Yuliana Heri Suselo
Sebelas Maret University

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Screening of Indonesian Pythochemicals as Glucagon-Like Peptide-1 Receptor Agonist In Silico in Type-2 Diabetes Mellitus Humamuddin .; R Aj Sri Wulandari; Yuliana Heri Suselo
Nexus Kedokteran Translasional Vol 6, No 1 (2017): Nexus Kedokteran Translasional
Publisher : Fakultas Kedokteran Universitas Sebelas Maret Surakarta

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Abstract

Background: Prevalence of diabetes mellitus (DM) continues to rise in the world, while DM therapy using oral antidiabetic drug (OAD) was still not effective. GLP-1R agonist was a drug that has been developed because it can lower blood sugar levels without hypoglycemic effect. However, GLP-1R agonists have severe side effects such as pancreatitis, thyroid cancer, and pancreatic cancer. Indonesia has 9,600 herbal plants, some of which have a pharmacological effect that could potentially be developed as a drug. This study aimed to identify the Indonesian pythochemicals that have activity as GLP-1R agonist in silico. Methods: The research was a bioinformatics study which utilized all phytochemicals in HerbalDB that had PubChem access code and met the criteria for Lipinski's rule of five as sample. Truncated Exendin-4 was used as standard compound. The structure of Exendin-4 bound to GLP-1R was obtained from the Protein Data Bank, code: 3C5T. Validation of truncated Exendin-4 with GLP-1R needed to get docking scores and binding site at GLP-1R. Molecular docking between phytochemical compounds with GLP-1R models was done using AutodockVina 1.1.2. Visualization of docking results was done using PyMOL 1.7.4. GLP-1R agonist candidates were analyzed based on binding affinity, binding site similarity, and Lipinski's rule of five criterias. Results: Weighteone and Eupatorin were two selected phytochemicals of the most potentially be GLP-1R agonist based on analysis of docking scores and binding site similarity with truncated Exendin-4. Weighteone and Eupatorin bound to Glu68, Glu127, and Glu128 of GLP-1R. Weighteone had docking scores of -5.12 kcal/mol, -6.22 kcal/mol, and -3.88 kcal/mol lower than truncated Exendin-4. Eupatorin had docking scores of -5.02 kcal/mol, -6 kcal/mol, and -3.58 kcal/mol lower than truncated Exendin-4. Conclusion: Weighteone and Eupatorin were the potential Indonesian phytochemicals that could be a GLP-1R agonist in silico. Future studies using Molecular Dynamics Simulation (MDS) method is required to validate this result. In vitro studies are also needed to evaluate these phytochemicals activity as GLP-1R agonists. Keywords: GLP-1R agonists, Indonesian phytochemicals, molecular docking, diabetes mellitus.
Identification of Herbal Compounds as Thymidylate Synthase Inhibitors that more Potent than 5-Fluorouracil using Molecular Docking Yoga Mulia Pratama; Dono Indarto; Yuliana Heri Suselo
Nexus Kedokteran Translasional Vol 4, No 2 (2015): Nexus Kedokteran Translasional
Publisher : Fakultas Kedokteran Universitas Sebelas Maret Surakarta

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Abstract

Background: Development of new selective anticancer drug is an important necessary. Because of that, some effective way to screen herbal compounds which have good potency for developing drug is needed, one of them is using molecular docking methods. In this study, researchers identify herbal compounds as new thymidylate synthase (TS) inhibitors which more potent than 5-Fluorouracil (5-FU) using molecular docking. Methods: Three-dimensional structure samples of herbal compounds from Indonesian herbal database (herbaldb.ui.ac.id) were docked with three-dimensional structure of TS protein using iGEMDOCK program. Then, the compounds which have lower docking score than fdUMP, as standard ligand, clustered using ChemMine. Results: The docking result showed that 27 herbal compounds have docking score lower than fdUMP in iGEMDOCK program. The 27 compounds have higher affinity to fdUMP and it can form a stable complex with TS protein. Protein-ligand complexes showed that all of 27 compounds have same binding site with fdUMP. But folic acid is excluded from the result because it is a TS ligand. fdUMP has similar structure with UMP, a TS ligand, but folic acid which has lowest docking score is not similar with UMP. Conclusions: The 26 compounds, except folic acid, are more potent than 5-FU as TS inhibitors by docking study. Further study to delineate the effectivity of molecular docking is needed. Keywords: 5-Fluorouracil, herbal compound, molecular docking, thymidylate synthase