
Frimayanti et al.  
Chempublish Journal, 9(2) 2025,183-195  
and Hommel,U. Structural Basic For  
The Activation of Flaviviral NS3  
Proteases From Dengue and West Nile  
Properties.  
Journal  
of  
Medicinal  
Chemistry. 2000; 43(20): 3714-3717.  
[23]. Banerjee, P.; Kemmler, E.; Dunkel, M.;  
Preissner, R. ProTox 3.0: a webserver  
for the prediction of toxicity of  
chemicals. Nucleic Acids Research. 2024.  
52:513-520.  
[24]. Yang, H.; Sun, L.; Li, W.; Liu, G.; and  
Tang, Y. In silico prediction of chemical  
toxicity for drug design using machine  
learning methods and structural alerts.  
Frontiers in chemistry. 2018; 6(30): 1-12.  
Virus. Nature Structural and Molecular  
Biology.  
2006;  
13(4):  
372-373.  
[19]. Daina, A.; Michielin, O.; and Zoete, V.  
SwissADME: a free web tool to evaluate  
pharmacokinetics, drug-likeness and  
medicinal chemistry friendliness of  
small  
2017;  
molecules. Scientific reports.  
7(1): 1-13.  
[20]. Lipinski, C.A. Lead- and Drug-Like  
Compounds:  
Revolution.  
Technologies  
The  
Drug Discovery  
2004; 1(4):  
Rule-Of-Five  
Today:  
337341.  
[25]. Siramshetty,  
V.B.;  
Nickel,  
J.;  
[21]. Veber, D. F., Johnson, S. R., Cheng, H. Y.,  
Smith, B. R., Ward, K. W., and Kopple, K.  
D. Molecular properties that influence  
Omieczynski, C.; Gohlke, B.O.; Drwal,  
M.N.; and Preissner, R. WITHDRAWN -  
A
Resource  
for  
Drugs.  
Withdrawn  
Nucleic  
and  
Acids  
Discontinued  
Research 2016; 44(D1): 10801086.  
the  
candidates.  
oral  
bioavailability  
Journal of  
of  
drug  
medicinal  
[26]. Regev, A. Drug-induced liver injury and  
chemistry. 2002. 45(12): 2615-2623.  
drug  
development:  
industry  
perspective. In Seminars in liver  
[22]. Ertl, P.; Rohde, B.; and Selzer, P. Fast  
Calculation of Molecular Polar Surface  
Area as a Sum of Fragment Based  
Contributions and its Application to the  
disease. Thieme Medical Publishers  
2014;  
34(2):  
227-239.  
Prediction  
of  
Drug  
Transport  
195