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All Journal ILMU KELAUTAN: Indonesian Journal of Marine Sciences Narra J
Kamarisima, Kamarisima
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Biochemistry, Genetics & Molecular Biology Earth & Planetary Sciences Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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Antibacterial compounds derived from marine Streptomyces aureofaciens A3 through in-silico molecular docking Srikandace, Yoice; Syani, Ira Rhabbiyatun; Wahhaab, Aisha; Kamarisima, Kamarisima; Putri, Sastia Prama; Aditiawati, Pingkan
ILMU KELAUTAN: Indonesian Journal of Marine Sciences Vol 29, No 3 (2024): Ilmu Kelautan
Publisher : Marine Science Department Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.14710/ik.ijms.29.3.403-413

Abstract

Streptomyces aureofaciens widely produces the antibiotic tetracycline and many other compounds during fermentation. The compounds have yet to be known for their antibacterial potential. This work aims to determine new antibiotics or other possible antibacterial compounds produced by marine S.aureofaceiens A3 through an in silico molecular docking method. The ethyl acetate (EA) extracts from fermented marine S. aureofaciens A3 in ISP4 medium enriched with seawater components showed strong antibacterial activity.  The antibacterial activity of EA extracts during 6-12 days of fermentation was carried out by the Kirby-Bauer method and the compounds of EA extracts were analyzed by GC/MS. Compounds identified by GC/MS were ligands for an in silico molecular docking study against four target proteins (DNA gyrase, topoisomerase IV, PBP 1a, and DHFR) of pathogenic bacteria. The drug-likeness of selected chemicals as antibacterial agents was assessed using Lipinski's Rule of Five. The results showed the prospective compounds as a narrow-spectrum antibacterial, including 3,5-di-tert-Butyl-4-hydroxyphenylpropionic acid against PBP 1a and Benzenepropanoic acid, and 3,5-bis (1,1-dimethyl ethyl)-4-hydroxy-, methyl esters against DHFR. Substances with broad-spectrum antibacterial activity, such as 3-Acetylphenanthrene and 3-(p-Ethoxyphenyl)-5-(O-tolyloxymethyl)-2-oxazolidone, against multitarget DNA gyrase B and DHFR, 7,9-Di-tert-butyl-1-oxaspiro (4,5) Deca-6,9-diene-2,8-dione against PBP1a and DHFR, and isobenzofuro [5,6-b] benzofuran-8-carboxylic acid, 1,3-dihydro-7,10-dimethoxy-9-methyl-1-oxo-, methyl ester against DNA gyrase B, PBP 1a, and DHFR. On the 12th day of fermentation, two compounds were identified: isobenzofuro[5,6-b] benzofuran-8-carboxylic acid, 1,3-dihydro-7,10-dimethoxy-9-methyl-1-oxo-, methyl ester, and 3-(p-Ethoxyphenyl)-5-(O-tolyl oxy methyl)-2-oxazolidone.  This is the first report that these two compounds, known as potential drugs like antibiotics through in silico molecular docking, were first produced by Streptomyces species.
Development of an inactivated viral transport medium for diagnostic testing in low-resource countries Rahmani, Silmi; Meitha, Karlia; Septiani, Popi; Priharto, Neil; Kamarisima, Kamarisima; Ningrum, Ratih A.; Angelina, Marissa; Agustiyanti, Dian F.; Wisnuwardhani, Popi H.; Nugroho, Herjuno A.; Tan, Marselina I.
Narra J Vol. 5 No. 3 (2025): December 2025
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v5i3.2068

Abstract

Viral transport medium (VTM) is crucial for retaining clinical specimens, such as the virus or its genetic material from the mucus of respiratory tract of coronavirus disease 2019 (COVID-19) suspected patients. However, the locally produced VTM in Indonesia lacks the ability to inactivate the virus, risking the safety of diagnostic personnel. The aim of this study was to formulate inactive VTM (iVTM) incorporating chaotropic agents like guanidine salt, along with anionic detergents, chelators, buffers, and surfactants, to inactivate the virus while maintaining RNA integrity. Viral RNA stability in iVTM (pH 4 and pH 6) was evaluated for 30 days at 4°C and 25–28°C. In vitro inactivation test was performed on SARS-CoV-2 isolate (variant B1). The stability test revealed that storing the clinical specimens in iVTM at pH 6 maintained severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) detectability by qPCR for up to 30 days at cold and room temperatures. Stability assessments conducted over a 4-month period (at 25–28°C) on iVTM with a pH of 6 revealed clear appearance, consistent pH stability, no alteration in the solution color, and no indications of bacterial or fungal contamination. Results from an in vitro inactivation assay demonstrated that iVTM pH 6 eliminated SARS-CoV-2 infectivity within just five minutes of contact. These findings suggest that iVTM pH 6 offers a safer and cost-effective alternative for handling and transportation of clinical specimens.
Co-Authors Agustiyanti, Dian F. Marissa Angelina Meitha, Karlia Ningrum, Ratih A. Nugroho, Herjuno A. PINGKAN ADITIAWATI Priharto, Neil Putri, Sastia Prama RAHMANI, SILMI Septiani, Popi Srikandace, Yoice Syani, Ira Rhabbiyatun Tan, Marselina I. Wahhaab, Aisha Wisnuwardhani, Popi H.