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The Identification of Peptide Inhibitors of the Coronavirus 3CL Protease from a Fucus ceranoides L. Hydroalcoholic Extract Using a Ligand-Fishing Strategy.
- Source :
-
Marine drugs [Mar Drugs] 2024 May 27; Vol. 22 (6). Date of Electronic Publication: 2024 May 27. - Publication Year :
- 2024
-
Abstract
- Brown seaweeds of the Fucus genus represent a rich source of natural antiviral products. In this study, a Fucus ceranoides hydroalcoholic extract (FCHE) was found to inhibit 74.2 ± 1.3% of the proteolytic activity of the free SARS-CoV-2 3CL protease (3CLpro), an enzyme that plays a pivotal role in polyprotein processing during coronavirus replication and has been identified as a relevant drug discovery target for SARS- and MERS-CoVs infections. To purify and identify 3CLpro ligands with potential inhibitory activity using a one-step approach, we immobilized the enzyme onto magnetic microbeads (3CLpro-MPs), checked that the enzymatic activity was maintained after grafting, and used this bait for a ligand-fishing strategy followed by a high-resolution mass spectrometry analysis of the fished-out molecules. Proof of concept for the ligand-fishing capacity of the 3CLpro-MPs was demonstrated by doping the FCHE extract with the substrate peptide TSAVLQ-pNA, resulting in the preferential capture of this high-affinity peptide within the macroalgal complex matrix. Ligand fishing in the FCHE alone led to the purification and identification via high-resolution mass spectrometry (HRMS) of seven hepta-, octa-, and decapeptides in an eluate mix that significantly inhibited the free 3CLpro more than the starting FCHE (82.7 ± 2.2% inhibition). Molecular docking simulations of the interaction between each of the seven peptides and the 3CLpro demonstrated a high affinity for the enzyme's proteolytic active site surpassing that of the most affine peptide ligand identified so far (a co-crystallographic peptide). Testing of the corresponding synthetic peptides demonstrated that four out of seven significantly inhibited the free 3CLpro (from 46.9 ± 6.4 to 76.8 ± 3.6% inhibition at 10 µM). This study is the first report identifying peptides from Fucus ceranoides with high inhibitory activity against the SARS-CoV-2 3CLprotease which bind with high affinity to the protease's active site. It also confirms the effectiveness of the ligand-fishing strategy for the single-step purification of enzyme inhibitors from complex seaweed matrices.
- Subjects :
- Ligands
SARS-CoV-2 drug effects
SARS-CoV-2 enzymology
Plant Extracts pharmacology
Plant Extracts chemistry
Peptides pharmacology
Peptides chemistry
Molecular Docking Simulation
Humans
Seaweed chemistry
Coronavirus 3C Proteases antagonists & inhibitors
Coronavirus 3C Proteases metabolism
Antiviral Agents pharmacology
Antiviral Agents chemistry
Antiviral Agents isolation & purification
Fucus chemistry
Protease Inhibitors pharmacology
Protease Inhibitors chemistry
Protease Inhibitors isolation & purification
Subjects
Details
- Language :
- English
- ISSN :
- 1660-3397
- Volume :
- 22
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- Marine drugs
- Publication Type :
- Academic Journal
- Accession number :
- 38921555
- Full Text :
- https://doi.org/10.3390/md22060244