Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which causes coronavirus disease-19 (COVID-19) has caused more than 2 million deaths around the globe. The high transmissibility rate of the disease is related to the strong interaction between the virus spike receptor-bi...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-09-01
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| Series: | Biochemistry and Biophysics Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405580821001187 |
| _version_ | 1818573839799418880 |
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| author | Marcelina Ogedjo Isaac Onoka Mtabazi Sahini Daniel M. Shadrack |
| author_facet | Marcelina Ogedjo Isaac Onoka Mtabazi Sahini Daniel M. Shadrack |
| author_sort | Marcelina Ogedjo |
| collection | DOAJ |
| description | The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which causes coronavirus disease-19 (COVID-19) has caused more than 2 million deaths around the globe. The high transmissibility rate of the disease is related to the strong interaction between the virus spike receptor-binding domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) as documented in several reports. In this study, using state-of-the-art computational methods, natural products were screened and their molecular mechanism to disrupt spike RBD-ACE2 recognition was evaluated. There is the sensitivity of results to receptor ensemble docking calculations. Binding free energy and MD simulation are important tools to evaluate the thermodynamics of binding stability and the capacity of top hits to disrupt RBD-ACE2 recognition. The free energy profiles provide a slight decrease in binding affinity of the virus-receptor interaction. Three flavonoids parvisoflavone B (3), alpinumisoflavone (5) and norisojamicin (2) were effective in blocking the viral entry by binding strongly at the spike RBD-ACE2 interface with the inhibition constant of 0.56, 0.78 and 0.93 μM, respectively. The same compounds demonstrated similar effect on free ACE2 protein. Compound (2), also demonstrated ability to bind strongly on free spike RBD. Well-tempered metadynamics established that parvisoflavone B (3) works by binding to three sites namely interface α, β and loop thereby inhibiting viral cell entry. Owing to their desirable pharmacokinetic properties, the presented top hit natural products are suggested for further SARS-COV-2 molecular targets and subsequent in vitro and in vivo evaluations. |
| first_indexed | 2024-12-15T00:18:16Z |
| format | Article |
| id | doaj.art-43a95beb7bfc4ddcb1faa800d4bca3b0 |
| institution | Directory Open Access Journal |
| issn | 2405-5808 |
| language | English |
| last_indexed | 2024-12-15T00:18:16Z |
| publishDate | 2021-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biochemistry and Biophysics Reports |
| spelling | doaj.art-43a95beb7bfc4ddcb1faa800d4bca3b02022-12-21T22:42:24ZengElsevierBiochemistry and Biophysics Reports2405-58082021-09-0127101024Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interfaceMarcelina Ogedjo0Isaac Onoka1Mtabazi Sahini2Daniel M. Shadrack3Department of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, P.O.Box 338, Dodoma, TanzaniaDepartment of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, P.O.Box 338, Dodoma, TanzaniaDepartment of Chemistry, College of Natural and Mathematical Sciences, University of Dodoma, P.O.Box 338, Dodoma, TanzaniaDepartment of Chemistry, Faculty of Natural and Applied Sciences, St. John's University of Tanzania, P.O.Box 47, Dodoma, Tanzania; Corresponding author.The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), which causes coronavirus disease-19 (COVID-19) has caused more than 2 million deaths around the globe. The high transmissibility rate of the disease is related to the strong interaction between the virus spike receptor-binding domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) as documented in several reports. In this study, using state-of-the-art computational methods, natural products were screened and their molecular mechanism to disrupt spike RBD-ACE2 recognition was evaluated. There is the sensitivity of results to receptor ensemble docking calculations. Binding free energy and MD simulation are important tools to evaluate the thermodynamics of binding stability and the capacity of top hits to disrupt RBD-ACE2 recognition. The free energy profiles provide a slight decrease in binding affinity of the virus-receptor interaction. Three flavonoids parvisoflavone B (3), alpinumisoflavone (5) and norisojamicin (2) were effective in blocking the viral entry by binding strongly at the spike RBD-ACE2 interface with the inhibition constant of 0.56, 0.78 and 0.93 μM, respectively. The same compounds demonstrated similar effect on free ACE2 protein. Compound (2), also demonstrated ability to bind strongly on free spike RBD. Well-tempered metadynamics established that parvisoflavone B (3) works by binding to three sites namely interface α, β and loop thereby inhibiting viral cell entry. Owing to their desirable pharmacokinetic properties, the presented top hit natural products are suggested for further SARS-COV-2 molecular targets and subsequent in vitro and in vivo evaluations.http://www.sciencedirect.com/science/article/pii/S2405580821001187Natural productsCovid-19SARS-CoV-2Molecular dockingMD simulation |
| spellingShingle | Marcelina Ogedjo Isaac Onoka Mtabazi Sahini Daniel M. Shadrack Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface Biochemistry and Biophysics Reports Natural products Covid-19 SARS-CoV-2 Molecular docking MD simulation |
| title | Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface |
| title_full | Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface |
| title_fullStr | Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface |
| title_full_unstemmed | Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface |
| title_short | Accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of SARS-COV-2 spike RBD-ACE2 interface |
| title_sort | accommodating receptor flexibility and free energy calculation to reduce false positive binders in the discovery of natural products blockers of sars cov 2 spike rbd ace2 interface |
| topic | Natural products Covid-19 SARS-CoV-2 Molecular docking MD simulation |
| url | http://www.sciencedirect.com/science/article/pii/S2405580821001187 |
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