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All Journal Eksakta : Berkala Ilmiah Bidang MIPA
Linda Erlina
Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Energy Engineering Environmental Science Materials Science & Nanotechnology Mathematics Mechanical Engineering

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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
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.  
In Silico Evaluation of Natural Compounds as Dual Inhibitors of Exotoxin A and LasB (Elastase) Virulence Proteins in Pseudomonas aeruginosa Andrias Bayu Fariska; Linda Erlina; Ade Arsianti; Aryo Tedjo
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 26 No. 04 (2025): 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/vol26-iss04/631

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen whose virulence is largely mediated by Exotoxin A and LasB (elastase), making them promising anti-virulence drug targets. This study aimed to evaluate the inhibitory potential of natural compounds against these two key proteins using an in silico approach. Pharmacophore-based virtual screening of HerbalDB compounds was performed by LigandScout software, followed by molecular docking using AutoDockTools-1.5.7 against Exotoxin A (PDB ID: 1AER) and LasB (PDB ID: 1U4G). Native ligands and co-crystallized inhibitors were used as docking controls to validate binding accuracy. Among the screened compounds, Epicatechin-(4β-6)-epicatechin-(4β-8)-catechin exhibited the strongest binding affinity to Exotoxin A (ΔG = −10.72 kcal·mol⁻¹), while Carpaine showed the highest affinity for LasB (ΔG = −8.91 kcal·mol⁻¹). The predicted interactions involved hydrogen bonds and hydrophobic interactions with active-site residues, comparable to the native inhibitors. Furthermore, ADMET analysis indicated favorable pharmacokinetic and drug-likeness properties. These findings suggest that selected natural compounds possess potential dual inhibitory activity against Exotoxin A and LasB, warranting further experimental validation as anti-virulence candidates for controlling P. aeruginosa infections.
Exploring the Chemopreventive Potential of Soybean Phytochemicals Targeting BRCA1 Protein: A Molecular Docking Study Regina Liviandari; Ari Estuningtyas; Kusmardi; Linda Erlina
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 27 No. 02 (2026): 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/vol27-iss02/671

Abstract

Breast cancer remains a significant cause of cancer-related mortality among women globally, highlighting the importance for preventive strategies targeting early molecular events. BRCA1 plays a critical role in maintaining genomic stability through DNA repair mechanisms. However, the potential of soybean phytochemicals to modulate BRCA1 activity at the molecular level, particularly through computational approaches, has not been extensively explored. This study aimed to evaluate the chemopreventive potential of soybean phytochemicals targeting the BRCA1 protein using an in silico approach. A total of 32 compounds were prepared and docked into the BRCA1 binding site using Autodock Tools 1.5.7, followed by interaction analysis and visualization, prediction of pharmacokinetic and toxicity profiles using SwissADME, pkCSM, and ProTox. The results showed that the top compounds exhibited binding energy ranging from -6.04 to -8.07 kcal/mol, which were lower than the reference compound. Interaction analysis revealed stable binding with key amino acid residues, including Met1775, Leu1839, and Lys1702 through hydrogen and hydrophobic interactions. Among the evaluated compounds, daidzin showed the most balanced profile in terms of binding affinity, interaction relevance, and favorable ADMET properties. This study provides a systematic in silico evaluation of soybean phytochemicals targeting BRCA1 and highlights their potential as candidates for breast cancer chemoprevention.
Integrative Transcriptomic and Docking Analysis of Coffee Bioactives Targeting CCNA2, AKT1, and CDK2 in TNBC Ida Neni Haryanti; Linda Erlina; Ade Arsianti; Aryo Tedjo
EKSAKTA: Berkala Ilmiah Bidang MIPA Vol. 27 No. 04 (2026): 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/vol27-iss04/707

Abstract

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype characterized by high proliferation rates, poor prognosis, and limited therapeutic options. Coffee-derived bioactive compounds have demonstrated potential anticancer properties, but their interactions with key TNBC-associated targets remain insufficiently understood. Therefore, this study aimed to identify molecular biomarkers and therapeutic targets in TNBC and evaluate the potential of major coffee bioactive compounds using an integrative in silico approach. Five Gene Expression Omnibus (GEO) datasets (GSE38959, GSE186102, GSE65194, GSE45827, and GSE7904) were analyzed to identify differentially expressed genes (DEGs) using |log2FC| ≥ 1 and adjusted p-value < 0.05. Protein–protein interaction analysis, machine-learning validation, Kaplan–Meier survival analysis, chemogenomic mapping, molecular docking, and ADMET prediction were subsequently performed. A total of 917 overlapping DEGs were identified, with CCNA2 emerging as a key hub gene associated with poor prognosis. Machine-learning validation achieved 97.7% accuracy and an AUC of 0.964. Chemogenomic analysis prioritized AKT1, CDK2, and CCNA2 as therapeutic targets. Molecular docking revealed favorable interactions of caffeic acid and chlorogenic acid, with caffeic acid showing the most consistent multitarget affinity (−5.94 to −6.96 kcal/mol). These findings suggest that caffeic acid is a promising multitarget candidate for TNBC therapy and warrants further experimental validation.
Co-Authors Ade Arsianti Andrias Bayu Fariska Ari Estuningtyas Aryo Tedjo Fadillah Fadillah Fatriansyah, Jaka Fajar Ida Neni Haryanti Kusmardi Nur Ayu Ramadanti Rafika Indah Paramita Regina Liviandari Surya Dwira Windy Dwininda