Towards anti-COVID-19 therapeutic development by targeting the viral papain-like proteinase [Added supplement: COVID-19 Variant Supplement]

When positive-stranded RNA viruses such as the causative agent for the 2019-2020 novel coronavirus (SARS-CoV-2) outbreak enter an infectious cycle in the cell, their RNA genomes hijack the host cell's protein production machinery to mass produce large continuous viral polyproteins in a process called translation. In order to make progeny viruses, these viral polypeptides need to be processed into smaller, individually functional protein programmed to perform specific tasks, e.g., replicating the RNA genome, assembling the protein coat for progeny viruses, packing the newly synthesized RNA genome into the assembled viral capsid, and subverting or disabling the host cell's antiviral defense mechanisms. Two virally encoded proteinases, the papain-like (PL) and the 3C-like (3CL) proteinases, carry out the job of "clipping" the viral polypeptides into individual viral proteins. The PL is translated before the 3CL hence it likely takes precedence in performing "cuts" in the polyprotein, releasing an initial batch of viral proteins to mount the first wave of suppressive attack on antiviral host defense. In addition, coronavirus PL directly participates in preventing type I interferon activation, an important step leading to antiviral defense. Last but not the least, PL1 is part of non-structural protein 3 (NSP3), which is an indispensable component of the membranous complex where viral RNA genome is replicated. Taken together, PL of the novel coronavirus makes a good antiviral target for the development of therapeutics. Inhibiting PL would not only halt viral protein and RNA production at an early stage but would also help restore host antiviral defense. In this proposal, we seek to solve the 3-dimensional structure of SARS-CoV-2 PL and then use the structural knowledge to aid our search of small molecules that can inhibit the functions of PL. We will work with our collaborators to optimize the top inhibitors and test these inhibitors in cell and animal infection models.