Inhibiting the interaction between the mitochondrial receptor Tom70 and SARS CoV 2 Orf9b with small molecules

The SARS CoV 2 accessory protein Orf9b is in a complex monomer-dimer equilibrium that influences its interactions with the host mitochondrial receptor Tom70. This interaction is critical for viral suppression of a Type-1 interferon response during infection. Modulating this equilibrium with a small molecule, either by stabilizing the Orf9b dimer or blocking its interaction with Tom70, represents a promising strategy for restoring interferon signaling and the antiviral response. To build tool molecules that could test this concept, we performed two screens: a crystallographic fragment screen against the Orf9b homodimer and a high-throughput fluorescence polarization screen for competitors of an Orf9b-derived peptide binding to Tom70. Fragment screening revealed two binding sites with potential to be developed into an inhibitor: one located at the peripheral dimer interface and the other just outside the lipid-binding channel that defines the central dimer interface. Functionalization of the fragments outside of the lipid-binding channel with hydrophobic moieties stabilized the Orf9b dimer thereby indirectly inhibiting association with Tom70. In parallel, the high throughput screen for competitive inhibitors of the Tom70:Orf9b interaction discovered a separate series of molecules. These molecules display dynamic structure activity relationship (SAR) and could be improved in the future to modulate the interaction between Tom70 and potentially a wide range of substrates. Collectively, these results demonstrate the feasibility of two distinct strategies to manipulate the Orf9b-Tom70 equilibrium, which is critical to the host response to SARS CoV 2 infection.