Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins
Abstract The ongoing global pandemic caused by the SARS-CoV-2 virus has demanded the urgent search for effective therapeutic interventions. In response, our research aimed at identifying natural products (NPs) with potential inhibitory effects on the entry of the SARS-CoV-2 spike (S) protein into ho...
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Nature Portfolio
2025-01-01
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| Series: | Scientific Reports |
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| Online Access: | https://doi.org/10.1038/s41598-024-83637-4 |
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| author | Muhammad Alqaaf Ahmad Kamal Nasution Mohammad Bozlul Karim Mahfujul Islam Rumman Muhammad Hendrick Sedayu Retno Supriyanti Naoaki Ono Md. Altaf-Ul-Amin Shigehiko Kanaya |
| author_facet | Muhammad Alqaaf Ahmad Kamal Nasution Mohammad Bozlul Karim Mahfujul Islam Rumman Muhammad Hendrick Sedayu Retno Supriyanti Naoaki Ono Md. Altaf-Ul-Amin Shigehiko Kanaya |
| author_sort | Muhammad Alqaaf |
| collection | DOAJ |
| description | Abstract The ongoing global pandemic caused by the SARS-CoV-2 virus has demanded the urgent search for effective therapeutic interventions. In response, our research aimed at identifying natural products (NPs) with potential inhibitory effects on the entry of the SARS-CoV-2 spike (S) protein into host cells. Utilizing the Protein Data Bank Japan (PDBJ) and BindingDB databases, we isolated 204 S-glycoprotein sequences and conducted a clustering analysis to identify similarities and differences among them. We subsequently identified 33,722 binding molecules (BMs) by matching them with the sequences of 204 S-glycoproteins and compared them with 52,107 secondary metabolites (SMs) from the KNApSAcK database to identify potential inhibitors. We conducted docking and drug-likeness property analyses to identify several SMs with potential as drug candidates based on binding energy (BE), no Lipinski’s rule violation (LV), psychochemical properties within the pink area of the bioavailability radar, and a bioavailability score (BAS) not less than 0.55. Fourteen SMs were predicted through computational analysis as potential candidates for inhibiting the three major types of S proteins. Our study provides a foundation for further experimental validation of these compounds as potential therapeutic agents against SARS-CoV-2. |
| format | Article |
| id | doaj-art-bcb26d57ba904c0caa8f1fbf9b380968 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-bcb26d57ba904c0caa8f1fbf9b3809682025-01-05T12:15:33ZengNature PortfolioScientific Reports2045-23222025-01-0115111910.1038/s41598-024-83637-4Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteinsMuhammad Alqaaf0Ahmad Kamal Nasution1Mohammad Bozlul Karim2Mahfujul Islam Rumman3Muhammad Hendrick Sedayu4Retno Supriyanti5Naoaki Ono6Md. Altaf-Ul-Amin7Shigehiko Kanaya8Graduate School of Science and Technology, Nara Institute of Science and TechnologyGraduate School of Science and Technology, Nara Institute of Science and TechnologyGraduate School of Science and Technology, Nara Institute of Science and TechnologyGraduate School of Science and Technology, Nara Institute of Science and TechnologyGraduate School of Science and Technology, Nara Institute of Science and TechnologyDepartment of Electrical Engineering, Jenderal Soedirman UniversityGraduate School of Science and Technology, Nara Institute of Science and TechnologyGraduate School of Science and Technology, Nara Institute of Science and TechnologyGraduate School of Science and Technology, Nara Institute of Science and TechnologyAbstract The ongoing global pandemic caused by the SARS-CoV-2 virus has demanded the urgent search for effective therapeutic interventions. In response, our research aimed at identifying natural products (NPs) with potential inhibitory effects on the entry of the SARS-CoV-2 spike (S) protein into host cells. Utilizing the Protein Data Bank Japan (PDBJ) and BindingDB databases, we isolated 204 S-glycoprotein sequences and conducted a clustering analysis to identify similarities and differences among them. We subsequently identified 33,722 binding molecules (BMs) by matching them with the sequences of 204 S-glycoproteins and compared them with 52,107 secondary metabolites (SMs) from the KNApSAcK database to identify potential inhibitors. We conducted docking and drug-likeness property analyses to identify several SMs with potential as drug candidates based on binding energy (BE), no Lipinski’s rule violation (LV), psychochemical properties within the pink area of the bioavailability radar, and a bioavailability score (BAS) not less than 0.55. Fourteen SMs were predicted through computational analysis as potential candidates for inhibiting the three major types of S proteins. Our study provides a foundation for further experimental validation of these compounds as potential therapeutic agents against SARS-CoV-2.https://doi.org/10.1038/s41598-024-83637-4SARS-CoV-2Spike proteinVirtual screeningNatural productsDrug discovery |
| spellingShingle | Muhammad Alqaaf Ahmad Kamal Nasution Mohammad Bozlul Karim Mahfujul Islam Rumman Muhammad Hendrick Sedayu Retno Supriyanti Naoaki Ono Md. Altaf-Ul-Amin Shigehiko Kanaya Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins Scientific Reports SARS-CoV-2 Spike protein Virtual screening Natural products Drug discovery |
| title | Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins |
| title_full | Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins |
| title_fullStr | Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins |
| title_full_unstemmed | Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins |
| title_short | Discovering natural products as potential inhibitors of SARS-CoV-2 spike proteins |
| title_sort | discovering natural products as potential inhibitors of sars cov 2 spike proteins |
| topic | SARS-CoV-2 Spike protein Virtual screening Natural products Drug discovery |
| url | https://doi.org/10.1038/s41598-024-83637-4 |
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