ANALYSIS OF MOLECULAR DOCKING QUERSETIN, GUAIJAVARIN AND

MORIN-3-O-α-L-ARABOPYRANOSIDE AS ANTIBACTERIAL

Raisa Fadilla, Asmiyenti Djaliasrin, Rina Herowati

Faculty of Pharmacy, Setia Budi University, Jl. Letjen Sutoyo Solo 57127

Email:Raisa.fadilla@gmail.com

ABSTRACT

Guava leaves have been shown to have antibacterial activity and have been

widely used for the prevention and therapeutic treatment of diarrhea. Guava leaves

contain many compounds which possess antibacterial activity. Some of these

compounds include quersetin, guaijavarin and morin-3-O-α-L-lyxopyranoside. This

study aims to understand the interaction and interaction patterns quersetin, guaijavarin

and morin-3-O-α-L-arabopiranosida of guava leaves (P. guajava L.) on 9 molecule

biology antibacterial targets through molecular docking. Molecule biology antibacterial

targets used, among other proteins SleB (4F55), protein SleL (4S3J), maltoporin

(1MPR), Agga (aggregative adherence fimbriae/1) (4PH8), Bc1960 peptidoglycan N-

acetylglucosamine deacetylase (4L1G), phosphatidylcholine-phospholipase C Bc

(2HUC), phospholipase C regulator + PapR (2QFC), penicillin binding protein 3 E. coli

(transferase) (4BJP) and gyrase + 4.5-dibromopyrolamide-based inhibitor (isomerase)

(4ZVI)

In this study, molecular docking performed on quersetin, guaijavarin and morin-

3-O-α-L-lyxopyranoside of guava leaves (P. guajava L.) as ligands to the 9 proteins as

a target using the software Autodock Vina and PyMOL as visualization tools.

Compounds guaijavarin, morin-3-O-α-L-arabopiranosida and quersetin of guava leaves

(P. guajava L.) have interaction of 7 molecule biology antibacterial targets because it

can bind to the active site and protein residues of protein macromolecules 4F55,
1MPR, 4L1G, 2HUC, 2QFC, 4ZVI and 4BJP with ΔG bind range -6,5-9,6 kcal/mol and

shows the interaction patterns that resemble the native ligand to the protein

macromolecules 2QFC and 4ZVI seen from visual observation.

Keywords: Diarrhea, molecular docking, quersetin, guaijavarin, morin-3-O-α-L-

lyxopyranoside

INTRODUCTION The use of traditional medicine

Diarrhea is a disease widely by society due in addition

characterized by increased frequency because it is natural, easy to obtain,

of defecation more than normal (>3 and the price is cheap, drug use herbs

times/day) with a change in stool traditionally did not produce side effects

consistency (to liquid), with/without such as is common in the treatment of

blood and/or mucus [1]. chemical, other than that there are still

Treatment of diarrhea allegedly many people who think that the use of

caused by invasive bacterial infections traditional medicine safer than synthetic

are treated with antibiotics. Treatment drugs [3].

with antibiotics is only required on Guava leaves (P. guajava L.)

bakteriil serious form of diarrhea. The has been widely used by the public as a

main choices are amoxicillin, treatment of diarrheal diseases. Arima

cotrimoxazole and fluoroquinolone and Danno (2002) concluded that the

compound. These drugs should not be compounds contained in guava leaves

given more than 7-10 days, except have antibacterial activity by MIC

where after recovering the diarrhea, the values were obtained. Some of these

patient was still issuing the bacteria in compounds include quersetin,

the stool [2]. guaijavarin and morin-3-O-α-L-

arabopiranosida [4].
 This study aimed to analyze acetylglucosamine deacetylase (4L1G),

whether the compound quersetin, phosphatidylcholine-phospholipase C

guaijavarin and morin-3-O-α-L- Bc (2HUC), phospholipase C regulator

arabopiranosida of guava leaves (P. + PapR (2QFC), penicillin binding

guajava L.) have interactions of 9 protein 3 E.coli (transferase) (4BJP)

molecule biology antibacterial targets and gyrase + 4.5-dibromopyrolamide-

and predict patterns of interaction of based inhibitor (isomerase) (4ZVI)

compounds quersetin, guaijavarin and downloaded from protein Data Bank.

morin-3-O-α-L-arabopiranosida against The ligands used are quersetin,

the 9 molecule biology antibacterial guaijavarin and morin-3-O-α-L-

targets through molecular docking. The arabopiranosida drawn and performed

method used in the study is molecular geometry optimization using

docking. Docking is a method that can ACD/ChemSketch. 3D structure can be

predict the orientation of a molecule to viewed using JMOL.

which another molecule when it binds Tools

to form a stable complex [5]. This The tools used in this study is a

method is useful to provide initial set of PC Laptop Asus Intel Core i7-

knowledge about the type of drug 4720 X450J HQ, 3.6 GHz, 4 GB RAM

compounds as ligand binding with with Microsoft Windows XP.

specific macromolecules [6]. The software used among

RESEARCH METHODS others JMOL, ACD/ChemSketch,

Materials Discovery Studio, PyRx-Autodock-Vina,

The materials used in this study PyMOL supported with internet access

include the protein SleB (4F55), protein to make connections with an online

SleL (4S3J), maltoporin (1MPR), Agga program.

(aggregative adherence fimbriae/1)

(4PH8), Bc1960 peptidoglycan N-

Procedures using ACD/ChemSketch. Furthermore

Preparation of molecule biology ligand format changed to .pdbqt using

antibacterial targets Discovery Studio. Optimization consists

Protein SleB (4F55), protein of adding hydrogen atoms in ligands

SleL (4S3J), maltoporin (1MPR), Agga that will automatically increase when

(aggregative adherence fimbriae/1) the Autodock Tools program opened

(4PH8), Bc1960 peptidoglycan N- and setting number of active sites

acetylglucosamine deacetylase (4L1G), torsion.

phosphatidylcholine-phospholipase C Validation of molecular docking

Bc (2HUC), phospholipase C regulator Validation docking of ligand and

+ PapR (2QFC), penicillin binding native ligand was added to Autodock-

protein 3 E.coli (transferase) (4BJP) PyRx-Vina program. Ligand and protein

and gyrase + 4.5-dibromopyrolamide- macromolecules selected to run the

based inhibitor (isomerase) (4ZVI) docking process. Ligands validation

downloaded from protein Data Bank. saved and compared with native ligand

Next step is optimization of these to see the Root Mean Square Deviation

targets with Autodock Tools saved (RMSD) value. Results docking

with .pdbqt format. Optimization otherwise be continued if the RMSD

consists of the removal of water value of ≤ 2 Å.

molecules and native ligand using Molecular docking

Discovery Studio and the addition of a The procedure is performed

hydrogen atom. similarly to the validation docking, but

Preparation of ligand structures will not do a comparison. The initial

The ligands used are quersetin, stage in docking with Autodock Vina is

guaijavarin. Quersetin, guaijavarin and open the file ligand and

morin-3-O-α-L-arabopiranosida drawn macromolecular protein after

and performed geometry optimization optimization. Then do the grid box

parameter settings, grid box parameter

for ligand 2QFC and ligand 4ZVI RESULTS AND DISCUSSION

equated with grid box parameter of Validation is performed on the

native ligand when validated. Then the regulator phospholipase C + PapR

grid box parameter for the other ligands (2QFC) and gyrase + 4.5-

governed by pointing to the active side dibromopyrolamide-based inhibitor

of the protein macromolecules. After (isomerase) (4ZVI) using PyRx-

setting the grid box, then continue with Autodock-Vina. Docking results

the process of docking. obtained show that the native ligand

Analysis and Visualization of may return to the same position prior to

molecular docking separation of the ligand to the protein

Determination of conformation macromolecules. This can be seen by

ligand done by selecting the looking at the amino acids bound to a

conformation of a ligand that has the ligand or in the surrounding areas.

lowest binding free energy (the best Amino acid protein macromolecules

pose) and see the interaction pattern is that are bound to a ligand prior to

formed, the similar patterns of separation can be seen through the

interaction that is formed it can be said binding pocket. The native Ligand

ligand has the same status as the 2QFC is ligand leu-pro-phe-glu-phe,

native ligand, protein-ligand complex ligands leu-pro-phe-glu-phe can be

increasingly stable and increasingly seen ligand bound to Asn 163, Asn

potent ligands. The position and 201, Lys 204 and Tyr 275, but it looks

orientation of the ligands on the amino acids surrounding, among

macromolecules, as well as amino others, Tyr 200, Glu 167 and Lys 197.

acids bound ligands were visualized by A comparison with the results of the

software PyMOL. validation docking, there are similarities

between the native ligand with the

results of the validation of the binding of bond at amino acid Asp 73 as well as

the amino acid residues via a second the validation results are visible through

overlay ligands, namely hydrogen the overlay both ligands with RMSD <2

bonds are formed at Lys 204 and amino Å, which is 1.178 Å in the center-x:

acids that bind around the same -14.1, center-y: 17.5, center z: 25.1,

ligands, namely Tyr 200 and Glu 167 size-x: 22.7, size-y: z size-20.5 and:

with RMSD <2 Å, which is 1.529 Å in 19.5. If an overlay between the native

the center-x: -22.1, center-y: 52.6, ligand with ligand docking results show

center-z: -0.3, size-x: 17.5, size-y: z that the native ligand with ligand

size-13.2 and: 20.2. The native ligand docking results have the position and

ie ligand 4S4 4ZVI visible hydrogen interaction patterns are similar.

Picture 1. 2QFC (ligan leu-pro-phe-glu-phe)

Picture 2. 4ZVI (ligan 4S4)

Table 1. Data compilation

morin-3-O-α-L-
Protein Guaijavarin Quersetin
arabopiranosida
4F55 No interaction on the Interaction occurs at Interaction occurs at

protein active site Glu 157 with ΔGbind Glu 157 with ΔGbind

-8.8 kcal/mol -7.9 kcal/mol

4S3J No interaction on the protein binding site

1MPR Interaction occurs at Interaction occurs at Interaction occurs at

Arg 8, Arg 33 and Glu Arg 8, Arg 33, Glu 43 Arg 8 and Arg 33

43 with ΔGbind -9.6 and Asp 116 with with ΔGbind -9.2

kcal/mol ΔGbind -9.0 kcal/mol kcal/mol

4PH8 No interaction on the protein binding site
4L1G Interaction occurs at No interaction on the Interaction occurs at

Pro 171 with ΔGbind protein active site Asp 80 with ΔGbind

-6.5 kcal/mol -7.2 kcal/mol

2HUC Interaction occurs at Interaction occurs at Interaction occurs at

122 Asp, Asn 147 Glu 146, Asn 147, Tyr 146 and His 142 Glu

and Trp 1 with 52 and Ala 3 with with ΔGbind -8.8

ΔGbind -9.2 kcal/mol ΔGbind -8.2 kcal/mol kcal/mol

2QFC Interaction occurs at Interaction occurs at No interaction on the

Asn 201 with ΔGbind Lys 204 with ΔGbind protein binding site

-6.8 kcal/mol -6.9 kcal/mol

4ZVI Interaction occurs at Interaction occurs at Interaction occurs at

Asp 73 with ΔGbind Asp 73 with ΔGbind Asp 73 with ΔGbind

-7.9 kcal/mol -7.0 kcal/mol -8.0 kcal/mol

4BJP Interaction occurs at Interaction occurs at Interactions occur at

Asn 361, Ser 307, Asn 361, Lys 310, Ser Ser 307, Thr 497 and

Ser 359 and Thr 497 307 and Ser 359 by Asn 361 with ΔGbind

with ΔGbind -7.3 ΔGbind -7.5 kcal/mol -7.0 kcal/mol

kcal/mol
 Based on the data compilation 1. Suraatmaja, Sudaryat. 2007. Kapita

analasis is found, it is suspected protein Selekta Gastroentrologi Anak.

SleL (4S3J) and Agga (aggregative Jakarta: CV Sagung Seto.

adherence fimbriae / 1) (4PH8) is not a 2. Tjay, Tan Hoan dan Kirana

targets of quersetin, guaijavarin and Rahardja. 2008. Obat-Obat Penting

morin-3-O-α-L-lyxopyranoside. Khasiat, Penggunaandan Efek-

Furthermore, seen from ΔGbind and Efek Sampingnya Edisi Keenam.

patterns of interaction that occurs, it Jakarta: PT. Elex Media

can be seen three best data, namely Komputindo.

the interaction of guaijavarin and 3. Thomas, A.N.S. 1989. Tanaman

quersetin in maltoporin (1MPR) and Obat Tradisional. Yogyakarta:

guaijavarin on the phosphatidylcholine- Kanisius.

phospholipase C Bc ( 2HUC). 4. Arima H dan Gen-ichi D. 2002.

CONCLUSION Isolation of Antimicrobial

Guaijavarin, morin-3-O-α-L- Compounds from Guava (Psidium

arabopiranosida and quersetin of guava guajava L.) and their structural

leaves (P. guajava L.) shows the elucidation. Bioscience,

interaction of biological molecules to 7 Biotechnology, and Biochemistry.

molecule biological antibacterial targets 66(8), 1727-1730.

4F55, 1MPR, 4L1G, 2HUC, 2QFC, 5. Lengauer T, Rarey M. 1996.

4ZVI and 4BJP and shows the Computational methods for

interaction patterns that resemble the biomolecular docking. Curr

native ligand against 2QFC and 4ZVI OpinStruct Biol. Jun;6(3):402-6.

seen from visual observations through Review. PubMed PMID: 8804827.

molecular docking. 6. Klebe, G. 2005. Virtual Screening:

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