Pharmacogn J.

2019; 11(6)Suppl:1471-1476
A Multifaceted Journal in the field of Natural Products and Pharmacognosy
Original Article
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Study of Molecular Docking of Vitexin in Binahong (Anredera

cordifolia (Ten.) Steenis) Leaves Extract on Glibenclamide-
CYP3A4 Interaction
Dwitiyanti1, Yahdiana Harahap2, Berna Elya3, Anton Bahtiar4,*

ABSTRACT
Introduction: Diabetes Mellitus is a disease that has a high prevalence in Indonesia. About
90-95% of all diabetes cases were caused by the failure or incapability of insulin target cells to
respond to the insulin in normal state. The use of glibenclamide antidiabetic drugs with herbs
has been occurred frequently in the community. Vitexin, one of active compounds in binahong
Dwitiyanti1, Yahdiana Harahap2,
(Anredera cordifolia (Ten.) Steenis) leaves, has been known to have an antidiabetic effects.
Berna Elya3, Anton Bahtiar4,*
This study aimed to determine the molecular docking interaction of glibenclamide and vitexin
1
Graduated Program of faculty of Pharmacy, in binahong leaves against CYP3A4 as antidiabetic drug. Method: Molecular docking methods
Universitas Indonesia, Kampus UI Depok, were carried out using Autodock Vina software and interaction was visualized using discovery
West Java 16424, INDONESIA. studio. Results: The study indicated that the value of glibenclamide complex free energy
2
Department of Bioanalysis, Faculty of
Pharmacy, Universitas Indonesia, Kampus UI
with CYP3A4 was -3.2 kcal/mol and the stability has increasing to -4.4 kcal/mol after docked
Depok, West Java 16424, INDONESIA. with vitexin. The glibenclamide and vitexin complexes had 7 Pi alkyl hydrophobic bonds, 1
3
Department of Phytochemistry, Faculty of hydrocarbon hydrogen bond 1 Pi-cation electrostatic interactions, other interactions between
Pharmacy, Universitas Indonesia, Kampus UI Pi bond and sulfur atoms in cysteine ​​amino acid residues, Pi bond interactions in phenylalamin
Depok, West Java 16424, INDONESIA.
4
Department of Pharmacology and
aromatic groups with electron pairs oxygen atom. Conclusion: This study concluded that
Toxicology, Faculty of Pharmacy, Universitas vitexin could improve glibenclamide stability.
Indonesia, Kampus UI Depok, West Java Key words: Molecular docking, Diabetes mellitus, Glibenclamide, Vitexin.
16424, INDONESIA.

Correspondence
INTRODUCTION ingredients that has the potential to reduce blood
Anton Bahtiar sugar levels is Binahong plant
Department of Pharmacology and Diabetes mellitus is a disease caused by various
Toxicology, Faculty of Pharmacy, factors. Diabetes mellitus is caused by insulin Binahong pharmacological activities included anti-
Universitas Indonesia, Kampus UI Depok, resistance, insulin deficiency and abnormal insulin hyperlipidemia, anti-inflammatory, analgesic, and
West Java 16424, INDONESIA.
secretion. Diabetes mellitus is a metabolic disorder antipyretic.4 Other studies reported that binahong
E-mail: [email protected] leaf extract can inhibit α-glucosidase with an IC50
characterized by high levels of glucose in the blood
History value of 54.24 μg/mL.5 Binahong leaf methanol
(hyperglycemia) and the detection of fat, fat, and
• Submission Date: 13-09-2019;
protein.1 International Diabetes Federation (IDF) extract at a dose of 50 mg/kg body weight and 200
• Review completed: 09-10-2019;
data for 2017 stated that diabetes mellitus (DM) mg/kg body weight could reduce the blood glucose
• Accepted Date: 16-10-2019. sufferers in the world are estimated to continue to levels of alloxan-induced mice on the 7th day by
DOI : 10.5530/pj.2019.11.227 increase by 48% from 425 million sufferers in 2017 61.02% and 60.68%, respectively. Meanwhile, on the
to increase by around 629 million in 2045, while in 14th day a decrease in glucose levels by 75.64% and
Article Available online
Asia according to IDF showed an increase of 84% 66.61% was observed, histologically could repair
http://www.phcogj.com/v11/i6s
from 82 million sufferers in 2017 increased to 151 β-pancreatic cell damage.6
Copyright million in 2045. Indonesia ranks 6th out of 10 as
© 2019 Phcogj.Com. This is an open- The pharmacological effects of Binahong plants can
the largest diabetes populated countries in the
access article distributed under the terms be used as an alternative to reducing blood glucose
of the Creative Commons Attribution 4.0 world with 10 million sufferers.2
levels. The amount of active content of Binahong
International license.
Diabetes treatment therapy is consisted of oral plants is possible for interaction if given together
antidiabetic drugs that can be used with one type with glibenclamide. Flavonoid glycoside compounds
of drug or combination. Drugs that are widely found in binahong leaves, namely vitexin (8-beta-D-
used in the treatment of diabetes mellitus, one of glucopiranosilapigenin) are active substances that are
which is sulfonylureas. One of the drugs used by responsible as antidiabetic agents. However, in many
people with type 2 diabetes is glibenclamide from cases the combination of herbs with synthetic drugs
sulfonylurea group. Glibenclamide is one of the causes interactions. Compounds contained in herbs
most well-known antidiabetic drugs and belongs can interact with synthetic drugs if used at the same
to the sulfonylurea group which reduces oxygen time. Previous studies have shown that apigenin
levels by production of insulin by Langerhans flavonoids were CYP3A47 enzymes inhibitors,
beta cells.3 In addition, drugs derived from natural and glibenclamide were primarily metabolized by
ingredients can be a therapeutic choice by patients CYP3A4 enzymes.8
with diabetes mellitus. The use of natural materials
as adjuvant to DM treatment has long been carried One way that can be done to determine the effect
out by the people of Indonesia. One of the natural of the combination of glibenclamide with herbal

Cite this article: Dwitiyanti, Harahap Y, Elya B, Bahtiar A. Study of Molecular Docking of Vitexin

Phcogj.com
in Binahong (Anredera cordifolia (Ten.) Steenis) Leaves Extract on Glibenclamide- CYP3A4
Interaction. Pharmacog J. 2019;11(6)Suppl:1471-6.

1471 Pharmacognosy Journal, Vol 11, Issue 6(Suppl), Nov-Dec, 2019

 Dwitiyanti, et al.: Study of Molecular Docking of Vitexin in Binahong (Anredera cordifolia (Ten.) Steenis) Leaves Extract on Glibenclamide- CYP3A4 Interaction

adjuvant in the treatment of diabetes is through molecular docking RESULT

simulations to predict bond conformation and binding affinity formed
between receptors and ligands which are very instrumental in further Receptor structure preparation
drug development.9
The receptor used in the study was CYP3A4 protein. The α-glucosidase
MATERIALS AND METHODS protein used is downloaded through the Protein Data Bank at the site
http://www.rcsb.org/pdb with PDB ID: 5G5J. The selection of 5G5J
Tools receptors based on experimental data was organism data (s) which
stated Homo sapiens (humans) and has a resolution value of 2.6 Å.11
A set of laptops with Intel (R) Core (TM) i7-4720 HQ CPU @ 2.60GHz, The results are shown in Figure 1.
̴2.60GHz processor, 16.0GB RAM memory, with operating system
windows 8.1 Pro Home 64-bit connected to the internet connection Ligand structure preparation and optimization
and linux operating system ubuntu (32-bit). Chimera 1.13, YASARA
version 10.1.8, AutoDockTools-1.5.6, Discovery Studio Visualizer The ligands that used were first downloaded in three-dimensional (3D)
version 17.2.0.16349 (http://accelrys.com/), Protein Data Bank (http:// format with the .sdf format from PubChem via https://pubchem.ncbi.
www.rcsb.org/pdb) and PubChem (http://PubChem.ncbi.nlm.nih. nlm.nih.gov/. After all files are downloaded, ligand preparation was
gov). done using the Chimera software. All ligands including comparison
ligands were prepared and reshaped in the pdbqt file format. The results
Material are shown in Figures 2 and 3.
This study used a 5G5J pdb receptor which was downloaded from Method validation and re-docking
RSCB PDB (http://www.rcsb.org/pdb). The glibenclamide and vitexin
as ligand compounds wereand downloaded from PubChem.10 Method validation and re-docking was done used Autodockvina with
native ligands and receptors. The results of re-docking were the default
Research procedures results from native ligands with receptors. It was used in virtual
screening for 2 ligands, namely vitexin and glibenclamid. Furthermore,
The procedure of this study was carried out by preparation of ligand from the re-docking stage also obtained Gibbs free energy (ΔG) re-
structure using Chimera with the aim of cleaning receptors and docking results of -5.2 kcal/mol. Then the results were analyzed through
ligands from all residues contained in these receptors and ligands. YASARA to observe the RMSD (Root Mean Square Deviation) value of
Then the method validation and re-docking was done using Autodock heavy atoms and the value was 1.9391 Å.
Vina which was aimed to validate the method that will be used. The
validation was also done to decide whether the method can be resumed Molecular docking results analysis
or not to the next phase and to search for pocket cavity receptors. The results analysis was carried out through screening of Gibbs
The next process was molecular docking simulation or can be referred free energy (ΔG) of each docking compound by selecting the
as virtual screening, aimed at finding drug candidates observed from conformational compound that had the lowest Gibbs free energy (ΔG).
Gibbs free energy (ΔG), generated from the formation of receptor-
ChemPLP score values. The next stage is the analysis of results based
ligand complex, could show the affinity of the ligand for the receptor.
on ChemPLP score values. The visualization was generated from
The docking results can be observed in Table 1 of the 2 analyzed ligands
molecular docking simulations using the Discovery Studio Visualizer
and 1 complex (glibenclamid and vitexin), the lowest Gibbs free energy
software. (ΔG) observed was in the complex compounds, namely glibenclamid

Figure 1: Experimental data of 5G5J as CYP3A4 receptor (Protein Data Bank 2018).

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 Dwitiyanti, et al.: Study of Molecular Docking of Vitexin in Binahong (Anredera cordifolia (Ten.) Steenis) Leaves Extract on Glibenclamide- CYP3A4 Interaction

comparison ligands which were prepared and reshaped in the. pdbqt

file format. This file format change was aimed to adjust to Autodock
Vina which used the .pdbqt file format so that the simulation process
could run.
Method validation and re-docking using Autodockvina with native
ligands and receptors aim to determine whether the docking method/
protocol used was acceptable. The results of re-docking were the
default results from native ligands with receptors. It was used in
virtual screening for 2 ligands, namely vitexin and glibenclamide.
Furthermore, from the re-docking stage also obtained Gibbs free
energy (ΔG) re-docking results of -5.2 kcal/mol. Then the results
were analyzed through YASARA to see the RMSD (Root Mean Square
Deviation) value of heavy atoms and the value obtained was 1.9391 Å.
Figure 2: Glibenclamide ligand (pubchem.ncbi.nlm.nih.gov). This means the method used was acceptable because the RMSD value
was less than 2.0 Å.13
RMSD value of heavy atoms showed the value of deviation between a
ligand conformation structure with native ligands. Smaller deviation
means smaller error in the prediction of the interaction of the ligand
with protein. It could be said that the conformation of the ligand with
native ligand has the same and parallel structure and atoms. The results
of the validation showed that the RMSD value of heavy atoms 1.9391
Å was still in the range of allowable RMSD values ​​that is less than 2
Å. After that is fulfilled, the method validation process can be used to
perform virtual screening with glibenclamide and vitexin.
Figure 4 is the result of validation using YASARA, it can be seen
that there were 2 compounds, namely docking ligand and native
ligand. Compounds with yellow carbon atoms were docking ligands
while compounds with blue carbon atoms were native ligands. After
the validation method/protocol docking stage was accepted, virtual
screening was performed. This stage was aimed to obtain Gibbs free
energy(ΔG) based on the interaction between the ligand with the
Figure 3: vitexin Ligand (pubchem.ncbi.nlm.nih.gov).
receptor. The receptors used were the same receptors on validation and
the ligands used were glibenclamide and vitexin.
Table 1: Molecular docking simulation results between Glibenclamid, vitexin
Analysis of the results was carried out through screening of Gibbs free
and combination compounds (glibenclamid and vitexin) with CYP3A4 using
vina autodock. energy (ΔG) of each docking compound by selecting the conformational
compound that had the lowest Gibbs free energy (ΔG). Gibbs Free
Gibbs free energy (ΔG)
No Ligand energy (ΔG) generated when the receptor-ligand complex was formed
(kcal/mol)
can show the affinity of the ligand for the receptor. The affinity of the
1 Glibenclamid + vitexin -4,4
ligand was shown to be negative, which means that if the affinity for
2 Glibenclamid -3,2
the receptor was high, the Gibbs free energy (ΔG) was getting smaller,
3 Vitexin -3,2
whereas if the affinity was small, the Gibbs free energy (ΔG) was greater.
and vitexin complexes that bind to CYP3A4 receptors with a ChemPLP Table 1 shows the Gibbs free energy (ΔG) which was evaluated and
score of -4,4 kcal/mol, while the Gibbs free energy(ΔG) glibenclamide was the result of docking simulation using the CYP3A4 receptor. The
with -3.2 kcal/mol receptors and vitexin with receptors is -3.2 kcal/mol. Gibbs free energy (ΔG) used was the lowest value, because the low
ChemPLP score shows good stability and high affinity in the molecular
DISCUSSION docking process.13 The docking results can be observed in Table 1 of
The selection of 5G5J receptors based on experimental data was the 2 of analyzed ligands and 1 complex (glibenclamide and vitexin),
organism data (s) which stated Homo sapiens (humans) and had a the lowest Gibbs free energy (ΔG) was in the complex compounds
resolution value of 2.6 Å. Resolution value is one of the receptors namely glibenclamide and vitexin complexes that bind to CYP3A4
selection parameters. Structure with resolution values less than 3 Å receptors with a ChemPLP score of -4 ,4 kcal/mol, while the Gibbs free
may affect the stability of the receptors. When performing molecular energy (ΔG) glibenclamide with -3.2 kcal/mol receptors and vitexin
docking, lower receptor resolution value may generate better receptor with receptors is -3.2 kcal/mol. These results indicate that the stability
stability. The resolution value on PDB ID stated that the protein between the complex compound glibenclamide and vitexin with the
structure has the same pose as the structure of the X-ray/original CYP3A4 receptor was better and had a higher affinity compared to the
protein.12 The 5G5J receptor binds to 2 ligands namely Protoporphyrin use of a single drug.
IX Containing Fe and Metformin which can be said to be native ligands.
The glibenclamide and vitexin complex had 7 Hydrophobic Pi-type
The ligands that used were first downloaded in three-dimensional Alkaline bonds, 1 Hydrocarbon-type hydrogen bond, 1 Pi-cation
(3D) format with the .sdf format from PubChem via https://pubchem. electrostatic interaction, other interactions between Pi bonds with
ncbi.nlm.nih.gov/. After all files were downloaded, ligand preparation sulfur atoms in cysteine amino
​​ acid residues, interaction of Pi bonds in
was done using the Chimera software. All ligands was also including phenylalamin aromatic groups with oxygen atom electron pairs.

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 Dwitiyanti, et al.: Study of Molecular Docking of Vitexin in Binahong (Anredera cordifolia (Ten.) Steenis) Leaves Extract on Glibenclamide- CYP3A4 Interaction

Figure 4: Superpose of validation results for docking ligand structures (yellow) with native ligand structures (blue).

Figure 5: Glibenclamid and vitexin complexes.

CONCLUSION REFERENCES
vitexin could increase the stability of the action of glibenclamide 1. Dipiro JT, Wells BG, Schwinghammer TL, Dipiro CV. Pharmacotherapy
handbook. Inggris: McGraw-Hill Education Companies. 2005.
against CYP3A4 receptors as antidiabetic.
2. International Diabetes Federation. Eighth edition 2017. Retrieved from http://
ACKNOWLEDGEMENT www.diabetesatlas.org/resources/2017-atlas.html
3. Katzung BG, Trevor AJ. Basic & Clinical Pharmacology Thirteenth Edition.
This research was support by The Ministry of Research, Technology and McGraw-Hill Education Companies. 2015.
Higher Education of Republic Indonesia Research Grant (Penelitian 4. Abou Zeid AHS; Soliman FM; Sleem AA; Mitry MNR. Phytochemical and bio-
activity investigations of the aerial parts of Anredera cordifolia (Ten.) Steenis.
Doktor) 2019. 2007.

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5. Elya B, Handayani R, Saurisari R, Azizahwati Hasyyati US, Permana IT, et al. 9. Trott O, Olson JA. Software news and update autodock vina: Improving
Antidiabetic activity and phytochemical screening of extracts from Indonesian the speed and accuracy of docking with a new scoring function, efficient
plants by inhibition of alpha amylase, alpha glucosidase and dipeptidyl peptidase optimization, and multithreading. Journal of Computational Chemistry.
IV. Ansinet. 2005;18(6):279-84. 2009;30(7):1174-8.
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madeiravine (Anredera cordifolia (TEN.)STEENIS) leaves on blood sugar in
diabetes mellitus model mice. 2011;1(4):1-10. 11. Sahu R, Shukla N. In-silico analysis of different plant protein and their essential
compound with sulfonylurea binding protein of β-cells of homo sapiens
7. Basheer L, Kerem Z. Interactions between CYP3A4 and dietary polyphenols. for curing diabetes mellitus type ii disease. European Chemical Bulletin.
Oxidative Medicine and Cellular Longevity. 2015. 2014;3(6):568-76.
8. Naritomi Y, Terashita S, Kagayama A. Identification and relative contributions of 12. Marcou G, Rognan D. Optimizing fragment and scaffold docking by use
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Senyawa Antikanker. 2013. Yogyakarta: Pustaka Pelajar.

GRAPHICAL ABSTRACT
Glibenclamide ligand
The receptor used in the study was
CYP3A4 protein, PDB ID: 5G5J

Analysis Molecular
Docking
vitexin Ligand

Gibs free energy (ΔG)

Ligand
No (kcal/mol)
1 Glibenclamid + vitexin -4,4

2 Glibenclamid -3,2

3 Vitexin -3,2

Glibenclamid and
vitexin complexes

SUMMARY
• The validation showed that the RMSD value of heavy atoms 1.9391 Å was still in the range of allowable RMSD values ​​that
is less than 2 Å.
• the stability between the complex compound glibenclamide and vitexin with the CYP3A4 receptor was better and had a
higher affinity compared to the use of a single drug.
• vitexin could increase the stability of the action of glibenclamide against CYP3A4 receptors as antidiabetic.
• The glibenclamide and vitexin complex had 7 Hydrophobic Pi-type Alkaline bonds, 1 Hydrocarbon-type hydrogen bond, 1
Pi-cation electrostatic interaction, other interactions between Pi bonds with sulfur atoms in cysteine ​​amino acid residues,
interaction of Pi bonds in phenylalamin aromatic groups with electron pairs oxygen atom.

ABOUT AUTHORS
Dr. Anton Bahtiar, M.Biomed., Apt. Obtained his Ph.D. degree in 2010 from Nara Institute of Science and
Technology, Japan. Currently, He is lecturer and researcher at faculty of pharmacy, University of Indonesia
since 1998. He is also a head of Pharmacology and Toxicology Laboratory. His research projects are
focus on Herbal medicine, and tried to solve the mechanism of action of herbal medicine, especially for
osteoporosis and menopause.

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 Dwitiyanti, et al.: Study of Molecular Docking of Vitexin in Binahong (Anredera cordifolia (Ten.) Steenis) Leaves Extract on Glibenclamide- CYP3A4 Interaction

Prof. Dr. Yahdiana Harahap, M.Si., Apt. got her undergraduate degree from Indonesian University in
1987 and finished her PhD from Bandung Institute of Technology in 2003. She is positioned as Professor
at Pharmacy at Faculty of Pharmacy Indonesian Univesity. Her research is in Pharmaceutical Chemistry
Analysis, especially Bioanalysis and DNA-Adduct Analysis.

Prof. Dr. Berna Elya, M.Si., Apt. Professor and Head of Phytochemistry and Pharmacognosy, Faculty
of Pharmacy, Universitas Indonesia (UI) Depok, West Java, Indonesia. She is expert in the area of
Pharmacognosy and Phytochemistry, working in drug discovery of herbal plants, extraction technology,
structure elucidation, and degenarative disease such as diabetes mellitus, antyhypertension, and
cholesterol.

Dwitiyanti, M.Farm., Apt. a Doctoral Student at Department of Pharmaceutical Sciences, Faculty of

Pharmacy, Universitas Indonesia, Depok, West Java, Indonesia, and also as a lecturer at Department
of Pharmacy, Faculty of Pharmacy and Sciences, University of Muhammadiyah Prof. Dr. HAMKA, East
Jakarta, Indonesia. The doctoral research focused on The Influence Of Binahong (Anredera Cordifolia
(Ten.) Steenis) Extract On Pharmacodynamics And Pharmacokinetic Glybenclamide.

Cite this article: Dwitiyanti, Harahap Y, Elya B, Bahtiar A. Study of Molecular Docking of Vitexin in Binahong (Anredera cordifolia
(Ten.) Steenis) Leaves Extract on Glibenclamide- CYP3A4 Interaction. Pharmacog J. 2019;11(6)Suppl:1471-6.

Pharmacognosy Journal, Vol 11, Issue 6(Suppl), Nov-Dec, 2019 1476