MOLECULAR DYNAMICS STUDIES OF FULL HUMAN MATRIX METALLOPROTEINASE 9 LIGANDED WITH N-HYDROXY-2-[(4-PHENYLPHENYL) SULFONYL-PROPAN-2-YLOXYAMINO] ACETAMIDE

Roy, Gunawan Wicaksono and Maywan, Hariono and Enade, Perdana Istyastono (2020) MOLECULAR DYNAMICS STUDIES OF FULL HUMAN MATRIX METALLOPROTEINASE 9 LIGANDED WITH N-HYDROXY-2-[(4-PHENYLPHENYL) SULFONYL-PROPAN-2-YLOXYAMINO] ACETAMIDE. JURNAL FARMASI SAINS DAN KOMUNITAS, 17 (1). pp. 1-7. ISSN 1693-5683

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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 Nhydroxy-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).

Item Type:	Article
Subjects:	R Medicine > RS Pharmacy and materia medica
Divisions:	Library of Congress Subject Areas > P Language and Literature > Farmasi Library of Congress Subject Areas > P Language and Literature > Fakultas Farmasi > Farmasi Fakultas Farmasi > Farmasi
Depositing User:	Unnamed user with email repo@umsb.ac.id
Date Deposited:	08 Sep 2022 02:17
Last Modified:	08 Sep 2022 02:17
URI:	http://eprints.umsb.ac.id/id/eprint/373

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