The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection

Sandoval, Daniel R.; Clausen, Thomas Mandel; Nora, Chelsea; Cribbs, Adam P.; Denardo, Andrea; Clark, Alex E.; Garretson, Aaron F.; Coker, Joanna K.C.; Narayanan, Anoop; Majowicz, Sydney A.; Philpott, Martin; Johansson, Catrine; Dunford, James E.; Spliid, Charlotte B.; Golden, Gregory J.; Payne, N. Connor; Tye, Mark A.; Nowell, Cameron J.; Griffis, Eric R.; Piermatteo, Ann; Grunddal, Kaare V.; Alle, Thibault; Magida, Jason A.; Hauser, Blake M.; Feldman, Jared; Caradonna, Timothy M.; Pu, Yuan; Yin, Xin; McVicar, Rachael N.; Kwong, Elizabeth M.; Weiss, Ryan J.; Downes, Michael; Tsimikas, Sotirios; Smidt, Aaron G.; Ballatore, Carlo; Zengler, Karsten; Evans, Ron M.; Chanda, Sumit K.; Croker, Ben A.; Leibel, Sandra L.; Jose, Joyce; Mazitschek, Ralph; Oppermann, Udo; Esko, Jeffrey D.; Carlin, Aaron F.; Gordts, Philip L.S.M.

Summary Paragraph We identify the prolyl-tRNA synthetase (PRS) inhibitor halofuginone1, a compound in clinical trials for anti-fibrotic and anti-inflammatory applications2, as a potent inhibitor of SARS-CoV-2 infection and replication. The interaction of SARS-CoV-2 spike protein with cell surface heparan sulfate (HS) promotes viral entry3. We find that halofuginone reduces HS biosynthesis, thereby reducing spike protein binding, SARS-CoV-2 pseudotyped virus, and authentic SARS-CoV-2 infection. Halofuginone also potently suppresses SARS-CoV-2 replication post-entry and is 1,000-fold more potent than Remdesivir4. Inhibition of HS biosynthesis and SARS-CoV-2 infection depends on specific inhibition of PRS, possibly due to translational suppression of proline-rich proteins. We find that pp1a and pp1ab polyproteins of SARS-CoV-2, as well as several HS proteoglycans, are proline-rich, which may make them particularly vulnerable to halofuginone’s translational suppression. Halofuginone is orally bioavailable, has been evaluated in a phase I clinical trial in humans and distributes to SARS-CoV-2 target organs, including the lung, making it a near-term clinical trial candidate for the treatment of COVID-19.