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The SARS-CoV-2 pandemic has triggered global efforts to develop therapeutics. The main protease of SARS-CoV-2 (M
pro
), critical for viral replication, is a key target for therapeutic development. An organoselenium drug called ebselen has been demonstrated to have potent M
pro
inhibition and antiviral activity. We have examined the binding modes of ebselen and its derivative in M
pro
via high resolution co-crystallography and investigated their chemical reactivity via mass spectrometry. Stronger M
pro
inhibition than ebselen and potent ability to rescue infected cells were observed for a number of derivatives. A free selenium atom bound with cysteine of catalytic dyad has been revealed in crystallographic structures of M
pro
with ebselen and MR6-31-2 suggesting hydrolysis of the enzyme bound organoselenium covalent adduct and formation of a phenolic by-product, confirmed by mass spectrometry. The target engagement with selenation mechanism of inhibition suggests wider therapeutic applications of these compounds against SARS-CoV-2 and other zoonotic
beta
-corona viruses.
Ebselen is an organoselenium drug that inhibits the SARS-CoV-2 main protease (M
pro
). Here, the authors co-crystallised M
pro
with ebselen and an ebselen derivative and observed an enzyme bound organoselenium covalent adduct in the crystal structures, which was also confirmed by mass spectrometry analysis.