Development of Broad-Spectrum Antiviral Therapeutics by Destabilizing the Main Protease of Coronaviruses

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Abstract At the moment, there is a worldwide outbreak of coronavirus disease 2019 (COVID-19) that is caused by the infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We urgently need effective anti-viral therapeutics against SARS-CoV-2 and related coronaviruses to avoid potential future outbreaks. This proposal seeks pilot funding to support the interdisciplinary collaboration between medicinal chemists and virologists to develop novel small molecules that can destabilize 3-chymotrypsin like protease (3CLpro), the main viral protease that is essential for the replication of SARS-CoV-2 and many related coronaviruses. The proposed small molecules are able to catalyze the degradation of 3CLpro through the host cell’s ubiquitin- proteasome-system, which routinely removes damaged or unfolded proteins. The proposed degraders are bifunctional molecules with a short linker between two ligands. One ligand binds with high selectivity to an E3 ubiquitin ligase while the other ligand simultaneously engages the viral protein target. As the binding event occurs, the viral protein is brought in close contact with the E3 ubiquitin ligase complex and is poly-ubiquitinated for degradation in the proteasome. The degrader is then released to continue its catalytic activity for the degradation of the viral protein. The degrader only needs to bind transiently to the target viral protein to induce its ubiquitination, which offers many advantages over traditional small molecule inhibitors. We selected 3CLpro as the primary target for selective degradation based on its key role in viral replication and the availability of selective inhibitors, which will serve as the ligand that binds to 3CLPro. Although inhibitors for 3CLpro exist, degraders’ catalytic properties will render them much more potent. By destabilizing and destroying the viral protein instead of stoichiometrically binding to the viral protein, degraders should also act faster than inhibitors. 3CLpro is conserved among many coronaviruses including SARS-CoV, MERS-CoV, and SARS-CoV-2. The proposed small molecule degraders can be potent antiviral therapeutics against a broad spectrum of coronaviruses, including viral strains that are resistant to antiviral inhibitors. In aim 1, we will prepare bifunctional small molecule degraders by linking ligands of E3 ligase and 3CLPro using our recently developed two-stage strategy. In aim 2, we will evaluate the degradation and anti-viral activities of 3CLPro degraders in cell-based assays. The research groups of PI and Co-Investigator are highly experienced in bifunctional small molecule degrader development and anti-viral research, respectively. The proposed study will produce important proof-of-concept data for the development of novel antiviral therapeutics against SARS-CoV-2 and related coronaviruses.