Structure-Guided Design of Potent and Selective Covalent Inhibitors Targeting the SARS-CoV-2 Papain-like Protease

Area of Science:

• Virology
• Medicinal Chemistry
• Drug Discovery

Background:

• The COVID-19 pandemic highlighted the urgent need for effective antiviral therapies.
• Existing treatments for COVID-19 infections may require novel mechanisms of action for improved efficacy and to combat resistance.
• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) papain-like protease (PLpro) is a key viral enzyme crucial for replication and pathogenesis, making it an attractive drug target.

Purpose of the Study:

• To design and develop novel covalent inhibitors targeting the SARS-CoV-2 PLpro enzyme.
• To evaluate the antiviral activity of these inhibitors against SARS-CoV-2 in vitro and in vivo.
• To explore the potential of these inhibitors for future antiviral drug development and pandemic preparedness.

Main Methods:

• Structure-guided design and synthesis of covalent inhibitors targeting SARS-CoV-2 PLpro.
• Biochemical assays to determine inhibitor potency and mechanism of action.
• Cell-based assays to assess antiviral activity against SARS-CoV-2 replication.
• In vivo efficacy studies in a mouse model of SARS-CoV-2 infection.

Main Results:

• Developed potent covalent inhibitors of SARS-CoV-2 PLpro with low nanomolar to subnanomolar antiviral activity.
• Identified N-propargylamide as an effective electrophilic warhead for covalent inhibition of PLpro.
• Demonstrated significant inhibition of viral replication in a mouse model of SARS-CoV-2 infection.

Conclusions:

• The developed covalent PLpro inhibitors represent a promising new class of antiviral agents against SARS-CoV-2.
• The unique N-propargylamide warhead offers a novel approach for designing covalent protease inhibitors.
• These findings provide a strong foundation for the further optimization of PLpro inhibitors as potential therapeutics for COVID-19 and future viral pandemics.