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Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates

VALENSI · Vol. ume No. 2 (2021) · hlm. 178–187

DOI
10.15408/jkv.v7i2.21634
ISSN
2548-3013, 2460-6065
Terbit
2021-11-25
Penerbit
Department of Chemistry, Faculty of Science and Technology Syarif Hidayatullah Jakarta State Islamic University
Bahasa
eng

Abstrak

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19). To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on developing inhibitors for this virus was performed using molecular dynamics simulation. 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. This study aimed to determine the stability of the selected protein-ligand complex through molecular dynamics simulation by Amber20 to propose bioactive compounds from natural products that have potential as a drug for COVID-19. Based on our previous study, the best value of free binding energy and protein-ligand interactions of the candidate compounds are obtained for each target protein through molecular docking. Corilagin (-14.42 kcal/mol), Scutellarein 7-rutinoside (-13.2 kcal/mol), Genistein 7-O-glucuronide (-10.52 kcal/mol), Biflavonoid-flavone base + 3O (-11.88 and -9.61 kcal/mol), and Enoxolone (-6.96 kcal/mol) has the best free energy value at each protein target. In molecular dynamics simulation, the 3CL-Pro-Corilagin complex was the most stable compared to other complexes, so that it was the most recommended compound. Further research is needed to test the selected ligand activity, which has the lowest free energy value of the six target proteins.

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  • IPB University
  • National Research and Innovation Agency
  • University of Hawaiʻi at Mānoa
  • Nara Institute of Science and Technology
  • Bandung Institute of Technology
  • Southeast Asian Regional Centre for Tropical Biology
  • Sumatera Institute of Technology
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Shadila Fira AsokaIPB University3
Utami Dyah SyafitriIPB University2
Laksmi AmbarsariIPB University2
Tony Ibnu SumaryadaIPB University2
Nampiah SukarnoIPB University2
Latifah Kosim DarusmanIPB University2
Mashuri WaiteUniversity of Hawaiʻi at Mānoa2
Muhammad Eka PrastyaNational Research and Innovation Agency2
Zahra Silmi MuscifaIPB University2
Zikri HamidiIPB University1
Rita Kartika SariIPB University1
Yanico Hadi PrayogoIPB University1
Wasrin SyafiiIPB University1
Adinda Zahra Marissa KasmiIPB University1
Bayu Febram PrasetyoIPB University1
Eva HarlinaIPB University1
Eka Winarni SapitriIPB University1
Rini KurniasihIPB University1
Agus KartonoIPB University1
Ajeng Widya RosliaIPB University1
Alfi AfifahIPB University1
I Nyoman Pugeg AryanthaBandung Institute of Technology1
Utut WidyastutiIPB University1
Rohani Cinta Badia GintingIPB University1
Sihegiko KanayaNara Institute of Science and Technology1
Sintho Wahyuning ArdieIPB University1
Soekisman TjitrosoedirdjoSoutheast Asian Regional Centre for Tropical Biology1
Za’aziza Ridha JuliaIPB University1
Sri ListiyowatiIPB University1
Rika Indri AstutiIPB University1
Nadila Fany AshafaniIPB University1
Vera PermatasariNational Research and Innovation Agency1
Dwi RetnowatiAfiliasi tidak diketahui1
Tjandrawati MozefIndonesian Institute of Sciences1
Indri YatiNational Research and Innovation Agency1
Erma SuryantiSumatera Institute of Technology1
Novita ArianiNational Research and Innovation Agency1

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Sumber metadata: OAI-PMH (metadata jurnal) http://journal.uinjkt.ac.id/index.php/valensi/oai, pertama di-harvest 10 Nov 2026, terakhir terlihat 10 Nov 2026.
Metadata asli (oai_dc) 
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	<dc:title xml:lang="en">Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates</dc:title>
	<dc:creator xml:lang="en">Awaluddin, Fikry</dc:creator>
	<dc:creator xml:lang="en">Batubara, Irmanida</dc:creator>
	<dc:creator xml:lang="en">Wahyudi, Setyanto Tri</dc:creator>
	<dc:subject xml:lang="en">Bioactive Compound</dc:subject>
	<dc:subject xml:lang="en">COVID-19</dc:subject>
	<dc:subject xml:lang="en">Molecular Dynamic</dc:subject>
	<dc:subject xml:lang="en">SARS-CoV-2</dc:subject>
	<dc:description xml:lang="en">Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19). To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on developing inhibitors for this virus was performed using molecular dynamics simulation. 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. This study aimed to determine the stability of the selected protein-ligand complex through molecular dynamics simulation by Amber20 to propose bioactive compounds from natural products that have potential as a drug for COVID-19. Based on our previous study, the best value of free binding energy and protein-ligand interactions of the candidate compounds are obtained for each target protein through molecular docking. Corilagin (-14.42 kcal/mol), Scutellarein 7-rutinoside (-13.2 kcal/mol), Genistein 7-O-glucuronide (-10.52 kcal/mol), Biflavonoid-flavone base + 3O (-11.88 and -9.61 kcal/mol), and Enoxolone (-6.96 kcal/mol) has the best free energy value at each protein target. In molecular dynamics simulation, the 3CL-Pro-Corilagin complex was the most stable compared to other complexes, so that it was the most recommended compound. Further research is needed to test the selected ligand activity, which has the lowest free energy value of the six target proteins.</dc:description>
	<dc:publisher xml:lang="en">Department of Chemistry, Faculty of Science and Technology Syarif Hidayatullah Jakarta State Islamic University</dc:publisher>
	<dc:date>2021-11-25</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://journal.uinjkt.ac.id/index.php/valensi/article/view/21634</dc:identifier>
	<dc:identifier>10.15408/jkv.v7i2.21634</dc:identifier>
	<dc:source xml:lang="en">Jurnal Kimia Valensi; Jurnal Kimia VALENSI Volume 7, No. 2, November 2021; 178-187</dc:source>
	<dc:source>2548-3013</dc:source>
	<dc:source>2460-6065</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>https://journal.uinjkt.ac.id/index.php/valensi/article/view/21634/pdf</dc:relation>
	<dc:rights xml:lang="en">Copyright (c) 2021 Irmanida Batubara, Setyanto Tri Wahyudi, Fikry Awaluddin</dc:rights>
</oai_dc:dc>