Main Article Content

Chenyue Fan
Ayesha Abdul Qadir Memon
Prajit Adhikari
Muhammad Osama
Calvin R. Wei


SARS-CoV-2, COVID-19, Mpro, Main Protease, Molecular Docking, Molecular Dynamics, ADMET, Toxicity, Drug Repurposing, Drug Discovery, Virtual Screening, Clinical, Trials


The novel coronavirus disease or Covid-19 is a global pandemic caused by the SARS-CoV-2 virus originated from Wuhan, China in December 2019. A rapidly spreading, contagious virus that caused more than 6.7 million deaths worldwide. The main protease of SARS-CoV-2 is believed to play a vital role in mediating viral replication and transcription, making it a potential target of interest against Covid-19. In this study, virtual drug screening methods were conducted against a current Mpro structure (Protein Data Bank ID: 8SXR) with 868 ligands from the NIH Clinical Collection of clinical trial molecules. Multiple possible hit compounds were identified with compound 1 and 2 outperforming the other compounds in binding conformation and binding free energy. Toxicity and ADMET properties of the top 5 compounds were further investigated computationally. To further validate the results, molecular dynamic simulations of the top 2 complexes were performed. The two complexes displayed stable affinity in respect to the root mean square distance (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA) and hydrogen bond.

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