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All Journal Narra J Journal of Pharmaceutical Sciences and Community
Fransiska Kurniawan
School Of Pharmacy, Bandung Institute Of Technology, Jalan Ganesha 10, Bandung 40132, Indonesia
Biochemistry, Genetics & Molecular Biology Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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Exploring the potential of Laportea decumana extract compounds as COX-1 and COX-2 inhibitors: An in silico study Simaremare, Eva S.; Kurniawan, Fransiska; Hartati, Rika; Tjahjono, Daryono H.
Narra J Vol. 5 No. 1 (2025): April 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narraj.v5i1.1627

Abstract

Laportea decumana (Roxb.) Wedd., known as itchy leaves, is traditionally used for pain relief due to its bioactive compounds. However, previous studies were limited by resource-intensive in vivo methods and a lack of mechanistic insights into cyclooxygenase (COX)-1 and COX-2 binding. The aim of this study was to identify compounds in the n-hexane and ethyl acetate extracts of L. decumana with potential as COX-1 and COX-2 inhibitors and to predict their binding affinity and stability within the binding pocket through molecular dynamics simulations. Leaves collected from Arso, Keerom Regency, Papua, Indonesia, were dried, sieved into simplicia, and macerated with n-hexane to obtain a n-hexane extract. The residual simplicia was further macerated with ethyl acetate to produce an ethyl acetate extract. N-hexane extract compounds were analyzed by gas chromatography-mass spectrometry (GC-MS), and ethyl acetate extract compounds by liquid chromatography-mass spectrometry (LC-MS). Identified chemicals were used in in silico evaluations targeting COX-1 and COX-2. This study identified ten compounds with high performance in docking analysis, which were further evaluated by molecular dynamics. The n-hexane extract contained 31 compounds, while the ethyl acetate extract contained 27. Among these, 4,8,12,16-tetramethylheptadecan-4-olide from the n-hexane extract demonstrated the strongest affinity for both COX-1 and COX-2, with binding free energies of -41.62±1.03 kcal/mol and -33.05±0.11 kcal/mol, respectively. Its interactions were comparable to those of native ligands, with superior binding free energy. In the ethyl acetate extract, pseudosantonim demonstrated the highest affinity for COX-1 (-24.41±1.32 kcal/mol), while arteamisinine showed strong potential as a COX-2 inhibitor (-23.53±0.30 kcal/mol). In conclusion, 4,8,12,16-tetramethylheptadecan-4-olide was the most potent COX-1 and COX-2 inhibitor, pseudosantonim was the most effective COX-1 inhibitor, and arteamisinine demonstrated COX-2 inhibitory potential. Further validation through in vitro or in vivo studies is recommended.
Employing Ensemble Protein-Ligand Interaction Fingerprints to Mimic Induced-Fit Theory in Structure-Based Virtual Screening Targeting Dipeptidyl Peptidase IV Enade Perdana Istyastono; Bonifacius Ivan Wiranata; Florentinus D.O. Riswanto; Fransiska Kurniawan; Tasia Amelia; Nunung Yuniarti; Eko Adi Prasetyanto
Journal of Pharmaceutical Sciences and Community Vol. 23 No. 1 (2026)
Publisher : Sanata Dharma University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24071/jpsc.v23i1.1070

Abstract

We have successfully employed PyPLIF HIPPOS in retrospective Structure-Based Virtual Screening (SBVS) campaigns targeting some G-protein coupled receptors (GPCRs), which could pinpoint the molecular determinants of the protein-ligand bindings and increase the quality of the SBVS protocols. We were then tempted to append with molecular dynamics simulations using YASARA-Structure to mimic the induced-fit theory in the construction of SBVS protocols targeting dipeptidyl peptidase IV (DPP4). The protocol was retrospectively validated by employing the DPP4 ligands and decoys provided by the Directory of Useful Decoys: Enhanced (DUDE). The best SBVS protocol from this research has the balanced accuracy (BA) value of 0.836, which could be used further in prospective screening campaigns. 
Co-Authors Bonifacius Ivan Wiranata Daryono H. Tjahjono Eko Adi Prasetyanto Enade Perdana Istyastono Florentinus D.O. Riswanto Nunung Yuniarti Rika Hartati Tasia Amelia