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All Journal Jurnal Farmasi Sains dan Komunitas
Enade Perdana Istyastono
Faculty of Pharmacy, Universitas Sanata Dharma
Medicine & Pharmacology

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Molecular Dynamics Simulations of Ethyl-4-[(α-L-rhamnosyloxy)-benzyl]carbamate from Moringa oleifera Lam. as a Dipeptidyl Peptidase-4 Inhibitor I Gusti Ayu Intan Puspita Dewi; Enade Perdana Istyastono
Jurnal Farmasi Sains dan Komunitas (Journal of Pharmaceutical Sciences and Community) Vol 22, No 2 (2025)
Publisher : Sanata Dharma University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24071/jpsc.009791

Abstract

Diabetes mellitus is a global health problem that requires innovative solutions. Ethyl-4-[(α-L-rhamnosyloxy)-benzyl]carbamate (ERBC) compound contained in Moringa oleifera Lam. showed potential as a potent dipeptidyl peptidase-4 (DPP4) inhibitor, with an IC50 value of 0.798 µM. Molecular dynamics simulations indicated that ERBC interacts specifically with the active site of DPP4, providing a mechanistic basis for its inhibitory activity. The research utilized the latest technique developed by previously published plug-ins. The molecular docking simulations were performed 100 times. Then, the poses were clustered to sample the probable poses which were then subjected as the inputs in molecular dynamics simulations. Molecular dynamics simulations have shown that the ERBC compound interacts with the DPP4 protein at two possible poses. PyPLIF HIPPOS analysis demonstrated that ERBC, during its second replication, interacts with Glu205 and Glu206, two key amino acids involved in DPP4 activity.
Comparison of GPU-accelerated Molecular Dynamics Simulation Efficiency for the Acetylcholinesterase-Huprine X Complex using YASARA, GROMACS, and AMBER Bonifacius Ivan Wiranata; Enade Perdana Istyastono
Jurnal Farmasi Sains dan Komunitas (Journal of Pharmaceutical Sciences and Community) Vol 22, No 1 (2025)
Publisher : Sanata Dharma University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24071/jpsc.009061

Abstract

Molecular dynamics simulations are a valuable tool in identifying potential acetylcholinesterase inhibitors for Alzheimer's disease therapy. Recent advancements in hardware and software, particularly the implementation of graphics processing units (GPUs), have significantly improved the efficiency of MD simulations. This study aims to compare GPU-accelerated molecular dynamics (MD) simulations of the acetylcholinesterase-Huprine X complex using YASARA, GROMACS, and AMBER. The complex was obtained from Protein Data bank with code 1E66 and was prepared with same conditions. MD simulations were performed for 50 ns with three replicates per software. GROMACS exhibited the shortest average simulation duration (45,104 seconds), followed by AMBER (48,884 seconds) and YASARA (649,208 seconds). RMSD analysis of protein backbone and ligand movement indicated stable simulations across all platforms. Interaction analysis at 25 ns and 35 ns of YASARA’s run revealed that Huprine X maintained key aromatic interactions within the AChE binding pocket, despite undergoing a 180° rotation. YASARA proved more efficient in MD preparation and produced more precise results, while GROMACS was most efficient in simulation runtime. The study highlights the trade-offs between ease of use, simulation speed, and result consistency among these software packages for AChE-HUX MD simulations.
Co-Authors Bonifacius Ivan Wiranata I Gusti Ayu Intan Puspita Dewi