Coronavirus Disease 2019 (COVID-19) outbreak has thrown the world into an unprecedented crisis. It has posed a challenge to scientists around the globe who are working tirelessly to combat this pandemic. We herein report a set of newly identified molecules, which can presumably act as potential inhibitors of SARS-CoV-2 main protease. A fast mode approach using a combinatorial structure-based strategy, which includes high throughput virtual screening, molecular docking, and WaterMap calculations, was applied to identify these molecules. The PDB structures 5R82 and 6Y2G was used as the basis for this study. Databases viz., Enamine, Drug Bank, Natural product, Specs, and few antiviral drugs were used for screening. Several molecules identified from the natural product database are promising and can be considered for future studies. The molecules screened from Drug Bank can be investigated for repurposing. Hydroxychloroquine and Ritonavir molecule used in treating COVID-19 have also been selected in the screening study. The results of WaterMap calculations used in the screening study and analysis gives insight into the thermodynamic properties of the hydration sites in the binding site. We believe that the identified molecules in this study will pave the way for the discovery and development of drugs for fighting the pandemic.

Rapid structure-based identification of potential SARS-CoV-2 main protease inhibitors

ACS Spring Meeting 2021

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