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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
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Pharmacophore-Based Virtual Screening from Indonesian Herbal Database to Find Putative Selective Estrogen Receptor Degraders Prawiningrum, Aisyah F; Paramita, Rafika Indah; Erlina, Linda
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 1, No. 1
Publisher : UI Scholars Hub

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Abstract

Most breast cancer cases are luminal subtypes which are estrogen receptor-sensitive or progesterone receptor-sensitive. Common treatments include surgery and adjuvant endocrine therapy by prescribing selective estrogen receptor degraders (SERD). SERD is a type of medication that inhibits estrogen receptor (ER) activity by degrading it, and as a result, downregulating it. The current FDA-approved SERD can only be administered through intramuscular injection. The aim of this study is to find orally non-toxic and bioavailable herbal alternatives of SERDs in Indonesian Herbal Database by doing virtual screening using LigandScout. The hit compounds were further analyzed using a molecular docking tool, AutoDock. Three compounds that gave the best results in molecular docking, namely kuwanon T, mulberrin, and curcumin, were analyzed in terms of their toxicity and drug-likeness. Based on toxicity and drug-likeness study, curcumin is considered to be the best candidates for SERD alternatives. This result is further supported by molecular dynamic simulation outcome in which curcumin is the most stable while binding with estrogen receptors.
MnSOD Gene Knockout Promotes Apoptosis in Triple-Negative Breast Cancer BT-549 Cells Through Survivin Inhibition and Caspase-3 and Caspase-9 Modulation Ghanny, Niken Rahmah; Wanandi, Septelia Inawati; Arumsari, Sekar; Paramita, Rafika Indah; Syahrani, Resda Akhra; Putri, Putu Indah Paramita Adi
Makara Journal of Science Vol. 28, No. 4
Publisher : UI Scholars Hub

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Abstract

Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype characterized by the lack of estro-gen, progesterone, and human epidermal growth factor receptor 2 (HER2) receptors. TNBC cells are becoming more aggressive due to the high expression of manganese superoxide dismutase (MnSOD) antioxidants to suppress reactive oxygen species-induced apoptosis and promote oncogenic signaling. This study was aimed to evaluate the effects of MnSOD knockout (KO) on TNBC cell apoptosis by assessing the survivin, caspase-9, and caspase-3 expressions. BT-549 TNBC cells containing the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-edited MnSOD gene were used to evaluate the messenger RNA (mRNA) expressions of survivin using the RT-qPCR assay. The West-ern blot assay was used to measure protein expressions of survivin, caspase-9, and caspase-3. Interactions between MnSOD and apoptosis-related proteins were simulated using computational methods based on molecular docking analysis and protein−protein interaction network. This study revealed that MnSOD KO decreased the binding affinity between MnSOD and survivin, in line with the significant reduction of survivin mRNA and protein expressions whereas the protein expressions of caspase-9 and caspase-3 increased in MnSOD KO cells. Therefore, MnSOD plays a pivotal role in BT-549 cell apoptosis by modulating survivin, caspase-9, and caspase-3 gene expressions. This study provides insights into a novel therapeutic strategy to mitigate the aggressiveness of TNBC by disrupting MnSOD gene expression. Further studies should elaborate the MnSOD signaling pathways involving closely related apoptotic proteins.
Identification of Antiviral Compounds against Hepatitis C Virus (HCV) targeting NS3 Protein by Pharmacophore Modeling, Molecular Docking, and ADMET Approach Rahayu, Ratih; Erlina, Linda; Ratnoglik, Suratno Lulut; Yasmon, Andi; Fadilah; Paramita, Rafika Indah
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 24 No. 04 (2023): 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/vol23-iss04/448

Abstract

Hepatitis C Virus (HCV) is a world health problem. HCV infection is initiated by various structural and non-structural proteins. The HCV NS3 protein has an important function in viral replication. The N-terminal domain of NS3 acts as a protease to process most of the viral polypeptides. NS3 also acts as an RNA helicase and NTPase and triggers liver fibrosis which accelerates the development of liver disease. Thus, this study aims to provide information on potential new antiviral candidates against HCV that target the NS3 protein. This study was conducted in-silico with a ligand-based and structure-based pharmacophore model to the cavity of the active protein site generated after virtual screening and molecular docking. The results of this study showed that three compounds, namely stigmasterol, gamma-mangostin, and erycristagallin, were found as HCV antiviral candidates that target the NS3 protein with a lower binding affinity than the native ligand. The binding energy of each compound is -9.23 Kcal/mol, -8.58 Kcal/mol, and -8.17 Kcal/mol. Based on ADMET analysis, the three compounds have high absorption in the small intestine. The cytotoxicity analysis of stigmasterol compounds is not potentially mutagenic, and the LD50 value of stigmasterol is also lower than other compounds.
Structure-Based Virtual Screening and Molecular Docking on the Indonesian Herbal Compound as a Promising Insulin Receptor (INSR) Inhibitor to Suppress Tumor Growth Candraningrum, Veronica Hesti; Erlina, Linda; Paramita, Rafika Indah; Fadillah, Fadillah; Dwira, Surya; Fatriansyah, Jaka Fajar
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 24 No. 04 (2023): 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/vol23-iss04/452

Abstract

A healthy cell maintains a homeostasis condition of glucose level, whereas cancer cells do not. Increased glucose uptake is a hallmark of cancer cells that helps them survive, proliferate, and spread. INSR is one of key feature that take part in glucose metabolism through insulin signaling. To block the entry of glucose into cells, researchers were aiming to disrupt the insulin signaling pathway as the upstream activation in glucose metabolism by inhibiting insulin receptor (INSR) using Indonesian herbal compounds. The approach during the screening was structure-based drug discovery (SBDD) method where INSR was determined as the macromolecules. Some parameters such as binding affinity, constant inhibition, drug-likeness, pharmacokinetics, and toxicity were applied to help the search of potential inhibitor. According to the test results, Heterophylin, Sanggenofuran A, and Epigallocatechin-3-O-caffeate had the strongest molecular binding activity against the INSR protein. Heterophylin is discovered in jackfruit fruit trees and Sanggenofuran A is present in mulberry trees. While Epigallocatechin-3-O-caffeate, is abundantly found in green tea plant
Genome-Wide Association Study for the Identification of Genetic Variants Associated with Facial Skin Phenotypes Rusma Yulita; Aswin, Yulia Ariani; Paramita, Rafika Indah
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 25 No. 02 (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-iss02/486

Abstract

Facial skin phenotypes such as pigmentation, wrinkles, and lentigines are determined by genetics and environmental factors. The genetic factor is known as the basic formation of facial skin phenotype variations in different populations. Genetic variations can be used as an approach to understanding genetic influences on the phenotype of interest and may influence molecular and cellular mechanisms. Genome wide-association study (GWAS) is used to identify common genetic variants associated with quantitative traits or complex human diseases. GWAS reveals a single phenotypic which is associated with a large number of SNPs and provides statistical information as significant SNPs. To perform GWAS analysis, bioinformatics tools are used as a rapid genetic data computation for large biological datasets which can report gene/locus with a related biological function viewed in silico. In this review, we summarize a common step-by-step workflow to conduct GWAS using bioinformatics analysis. The step-by-step workflow helps researchers understand how to identify SNPs with phenotypes of interest using bioinformatics approaches. Then, we explore common SNP and gene of facial skin phenotypes from several populations originating from various countries that can provide insights into the genetic contributions to facial skin phenotypes.
FOXO1 and FYN Expression Trends in Breast Cancer Stem Cells: An Integrative Study of Single Nucleotide Polymorphism (SNP) Array and Quantitative PCR (qPCR) Analysis Margaret, Ay Ly; Wanandi, Septelia Inawati; Fadilah, Fadilah; Paramita, Rafika Indah
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
The Bioinformatics Application in Detecting Germline and Somatic Variants towards Breast Cancer using Next Generation Sequencing Retnomawarti, Rizka; Panigoro, Sonar Soni; Paramita, Rafika Indah
Journal of Applied Science, Engineering, Technology, and Education Vol. 5 No. 1 (2023)
Publisher : PT Mattawang Mediatama Solution

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35877/454RI.asci1608

Abstract

Breast cancer is the type of cancer with the most and the highest cases causing mortality in Indonesia, so an effective treatment is required to reduce the incidence and mortality rate due to cancer breasts. Most breast cancer patients are diagnosed at an advanced stage so the treatment used are limited and the risk of death becomes higher. Along with the development of human genome sequencing technology, the genetic examination of breast cancer is considered as an examination that can be used for early prevention and treatment management personally. Based on the target variants detected, the genetic examination of breast cancer can be divided into two, namely the examination of germline variants and somatic variants. Germline variant examination is intended to predict the risk of breast cancer which can be used as an early preventive measure, while somatic variant examination is intended for cancer diagnosis and management therapy. NGS technology is able to detect both types of variants in a number of genes associated with breast cancer in several samples effectively and quickly. However, the data generated from NGS technology is very large and complex, so the role of bioinformatics is required in analyzing and interpreting data. By utilizing bioinformatics pipelines and tools, analysis of germline variants and somatic variants in breast cancer can be carried out accurately so that the results of genetic examinations can be used as a step to treat breast cancer.
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.
Co-Authors Andi Yasmon Aswin, Yulia Ariani Ay Ly Margaret, Ay Ly Candraningrum, Veronica Hesti Cendani, Gabriella Regita Cristina, Artha Uli Dwira, Surya Erlina, Linda Fadilah Fadilah Fadilah, Fadilah Fadillah Fadillah Fatriansyah, Jaka Fajar Ghanny, Niken Rahmah Harimurti, Putri Saskia Insani, Fauzi Azhar Monica, Maria Diyan Prawiningrum, Aisyah F Putri, Putu Indah Paramita Adi Rahayu, Ratih Ratnoglik, Suratno Lulut Retnomawarti, Rizka Rusma Yulita SEKAR ARUMSARI, SEKAR SEPTELIA INAWATI WANANDI Sonar Soni Panigoro Stevina, Lany Sugito, Syailendra Karuna Syahrani, Resda Akhra Tjampakasari, Conny Riana