Identification of Small-Molecule Inhibitors of Coronaviruses by Targeting Protein-Protein Interaction RdRp Complex

The arsenal of antiviral drugs is currently very limited. It consists of only ~90 molecules primarily targeting the activity of viral enzymes, which leaves other biological features vastly underexplored. This might complicate the rapid and effective answers to emerging viruses. For example, the ongoing COVID-19 pandemic highlighted the critical needs for the proactive identification of antiviral drugs with complementary modes of action and broad-spectrum activity. Here, to develop pan-coronavirus inhibitors that potentially reduce the frequency of adaptive evolution compared to enzymatic drugs, we have targeted a conserved protein-protein interaction (PPI) within the core SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex. We have first demonstrated that the Nsp12-Nsp8 interface is a better target than Nsp12-Nsp7 for direct PPI inhibition. Using advanced interactomic tools in human cells, we then subjected the Nsp12-Nsp8 target to ~18,000 candidate inhibitors. To select for interaction-specific compounds, we performed a parallel counter-screen using an irrelevant PPI. This led us to identify three specific Nsp12-Nsp8 inhibitors with minimal cytotoxicity and potent antiviral activity. These new molecules significantly decreased viral replication when combined to Remdesivir, which highlights the potential for combinatorial therapies. Importantly, they are very effective against different SARS-CoV-2 variants, as well as other coronaviruses. Overall, our results position the conserved RdRp complex as a central element to identify small molecules with complementary modes of action to existing drugs.They also shade lights on strategies to improve pandemic preparedness.