Indonesian Journal of Computational Biology (IJCB)
IJCB (Indonesian Journal of Computational Biology) 3 times a year to provide a peer-reviewed scientific journal covering computational biology and bioinformatics and publishing in-fields statistical, mathematical, and computational analysis of methods. It was established by Indonesian Society for Bioinformatics and Biodiversity (MABBI) and Research Centre of Molecular Biotechnology and Bioinformatic, Universitas Padjadjaran. We open wide to all researchers or practitioners who have scientific work or research results in this field to be published in our journal. All articles submitted will be reviewed by a minimum of 2 reviewers who are experienced in their field. ISSN: 2962-1313 (Print) eISSN: 2963-4938 (Online)
Potential of Indonesian Medicinal Plant Biodiversity as CHK1 Inhibitor Agent for Cancer Treatment by Bioinformatics and Computational Chemistry
Indonesia is rich in flora diversity thanks to its biodiversity that has the potential as compounds that can be validated as candidate CHK1 inhibitor agents. The research was conducted in silico by performing molecular tethering using Autodock tools. The reference ligand was found from the 4FT3 receptor with the H1K code on the PDB. The result of docking in reference ligand obtained a Gibbs free energy value of -6.48 kcal/mol. The next process was carried out molecular tethering to 24 selected test compounds. The processes carried out are molecular docking, molecular visualisation, "Lipinski's Rule of Five" testing and Pre-ADMET testing. Based on Gibbs free energy, 18 molecules met the criteria and the best 3 were selected for analysis, namely stigmasterol, laurifolin, and quercetin with Gibbs free energy values of -10.40 kcal/mol, -8.70 kcal/mol, and -8.04 kcal/mol respectively. Based on the Pre-ADMET test, quercetin belongs to GSH toxicity class 4 which means the compound has a mild toxicity effect compared to other compounds. The molecular dynamics results showed that quercetin is the most stable compound and binds the longest compared to the others. The results can be continued for further research through laboratory testing stages in vitro and in vivo.
Computational Simulation of Indonesian Natural Compounds as Mainprotease Inhibitors of SARS CoV 2
The computational method provides an alternative approach for conducting screening of natural substances antiviral properties against the SARS-CoV-2 virus. This research focuses on the Main Protease, a target protein that plays a central role in viral replication by producing an enzyme that cleaves the host protein nuclear factor (NF)-κB in SARS-CoV-2. The study used a thousand natural compound structures from the Indonesian Natural Compound Database (Herbaldb), filtered based on the similarity of their pharmacophore features with Mainprotease inhibitors. In compounds with good pharmacophore properties, docking will be carried out to determine the binding affinity with the target protein and obtain the complex structure. The ADMETSAR test was used to determine the pharmacology and pharmacokinetics of the five best natural compounds. Finally, molecular dynamics simulation of the complex structure was performed to assess the stability of the best compound interactions with the SARS-CoV-2 Mainprotease. The compounds identified as Mainprotease inhibitors in this study were cosmosiin, glucobrassicin, and isobavachin.
Copyright (c) 2023 Setyanto Tri Wahyudi, Zahra Silmi Muscifa, Tony Ibnu Sumaryada, Laksmi Ambarsari
Interaction of Singawalang Leaves (Petiveria alliacea) Compounds as a Reduction of Blood Glucose Levels in Treatment of Type 2 Diabetes Mellitus Disease
AMPK-α2 has an important role in controlling glucose homeostasis, carbohydrate, fat, and protein metabolism, so AMPK-α2 plays an important role in the pathophysiology of type 2 diabetes. Therefore, AMPK-α2 is an important therapeutic target in the management of type 2 diabetes. (Petiveria alliacea) is a type of plant in Indonesia and is empirically used by residents to treat diabetes mellitus. The purpose is to examine the interaction and affinity of compounds from singawalang to the AMPK-α2 receptor and its toxicity prediction so that it becomes an alternative treatment for type 2 diabetes mellitus with minimum risk of side effects. The methods of this study are molecular docking simulations and prediction toxicity. The results of the simulation molecular docking of the singawalang isolate compound against the AMPK-α2 receptor obtained the best test ligands which have ΔG -5.16 kcal/mol. While the prediction of toxicity shows that the benzyl 2-hydroxyethyl trisulphide test ligand has the potential to be mutagenic but not carcinogenic. Therefore, it is necessary to modify the structure to be able to provide a lower toxicity effect. The conclusion is that benzyl 2-hydroxyethyl trisulphide is the most potential candidate compound with the highest affinity and low risk of toxicity.
Copyright (c) 2023 Meilinda setya praceka
Insight into Jasminum sambac Molecular Docking Interaction with GCK related to Diabetes Mellitus
Diabetes mellitus is one of non comunicable disease witrh high prevalencies in Indonesia. The aim of thie study are exploring the potential of J sambac phytochemical constituen for treating DM. The potential of J sambac as a DM therapy candidate was demonstrated through in silico analysis using several databases and computer aided drug discovery tools. The bioactive compounds analyzed were obtained from pubchem data, for the protein database taken from RSCB PDB, to predict or test ADME using SWISSADME and to analyze target proteins and metabolic pathways, biological activity and related diseases using Swiss prediction target prediction and string DB. Performing molecular docking using BIOAVIA Discovery Studio Visualizer version 4.5 and PyRx version 0.8. From the search results for the compounds contained in Jasminum sambacit was found that there were several active compounds contained in it and some of these compounds passed the ADME criteria, namely compounds (Z,Z,Z)-3,6,9-Dodecatrien -1-ol,( Z)-Jasmone, linalool, Nerolidol, (-)-alpha-Cadinol, Benzenemethanol, Benzaldehyde, Linalyl benzoate, 2,2,3,4-Tetramethylpentane. And an in-depth analysis was carried out regarding the bonds that occur and how these compounds bind to the Glucokynase enzymes found in humans and also how their potential is to become an inhibitor of diabetes mellitus. The GCK enzyme protein contained in J.sambac binds to compounds present in J.sambac such as Linalyl Benzoate and also Benzenemethanol, which may result in the bonding that can make these compounds into medicinal compounds for diabetes mellitus.
Copyright (c) 2023 Ahmad Shobrun Jamil, Mochammad Rehan Alghifari
Molecular interaction analysis and visualization of protein-ligand docking using Biovia Discovery Studio Visualizer
Molecular docking interpretation is one of the crucial part before determining the result. Docking is commonly used to study the biomolecular interaction, usually for protein-ligand interaction, and to study about the molecular mechanism. Analysis of molecular interaction can help user to determine the strengthened of docking results, besides free energy of binding. In this protocol, analysis of molecular interaction as well as the surface characteristic of receptor was discussed in detail. In addition, the visualization to obtain suitable pictures for publications also included. The entire protocol will spend more of less 2 hours.
Copyright (c) 2023 Umi Baroroh, S.Si., M.Biotek., Zahra Silmi Muscifa, Wanda Destiarani, Fauzian Giansyah Rohmatullah, Muhammad Yusuf