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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences METAMORFOSA Journal of Biological Sciences Jurnal Penelitian Pascapanen Pertanian Cannarium (Jurnal Ilmu-ilmu Pertanian) Jurnal Pangan dan Agroindustri Jurnal Keteknikan Pertanian Tropis dan Biosistem TEKNOLOGI PANGAN : Media Informasi dan Komunikasi Ilmiah Teknologi Pertanian Jurnal Teknologi Pertanian Andalas Agrica: Journal of Sustainable Dryland Agriculture Spizaetus: Jurnal Biologi dan Pendidikan Biologi Jurnal Teknologi Pangan CHEMTAG Journal of Chemical Engineering Jurnal Riset Teknologi Pangan Dan Hasil Pertanian (RETIPA) Journal of Food and Agricultural Product Jurnal Ilmiah Pangan Halal
Nelsy Dian Permatasari
Politeknik Tonggak Equator
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Control & Systems Engineering Economics, Econometrics & Finance Education Electrical & Electronics Engineering Energy Environmental Science Immunology & microbiology Industrial & Manufacturing Engineering Mechanical Engineering Social Sciences Other

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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 Alvianto, Dikianur Bambang Dwi Argo Brahmanti, Ajeng Astrini Fransiska Fransiska Hyldegardis Naisali Jatmiko Eko Witoyo Jaya Mahar Maligan Masruri Masruri Masruri Ni'maturohmah, Eva Pamungkas, Bangkit Puji Putra Panggulu Ahmad Ramadhani Utoro Renny Anggraini SARASWATI, Ayu Rahayu SIMON BAMBANG WIDJANARKO Sudarminto Setyo Yuwono Susilo, Donor Utomo M. T. Winny Kurniawan