The Identification of Peptide Inhibitors of the Coronavirus 3CL Protease from a Fucus ceranoides L. Hydroalcoholic Extract Using a Ligand-Fishing Strategy.

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.

Dereplication of tropane alkaloids from four Erythroxylum species using liquid chromatography coupled with ESI-MSn and HRESIMS.

RATIONALE: Tropane alkaloids represent an important class of secondary metabolites, but many of these compounds are already described in the scientific literature, so the use of guided identification and isolation strategies, such as dereplication, represent a fast and safe alternative. METHODS: For the annotation of the tropane alkaloids the chloroform phases of the four Erythroxylum species were analyzed by high-performance liquid chromatography coupled to mass spectrometry with positive-mode electrospray ionization, then the ions of their protonated molecules, molecular formulas and fragmentation patterns were observed and a comparison of the obtained data with those present in the scientific literature was performed. The compounds not fully annotated were isolated and characterized by 1 H and 13 C nuclear magnetic resonance spectroscopy. RESULTS: The annotation of 29 tropane alkaloids was performed, some being described for the first time in the family Erythroxylaceae. The chemical profiles of these secondary metabolites in the four Erythroxylum species analyzed were traced and compared. Isolation of three compounds whose mass spectral data were not sufficient for their full annotation was performed. They were 6-(benzoyloxy)-3-(3,5-dimethoxy-4-hydroxybenzoyloxy)tropane, 6-(benzoyloxy)-3-(3,4,5-trimethoxybenzoyloxy)tropane and 6-(benzoyloxy)-3-(3,4,5-trimethoxycinamoyloxy)tropane, first reported in the species Erythroxylum revolutum Mart. CONCLUSIONS: This work contributes to the phytochemical knowledge of the genus Erythroxylum, and demonstrates the efficiency and importance of using guided isolation methodologies of secondary metabolites in natural products research. Since safe results were presented in the annotation of the compounds evidenced, employing small quantities of organic solvents, when compared to classical methodologies, besides promoting an optimization in the research time.