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Ade Arsianti
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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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.
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 Andrias Bayu Fariska Aryo Tedjo Ida Neni Haryanti Linda Erlina