A Systematic Host-Centric Approach to Identifying Repurposed Drugs for Viral Infections

<p xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" class="first" dir="auto" id="d7181933e174">Today, most antiviral screening approaches evaluate the drug activity targeting virus proteins, while often overlooking the host proteins essential to virus replication. This virus-centric approach rapidly leads to therapy resistance due to mutation-prone viral genomes, underscoring the need of alternative antiviral strategies. Here, we explore host-targeting compounds, using SARS-CoV-2 as a model as an alternative approach. With systematic screening approaches, we have investigated the antiviral activity of 5275 compounds from the SPECS drug repurposing library. Our primary screening pipeline included: 1) host cell morphology changes by the phenomics assay Cell Painting (CP), 2) detecting SARS-CoV-2 infection rate by antibody-detection of, and 3) viability rescue, the gold standard for antiviral evaluation. We demonstrate how SARS-CoV-2 infection induced a specific phenotypic signature in Vero E6 and A549-ACE2 cells, which was reversed by antiviral controls such as remdesivir. Our unbiased host-focused approach identified 324 compounds with antiviral activity against SARS-CoV-2 (6% of SPECS library), including 150, 117, and 210 from respective screening assay. Compounds exhibiting antiviral activity were further validated in a dose-response manner by CP and counter screened using a live-cell assay assessing drug-induced phopholipidosis (DIPL). Validation screens identified 33 (0.6% of the SPECS library) compounds that restored host cell morphology without inducing DIPL, representing both new and previously investigated drug repurposing candidates against SARS-CoV-2 with activity to the host cell. This research establishes a systematic methodological approach to identify host-targeted antivirals, applicable to other emerging viruses in global need of antiviral drugs, while highlighting their potential to mitigate drug resistance.