Exploring Nirmatrelvir Derivatives Through P2 Substituent Modifications and Warhead Innovations Targeting the Main...

The COVID-19 pandemic underscored the urgent need for effective antiviral agents, particularly against coronaviruses, which pose a continuing threat of future outbreaks. Targeting the main protease (M^pro), a key enzyme in viral replication, represents a promising therapeutic strategy. This study investigates structural modifications to known M^pro inhibitors, focusing on substitutions at the P2 position to explore alterations in both inhibitory potency and metabolic stability. Computational modeling and biochemical assays revealed that incorporating large, hydrophobic, and π-rich groups, such as the 4-phenylproline, significantly enhances binding affinity. Additionally, we evaluated warheads that have not yet been explored in the context of SARS-CoV-2 M^pro inhibition. Among these, fluoro-vinylsulfone and nitrile groups demonstrated superior inhibitory activity. A fragment-merging strategy combining an optimized P2 substituent with the nitrile warhead yielded a hybrid molecule with binding affinity comparable to nirmatrelvir. However, other analogs incorporating individual warhead optimizations displayed similar potency. These findings generate valuable insights into the design of robust M^pro inhibitors and support their potential development as broad-spectrum antiviral agents.