Progress and Challenges in Targeting the SARS-CoV-2 Papain-like Protease

SARS-CoV-2 is the causative agent of the COVID-19 pandemic. The approval of vaccines and small-molecule antivirals is vital in combating the pandemic. The viral polymerase inhibitors remdesivir and molnupiravir and the viral main protease inhibitor nirmatrelvir/ritonavir have been approved by the U.S. FDA. However, the emergence of variants of concern/interest calls for additional antivirals with novel mechanisms of action. The SARS-CoV-2 papain-like protease (PL^pro) mediates the cleavage of viral polyprotein and modulates the host's innate immune response upon viral Infection, rendering it a promising Antiviral drug target. This Perspective highlights major achievements in structure-based design and high-throughput screening of SARS-CoV-2 PL^pro inhibitors since the beginning of the pandemic. Encouraging progress includes the design of non-covalent PL^pro inhibitors with favorable pharmacokinetic properties and the first-in-class covalent PL^pro inhibitors. In addition, we offer our opinion on the knowledge gaps that need to be filled to advance PL^pro inhibitors to the clinic.