IN SILICO SCREENING OF Syzygium myrtifolium FLAVONOID COMPOUNDS 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

doi:10.11594/jtls.12.03.02

Authors

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, Indonesia
Jatmiko Eko Witoyo Department of Agroindustrial Technology, Faculty of Agricultural Technology, Universitas Brawijaya, Jalan Veteran, Malang, 65141, Indonesia
Masruri Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Brawijaya, Jalan Veteran, Malang, 65141, Indonesia
Sudarminto Setyo Yuwono Department of Food Science and Biotechnology, Faculty of Agricultural Technology, Universitas Brawijaya, Jalan Veteran, Malang, 65141, Indonesia
Simon Bambang Widjanarko Department of Food Science and Biotechnology, Faculty of Agricultural Technology, Universitas Brawijaya, Jalan Veteran, Malang, 65141, Indonesia

DOI:

https://doi.org/10.11594/jtls.12.03.02

Abstract

acterial infection and antibiotic resistance are popular issues nowadays. Several previous 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
the 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 benzoate. 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.
Keywords: Alanine racemase, Flavonoids, In silico, Transglycosylase