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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) · pp. 567–575

DOI
10.14710/ik.ijms.29.4.567-575
ISSN
2406-7598, 0853-7291
Published
2024-12-11
Publisher
Marine Science Department Diponegoro University
Language
eng
License
creativecommons.org/licenses/by-sa/4.0

Abstract

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.

Keywords

Collaboration network of the authors

40 authors · 169 co-authorship links · showing the 40 most connected

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  • Diponegoro University
  • Affiliation unknown
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  • Same organisation
  • Affiliation unknown
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Co-authorOrganisationJoint articles
OCKY KARNA RADJASAAffiliation unknown9
Hadi EndrawatiAffiliation unknown6
Agus TriantoAffiliation unknown6
Retno HartatiAffiliation unknown5
Widianingsih WidianingsihAffiliation unknown5
Nenik KholilahAffiliation unknown4
Wilis Ari SetyatiAffiliation unknown4
Endang KusdiyantiniAffiliation unknown4
Diah Permata WijayantiAffiliation unknown4
Chrisna A SuryonoAffiliation unknown4
Ambariyanto AmbariyantoAffiliation unknown3
Anto BudiharjoAffiliation unknown3
Chrisna Adhi SuryonoAffiliation unknown3
Ria AzizahAffiliation unknown3
Norma AfiatiAffiliation unknown3
Ita WidowatiAffiliation unknown3
Bambang YuliantoAffiliation unknown3
Sutrisno AnggoroDiponegoro University3
TONNY BACHTIARAffiliation unknown2
Suryono SuryonoAffiliation unknown2
Agus IndarjoAffiliation unknown2
Galung Dhiva MaharaniAffiliation unknown2
Ervia YudiatiDiponegoro University2
Rabia AlghazeerAffiliation unknown2
Anindya WirasatriyaAffiliation unknown2
Denny Nugroho SugiantoAffiliation unknown2
Wilis A SetyatiAffiliation unknown2
Ali RidloAffiliation unknown2
Muhammad ZaenuriAffiliation unknown2
Sri RedjekiAffiliation unknown2
Witria WitriaAffiliation unknown2
Baskoro RochaddiAffiliation unknown2
Elis IndrayantiAffiliation unknown2
Dwi Haryo IsmunartiAffiliation unknown2

Affiliations come from OpenAlex; journal OAI-PMH metadata carries none. Authors without an OpenAlex ID are matched by name, which can merge or split people.

Metadata source: OAI-PMH (metadata jurnal) http://ejournal.undip.ac.id/index.php/ijms/oai, first harvested 8 Nov 2026, last seen 8 Nov 2026.
Original metadata (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>
</oai_dc:dc>