Novel adenosine derivatives against SARS-CoV-2 RNA-dependent RNA polymerase: an in silico perspective

Type
Article

Authors
Sonousi, Amr
Mahran, Hanan A.
Ibrahim, Ibrahim M.
Ibrahim, Mohamed N.
Elfiky, Abdo A.
Elshemey, Wael M.

Online Publication Date
2021-06-24

Print Publication Date
2021-12

Date
2021-06-24

Abstract
Background: SARS-CoV-2 is a newly emerged human coronavirus that severely affected human health and the economy. The viral RNA-dependent RNA polymerase (RdRp) is a crucial protein target to stop virus replication. The adenosine derivative, remdesivir, was authorized for emergency use 10 months ago by the United States FDA against COVID-19 despite its doubtful efficacy against SARS-CoV-2. Methods: A dozen modifications based on remdesivir are tested against SARS-CoV-2 RdRp using combined molecular docking and dynamics simulation in this work. Results: The results reveal a better binding affinity of 11 modifications compared to remdesivir. Compounds 8, 9, 10, and 11 show the best binding affinities against SARS-CoV-2 RdRp conformations gathered during 100 ns of the Molecular Dynamics Simulation (MDS) run (− 8.13 ± 0.45 kcal/mol, − 8.09 ± 0.67 kcal/mol, − 8.09 ± 0.64 kcal/mol, and − 8.07 ± 0.73 kcal/mol, respectively). Conclusions: The present study suggests these four compounds as potential SARS-CoV-2 RdRp inhibitors, which need to be validated experimentally. Graphic abstract: [Figure not available: see fulltext.]

Citation
Sonousi, A., Mahran, H. A., Ibrahim, I. M., Ibrahim, M. N., Elfiky, A. A., & Elshemey, W. M. (2021). Novel adenosine derivatives against SARS-CoV-2 RNA-dependent RNA polymerase: an in silico perspective. Pharmacological Reports. doi:10.1007/s43440-021-00300-9

Acknowledgements
Shaheen supercomputer of King Abdullah University of Science and Technology (KAUST) is used to perform the after dockings MDS calculations (under Project Number k1482). In addition, the Bibliotheca Alexandrina is used to perform the initial MDS calculations. This work is supported by the Cairo University COVID-19 fund received by AAE.

Publisher
Springer Science and Business Media LLC

Journal
PHARMACOLOGICAL REPORTS

DOI
10.1007/s43440-021-00300-9

PubMed ID
34165771

PubMed Central ID
PMC8222949

Additional Links
https://link.springer.com/10.1007/s43440-021-00300-9

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