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Duarte Filho LAMDS, Yanaguibashi Leal CE, Bodet PE, Beserra de Alencar Filho E, Almeida JRGDS, Porta Zapata M, Achour O, Groult H, Gouveia Veloso CA, Viegas Júnior C, Bourgougnon N, Picot L. The Identification of Peptide Inhibitors of the Coronavirus 3CL Protease from a Fucus ceranoides L. Hydroalcoholic Extract Using a Ligand-Fishing Strategy. Mar Drugs 2024; 22:244. [PMID: 38921555 PMCID: PMC11205194 DOI: 10.3390/md22060244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/27/2024] Open
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.
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Affiliation(s)
| | - Cintia Emi Yanaguibashi Leal
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Université de Picardie Jules Verne, 80039 Amiens, France;
| | - Pierre-Edouard Bodet
- Plateforme D’analyse Haute Résolution des Biomolécules, UMR CNRS 7266 LIENSs, La Rochelle Université, 17042 La Rochelle, France;
| | | | | | - Manon Porta Zapata
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Oussama Achour
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Hugo Groult
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Carlos Arthur Gouveia Veloso
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
| | - Claudio Viegas Júnior
- Institute of Chemistry, Federal University of Alfenas, Alfenas 37130-000, MG, Brazil;
| | - Nathalie Bourgougnon
- Laboratoire de Biotechnologie et Chimie Marines, LBCM, Université Bretagne Sud, EMR CNRS 6076, IUEM, 56000 Vannes, France;
| | - Laurent Picot
- Littoral Environnement et Societés (LIENSs), UMRi CNRS 7266, La Rochelle Université, 17042 La Rochelle, France; (L.A.M.d.S.D.F.); (M.P.Z.); (O.A.); (H.G.)
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Vauthier M, Serra CA. Controlled reversible aggregation of thermoresponsive polymeric nanoparticles by interfacial Diels-Alder reaction. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abdurahim J, Serra CA, Blanck C, Vauthier M. One-step production of highly monodisperse size-controlled poly(lactic-co-glycolic acid) nanoparticles for the release of a hydrophobic model drug. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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