Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine.

ABSTRACT: The kinase-like nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain of nsp12 in SARS-CoV-2 catalyzes the formation of the 5' RNA cap structure. This activity is required for viral replication, offering a new target for the development of antivirals. Here, we develop a high-throughput assay to screen for small molecule inhibitors targeting the SARS-CoV-2 NiRAN domain. We identified NiRAN covalent inhibitor 2 (NCI-2), a compound with a reactive chloromethyl group that covalently binds to an active site cysteine (Cys53) in the NiRAN domain, inhibiting its activity. NCI-2 can enter cells, bind to, and inactivate ectopically expressed nsp12. A cryo-EM reconstruction of the SARS-CoV-2 replication-transcription complex bound to NCI-2 offers a detailed structural blueprint for rationa

SUBMITTER: Hernandez G 

PROVIDER: S-EPMC12013494 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature