Host-pathogen interactions of highly pathogenic coronaviruses reveal drug targets

Background: The novel coronavirus SARS-CoV-2, the causative agent of COVID-19, has caused worldwide social and economic disruption. Initial efforts to treat SARS-CoV-2 were hampered by limited knowledge of the molecular details of SARS-CoV-2 infection. To identify molecular targets for SARS-CoV-2 therapeutics, we mapped the host-pathogen protein interactions of SARS-CoV- 2, and investigated host dependency pathways that are required for SARS-CoV-2 infection using drug, knockdown and knockout screens. Concerns regarding the mutagenic potential of SARS-CoV-2 also led us to inquire whether a conserved set of human host factors may be required for infection by all highly pathogenic coronaviruses, thus representing pan-coronavirus drug targets. Therefore, we also mapped the host protein interactions of SARS-CoV-1 and MERS-CoV. Methods: We cloned, tagged and expressed proteins encoded by SARS-CoV-2, SARS-CoV-1, and MERS-CoV in HEK-293T cells, which are permissive to infection by all three viruses. Cells expressing individual proteins were harvested, affinity purifications performed in 96-well format, and protein mass spectrometry was utilized to identify physical interaction partners of each viral protein. Drug treatments, RNAi knockdowns and CRISPR/Cas9 knockouts were tested for SARS-CoV-2 viral phenotypes in Vero, Caco2 or A549-ACE2 cells. Results: We report 389 high-confidence interactors of SARS-CoV-2, 366 interactions for SARS-CoV-1, and 296 interactions for MERS-CoV. Among the SARS-CoV-2 interactors, we identified at least 66 druggable human proteins or host factors, and screening small molecules targeting these pathways using multiple viral assays have identified at least four sets of pharmacological agents that demonstrate antiviral activity against SARS-CoV-2. Comparison of the host-pathogen interactomes of SARS-CoV-2 with the other highly pathogenic coronaviruses SARS-CoV-1 and MERS highlights shared host interactions which may represent pan-coronavirus drug targets. Conclusion: We successfully utilized systematic protein interaction mapping to identify drug targets for SARS-CoV-2, leading to several Covid-19 clinical studies investigating the efficacy of drugs perturbing these pathways. Furthermore, comparative proteomics of the related coronaviruses SARS-CoV-1 and MERS-CoV identified shared host interactions which may represent pan-coronavirus drug targets. For a full list of contributing authors see: Gordon, D. E. et al. Nature 583, 459-468 (2020);Gordon, D. E. et al. Science 370 (2020).