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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Nelsy Dian Permatasari
Department of Food Technology, Politeknik Tonggak Equator, Jl. Fatimah No 1-2, Pontianak, 78243, Indonesia Department of Food Science and Biotechnology, Faculty of Agricultural Technology, Universitas Brawijaya, Jalan Veteran, Malang, 65141, Indonesi
Agriculture, Biological Sciences & Forestry Environmental Science

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In Silico Screening of Syzygium myrtifolium Flavonoid Compoinds as Anti-bacterial Activity: In Silico Screening of Syzygium myrtifolium Flavonoid Compounds Nelsy Dian Permatasari; Jatmiko Eko Witoyo; Masruri; Sudarminto Setyo Yuwono; Simon Bambang Widjanarko
Journal of Tropical Life Science Vol. 12 No. 3 (2022)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.12.03.02

Abstract

Bacterial infection and antibiotic resistance are popular issues nowadays. Several pre[1]vious reports performed antibacterial screening activities involving natural herbs and synthetic drugs. Alanine racemase and transglycosylase are essential proteins for peptidoglycan membrane synthesis in bacteria and an alternative target for antibacterial performance. This study identified six flavonoid compounds in Syzygium myrtifolium to perform the antibacterial activity. In silico study was conducted for modelling flavonoids – protein complexes. Five flavonoids from S. myrtifolium were taken out of he canonical smiles from the PubChem database and modelled three-dimensional structure using ChemDraw and molView. Targeted protein, alanine racemase and transglycosylase were downloaded from Protein Data Bank with ID 4WR3 and 1SLY. Ligands and proteins were interacted by Molegro virtual Docker 5.0 and visualized by Discovery studio version 21.1.1. Five flavonoids showed inhibition with alanine racemase and transglycosylase in the same active sites of control and sodium benzo[1]ate. According to the binding energy, calopiptin performed the lowest binding energy value in alanine racemase complexes, while 2-Propanone, 1,3-bis(5-nitro-2-furanyl) showed the lowest value of four other flavonoids at transglycosylase complexes. The type of interactions were electrostatic, hydrogen bonds, hydrophobic interactions and unfavorable ones. Low binding energy and varied interaction types indicated tight of ligand-protein interaction. In summary, five flavonoids inhibited alanine racemase and transglycosylase, and the peptidoglycane membrane synthesis in bacteria might be inferred.
Co-Authors Jatmiko Eko Witoyo Masruri Masruri SIMON BAMBANG WIDJANARKO Sudarminto Setyo Yuwono