biostudies-literatureMercaldi GFFinanciadora de Estudos e Projetos18500https://www.ebi.ac.uk/biostudies/studies/S-EPMC9628480biostudies-literatureUnknown12(1)The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, ¹H-STD and ¹⁵N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARSScientific reportsDiscovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.PMC962848001.20.0003.00Filho HVRda Silva JCShimizu JFFigueira ACMCordeiro ATProenca-Modena JLMercaldi GFZeri ACMRocco SAMarques REBezerra EHSTonoli CCCSoprano ASLopes-de-Oliveira PSSforca MLdo Nascimento Faria JBenedetti CEda Cunha MGBruder MBatista FAHNagai ABajgelman MCFranchini KGNascimento AFZTrivella DBBfalseDiscovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.The nucleocapsid (N) protein plays critical roles in coronavirus genome transcription and packaging, representing a key target for the development of novel antivirals, and for which structural information on ligand binding is scarce. We used a novel fluorescence polarization assay to identify small molecules that disrupt the binding of the N protein to a target RNA derived from the SARS-CoV-2 genome packaging signal. Several phenolic compounds, including L-chicoric acid (CA), were identified as high-affinity N-protein ligands. The binding of CA to the N protein was confirmed by isothermal titration calorimetry, ¹H-STD and ¹⁵N-HSQC NMR, and by the crystal structure of CA bound to the N protein C-terminal domain (CTD), further revealing a new modulatory site in the SARS2022-01-01T00:00:00Z2022 Nov2026-05-27T23:47:04.744Z2024-12-04T12:33:06.027ZS-EPMC96284803632373210.1038/s41598-022-22576-4