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All Journal Jurnal Neutrino : jurnal fisika dan aplikasinya Journal of Biomedicine and Translational Research Berkala Kedokteran Jurnal Ilmu Kedokteran dan Kesehatan Jurnal Entomologi Indonesia Bioscientia Medicina : Journal of Biomedicine and Translational Research Journal of the Indonesian Medical Association : Majalah Kedokteran Indonesia Jurnal Health Sains Bioscientia Medicina : Journal of Biomedicine and Translational Research Makara Journal of Science Indonesian Journal of Medical Chemistry and Bioinformatics Journal of Global Pharma Technology Indonesian Journal of Biomedicine and Clinical Sciences
Dwi Anita Suryandari
Department Of Medical Biology, Faculty Of Medicine, Universitas Indonesia, Jakarta 10430
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Computer Science & IT Dentistry Education Health Professions Immunology & microbiology Medicine & Pharmacology Neuroscience Nursing Physics Public Health Veterinary

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A Computational Exploration: Docking Analysis of Compounds from Foeniculum vulgare as Potential Aromatase Inhibitors for Endometriosis Candidate Therapy Suryandari, Dwi Anita; Sari, Puji; Sunaryo, Hadi; Istiadi, Khaerunissa Anbar
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 2, No. 2
Publisher : UI Scholars Hub

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Abstract

Aromatase inhibitors (AI) have controlling symptoms and size of endometriotic implants, making them a promising second-line therapy for endometriosis treatment.pretreatment with letrozole, an AI, combined with leuprolide acetate and resveratrol has been found to improve in vitro fertilization (IVF) outcomes in women mild endometriosis.in this study we screening and analysis of ten phenolic compounds from Foeniculum vulgare using molecular docking with Mcole server.from this results showed that three phenolic trans resveratrol (TR), caempherol coumaril (CC) have low gibbs energy compare with resveratrol (R). The binding modalities of compound TR and compound R were hydrogen-bonding between the hydroxyl and oxygen atom and Thr310 and hydrophobic interactions with Phe187, Ala272, Asp275, Ala189.and compound R exhibited cation-π interactions between Val336 as binding activity from aromatase.aromatase inhibitors and resveratrolfrom fennel lies in the potential of resveratrol to modulate hormonal pathways, including aromatase inhibition.
Molecular Insights into Propylthiouracil as a Thyroid Peroxidase Inhibitor: A Computational Study Approach Suryandari, Dwi Anita; Yunaini, Luluk; Sunaryo, Hadi; Istiadi, Khaerunissa Anbar; Pratomo, Irandi Putra
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 3, No. 1
Publisher : UI Scholars Hub

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Thyroid peroxidase (TPO) is a crucial enzyme in the biosynthesis of thyroid hormones, catalyzing the iodination of tyrosine residues in thyroglobulin and the coupling of iodotyrosines to form thyroxine (T4) and triiodothyronine (T3). Propylthiouracil (PTU) is an antithyroid drug commonly used to manage hyperthyroidism by inhibiting TPO. Understanding the molecular interactions between TPO and PTU can provide insights into the inhibitory mechanisms and guide the design of more effective antithyroid medications. Objective: This study aims to elucidate the binding interactions between TPO and PTU through molecular docking, providing a detailed understanding of how PTU inhibits TPO activity. Methods: The three-dimensional structure of TPO was obtained from Prosite and modelling by swissmodel and prepared for docking. The structure of PTU was optimized, and molecular docking was performed using AutoDock. The binding affinity, binding poses, and key interactions between TPO and PTU were analyzed. Visualization of the docking results was performed using PyMOL to identify critical residues involved in PTU binding. Results: The docking analysis revealed that PTU binds effectively to the active site of TPO with a binding affinity of -5.45 kcal/mol. The interaction involves coordination with the heme group and several key residues, including His239, which coordinates the heme, and Ser314, which forms hydrogen bonds with PTU. Additionally, hydrophobic interactions with residues Phe241 and Ile399 stabilize the binding of PTU in the active site. Conclusion: The docking study highlights the significant interactions between PTU and TPO, elucidating the molecular basis of TPO inhibition by PTU. The binding affinity and key interactions identified in this study provide a foundation for the design of more potent antithyroid drugs.
Association of fat mass and obesity associate (FTO) single nucleotide polymorphisms in the first intron and obesity risk among Indonesians Benedikta Diah Saraswati; Luluk Yunaini; Dwi Anita Suryandari
Indonesian Journal of Biomedicine and Clinical Sciences Vol 56 No 01 (2024)
Publisher : Published by Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/inajbcs.v56i01.11771

Abstract

Obesity is one of the global pandemics characterized by an excessive fat buildup due to disruption of energy homeostasis in the body. As obesity is a risk factor for many other non-communicable diseases such as diabetes and coronary heart disease, it is crucial to understand the risk factors that contribute to the pathogenesis of obesity. Although obesity is mainly caused due to unhealthy lifestyles, genetic predisposition also plays a part in the pathogenesis of obesity. Individuals who carry risk alleles for genes that control energy balance in the body have a greater risk of developing obesity. Fat mass and obesity associate (FTO) is a gene strongly correlated with obesity and is widely expressed in the hypothalamus. This gene is predicted to have 89 common variations that affect obesity-related phenotypes. Among Indonesians, the three most studied single nucleotide polymorphisms (SNPs) in the first intron of the FTO gene are rs1421085, rs17817449, and rs9939609. They are strongly associated with obesity’s related traits such as weight gain, fat mass, body mass index (BMI), waist, and hip sizes. rs993609 is the most studied among diverse ethnicities in Indonesia, with AA genotype and allele A as a risk allele.
In Silico Analysis of CD40 Mutations and Their Implications for Quinoline-benzoic acid derivatives Based Therapy in Graves' Disease Yunaini, Luluk; Kristanty, Diyah; Sari, Puji; Dwira, Surya; Suryandari, Dwi Anita; Bustami, Arleni
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 3, No. 2
Publisher : UI Scholars Hub

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Graves' disease is an autoimmune disorder in which the CD40-CD154 interaction plays a critical role in T-cell activation. In this study, in silico methods were employed to analyze the binding interactions of quinoline-benzoic acid derivatives (NSB, FSB, and NQB) with the CD40 receptor and to investigate the implications of specific CD40 mutations for drug efficacy. In this reseach conducted by molecular simulation approach with molecular docking Results Mutation analysis of CD40 identified alterations in key residues, such as R203C, which may impact ligand-independent activation and downstream TRAF binding, crucial for signal transduction. These findings highlight the therapeutic potential of quinoline-benzoic acid derivatives for targeting CD40 in Graves' disease, particularly in the context of receptor mutations. The integration of molecular docking, mutation analysis, and pharmacokinetic profiling provides a comprehensive framework for designing effective CD40-targeted therapies.
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
Publisher : UI Scholars Hub

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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.
VEGF mRNA Expression in Epithelial Ovarian Cancer: Correlation with rs699947 Gene Variant Prameswari, Yuda Nabella; Suryandari, Dwi Anita; Sukmawati, Dewi; Yunaini, Luluk; Kodariah, Ria
Journal of Biomedicine and Translational Research Vol 11, No 2 (2025): August 2025
Publisher : Faculty of Medicine, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/jbtr.v11i2.26156

Abstract

Background: Angiogenesis is the formation of new blood vessels, is crucial for cancer growth and metastasis, including in epithelial ovarian cancer (EOC). Vascular Endothelial Growth Factor (VEGF) regulates angiogenesis, and its elevated mRNA expression is linked to poor prognosis in cancer. Genetic variations, such as the rs699947 polymorphism in the VEGF gene, can affect VEGF expression and contribute to cancer progression.Objective: The primary aim of this study is to examine the distribution of the VEGF rs699947 polymorphism and its correlation with VEGF mRNA expression levels in patients with low-grade and high-grade EOC at Dr. Cipto Mangunkusumo Hospital, Indonesia.Methods: This research is a cross-sectional analysis involving 65 normal female whole blood samples and a total of 80 ovarian cancer biopsy samples, including 15 ovarian cysts as expression calibrators, along with 36 low-grade and 29 high-grade EOC samples. The distribution of genotypes and alleles of the VEGF rs699947 polymorphism was assessed through ARMS PCR analysis, while VEGF mRNA expression was quantified using real-time qPCR.Results: Significant differences were observed in both genotype (p<0,01) and allele (p=0,000) distributions between the normal and cases group. The relative mRNA expression of VEGF was significantly elevated in both low-grade and high-grade EOC. Individuals with the homozygous VEGF rs699947 AA genotype exhibited the highest mRNA expression compared to other genotypes. In contrast, individuals carrying the CC genotype showed the lowest correlation with VEGF mRNA expression in both low-grade and high-grade EOC.Conclusion: This study shows that the A allele of VEGF rs699947 is correlated with increased VEGF mRNA expression in EOC patients, particularly in those with the AA genotype. Conversely, the C allele may offer a protective effect against EOC, as the CC genotype is linked to lower VEGF mRNA expression. Genetic screening for VEGF rs699947 could facilitate early detection and inform targeted therapeutic strategies.
Correlation Epidermal Growth Factor Receptor Mutation with Non-small Cell Lung Cancer in Passive Smokers: A Review Prameswari, Yuda Nabella; Dwi Anita Suryandari
Bioscientia Medicina : Journal of Biomedicine and Translational Research Vol. 6 No. 4 (2022): Bioscientia Medicina: Journal of Biomedicine & Translational Research
Publisher : HM Publisher

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37275/bsm.v6i4.484

Abstract

Epidermal growth factor receptor (EGFR) is a transmembrane glycoprotein with an extracellular epidermal growth factor binding domain and an intracellular tyrosine kinase domain through signaling pathways to regulate cellular proliferation. Epidermal growth factor receptor binding to its ligand will result in autophosphorylation by intrinsic tyrosine kinase activity, thereby triggering multiple signal transduction cascades. Constant or sustained activation of these downstream target sequences is thought to result in a more aggressive tumor phenotype. Mutations in EGFR are associated with non-small cell lung cancer in passive smokers.
Correlation Epidermal Growth Factor Receptor Mutation with Non-small Cell Lung Cancer in Passive Smokers: A Review Prameswari, Yuda Nabella; Dwi Anita Suryandari
Bioscientia Medicina : Journal of Biomedicine and Translational Research Vol. 6 No. 4 (2022): Bioscientia Medicina: Journal of Biomedicine & Translational Research
Publisher : HM Publisher

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37275/bsm.v6i4.484

Abstract

Epidermal growth factor receptor (EGFR) is a transmembrane glycoprotein with an extracellular epidermal growth factor binding domain and an intracellular tyrosine kinase domain through signaling pathways to regulate cellular proliferation. Epidermal growth factor receptor binding to its ligand will result in autophosphorylation by intrinsic tyrosine kinase activity, thereby triggering multiple signal transduction cascades. Constant or sustained activation of these downstream target sequences is thought to result in a more aggressive tumor phenotype. Mutations in EGFR are associated with non-small cell lung cancer in passive smokers.
Anopheles species diversity and potential vectors of zoonotic malaria in Central Kalimantan, Indonesia: Diversitas spesies Anopheles dan vektor potensial malaria zoonotik di Kalimantan Tengah, Indonesia Permana, Dendi Hadi; Asih, Puji Budi Setia; Suryandari, Dwi Anita; Murhandarwati, Elsa Herdiana; Rozi, Ismail Ekoprayitno; Syahrani, Lepa; Kartapradja, Hannie Dewi Hadyani; Hidayah, Najdah; Bahrani; Irdayanti; Juliawaty, Rita; Coutrier , Elisabeth Farah Novita; Syafruddin, Din
Jurnal Entomologi Indonesia Vol 22 No 3 (2025): November
Publisher : Perhimpunan Entomologi Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5994/jei.22.3.165

Abstract

Zoonotic malaria is an emerging public health issue in Indonesia, particularly in regions with significant forest cover and frequent interaction between humans and non-human primates. Information regarding the diversity and behaviour of mosquito vectors in these areas is very limited. This study aims to identify the diversity and bionomics of mosquitoes, particularly Anopheles sp., across five ecologically diverse locations in Palangkaraya, Central Kalimantan, to gain an understanding of their potential role in zoonotic malaria transmission. Cross-sectional entomological surveys were conducted during November 2022 (during the rainy season) and October 2024 (at the beginning of the rainy season). Adult mosquitoes were collected using human landing catches (HLC) from 18:00 to 06:00, and larval habitats were surveyed and characterized following the WHO protocol. A total of 1,278 mosquitoes were collected from six genera, with Anopheles letifer Sandosham dominating the Anopheles group (97%), particularly in swampy secondary forests, such as Nyaru Menteng. This species exhibited peak outdoor biting activity shortly after dusk and late at night, posing a greater risk to those outside or in unscreened homes. Larval surveys conducted at 48 sites revealed Anopheles larvae in 27% of habitats, predominantly in swamps (67% positive). Although no significant associations were found with environmental factors, natural and semi-natural water bodies appear key to sustaining vector populations. These findings highlight the ecological flexibility of An. letifer and its potential impact on zoonotic malaria transmission in forest-edge communities. Vector control strategies should include integrated methods, such as larval source management and community-based interventions, particularly in peat swamp regions where interactions between humans and non-human primates are frequent.
Co-Authors Arleni Bustami Bahrani Barasila, Atikah Chalida Benedikta Diah Saraswati Budi Wiweko Christina Agusta Deviana Tanifan Coutrier , Elisabeth Farah Novita Dewi Sukmawati Din Syafruddin Dwi Yanti E. Elsa Herdiana Murhandarwati Fatimah Eliana Fatimah Eliana Ghaniyyatul Khudri Hadi Sunaryo Hidayah, Najdah Irandi Putra Pratomo Irdayanti Juliawaty, Rita Kartapradja, Hannie Dewi Hadyani Khaerunissa Anbar Istiadi Khatimah, Husnul Kristanty, Diyah Kurniati, Mala Luluk Yunaini Mala Kurniati Muchtaruddin Mansyur Muhammad Ilyas Iqbal Nukman Moeloek Nukman Moeloek Nukman Moeloek Panghiyangani, Roselina Permana, Dendi Hadi Pramudianto Prawiningrum, Aisyah Pudji Sari Pudji Sari Puji Budi Setia Asih, Puji Budi Puji Sari Puji Sari Puji Sari Ria Kodariah Rozi, Ismail Ekoprayitno Surya Dwira Syahrani, Lepa Trisia Lusiana Amir Umiatin, Umiatin Widia Bela Oktaviani Yoel Asmida Yoel Asmida Yuda Nabella Prameswari Yurnadi Yurnadi