Discovery of an Antiviral PROTAC Targeting the SARS-CoV-2 Main Protease Using an Allosteric Warhead

ABSTRACT Targeted protein degradation represents a new paradigm in drug development. By hijacking the cellular ubiquitin-proteasome-system pathogenic proteins are degraded via heterobifunctional molecules, referred to as proteolysis targeting chimeras (PROTACs). However, to date, only few PROTACs targeting viral or proviral proteins have been developed. To explore the possibilities and advantages of antiviral PROTACs, we have developed an antiviral PROTAC against the SARS-CoV-2 main protease (M Pro ) using an allosteric warhead. Here, we present the design of ten M Pro degraders that were developed using pelitinib as a warhead, an allosteric binder of M Pro . Among several candidates, LLP019 emerged as the most potent molecule, capable of degrading up to 90% of M Pro after ectopic expression in HEK293F cells. LLP019 displayed significant antiviral activity against several variants of concern of SARS-CoV-2 in infected Calu3 cells. In conclusion, we show that the development of antiviral PROTACs using an allosteric warhead represents a promising antiviral strategy, expanding the range of possible target proteins and ligands. SYNPOSIS We present a proof-of-concept study to construct a PROTAC targeting the SARS-CoV-2 main protease (M Pro ) using a warhead that binds outside the catalytic pocket.