In Silico Analysis of Antiviral Activity and Pharmacokinetic Prediction of Brazilein Sappan Wood (Caesalpinia sappan L.
Against SARS-CoV-2 Spike Glycoproteins Dwi Krihariyani1.
Edy Haryanto1.
Retno Sasongkowati1 Department of Medical Laboratory Technology.
Poltekkes Kemenkes Surabaya.
Indonesia Correspondence:
Dwi Krihariyani.
Jl.
Wiguna Tengah XIX No.
Surabaya.
East Java.
Indonesia Zip Code: 60294 Email: dwikrihariyani@gmail.
Received: December 18th, 2020 Revised: March 20th, 2021 Accepted: March 22th, 2021 Published: April 28th, 2021 DOI: 10.
33086/ijmlst.
Abstract Brazilein is one of the secondary sappan wood metabolites which can be used empirically as an antivirus.
The SARSCoV-2 spike (S) glycoproteins play significant roles in attaching and entering the virus into the host cell.
This study aims to predict the antiviral activity and pharmacokinetic properties of brazilein of the sappan wood against the in silico SARS-CoV-2 S glycoproteins with vitamin C as the reference compound.
Molegro Virtual Docker 5.
5 was used to predict antiviral activity by docking process.
SARS-CoV2 S glycoprotein with NAG ligand available in Protein Data Bank (PDB) (PDB ID: 7C.
was the receptor used.
The pkCSM online tool was used to predict the pharmacokinetic properties and toxicity of brazilein.
Data were analyzed on the target receptors by comparing the docking bond energies between NAG, brazilein, and vitamin C.
The smaller the ligandsAo bond energy to the target receptor, the more stable the bonds are.
The bond energy of NAG, brazilein, and vitamin C was Ae59.
2864 kcal/mol.
Ae65.
8911 kcal/mol, and Ae53.
9093 kcal/mol, respectively.
These results suggested that brazilein has a greater capacity as an antivirus compared to NAG and vitamin C.
In silico test using the pkCSM online tool demonstrated that brazilein had strong pharmacokinetic properties and relatively low toxicity.
Keywords ADME.
Brazilein.
NAG.
Toxicology.
Vitamin C.
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.
A2021 by author.
INTRODUCTION
9-nCoV).
On February 11.
In December 2019, mysterious cases of 2020.
World Health Organization (WHO) pneumonia were first recorded in Wuhan, declared a new name which was coronavirus Hubei Province.
China .
This disease disease 2019 (COVID-.
The disease was was initially referred to as the 2019 novel caused by severe acute respiratory syndrome Dwi Krihariyani, et al.
coronavirus 2 (SARS-CoV-.
To date.
SARS-CoV-2 does not only infect the human COVID-19 has become a pandemic.
respiratory system, but also other organs.
Coronavirus is one of the significant The host cell receptor for SARS-CoV-2 pathogens that can infect the human is the same as SARS-CoV which is ACE2.
respiratory system and cause mild to severe The Seven coronaviruses are known that can infect humans.
Four of them (HCoV- receptor-binding NL63, specifically contacts the ACE2.
SARS-CoV- HCoV-HKU.
can infect immunocompetent 2 RBM interacts with ACE2 in humans with patients with only moderate symptoms.
residual effects (Gln.
, thereby making contrast.
Middle East Respiratory Syndrome SARS-CoV-2 capable of infecting human Coronavirus (MERS-CoV).
Severe Acute cells .
,11,.
HCoV-229E.
HCoV-OC43, receptor-binding (RBD) SARS-CoV-2
(RBM)
Respiratory Syndrome Coronavirus (SARS- COVID-19 pandemic is a major health CoV), and SARS-CoV-2 cause severe concern which requires immediate treatment.
symptoms in patients .
One of the efforts that can be made to combat The pathogenesis of SARS-CoV-2 is still this disease includes enhancing the humansAo unknown, although it is believed not too immune systems.
Flavonoids, curcumin, different from that of SARS-CoV.
SARS-
CoV-2 mainly infects alveoli-lining airway .
, cells .
Host tropism is the key for virus candidates which can strengthen the immune If SARS-CoV-2 has identified the system .
host cell according to its viral tropism, it will Sappan wood (Caesalpinia sappan L.
bind to the host cell via spike (S) glycoprotein consists of five flavonoid compounds, .
The S glycoprotein binds to the host cell receptor which is the angiotensin- methylbrazilin, sappanin, chalcone, and converting enzyme 2 (ACE.
ACE2 is also Brazilein is the major present in other organs, such as the oral and constituent in sappan wood that is used nasal mucosa, nasopharynx, lung, stomach, empirically as an antivirus.
The five small intestine, large intestine, skin, thymus, compounds can be used as anti-stressants, bone marrow, spleen, liver, kidney, brain, enterocyte cells of the small intestine, 3'-O- antimicrobial agents .
In silico test to determine the potential smooth muscle cells .
Therefore, use of brazilein as an antivirus is an attractive Ina.
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method due to several reasons.
This test is from PubChemA.
The tool used in this study safe, free of chemical waste, simple, cost- effective, and can shorten research time specifications: Windows 8 64-bit.
The .
This test is an approach to the software used was ChemDraw Professional 0.
Chem3D 16.
0, and Molegro Virtual .
Docker 5.
Prediction metabolism, and excretion (ADME)), the Dockin.
Operation (Molecular interaction of compounds with receptors.
ChemDraw Professional 16.
0 was used mechanisms of action, compound selectivity, to draw the 2D structures of the NAG, and compound toxicity.
brazilein, and vitamin C ligands.
Chem3D Vitamin C, which has been demonstrated 0 was then used to convert them to 3D to have a role in the treatment of COVID-19.
This software was also used to was used as a reference in this study .
The find the most stable conformation.
After the Protein Data Bank (PDB) 7C01 .
olecular minimum energy of NAG, brazilein, and basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD) was {SYBYL2 (*.
Mol.
} was stored in the used for ligands that have demonstrated good format of mol2.
The results were in the form biological activities and are able to bind to the of rerank score (RS), which was the energy desired biological target .
of the needed in the process of ligand-receptor From this score, the antiviral Here, we present a study on the activity of brazilein can be predicted.
prediction of the antiviral activity and Physicochemical, pharmacokinetic, and pharmacokinetic properties of brazilein of the sappan wood against the in silico SARS- .
kCSM) CoV-2 S glycoprotein with vitamin C as the reference compound.
The pkCSM online method has been used to predict physicochemical properties, such as the molecular weight (MW), octanol/water MATERIALS AND METHODS partition coefficient logarithm (Log P), the The materials included the 3D structures number of bonds between atoms that can of 7C01 which were downloaded from RCSB rotate .
, hydrogen bond acceptors PDB.
The 3D structures of 2-acetamido-2- (HBA), hydrogen bond donors (HBD), and deoxy-beta-D-glucopyranose (NAG), polar surface area (PSA).
In this study, the brazilein, and vitamin C were downloaded pkCSM online tool was used to predict the Ina.
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pharmacokinetic properties and toxicity of ADME and toxicity.
Protox online tool NAG, brazilein and vitamin C.
Firstly, the 2D .
ttp://tox.
de/tox/) molecular structures of NAG, brazilein, and predict the oral toxicity (LD.
in the vitamin C were drawn with the ChemDraw Globally Harmonized System (GSH) .
Professional 16.
0 program.
Secondly, they were copied to the Chem3D 16.
0 program to RESULTS be converted into 3D structures .
aved as Thirdly.
Prediction SMILES Operation (Molecular Dockin.
Translator was used to transform the The 2D structures of NAG, brazilein, and structures of NAG, brazilein, and vitamin C vitamin C are depicted in Figure 1, whereas into SMILES format.
Compounds are the 3D structures of NAG, brazilein, and subsequently processed in SMILES format vitamin C are depicted in Figure 2.
using the pkCSM online tool to predict the .
Figure 1.
2D structures.
NAG, .
brazilein, .
and vitamin C (ChemDraw Professional 16.
Figure 2.
3D structures.
NAG, .
brazilein, .
and vitamin C (Chem3D 16.
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Prediction of Docking and Amino Acid Figure 5 and Table 1 indicate the amino The protein structures of PDB 7C01 are acids involved in the interactions of NAG, depicted in Figure 3, whilst the interaction brazilein, and vitamin C compounds with the between the ligands (NAG, brazilein, and 7C01 protein receptor.
Table 2 displays the vitamin C) and receptors on the 7C01 protein redocking effects of NAG, brazilein, and is depicted in Figure 4.
vitamin C with 7C01 protein receptor.
Figure 3.
Protein structures (PDB 7C.
(Molegro Virtual Docker 5.
Figure 4.
Receptor interactions between the ligands of .
NAG, .
brazilein, .
and vitamin C (Molegro Virtual Docker 5.
Figure 5.
Amino acids involved in the interactions of .
NAG, .
brazilein, .
and vitamin C .
with 7C01 protein receptor (H-bond, electrostatic, and steri.
(Molegro Virtual Docker 5.
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Table 1.
Amino acids involved in the interactions of NAG .
, brazilein .
, and vitamin C .
with 7C01 protein receptor (H-bond, electrostatic, and steri.
Hydrogen bonds and amino acid Ae Ligands NAG Electrostatic interactions and amino acid residues Ae Brazilein Asn 343(A) Ae Vitamin C Asn 343(A) Ae Steric interactions and amino acid Asn 343(A) Asn 343(A) Leu 368(A) Asn 343(A) Table 2.
Redocking results using the Molegro Virtual Docker 5.
Redocking/Ligand NAG Brazilein Vitamin C Ae51.
Ae58.
Ae45.
Ae59.
Ae65.
Ae53.
i Ae51.
Ae55.
Ae46.
Physicochemical, pharmacokinetic, and brazilein, and vitamin C are presented in Table 3.
kCSM) The The results of the in silico predictions for NAG, pharmacokinetic properties and toxicity of NAG, brazilein, and vitamin C are presented in Table 4.
Table 3.
In silico predictions for physicochemical parameters of NAG, brazilein, and vitamin C.
Struktur
SMILES
NAG
Brazilein Vitamin C Log P Ae3.
Ae1.
Torsion
HBA
HBD
PSA (A.
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log P = logarithm of the octanol/water partition coefficient.
torsion = bonds between atoms that can rotate.
HBA = hydrogen bond acceptors.
HBD = hydrogen bond donors.
PSA = polar surface area.
Dwi Krihariyani, et al.
Table 4.
In silico predictions of pharmacokinetic properties and toxicity of NAG, brazilein, and vitamin C.
Pharmacokinetic properties and toxicity NAG Brazilein Intestinal absorption .
(%) Vitamin Skin permeability .
og K.
Ae3.
Ae3.
Ae3.
Vss .
og L/k.
Ae0.
Ae0.
b permeability .
og BB) Ae1.
Ae0.
Ae1.
CYP2D6 substrate (Yes/N.
CYP2D6 inhibitior (Yes/N.
Total Clearance .
og ml/min/k.
OCT2 substrate (Yes/N.
Ames toxicity (Yes/N.
Yes LD50 .
ol/k.
Vss: steady-state volume of distribution.
b: blood-brain barrier.
CYP2D6: cytochrome P2D6.
OCT2: organic cation transporter 2.
DISCUSSION
Activity Prediction (Molecular Dockin.
electrostatic, and steric/geometric properties of the functional groups, were searched using glycoprotein with NAG_601[A] ligand (PDB Molegro Virtual Docker 5.
This was 7C.
was the target molecular receptor.
conducted in order to design the minimum PDB 7C01 was selected since it is structural characteristics needed for further medicine production development .
SARS-CoV-2 SARS-CoV-2 The host cell receptor for Physical and chemical properties .
SARS-CoV-2 is the same as SARS-CoV lipophilic and electrostatic propertie.
of the which is ACE2.
The RBD sequence involves drugs play an essential role in transporting SARS-CoV-2 RBM in direct contact with the the drugs to reach the virus .
ACE2 .
and deliver.
Only drugs that have a high NAG_601[A] ligand was specificity structure can interact and cause biological activity and can bind to the desired biological target during the docking process Furthermore, the drugsAo electrostatic and to determine the moleculesAo physical and steric properties play a role in promoting the chemical properties.
The functional groups of precise orientation of the receptor surface NAG, brazilein, and vitamin C responsible molecule .
for pharmacophores which can reduce Ina.
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Docking and Amino Acid Analysis Activity vitamin C ligands.
Brazil had a RS of Prediction Ae65,8911 kcal/mol, whereas NAG and The protein receptor (PDB 7C.
that vitamin C had RSs of Ae59,2864 kcal/mol and was downloaded and imported into the Ae53,9093 kcal/mol, respectively.
It indicated Molegro Virtual Docker 5.
5 is presented in that brazilein supplied lower energy than Figure 3.
Figure 4 depicts the detection NAG and vitamin C, hence binding to the results of the interaction between the three receptor would be more stable compared to ligands and S glycoprotein.
Cavity .
olume NAG and vitamin C.
with active NAG_601[A] ligand
was used because there is a region where the Physicochemical, pharmacokinetic, and NAG
kCSM) There was a ligand interaction with The results of the in silico prediction of multiple amino acid residues from the 7C01
NAG,
protein receptor in the interaction between the ligands and receptors.
Figure 5 and Table displayed in Table 3.
Lipinski et al.
1 indicate the amino acids involved in the analyzed 2,245 drugs from the baseline NAG, brazilein, and vitamin C interaction World Drugs Index and concluded that if the pathway with the 7C01 protein receptor.
The molecular weight is greater than 500 Da, the lipophilic/hydrophobic bond, electronic, and compounds would be difficult to be absorbed, steric interactions of the amino acid residues have low permeability, have a log value of 5 of the protein receptor with these compounds octanol/water .
og P) partition coefficient, take place.
There were variations in the have HBD expressed by the number of interactions with the S glycoprotein receptor groups O-H and N-H greater than 5, and have between each of the NAG, brazilein, and an H-bond.
Since all values are the vitamin C compounds (Figure 5 and Table .
multiplication of five, this analysis is known since there were differences in the spatial as Lipinski's Rule of Five .
It can be analyzed from Table 3 that NAG, brazilein, and vitamin C had molecular weight of less The effects of redocking with the 7C01 than 500 Da, logP values of less than 5, protein receptor for NAG, brazilein, and acceptor and donor values of less than 10, vitamin C are displayed in Table 2.
The hence it can be inferred that it is easy to binding energy of brazilein with the 7C01 absorb these three compounds.
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The in silico pharmacokinetic properties state volume of distribution (Vs.
values for and toxicity predictions of NAG, brazilein.
NAG, brazilein, and vitamin C were Ae0.
and vitamin C are presented in Table 4.
194, and Ae0.
156 (Table .
, thus it could be According to Chander et al.
, a compound estimated that all the derivatives of these is categorized as having strong absorption compounds can be uniformly distributed to capacity if the absorption value is > 80%, have the same concentration as in blood whereas it has poor absorption capacity if the absorption value is < 30%.
The primary site Another for absorption of oral medications is the consider is the ability of drugs to cross the intestine .
Table 4 shows that NAGAos blood-brain barrier .
to help decrease human intestinal absorption value was less side effects and toxicity, or to improve the than 30%, whereas brazileinAos and vitamin CAos were more than 80%.
These results pharmacological activity is present in the suggested that brazilein and vitamin C had b permeability is calculated as log better absorption capacity than NAG.
BB .
he logarithmic ratio of brain-to-plasma Pires et al.
stated that a compound is concentration.
in vivo in an animal model.
described to have relatively low skin Pires et al.
stated that compounds are permeability if its value is log Kp > Ae2.
believed to be able to pass the b Table 4 displays that the skin permeability effectively if their log BB values are > 0.
og K.
of NAG, brazilein, and vitamin C and cannot be adequately distributed if their was lower than Ae2.
5, hence these three log BB values are < Ae1 .
The log BB compounds were supposed to have strong values of NAG, brazilein, and vitamin C were skin permeability.
Ae1.
Ae0.
662, and Ae1.
031, respectively The volume of distribution (V.
refers to (Table .
The log BB value of brazilein was the theoretical volume that is required to higher than Ae1, while NAGAos and vitamin CAos distribute the total dose of the medicine were lower than Ae1, hence it was expected that brazilein was capable of penetrating the concentration as in the blood plasma.
The b moderately, while NAG and vitamin C higher the Vd value, the more drugs than compounds were less capable.
blood plasma are distributed to the bodyAos Most of the metabolic reactions require Pires et al.
stated that a oxidation process.
Cytochrome P450 is an compound is described to have high Vd if the essential detoxification enzyme in the body, value of log Vd is > 0.
45, but low Vd if the and it is primarily found in the liver.
value of log Vd is < Ae0.
The steady- Cytochrome P450 acts by oxidizing and Ina.
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promoting the excretion of unidentified compounds did not affect the OCT2 organic compounds, including narcotics.
substrates (Table .
, thus it could be Enzyme inhibitors, such as grapefruit juice, interpreted that the NAG, brazilein, and are contraindicated against cytochrome P450 vitamin C derivatives were not substrates of enzymes since it can affect drug metabolism.
OCT2.
It is therefore important to assess the ability To assess the toxicity of the compounds, of compounds to inhibit cytochrome P450, the Ames toxicity test was carried out.
The which is represented as the cytochrome P2D6 Ames Toxicity Test is a commonly used (CYP2D.
isoform in this study.
Table 4 method to determine the mutagenic ability of displays that the CYP2D6 enzyme is not bacteria-based compounds.
A positive test impaired or inhibited by NAG, brazilein, and result indicates the mutagenicity of the vitamin C, thus it could be expected that these compound and may thus serve as a derivatives appear to be metabolized by the carcinogen .
Brazilein might cause P450 enzyme .
mutagenic effects, while NAG and vitamin C The compound excretion process can be carried out by calculating the total clearance were not expected to cause mutagenic effects (Table .
(CLto.
and renal organic cation transporter 2 (OCT.
substrate constants.
CLtot is a CONCLUSIONS mixture of liver clearance .
iver and bile The bond energy of brazilein was lower metabolis.
and renal clearance .
xcretion than NAG and vitamin C.
The comparison of through the kidney.
This is related to the bond energy values showed that brazilein steady-state had higher antiviral capacity than NAG and concentrations, it is necessary to determine vitamin C in silico using the molecular the dosage level .
CLtot values of NAG, docking process.
The brazilein, and vitamin C were 0.
718, 0.
pharmacokinetic, and toxicity properties of 631, respectively (Table .
Therefore, brazilein showed that it was projected to have the rate of compound excretion could be strong skin permeability, be distributed estimated from these values.
uniformly to provide the same concentration OCT2 is a kidney-based transporter that as in the blood plasma, be penetrating the plays a significant role in drug and b moderately, be very well absorbed in the intestine, be metabolized by the P450 When given along with OCT2 enzyme, and have relatively low toxicity.
OCT2 substrates also have the Ina.
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The three Dwi Krihariyani, et al.
AUTHOR CONTRIBUTIONS
Dwi Krihariyani:
ACKNOWLEDGMENT
Utmost gratitude was given to Prof.
Dr.
software, formal analysis, writing the original Siswandono.
Apt.
from Faculty of draft, and visualization.
Edy Haryanto:
Pharmacy.
Universitas Airlangga (Surabaya, methodology, validation, writing, review.
Indonesi.
who gave the authors the Molegro Virtual Docker license 5.
Retno Sasongkowati:
supervision, writing, review, and editing.
CONFLICT OF INTEREST
None to declare.
REFERENCES