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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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Molecular Docking Study of Caffeic Acid as Acetylcholinesterase Inhibitor Wira Waskitha, Stephanus Satria; Istyastono, Enade Perdana; Octa Riswanto , Florentinus Dika
Journal of Food and Pharmaceutical Sciences Vol 11, No 3 (2023): 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.7665

Abstract

Abstract: Acetylcholinesterase (AChE) receptor is a receptor that has been widely used as a potential drug target for Alzheimer's disease. Caffeic acid is a phenolic compound that had been experimentally proven to be an inhibitor of AChE. In this study, 100 molecular docking simulations were performed to study the interaction of caffeic acid in inhibiting AChE. The molecular docking simulations were performed using YASARA software with an in-house developed plug-in. Redocking results showed that there were 99 out of 100 docking poses had an RMSD value of ≤ 2.000 Å, which indicated that the molecular docking procedure could be used for further processes. The molecular docking of caffeic acid showed that all docking poses had an RMSD value of ≤ 2.000 Å relative to the best pose of the first simulation, revealing that there was only one dominant docking pose in the AChE active site. Caffeic acid interacted favorably in the AChE active site with binding energy of about -8.022 kcal/mol. Its interactions were stabilized by hydrophobic and pi-anion interactions, in which some of the interactions resemble the same interaction of the native ligand. Keywords: Acetylcholinesterase, Alzheimer's disease, caffeic acid, molecular docking
PERAN EDUKASI DALAM OPTIMALISASI GERAKAN CEGAH STUNTING SEJAK DINI DI KABUPATEN GUNUNG KIDUL Pramono, Zita Dhirani; Waskitha, Stephanus Satria Wira; Chrisanti, Marcella Widya; Rekso, Putri Ayu Dharmo; Berlina, Violita Yessi; Istyastono, Enade Perdana
Jurnal Pengabdian Kesehatan Masyarakat Vol 5, No 2 (2024): November: Jurnal Pengabdian Kesehatan Masyarakat
Publisher : Program Studi Kesehatan Masyarakat Universitas Negeri Gorontalo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37905/jpkm.v5i2.27521

Abstract

Stunting merupakan gangguan pertumbuhan maupun perkembangan anak akibat gizi yang buruk, kekurangan protein dan vitamin, infeksi, serta stimulasi psikosial yang kurang memadahi. Pada negara berkembang termasuk Indonesia, stunting merupakan salah satu permasalahan kesehatan anak usia balita hingga saat ini. Gunung Kidul merupakan salah satu kabupaten di Daerah Istimewa Yogyakarta yang menjadi perhatian pemerintah dalam mengupayakan penurunan angka stunting. Tujuan dari penelitian dan pengabdian kepada masyarakat ini adalah untuk memberikan edukasi kepada ibu dan ibu hamil di Desa Wonosari, Kabupaten Gunung Kidul dengan memberdayakan Tim Percepatan Penurunan Stunting Puskesmas Wonosari II. Metode pelaksanaan upaya pemberian edukasi pencegahan stunting dilakukan melalui video edukasi dan paparan materi oleh tim Puskesmas Wonosari II dan dosen Fakultas Farmasi Universitas Sanata Dharma. Pemahaman pada ibu dan ibu hamil mengenai strategi pencegahan stunting dievaluasi menggunakan nilai pre-test dan post-test. Hasil pelaksanaan kegiatan menunjukkan bahwa nilai rata-rata post-test memiliki nilai yang lebih tinggi dibandingkan pre-test pada jumlah sampel sebanyak 68 peserta ibu dan ibu hamil. Uji statistika t berpasangan (paired t-test) mengindikasikan bahwa terdapat perbedaan nilai rata-rata pre-test dan post-test dengan tingkat kepercayaan sebesar 95% yang mengindikasikan peningkatan rata-rata skor pengetahuan para ibu dan ibu hamil mengenai edukasi yang diberikan. Kesimpulan bahwa pemberian edukasi meningkatkan pemahaman dan pengetahuan ibu serta ibu hamil terkait pencegahan stunting sejak dini.Kata Kunci: Stunting; Pencegahan stunting; Edukasi.
Identifikasi Determinan Molekul Interaksi STK630921 pada Interleukin-17A Riandono, Fransiscus Deddy; Istyastono, Enade Perdana
JSFK (Jurnal Sains Farmasi & Klinis) Vol 9 No 1 (2022): J Sains Farm Klin 9(1), April 2022
Publisher : Fakultas Farmasi Universitas Andalas

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.25077/jsfk.9.1.57-63.2022

Abstract

Interleukin-17A (IL-17A) merupakan sitokin pro-inflamasi yang terlibat dalam patogenesis beberapa penyakit, antara lain psoriasis, rheumatoid arthritis, kanker, diabetes dan penyakit ginjal stadium akhir. Peningkatan kadar serum IL-17A memberikan petunjuk adanya keterkaitan antara IL-17A pada kejadian nefropati diabetik. Keterkaitan ini juga diperjelas dengan temuan bahwa penghambatan aktivitas IL-17A dapat menurunkan albuminuria, cedera ginjal dan menunda perkembangan nefropati diabetik. Peranan IL-17A ini menjadikannya sebagai pilihan target potensial terapi nefropati diabetik yang sejauh ini bertumpu pada pengendalian optimal sistem renin angiotensin. Penelitian ini bertujuan mengidentifikasi determinan molekul interaksi STK630921 pada IL-17A. Penelitian dilakukan dengan penambatan molekul STK630921 pada protein IL-17A, dilanjutkan dengan simulasi dinamika molekul selama 15 ns. Identifikasi determinan molekul dilakukan menggunakan bantuan perangkat lunak PyPLIF-HIPPOS terhadap hasil simulasi dinamika molekul. Penelitian ini berhasil mengidentifikasikan asam-asam amino yang berperan penting yaitu His29, Trp67, Asn27, Lys114 dan Glu95 dengan interaksi aromatik dan interaksi hidrogen sebagai jenis interaksi yang berperan pada aktivitas STK630921 pada struktur protein 4HR9.
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.
Studi Dinamika Molekul Stabilisasi Metaloproteinase Matriks 9 oleh Asam Kafeat: Molecular Dynamics Studies of Matrix Metalloprotenase-9 Stabilization by Caffeic Acid Istyastono, Enade Perdana
Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal) Vol. 6 No. 2 (2020): (October 2020)
Publisher : Universitas Tadulako

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22487/j24428744.2020.v6.i2.15131

Abstract

Caffeic acid, a cathecol-containing phytochemical found in coffee, has been reported as a potent matrix metalloproteinase 9 (MMP9) inhibitor. The IC50 value of caffeic acid as MMP9 inhibitor could reach below 20 nM. The research presented in this article employed molecular dynamics simulations to unravel the atomic mechanism of the MMP9 inhibition by caffeic acid. Molecular dynamics simulations of MMP9 for 10 ns using YASARA-Structure were performed with and without caffeic acid as the studied ligand. The results showed that caffeic acid stabilized the stucture of the MMP9.
Identification of Interactions of ABT-341 to Dipeptidyl Peptidase IV during Molecular Dynamics Simulations: Identikasi Interaksi-interaksi ABT-341 dengan Dipeptidil Peptidase IV pada Simulasi Dinamika Molekul Istyastono, Enade; Gani, Michael
Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal) Vol. 7 No. 2 (2021): (October 2021)
Publisher : Universitas Tadulako

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22487/j24428744.2021.v7.i2.15516

Abstract

Background: Dipeptidyl Peptidase IV (DPP-IV) is an established drug discovery target for type 2 diabetes mellitus (T2DM) therapy. On the other hand, molecular dynamics (MD) simulations have been widely employed to obtain insights of the protein-ligand interactions in structure-based drug design research projects. Moreover, a software to identify protein-ligand interactions called PyPLIF HIPPOS was made publicly available recently. Employing PyPLIF HIPPOS to identify the interactions of DPP-IV and its ligand ABT-341 during MD simulations was then of considerable interest. Objectives: The main aim of this study was to identify protein-ligand interactions of ABT-341 to DPP-IV during MD simulations. Material and Methods: The crystal structure of DPP-IV co-crystallized with ABT-341 obtained from the Protein Data Bank with code of 2I78 was used as the main material. YASARA-Structure was employed for performing 10 ns prodution run MD simulations with snapshots in every 100 ps and PyPLIF HIPPOS was used to identify the protein-ligand interactions. Results: There were 23 interactions involving 13 residues identified by employing PyPLIF HIPPOS during the MD simulations. Two of them identified in all snapshots, i.e., hydrophobic interactions to PHE357 and TYR666. Conclusions: PyPLIF HIPPOS was succesfully employed to identify the interactions of ABT-341 to DPP-IV during MD simulations.
Molecular Docking Study of Caffeic Acid as Acetylcholinesterase Inhibitor Wira Waskitha, Stephanus Satria; Istyastono, Enade Perdana; Octa Riswanto , Florentinus Dika
Journal of Food and Pharmaceutical Sciences Vol 11, No 3 (2023): 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.7665

Abstract

Abstract: Acetylcholinesterase (AChE) receptor is a receptor that has been widely used as a potential drug target for Alzheimer's disease. Caffeic acid is a phenolic compound that had been experimentally proven to be an inhibitor of AChE. In this study, 100 molecular docking simulations were performed to study the interaction of caffeic acid in inhibiting AChE. The molecular docking simulations were performed using YASARA software with an in-house developed plug-in. Redocking results showed that there were 99 out of 100 docking poses had an RMSD value of ≤ 2.000 Å, which indicated that the molecular docking procedure could be used for further processes. The molecular docking of caffeic acid showed that all docking poses had an RMSD value of ≤ 2.000 Å relative to the best pose of the first simulation, revealing that there was only one dominant docking pose in the AChE active site. Caffeic acid interacted favorably in the AChE active site with binding energy of about -8.022 kcal/mol. Its interactions were stabilized by hydrophobic and pi-anion interactions, in which some of the interactions resemble the same interaction of the native ligand. Keywords: Acetylcholinesterase, Alzheimer's disease, caffeic acid, molecular docking
Computational Studies of Donepezil and Acetylcholinesterase Dynamics Interactions Windah, Axl Laurens Lukas; Istyastono, Enade Perdana
Jurnal Farmasi Sains dan Komunitas (Journal of Pharmaceutical Sciences and Community) Vol 21, No 1 (2024)
Publisher : Sanata Dharma University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24071/jpsc.006967

Abstract

Donepezil is an acetylcholinesterase (AChE) inhibitor commonly used as an anti-dementia medication for patients with Alzheimer's Disease. This research aims to determine the stability of each enantiomer R and S of donepezil as an AChE inhibitor using molecular dynamics (MD) simulations. The MD simulations were performed on a Cloud Protein Simulator (CPS) with YASARA-Structure as the main software and PyPLIF HIPPOS as the software to identify protein-ligand interactions. The MD simulations were performed in three replications of 50 ns for each enantiomer complexed to AChE. The stabilities of the AChE-donepezil complexes were analyzed by assessing the root-mean-squared deviation (RMSD) values of the AChE backbone atoms (RMSDBb) and the ligand (RMSDLigMov) during the last 5 ns of simulation time. The dynamics of the protein-ligand interactions were also analyzed during the last 5 ns. The results of these MD simulations indicate that the S-donepezil serves as a better AChE inhibitor compared to the R-donepezil. 
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.
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