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All Journal VALENSI Journal of Mathematical and Fundamental Sciences Acta Pharmaceutica Indonesia JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA Farmasains : Jurnal Ilmiah Ilmu Kefarmasian
Daryono Hadi Tjahjono
School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung 40132
Astronomy Chemistry Earth & Planetary Sciences Education Health Professions Mathematics Medicine & Pharmacology Physics Other

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Pharmacophore Modeling, Docking, and Molecular Dynamics Simulation of Flavonoids as Inhibitors of Urokinase-type Plasminogen Activator Bina Lohita Sari; Slamet Ibrahim; Daryono Hadi Tjahjono
Journal of Mathematical and Fundamental Sciences Vol. 53 No. 3 (2021)
Publisher : Institute for Research and Community Services (LPPM) ITB

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.5614/j.math.fund.sci.2021.53.3.8

Abstract

The urokinase-type plasminogen activator (uPA) system plays a significant role in the invasion and metastasis of cancer cells. The present study was conducted to investigate natural product compounds as inhibitors and hit molecules of uPA using in-silico analysis. A pharmacophore model was built to screen the Indonesian Herbal Database (HerbalDB) to obtain inhibitors of different scaffolds. Based on the molecular docking score, four ligands were selected as potential uPA inhibitors. Subsequently, the stability of the ligand-uPA complex was analyzed using molecular dynamics (MD) simulation. An RMSD graph of the backbone protein and the RMSF values of the amino acid residues were also determined. In addition, the MM-PBSA method was applied to calculate the free binding energy. According to the results, Model_3, characterized by aromatic rings 23 (F1 and F2), cationic H-bond donor (F3), and metal ligator (F4) features, had an adequate goodness-of-hit score (GH). The four top-ranked ligands, isorhamnetin, rhamnetin, quercetin, and kaempferol, showed higher docking scores compared to the others. This study confirmed that isorhamnetin, rhamnetin, and kaempferol build stable complexes with uPA with lower binding energy than quercetin.
Co-Authors . Patonah Andry Nur Hidayat Arba, Muhammad Arry Yanuar Asmiyenti Djaliasrin Djalil Bina Lohita Sari Elin Yulinah Sukandar Fadhilah, Qoonita Farida Suhud Ferlianti Oktaviani Pangestoe Galih Satrio Putra Hamzah, Nursalam I Ketut Adnyana Maulidiyah Maulidiyah Melanny Ika Sulistyowaty Muhammad Arba Muhammad Sulaiman Zubair Nursalam Hamzah Nursan Nursan Pangestoe, Ferlianti Oktaviani Rahmana Emran Kartasasmita Rahmana Emran Kartasasmita Rina Anugrah, Rina Ruslin Ruslin Ruslin Ruslin Sanang Nur Safitri Slamet Ibrahiim Slamet Ibrahim Tegar Achsendo Yuniarta Yeni Yeni