Structural Elucidation and Antiviral Activity of Covalent Cathepsin L Inhibitors

Area of Science:

• Virology
• Drug Discovery
• Structural Biology

Background:

• Emerging RNA viruses like SARS-CoV-2 pose significant global health threats.
• Cellular entry of SARS-CoV-2 involves the endosomal pathway and cysteine cathepsins.
• Cathepsin L (CatL), due to its widespread expression, is a key drug target for viral and lysosomal diseases.

Purpose of the Study:

• To evaluate the anti-SARS-CoV-2 efficacy of epoxide-based inhibitors targeting cathepsins.
• To understand the structure-activity relationships of these inhibitors with CatL.
• To provide a basis for structure-guided optimization of CatL inhibitors for drug development.

Main Methods:

• Screening of carbonyl- and succinyl epoxide-based inhibitors for antiviral activity against SARS-CoV-2 in Vero E6 cells.
• Biochemical assays to determine CatL inhibition constants (K_i).
• X-ray crystallography to determine the structures of CatL in complex with inhibitors.

Main Results:

• Several inhibitors, including Calpain inhibitor XII, MG-101, and CatL inhibitor IV, demonstrated potent antiviral activity (EC₅₀ in the nanomolar range).
• These compounds effectively inhibited CatL activity (K_i in the picomolar range).
• Crystal structures of CatL complexed with 14 compounds were obtained at high resolution (<2 Å), revealing detailed binding interactions.

Conclusions:

• Epoxide-based inhibitors targeting CatL exhibit significant anti-SARS-CoV-2 potential.
• Structure-based insights facilitate the design and optimization of novel CatL inhibitors.
• This work supports the development of CatL-targeted therapeutics for viral infections.