Covalent inhibition of the SARS-CoV-2 NiRAN domain via an active-site cysteine
Year: 2025
Type: article
Abstract: The kinase-like 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 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 (RTC) bound to NCI-2 offers a detailed structural blueprint for rational drug design. Although NCI-2 showed limited potency against SARS-CoV-2 replication in cells, our work lays the groundwork for developing more potent and selective inhibitors targeting the NiRAN domain. This approach presents a promising therapeutic strategy for effectively combating COVID-19 and potentially mitigating future coronavirus outbreaks.
Source: Journal of Biological Chemistry
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $3,430
Funders: Howard Hughes Medical Institute, W. M. Keck Foundation, Welch Foundation, Cancer Prevention and Research Institute of Texas, University of Texas Southwestern Medical Center, Searle Scholars Program, National Institutes of Health, NIH Office of the Director, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases
Awards: Establish a New Cryo-Electron Microscopy Core Facility and Service for Structure Determination at UT Southwestern Medical Center, G1065445663, G1271325796, Establish New Cryo-EM Core Services to Drive Cancer Research and Drug Discovery at UTSouthwestern Medical Center, G179861173, A functional evolutionary genetic approach to combat viral infection, An acoustic droplet ejection liquid dipenser for our UTSW HTS Core, G5451725915, Antioxidant signaling by protein AMPylation, G626896620, G7073091334, Recruitment of First-Time, Tenure-Track Faculty Members
OpenAlex ID: W4408129215