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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.
HOMOLOGY MODELING EPITOP ISOCITRATE DEHYDROGENASE TIPE 1 (R132H) MENGGUNAKAN MODELLER, I-TASSER DAN (PS)2 UNTUK VAKSIN GLIOMA Yeni, Yeni; Tjahjono, Daryono Hadi
Farmasains : Jurnal Ilmiah Ilmu Kefarmasian Vol. 4 No. 1 (2017)
Publisher : Universitas Muhammadiyah Prof. DR. HAMKA

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22236/farmasains.v4i1.189

Abstract

Glioma is a type of primary malignant brain tumor. The presence of gliomas can be characterized by a mutation R132H of isocitrate dehydrogenase type 1 (IDH1). IDH1 (R132H) contains specific immunogenic epitopes to the tumor. It is appropriate to be used as a gliomas vaccine. Therefore, it was necessary to do homology modeling for IDH1 (R132H) epitopes. TMHMM, MEMSAT-SVM and MEMSAT3 were used to predict transmembrane topology of IDH1 (R132H). Analysis of IDH1 (R132H) epitopes was performed using NetMHCII and IEDB®. The antigenicity of epitopes were predicted using VaxiJen to obtained 91 epitopes. Homology modeling using Modeller, I-TASSER and (PS)2 was established for the epitopes that have probability as tumor antigen. The results of homology modeling of IDH1 (R132H) epitopes were validated by MolProbity, ProSA-web dan QMEAN. A 3D stucture model of the epitopes was selected from three models from the homology modeling based on the validation results. Refinement was established on the epitopes using GalaxyRefine and GROMACS for energy minimization.
Co-Authors . Patonah Andry Nur Hidayat Arba, Muhammad Arry Yanuar Asmiyenti Djaliasrin Djalil Bina Lohita Sari Elin Yulinah Fadhilah, Qoonita Farida Suhud Ferlianti Oktaviani Pangestoe Galih Satrio Putra 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