Coronaviruses
(CoVs) cause numerous diseases, including Middle
East respiratory syndrome and severe acute respiratory syndrome, generating
significant health-related and economic consequences. CoVs encode
the nucleocapsid (N) protein, a major structural protein that plays
multiple roles in the virus replication cycle and forms a ribonucleoprotein
complex with the viral RNA through the N protein’s N-terminal
domain (N-NTD). Using human CoV-OC43 (HCoV-OC43) as a model for CoV,
we present the 3D structure of HCoV-OC43 N-NTD complexed with ribonucleoside
5′-monophosphates to identify a distinct ribonucleotide-binding
pocket. By targeting this pocket, we identified and developed a new
coronavirus N protein inhibitor, N-(6-oxo-5,6-dihydrophenanthridin-2-yl)(N,N-dimethylamino)acetamide hydrochloride
(PJ34), using virtual screening; this inhibitor reduced the N protein’s
RNA-binding affinity and hindered viral replication. We also determined
the crystal structure of the N-NTD–PJ34 complex. On the basis
of these findings, we propose guidelines for developing new N protein-based
antiviral agents that target CoVs.