Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Discovery of Natural Products to SARS-CoV-2 with Comparative Molecular Docking and Moderate Cell Proliferation Inhibition in vitro

Shiwei Yang
* ORCID logo ,
Xinming Hu
,
Jinmiao Zhu
,
Bin Zheng
ORCID logo ,
Heng Tian
,
Jifeng Zhang
,
Zhixian Wang
,
Shan Gao
,
Zhaoyi Chu
,
Shengnan Li
,
Xiaohong Wang
,
Wenjie Bi
,
Xinsong Yuan
,
Liang Yang
ORCID logo ,
Penglin Xu
Version 1 : Received: 29 March 2024 / Approved: 29 March 2024 / Online: 1 April 2024 (11:54:06 CEST)

How to cite: Yang, S.; Hu, X.; Zhu, J.; Zheng, B.; Tian, H.; Zhang, J.; Wang, Z.; Gao, S.; Chu, Z.; Li, S.; Wang, X.; Bi, W.; Yuan, X.; Yang, L.; Xu, P. Discovery of Natural Products to SARS-CoV-2 with Comparative Molecular Docking and Moderate Cell Proliferation Inhibition in vitro. Preprints 2024, 2024031884. https://doi.org/10.20944/preprints202403.1884.v1 Yang, S.; Hu, X.; Zhu, J.; Zheng, B.; Tian, H.; Zhang, J.; Wang, Z.; Gao, S.; Chu, Z.; Li, S.; Wang, X.; Bi, W.; Yuan, X.; Yang, L.; Xu, P. Discovery of Natural Products to SARS-CoV-2 with Comparative Molecular Docking and Moderate Cell Proliferation Inhibition in vitro. Preprints 2024, 2024031884. https://doi.org/10.20944/preprints202403.1884.v1

Abstract

Based on screening in computational biology and biological in vitro assays, five natural products isolated from extracts of the herbal medicine toad skin, such as cinobufagin (CBFi), bufalin (BFi), arenobufagin (ABFi), telocinobufagin (TBFi), bufotalin (BFTi), were subjected to molecular docking calculations with the use of SARS-CoV-2 main protease (PDB 6LU7 and 7BTF) and top-scoring ligand-receptor complexes were obtained. The results showed that the binding energy of ABFi to the 3CL protein was -17.044kcal/mol, which was higher than CBFi and TBFi. However, the binding energy of ABFi to the RdRp protease was -23.250 kcal/mol, which was much lower than that of CBFi and TBFi, EVEN lower than that of ABFi to the 3CL protein. ABFi also has polar interactions with amino acids such as Glu811, Ser814, Ser681 and Thr680 of RdRp enzyme. The results revealed that ABFi had a moderate inhibitory effect on the cell proliferation of SARS-CoV-2 in vitro, with an inhibition rate of 61.12%, even weaker than Remdesivir. This new discovery provides us with new ideas for in-depth studies on the development of natural products with this class of structural generalizations as inhibitors of SARS-CoV-2, and provides an experimental basis for the next step of mechanistic studies.

Keywords

Natural products; Molecular Docking, Antiviral Activity; SARS-CoV-2; Cell Proliferation Inhibition

Subject

Medicine and Pharmacology, Medicine and Pharmacology

Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Download PDF

Comments (0)

We encourage comments and feedback from a broad range of readers. See criteria for comments and our Diversity statement.

Leave a public comment
Send a private comment to the author(s)
* All users must log in before leaving a comment
Views 0
Downloads 0
Comments 0
Metrics 0
Get PDF Cite Share 0
Bookmark BibSonomy Mendeley Reddit Delicious
×
Alerts
Notify me about updates to this article or when a peer-reviewed version is published.
We use cookies on our website to ensure you get the best experience.
Read more about our cookies here.