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All Journal Journal of Food and Pharmaceutical Science Pharmaciana: Jurnal Kefarmasian Jurnal Ilmu Farmasi dan Farmasi Klinik (Journal of Pharmaceutical Science and Clinical Pharmacy) Majalah Obat Tradisional MPI (Media Pharmaceutica Indonesiana) INDONESIAN JOURNAL OF PHARMACY Pharmascience Jurnal Farmasi Sains dan Komunitas Majalah Farmaseutik Indonesian Journal of Chemistry JURNAL PENGABDI Cendekia Journal of Pharmacy Jurnal Pengabdian Kesehatan Rengganis Jurnal Pengabdian Masyarakat Abdimas Altruis: Jurnal Pengabdian Kepada Masyarakat MEDICINUS JURNAL JAMU KUSUMA Journal of Food and Pharmaceutical Sciences
Florentinus Dika Octa Riswanto
Faculty Of Pharmacy, Sanata Dharma University, Yogyakarta 55282
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Control & Systems Engineering Economics, Econometrics & Finance Education Energy Environmental Science Health Professions Immunology & microbiology Materials Science & Nanotechnology Mathematics Mechanical Engineering Medicine & Pharmacology Neuroscience Nursing Public Health Social Sciences Veterinary Other

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Authentication of Drimys piperita Hook f. Tree Bark Infusion from the Adulteration of Cinnamomum burmannii Nees Ex Bl. using the Combination of UV Spectroscopy and Chemometrics Techniques Sabela, Vivian Yulias; Laurendy, Chesie; Prarathana, Dicky; Riswanto, Florentinus Dika Octa
MPI (Media Pharmaceutica Indonesiana) Vol. 7 No. 2 (2025): DECEMBER
Publisher : Fakultas Farmasi, Universitas Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24123/mpi.v7i2.7964

Abstract

This study aims to develop a method to authenticate akway bark (Drimys piperita Hook f.) infusion using UV spectroscopy and chemometrics techniques. The background initiative of this study is the consideration of the high economic value of akway bark which may potentially lead to the adulteration of the akway raw materials for traditional medicine. The sample used in this study was akway bark obtained from Manokwari, Papua, Indonesia. Samples of akway bark, cinnamon, and a mixture of both were prepared in the form of powder and then infused. The infusion was examined using UV spectroscopy to obtain the absorption value of each wavelength. Chemometrics techniques including principal component analysis (PCA) and multivariate calibration using principal component regression (PCR) and partial least squares (PLS) regression were carried out during the study. Additionally, computational discrimination using sparse partial least squares discriminant analysis (sPLS-DA) was performed afterwards. A total of 36 distinctive wavelengths were obtained. The absorption values were then used to form a PCA model. The best multivariate calibration model was derived from PCR data processing on the original spectra for both akway and cinnamon bark infusion samples. The AUC-ROC values obtained from the application of the sPLS-DA technique for each sample were 1.000, 0.956, and 0.633 for akway bark, cinnamon, and the mixture of both, respectively. Authentication of akway bark infusion has been successfully conducted on the presence of cinnamon as the adulterant.
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.
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 Abdul Rohman Abdul Rohman Adelsiana Leda Adithya Guntur Agatha Kania Ugahari Dyatmika Agnes Margaretta Sihombing Agustina Setiawati Alni Desra Anandha Nabila Prjanaparamita Anastasia Bella Anastasia Melin Fitria Wulandari Angelina Kinsha Pandhita Ardine, Glory Ivana Arief Dzulfianto Arini Safti Sandrapitaloka Arya Pratama Nugraha Pede Bili, Juita Putrinda Bintari, Resita Widya Birgita Elsia Setiarini Bramantyo , Dominicus Adyatma Christofori Maria Ratna Rini Nastiti Corina Febrianti Isabel Darmawangzah, Muhammad Debby Yunita Debi Kristiananda Debi Kristiananda Desy Natalia Rambu Padji Mahemba Dewi Setyaningsih DEWI SETYANINGSIH Dina Christin Ayuning Putri Dita Maria Virginia Enade Perdana Istyastono Enade Perdana Istyastono Enade Perdana Istyastono Enade Perdana Istyastono Familia Putri Wulandari Faustina Evania Ngai Febrina Dameria Marbun Filisia Putri Rosari Florentina Yohana Ngelu Fransisca Wahyu Indriastuti Indriastuti Fransiska Revana Restiana Gani, Michael Raharja Giovanny Leonarda Indriastuti, Fransisca Wahyu Indriastuti Indriastuti, Fransisca Wahyu Indriastuti Irnawati Irnawati Jeanne Magistra Noverita Jeanne Magistra Noverita Jeffry Julianus Jihan, Rimatul Jullius Ivan Mahadhika Juvita Lisu Allo Juvita Lisu Allo Katharina Floransia Walburga Resmianto Katrina Imaculata Tema Pedha Khrisna Agung Cendekiawan Kinanti, Valentina Putri Embun Klemen Wahyu Kurniadi Krisantia, Herluin Sekar Kristina, Natalia Kurniadi, Klemen Wahyu Kurniadi, Klemen Wahyu Laurendy, Chesie Lintang Adelya Lusiana Lusiana Lusiana Lusiana Mahenu, Novia Indah Permatasari Putri Mahenu, Novia Indah Permatasari Putri Marchaban Marchaban Maria Aurelia Afila Tutonugi Maria Theresia Mawarni Mark, Julyus Jason Mase Mase Maywan Hariono Meissy, Angelina Michael Raharja Gani Monica Selena nafisah isnawati Ni Gusti Ayu Diantari Novia Indah Permatasari Putri Mahenu Noviayanti Chandra Oka, Mitsue Padmadiayu, Hana Paulina Nadya Feranti Pebby Lorenza Petrus Damiani Tosan Aji Phebe Hendra, Phebe Pisga Chrisita Dewi Pramono, Zita Dhirani Prarathana, Dicky Prasetyo, Chrisologus Ivan Primana, Mala Hikmawan Putri , Elsha Tiany Putri Natasya Br Siregar Radhita Tyastu Puteri Winengku Rajagukguk, ⁠Greysianita Rini Dwiastuti Rini Dwiastuti Rinjani Mustika Sari RR. Endang Lukitaningsih Sabela, Vivian Yulias Santi , Nyoman Pradnya Yoni Meytri Setiarini, Birgita Elsia Setiarini, Birgita Elsia Shinta Mayasari Siallagan , Angela Meirella Sri Hartati Yuliani Sudibyo Martono Sudibyo Martono Susanti, Dhina Ayu Suwidjiyo Pramono Teresia Kiki Oktavianti Theodora Dominika Gadi Seran Theresia Helena Tokan Tiara, Carolina Titien Siwi Hartayu Valentino Thomas Vania Rambu Kaha Milla Ate Veronica Arien Widyarahma Veronica Arien Widyarahma Vinsensia Nalita Maharani Wahyuning Setyani Wira Waskitha, Stephanus Satria Wiranata, Bonifacius Ivan Wulandari, Familia Putri Wulandari, Familia Putri Yoanes Fransiskus Regis Widyo Utomo Yohana Manalu Yohana Maria Bina Zerlinda Clara Auw