Targeting programmed ribosomal frameshifting as a therapeutic strategy against 2019-nCoV [Added supplement: COVID-19 Variant Supplement]

The new coronavirus 2019-nCoV has spread rapidly in the last 3 months, infecting tens of thousands of people in dozens of countries and killing over 1,000, with no preventive vaccines or medications that can treat it. We propose to search for possible drugs to treat 2019-nCoV by targeting the ability of the virus to hijack the cell's machinery and recode how the genome is read via programmed ribosomal frameshifting (PRF). Coronaviruses use PRF, which is triggered by a specific structure (a 'pseudoknot') in the viral genome, to produce essential enzymes in specific ratios. Suppressing PRF in SARS coronavirus-which is very closely related to 2019-nCoV-disrupts viral propagation and significantly reduces infectivity, suggesting that PRF inhibitors could be used to combat 2019-nCoV. We will search for potential drugs that bind to the 2019-nCoV pseudoknot and disrupt PRF. We will first build a structural model of the pseudoknot by combining computational simulations with measurements revealing the base-pairing patterns and higher-order structures in the RNA. We will then use high-throughput computational tools to screen large libraries of existing approved drugs (which could be deployed rapidly), as well as publicly-available chemical compounds, for binding to the pseudoknot. Compounds predicted to have high binding affinity will be tested experimentally to confirm their binding-quantifying the binding affinity, identifying the binding site, and showing that binding alters the pseudoknot structural dynamics (thought to be important for triggering PRF)-and to measure their effectiveness at inhibiting PRF in cell extracts. We will examine if the effects of the compounds are specific to 2019-nCoV by repeating all measurements using other RNA structures as controls. Lead compounds will be passed on to collaborators for future studies assessing their effectiveness against live virus and suitability for deployment as therapeutics.