Structural basis of main proteases of HCoV-229E bound to inhibitor PF-07304814 and PF-07321332

PF-07321332 and PF-07304814, inhibitors against SARS-CoV-2 developed by Pfizer, exhibit broad-spectrum inhibitory activity against the main protease (M^pro) from various coronaviruses. Structures of PF-07321332 or PF-07304814 in complex with M^pros of various coronaviruses reveal their inhibitory mechanisms against different M^pros. However, the structural information on the lower pathogenic coronavirus M^pro with PF-07321332 or PF-07304814 is currently scarce, which hinders our comprehensive understanding of the inhibitory mechanisms of these two inhibitors. Meanwhile, given that some immunocompromised individuals are still affected by low pathogenic coronaviruses, we determined the structures of lower pathogenic coronavirus HCoV-229E M^pro with PF-07321332 and PF-07304814, respectively, and analyzed and defined in detail the structural basis for the inhibition of HCoV-229E M^pro by both inhibitors. Further, we compared the crystal structures of multiple coronavirus M^pro complexes with PF-07321332 or PF-07304814 to illustrate the differences in the interaction of M^pros, and found that the inhibition mechanism of lower pathogenic coronavirus M^pro was more similar to that of moderately pathogenic coronaviruses. Our structural studies provide new insights into drug development for low pathogenic coronavirus M^pro, and provide theoretical basis for further optimization of both inhibitors to contain potential future coronaviruses.