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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 Indonesian Journal of Chemistry Journal of Multidisciplinary Applied Natural Science Makara Journal of Science Molekul: Jurnal Ilmiah Kimia Journal of Food and Pharmaceutical Sciences Indonesian Journal of Pharmacology and Therapy
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 Neuroscience Physics

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Molecular docking study of Indonesian phytochemicals as inhibitor of 6-HB formation by binding to HR1 subunit of SARSCOV-2 S2 protein Julianus, Jeffry; Phebe Hendra; Maywan Hariono; Nico Frederick; Satrio Ardyantoro; Mustofa; Jumina
Indonesian Journal of Pharmacology and Therapy Vol 2 No 3 (2021): Special Issue: COVID-19
Publisher : Faculty of Medicine, Public Health, and Nursing Universitas Gadjah Mada and Indonesian Pharmacologist Association or Ikatan Farmakologi Indonesia (IKAFARI)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijpther.2392

Abstract

Coronavirus disease 2019 (COVID-19) is still as global pandemic. No officially drugs to treat COVID-19 are available until now. Increasing number of patients and deaths trigger new antiCOVID-19 discovery efforts. In this study, we have conducted in silico screening employing molecular docking for Indonesian phytochemicals. Docking process was performed by employing AutoDock4 software on crystal structure 6VSB. Based on molecular docking results, several compounds had potential as antiCOVID-19 drugs, such as β-carotene, veramiline, ecliptalbine, betulinic acid, and lupeol. β-carotene was the most potential compound to treat COVID-19.
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

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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 Abdul Karim Zulkarnain ADITYA NUGRAHA Agus Dwi Ananto, Agus Alfiyah, Viny Anggraeni, Putri Dian Anita Dwi Puspitasari Chairil Anwar Desi Suci Handayani Dhina Fitriastuti Dwi Aris Agung Nugrahaningsih Dwi Siswanta Eti Nurwening Sholikhah Faris Hermawan, Faris Fatimi, Hana Anisa Fatmasari, Nela Fitria, Anggit Harizal Harizal Harno Dwi Pranowo Hidetaka Kawakita Iin Narwanti Ikhsan Nur Salim Jeffry Julianus Kasta Gurning Keisuke Ohto Kurniawan, Yehezkiel Steven Laela Hayu Nurani Lathifah Puji Hastuti Marlina, Lala Adetia Maulidan Firdaus Maywan Hariono Mia Munawaroh Yuniyanti Muhammad Idham Darussalam Mardjan Muhammad Yusron Maulana El-Yunusi Mustofa . Mustofa Mustofa Nico Frederick Nisa, Siti Astika Nursofia, Baiq Ike Phebe Hendra Pratama, Ardhya Ayu Priastomo, Yoga Priyangga, Krisfian Tata Aneka Putra, Nicky Rahmana RATNA SARI Reinner Ishaq Lerrick Rul Afiyah Syarif S Matsjeh S Mursiti Sabirin Matsjeh Satrio Ardyantoro Sri Juari Santosa Susy Yunita Prabawati Triana Kusumaningsih Wahyu Widyaningsih Wibowo, Susalit Setya Yogaswara, Radite Yudha, Ervan