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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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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.
Pharmacophore Modeling, Molecular Docking, and ADMET Approach for Identification of Anti-Cancer Agents Targeting the C-Jun N-Terminal Kinase (JNK) Protein Nur Ayu Ramadanti; Linda Erlina; Rafika Indah Paramita; Aryo Tedjo; Fadillah Fadillah; Surya Dwira
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 24 No. 01 (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/vol24-iss01/391

Abstract

One of the most prevalent cancers in Indonesia is breast cancer, based on Indonesia's pathological-based registration.    Breast cancer is a complex, heterogeneous disease classified into hormone-receptor-positive, human epidermal growth factor receptor-2 overexpressing (HER2+) and triple-negative breast cancer (TNBC) based on histological features. Patients with HR+, HER2- Early Breast Cancer (EBC) do not experience recurrence or recurrence for a long time with currently available standard therapy [11]. However, up to 30% of patients with high-risk clinical and/or pathological features may experience a relapse in the first few years. This results in the need for research and development regarding updates in medicine both in terms of treatment and targets and drug compounds used. The c-Jun N-terminal kinase (JNK) protein functions in signaling and influences the apoptotic pathway as well as cancer cell survival. In this study, an insilico screening experiment of inhibitory compounds was carried out on the JNK protein receptor target by screening compounds and molecular docking of compounds for breast cancer therapy.Two novel herbal compounds, Mangostin and ent-Copalyl Dyphospate, have the potential to be turned into medicines that may cause apoptosis through JNK protein targets according to an in-silico-based molecular simulation technique
Genome-Wide Association Study in Pigmentation as One of Skin Aging Characteristics Farah Shabihah; Rafika Indah Paramita
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 24 No. 02 (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/vol24-iss02/412

Abstract

Skin aging is a physiological process marked by changes in the skin's structure, giving rise to the characteristics of skin aging, such as pigmentation. Genome-Wide Association Studies (GWAS) identify genetic profiles that play a role in skin aging characteristics such as pigmentation. This study aimed to gather information about candidate SNPs and genes related to pigmentation characteristics of skin aging across different populations. We systematically searched relevant articles published in PubMed and ProQuest in the last ten years. Out of 212 articles screened, seven studies pertinent to our research are included in the analysis. Results indicated that in European and East Asian populations, several gene candidates such as IRF4, MC1R, ASIP, BNC2, PPARGC1B, RAB11FIP2, and CYP1A associated with SNPs that are known to have functions related to skin aging. However, further comprehensive analysis is needed to understand the functional correlation between SNP or gene candidates and pigmentation. In addition, the diversity of the subjects in the GWAS is still concerning. The future comprehensive analysis of GWAS, which involves underrepresented ones, is needed to broaden the knowledge of skin aging mechanisms across different populations.
Ligand Based Pharmacophore Modelling, Virtual Screening, Molecular Docking, and ADMETOX of Natural Compounds as Antibiotic Candidates against Urinary Tract Infections (UTI) Windy Dwininda; Linda Erlina; Rafika Indah Paramita; Fadillah Fadillah; Surya Dwira; Jaka Fajar Fatriansyah
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 24 No. 02 (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/vol24-iss02/404

Abstract

The use of antibiotic drugs requires close supervision that patients take antibiotics according to the rules. Irregular antibiotic use led to increased ADR cases (Antibiotic Drug-resistant). ADR is when an individual becomes resistant to an antibiotic drug that cannot kill bacteria. The high number of ADR cases prompted drug discovery to be implemented in analysis for Antibiotic candidates with good effectiveness through the Molecular Docking approach. The search for candidate test compounds as antibiotics were performed using the pharmacophore modelling method and molecular docking. And piperine, withaferin, has some of the same amino acids Ala101, Val103, Glu166, Trp165, and Leu102. Based on the prediction of the promising potential test ligand compound is Corosolic acid. In addition to assessing drug-likeness, pharmacokinetic and toxicity parameters, corosolic acid also has the lowest binding energy among other compounds. Through a textual bioinformatics approach, molecular docking simulations can be used as a first step in the search for new drug candidates in silico by considering various aspects, starting from the physicochemical properties of protein-ligand compounds and the environment. Analysis during the docking process to ADMETOX is an analysis to see the effectiveness and in silico compound safety.  
Amino Acid Profile of Luminal A and B Subtypes Breast Cancer Sonar Soni Panigoro; Arif Kurniawan; Ramadhan Ramadhan; Ninik Sukartini; Herqutanto Herqutanto; Rafika Indah Paramita; Ferry Sandra
The Indonesian Biomedical Journal Vol 15, No 3 (2023)
Publisher : The Prodia Education and Research Institute (PERI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18585/inabj.v15i3.2109

Abstract

BACKGROUND: Amino acids are important for proliferation and maintenance of tumor cells. Breast cancer patients were found to have significant changes in the number of amino acids, which are assumed to be correlated with the molecular subtypes of breast cancer. Therefore, current study was conducted to analyze plasma amino acids in breast cancer patients with luminal A and B subtypes.METHODS: Breast cancer and control subjects were recruited, and venous blood was collected for the measurement of plasma amino acids. Total 19 plasma amino acids were measured using reverse-phase high-performance liquid chromatography with C18 column. Mean comparison for normally distributed and homogeneous data was further analzyed using independent sample T-test, with p<0.05 was considered as significant.RESULTS: From total 19 amino acids, only 7 amino acids; cysteine, glutamic acid, histidine, ornithine, threonine, tyrosine, valine, were statistically different between the healthy control and breast cancer subjects. Eventhough no amino acids was found to be statistically different between breast cancer subjects with luminal A and B subtypes, but some amino acids were found to be significantly different when correlated to various breast cancer risk factors.CONCLUSION: Amino acid profile of patients with Luminal A and B subtypes of breast cancer differs compared to healthy controls and is also correlated with breast cancer risk factors. Increase in cysteine level in Luminal A subtype patients and decrease of alanine and leucine in Luminal B subtype patients can be used as a biomarker.KEYWORDS: amino acid, plasma, breast cancer, risk factor, biomarker
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.
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.
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