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All Journal Journal of Food and Pharmaceutical Science Jurnal Farmasi Sains dan Komunitas Journal of Food and Pharmaceutical Sciences
Wiranata, Bonifacius Ivan
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Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience

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Interaction Dynamics of Caffeine in the Human Acetylcholinesterase Binding Pocket Wiranata, Bonifacius Ivan; Istyastono, Enade Perdana
Journal of Food and Pharmaceutical Sciences Vol 13, No 1 (2025): J.Food.Pharm.Sci
Publisher : Integrated Research and Testing Laboratory (LPPT) Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jfps.16533

Abstract

Alzheimer’s disease (AD) cases are increasing in Indonesia, with no effective therapy due to multiple hypotheses about its causes. The cholinergic hypothesis, focusing on acetylcholinesterase (ACHE) inhibition, is a key therapeutic approach. Caffeine, a natural compound, shows a potent activity as an AChE inhibitor. This study used computational methods to investigate the interaction dynamics of caffeine with the AChE’s active site. This study performed 100 redocking simulations of donepezil to validate the docking protocol followed by 100 molecular docking simulations of caffeine. The 50-ns molecular dynamics (MD) production phase simulations of donepezil and caffeine were performed to study the interaction dynamics, such as conformational stability and binding free energies. The interaction hotspots during the simulations were identified using PyPLIF HIPPOS. Our findings reveal that caffeine interacted in the active site during the simulations and the importance of Glu202 and Phe338 in helping caffeine reside within the esteratic site of AChE.
Interaction Dynamics of Caffeine in the Human Acetylcholinesterase Binding Pocket Wiranata, Bonifacius Ivan; Istyastono, Enade Perdana
Journal of Food and Pharmaceutical Sciences Vol 13, No 1 (2025): J.Food.Pharm.Sci
Publisher : Integrated Research and Testing Laboratory (LPPT) Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/jfps.16533

Abstract

Alzheimer’s disease (AD) cases are increasing in Indonesia, with no effective therapy due to multiple hypotheses about its causes. The cholinergic hypothesis, focusing on acetylcholinesterase (ACHE) inhibition, is a key therapeutic approach. Caffeine, a natural compound, shows a potent activity as an AChE inhibitor. This study used computational methods to investigate the interaction dynamics of caffeine with the AChE’s active site. This study performed 100 redocking simulations of donepezil to validate the docking protocol followed by 100 molecular docking simulations of caffeine. The 50-ns molecular dynamics (MD) production phase simulations of donepezil and caffeine were performed to study the interaction dynamics, such as conformational stability and binding free energies. The interaction hotspots during the simulations were identified using PyPLIF HIPPOS. Our findings reveal that caffeine interacted in the active site during the simulations and the importance of Glu202 and Phe338 in helping caffeine reside within the esteratic site of AChE.
Comparison of GPU-accelerated Molecular Dynamics Simulation Efficiency for the Acetylcholinesterase-Huprine X Complex using YASARA, GROMACS, and AMBER Wiranata, Bonifacius Ivan; Istyastono, Enade Perdana
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.
Caffeine and Caffeic Acid as Acetylcholinesterase Inhibitors: In Silico Perspectives Wira Waskitha, Stephanus Satria; Wiranata, Bonifacius Ivan; Mark, Julyus Jason; Krisantia, Herluin Sekar; Kristina, Natalia; Ardine, Glory Ivana; Prasetyo, Chrisologus Ivan; Gani, Michael Raharja; Riswanto, Florentinus Dika Octa; Istyastono, Enade Perdana
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.009687

Abstract

Alzheimer's disease (AD) has been recognized as a significant issue affecting population health globally and tended to increase over the years. The utilization of natural products for AD treatments has been widely studied, which possibly offers better outcomes with minimum side effects. Coffee consumption has been subjected as a lifestyle propensity, which offers beneficial advantages including reducing the risk of AD. Bioactive natural compounds contained in coffee such as caffeine and caffeic acid have been experimentally proven to be acetylcholinesterase (AChE) inhibitors, a pivotal target enzyme for AD treatments. This research aimed to explore the dynamics interactions of caffeine and caffeic acid in the AChE active site using the in silico approach. In this study, 100 redocking and docking simulations were implemented before the molecular dynamics (MD) simulations. The 55-ns MD simulations of huprine X, caffeine, and caffeic acid were implemented to study the dynamics interactions. Conformational stability, free energies of binding, and interaction hotspots were identified during the simulations. Our findings informed that caffeine interacted in the active site during the simulations, revealing the importance of the imidazole ring in maintaining the interactions. In contrast, caffeic acid interacted longer in the plausible allosteric site, forming ionic, hydrogen bonds, and aromatic interactions.
Co-Authors Ardine, Glory Ivana Enade Perdana Istyastono Florentinus Dika Octa Riswanto Gani, Michael Raharja Krisantia, Herluin Sekar Kristina, Natalia Mark, Julyus Jason Prasetyo, Chrisologus Ivan Wira Waskitha, Stephanus Satria