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

Simple item page
dc.contributor.authorOgedjo, M.
dc.contributor.authorOnoka, I.
dc.contributor.authorSahini, M.
dc.contributor.authorShadrack, D. M.
dc.date.accessioned2023-05-25T10:20:06Z
dc.date.available2023-05-25T10:20:06Z
dc.date.issued2021
dc.descriptionFull text article. Also available at https://doi.org/10.1016/j.bbrep.2021.101024en_US
dc.description.abstractThe 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 hermodynamics 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.en_US
dc.identifier.citationOgedjo, M., Onoka, I., Sahini, M., & Shadrack, D. M. (2021). 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, 27, 101024.en_US
dc.identifier.otherDOI: https://doi.org/10.1016/j.bbrep.2021.101024
dc.identifier.otherURL: https://www.sciencedirect.com/science/article/pii/S2405580821001187?via%3Dihub
dc.identifier.urihttp://hdl.handle.net/20.500.12661/3993
dc.language.isoenen_US
dc.publisherElsevieren_US
dc.subjectNatural productsen_US
dc.subjectCOVID-19en_US
dc.subjectSARS-CoV-2en_US
dc.subjectMolecular dockingen_US
dc.subjectRBD-ACE2en_US
dc.subjectReceptor-Binding Domainen_US
dc.subjectAngiotensin-Converting Enzyme 2en_US
dc.subjectCoronavirus diseaseen_US
dc.subjectMedicinal plantsen_US
dc.subjectPharmacokinetics propertiesen_US
dc.subjectAfrican medicinal plantsen_US
dc.titleAccommodating 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 interfaceen_US
dc.typeArticleen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Isaac Onoka _ Accommodating receptor flexibility.pdf
Size:
4.28 MB
Format:
Adobe Portable Document Format
Description:
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Journal Articles