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All Journal Eksakta : Berkala Ilmiah Bidang MIPA Health Information : Jurnal Penelitian Narra J Pharmaceutical Sciences and Research (PSR) Makara Journal of Science Indonesian Journal of Medical Chemistry and Bioinformatics
Erlina, Linda
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Epigenetic Diet to Modulate Immune Response against SARS-CoV-2 Andika, Andika; Ahdyani, Risa; Erlina, Linda; Azminah, Azminah; Yanuar, Arry
Pharmaceutical Sciences and Research Vol. 7, No. 2
Publisher : UI Scholars Hub

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Abstract

The COVID-19 pandemic has spread to various parts of the world and caused many deaths. The victims are infected by SARS-CoV-2, a new type of coronavirus that has appeared since December 2019 and caused respiratory symptoms, fever, coughing, and shortness of breath. In addition to social distancing, wearing masks and washing hands, diet is important as a defense of the body against SARS-CoV-2. In this review, researchers conducted epigenetic diet studies that could potentially inhibit SARS-CoV-2, and can be consumed and used on a daily basis.
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.
Metabolite Biomarker Discovery for Lung Cancer Using Machine Learning Fajarido, Ariski; Erlina, Linda; Tedjo, Aryo; Fadilah, Fadilah; Arozal, Wawaimuli
Indonesian Journal of Medical Chemistry and Bioinformatics Vol. 3, No. 1
Publisher : UI Scholars Hub

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Abstract

Lung cancer is the leading cause of cancer death worldwide. About 2.1 million lung cancer patients were diagnosed in 2018, accounting for about 11.6% of all newly diagnosed cancer cases. For lung cancer, blood is the first choice as a source of screening biomarker candidates. Blood biomarkers provide a snapshot of the patient's entire body, including the primary tumor, metastatic disease, immune response, and peritumoral stroma. However, sputum sampling, bronchial lavage or aspiration, exhaled breath (EB), and airway epithelial sampling represent unique samples for lung cancer and other airway cancers as potential sources for alternative biomarkers. Metabolites are products of cell metabolism that are unique biomarkers in a disease. In this article, we aim to find metabolite biomarkers using machine learning. Metabolite data were obtained from Metabolomic workbench, while detection and identification were performed in silico. From 82 samples, controls and cancers, we found 158 metabolites and analyzed them. From the analysis, we found 3 metabolites that play an important role in lung cancer and found 1 metabolite that is the most influential. From there we found that glutamic acid is one of the best biomarker candidates we provide for detecting lung cancer. However, this simulation still needs to be improved in order to find other biomarkers that can provide a better detection of lung cancer
The Whole Genome Sequencing Of Mycobacterium Tuberculosis For Drug Resistance Prediction Puspitasari, Melya; Andriansjah, Andriansjah; Erlina, Linda
Health Information : Jurnal Penelitian Content Digitized
Publisher : Poltekkes Kemenkes Kendari

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Abstract

Whole-genome sequencing (WGS) has shown tremendous potential in rapid diagnosis of drug-resistant tuberculosis (TB). In the current study, we performed WGS on drug-resistant Mycobacterium tuberculosis isolates obtained from Shanghai (n = 137) and Russia (n = 78). We aimed to characterise the underlying and high-frequency novel drug-resistance-conferring mutations, and also create valuable combinations of resistance mutations with high predictive sensitivity to predict multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB) phenotype using a bootstrap method. Most strains belonged to L2.2, L4.2, L4.4, L4.5 and L4.8 lineages. We found that WGS could predict 82.07% of phenotypically drug-resistant domestic strains. The prediction sensitivity for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STR), ofloxacin (OFL), amikacin (AMK) and capreomycin (CAP). The mutation combination with the highest sensitivity for MDR prediction was rpoB S450L + rpoB H445A/P + katG S315T + inhA I21T + inhA S94A, with a sensitivity of 92.17%, and the mutation combination with highest sensitivity for XDR prediction was rpoB S450L + katG S315T + gyrA D94G + rrs A1401G, with a sensitivity of 92.86%. The molecular information presented here will be of particular value for the rapid clinical detection of MDR- and XDR-TB isolates through laboratory diagnosis.
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
Roles of the Survivin BIR Domain in Cellular Apoptosis and Proliferation: An In Silico Study Nihayah, Silviatun; Wanandi, Septelia Inawati; Erlina, Linda; Syahrani, Resda Akhra
Makara Journal of Science Vol. 29, No. 1
Publisher : UI Scholars Hub

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Abstract

Survivin is an antiapoptotic protein that is highly expressed in cancer cells. We investigated the dual roles of the Bacu-lovirus IAP Repeats (BIR) domain within survivin, encompassing both apoptosis and proliferation, through an in silico study. The protein-protein interaction (PPI) network of survivin was analyzed using Cytoscape software. Functional enrichment (FE) analysis and data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to identify the implicated signaling pathways. The binding affinity of the BIR domain with the targeted proteins was visualized via molecular docking analysis. Drawing insights from the PPI network and FE analysis, we identified two key proteins in-volved in apoptosis such as X-linked Inhibitor of Apoptosis Proteins (XIAP) and caspase-9, and proliferation such as Cyclin-dependent Kinase 1 (CDK1) and Inner Centromere Protein (INCENP) for further analysis of their binding with the survivin BIR domain. These proteins were found to bind to the BIR domain at the Thr34, Thr48, and Ser20 resi-dues that have critical roles to regulate the apoptosis and proliferation. This study provides future insights into how the BIR domain of survivin could emerge as a potential target for cancer treatment, such as determining knockout targets for the development of genome editing technology
Beetroot (Beta vulgaris) potential in preventing colorectal cancer using in-silico analysis Dwijayanti, Adisti; Azizah, Norma N.; Erlina, Linda; Kusmardi, Kusmardi; Ningsih, Sri S.; Fadilah, Fadilah; Hashim, Najihah M.
Narra J Vol. 5 No. 2 (2025): August 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i2.1578

Abstract

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality worldwide, necessitating the need for an effective therapeutic strategy. Beta vulgaris (beetroot) possesses active compounds that exert anti-cancer properties. The aim of this study was to evaluate the potential of beetroot as a preventative agent against the progression of CRC using differentially expressed gene (DEG) analysis and network pharmacology approaches. The protein-protein interaction network and molecular docking analyses were employed to assess the key interactions of beetroot active compounds with CRC-related target protein. Cytotoxicity of beetroot extract was experimentally evaluated using 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyl tetrazolium bromide (MTT) assay on the HT29 cell line. The result of this study showed that protein in the cell cycle was significantly enriched in CRC, with cyclin-dependent kinase 4 (CDK4) gene as one of the specific genes. Quercetin, galangin, hesperidin, farrerol, and betanin were the most typical compounds of beetroot based on the Comparative Toxicogenomics Database (CTD). Molecular docking studies revealed the strong binding affinity between quercetin (-7.04 kcal/mol) and bentanin (-8.11 kcal/mol) with CDK4. Beetroot demonstrated anticancer properties against the HT29 cell line with IC50 value of 39.03±1.4 µg/mL. In conclusion, the beetroot extract has inhibitory activity against HT29 cell line proliferation, highlighting its potential in preventing the development of CRC through the substantial suppression of gene expression within the cell cycle pathway.
Flavonoid Role as Autophagy Modulators in Breast Cancer Treatment Strategy Dany, Frans; Arsianti, Ade; Erlina, Linda; Rinendyaputri, Ratih
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 26 No. 04 (2025): Eksakta : Berkala Ilmiah Bidang MIPA (E-ISSN : 2549-7464) In Progress
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/vol26-iss04/624

Abstract

Autophagy is a tightly regulated catabolic process that enables cancer cells to survive under metabolic stress and contributes to the development of chemoresistance. Targeting autophagy has therefore emerged as a promising strategy to enhance cancer therapy efficacy. Flavonoids, a diverse class of polyphenolic compounds abundantly found in plants, have gained considerable attention due to their broad-spectrum biological activities, including anticancer effects. Recent studies highlight their ability to modulate key signaling pathways involved in cell proliferation, apoptosis, and autophagy. Several flavonoids, such as fisetin, apigenin, and quercetin, exhibit roles as autophagy modulators depending on the cellular context, offering therapeutic flexibility. Their low toxicity and synergistic potential with conventional drugs underscore their relevance as adjuvant agents. This review discusses the critical role of autophagy in cancer progression and drug resistance, and examines current evidence supporting the integration of flavonoids as autophagy modulators in the design of more effective and targeted anticancer strategies, particularly in breast cancer therapy.
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.
Co-Authors . Andriansjah Abiyyi, Mohammad Wildan Adisti Dwijayanti Ahdyani, Risa Andi Yasmon Andika Andika Arleni Bustami Arry Yanuar Arsianti, Ade Aryo Tedjo Azizah, Norma N. Azminah Azminah Candraningrum, Veronica Hesti Cendani, Gabriella Regita Cristina, Artha Uli Dwira, Surya Fadilah Fadilah Fadilah, Fadilah Fadillah Fadillah Fajarido, Ariski Fatriansyah, Jaka Fajar Frans Dany, Frans Harimurti, Putri Saskia Hashim, Najihah M. Insani, Fauzi Azhar Kezia, Immanuelle Kusmardi Kusmardi Monica, Maria Diyan Nihayah, Silviatun Paramita, Rafika Indah Prawiningrum, Aisyah F Puspitasari, Melya Rahayu, Ratih Ratih Rinendyaputri Ratnoglik, Suratno Lulut Rosa, Feby Lilia SEPTELIA INAWATI WANANDI Sri S. Ningsih, Sri S. Sugito, Syailendra Karuna Syahrani, Resda Akhra Wawaimuli Arozal