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All Journal Health Science Journal of Indonesia Jurnal Neutrino : jurnal fisika dan aplikasinya Medical Journal of Indonesia 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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Journal : Indonesian Journal of Medical Chemistry and Bioinformatics

 1 
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
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.
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
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
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.
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 Trisia Lusiana Amir Umiatin, Umiatin Widia Bela Oktaviani Yuda Nabella Prameswari Yurnadi Yurnadi