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Email:Raisa.fadilla@gmail.com
ABSTRACT
Guava leaves have been proven to have antibacterial activity and have been
widely used for the prevention and therapeutic treatment of diarrhea. Guava leaves
contain many compounds that have antibacterial activity. Some of these compounds
understand the interaction and interaction patterns of quercetin, guaijavarin and morin-
molecule antibacterial targets used were SleB protein (4F55), SleL protein (4S3J),
antibacterial targets because it can bind to the active site residues of the
macromolecular protein 4F55, 1MPR, 4L1G, 2HUC, 2QFC, 4ZVI and 4BJP with Gbind
range -6,5-9,6 kcal/mol and shows the interaction patterns that resemble the original
ligand to the protein macromolecules 2QFC and 4ZVI AS seen from visual observation.
lyxopyranoside
INTRODUCTION
usual (> 3 times/day) along with a change in feces consistency (to liquid), with / without
blood and / or mucus [1]. Bacteria that cause diarrhea can be divided into two major
categories, the bacteria non-invasive and invasive bacteria. Included in the class of
non-invasive bacteria are: V. cholerae, pathogenic E. coli (EPEC, ETEC, EIEC), while
groups of invasive bacteria are Salmonella sp [2]. Most microorganisms that cause
diarrhea spread via fecal-oral route through food, contaminated water or transmitted
treated with antibiotics. Treatment with antibiotics is only needed on serious form of
diarrhea bacteria. The main choices are amoxicillin, cotrimoxazole and fluoroquinolone
compound. These drugs should not be given more than 7-10 days, except where after
recovering the diarrhea, the patient was still issuing the bacteria in the feces [4]. Giving
antimicrobials should consider the clinical benefits with cost, risk of side effects,
eradication of the normal flora intestinal that is harmful, induction of Shiga toxin
obtain, and the price is cheap, the use of traditional herbs does not create side effects,
as it often happens in the chemical treatment, other than that there are still many
people who believe that the use traditional medicine is safer than synthetic drugs [6].
Guava leaf (P.guajava L.) has been widely used by the public as a treatment of
activity based on the acquired MIC values. Some of these compounds include
This study aimed to analyze whether the quercetin, guaijavarin and morin-3-O-
method that can predict the orientation of a molecule to another molecule when it binds
biological screening, the goal is to find the value, rank or filter the set of data structures
using one or more procedures computing [9]. This method is useful to provide initial
knowledge about the type of drug compounds as ligand binding with specific
macromolecules [10].
EXPERIMENTAL SECTION
Materials
The materials used in this study were SleB protein (PDB ID: 4F55), SleL protein
(PDB ID: 4S3J), maltoporin (PDB ID: 1MPR), Agga (aggregative adherence fimbriae /
ID: 4ZVI) downloaded from the protein Data Bank. The ligands used were quercetin,
JMOL.
Instrumentation
The instruments used in this study were a set of PC Laptop Asus Intel Core i7-
4720 X450J HQ, 3.6 GHz, 4 GB RAM with Microsoft Windows XP. The software used
PyMOL which supported with internet access to make connections with an online
program.
Procedure
(4ZVI) were downloaded from the protein Data Bank. Furthermore these targets were
optimized with Autodock Tools saved with .pdbqt format. The conducted optimization
was the removal of water molecules and original ligand bound by using Discovery
structure could be viewed by using JMOL. Furthermore ligand format converted into
.pdbqt by using Discovery Studio. The conducted optimization was the addition of a
hydrogen atom in the ligand which will automatically increase when the Autodock Tools
Ligand docking validation and ligand was added to the original program-
Autodock PyRx-Vina. Selected ligand and macromolecular protein were used to run
docking process. Ligand resulted from docking process were saved (ligand validation)
and compared with original ligand to see the value Root Mean Square Deviation
Molecular docking
Autodock PyRx-Vina program. The performed procedure was similar to the docking
validation; however comparison would not be done. The initial stage in conducting
docking with Autodock Vina was by opening the ligand file and macromolecular protein
after optimization. Then the grid box parameter settings, parameter box for ligand
2QFC grid was done and 4ZVI equated with grid box parameter of original ligand when
validation was conducted. Then the parameter of grid box test ligand controlled by
pointing to the active side of the macromolecules protein. After setting the grid box,
ligand conformations which had the lowest binding free energy (best pose) and looking
at the pattern of formed interaction, the more similar the patterns of formed interaction
it means ligand had the same status as the original and complex ligand-protein became
more stable and ligan became more potent. The position and orientation of the ligands
software PyMOL.
Autodock-Vina. The obtained docking results showed that the original tethered ligand
could return to the same position prior to separation of the ligand to the protein
macromolecules. It could be seen by looking at the amino acids that was bound or
nearby to a ligand. Amino acid protein macromolecules that were bound to a ligand
prior to separation could be seen through the binding pocket. Original ligands 2QFC
bound with 163 Asn, 201 Asn, 204 Lys and 275 Tyr, beside that the other visible amino
acids were 200 Tyr, 167 Glu and 197 Lys. After being compared with the results of the
validation docking, there were similarities between the original ligand with the results of
the binding validation of the amino acid residues via second overlay ligands, which
hydrogen bonds were formed at Lys 204 and the same amino acid binding around
ligands, which were Tyr 200 and Glu 167 with RMSD <2 , which was 1.529 in the
center-x: -22.1, center-y: 52.6, center-z: -0.3, size-x: 17, 5, size-y: z size-13.2 and:
20.2. The original ligand was ligand 4S4 4ZVI could be seen hydrogen bond at amino
acid Asp 73 as well as the validation results were visible through the overlay both
ligands with RMSD <2 , which is 1.178 in the center-x: -14.1, center-y: 17.5, center
z: 25.1, size-x: 22.7, size-y: z size-20.5 and: 19.5. Overlay results between the original
ligand with ligand docking results showed that the original ligand with ligand docking
Based on the analysis of the obtained compiled data, it was suspected that
and patterns of interaction that occurred, three best data could be seen, which are the
CONCLUSION
leaves (P. guajava L.) shows the interaction towards 7 biological molecule antibacterial
targets 4F55, 1MPR, 4L1G, 2HUC, 2QFC, 4ZVI and 4BJP and have interaction
patterns that resemble the original ligand towards a biological molecule antibacterial
targets 2QFC and 4ZVI when viewed from visual observations through molecular
docking.
REFERENCES
Sagung Seto.
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3. Wong, L.D., Eaton, H.M., Wilson, D., Winkelstein, L.M., dan Schwart, P., 2009.
4. Tjay, Tan Hoan dan Kirana Rahardja. 2008. Obat-Obat Penting Khasiat,
Penggunaan dan Efek-Efek Sampingnya Edisi Keenam. Jakarta: PT. Elex Media
Komputindo.
9. Leach, A., Shoicet, B., & Peishoff, C. 2006. Docking and Scoring. J Med Chem 49
(20).
10. Klebe, G. 2005. Virtual Screening: Scope and Limitations. In J. Alvarez, & B.
Shoichet (Ed). Virtual Screening in Drug Discovery. Boca Raton: Taylor & Francis
Group.
morin-3-O--L-
Protein Guaijavarin Quercetin
arabopiranocid
1MPR Arg 8, Arg 33 and Glu Arg 8, Arg 33, Glu 43 Arg 8 and Arg 33
2HUC Asp 122, Asn 146 and Glu 146, Asn 147, Tyr Glu 146 and His 142
4BJP Asn 361, Ser 307, Ser Asn 361, Lys 310, Ser Ser 307, Thr 497 and
359 and Thr 497 307 and Ser 359 Asn 361 (Gbind-7,0