Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor

• Published in: Scientific reports Vol. 12; no. 1; p. 18500
• Main Authors: Mercaldi, Gustavo Fernando, Bezerra, Eduardo Henrique Salviano, Batista, Fernanda Aparecida Heleno, Tonoli, Celisa Caldana Costa, Soprano, Adriana Santos, Shimizu, Jacqueline Farinha, Nagai, Alice, da Silva, Jaqueline Cristina, Filho, Helder Veras Ribeiro, do Nascimento Faria, Jéssica, da Cunha, Marcos Guilherme, Zeri, Ana Carolina Mattos, Nascimento, Andrey Fabricio Ziem, Proenca-Modena, José Luiz, Bajgelman, Marcio Chaim, Rocco, Silvana Aparecida, Lopes-de-Oliveira, Paulo Sérgio, Cordeiro, Artur Torres, Bruder, Marjorie, Marques, Rafael Elias, Sforça, Mauricio Luis, Franchini, Kleber Gomes, Benedetti, Celso Eduardo, Figueira, Ana Carolina Migliorini, Trivella, Daniela Barretto Barbosa
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 02.11.2022; Nature Publishing Group UK; Nature Portfolio
• Subjects: Acids; Antiviral agents; Antiviral Agents - pharmacology; Calorimetry; Candidates; Coronaviruses; COVID-19; Crystal structure; Drugs; Experiments; Fluorescence polarization; Genomes; Humans; Kinases; Ligands; N protein; NMR; Nuclear magnetic resonance; Nucleocapsid Proteins - genetics; Nucleocapsids; Packaging; Phenols; Protein Binding; Protein C; Proteins; RNA - metabolism; RNA polymerase; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Titration; Viruses
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-22576-4

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, H-STD and N-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 SARS-CoV-2 N protein. Moreover, CA reduced SARS-CoV-2 replication in cell cultures. These data thus open venues for the development of new antivirals targeting the N protein, an essential and yet underexplored coronavirus target.