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In silico virtual screening of known drugs against SARS-CoV-2 3CL protease: A drug repurposing approach for COVID-19
1 , * 1, 2 , * 1 , 1
1  Department of Pharmacy, International Islamic University Chittagong, Chittagong 4318, Bangladesh
2  Department of Bio-Health Technology, Kangwon National University, Chuncheon 24341, Korea

Abstract:

Since the outbreak of the novel coronavirus disease (COVID-19) in late December 2019, it rapidly spread throughout the world. Besides, no specific treatment has been reported so far against the disease. In such cases, the drug repurposing approach can be an effective way to determine potential candidates to treat COVID-19. Therefore, this study is focused on screening drugs that could inhibit the viral receptor. Structure of SARS-CoV-2 3CL protease with a complex (baicalein) was employed for the generation of pharmacophore hypothesis using Schrödinger Maestro. Initially, 8820 approved, investigational and experimental drugs from DrugBank database were screened on the basis of generated hypothesis features. Among those, 1000 drugs were subjected to molecular docking-based virtual screening to evaluate the glide score and glide energy. Moreover, receptor-ligand interactions of the best hits were analyzed using discovery studio software. The virtual screening revealed several drug classes including CYP3A4 inhibitor, anti-tumor, anti-platelet, antiviral, neurological, anticancer, Vit-B2 deficiency, anti-inflammatory, antidiabetic, and anti-asthmatic which are capable of inhibiting viral receptor. In particular, six drugs namely rutin, fosifloxuridine-nafalbenamide, eluxadoline, telmisartan, fostemsavir, and capmatinib demonstrated extra precision docking with promising binding affinities. Interaction analysis revealed several hydrogens and hydrophobic bonds with the amino acids of the active site. Additionally, 19 experimental drugs were found to possess higher docking scores than the bound complex with the receptor indicating a possibility of discovering novel drugs to treat COVID-19. However, further in vitro and in vivo studies are required for the evaluation of the antiviral activity of the mentioned drugs.

Keywords: COVID-19, drug repurposing, molecular docking, pharmacophore hypothesis, virtual screening
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