Integrated computational screen and validation of thalidomide-based PROTACs targeting SARS-CoV-2 main protease.

Area of Science:

• Virology
• Medicinal Chemistry
• Biochemistry

Background:

• SARS-CoV-2's persistent evolution necessitates novel antiviral strategies.
• The viral main protease (Mpro) is crucial for replication and a conserved target.
• Conventional inhibitors face resistance and toxicity; PROTACs offer an alternative degradation approach.

Purpose of the Study:

• To design and validate thalidomide-based PROTACs targeting SARS-CoV-2 Mpro.
• To assess the efficacy and mechanism of Mpro degradation by novel PROTACs.

Main Methods:

• Computational simulations including molecular docking and dynamics.
• Experimental validation using cell-based assays in HEK293 cells.
• Analysis of protein degradation via ubiquitin-proteasome system markers.

Main Results:

• PROTACs A, B, and C showed favorable binding free energies and stable interactions with Mpro.
• These PROTACs induced dose-dependent Mpro degradation with high selectivity.
• Degradation occurred via the ubiquitin-proteasome system, evidenced by K48-linked polyubiquitination.

Conclusions:

• Thalidomide-based PROTACs are effective degraders of SARS-CoV-2 Mpro.
• PROTACs demonstrate therapeutic potential against drug-resistant viral targets through catalytic degradation.