Repurposing screens reveal a role for PKCη and NF1 in SARS-CoV-2 infection

SARS-CoV-2 continues to circulate with the emergence of variants that evade existing immunity. However, all strains rely on conserved host factors for entry, making them attractive targets for host-directed antivirals. SARS-CoV-2 engages the ACE2 receptor and can enter cells through two alternative pathways depending on cell type: Spike cleavage at the plasma membrane by TMPRSS2, or within endocytic compartments by cathepsins. Cleavage triggers Spike-mediated membrane fusion and release of the viral genome. To discover small-molecule inhibitors of entry, we first screened compounds against live virus and active candidates were then tested using recombinant VSV expressing SARS-CoV-2 Spike, with VSV expressing its native glycoprotein serving as a control. This approach identified known and novel TMPRSS2 inhibitors, as well as Staurosporine and Retro-2.1. Both compounds inhibited infection in both TMPRSS2-dependent and -independent cell types. Entry bypass studies revealed that Staurosporine acts upstream of Spike cleavage, while Retro-2.1 functions downstream. Mechanistic studies in Calu-3 cells showed that Staurosporine, a pan-PKC inhibitor, blocks entry via PKCη, a pro-viral factor acting before Spike cleavage. Retro-2.1 targets NF1, which promotes infection downstream of Spike cleavage. Together, our screening pipeline identified inhibitors that block SARS-CoV-2 entry at distinct stages and revealed host factors that may inform the development of current and novel antiviral strategies.