Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2

Deborah 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

doi:10.1021/acsmedchemlett.3c00498

Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2

ACS Med Chem Lett. 2024 Jan 10;15(2):250-257. doi: 10.1021/acsmedchemlett.3c00498. eCollection 2024 Feb 8.

Authors

Deborah Grifagni^{1

2}, Elena Lenci², Alessia De Santis^{1

2}, Andrea Orsetti^{1

2}, Carlo Giorgio Barracchia³, Filomena Tedesco², Raffaele Bellini Puglielli², Francesca Lucarelli^{1

2}, Angela Lauriola³, Michael Assfalg³, Francesca Cantini^{1

2}, Vito Calderone^{1

2}, Daniele Guardavaccaro³, Andrea Trabocchi², Mariapina D'Onofrio³, Simone Ciofi-Baffoni^{1

2

4}

Affiliations

¹ Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy.
² Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Florence, Italy.
³ Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
⁴ Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.

PMID: 38352832
PMCID: PMC10860180 (available on 2025-02-08)
DOI: 10.1021/acsmedchemlett.3c00498

Abstract

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 (3CL^Pro). The PROTAC molecule was designed by conjugating a GC-376 based dipeptidyl 3CL^Pro 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 3CL^Pro 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 3CL^Pro in cultured cells. This study paves the way for the future applicability of peptidomimetic PROTACs to tackle 3CL^Pro-dependent viral infections.