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Ade Arsianti
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INDONESIA
Indonesian Journal of Medical Chemistry and Bioinformatics
Published by Universitas Indonesia
ISSN : -     EISSN : 29633818     DOI : https://doi.org/10.7454/ijmcb
Core Subject : Science,
Chemistry Computer Science & IT
The Indonesian Journal of Medical Chemistry and Bioinformatics (IJMCB) provides a forum for disseminating information on both the theory and the application of in silico, in vitro, and in vivo methods in the analysis and design of molecules, phytochemistry, medicinal chemistry and bioinformatics. Indonesian Journal of Medical Chemistry and Bioinformatics was published by Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia. This peer-reviewed academic open access journal has its first publish in in August 2022 and formerly publish every March and August. The scope of the journal encompasses papers which report new and original research and applications in the following areas: 1. Phytochemical and Medicinal chemistry (identification of targets, design, synthesis and evaluation of biological target) 2. Bioinformatics (genomic profiling, mutation analysis) 3. Molecular modeling (pharmacophore, molecular docking, molecular dynamic simulation) 4. Protein Modeling 5. Network Pharmacology and protein-protein interaction 6. Genomic 7. Metagenomics
Arjuna Subject : Kedokteran - Kedokteran (Lain-Lain)
Articles 5 Documents
 1 
Search results for , issue "Vol. 4, No. 2" : 5 Documents clear
Prediction of Structure and Function of a Novel β-Lactamase Protein in Gram-Negative Bacteria Using Homology Modeling and Molecular Docking Kiranasari, Ariyani; Dwira, Surya; Merizka, Engla
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 2
Publisher : UI Scholars Hub

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Abstract

The emergence of β-lactamase–producing Gram-negative bacteria represents a major global challenge due to increasing resistance to β-lactam antibiotics. In this study, we performed in silico structural and functional prediction of a newly identified β-lactamase protein sequence obtained from a Gram-negative bacterial isolate. Homology modeling was used to construct a reliable 3D model of the protein based on structurally resolved β-lactamases. The model was further evaluated using stereochemical validation parameters. Molecular docking was conducted to assess binding affinity and interaction patterns between the predicted β-lactamase and clinically relevant β-lactam antibiotics, including ampicillin, cefotaxime, and imipenem. The results revealed conserved catalytic residues typical of class A β-lactamases, strong binding affinities toward penicillin and cephalosporin substrates, and key hydrogen bond interactions within the active site. This study provides a structural framework for understanding the function of the new β-lactamase and offers insights for developing β-lactamase inhibitors targeting resistant Gram-negative pathogens.
A Comparison of The Effectiveness of Salmonella-Shigella (SS) Agar and Xylose Lysine Deoxycholate (XLD) Agar in Supporting The Growth of Salmonella sp. and Shigella sp. Ningsih, Ika; Tiro, Kharisma Winnie Chryssantium
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 2
Publisher : UI Scholars Hub

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Abstract

Diarrheal diseases caused by Salmonella sp. and Shigella sp. are among the most significant public health challenges worldwide, especially among children. To identify these bacteria, Salmonella-Shigella (SS) and Xylose Lysine Deoxycholate (XLD) agar media are used, which are selective and differential for Salmonella sp. and Shigella sp. Although these media share similar properties and functions for growing Salmonella sp. and Shigella sp., results from previous studies differ from those obtained in tests conducted by the Department of Microbiology, Faculty of Medicine, University of Indonesia. This laboratory-based experimental study used serial dilution with three replicates (triplicate). Based on SNI 2897 of 2008 concerning Standard Plate Count, which is considered valid at 30 -300 colonies, data with a value of 300 will be excluded, and the remaining valid data will be processed using SPSS for Windows version 29. The average growth of Salmonella typhimurium ATCC 14028 on SS agar was 417 × 106 CFU/mL, and on XLD agar was 420 × 106 CFU/mL, a difference that was not statistically significant. Then, the average growth of Shigella sonnei on SS agar was 317 × 106 CFU/mL, whereas on XLD agar it was 183 × 106 CFU/mL, a statistically significant difference. There was no difference in growth effectiveness between Salmonella sp. and Shigella sp. bacteria grown on SS and XLD agar media. Shigella sp. grew more effectively on SS agar.
Larvicidal activity of β-asarone and Acorus calamus Linn. (sweet flag) extract against Aedes aegypti (Dipotera: Culicidae): Enzyme inhibition, midgut histopathology, and in silico analysis Subahar, Rizal; Dwira, Surya
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 2
Publisher : UI Scholars Hub

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Abstract

Aedes aegypti (Diptera: Culicidae), the primary vector of dengue, poses a significant public health threat in tropical and subtropical regions. Botanical insecticides and phytochemicals such as β- asarone, derived from essential oils,offer a promising alternative to synthetic larvicides. The rhizome of Acorus calamus L. (sweet flag), traditionally known for its neuroprotective and antioxidant properties, contains β-asarone as its principal bioactive constituent.This study evaluated the larvicidal efficacy of β-asarone and A. calamus rhizome extract against Ae. aegypti larvae, focusing on detoxification enzyme inhibition, midgut histopathology, and in silico molecular interactions.Third- and fourth-instar larvae were exposed to β-asarone and crude extract at concentrations ranging from 0.25 to 24.25 μg/mL. Larval mortality was recorded at 24, 48, and 72 hours post-exposure following WHO guidelines. Activities of acetylcholinesterase (AChE), glutathione-S-transferase (GST), and oxidase were measured using biochemical assays. Midgut histopathological changes were assessed via hematoxylin and eosin staining. Molecular docking (CB-Dock2) was used to evaluate β-asarone interactions with AChE, GST, and oxidase. β-asarone showed significantly higher larvicidal potency (LC₅₀ = 6.768 μg/mL) than the crude extract (LC₅₀ = 54.566 μg/mL). Both treatments markedly inhibited AChE and oxidase and caused extensive midgutdamage, including epithelial degeneration, ruptured peritrophic membrane, and loss of microvilli. These results demonstrate the potential of β-asarone as plant-derived larvicides acting through enzymatic inhibition and midgut disruption, offering a promising strategy for mosquito control.
Prediction of Antidiabetic Activity of Swietenia mahagoni Compounds through PPARγ Activation: Machine Learning and Molecular Docking Analysis Veranita, Weri; Nurbaya, Siti
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 2
Publisher : UI Scholars Hub

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Abstract

Type 2 diabetes mellitus is a chronic metabolic disorder requiring long-term therapy, yet current synthetic PPARγ agonists like thiazolidinediones are often associated with serious adverse effects. Therefore, identifying natural alternatives from sources such as Swietenia mahagoni is essential to provide effective therapy with potentially lower toxicity profiles. This study employed an in silico machine learning approach using SkelSpheres descriptors to predict the IC₅₀ values of compounds derived from the seeds of Swietenia mahagoni against PPARγ, followed by molecular docking validation using Molegro Virtual Docker (MVD). The predictive model for PPARγ agonists demonstrated acceptable validity (R²-test = 0.5308; accuracy = 84.01%). Four compounds from S. mahagoni showed predicted IC₅₀ values below 1 µM (0.0973–0.9527 µM), categorized as “Predicted Excellent activity.” Docking simulations revealed that the bibenzyl derivative 2-Carboxy-3,5-Dihydroxy-4-Geranylbibenzyl (CID: 25135579) and β,β-Carotene tetrol (CID: 23258402) exhibited binding affinities comparable to the control ligand thiazolidinedione, with Rerank Scores of-114.991 and -109.764 kJ/mol, respectively. In conclusion, the bibenzyl derivative and carotene tetrol from S. mahagoni represent promising natural candidates for PPARγ agonists, providing a strong rationale for further in vitro and in vivo investigations as potential antidiabetic agents.
In Silico Molecular Docking Study Of Antidiabetic Bioactive Compounds From Brotowali (Tinospora cordifolia) Targeting GLUT4 In Type II Diabetes Mellitus Tarigan, Gita Euaggelion; Dwira, Surya
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 2
Publisher : UI Scholars Hub

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Abstract

Type 2 diabetes mellitus (T2DM) is a global metabolic disorder characterized by insulin resistance and impaired glucose uptake. Despite the availability of pharmacological therapies, limitations such as adverse effects and high costs highlight the need for alternative therapeutic candidates. Tinospora cordifolia has been widely reported to contain bioactive compounds with antidiabetic potential; however, comparative evaluation of their interaction with glucose transporter type 4 (GLUT4) remains limited. This study aimed to identify the most promising bioactive compounds from Tinospora cordifolia targeting GLUT4 using an in silico molecular docking approach, followed by pharmacokinetic and toxicity (ADMET) prediction. Molecular docking was performed using Molegro Virtual Docker with GLUT4 (PDB ID: 7WSM), and six ligands retrieved from the PubChem database. Model validation was conducted using redocking with RMSD < 2 Å. The results demonstrated that hesperetin 7-rhamnoglucoside, verbascoside, and cyanidin 3-O-sambubiosyl 5-O-glucoside exhibited stronger binding affinities than the native ligand, with rerank scores of −137.228, −132.756, and −131.726 kJ/mol, respectively. These compounds formed stable hydrogen bonds with key residues, including Asn176, Gln298/Gln299, and Trp404/Trp428. ADMET analysis indicated that hesperetin 7-rhamnoglucoside and verbascoside possessed more favorable pharmacokinetic profiles with relatively low toxicity risks. In conclusion, hesperetin 7-rhamnoglucoside and verbascoside are identified as the most promising candidates for GLUT4-targeted antidiabetic therapy. These findings provide a computational basis for further experimental validation in the development of novel antidiabetic agents.

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