ORIGINAL ARTICLE
Year : 2021  |  Volume : 20  |  Issue : 4  |  Page : 371-392

Repurposing of available antiviral drugs against SARS-CoV-2 by targeting crucial replication machinery proteins: a molecular docking study


1 Department of Microbial Genetic, Genetic Engineering and Biotechnology Division, National Research Centre, Giza, Egypt
2 Department of Biochemistry, Genetic Engineering and Biotechnology Division, National Research Centre, Giza, Egypt
3 Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Sadat University, Menoufia, Egypt
4 Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt

Correspondence Address:
PhD Ahmed F El-Sayed
Researcher at Department of Microbial Genetics, Genetic Engineering and Biotechnology Division, National Research Centre, Giza
Egypt
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/epj.epj_70_21

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Background and objectives The newly emerged severe acute respiratory syndrome coronavirus is spreading worldwide rapidly with increasing incidence rates. Due to lack of effective treatments and vaccines, various drug repurposing studies are being developed. Searching for available antiviral drug libraries is the best and fast option to advance to clinical trials and spread their application among infected patients. Materials and methods Molecular docking study was performed utilizing AutoDock 4.2 system and Discovery Studio 4.5, which were utilized to predict the activity pocket of the target proteins. Results and conclusion The results found that the interacting affinities resulted from the molecular simulation of 3CL protease with ligands Ledipasvir, Sofosbuvir, Ribavirin, Galidesivir, Tenofovir, and Remdesivir were −7.2, −7.4, −7.2, −6.3, −6.1 and −6.6 kcal/mol, respectively. Similarly, the interacting energies obtained from the docking of RNA helicase with ligands were −7.9, −7.4, −6.4, −7.9, −6.2, and −6.9 kcal/mol. Also, the binding energies obtained from the docking of 3′-5′ exoribonuclease with ligands were −10.6, −10.1, −6.5, −7.1, −6.1, and −9.3 kcal/mol. Finally, the binding energies score from the docking of the RNA-dependent RNA polymerase with ligands was −9.6, −6.9, −6.2, −6.6, −6.7, and −6.4 kcal/mol. Based on the binding energy score and docking result, Ledipasvir and Sofosbuvir have a higher affinity of the drug molecule such as against RNA-dependent RNA polymerase, exonuclease, and 3CL protease. Besides, Ledipasvir and Galidesivir show prominent binding interaction with severe acute respiratory syndrome coronavirus RNA helicase. The results are promising for evaluated drugs especially Ledipasvir and Sofosbuvir and could be useful in emergency treatment of coronavirus disease 2019 patients.


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