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All Journal The Indonesian Biomedical Journal Syntax Literate: Jurnal Ilmiah Indonesia Eksakta : Berkala Ilmiah Bidang MIPA Journal of Applied Science, Engineering, Technology, and Education Makara Journal of Science Indonesian Journal of Medical Chemistry and Bioinformatics
Paramita, Rafika Indah
Department Of Chemistry, Faculty Of Faculty Of Medicine, Universitas Indonesia, Jakarta, Indonesia
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Molecular Docking of ftsZ Protein of Staphylococcus aureus to Indonesian Herbal Compound Monica, Maria Diyan; Erlina, Linda; Fadilah, Fadilah; Paramita, Rafika Indah
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 25 No. 01 (2024): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464)
Publisher : Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24036/eksakta/vol25-iss01/431

Abstract

Microbial resistance to antibiotics is a growing global problem, and new antibacterial agents are needed to overcome this. One of the bacteria with a high level of resistance is Staphylococcus aureus. Herbal compounds are an alternative as a source of new antibacterial agents. Molecular docking can be used in screening herbal compounds that can become new antibacterial agents against Staphylococcus aureus. Virtual screening was conducted using Ligandscout, and molecular docking was conducted via Autodock. LigPlot was used to analyze the interaction between hit compounds to the protein target, and finally, the pharmacokinetic characteristics were assessed in SWISSADME and ADMETsar programs. From 1377 compounds in the Indonesian Herbal Database, 12 hit compounds have an affinity to the target protein ftsZ of Staphylococcus aureus. Further analysis of the interaction with target protein and pharmacokinetics properties considers Alpha Santalol a compound with good potential for further development as an antibacterial agent against Staphylococcus aureus. However, in vitro and in vivo study is needed to validate this result.
Profil Genotipik Extraintestinal pathogenic Escherichia coli (ExPEC) Penyebab Bloodstream Infection Menggunakan Whole Genome Sequencing: Literatur Review Stevina, Lany; Tjampakasari, Conny Riana; Paramita, Rafika Indah
Syntax Literate Jurnal Ilmiah Indonesia
Publisher : Syntax Corporation

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.36418/syntax-literate.v9i7.15845

Abstract

Penelitian ini bertujuan untuk menganalisa profil fenotipik dan genotipik pola kepekaan antibiotik pada Escherichia coli (E.coli) penyebab Bloodstream infection (BSI). Metode penelitian yang digunakan adalah literature review. Pencarian literatur menggunakan data dari publikasi ilmiah mulai dari tahun 2020 hingga tahun 2024 dengan menggunakan beberapa pencarian database seperti ScienceDirect (https://www.sciencedirect.com); PubMed (https://pubmed.ncbi.nml.nih.gov); dan Google Scholar (https://www. scholar.google.com). Berdasarkkan kata kunci dan kriteria inklusi yang digunakan, total ditemukan 236 artikel. Setelah dilakukan penyaringan didapatkan empat artikel yang ditinjau dan ditelaah lebih lanjut berdasarkan kecocokan judul dan abstrak. Berdasarkan hasil review jurnal, penelitian menyimpulkan bahwa karakterisasi secara fenotipik dan genotipik tidak hanya akan meningkatkan ketepatan diagnostik bakteri penyebab BSI tetapi juga dapat memberikan pemahaman mendalam mengenai sifat biologis dan epidemiologi penyakit. Sehingga, tidak hanya mendukung pengambilan keputusan klinis yang lebih akurat melainkan juga memungkinkan upaya pencegahan serta pengendalian infeksi.
Virtual Screening on Indonesian Herbal Compounds as SARS-CoV-2 Spike (S2) Glycoprotein Inhibitors: Pharmacophore Modelling & Molecular Docking Approaches Sugito, Syailendra Karuna; Cristina, Artha Uli; Harimurti, Putri Saskia; Cendani, Gabriella Regita; Insani, Fauzi Azhar; Erlina, Linda; Paramita, Rafika Indah; Fadilah, Fadilah
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 1, No. 2
Publisher : UI Scholars Hub

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Abstract

Background: There are still no specific treatments for coronavirus disease (COVID-19) until present days. Several studies have been conducted to determine whether herbal medicine can be an option to be used as a definitive medicine for COVID-19. S2 subunit of spike protein which is responsible for SARS-CoV-2 entry to the host cell, is a potential drug target to inhibit the viral infection. In this study, we aimed to find some compounds from the HerbalDB database that have potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor. Methods: The 6LXT protein was used as the target protein. The procedure in this study consisted of these following steps: protein and ligand preparation, pharmacophore modelling and compound screening, molecular docking, ADME, and toxicity analysis. The docking of hit compounds to the target protein were compared to arbidol and quercetin as positive controls. Results: Four hit compounds were screened from HerbalDB compounds. Two of them, octopamine and L-noradrenaline, showed lower binding energies (respectively, -5.19 and -4.98 kcal/mol) than positive controls whereas the other two compounds, mimosine and L-theanine, showed higher binding energies (respectively, -3.99 and -3.62 kcal/mol) compared to positive controls. Mimosine, L-noradrenaline, octopamine, and L-theanine had toxicity classes of IV, II, IV, and IV, respectively. Conclusion: Octopamine shows the best potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor. However, this compound also poses several toxicity risks and therefore, needs a more elaborate considera-tion upon using. There are still no specific treatments for coronavirus disease (COVID-19) until present days. Several studies have been conducted to determine whether herbal medicine can be an option to be used as a definitive medicine for COVID-19. S2 subunit of spike protein which is responsible for SARS-CoV-2 entry to the host cell, is a potential drug target to inhibit the viral infection. In this study, we aimed to find some compounds from the HerbalDB database that have potential as SARS-CoV-2 spike (S2) glycoprotein inhibitor.
Identification of Novel Intronic Variants Implicating L3MBTL4 and AOAH in Indonesian Ovarian Endometriosis Trijayani Trijayani; Surya Dwira; Raden Muharam; Rafika Indah Paramita
The Indonesian Biomedical Journal Vol 17, No 6 (2025)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v17i6.3732

Abstract

BACKGROUND: Genetic factors are contributing substantially to endometriosis risk, however, there is limited data on genetic variant associations specific to ovarian endometriosis, especially in Indonesian populations. Understanding the genetic variants associated with this condition is essential for improving diagnosis and identifying potential therapeutic targets. Therefore, this study was conducted to analyze the association of genetic variants with ovarian endometriosis in Indonesian women using the single nucleotide polymorphisms (SNP)-array method, followed by an in-silico functional enrichment and gene expression analysis to explore their biological context.METHODS: This case-control study utilized the Infinium Asian Screening Array microarray platform to examine 46 samples, consisting of 22 ovarian endometriosis and 24 controls. The analysis included quality control, genetic association testing, and enrichment analysis. Genotypes were analyzed under dominant and recessive inheritance models, and functional insights were explored using gene expression databases.RESULTS: Ten intronic SNPs were significantly associated with endometrioma (p<0.05). Eight variants conferred increased risk (OR>1): rs77360595 (IFNLR1), rs2325558 (KLF12), rs1654499 (NLRP2), rs4809494 (LOC105376996), rs168482 (TMPRSS11A), rs17026725 (STPG2-AS1), rs59330070 (GFOD1), and rs58909364 (AOAH). Two variants were protective (OR<1): rs180732 (L3MBTL4) and rs7356507 (CRMP1). Notably, AOAH variant showed the highest odds ratio among risk variants, while L3MBTL4 variant showed the strongest statistical significance among protective variants in the dominant model. In-silico expression analysis confirmed that key implicated genes (KLF12, L3MBTL4, AOAH, and GFOD1) are expressed in relevant female reproductive tissues, generally at low-to-moderate levels.CONCLUSION: Ten novel genetic variants associated with ovarian endometriosis in Indonesian were identified. In particular, variants in L3MBTL4 and AOAH represent promising candidates that may play roles in disease pathophysiology of endometriosis, suggesting the importance of population-specific genetic studies and these specific loci as potential biomarkers or therapeutic targets.KEYWORDS: ovarian endometriosis, SNP, microarray, genetic association, plink, bioinformatics
FOXO1 and FYN Expression Trends in Breast Cancer Stem Cells: An Integrative Study of Single Nucleotide Polymorphism (SNP) Array and Quantitative PCR (qPCR) Analysis Ay Ly Margaret; Septelia Inawati Wanandi; Fadilah Fadilah; Rafika Indah Paramita
The Indonesian Biomedical Journal Vol 17, No 4 (2025)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v17i4.3656

Abstract

BACKGROUND: Currently, identification of breast cancer stem cells (BCSCs) commonly relies on CD24-/CD44+ expression profiles. However, few studies have integrated genomic mutation data with experimental gene expression validation in CSC and non-CSC populations. Genotyping results of CD24-/CD44+ MDAMB-231 cells revealed 36 mutations in BCSCs compared to non-BCSCs, with upregulated FOXO1 and FYN that might represent promising candidate biomarkers for this subpopulation. Therefore, in this study, single nucleotide polymorphism (SNP) and quantitative polymerase chain reaction (qPCR) analysis were performed to assess the association between mutations and expression trends of FOXO1 and FYN in MDAMB-231 cell, as breast cancer cell model with stem-like traits and well-characterized profile.METHODS: Genomic DNA was isolated from BCSC and non-BCSC DNA from the MDAMB-231 cell line. Mutation analysis was conducted using PLINK, while gene expressions of FOXO1 and FYN were quantified by one-step SYBR Green-based qPCR, using 18s rRNA as a reference. Data was then analyzed with the Livak (2−∆∆Ct) method.RESULTS: Among 36 mutations found in BCSCs of the MDAMB-231 cell line, PTEN (rs786204914) and CHEK2 (rs587782401) were identified as pathogenic. While FOXO1 (2.989±2.817 vs. 1.072±0.388) and FYN (1.405±0.072 vs. 0.855±0.140) mRNA levels were found to be higher in CSCs compared to non-CSCs, though these differences was not statistically significant.CONCLUSION: Pathogenic mutations in CHEK2 and PTEN were detected within BCSC population, implying a potential influence on the expression of FOXO1 and FYN, though not statistically significant. These findings suggest a possible, but as yet unverified, association between gene mutations and expression patterns, emphasizing the importance of further functional studies to validate FOXO1 and FYN as biomarkers for BCSCs.KEYWORDS: breast cancer stem cells, FOXO1, FYN, PTEN, CHEK2, mutation, biomarker
Evaluation of the DHCR7/NADSYN1 rs4944946 Variant and Breast Cancer Susceptibility: A Case-Control Study in an Indonesian Cohort Wahyudi, Dian Tri; Paramita, Rafika Indah; Panigoro, Sonar Soni
Indonesian Journal of Medical Chemistry and Bioinformatics
Publisher : UI Scholars Hub

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Abstract

Background: The rs4944946 variant, located in the 5’UTR of the DHCR7 gene and upstream of NADSYN1, is biologically implicated in vitamin D and cholesterol metabolism pathways closely linked to cancer pathogenesis. This study aimed to experimentally validate the association between the rs4944946 polymorphism and breast cancer susceptibility in an independent cohort of Indonesian women. Method: A case-control study was conducted involving 36 breast cancer patients and 39 healthy adult females. Genotyping of the rs4944946 variant was performed using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). The genetic association was evaluated across codominant, dominant, and recessive models. Luminal B was the predominant molecular subtype (36.1%) within the case group. Results: Validation results demonstrated no significant association between the rs4944946 variant and breast cancer susceptibility across all tested genetic models. The discordance between our validation cohort and prior in silico predictions is likely attributable to the low frequency of the mutant allele, limited sample size, and the "winner’s curse" phenomenon. Furthermore, technical constraints inherent to PCR-RFLP, such as the risk of incomplete enzymatic digestion, may have influenced genotyping accuracy. Conclusion: This experimental validation did not establish a significant association between the rs4944946 variant and breast cancer in the studied cohort. Future multicenter studies utilizing larger cohorts and more advanced, precise genotyping technologies (e.g., Next-Generation Sequencing) are required to definitively determine the clinical significance of this variant.
Co-Authors Andi Yasmon Arif Kurniawan Aryo Tedjo Aswin, Yulia Ariani Ay Ly Margaret Candraningrum, Veronica Hesti Cendani, Gabriella Regita Cristina, Artha Uli Erlina, Linda Fadilah Fadilah Fadilah Fadillah Fadillah Fadillah Fadillah Farah Shabihah Fatriansyah, Jaka Fajar Ferry Sandra Ghanny, Niken Rahmah Harimurti, Putri Saskia Herqutanto - Insani, Fauzi Azhar Monica, Maria Diyan Ninik Sukartini Nur Ayu Ramadanti Prawiningrum, Aisyah F Putri, Putu Indah Paramita Adi Raden Muharam Natadisastra Rahayu, Ratih Ramadhan Ramadhan Retnomawarti, Rizka Rusma Yulita SEKAR ARUMSARI, SEKAR Septelia I. Wanandi Sonar Panigoro Stevina, Lany Sugito, Syailendra Karuna Suratno Lulut Ratnoglik Surya Dwira Syahrani, Resda Akhra Tjampakasari, Conny Riana Trijayani Trijayani Wahyudi, Dian Tri Windy Dwininda