Screen for Modulation of Nucleocapsid Protein Condensation Identifies Small Molecules with Anti-Coronavirus Activity

Biomolecular condensates formed by liquid–liquid
phase separation
have been implicated in multiple diseases. Modulation of condensate
dynamics by small molecules has therapeutic potential, but so far,
few condensate modulators have been disclosed. The SARS-CoV-2 nucleocapsid
(N) protein forms phase-separated condensates that are hypothesized
to play critical roles in viral replication, transcription, and packaging,
suggesting that N condensation modulators might have anti-coronavirus
activity across multiple strains and species. Here, we show that N
proteins from all seven human coronaviruses (HCoVs) vary in their
tendency to undergo phase separation when expressed in human lung
epithelial cells. We developed a cell-based high-content screening
platform and identified small molecules that both promote and inhibit
condensation of SARS-CoV-2 N. Interestingly, these host-targeted small
molecules exhibited condensate-modulatory effects across all HCoV
Ns. Some have also been reported to exhibit antiviral activity against
SARS-CoV-2, HCoV-OC43, and HCoV-229E viral infections in cell culture.
Our work reveals that the assembly dynamics of N condensates can be
regulated by small molecules with therapeutic potential. Our approach
allows for screening based on viral genome sequences alone and might
enable rapid paths to drug discovery with value for confronting future
pandemics.