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Ade Arsianti
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arsi_ade2002@yahoo.com
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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 39 Documents
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Analysis of Differentially Expressed Genes (DEGS) Related to Interleukin-17 Signaling for Biomarker Identification and Therapeutic Targets in Atopic Eczema Fauziah, Siva; Veranita, Weri; Nurbaya, Siti; Sari, Puji
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 3, No. 2
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Abstract

Atopic eczema, also known as atopic dermatitis, is a chronic inflammatory skin condition characterized by itchy, red, and swollen skin. It is often associated with other atopic diseases such as asthma and hay fever. Interleukin-17 (IL-17), a pro-inflammatory cytokine, plays a crucial role in various inflammatory and autoimmune conditions, including atopic eczema. This study aims to identify potential therapeutic targets for managing atopic eczema based on the analysis of differentially expressed genes (DEGs). The expression of these gene targets was subsequently validated for their potential as biomarkers. Additionally, upstream regulator protein (URP) searches for the resulting DEGs were conducted. DEG analysis of the Gene Expression Omnibus (GEO) dataset, GSE6012 (atopic eczema vs. healthy donor skin), revealed that genes related to IL-17 signaling—FOSL1, MMP1, DEFB4B, S100A7, S100A8, and S100A9—can serve as biomarkers for atopic eczema with sensitivity and specificity values of 1.000. URP analysis suggested that inhibition of IL1A and NOG, as well as TGFB1 activity, are potential therapeutic targets to downregulate these six DEGs, thereby restoring their expression to the levels observed in healthy skin.
Targeting Detoxifying Enzymes in the Lymphatic Filariasis Vector: An In Silico Study on Curcumin, Camphor, and Menthol Subahar, Rizal; Winita, Rawina; Dwira, Surya; El Bayani, Gulshan Fahmi
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 1
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Abstract

Vector control remains a critical component in the prevention of lymphatic filariasis, a disease transmitted by insect vectors. Natural compounds such as curcumin, camphor, and menthol are being explored for their bio-insecticidal properties due to their potential to inhibit key detoxification and neurological enzymes in insects, including acetylcholinesterase (AChE), glutathione S-transferase (GST), and cytochrome P450 oxidases (CYP450). A molecular docking study using SwissDock was conducted to evaluate the interaction of curcumin, camphor, and menthol with AChE, GST, and CYP450 enzymes. Binding affinity (ΔG), hydrogen bonding, and active site interactions were analyzed to assess the inhibitory potential of each compound. Curcumin showed the highest binding affinity across all target enzymes. AChE (-8.2 kcal/mol), GST (-7.9 kcal/mol), and CYP450 (-7.5 kcal/mol). It formed strong hydrogen bonds with key catalytic residues, suggesting effective inhibition of neurotoxicity and detoxification pathways. Camphor displayed moderate binding affinities with AChE (-7.1 kcal/mol), GST (-6.5 kcal/mol), and CYP450 (-7.2 kcal/mol), primarily through hydrophobic interactions. Menthol exhibited the weakest binding, with limited hydrogen bonding and lower affinities (AChE: -6.4 kcal/mol, GST:-5.9 kcal/mol, CYP450: -6.3 kcal/mol). The findings suggest that curcumin is a promising candidate for insect vector control through inhibition of critical enzyme systems involved in neurotransmission and detoxification. Camphor may offer moderate bioactivity, while menthol appears less potent. These insights support further exploration of phenolic compounds as environmentally friendly, natural insecticidal agents against vectors of lymphatic filariasis.
The Effect of Temperature for Producing Thayer-Martin Agar Media Using Sheep Blood on Neisseria Gonorrhoeae Growth with Various Inoculums Ningsih, Ika; Sumadiyo, Kayla Adyapratista
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 1
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Abstract

Neisseria gonorrhoeae is a Gram-negative bacterium in the form of diplococci that infects mucous membranes through direct inoculation, is fastidious, and requires special media for growth because it is susceptible to heating and dryness, so it cannot survive long outside its host. Thayer-Martin agar media is a selective culture medium for the diagnosis of Neisseria gonorrhoeae bacterial infections enriched with sheep blood. The purpose of this study was to determine the optimum temperature for various temperature variations of making Thayer-Martin agar when mixing with sheep blood, compared to the temperature according to the manufacturer's procedure. Determining this ideal temperature may help improve the accuracy of the diagnosis of Neisseria gonorrhoeae infection. This study used an experimental laboratory design. Sheep blood was mixed into Thayer-Martin agar at several different temperatures: 56°C, 65°C, 75°C, and 85°C. After agar preparation, Neisseria gonorrhoeae ATCC 43069 was inoculated onto the agar with McFarland standards of 0.5, 1.0, 2.0, and 3.0. The plates were then incubated under appropriate conditions to observe bacterial growth. Neisseria gonorrhoeae showed varying growth patterns at different Thayer-Martin agar preparation temperatures, which was confirmed using ANOVA analysis with a p-value of 0.002. At 56°C, full growth was observed consistently across all McFarland turbidity standards (0.5, 1.0, 2.0, and 3.0). At 65°C, growth varied with a combination of full and half-full growth in all standards. However, temperatures of 75°C and 85°C resulted in significantly reduced growth, showing only half-full growth in all standards. Post hoc tests revealed that agar preparation at 56°C provided the most favorable conditions for Neisseria gonorrhoeae growth compared to the other temperatures tested. This study found that 56°C provided optimal conditions for the growth of Neisseria gonorrhoeae because it resulted in maximum bacterial growth. Higher temperatures, such as 65°C, 75°C, and 85°C, resulted in reduced bacterial growth, possibly due to protein denaturation or bacterial cell damage at these temperatures.
Exploring Differentially Expressed Genes to Identify Biomarkers of Cervical Cancer: A Bioinformatics Approach Suryandari, Dwi Anita; Yunaini, Luluk; Kristanty, Diyah; Prawiningrum, Aisyah
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 1
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Abstract

This study explores the molecular landscape of cervical cancer through the identification and analysis of differentially expressed genes (DEGs) from the GSE63514 dataset. A high-confidence protein–protein interaction (PPI) network was constructed using the STRING database (v11.5) and visualized via Cytoscape, identifying 178 nodes and 1,052 edges. Using the CytoHubba plugin, the top 10 hub genes—TOP2A, MKI67, CDK1, BUB1, CCNB1, CCNA2, AURKA, CDC20, PLK1, and RFC4—were highlighted based on degree centrality. These genes are predominantly associated with cell cycle regulation, DNA replication, and mitotic division, and are potentially valuable as biomarkers or therapeutic targets for cervical cancer. Functional enrichment using DAVID and Enrichr tools revealed significant involvement of DEGs in ATP binding, spindle microtubule formation, and protein kinase activity, particularly within the chromosome centromeric region and nucleoplasm. KEGG pathway analysis identified key associations with the cell cycle, DNA replication, p53 signaling, and complement and coagulation cascades. Further heatmap analysis of treatment responders versus non-responders demonstrated distinct gene expression profiles, particularly of immune-related genes like C1QA, C3, and SERPING1, and proliferative markers such as TOP2A and MKI67. These findings underscore the dual role of immune and proliferative pathways in cervical cancer progression and suggest their utility in developing predictive biomarkers and personalized treatment strategies.
Immunocytochemistry Evaluation of Fibroblast Response to Garlic (Allium sativum) Extract Targeting MMP9: In Vitro and In Silico Approaches Ningsih, Sri Suciati; Zuraidah, Endah; Handayani, Supri Irianti; Ardiansyah, Ahmad Ali Irfan; Wahyuni, Ningrum
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 1
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Abstract

Background: Fibrosis involves excessive extracellular matrix (ECM) deposition, with matrix metalloproteinase-9 (MMP-9) playing a critical role. Natural compounds targeting MMP-9 may offer therapeutic potential. Objective: This study evaluated the antifibrotic effect of Allium sativum extract on fibroblast cells through in vitro and in silico approaches targeting MMP-9. Methods: Human dermal fibroblasts were treated with A. sativum extract (25, 50, and 100 µg/mL) for 24 and 48 hours. Cell viability was assessed using MTT assay. MMP-9 expression was analyzed via quantitative real-time PCR (qRT-PCR) and immunocytochemistry (ICC). Major garlic compounds were docked to MMP-9 using AutoDock Vina. Results: The 50 µg/mL concentration maintained >85% cell viability and significantly reduced MMP-9 gene and protein expression. S-allyl cysteine exhibited the strongest binding affinity (−6.8 kcal/mol) and formed hydrogen bonds with key residues (Glu402, Ala189, His405) of MMP-9. Conclusion: Allium sativum extract demonstrates antifibrotic activity by downregulating MMP-9 expression and inhibiting its function, supporting its potential as a natural MMP-9 inhibitor for fibrosis-related disorders.
Phytochemisty and Antioxidant Activity of Ethanol, Ethyl Acetate, and n-Hexane Extracts of Suruhan Leaves (Peperomia pellucida) Arsianti, Ade; Gill, Steven; Kristanty, Diyah
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 4, No. 1
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Abstract

Background: Free radicals are natural byproducts of cellular metabolism, in which, their excessive accumulation can lead to oxidative stress, which plays a key role in the development of various chronic diseases, including cancer, cardiovascular disorders, and neurodegenerative conditions. Antioxidants are compounds capable of scavenging free radicals and minimizing oxidative damage. Peperomia pellucida, commonly known as Suruhan leaves, is a tropical herb traditionally used in folk medicine that contain bioactive compounds correlated with a strong radical-scavenging activity, suggesting its potential as a natural antioxidant source. This study aims to conduct a phytochemical analysis and evaluate the antioxidant activity of ethanol, ethyl acetate and n-hexane extracts of Suruhan leaves (P. pellucida). Method: Suruhan leaf powder obtained from Situbondo, East Java, was macerated in three different solvents of ethanol, ethyl acetate and n-hexane to produce its corresponding ethanol extract, ethyl acetate extract, and n-hexane extract of P. pellucida. The phytochemical components in P. pellucida extracts were determined using phytochemistry test. Antioxidant activity of the extracts was assessed using the DPPH method. Results: P. pellucida extracts comprise alkaloids, flavonoids, tannins, steroids, and triterpenoids as its phytochemical constituents. The ethanol and ethyl acetate extracts of P. pellucida displayed extremely strong antioxidant properties on DPPH with IC50 value of 14.45 µg/mL and 22.12 µg/mL respectively, while the n-hexane extract exhibited moderate antioxidant activity with IC50 value of 102.71 µg/mL on DPPH. Conclusion: P. pellucida extracts containing several phytochemical constituents that showed moderate-to-strong antioxidant activity towards DPPH free radical.
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
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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
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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
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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.

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