The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy
The global pandemic of COVID-19 caused by SARS-CoV-2 has caused more than 400 million infections with more than 5.7 million deaths worldwide, and the number of validated therapies from natural products for treating coronavirus infections needs to be increased. Therefore, the virtual screening of bio...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-04-01
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| Series: | Journal of King Saud University: Science |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1018364722007145 |
| _version_ | 1797947041054195712 |
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| author | Fiddy S. Prasetiya Wanda Destiarani Rina F. Nuwarda Fauzian G. Rohmatulloh Wiwin Natalia Mia T. Novianti Taufik Ramdani Mochamad U.K. Agung Sulastri Arsad Luthfiana A. Sari Pipit Pitriani Suryanti Suryanti Gilang Gumilar Jean-Luc Mouget Muhammad Yusuf |
| author_facet | Fiddy S. Prasetiya Wanda Destiarani Rina F. Nuwarda Fauzian G. Rohmatulloh Wiwin Natalia Mia T. Novianti Taufik Ramdani Mochamad U.K. Agung Sulastri Arsad Luthfiana A. Sari Pipit Pitriani Suryanti Suryanti Gilang Gumilar Jean-Luc Mouget Muhammad Yusuf |
| author_sort | Fiddy S. Prasetiya |
| collection | DOAJ |
| description | The global pandemic of COVID-19 caused by SARS-CoV-2 has caused more than 400 million infections with more than 5.7 million deaths worldwide, and the number of validated therapies from natural products for treating coronavirus infections needs to be increased. Therefore, the virtual screening of bioactive compounds from natural products based on computational methods could be an interesting strategy. Among many sources of bioactive natural products, compounds from marine organisms, particularly microalgae and cyanobacteria, can be potential antiviral agents. The present study investigates bioactive antiviral compounds from microalgae and cyanobacteria as a potential inhibitor of SARS-CoV-2 by targeting Angiotensin-Converting Enzyme II (ACE2) using integrated in silico and in vitro approaches. Our in silico analysis demonstrates that C-Phycocyanin (CPC) can potentially inhibit the binding of ACE2 receptor and SARS-CoV-2 with the docking score of −9.7 kcal mol−1. This score is relatively more favorable than the native ligand on ACE2 receptor. Molecular dynamics simulation also reveals the stability interaction between both CPC and ACE2 receptor with a root mean square deviation (RMSD) value of 1.5 Å. Additionally, our in vitro analysis using the surface plasmon resonance (SPR) method shows that CPC has a high affinity for ACE2 with a binding affinity range from 5 to 125 µM, with KD 3.37 nM. This study could serve as a reference to design microalgae- or cyanobacteria-based antiviral drugs for prophylaxis in SARS-CoV-2 infections. |
| first_indexed | 2024-04-10T21:21:32Z |
| format | Article |
| id | doaj.art-3f87149d76924aefb9b56e1a529d9e83 |
| institution | Directory Open Access Journal |
| issn | 1018-3647 |
| language | English |
| last_indexed | 2024-04-10T21:21:32Z |
| publishDate | 2023-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of King Saud University: Science |
| spelling | doaj.art-3f87149d76924aefb9b56e1a529d9e832023-01-20T04:24:16ZengElsevierJournal of King Saud University: Science1018-36472023-04-01353102533The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapyFiddy S. Prasetiya0Wanda Destiarani1Rina F. Nuwarda2Fauzian G. Rohmatulloh3Wiwin Natalia4Mia T. Novianti5Taufik Ramdani6Mochamad U.K. Agung7Sulastri Arsad8Luthfiana A. Sari9Pipit Pitriani10Suryanti Suryanti11Gilang Gumilar12Jean-Luc Mouget13Muhammad Yusuf14Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency Republic of Indonesia (BRIN), Jalan Raya Bogor Km 46, Cibinong, West Java 16911, Indonesia; Marine Science Department, Faculty of Fisheries and Marine Sciences, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM. 21, 45363 Jatinangor, Indonesia; Corresponding authors at: Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency Republic of Indonesia (BRIN), Jalan Raya Bogor Km 46, Cibinong, West Java 16911, Indonesia (F.S. Prasetiya).Research Center for Biotechnology and Bioinformatics Universitas Padjadjaran, Jl. Singaperbangsa No. 2, 40132 Bandung, IndonesiaDepartment of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM. 21, 45363 Jatinangor, IndonesiaResearch Center for Biotechnology and Bioinformatics Universitas Padjadjaran, Jl. Singaperbangsa No. 2, 40132 Bandung, Indonesia; Study Programme of Master Biotechnology, Faculty of Postgraduate School, Universitas Padjadjaran, Jl. Dipatiukur No. 35, Bandung, IndonesiaResearch Center for Biotechnology and Bioinformatics Universitas Padjadjaran, Jl. Singaperbangsa No. 2, 40132 Bandung, IndonesiaResearch Center for Biotechnology and Bioinformatics Universitas Padjadjaran, Jl. Singaperbangsa No. 2, 40132 Bandung, IndonesiaResearch Center for Biotechnology and Bioinformatics Universitas Padjadjaran, Jl. Singaperbangsa No. 2, 40132 Bandung, IndonesiaMarine Science Department, Faculty of Fisheries and Marine Sciences, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM. 21, 45363 Jatinangor, IndonesiaAquatic Resources Management Study Program, Faculty of Fisheries and Marine Science, Universitas Brawijaya, Jl. Veteran, 65145 Malang, IndonesiaDepartment of Fish Health Management and Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Campus C Unair Jl. Mulyosari, 60113 Surabaya, IndonesiaDepartment of Coaching Education, Faculty of Sports and Health Education, Universitas Pendidikan Indonesia, Jl. Dr. Setiabudi No. 299, 40154 Bandung, IndonesiaDepartment of Aquatic Resources, Faculty of Fisheries and Marine Sciences, Universitas Diponegoro, Jl. Prof. H. Soedarto, S.H., 50275 Semarang, IndonesiaWelding and Fabrication Engineering Technology Department, Institut Teknologi Sains Bandung, Central Cikarang, 17530 Bekasi, IndonesiaBiOSSE Laboratory, Faculty of Science & Technology, Le Mans Université, Avenue O. Messiaen, 72085 Le Mans Cedex 9, FranceResearch Center for Biotechnology and Bioinformatics Universitas Padjadjaran, Jl. Singaperbangsa No. 2, 40132 Bandung, Indonesia; Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jl. Raya Bandung Sumedang KM. 21, 45363 Jatinangor, Indonesia; Corresponding authors at: Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency Republic of Indonesia (BRIN), Jalan Raya Bogor Km 46, Cibinong, West Java 16911, Indonesia (F.S. Prasetiya).The global pandemic of COVID-19 caused by SARS-CoV-2 has caused more than 400 million infections with more than 5.7 million deaths worldwide, and the number of validated therapies from natural products for treating coronavirus infections needs to be increased. Therefore, the virtual screening of bioactive compounds from natural products based on computational methods could be an interesting strategy. Among many sources of bioactive natural products, compounds from marine organisms, particularly microalgae and cyanobacteria, can be potential antiviral agents. The present study investigates bioactive antiviral compounds from microalgae and cyanobacteria as a potential inhibitor of SARS-CoV-2 by targeting Angiotensin-Converting Enzyme II (ACE2) using integrated in silico and in vitro approaches. Our in silico analysis demonstrates that C-Phycocyanin (CPC) can potentially inhibit the binding of ACE2 receptor and SARS-CoV-2 with the docking score of −9.7 kcal mol−1. This score is relatively more favorable than the native ligand on ACE2 receptor. Molecular dynamics simulation also reveals the stability interaction between both CPC and ACE2 receptor with a root mean square deviation (RMSD) value of 1.5 Å. Additionally, our in vitro analysis using the surface plasmon resonance (SPR) method shows that CPC has a high affinity for ACE2 with a binding affinity range from 5 to 125 µM, with KD 3.37 nM. This study could serve as a reference to design microalgae- or cyanobacteria-based antiviral drugs for prophylaxis in SARS-CoV-2 infections.http://www.sciencedirect.com/science/article/pii/S1018364722007145Bioactive compoundsMicroalgaeMolecular dockingMolecular dynamicsSARS-CoV-2Surface plasmon resonance |
| spellingShingle | Fiddy S. Prasetiya Wanda Destiarani Rina F. Nuwarda Fauzian G. Rohmatulloh Wiwin Natalia Mia T. Novianti Taufik Ramdani Mochamad U.K. Agung Sulastri Arsad Luthfiana A. Sari Pipit Pitriani Suryanti Suryanti Gilang Gumilar Jean-Luc Mouget Muhammad Yusuf The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy Journal of King Saud University: Science Bioactive compounds Microalgae Molecular docking Molecular dynamics SARS-CoV-2 Surface plasmon resonance |
| title | The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy |
| title_full | The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy |
| title_fullStr | The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy |
| title_full_unstemmed | The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy |
| title_short | The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy |
| title_sort | nanomolar affinity of c phycocyanin from virtual screening of microalgal bioactive as potential ace2 inhibitor for covid 19 therapy |
| topic | Bioactive compounds Microalgae Molecular docking Molecular dynamics SARS-CoV-2 Surface plasmon resonance |
| url | http://www.sciencedirect.com/science/article/pii/S1018364722007145 |
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