posted on 2024-01-10, 16:05authored byDeborah Grifagni, Elena Lenci, Alessia De Santis, Andrea Orsetti, Carlo Giorgio Barracchia, Filomena Tedesco, Raffaele Bellini Puglielli, Francesca Lucarelli, Angela Lauriola, Michael Assfalg, Francesca Cantini, Vito Calderone, Daniele Guardavaccaro, Andrea Trabocchi, Mariapina D’Onofrio, Simone Ciofi-Baffoni
We
have applied a proteolysis targeting chimera (PROTAC) technology
to obtain a peptidomimetic molecule able to trigger the degradation
of SARS-CoV-2 3-chymotrypsin-like protease (3CLPro). The
PROTAC molecule was designed by conjugating a GC-376 based dipeptidyl
3CLPro ligand to a pomalidomide moiety through a piperazine–piperidine
linker. NMR and crystallographic data complemented with enzymatic
and cellular studies showed that (i) the dipeptidyl moiety of PROTAC
binds to the active site of the dimeric state of SARS-CoV-2 3CLPro forming a reversible covalent bond with the sulfur atom
of catalytic Cys145, (ii) the linker and the pomalidomide cereblon-ligand
of PROTAC protrude from the protein, displaying a high degree of flexibility
and no interactions with other regions of the protein, and (iii) PROTAC
reduces the protein levels of SARS-CoV-2 3CLPro in cultured
cells. This study paves the way for the future applicability of peptidomimetic
PROTACs to tackle 3CLPro-dependent viral infections.