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All Journal Journal of Food and Pharmaceutical Science Pharmaciana: Jurnal Kefarmasian Indonesian Journal of Mathematics and Natural Sciences Teknosains: Media Informasi Sains dan Teknologi Alchemy Jurnal Penelitian Kimia Indonesian Journal of Chemistry Journal of Multidisciplinary Applied Natural Science Makara Journal of Science Molekul: Jurnal Ilmiah Kimia
Jumina Jumina
Department of Chemistry, Faculty of Mathematics and Natural Sciences Universitas Gadjah Mada Yogyakarta
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Control & Systems Engineering Energy Environmental Science Immunology & microbiology Materials Science & Nanotechnology Mathematics Medicine & Pharmacology Physics

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Journal : Journal of Multidisciplinary Applied Natural Science

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Allyl-Modified of Calix[4]resorcinarene Derivatives for HER2 Inhibition Agents: An In Silico Study Fitria, Anggit; Kurniawan, Yehezkiel Steven; Ananto, Agus Dwi; Jumina, Jumina; Sholikhah, Eti Nurwening; Pranowo, Harno Dwi
Journal of Multidisciplinary Applied Natural Science Vol. 5 No. 2 (2025): Journal of Multidisciplinary Applied Natural Science
Publisher : Pandawa Institute

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.47352/jmans.2774-3047.250

Abstract

Breast cancer is one of the deathliest cancer diseases for women, with high mortality cases. Since breast cancer cells overexpressed HER2 receptors, a computerized structure-based screening was conducted to identify potential HER2 inhibitors as an anti-breast cancer agent. This method can investigate the potency of proposed compounds as potential protein inhibitors. Researchers were interested in studying some synthetic macromolecules, i.e., allyl-modified calix[4]resorcinarenes, through in silico studies as HER2 inhibitors using molecular docking studies. Prospective protein-ligand complexes for HER2 inhibition were further investigated by molecular dynamics simulations for 200 ns on different binding pockets. The allyloxycalix[4]resorcinarene derivative (5A) was identified as the most potential HER2 inhibitor through a computational approach, including molecular docking studies and molecular dynamics simulations. The HER2-5A complex was relatively stable during the 200 ns molecular dynamics run. In addition, the hydrogen bonds formed between blind docking and molecular dynamics simulations are almost unchanged for the HER2-5A complex. The HER2-5A formed with two crucial amino acid residues, i.e., Asp845 and Asn850. Moreover, the data of the molecular dynamics simulations of compounds 5A and 2A demonstrate the stability of both complexes in different binding sites of HER2. These computational results are preliminary data for further synthesis and in vitro evaluation.
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.
Co-Authors Abdul Karim Zulkarnain Agus Dwi Ananto, Agus Alfiyah, Viny Anggraeni, Putri Dian Anita Dwi Puspitasari Chairil Anwar Desi Suci Handayani Dhina Fitriastuti Dwi Siswanta Eti Nurwening Sholikhah Faris Hermawan, Faris Fatimi, Hana Anisa Fatmasari, Nela Fitria, Anggit Harizal Harizal Harno Dwi Pranowo Hidetaka Kawakita Iin Narwanti Jeffry Julianus Kasta Gurning Keisuke Ohto Kurniawan, Yehezkiel Steven Laela Hayu Nurani Lathifah Puji Hastuti Marlina, Lala Adetia Maulidan Firdaus Muhammad Idham Darussalam Mardjan Muhammad Yusron Maulana El-Yunusi Mustofa . Mustofa Mustofa Nisa, Siti Astika Nursofia, Baiq Ike Pratama, Ardhya Ayu Priastomo, Yoga Priyangga, Krisfian Tata Aneka Putra, Nicky Rahmana Reinner Ishaq Lerrick S Matsjeh S Mursiti Sabirin Matsjeh Sri Juari Santosa Susy Yunita Prabawati Triana Kusumaningsih Wahyu Widyaningsih Wibowo, Susalit Setya Yudha, Ervan