Marine Streptomyces-Derived Lipids Inhibit SARS-CoV-2 3CLpro Through In Vitro and Predicted Multi-Site Binding...

Area of Science:

• Microbiology
• Biochemistry
• Drug Discovery

Background:

• The SARS-CoV-2 3CLpro enzyme is crucial for viral replication and a key target for antiviral therapies.
• Inhibition strategies beyond the catalytic site, such as targeting the dimerization interface or allosteric pockets, are being explored.

Purpose of the Study:

• To investigate lipid metabolites from marine Streptomyces sp. DSD454^T as potential multi-site inhibitors of SARS-CoV-2 3CLpro.
• To identify specific lipids and elucidate their binding mechanisms to the 3CLpro enzyme.

Main Methods:

• Metabolite extraction and characterization using LCMS-QTOF, MS/MS, and ¹H NMR.
• Inhibition assays (FRET-based) and molecular modeling (docking, MM/GBSA) to assess enzyme activity and binding interactions.
• Lipidomic analysis of Streptomyces strains and lipid staining.

Main Results:

• Palmitoleic acid and linoleic acid identified as potent SARS-CoV-2 3CLpro inhibitors (IC₅₀ values 1.59 µg/mL and 5.29 µg/mL, respectively).
• Molecular docking revealed multi-site binding of these fatty acids to the catalytic, dimerization, and allosteric sites of 3CLpro.
• Significant lipid accumulation (~63%) in Streptomyces sp. DSD454^T and a conserved lipid signature correlating with 3CLpro inhibition across strains.

Conclusions:

• Microbial lipids from marine Streptomyces are promising scaffolds for developing novel catalytic and allosteric SARS-CoV-2 3CLpro inhibitors.
• Marine Streptomyces represent a valuable resource for discovering versatile antiviral metabolites with potential for COVID-19 therapeutics.