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All Journal Health Science Journal of Indonesia Jurnal Neutrino : jurnal fisika dan aplikasinya Journal of Biomedicine and Translational Research Universa Medicina Indonesian Journal of Obstetrics and Gynecology (Majalah Obstetri dan Ginekologi Indonesia) Jurnal Ilmu Kedokteran dan Kesehatan Jurnal Health Sains Indonesian Journal of Medical Chemistry and Bioinformatics Journal of Global Pharma Technology Indonesian Journal of Biomedicine and Clinical Sciences
Luluk Yunaini
Department Of Medical Biology, Faculty Of Medicine, University Of Indonesia, Jakarta
Biochemistry, Genetics & Molecular Biology Chemistry Computer Science & IT Dentistry Health Professions Immunology & microbiology Medicine & Pharmacology Neuroscience Nursing Physics Public Health Veterinary

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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.
Co-Authors Arleni Bustami Benedikta D. Saraswati Benedikta Diah Saraswati Budi Wiweko Christina Agusta Deviana Tanifan Debby Desmarini Dewi Sukmawati Dewi Sukmawati Dwi A. Suryandari Dwi A. Suryandari Dwi Anita Suryandari Dwi Ari Pujianto Dwi Yanti Dwira, Surya Fadilah Fadilah Fatimah Eliana Fatimah Eliana Hadi Sunaryo Irandi Putra Pratomo Khaerunissa Anbar Istiadi Kristanty, Diyah Kurniati, Mala Murdani Abdullah Panghiyangani, Roselina Prawiningrum, Aisyah Primariadewi Rustamadji Pudji Sari Puji Sari Puji Sari Puji Sari Puji Sari Ria Kodariah Ria Kodariah Sisca Sisca, Sisca Sofy Meilaini Trisia Lusiana Amir Umiatin, Umiatin Widia Bela Oktaviani Yuda Nabella Prameswari Yurnadi Yurnadi