Dynamic Profiling of β-Coronavirus 3CL M^pro Protease Ligand-Binding Sites

Area of Science:

• Virology
• Structural Biology
• Drug Discovery

Background:

• Beta-coronaviruses (CoVs) have caused three major 21st-century pandemics, necessitating rapid therapeutic development.
• The main protease (Mpro) is crucial for viral replication and a key target for antiviral drugs.
• Existing SARS-CoV-2 vaccines highlight the need for alternative strategies against emerging variants.

Purpose of the Study:

• To comprehensively compare ligand-binding sites across SARS-CoV-2, SARS-CoV, and MERS-CoV Mpro.
• To investigate the structural conservation and conformational dynamics of Mpro ligand-binding sites.
• To assess the feasibility of developing a single pan-inhibitor for multiple beta-CoVs.

Main Methods:

• Utilized adaptive sampling and Markov state models (MSMs) to analyze structural conservation.
• Employed deep learning (convolutional variational auto-encoder) to compare conformational dynamics.
• Performed a comparative analysis of over 270 Mpro X-ray structures with inhibitors.

Main Results:

• Identified significant differences in ligand-binding site dynamics despite high sequence and structural conservation among beta-CoV Mpro homologs.
• Demonstrated that not all ligand-binding sites are dynamically conserved across different beta-CoVs.
• Highlighted complexities in targeting conserved Mpro enzymes with a single pan-inhibitor.

Conclusions:

• The dynamic variability of Mpro ligand-binding sites presents a challenge for developing universal inhibitors.
• Targeting Mpro for pan-coronavirus therapeutics requires consideration of distinct conformational behaviors.
• Further research into specific Mpro dynamics is essential for effective antiviral drug design against beta-CoVs.