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Molecular Docking Studies of Marine Sulfated Polysaccharides: Exploring Green Seaweed’s Role Against SARS-CoV-2 Spike Glycoprotein

ILMU KELAUTAN: Indonesian Journal of Marine Sciences · Vol. 29 No. 4 (2024) · hlm. 567–575

DOI
10.14710/ik.ijms.29.4.567-575
ISSN
2406-7598, 0853-7291
Terbit
2024-12-11
Penerbit
Marine Science Department Diponegoro University
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-sa/4.0

Abstrak

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is a virus responsible for the infectious disease of COVID-19 (Coronavirus Disease 2019), whose development is still being monitored. One way to deal with the virus’s development is by searching for natural-based medicines that prevent and treat SARS-CoV-2 infection. The abundant biodiversity can be used as a source of treatment. Among many natural resources, seaweed is one of the natural resources rich in bioactive components. Sulfated polysaccharide is one of the potential bioactive compounds in seaweed because it has antiviral effects and the potential to treat SARS-CoV-2. This research aims at increasing the potential of Karimunjawa green seaweed sulfate polysaccharides for antiviral capabilities in SARS-CoV-2 through molecular docking. This research began with identifying the morphology of Karimunjawa seaweed. Identify the components of sulfated polysaccharide compounds based on literature studies according to the species that have been identified. Analysis of the antiviral ability of SARS-CoV-2 based on its binding ability to the SARS-CoV-2 target protein through a molecular docking computational program and testing drug compounds using the Lipinski rule. Based on the research results, it is known that the seaweed obtained from Karimunjawa based on morphology, belongs to the genus Kappaphycus. Molecular docking with a ligand and spike glycoprotein (6LZG) resulted in the hexadecanoic acid compound having a binding free energy of -5.3 kcal.mol-1, which was the compound with the lowest yield compared to other test compounds. The prediction of the physicochemical properties of all test compounds fulfills Lipinski's five rules and has the potential to be used as medicinal compounds.

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  • Diponegoro University
  • Cenderawasih University
  • Jenderal Soedirman University
  • University of the Ryukyus
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Rekan penulisOrganisasiArtikel bersama
Ocky Karna RadjasaDiponegoro University8
Hadi EndrawatiDiponegoro University7
Diah Permata WijayantiDiponegoro University6
Chrisna Adhi SuryonoDiponegoro University6
Wilis Ari SetyatiDiponegoro University5
Agus TriantoDiponegoro University5
Endang KusdiyantiniDiponegoro University5
Retno HartatiDiponegoro University5
Widianingsih WidianingsihDiponegoro University5
Ambariyanto AmbariyantoDiponegoro University3
Norma AfiatiDiponegoro University3
Ita WidowatiDiponegoro University3
Sutrisno AnggoroDiponegoro University3
Agus IndarjoDiponegoro University2
Galung Dhiva MaharaniDiponegoro University2
Anindya WirasatriyaDiponegoro University2
Denny Nugroho SugiantoDiponegoro University2
Nenik KholilahDiponegoro University2
Sri RedjekiDiponegoro University2
Dio DirgantaraUniversity of the Ryukyus2
Mada Triandala SiberoDiponegoro University2
Elis IndrayantiDiponegoro University2
Ria AzizahDiponegoro University2
Dwi Haryo IsmunartiDiponegoro University2
Bambang YuliantoDiponegoro University2
Popi IL AyerAfiliasi tidak diketahui1
Lolita Lolita TuhumenaAfiliasi tidak diketahui1
Imam MishbachCenderawasih University1
Lalu Panji Imam AgamawanCenderawasih University1
Baigo HamunaCenderawasih University1
Liyatin GeaCenderawasih University1
Yuriza EshanandaJenderal Soedirman University1
Synta Haqqul FadlilahJenderal Soedirman University1
Nabela FikriyyaJenderal Soedirman University1

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Sumber metadata: OAI-PMH (metadata jurnal) http://ejournal.undip.ac.id/index.php/ijms/oai, pertama di-harvest 8 Nov 2026, terakhir terlihat 8 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en-US">Molecular Docking Studies of Marine Sulfated Polysaccharides: Exploring Green Seaweed’s Role Against SARS-CoV-2 Spike Glycoprotein</dc:title>
	<dc:creator>Herida, Azalia Puspa</dc:creator>
	<dc:creator>Kusumaningrum, Hermin Pancasakti</dc:creator>
	<dc:creator>Zainuri, Muhammad</dc:creator>
	<dc:creator>Sabdono, Agus</dc:creator>
	<dc:creator>Subagiyo, Subagiyo</dc:creator>
	<dc:creator>Wahyuningsih, Candra</dc:creator>
	<dc:subject xml:lang="en-US">Seaweed; Sulfated Polysaccharide; Karimunjawa; Antiviral; SARS-CoV-2</dc:subject>
	<dc:description xml:lang="en-US">SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is a virus responsible for the infectious disease of COVID-19 (Coronavirus Disease 2019), whose development is still being monitored. One way to deal with the virus’s development is by searching for natural-based medicines that prevent and treat SARS-CoV-2 infection. The abundant biodiversity can be used as a source of treatment. Among many natural resources, seaweed is one of the natural resources rich in bioactive components. Sulfated polysaccharide is one of the potential bioactive compounds in seaweed because it has antiviral effects and the potential to treat SARS-CoV-2. This research aims at increasing the potential of Karimunjawa green seaweed sulfate polysaccharides for antiviral capabilities in SARS-CoV-2 through molecular docking. This research began with identifying the morphology of Karimunjawa seaweed. Identify the components of sulfated polysaccharide compounds based on literature studies according to the species that have been identified. Analysis of the antiviral ability of SARS-CoV-2 based on its binding ability to the SARS-CoV-2 target protein through a molecular docking computational program and testing drug compounds using the Lipinski rule. Based on the research results, it is known that the seaweed obtained from Karimunjawa based on morphology, belongs to the genus Kappaphycus. Molecular docking with a ligand and spike glycoprotein (6LZG) resulted in the hexadecanoic acid compound having a binding free energy of -5.3 kcal.mol-1, which was the compound with the lowest yield compared to other test compounds. The prediction of the physicochemical properties of all test compounds fulfills Lipinski's five rules and has the potential to be used as medicinal compounds.</dc:description>
	<dc:publisher xml:lang="en-US">Marine Science Department Diponegoro University</dc:publisher>
	<dc:date>2024-12-11</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:type xml:lang="en-US"></dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://ejournal.undip.ac.id/index.php/ijms/article/view/67088</dc:identifier>
	<dc:identifier>10.14710/ik.ijms.29.4.567-575</dc:identifier>
	<dc:source xml:lang="en-US">ILMU KELAUTAN: Indonesian Journal of Marine Sciences; Vol 29, No 4 (2024): Ilmu Kelautan; 567-575</dc:source>
	<dc:source>2406-7598</dc:source>
	<dc:source>0853-7291</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://ejournal.undip.ac.id/index.php/ijms/article/view/67088/pdf</dc:relation>
	<dc:rights xml:lang="en-US">Copyright (c) 2024 ILMU KELAUTAN: Indonesian Journal of Marine Sciences</dc:rights>
	<dc:rights xml:lang="en-US">https://creativecommons.org/licenses/by-sa/4.0</dc:rights>
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