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

AbstractAt the moment, there is a worldwide outbreak of coronavirus disease 2019 (COVID-19) that is caused by theinfection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We urgently need effectiveanti-viral therapeutics against SARS-CoV-2 and related coronaviruses to avoid potential future outbreaks. Thisproposal seeks pilot funding to support the interdisciplinary collaboration between medicinal chemists andvirologists to develop novel small molecules that can destabilize 3-chymotrypsin like protease (3CLpro), themain viral protease that is essential for the replication of SARS-CoV-2 and many related coronaviruses. Theproposed 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 bindswith high selectivity to an E3 ubiquitin ligase while the other ligand simultaneously engages the viral proteintarget. As the binding event occurs, the viral protein is brought in close contact with the E3 ubiquitin ligasecomplex and is poly-ubiquitinated for degradation in the proteasome. The degrader is then released tocontinue its catalytic activity for the degradation of the viral protein. The degrader only needs to bind transientlyto the target viral protein to induce its ubiquitination, which offers many advantages over traditional smallmolecule inhibitors.We selected 3CLpro as the primary target for selective degradation based on its key role in viral replication andthe availability of selective inhibitors, which will serve as the ligand that binds to 3CLPro. Although inhibitors for3CLpro exist, degraders' catalytic properties will render them much more potent. By destabilizing anddestroying the viral protein instead of stoichiometrically binding to the viral protein, degraders should also actfaster than inhibitors. 3CLpro is conserved among many coronaviruses including SARS-CoV, MERS-CoV, andSARS-CoV-2. The proposed small molecule degraders can be potent antiviral therapeutics against a broadspectrum of coronaviruses, including viral strains that are resistant to antiviral inhibitors. In aim 1, we willprepare bifunctional small molecule degraders by linking ligands of E3 ligase and 3CLPro using our recentlydeveloped two-stage strategy. In aim 2, we will evaluate the degradation and anti-viral activities of 3CLProdegraders in cell-based assays.The research groups of PI and Co-Investigator are highly experienced in bifunctional small molecule degraderdevelopment and anti-viral research, respectively. The proposed study will produce important proof-of-conceptdata for the development of novel antiviral therapeutics against SARS-CoV-2 and related coronaviruses.