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All Journal Jurnal Farmasi Sains dan Komunitas
Enade Perdana Istyastono
Faculty of Pharmacy, Sanata Dharma University, Yogyakarta
Medicine & Pharmacology

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VIRTUAL SCREENING CAMPAIGNS ON ISOFLAVONES TO DISCOVER POTENT CYCLOOXYGENASE-2 INHIBITORS Enade Perdana Istyastono
Jurnal Farmasi Sains dan Komunitas (Journal of Pharmaceutical Sciences and Community) Vol 14, No 2 (2017)
Publisher : Sanata Dharma University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (505.928 KB) | DOI: 10.24071/jpsc.00698

Abstract

By employing recently published structure-based virtual screening (SBVS) to identify potent cyclooxygenase-2 (COX-2) inhibitors, all isoflavones collected by ZINC15 database were virtually screened. There were 3371 isoflavones in ZINC15 database and 1356 compounds out of them met the Lipinskis rule of 5. Notably, only 3 isoflavones out of those 1356 compounds were identified as potent COX-2 inhibitors.
MOLECULAR DYNAMICS STUDIES OF FULL HUMAN MATRIX METALLOPROTEINASE 9 LIGANDED WITH N-HYDROXY-2-[(4-PHENYLPHENYL) SULFONYL-PROPAN-2-YLOXYAMINO] ACETAMIDE Roy Gunawan Wicaksono; Maywan Hariono; Enade Perdana Istyastono
Jurnal Farmasi Sains dan Komunitas (Journal of Pharmaceutical Sciences and Community) Vol 17, No 1 (2020)
Publisher : Sanata Dharma University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1038.827 KB) | DOI: 10.24071/jpsc.001970

Abstract

The research presented in this article aimed to provide a full quarternary structure of human matrix metalloproteinase 9 (MMP9) enzyme with a ligand in the catalytic site for structure-based virtual screening. The enzyme plays an important role in wound healing of diabetic foot ulcer. By employing the primary structure of the enzyme obtained from UniProt database (UniProt:P14780), the theoretical structure of full apoenzyme of the human MMP9 (PDB:1LKG), the crystal structures of the catalytic domain (PDB:4H3X) and the hemopexin domain (PDB:1ITV) of the human MMP9, homology modeling studies have been performed. The ligand N-2-(biphenyl-4-yl-sulfonyl)-N-2-(isopropyloxy)-acetohydroxamic acid (CC27) or N-hydroxy-2-[(4-phenylphenyl)sulfonyl-propan-2-yloxyamino]acetamide (IUPAC version) from PDB:4H3X was embedded in the catalytic site of the enzyme. The modeling made use of the modules of homology modeling in YASARA structure. Subsequently, molecular dynamics (MD) simulations in YASARA structure were performed to examine the stability of the enzyme. The homology model was found stable after 5.05 ns and the lowest energy of the model was found at the 6.40 ns of the MD production run. This lowest energy snapshot was then energetically minimized and analyzed for its applicability for virtual screening. This optimized model was then stored in Mendeley Data (DOI: 10.17632/4gsb4p75gz.1).
Co-Authors Maywan Hariono Roy Gunawan Wicaksono