The current COVID-19 pandemic caused by the severe acute respiratory syndrome
coronavirus-2 (SARS-CoV-2) created a global health crisis. The ability of vaccines to
protect immunocompromised individuals and from emerging new strains are major concerns.
Hence antiviral drugs against SARS-CoV-2 are essential. The SARS-CoV-2 main protease
M
pro
is vital for replication and an important target for antivirals. Using
CMap analysis and docking studies, withaferin A (wifA) and withanone (win), two natural
products from the medicinal herb
Withania somnifera
(ashwagandha), were
identified as promising candidates that can covalently inhibit the viral protease
M
pro
. Cell culture, enzymatic, LC-MS/MS, computational, and equilibrium
dialysis based assays were performed. DFT calculations indicated that wifA and win can
form stable adducts with thiols. The cytotoxicity of M
pro
was significantly
reduced by wifA and win. Both wifA and win were found to irreversibly inhibit 0.5
μM M
pro
with IC
50
values of 0.54 and 1.8 μM,
respectively. LC-MS/MS analysis revealed covalent adduct formation with wifA at
cysteines 145 and 300 of M
pro
. The natural products wifA and win can
irreversibly inhibit the SARS-CoV-2 main protease M
pro
. Based on the work
presented here we propose that both wifA and win have the potential to be safely used as
preventative and therapeutic interventions for COVID-19.