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All Journal Jambura Journal of Educational Chemistry JIKA (Jurnal Informatika) Journal of Multidisciplinary Applied Natural Science Makara Journal of Science
Fatmasari, Nela
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Education Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Physics Other

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Design of Hydroxyxanthone Derivatives as Breast Cancer Inhibitors: A QSAR Modeling, Molecular Docking, Molecular Dynamics, MM-PBSA and ADMET Prediction Fatmasari, Nela; Hermawan, Faris; Jumina, Jumina; Kurniawan, Yehezkiel Steven; Pranowo, Harno Dwi; Puspitasari, Anita Dwi; Hastuti, Lathifah Puji; Marlina, Lala Adetia; Putra, Nicky Rahmana
Journal of Multidisciplinary Applied Natural Science Articles in Press
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.283

Abstract

A comprehensive QSAR analysis, in conjunction with molecular docking, molecular dynamics simulations, MM-PBSA binding energy estimations, and ADMET profiling, was conducted to facilitate the development of novel anticancer agents based on hydroxyxanthone derivatives. Molecular and electronic descriptors were calculated using the DFT method with the 3-21G basis set. The best QSAR model identified several descriptors that significantly influence anticancer activity, including the atomic charges at positions C1, C3, C4a, and C7, as well as the highest occupied molecular orbital (HOMO), surface area (SA), molecular volume (VOL), and molecular weight (MW). This model was used to design novel hydroxyxanthone derivatives (X27 to X47). The docking result showed that compounds 7-bromo-3-hydroxy-1-(methylamino)-9H-xanthen-9-one (X43), 6-hydroxy-8-(methylamino)-9-oxo-9H-xanthene-2-carbonitrile (X44), and 3-hydroxy-7-mercapto-1-(methylamino)-9H-xanthen-9-one (X45) had stronger binding energy values than gefitinib as a native ligand. Gefitinib had a binding energy of -6.84 kcal/mol, while those compounds had values of -6.92, -7.12, and -6.92 kcal/mol, respectively. In a molecular dynamics simulation of 100 ns, compounds X43, X44, and X45 exhibited stability comparable to that of gefitinib against the EGFR protein. Additionally, the binding energy MM-PBSA of compound X43 was the lowest (-29.18 kcal/mol), followed by X44 (-27.11 kcal/mol), gefitinib (-26.06 kcal/mol), and X45 (-25.21 kcal/mol). Furthermore, these compounds met Lipinski's rule parameters and the minimal standard parameters in terms of ADMET characteristics, as predicted by physicochemical properties. In conclusion, compounds X43, X44, and X45 are potential anticancer agents for MDA-MB-231 breast cancer cells.
Development of Teaching Modules Based on Problem Based Learning Integrated with Scientific Literacy on Acid Base Material Septiana, Ilham; Aisyah, Ratna Sari Siti; Fatmasari, Nela
Jambura Journal of Educational Chemistry Vol 7, No 2 (2025): August
Publisher : Universitas Negeri Gorontalo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.37905/jjec.v7i2.30460

Abstract

Scientific literacy in Indonesia is not yet a major concern, this is proven by data from the Program for International Student Assessment (PISA) which shows that Indonesia's scientific literacy ranking is in 71st position out of 77 countries. The Problem Based Learning (PBL) model is a learning model that can improve students' scientific literacy skills in explaining problems in everyday life, including those related to acids and bases, based on scientific data. The PBL model is suitable for application in an independent curriculum. One of the problems faced by educators in the independent curriculum is a lack of understanding in compiling teaching modules. The aim of this research is to develop a teaching module based on problem-based learning integrated with scientific literacy in acid-base material. This research is research and development research with the ADDIE model (analysis, design, development, implementation, evaluation). Data collection techniques used validation tests from material experts, media experts and limited trials on 30 students. Analysis of validation data using the Aiken's formula with a V table value of 0.79. The research results show that the Vcount value ≥ Vtable, the material validation Vcount value is 0.88, while the media validation value is 0.90 so it can be declared valid. The limited trial for students obtained a percentage score of 91.18% in the "very good" category. Based on the research results, the teaching module developed was declared valid and suitable for use as a learning tool
PENGEMBANGAN SISTEM PARKIR CERDAS BERBASIS ANDROID UNTUK FAKULTAS TEKNIK UNTIRTA Hardiansyah, Alim; Fatmasari, Nela; Sukarna, Royan Habibie; Umam, Ahmad Khoirul
Jurnal Informatika Vol 9, No 4 (2025): JIKA (Jurnal Informatika)
Publisher : University of Muhammadiyah Tangerang

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31000/jika.v9i4.14769

Abstract

Sistem parkir cerdas memanfaatkan kemajuan teknologi untuk mengatasi permasalahan yang melekat pada sistem parkir konvensional. Sistem parkir cerdas yang dikembangkan berbasis mobile, mengharuskan mahasiswa, dosen, dan pengguna lainnya untuk mendaftar dan akunnya diverifikasi oleh administrator departemen masing-masing. Penelitian ini menggunakan metode eksperimental prototyping yang menggambarkan sistem parkir cerdas berbasis Android menggunakan kode QR dan pemindaian kode QR. Kode QR berisi data identitas kendaraan, bersama dengan kunci yang dihasilkan dari string acak, yang di-cache dan dihasilkan setiap 10 menit. Dengan pembuatan prototipe, hasil dari sistem parkir cerdas diperlihatkan. Dalam pengembangannya (SDLC), penelitian ini menggunakan model Extreme Programming (XP). Extreme Programming (XP) dipilih sebagai metode pengembangan karena dinilai paling efektif untuk penelitian ini. Melalui iterasi singkat, pengujian berkelanjutan, dan komunikasi intensif antara pengembang dan pengguna, XP memastikan produk akhir tidak hanya memenuhi ekspektasi tetapi juga melampaui ekspektasi. Sistem parkir cerdas berbasis Android yang dibangun berfungsi untuk membantu keamanan dan mahasiswa dalam proses parkir di fakultas teknik Untirta.
Design and In Silico Modeling of Heterocyclic-based Xanthone Derivatives as Potential Anticancer Agents Through Tyrosine Kinase Inhibition Kurniawan, Yehezkiel Steven; Yudha, Ervan; Fatmasari, Nela; Yogaswara, Radite; Pranowo, Harno Dwi; Sholikhah, Eti Nurwening; Jumina, Jumina
Makara Journal of Science Vol. 30, No. 1
Publisher : UI Scholars Hub

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

Abstract

Cancer is one of the deadliest diseases nowadays, and tyrosine kinase receptors play crucial roles in cancer cell survival, differentiation, proliferation, and migration. This study designed and developed a new inhibitor from heterocyclic-based xanthone derivatives to target two tyrosine kinase receptors, epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor (PDGFR), through in silico screening. Eighteen heterocyclic-based xanthones were evaluated through molecular docking for both receptors. All heterocyclic-based xanthones gave the root mean square deviation (RMSD) value lower than 2.00 Å. Xanthone with isobenzothiazole substituent (iBzThio) was found as the most potent inhibitor with binding energies of -10.60 and -12.90 kcal/mol against EGFR and PDGFR, respectively. Further investigation has been performed through molecular dynamics (MD) simulation for 100 ns. From the results of MD simulations, i.e., RMSD, root mean square fluctuation, radius of gyration, solvent accessible surface area, hydrogen bonds, and binding energy parameters, as well as secondary structure fraction, dictionary of protein secondary structure, and Ramachandran plot, iBzThio demonstrated good stability to interact with the active site of both receptors. The binding energies of IBzThio against EGFR and PDGFR receptors were -12.58 and -12.61 kcal/mol after the MD simulations, indicating its potential application as an effective tyrosine kinase inhibitor.
Co-Authors Ahmad Khoirul Umam Anita Dwi Puspitasari Eti Nurwening Sholikhah Faris Hermawan, Faris hardiansyah, alim Harno Dwi Pranowo Jumina Jumina Kurniawan, Yehezkiel Steven Lathifah Puji Hastuti Marlina, Lala Adetia Putra, Nicky Rahmana Ratna Sari Siti Aisyah Septiana, Ilham Sukarna, Royan Habibie Yogaswara, Radite Yudha, Ervan