Defining therapeutic drug targets for SARS-CoV-2-specific and pan-coronavirus inhibition

Project Summary COVID-19 disease, caused by severe respiratory distress syndrome coronavirus 2 (SARS-CoV-2), is currently ravaging the world. Infection of humans causes symptoms spanning the spectrum from asymptomatic infection to severe respiratory distress and death. Despite the fact that vaccines and repurposed drugs are currently under study, it is uncertain whether they will be efficacious and so efforts to develop additional treatment and preventative options are crucial. This study will leverage results from multiple bulk CRISPR knockout screens already performed in the lab that identify host factors that SARS-CoV-2 and other human coronaviruses require for replication. These screens utilized cells from two tissue sources, lung and liver, four human coronaviruses including SARS-CoV-2, two temperatures that mimic the upper and lower airway, and five different CRISPR libraries including three druggable genome libraries, a library focused on human factors recently discovered to interact with proteins of SARS-CoV-2 and a full genome library. In the first aim, factors identified as hits in each of the screens will be cross compared and prioritized into three categories: 1) specific to SARS-CoV-2, 2) common to SARS-CoV-2 and at least one other coronavirus, or 3) specific to the lung for any of the viruses (Aim 1a). Hits from these categories will be subjected to refinement using a semi-arrayed CRISPR approach (Aim 1b) as well as drug and small molecule inhibition assays (Aim 1c) in the context of a panel of coronaviruses. In the second aim, gene disruption of the prioritized targets will be performed in primary human lung cells (Aim 2a) and the effect on the replication and cell killing by a panel of coronaviruses, including SARS-CoV-2 will be determined (Aim 2b). Drugs and compounds found as antiviral in Aim 1c will be tested in the primary human lung cells for their antiviral activity against the coronavirus panel. Validated factors, which could be SARS-CoV-2-specific, or possibly factors required generally for coronaviruses, would be targets for future in depth mechanistic studies and drug development.