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

Abstract

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.