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All Journal Journal of Food and Pharmaceutical Science PROSIDING SEMINAR NASIONAL Jurnal Ilmiah Farmasi Journal of Mathematical and Fundamental Sciences Jurnal Riset Kimia JPS Unimus Majalah Obat Tradisional INDONESIAN JOURNAL OF PHARMACY Jurnal Farmasi Sains dan Komunitas Unnes Science Education Journal Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) Indonesian Journal of Chemistry JSFK (Jurnal Sains Farmasi & Klinis) Jurnal Ilmu Kefarmasian Indonesia Jurnal Pengabdian Kesehatan Masyarakat Jurnal Farmasi Sains dan Praktis Prosiding Seminar Nasional Universitas Ma Chung Jurnal Manusia dan Lingkungan Journal of Food and Pharmaceutical Sciences Journal of Pharmascience Journal of Pharmaceutical Sciences and Community
Enade Perdana Istyastono
Department Of Pharmacy, Faculty Of Medicine And Health Sciences, Atma Jaya Catholic University Of Indonesia, Jalan Pluit Raya 2, Jakarta 14440, Indonesia
Agriculture, Biological Sciences & Forestry Humanities Astronomy Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Dentistry Earth & Planetary Sciences Education Engineering Environmental Science Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Neuroscience Nursing Physics Public Health Social Sciences Veterinary Other

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A Structure-Based Virtual Screening Protocol Utilizing PyPLIF HIPPOS and Vina for Targeting BACE-1 Primana, Mala Hikmawan; Oka, Mitsue; Istyastono, Enade Perdana; Riswanto, Florentinus Dika Octa
Journal of Food and Pharmaceutical Sciences Vol 13, No 4 (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.24790

Abstract

Alzheimer’s Disease (AD) is a leading cause of dementia, characterized by progressive cognitive decline driven in part by amyloid-β (Aβ) accumulation. The β-site amyloid precursor protein cleaving enzyme 1 (BACE-1) is responsible for initiating Aβ generation, making it a central therapeutic target. Yet, developing effective BACE-1 inhibitors has proven difficult due to structural complexity and pharmacological limitation. This study aimed to construct and validate a structure-based virtual screening (SBVS) workflow combining Vina and PyPLIF HIPPOS to facilitate the identification of promising BACE-1 ligands. The protocol was validated through 100 independent redocking experiments of the native ligand (PDB ID: 3L5F), all reproducing the crystallographic pose with RMSD < 2.0 Å. Large-scale screening of the DUDE dataset (283 active ligands; 18,100 decoys) generated interaction fingerprint, which were subsequently analyzed using Recursive Partitioning and Regression Trees (RPART) under varying prior probabilities. At the optimal prior ratio of 0.82:0.18, the model achieved an enrichment factor (EF) of 10.03, surpassing the DUDE benchmark (EF = 8.1). analysis consistently highlighted ionic interactions with Asp289 and hydrophobic contacts with Trp137 as key determinants of ligand activity. From 283 active ligands, 32 were classified as true positives, narrowing the pool of candidates and interpretable SBVS protocol and proposing a dual anchoring strategy involving Asp289 and Trp137 as a rational design principle for novel BACE-1 inhibitors in AD therapy.
Integrative Study on the Binding Energy Calculation: Molecular Docking and Molecular Mechanics with Generalized Born Surface Area Targeting Acetylcholinesterase Ignasius Widya Parahita Putranto; Bonifacius Ivan Wiranata; Enade Perdana Istyastono; Florentinus Dika Octa Riswanto
Jurnal Pharmascience Vol. 13 No. 1 (2026): Jurnal Pharmascience
Publisher : Universitas Lambung Mangkurat

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20527/jps.v13i1.24094

Abstract

Alzheimer's disease (AD) imposes a significant global financial burden. Previous studies have reported that acetylcholinesterase (AChE) activity is strongly associated with AD, making it a key target in therapeutic research. Molecular docking and computational techniques are increasingly used to study these associations, yet a surge in publications has led to a departure from strictly designed paradigms. This study evaluates the accuracy of the Gibbs free energy of binding (ΔG) from molecular docking scores, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA), and local Vina scores. The Spearman rank test was applied to compare ΔG predictions and the in vitro results from our previous study. The correlation coefficient for molecular docking was -0.491, the MM/GBSA correlation coefficient calculated at the best molecular docking pose was -0.309, the MM/GBSA correlation coefficient calculated at the last 5 nanoseconds (ns) snapshots was 0.164, and the correlation coefficient of the Vina local score calculated at the last 5 ns snapshots was 0.273. Our findings indicate that the ΔG prediction from the Vina local score for the last 5 ns shows the strongest correlation with in vitro results.
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.
Caffeine and Caffeic Acid as Acetylcholinesterase Inhibitors: In Silico Perspectives Stephanus Satria Wira Waskitha; Bonifacius Ivan Wiranata; Julyus Jason Mark; Herluin Sekar Krisantia; Natalia Kristina; Glory Ivana Ardine; Chrisologus Ivan Prasetyo; Michael Raharja Gani; Florentinus Dika Octa Riswanto; 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.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.
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.
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. 
PEMODELAN MOLEKUL MITRAGYNINE SEBAGAI AGONIS PARSIAL PADA RESEPTOR OPIOID KELAS MU Enade Istyastono
Prosiding Seminar Nasional Universitas Ma Chung (Informatika & Sistem Informasi Bahasa dan Seni
Publisher : Ma Chung Press

Show Abstract | Download Original | Original Source | Check in Google Scholar

Abstract

Senyawa aktif mitragynine (MIT) yang terdapat dalam tanaman Kratom (Mitragyna speciosa) dilaporkan memiliki aktivitas biologi sebagai agonis parsial reseptor opioid kelas Mu (Mu opioid receptor (MOR). Hal ini berakibat pada polemik terkait regulasi pemanfaatan tanaman ini, karena pada dosis yang tepat dapat bermanfaat sebagai analgesik maupun untuk penanganan adiksi opioid, namun diduga berpotensi menimbulkan adiksi. Penelitian ini bertujuan meneliti aktivitas biologi di level atomik terutama dinamika interaksi MIT dalam kantung ikatan MOR serta menyediakan target virtual untuk pengembangan protokol uji in silico atau penapisan virtual. Titik awal penelitian dengan menggunakan struktur kristal MOR dengan ligan kokristal morfin (http://rcsb.org/structure/8EF6). Berbantuan kecerdasan artifisial dan computational tools pada software YASARA-Structure dilakukan inspeksi visual dan koreksi struktur, yang dilanjutkan dengan validasi protokol docking dengan penambatan ulang morfin. Dengan memanfaatkan protokol yang tervalidasi dilakukan penambatan MIT pada MOR yang dilanjutkan simulasi dinamika molekul 0,5 ns. Hasil penelitian menunjukkan bahwa MIT berikatan dengan MOR dengan mempertahanka interaksi-interaksi kunci yang dimiliki oleh morfin.
Co-Authors ., Jumina Abdul Mutholib Aditya Asyhar Agnes Mutiara Kurniawan Agnes Nora Iska Harnita Agnes Nora Iska Harnita Agung Endro Nugroho Agustina Setiawati Akhmad Darmawan Andreas Asdi Utama ARGUN WIDARSA ARIEF NURROCHMAD As'ari Nawawi Berlina, Violita Yessi Bonifacius Ivan Wiranata Bonifacius Ivan Wiranata Bonifacius Ivan Wiranata Chrisanti, Marcella Widya Chrisologus Ivan Prasetyo David Chandra Putra Dewi Setyaningsih Dina Christin Ayuning Putri Dita Maria Virginia Eko Yuliyanto Eko Yuliyanto, Eko Esti Mumpuni Evy Fenny Veronica Fajar Agung Dwi Hartanto Fajar Ira Juwita Farach Khanifah Felicia Felicia Felicia Fraulein Setiawan Fitria Fatichatul Hidayah Fitria Fatichatul Hidayah Fitria Fatichatul Hidayah Florentinus D.O. Riswanto Florentinus Dika Octa Riswanto Florentinus Dika Octa Riswanto Florentinus Dika Octa Riswanto Florentinus Dika Octa Riswanto Fransiscus Deddy Riandono Fransiska Kurniawan Gani, Michael Gatot Nugroho Susanto Gerry Nugraha Glory Ivana Ardine Harno Dwi Pranowo Harno Dwi Pranowo Harno Dwi Pranowo Herluin Sekar Krisantia I Gusti Ayu Intan Puspita Dewi Ignasius Widya Parahita Putranto Ignatius Yulius Kristio Budiasmoro Iqmal Tahir Iwan J. P. de Esch Jeffry Julianus Julyus Jason Mark Jutti Levita Liana Roh Widiyani Liliana Liliana Lukman Hakim Marchaban Marchaban Marchaban Marchaban Marchaban Marchaban Maria Ludya Pulung Maywan Hariono Maywan Hariono Michael Raharja Gani Michael Raharja Gani Michael Raharja Gani Michael Resta Surya Yanuar Muhamad Hanafi MUHAMMAD RADIFAR Muhammad Radifar Muhammad Radifar Muhammad Radifar Natalia Kristina Nugraha, Gerry Nunung Priyatni Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Nunung Yuniarti Octa Riswanto , Florentinus Dika OISAN OISAN Oka, Mitsue Perdana Adhi Nugroho Pramono, Zita Dhirani Primana, Mala Hikmawan Pudjono Pudjono Radite Yogaswara Rekso, Putri Ayu Dharmo reza eka putra Riandono, Fransiscus Deddy Rini Dwiastuti Rizna Triana Dewi Roy Gunawan Wicaksono Rr. Sri Untari Siwi S.M.P Sardjiman Sardjiman Slamet Ibrahim - Sri Hartati Yuliani Sri Noegrohati Sri Noegrohati St. Layli Prasojo Stefanus Layli Prasojo Stephanus Satria Wira Waskitha Sudibyo Martono Sudibyo Martono Sudibyo Martono Sudibyo Martono Sudibyo Martono Supardjan . Supardjan . Supardjan A. Margono Supardjan A. Margono Supardjan A.M Supardjan A.M. Supardjan AM Tasia Amelia Titien Siwi Hartayu Umar Anggara Jenie Vivitri Dewi Prasasty Waskitha, Stephanus Satria Wira Widayati, Aris Windah, Axl Laurens Lukas Wira Waskitha, Stephanus Satria Wiranata, Bonifacius Ivan YANTI SUSILAWATI Yohanes Eko Adi Prasetyanto Yosef Wijoyo Yosef Wijoyo Yosef Wijoyo, Yosef Yosi Bayu Murti Yulia Anita YUMI RAHMADANI Yuniarti, Nunung Zullies Ikawati Zullies Ikawati