Structure-based discovery of highly bioavailable, covalent, broad-spectrum coronavirus M <sup>Pro</sup> inhibitors with potent in vivo efficacy
Tyler C. Detomasi, Gilles Degotte, Sijie Huang, Rahul K. Suryawanshi, Amy Diallo, Luca Lizzadro, Francisco J. Zaptero-Belinchón, Taha Y. Taha, Jiapeng Li, Alicia Richards, Eric R. Hantz, Zain Alam, Mauricio Montaño, Maria McCavitt-Malvido, R. Gumpena, James R. Partridge, G.J. Correy, Yusuke Matsui, Annemarie F. Charvat, Isabella Glenn, Julia Rosecrans, Jezrael L. Revalde, Dashiell Anderson, Judd F. Hultquist, Michelle R. Arkin, R. Jeffrey Neitz, Danielle L. Swaney, Nevan J. Krogan, Brian K. Shoichet, Kliment A. Verba, Mélanie Ott, Adam R. Renslo, Charles S. Craik
Abstract
The main protease (M Pro ) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a validated drug target. Starting with a lead-like dihydrouracil chemotype identified in a large-library docking campaign, we improved M Pro inhibition >1000-fold by engaging additional M Pro subsites and using a latent electrophile to engage Cys 145 . Advanced leads from this series show pan-coronavirus antiviral activity, low clearance in mice, and for AVI-4773 , a rapid reduction in viral titers >1,000,000 after just three doses. Both compounds are well distributed in mouse tissues, including brain, where concentrations >1000× the 90% effective concentration are observed 8 hours after oral dosing for AVI-4773 . AVI-4516 shows minimal inhibition of major cytochrome P450s and human proteases. AVI-4516 also exhibits synergy with the RNA-dependent RNA polymerase inhibitor, molnupiravir, in cellular infection models. Related analogs strongly inhibit nirmatrelvir-resistant M Pro mutant virus. The properties of this chemotype are differentiated from existing clinical and preclinical M Pro inhibitors and will advance therapeutic development against emerging SARS-CoV-2 variants and other coronaviruses.