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Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a dreaded pandemic in lack of specific therapeutic agent. SARS-CoV-2 M pro , an essential factor in viral pathogenesis, is recognized as a prospective therapeutic target in drug discovery against SARS-CoV-2. To tackle this pandemic, Food and Drug Administration-approved drugs are being screened against SARS-CoV-2 M pro  via  in silico  and  in vitro  methods to detect the best conceivable drug candidates. However, identification of natural compounds with anti-SARS-CoV-2 M pro  potential have been recommended as rapid and effective alternative for anti-SARS-CoV-2 therapeutic development. Thereof, a total of 653 natural compounds were identified against SARS-CoV-2 M pro  from NP-lib database at MTi-OpenScreen webserver using virtual screening approach. Subsequently, top four potential compounds, i.e. 2,3-Dihydroamentoflavone (ZINC000043552589), Podocarpusflavon-B (ZINC3594862), Rutin (ZINC3947429) and Quercimeritrin 6”-O-L-arabinopyranoside (ZINC000070691536), and co-crystallized N3 inhibitor as reference ligand were considered for stringent molecular docking after geometry optimization by DFT method. Each compound exhibited substantial docking energy &gt;−12 kcal/mol and molecular contacts with essential residues, including catalytic dyad (His 41  and Cys 145 ) and substrate binding residues, in the active pocket of SARS-CoV-2 M pro  against N3 inhibitor. The screened compounds were further scrutinized via absorption, distribution, metabolism, and excretion - toxicity (ADMET), quantum chemical calculations, combinatorial molecular simulations and hybrid QM/MM approaches. Convincingly, collected results support the potent compounds for druglikeness and strong binding affinity with the catalytic pocket of SARS-CoV-2 M pro . Hence, selected compounds are advocated as potential inhibitors of SARS-CoV-2 M pro  and can be utilized in drug development against SARS-CoV-2 infection.

Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 M pro