Aims: To predict potential drugs for COVID-19 by using molecular docking for virtual
screening of drugs approved for other clinical applications.
Background: SARS-CoV-2 is the betacoronavirus responsible for the COVID-19 pandemic. It was
listed as a potential global health threat by the WHO due to high mortality, high basic reproduction
number, and lack of clinically approved drugs and vaccines. The genome of the virus responsible
for COVID-19 has been sequenced. In addition, the three-dimensional structure of the main protease
has been determined experimentally.
Objective: To identify potential drugs that can be repurposed for treatment of COVID-19 by using
molecular docking based virtual screening of all approved drugs.
Methods: A list of drugs approved for clinical use was obtained from the SuperDRUG2 database.
The structure of the target in the apo form, as well as structures of several target-ligand complexes,
were obtained from RCSB PDB. The structure of SARS-CoV-2 Mpro determined from X-ray diffraction
data was used as the target. Data regarding drugs in clinical trials for COVID-19 was obtained
from clinicaltrials.org. Input for molecular docking based virtual screening was prepared by
using Obabel and customized python, bash, and awk scripts. Molecular docking calculations were
carried out with Vina and SMINA, and the docked conformations were analyzed and visualized
with PLIP, Pymol, and Rasmol.
Results: Among the drugs that are being tested in clinical trials for COVID-19, Danoprevir and
Darunavir were predicted to have the highest binding affinity for the Main protease (Mpro) target
of SARS-CoV-2. Saquinavir and Beclabuvir were identified as the best novel candidates for
COVID-19 therapy by using Virtual Screening of drugs approved for other clinical indications.
Conclusion: Protease inhibitors approved for treatment of other viral diseases have the potential to
be repurposed for treatment of COVID-19.
Keywords: Virtual screening, molecular docking, drug repurposing, drug repositioning, anti-viral drugs, coronavirus,
COVID-19, 2019-nCoV, SARS-CoV-2.
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