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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Journal of Innovation and Applied Technology Indonesian Green Technology Journal Jurnal Pangan dan Agroindustri Jurnal Keteknikan Pertanian Tropis dan Biosistem Jurnal Teknologi Pertanian Aquahayati agriTECH Jurnal Ilmu Pangan dan Hasil Pertanian JPPM (Jurnal Pengabdian dan Pemberdayaan Masyarakat) Advances in Food Science, Sustainable Agriculture and Agroindustrial Engineering (AFSSAAE) International Journal of Advance Tropical Food (IJATF)
Sudarminto Setyo Yuwono
Universitas Brawijaya
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Civil Engineering, Building, Construction & Architecture Computer Science & IT Control & Systems Engineering Earth & Planetary Sciences Electrical & Electronics Engineering Energy Engineering Environmental Science Immunology & microbiology Industrial & Manufacturing Engineering Mechanical Engineering Medicine & Pharmacology Public Health 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 Abisatya Widya Swadana Ahmad Faruq Abidin Ahmad Subagio Ahmad Zaki Mubarok Aji Sutrisno Annisa Oktafianti Nurlatifah, Annisa Oktafianti Ardyanti, Dwi Kusuma Arrida Ad'hi Zulfiah Atikah Atikah Bambang Dwi Argo Beauty Suestining Diyah Dewanti Dani Ali Kusuma Dedy Nur Midayanto Dego Y. Ali Dego Yusa Ali Desyandri Desyandri Devy Sekarlianty Dhira Ananta Wijaya Dian Widya Ningtyas Disafitri Candra Ayu Diwyacitta Antya Putri, Diwyacitta Antya Dyah Ayu Kurniasari Ella Saparianti Elok Waziiroh Ericha Nurvia Alami Erni Sofia Murtini Erryana Martati Esy Apriyana Feronika Heppy Sriherfyna Fithri Choirun Nisa Galih Pramuditya Galih Wiranata, Galih Ha Mi Thah Hamidin Rasulu Hari Purnomo HARI PURNOMO Hasna Nadhiroh Imam Santoso Imro’ah Ikarini Indria Purwantiningrum Insaniyatus Sakinah Irawan Setya Wardhana Jatmiko Eko Witoyo Jaya Mahar Maligan Jodi Sangga Bagja Joni Kusnadi Kartika Ken Hayati Karunia Widhianingputri, Karunia Khusnia, Nastasya Kiki Febrianto KIKI FIBRIANTO Kobajashi T. Isamu Kobajashi T. Isamu Laila Yum Wahibah Lisna Mayani Liyundzira, Fasandra Novi Luchis Rubianto M Subhan Edi Wasono Masruri Masruri Masruri Mawar Sarastuti Michelle Noviria Michelle Noviria Miftahus Saadah Mochamad Affandi Mohammad Andi Cahyono Mohammad Rizal Amaluddin Nelsy Dian Permatasari Ni'maturohmah, Eva Nidha Arfa Ladamay Novi Sintya Dewi Novita Wijayanti Nur Ida Panca Nugrahini Nur Istianah Nur Istianah Nuriska Yulianingsih Nurrizaq Karunia Pamungkas, Bangkit Puji Putra Pinctada Putri Pamungkas Prabowo, Ivy Dian Puspitasari Puspaningrum, Lilianti Reza Widyasaputra Riska Septifani Rizkhia J.A. Aghata Sabathani, Anniversary SARASWATI, Ayu Rahayu Shela Maliaentika, Shela SIMON BAMBANG WIDJANARKO Siti Narsito Wulan Soemarno Soemarno Suhartini Suhartini Sulthon Fathoni Suprihhartini Nurani Susilo, Donor Utomo M. Syamsiar, Syamsiar Tika Pusparani Tri Susanto Vivien Fathuroya, Vivien Wenny B. Sunarharum Wenny Bekti Sunarharum Wintari Devita, Wintari Wulandari, Eka Shinta Yenny Puspita Anggraeni Yunita Prameswari, Yunita Zamnia Wahyuli